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Yue T, Guo Y, Qi X, Zheng W, Zhang H, Wang B, Liu K, Zhou B, Zeng X, Ouzhuluobu, He Y, Su B. Sex-biased regulatory changes in the placenta of native highlanders contribute to adaptive fetal development. eLife 2024; 12:RP89004. [PMID: 38869160 PMCID: PMC11175615 DOI: 10.7554/elife.89004] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/14/2024] Open
Abstract
Compared with lowlander migrants, native Tibetans have a higher reproductive success at high altitude though the underlying mechanism remains unclear. Here, we compared the transcriptome and histology of full-term placentas between native Tibetans and Han migrants. We found that the placental trophoblast shows the largest expression divergence between Tibetans and Han, and Tibetans show decreased immune response and endoplasmic reticulum stress. Remarkably, we detected a sex-biased expression divergence, where the male-infant placentas show a greater between-population difference than the female-infant placentas. The umbilical cord plays a key role in the sex-biased expression divergence, which is associated with the higher birth weight of the male newborns of Tibetans. We also identified adaptive histological changes in the male-infant placentas of Tibetans, including larger umbilical artery wall and umbilical artery intima and media, and fewer syncytial knots. These findings provide valuable insights into the sex-biased adaptation of human populations, with significant implications for medical and genetic studies of human reproduction.
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Affiliation(s)
- Tian Yue
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of SciencesKunmingChina
- Kunming College of Life Science, University of Chinese Academy of SciencesBeijingChina
| | - Yongbo Guo
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of SciencesKunmingChina
- Kunming College of Life Science, University of Chinese Academy of SciencesBeijingChina
| | - Xuebin Qi
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of SciencesKunmingChina
- Fukang Obstetrics, Gynecology and Children Branch Hospital, Tibetan Fukang HospitalKunmingChina
- State Key Laboratory of Primate Biomedical Research, Institute of Primate Translational Medicine, Kunming University of Science and TechnologyKunmingChina
| | - Wangshan Zheng
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of SciencesKunmingChina
| | - Hui Zhang
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of SciencesKunmingChina
- State Key Laboratory of Primate Biomedical Research, Institute of Primate Translational Medicine, Kunming University of Science and TechnologyKunmingChina
| | - Bin Wang
- Fukang Obstetrics, Gynecology and Children Branch Hospital, Tibetan Fukang HospitalKunmingChina
| | - Kai Liu
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of SciencesKunmingChina
| | - Bin Zhou
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of SciencesKunmingChina
- Kunming College of Life Science, University of Chinese Academy of SciencesBeijingChina
| | - Xuerui Zeng
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of SciencesKunmingChina
- Kunming College of Life Science, University of Chinese Academy of SciencesBeijingChina
| | - Ouzhuluobu
- Fukang Obstetrics, Gynecology and Children Branch Hospital, Tibetan Fukang HospitalKunmingChina
| | - Yaoxi He
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of SciencesKunmingChina
| | - Bing Su
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of SciencesKunmingChina
- Center for Excellence in Animal Evolution and Genetics, Chinese Academy of SciencesKunmingChina
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2
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Gutierrez Guarnizo SA, Kellogg MK, Miller SC, Tikhonova E, Karamysheva ZN, Karamyshev AL. Pathogenic signal peptide variants in the human genome. NAR Genom Bioinform 2023; 5:lqad093. [PMID: 37859801 PMCID: PMC10583284 DOI: 10.1093/nargab/lqad093] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2023] [Revised: 09/05/2023] [Accepted: 09/29/2023] [Indexed: 10/21/2023] Open
Abstract
Secreted and membrane proteins represent a third of all cellular proteins and contain N-terminal signal peptides that are required for protein targeting to endoplasmic reticulum (ER). Mutations in signal peptides affect protein targeting, translocation, processing, and stability, and are associated with human diseases. However, only a few of them have been identified or characterized. In this report, we identified pathogenic signal peptide variants across the human genome using bioinformatic analyses and predicted the molecular mechanisms of their pathology. We recovered more than 65 thousand signal peptide mutations, over 11 thousand we classified as pathogenic, and proposed framework for distinction of their molecular mechanisms. The pathogenic mutations affect over 3.3 thousand genes coding for secreted and membrane proteins. Most pathogenic mutations alter the signal peptide hydrophobic core, a critical recognition region for the signal recognition particle, potentially activating the Regulation of Aberrant Protein Production (RAPP) quality control and specific mRNA degradation. The remaining pathogenic variants (about 25%) alter either the N-terminal region or signal peptidase processing site that can result in translocation deficiencies at the ER membrane or inhibit protein processing. This work provides a conceptual framework for the identification of mutations across the genome and their connection with human disease.
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Affiliation(s)
| | - Morgana K Kellogg
- Department of Cell Biology and Biochemistry, Texas Tech University Health Sciences Center, Lubbock, TX 79430, USA
| | - Sarah C Miller
- Department of Cell Biology and Biochemistry, Texas Tech University Health Sciences Center, Lubbock, TX 79430, USA
| | - Elena B Tikhonova
- Department of Cell Biology and Biochemistry, Texas Tech University Health Sciences Center, Lubbock, TX 79430, USA
| | | | - Andrey L Karamyshev
- Department of Cell Biology and Biochemistry, Texas Tech University Health Sciences Center, Lubbock, TX 79430, USA
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3
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Rehan S, Tranter D, Sharp PP, Craven GB, Lowe E, Anderl JL, Muchamuel T, Abrishami V, Kuivanen S, Wenzell NA, Jennings A, Kalyanaraman C, Strandin T, Javanainen M, Vapalahti O, Jacobson MP, McMinn D, Kirk CJ, Huiskonen JT, Taunton J, Paavilainen VO. Signal peptide mimicry primes Sec61 for client-selective inhibition. Nat Chem Biol 2023; 19:1054-1062. [PMID: 37169961 PMCID: PMC10449633 DOI: 10.1038/s41589-023-01326-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2022] [Accepted: 04/06/2023] [Indexed: 05/13/2023]
Abstract
Preventing the biogenesis of disease-relevant proteins is an attractive therapeutic strategy, but attempts to target essential protein biogenesis factors have been hampered by excessive toxicity. Here we describe KZR-8445, a cyclic depsipeptide that targets the Sec61 translocon and selectively disrupts secretory and membrane protein biogenesis in a signal peptide-dependent manner. KZR-8445 potently inhibits the secretion of pro-inflammatory cytokines in primary immune cells and is highly efficacious in a mouse model of rheumatoid arthritis. A cryogenic electron microscopy structure reveals that KZR-8445 occupies the fully opened Se61 lateral gate and blocks access to the lumenal plug domain. KZR-8445 binding stabilizes the lateral gate helices in a manner that traps select signal peptides in the Sec61 channel and prevents their movement into the lipid bilayer. Our results establish a framework for the structure-guided discovery of novel therapeutics that selectively modulate Sec61-mediated protein biogenesis.
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Affiliation(s)
- Shahid Rehan
- Institute of Biotechnology, HiLIFE, University of Helsinki, Helsinki, Finland
| | - Dale Tranter
- Institute of Biotechnology, HiLIFE, University of Helsinki, Helsinki, Finland
| | - Phillip P Sharp
- Department of Cellular and Molecular Pharmacology, University of California, San Francisco, CA, USA
| | - Gregory B Craven
- Department of Cellular and Molecular Pharmacology, University of California, San Francisco, CA, USA
| | - Eric Lowe
- Kezar Life Sciences, South San Francisco, CA, USA
| | | | | | - Vahid Abrishami
- Institute of Biotechnology, HiLIFE, University of Helsinki, Helsinki, Finland
| | - Suvi Kuivanen
- Institute of Virology, Charité-Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Berlin, Germany
| | - Nicole A Wenzell
- Department of Cellular and Molecular Pharmacology, University of California, San Francisco, CA, USA
| | | | - Chakrapani Kalyanaraman
- Department of Pharmaceutical Chemistry, Faculty of Pharmacy, University of California, San Francisco, CA, USA
| | - Tomas Strandin
- Department of Virology, Faculty of Medicine, University of Helsinki, Helsinki, Finland
| | - Matti Javanainen
- Institute of Biotechnology, HiLIFE, University of Helsinki, Helsinki, Finland
| | - Olli Vapalahti
- Department of Virology, Faculty of Medicine, University of Helsinki, Helsinki, Finland
| | - Matthew P Jacobson
- Department of Pharmaceutical Chemistry, Faculty of Pharmacy, University of California, San Francisco, CA, USA
| | | | | | - Juha T Huiskonen
- Institute of Biotechnology, HiLIFE, University of Helsinki, Helsinki, Finland
| | - Jack Taunton
- Department of Cellular and Molecular Pharmacology, University of California, San Francisco, CA, USA.
| | - Ville O Paavilainen
- Institute of Biotechnology, HiLIFE, University of Helsinki, Helsinki, Finland.
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4
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Pirkalkhoran S, Grabowska WR, Kashkoli HH, Mirhassani R, Guiliano D, Dolphin C, Khalili H. Bioengineering of Antibody Fragments: Challenges and Opportunities. Bioengineering (Basel) 2023; 10:bioengineering10020122. [PMID: 36829616 PMCID: PMC9952581 DOI: 10.3390/bioengineering10020122] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2022] [Revised: 01/09/2023] [Accepted: 01/11/2023] [Indexed: 01/18/2023] Open
Abstract
Antibody fragments are used in the clinic as important therapeutic proteins for treatment of indications where better tissue penetration and less immunogenic molecules are needed. Several expression platforms have been employed for the production of these recombinant proteins, from which E. coli and CHO cell-based systems have emerged as the most promising hosts for higher expression. Because antibody fragments such as Fabs and scFvs are smaller than traditional antibody structures and do not require specific patterns of glycosylation decoration for therapeutic efficacy, it is possible to express them in systems with reduced post-translational modification capacity and high expression yield, for example, in plant and insect cell-based systems. In this review, we describe different bioengineering technologies along with their opportunities and difficulties to manufacture antibody fragments with consideration of stability, efficacy and safety for humans. There is still potential for a new production technology with a view of being simple, fast and cost-effective while maintaining the stability and efficacy of biotherapeutic fragments.
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Affiliation(s)
- Sama Pirkalkhoran
- School of Biomedical Science, University of West London, London W5 5RF, UK
| | | | | | | | - David Guiliano
- School of Life Science, College of Liberal Arts and Sciences, University of Westminster, London W1W 6UW, UK
| | - Colin Dolphin
- School of Biomedical Science, University of West London, London W5 5RF, UK
| | - Hanieh Khalili
- School of Biomedical Science, University of West London, London W5 5RF, UK
- School of Pharmacy, University College London, London WC1N 1AX, UK
- Correspondence:
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5
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Cytosolic Quality Control of Mitochondrial Protein Precursors-The Early Stages of the Organelle Biogenesis. Int J Mol Sci 2021; 23:ijms23010007. [PMID: 35008433 PMCID: PMC8745001 DOI: 10.3390/ijms23010007] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2021] [Revised: 12/15/2021] [Accepted: 12/16/2021] [Indexed: 12/12/2022] Open
Abstract
With few exceptions, proteins that constitute the proteome of mitochondria originate outside of this organelle in precursor forms. Such protein precursors follow dedicated transportation paths to reach specific parts of mitochondria, where they complete their maturation and perform their functions. Mitochondrial precursor targeting and import pathways are essential to maintain proper mitochondrial function and cell survival, thus are tightly controlled at each stage. Mechanisms that sustain protein homeostasis of the cytosol play a vital role in the quality control of proteins targeted to the organelle. Starting from their synthesis, precursors are constantly chaperoned and guided to reduce the risk of premature folding, erroneous interactions, or protein damage. The ubiquitin-proteasome system provides proteolytic control that is not restricted to defective proteins but also regulates the supply of precursors to the organelle. Recent discoveries provide evidence that stress caused by the mislocalization of mitochondrial proteins may contribute to disease development. Precursors are not only subject to regulation but also modulate cytosolic machinery. Here we provide an overview of the cellular pathways that are involved in precursor maintenance and guidance at the early cytosolic stages of mitochondrial biogenesis. Moreover, we follow the circumstances in which mitochondrial protein import deregulation disturbs the cellular balance, carefully looking for rescue paths that can restore proteostasis.
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6
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Wu B, Zhao TV, Jin K, Hu Z, Abdel MP, Warrington KJ, Goronzy JJ, Weyand CM. Mitochondrial aspartate regulates TNF biogenesis and autoimmune tissue inflammation. Nat Immunol 2021; 22. [PMID: 34811544 PMCID: PMC8756813 DOI: 10.1038/s41590-021-01065-2 10.1038/s41590-021-01065-2] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023]
Abstract
Misdirected immunity gives rise to the autoimmune tissue inflammation of rheumatoid arthritis, in which excess production of the cytokine tumor necrosis factor (TNF) is a central pathogenic event. Mechanisms underlying the breakdown of self-tolerance are unclear, but T cells in the arthritic joint have a distinctive metabolic signature of ATPlo acetyl-CoAhi proinflammatory effector cells. Here we show that a deficiency in the production of mitochondrial aspartate is an important abnormality in these autoimmune T cells. Shortage of mitochondrial aspartate disrupted the regeneration of the metabolic cofactor nicotinamide adenine dinucleotide, causing ADP deribosylation of the endoplasmic reticulum (ER) sensor GRP78/BiP. As a result, ribosome-rich ER membranes expanded, promoting co-translational translocation and enhanced biogenesis of transmembrane TNF. ERrich T cells were the predominant TNF producers in the arthritic joint. Transfer of intact mitochondria into T cells, as well as supplementation of exogenous aspartate, rescued the mitochondria-instructed expansion of ER membranes and suppressed TNF release and rheumatoid tissue inflammation.
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Affiliation(s)
- Bowen Wu
- Department of Medicine, Mayo College of Medicine, Rochester, MN 55905, USA
| | - Tuantuan V. Zhao
- Department of Medicine, Mayo College of Medicine, Rochester, MN 55905, USA
| | - Ke Jin
- Department of Medicine, Mayo College of Medicine, Rochester, MN 55905, USA
| | - Zhaolan Hu
- Department of Medicine, Mayo College of Medicine, Rochester, MN 55905, USA
| | - Matthew P. Abdel
- Department of Orthopedic Surgery, Mayo College of Medicine, Rochester, MN 55905, USA
| | - Ken J. Warrington
- Department of Medicine, Mayo College of Medicine, Rochester, MN 55905, USA
| | - Jörg J. Goronzy
- Department of Medicine, Mayo College of Medicine, Rochester, MN 55905, USA
| | - Cornelia M. Weyand
- Department of Medicine, Mayo College of Medicine, Rochester, MN 55905, USA,Corresponding author: Cornelia M. Weyand, Department of Medicine, Mayo College of Medicine and Sciences, Rochester, MN 55901;
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7
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Wu B, Zhao TV, Jin K, Hu Z, Abdel MP, Warrington KJ, Goronzy JJ, Weyand CM. Mitochondrial aspartate regulates TNF biogenesis and autoimmune tissue inflammation. Nat Immunol 2021; 22:1551-1562. [PMID: 34811544 PMCID: PMC8756813 DOI: 10.1038/s41590-021-01065-2] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2021] [Accepted: 10/01/2021] [Indexed: 01/03/2023]
Abstract
Misdirected immunity gives rise to the autoimmune tissue inflammation of rheumatoid arthritis, in which excess production of the cytokine tumor necrosis factor (TNF) is a central pathogenic event. Mechanisms underlying the breakdown of self-tolerance are unclear, but T cells in the arthritic joint have a distinctive metabolic signature of ATPlo acetyl-CoAhi proinflammatory effector cells. Here we show that a deficiency in the production of mitochondrial aspartate is an important abnormality in these autoimmune T cells. Shortage of mitochondrial aspartate disrupted the regeneration of the metabolic cofactor nicotinamide adenine dinucleotide, causing ADP deribosylation of the endoplasmic reticulum (ER) sensor GRP78/BiP. As a result, ribosome-rich ER membranes expanded, promoting co-translational translocation and enhanced biogenesis of transmembrane TNF. ERrich T cells were the predominant TNF producers in the arthritic joint. Transfer of intact mitochondria into T cells, as well as supplementation of exogenous aspartate, rescued the mitochondria-instructed expansion of ER membranes and suppressed TNF release and rheumatoid tissue inflammation.
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Affiliation(s)
- Bowen Wu
- Department of Medicine, Mayo Clinic College of Medicine and Science, Rochester, MN, USA
| | - Tuantuan V Zhao
- Department of Medicine, Mayo Clinic College of Medicine and Science, Rochester, MN, USA
| | - Ke Jin
- Department of Medicine, Mayo Clinic College of Medicine and Science, Rochester, MN, USA
| | - Zhaolan Hu
- Department of Medicine, Mayo Clinic College of Medicine and Science, Rochester, MN, USA
| | - Matthew P Abdel
- Department of Orthopedic Surgery, Mayo Clinic College of Medicine and Science, Rochester, MN, USA
| | - Ken J Warrington
- Department of Medicine, Mayo Clinic College of Medicine and Science, Rochester, MN, USA
| | - Jörg J Goronzy
- Department of Medicine, Mayo Clinic College of Medicine and Science, Rochester, MN, USA
- School of Medicine, Stanford University, Stanford, CA, USA
| | - Cornelia M Weyand
- Department of Medicine, Mayo Clinic College of Medicine and Science, Rochester, MN, USA.
- School of Medicine, Stanford University, Stanford, CA, USA.
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8
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Thoma J, Burmann BM. Architects of their own environment: How membrane proteins shape the Gram-negative cell envelope. ADVANCES IN PROTEIN CHEMISTRY AND STRUCTURAL BIOLOGY 2021; 128:1-34. [PMID: 35034716 DOI: 10.1016/bs.apcsb.2021.10.001] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/14/2023]
Abstract
Gram-negative bacteria are surrounded by a complex multilayered cell envelope, consisting of an inner and an outer membrane, and separated by the aqueous periplasm, which contains a thin peptidoglycan cell wall. These bacteria employ an arsenal of highly specialized membrane protein machineries to ensure the correct assembly and maintenance of the membranes forming the cell envelope. Here, we review the diverse protein systems, which perform these functions in Escherichia coli, such as the folding and insertion of membrane proteins, the transport of lipoproteins and lipopolysaccharide within the cell envelope, the targeting of phospholipids, and the regulation of mistargeted envelope components. Some of these protein machineries have been known for a long time, yet still hold surprises. Others have only recently been described and some are still missing pieces or yet remain to be discovered.
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Affiliation(s)
- Johannes Thoma
- Wallenberg Centre for Molecular and Translational Medicine, University of Gothenburg, Göteborg, Sweden; Department of Chemistry and Molecular Biology, University of Gothenburg, Göteborg, Sweden.
| | - Björn M Burmann
- Wallenberg Centre for Molecular and Translational Medicine, University of Gothenburg, Göteborg, Sweden; Department of Chemistry and Molecular Biology, University of Gothenburg, Göteborg, Sweden
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9
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Budowa i znaczenie II systemu sekrecji białek w ekologii i patogenezie Legionella pneumophila. POSTEP HIG MED DOSW 2021. [DOI: 10.2478/ahem-2021-0034] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Abstract
Pałeczki Legionella pneumophila pasożytują w komórkach odległych filogenetycznie gospodarzy, w środowisku wodnym w pierwotniakach, a w organizmie człowieka w makrofagach alweolarnych. Zdolność tych bakterii do wewnątrzkomórkowego namnażania się w komórkach fagocytujących, wyspecjalizowanych do niszczenia mikroorganizmów, ma podstawowe znaczenie dla rozwoju nietypowego zapalenia płuc zwanego chorobą legionistów. Umiejscowione na kilku różnych loci chromosomu bakteryjnego geny II systemu sekrecji L. pneumophila kodują co najmniej 25 białek, w tym enzymy o aktywności lipolitycznej, proteolitycznej, rybonukleazy oraz białka unikalne bakterii Legionella. W środowisku naturalnym T2SS L. pneumophila odgrywa decydującą rolę w ekologii tych drobnoustrojów determinując ich zdolność do przeżycia zarówno w postaci planktonicznej, jak i w strukturach biofilmu w słodkowodnych zbiornikach o niskiej temperaturze. Białka T2SS umożliwiają L. pneumophila zakażenie różnych gatunków pierwotniaków, a substraty tego systemu określają zakres pierwotniaczego gospodarza. Namnażanie się bakterii w różnorodnych pierwotniakach przyczynia się do ich rozsiewania oraz transmisji do antropogenicznych źródeł. Białka wydzielane za pomocą II systemu sekrecji determinują również zdolność L. pneumophila do zakażania mysich makrofagów alweolarnych i szpiku kostnego, ludzkich makrofagów linii U937 i THP-1 oraz komórek nabłonkowych pęcherzyków płucnych. Enzymy wydzielane za pomocą tego systemu, takie jak: proteazy, aminopeptydazy czy fosfolipazy umożliwiają pozyskanie substancji pokarmowych oraz powodują destrukcję tkanki płucnej myszy. W organizmie człowieka białka T2SS przyczyniają się do osłabienia wrodzonej odpowiedzi immunologicznej na zakażenie L. pneumophila przez hamowanie indukcji prozapalnych cytokin (IL-6, TNF-α, IL-1 oraz IL-8).
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10
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Selective promiscuity in the binding of E. coli Hsp70 to an unfolded protein. Proc Natl Acad Sci U S A 2021; 118:2016962118. [PMID: 34625496 DOI: 10.1073/pnas.2016962118] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 08/26/2021] [Indexed: 01/16/2023] Open
Abstract
Heat shock protein 70 (Hsp70) chaperones bind many different sequences and discriminate between incompletely folded and folded clients. Most research into the origins of this "selective promiscuity" has relied on short peptides as substrates to dissect the binding, but much less is known about how Hsp70s bind full-length client proteins. Here, we connect detailed structural analyses of complexes between the Escherichia coli Hsp70 (DnaK) substrate-binding domain (SBD) and peptides encompassing five potential binding sites in the precursor to E. coli alkaline phosphatase (proPhoA) with SBD binding to full-length unfolded proPhoA. Analysis of SBD complexes with proPhoA peptides by a combination of X-ray crystallography, methyl-transverse relaxation optimized spectroscopy (methyl-TROSY), and paramagnetic relaxation enhancement (PRE) NMR and chemical cross-linking experiments provided detailed descriptions of their binding modes. Importantly, many sequences populate multiple SBD binding modes, including both the canonical N to C orientation and a C to N orientation. The favored peptide binding mode optimizes substrate residue side-chain compatibility with the SBD binding pockets independent of backbone orientation. Relating these results to the binding of the SBD to full-length proPhoA, we observe that multiple chaperones may bind to the protein substrate, and the binding sites, well separated in the proPhoA sequence, behave independently. The hierarchy of chaperone binding to sites on the protein was generally consistent with the apparent binding affinities observed for the peptides corresponding to these sites. Functionally, these results reveal that Hsp70s "read" sequences without regard to the backbone direction and that both binding orientations must be considered in current predictive algorithms.
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11
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Zhao L, Fu G, Cui Y, Xu Z, Cai T, Zhang D. Compensating Complete Loss of Signal Recognition Particle During Co-translational Protein Targeting by the Translation Speed and Accuracy. Front Microbiol 2021; 12:690286. [PMID: 34305852 PMCID: PMC8299109 DOI: 10.3389/fmicb.2021.690286] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2021] [Accepted: 06/09/2021] [Indexed: 11/23/2022] Open
Abstract
Signal recognition particle (SRP) is critical for delivering co-translational proteins to the bacterial inner membrane. Previously, we identified SRP suppressors in Escherichia coli that inhibit translation initiation and elongation, which provided insights into the mechanism of bypassing the requirement of SRP. Suppressor mutations tended to be located in regions that govern protein translation under evolutionary pressure. To test this hypothesis, we re-executed the suppressor screening of SRP. Here, we isolated a novel SRP suppressor mutation located in the Shine–Dalgarno sequence of the S10 operon, which partially offset the targeting defects of SRP-dependent proteins. We found that the suppressor mutation decreased the protein translation rate, which extended the time window of protein targeting. This increased the possibility of the correct localization of inner membrane proteins. Furthermore, the fidelity of translation was decreased in suppressor cells, suggesting that the quality control of translation was inactivated to provide an advantage in tolerating toxicity caused by the loss of SRP. Our results demonstrated that the inefficient protein targeting due to SRP deletion can be rescued through modulating translational speed and accuracy.
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Affiliation(s)
- Liuqun Zhao
- Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, China.,Tianjin Institute of Industrial Biotechnology, University of Chinese Academy of Sciences, Beijing, China
| | - Gang Fu
- Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, China.,Key Laboratory of Systems Microbial Biotechnology, Chinese Academy of Sciences, Tianjin, China.,National Engineering Laboratory for Industrial Enzymes, Chinese Academy of Sciences, Tianjin, China
| | - Yanyan Cui
- Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, China
| | - Zixiang Xu
- Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, China.,National Engineering Laboratory for Industrial Enzymes, Chinese Academy of Sciences, Tianjin, China
| | - Tao Cai
- Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, China
| | - Dawei Zhang
- Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, China.,Tianjin Institute of Industrial Biotechnology, University of Chinese Academy of Sciences, Beijing, China.,Key Laboratory of Systems Microbial Biotechnology, Chinese Academy of Sciences, Tianjin, China.,National Engineering Laboratory for Industrial Enzymes, Chinese Academy of Sciences, Tianjin, China
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12
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Faoro C, Ataide SF. Noncanonical Functions and Cellular Dynamics of the Mammalian Signal Recognition Particle Components. Front Mol Biosci 2021; 8:679584. [PMID: 34113652 PMCID: PMC8185352 DOI: 10.3389/fmolb.2021.679584] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2021] [Accepted: 04/29/2021] [Indexed: 12/24/2022] Open
Abstract
The signal recognition particle (SRP) is a ribonucleoprotein complex fundamental for co-translational delivery of proteins to their proper membrane localization and secretory pathways. Literature of the past two decades has suggested new roles for individual SRP components, 7SL RNA and proteins SRP9, SRP14, SRP19, SRP54, SRP68 and SRP72, outside the SRP cycle. These noncanonical functions interconnect SRP with a multitude of cellular and molecular pathways, including virus-host interactions, stress response, transcriptional regulation and modulation of apoptosis in autoimmune diseases. Uncovered novel properties of the SRP components present a new perspective for the mammalian SRP as a biological modulator of multiple cellular processes. As a consequence of these findings, SRP components have been correlated with a growing list of diseases, such as cancer progression, myopathies and bone marrow genetic diseases, suggesting a potential for development of SRP-target therapies of each individual component. For the first time, here we present the current knowledge on the SRP noncanonical functions and raise the need of a deeper understanding of the molecular interactions between SRP and accessory cellular components. We examine diseases associated with SRP components and discuss the development and feasibility of therapeutics targeting individual SRP noncanonical functions.
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Affiliation(s)
- Camilla Faoro
- School of Life and Environmental Sciences, The University of Sydney, Sydney, NSW, Australia
| | - Sandro F Ataide
- School of Life and Environmental Sciences, The University of Sydney, Sydney, NSW, Australia
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13
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Schmaltz-Panneau B, Pagnier A, Clauin S, Buratti J, Marty C, Fenneteau O, Dieterich K, Beaupain B, Donadieu J, Plo I, Bellanné-Chantelot C. Identification of biallelic germline variants of SRP68 in a sporadic case with severe congenital neutropenia. Haematologica 2021; 106:1216-1219. [PMID: 32273475 PMCID: PMC8018125 DOI: 10.3324/haematol.2020.247825] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2020] [Indexed: 01/14/2023] Open
Affiliation(s)
- Barbara Schmaltz-Panneau
- INSERM U1287, Gustave Roussy, Villejuif, France; Paris Saclay University, U1287, Villejuif, France
| | - Anne Pagnier
- Department of Pediatric Hematology and Oncology, CHU Grenoble Alpes, Grenoble, France
| | - Séverine Clauin
- Department of Genetics, Pitié-Salpêtrière Hospital, APHP, Paris, France
| | - Julien Buratti
- Department of Genetics, Pitié-Salpêtrière Hospital, APHP, Paris, France
| | - Caroline Marty
- INSERM U1287, Gustave Roussy, Villejuif, France; Paris Saclay University, U1287, Villejuif, France
| | - Odile Fenneteau
- Laboratory of Hematology, Robert Debré Hospital - Université de Paris, France
| | - Klaus Dieterich
- Department of Medical Genetics, Univ. Grenoble Alpes, INSERM U1216, CHU Grenoble Alpes, Grenoble
| | - Blandine Beaupain
- French Registry of Chronic Neutropenia, Trousseau Hospital, Paris, France
| | - Jean Donadieu
- Department of Pediatric Hematology and Oncology, Trousseau Hospital, AP-HP, Paris, France
| | - Isabelle Plo
- INSERM U1287, Gustave Roussy, Villejuif, France; Paris Saclay University, U1287, Villejuif, France
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14
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Gershberg J, Braverman D, Sal-Man N. Transmembrane domains of type III-secreted proteins affect bacterial-host interactions in enteropathogenic E. coli. Virulence 2021; 12:902-917. [PMID: 33729090 PMCID: PMC7993127 DOI: 10.1080/21505594.2021.1898777] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
Many bacterial pathogens utilize a specialized secretion system, termed type III secretion system (T3SS), to translocate effector proteins into host cells and establish bacterial infection. The T3SS is anchored within the bacterial membranes and contains a long needle/filament that extends toward the host-cell and forms, at its distal end, a pore complex within the host membrane. The T3SS pore complex consists of two bacterial proteins, termed SctB and SctE, which have conflicting targeting indications; a signal sequence that targets to secretion to the extracellular environment via the T3SS, and transmembrane domains (TMDs) that target to membrane localization. In this study, we investigate whether the TMD sequences of SctB and SctE have special features that differentiate them from classical TMDs and allow them to escape bacterial membrane integration. For this purpose, we exchanged the SctB and SctE native TMDs for alternative hydrophobic sequences and found that the TMD sequences of SctB and SctE dictate membrane destination (bacterial versus host membrane). Moreover, we examined the role of the SctB TMD sequence in the activity of the full-length protein, post secretion, and found that the TMD does not serve only as a hydrophobic segment, but is also involved in the ability of the protein to translocate itself and other proteins into and across the host cell membrane.
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Affiliation(s)
- Jenia Gershberg
- The Shraga Segal Department of Microbiology, Immunology and Genetics, Faculty of Health Sciences, Ben-Gurion University of the Negev, Beer Sheva, Israel
| | - Dor Braverman
- The Shraga Segal Department of Microbiology, Immunology and Genetics, Faculty of Health Sciences, Ben-Gurion University of the Negev, Beer Sheva, Israel
| | - Neta Sal-Man
- The Shraga Segal Department of Microbiology, Immunology and Genetics, Faculty of Health Sciences, Ben-Gurion University of the Negev, Beer Sheva, Israel
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15
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Berke K, Sun P, Ong E, Sanati N, Huffman A, Brunson T, Loney F, Ostrow J, Racz R, Zhao B, Xiang Z, Masci AM, Zheng J, Wu G, He Y. VaximmutorDB: A Web-Based Vaccine Immune Factor Database and Its Application for Understanding Vaccine-Induced Immune Mechanisms. Front Immunol 2021; 12:639491. [PMID: 33777032 PMCID: PMC7994782 DOI: 10.3389/fimmu.2021.639491] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2020] [Accepted: 02/18/2021] [Indexed: 01/07/2023] Open
Abstract
Vaccines stimulate various immune factors critical to protective immune responses. However, a comprehensive picture of vaccine-induced immune factors and pathways have not been systematically collected and analyzed. To address this issue, we developed VaximmutorDB, a web-based database system of vaccine immune factors (abbreviated as “vaximmutors”) manually curated from peer-reviewed articles. VaximmutorDB currently stores 1,740 vaccine immune factors from 13 host species (e.g., human, mouse, and pig). These vaximmutors were induced by 154 vaccines for 46 pathogens. Top 10 vaximmutors include three antibodies (IgG, IgG2a and IgG1), Th1 immune factors (IFN-γ and IL-2), Th2 immune factors (IL-4 and IL-6), TNF-α, CASP-1, and TLR8. Many enriched host processes (e.g., stimulatory C-type lectin receptor signaling pathway, SRP-dependent cotranslational protein targeting to membrane) and cellular components (e.g., extracellular exosome, nucleoplasm) by all the vaximmutors were identified. Using influenza as a model, live attenuated and killed inactivated influenza vaccines stimulate many shared pathways such as signaling of many interleukins (including IL-1, IL-4, IL-6, IL-13, IL-20, and IL-27), interferon signaling, MARK1 activation, and neutrophil degranulation. However, they also present their unique response patterns. While live attenuated influenza vaccine FluMist induced significant signal transduction responses, killed inactivated influenza vaccine Fluarix induced significant metabolism of protein responses. Two different Yellow Fever vaccine (YF-Vax) studies resulted in overlapping gene lists; however, they shared more portions of pathways than gene lists. Interestingly, live attenuated YF-Vax simulates significant metabolism of protein responses, which was similar to the pattern induced by killed inactivated Fluarix. A user-friendly web interface was generated to access, browse and search the VaximmutorDB database information. As the first web-based database of vaccine immune factors, VaximmutorDB provides systematical collection, standardization, storage, and analysis of experimentally verified vaccine immune factors, supporting better understanding of protective vaccine immunity.
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Affiliation(s)
- Kimberly Berke
- College of Literature, Science, and the Arts, University of Michigan, Ann Arbor, MI, United States.,Central Michigan College of Medicine, Mt. Pleasant, MI, United States
| | - Peter Sun
- College of Literature, Science, and the Arts, University of Michigan, Ann Arbor, MI, United States
| | - Edison Ong
- Department of Computational Medicine and Biology, University of Michigan, Ann Arbor, MI, United States
| | - Nasim Sanati
- Department of Medical Informatics and Clinical Epidemiology, Oregon Health and Science University, Portland, OR, United States
| | - Anthony Huffman
- Department of Computational Medicine and Biology, University of Michigan, Ann Arbor, MI, United States
| | - Timothy Brunson
- Department of Medical Informatics and Clinical Epidemiology, Oregon Health and Science University, Portland, OR, United States
| | - Fred Loney
- Department of Medical Informatics and Clinical Epidemiology, Oregon Health and Science University, Portland, OR, United States
| | - Joseph Ostrow
- College of Literature, Science, and the Arts, University of Michigan, Ann Arbor, MI, United States
| | - Rebecca Racz
- College of Literature, Science, and the Arts, University of Michigan, Ann Arbor, MI, United States
| | - Bin Zhao
- College of Literature, Science, and the Arts, University of Michigan, Ann Arbor, MI, United States
| | - Zuoshuang Xiang
- College of Literature, Science, and the Arts, University of Michigan, Ann Arbor, MI, United States
| | - Anna Maria Masci
- Department of Biostatistics and Bioinformatics, Duke University School of Medicine, Durham, NC, United States
| | - Jie Zheng
- Department of Genetics, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, United States
| | - Guanming Wu
- Department of Medical Informatics and Clinical Epidemiology, Oregon Health and Science University, Portland, OR, United States
| | - Yongqun He
- Unit for Laboratory Animal Medicine, University of Michigan Medical School, Ann Arbor, MI, United States.,Department of Microbiology and Immunology, University of Michigan Medical School, Ann Arbor, MI, United States.,Center for Computational Medicine and Biology, University of Michigan, Ann Arbor, MI, United States
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16
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Signal Recognition Particle Suppressor Screening Reveals the Regulation of Membrane Protein Targeting by the Translation Rate. mBio 2021; 12:mBio.02373-20. [PMID: 33436432 PMCID: PMC7844537 DOI: 10.1128/mbio.02373-20] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022] Open
Abstract
The signal recognition particle (SRP) is conserved in all living organisms, and it cotranslationally delivers proteins to the inner membrane or endoplasmic reticulum. Recently, SRP loss was found not to be lethal in either the eukaryote Saccharomyces cerevisiae or the prokaryote Streptococcus mutans In Escherichia coli, the role of SRP in mediating inner membrane protein (IMP) targeting has long been studied. However, the essentiality of SRP remains a controversial topic, partly hindered by the lack of strains in which SRP is completely absent. Here we show that the SRP was nonessential in E. coli by suppressor screening. We identified two classes of extragenic suppressors-two translation initiation factors and a ribosomal protein-all of which are involved in translation initiation. The translation rate and inner membrane proteomic analyses were combined to define the mechanism that compensates for the lack of SRP. The primary factor that contributes to the efficiency of IMP targeting is the extension of the time window for targeting by pausing the initiation of translation, which further reduces translation initiation and elongation rates. Furthermore, we found that easily predictable features in the nascent chain determine the specificity of protein targeting. Our results show why the loss of the SRP pathway does not lead to lethality. We report a new paradigm in which the time delay in translation initiation is beneficial during protein targeting in the absence of SRP.IMPORTANCE Inner membrane proteins (IMPs) are cotranslationally inserted into the inner membrane or endoplasmic reticulum by the signal recognition particle (SRP). Generally, the deletion of SRP can result in protein targeting defects in Escherichia coli Suppressor screening for loss of SRP reveals that pausing at the translation start site is likely to be critical in allowing IMP targeting and avoiding aggregation. In this work, we found for the first time that SRP is nonessential in E. coli The time delay in initiation is different from the previous mechanism that only slows down the elongation rate. It not only maximizes the opportunity for untranslated ribosomes to be near the inner membrane but also extends the time window for targeting translating ribosomes by decreasing the speed of translation. We anticipate that our work will be a starting point for a more delicate regulatory mechanism of protein targeting.
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17
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Juaire KD, Lapouge K, Becker MMM, Kotova I, Michelhans M, Carapito R, Wild K, Bahram S, Sinning I. Structural and Functional Impact of SRP54 Mutations Causing Severe Congenital Neutropenia. Structure 2020; 29:15-28.e7. [PMID: 33053321 DOI: 10.1016/j.str.2020.09.008] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2020] [Revised: 07/22/2020] [Accepted: 09/23/2020] [Indexed: 01/12/2023]
Abstract
The SRP54 GTPase is a key component of co-translational protein targeting by the signal recognition particle (SRP). Point mutations in SRP54 have been recently shown to lead to a form of severe congenital neutropenia displaying symptoms overlapping with those of Shwachman-Diamond syndrome. The phenotype includes severe neutropenia, exocrine pancreatic deficiency, and neurodevelopmental as well as skeletal disorders. Using a combination of X-ray crystallography, hydrogen-deuterium exchange coupled to mass spectrometry and complementary biochemical and biophysical methods, we reveal extensive structural defects in three disease-causing SRP54 variants resulting in critical protein destabilization. GTP binding is mostly abolished as a consequence of an altered GTPase core. The mutations located in conserved sequence fingerprints of SRP54 eliminate targeting complex formation with the SRP receptor as demonstrated in yeast and human cells. These specific defects critically influence the entire SRP pathway, thereby causing this life-threatening disease.
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Affiliation(s)
- Keven D Juaire
- Heidelberg University Biochemistry Center (BZH), Im Neuenheimer Feld 328, D-69120 Heidelberg, Germany
| | - Karine Lapouge
- Heidelberg University Biochemistry Center (BZH), Im Neuenheimer Feld 328, D-69120 Heidelberg, Germany
| | - Matthias M M Becker
- Heidelberg University Biochemistry Center (BZH), Im Neuenheimer Feld 328, D-69120 Heidelberg, Germany
| | - Irina Kotova
- BIOMICA SAS, 4 rue Boussingault, 67000 Strasbourg, France
| | - Michelle Michelhans
- Heidelberg University Biochemistry Center (BZH), Im Neuenheimer Feld 328, D-69120 Heidelberg, Germany
| | - Raphael Carapito
- Laboratoire d'ImmunoRhumatologie Moléculaire, plateforme GENOMAX, INSERM UMR_S 1109, Faculté de Médecine, Fédération Hospitalo-Universitaire OMICARE, Fédération de Médecine Translationnelle de Strasbourg (FMTS), LabEx TRANSPLANTEX, Université de Strasbourg, 4 rue Kirschleger, 67085 Strasbourg, France
| | - Klemens Wild
- Heidelberg University Biochemistry Center (BZH), Im Neuenheimer Feld 328, D-69120 Heidelberg, Germany
| | - Seiamak Bahram
- Laboratoire d'ImmunoRhumatologie Moléculaire, plateforme GENOMAX, INSERM UMR_S 1109, Faculté de Médecine, Fédération Hospitalo-Universitaire OMICARE, Fédération de Médecine Translationnelle de Strasbourg (FMTS), LabEx TRANSPLANTEX, Université de Strasbourg, 4 rue Kirschleger, 67085 Strasbourg, France
| | - Irmgard Sinning
- Heidelberg University Biochemistry Center (BZH), Im Neuenheimer Feld 328, D-69120 Heidelberg, Germany.
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18
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Fujiwara K, Katagi Y, Ito K, Chiba S. Proteome-wide Capture of Co-translational Protein Dynamics in Bacillus subtilis Using TnDR, a Transposable Protein-Dynamics Reporter. Cell Rep 2020; 33:108250. [DOI: 10.1016/j.celrep.2020.108250] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2020] [Revised: 09/03/2020] [Accepted: 09/17/2020] [Indexed: 11/29/2022] Open
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19
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Singh AP, Salvatori R, Aftab W, Kohler A, Carlström A, Forne I, Imhof A, Ott M. Molecular Connectivity of Mitochondrial Gene Expression and OXPHOS Biogenesis. Mol Cell 2020; 79:1051-1065.e10. [PMID: 32877643 DOI: 10.1016/j.molcel.2020.07.024] [Citation(s) in RCA: 28] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2020] [Revised: 07/20/2020] [Accepted: 07/21/2020] [Indexed: 01/05/2023]
Abstract
Mitochondria contain their own gene expression systems, including membrane-bound ribosomes dedicated to synthesizing a few hydrophobic subunits of the oxidative phosphorylation (OXPHOS) complexes. We used a proximity-dependent biotinylation technique, BioID, coupled with mass spectrometry to delineate in baker's yeast a comprehensive network of factors involved in biogenesis of mitochondrial encoded proteins. This mitochondrial gene expression network (MiGENet) encompasses proteins involved in transcription, RNA processing, translation, or protein biogenesis. Our analyses indicate the spatial organization of these processes, thereby revealing basic mechanistic principles and the proteins populating strategically important sites. For example, newly synthesized proteins are directly handed over to ribosomal tunnel exit-bound factors that mediate membrane insertion, co-factor acquisition, or their mounting into OXPHOS complexes in a special early assembly hub. Collectively, the data reveal the connectivity of mitochondrial gene expression, reflecting a unique tailoring of the mitochondrial gene expression system.
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Affiliation(s)
- Abeer Prakash Singh
- Department of Biochemistry and Biophysics, Stockholm University, 10691 Stockholm, Sweden; Department of Medical Biochemistry and Cell Biology, University of Gothenburg, 40530 Gothenburg, Sweden
| | - Roger Salvatori
- Department of Biochemistry and Biophysics, Stockholm University, 10691 Stockholm, Sweden; Department of Medical Biochemistry and Cell Biology, University of Gothenburg, 40530 Gothenburg, Sweden
| | - Wasim Aftab
- BioMedical Center, Faculty of Medicine, Ludwig Maximilians University of Munich, 82152 Planegg-Martinsried, Germany; Graduate School for Quantitative Biosciences (QBM), Ludwig Maximilians University of Munich, 81377 Munich, Germany
| | - Andreas Kohler
- Department of Biochemistry and Biophysics, Stockholm University, 10691 Stockholm, Sweden
| | - Andreas Carlström
- Department of Biochemistry and Biophysics, Stockholm University, 10691 Stockholm, Sweden
| | - Ignasi Forne
- BioMedical Center, Faculty of Medicine, Ludwig Maximilians University of Munich, 82152 Planegg-Martinsried, Germany
| | - Axel Imhof
- BioMedical Center, Faculty of Medicine, Ludwig Maximilians University of Munich, 82152 Planegg-Martinsried, Germany
| | - Martin Ott
- Department of Biochemistry and Biophysics, Stockholm University, 10691 Stockholm, Sweden; Department of Medical Biochemistry and Cell Biology, University of Gothenburg, 40530 Gothenburg, Sweden.
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20
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ER Stress-Induced Secretion of Proteins and Their Extracellular Functions in the Heart. Cells 2020; 9:cells9092066. [PMID: 32927693 PMCID: PMC7563782 DOI: 10.3390/cells9092066] [Citation(s) in RCA: 22] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2020] [Revised: 09/02/2020] [Accepted: 09/03/2020] [Indexed: 12/12/2022] Open
Abstract
Endoplasmic reticulum (ER) stress is a result of conditions that imbalance protein homeostasis or proteostasis at the ER, for example ischemia, and is a common event in various human pathologies, including the diseased heart. Cardiac integrity and function depend on the active secretion of mature proteins from a variety of cell types in the heart, a process that requires an intact ER environment for efficient protein folding and trafficking to the secretory pathway. As a consequence of ER stress, most protein secretion by the ER secretory pathway is decreased. Strikingly, there is a select group of proteins that are secreted in greater quantities during ER stress. ER stress resulting from the dysregulation of ER Ca2+ levels, for instance, stimulates the secretion of Ca2+-binding ER chaperones, especially GRP78, GRP94, calreticulin, and mesencephalic astrocyte-derived neurotrophic factor (MANF), which play a multitude of roles outside the cell, strongly depending on the cell type and tissue. Here we review current insights in ER stress-induced secretion of proteins, particularly from the heart, and highlight the extracellular functions of these proteins, ranging from the augmentation of cardiac cell viability to the modulation of pro- and anti-apoptotic, oncogenic, and immune-stimulatory cell signaling, cell invasion, extracellular proteostasis, and more. Many of the roles of ER stress-induced protein secretion remain to be explored in the heart. This article is part of a special issue entitled “The Role of Proteostasis Derailment in Cardiac Diseases.”
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21
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Goldberg L, Simon AJ, Rechavi G, Lev A, Barel O, Kunik V, Toren A, Schiby G, Tamary H, Steinberg-Shemer O, Somech R. Congenital neutropenia with variable clinical presentation in novel mutation of the SRP54 gene. Pediatr Blood Cancer 2020; 67:e28237. [PMID: 32277798 DOI: 10.1002/pbc.28237] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/08/2019] [Revised: 02/08/2020] [Accepted: 02/12/2020] [Indexed: 12/18/2022]
Abstract
BACKGROUND The SRP54 (signal recognition protein 54) is a conserved component of the ribonucleoprotein complex that mediates cotranslational targeting and translocation of proteins to the endoplasmic reticulum. In 2017, mutations in the gene have been described as a cause of congenital neutropenia with or without pancreatic insufficiency, and since then, only limited cases were added to the literature. METHODS Two patients with neutropenia underwent hematological, immunological, and genetic work-up, including lymphocyte phenotyping, immunoglobulins, and complement levels, antineutrophil and antinuclear antibodies, bone marrow FISH panel for myelodysplastic syndrome, whole-exome sequencing, and in silico proteomic analysis. RESULTS Clinical findings in the two families revealed a wide spectrum of immunological and clinical manifestations, ranging from mild asymptomatic neutropenia during febrile illnesses to severe neutropenia and life-threatening infection requiring leg amputation. Immunological and hematological work-up showed isolated neutropenia with normal lymphocyte subpopulations, immunoglobulin and complement levels, and negative autoimmune tests. Bone marrow aspirations showed variability ranging from normal myelopoiesis to myeloid maturation arrest at the promyelocytic stage, with normal FISH panel for myelodysplastic syndrome. Genetic analysis identified a novel, de novo, in-frame deletion in the SRP54 gene, c.342-344delAAC, p.T115del. In silico proteomic analysis suggested impaired SRP54 protein function due to reduced GTP activity and stability. CONCLUSIONS We describe congenital neutropenia with variable clinical presentation in novel mutation of the SRP54 gene.
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Affiliation(s)
- Lior Goldberg
- Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel.,Pediatric Department A, Pediatric Immunology Service, "Edmond and Lily Safra" Children's Hospital, Jeffrey Modell Foundation (JMF) Center, Tel HaShomer, Israel
| | - Amos J Simon
- Pediatric Department A, Pediatric Immunology Service, "Edmond and Lily Safra" Children's Hospital, Jeffrey Modell Foundation (JMF) Center, Tel HaShomer, Israel.,The Wohl Institute for Translational Medicine, Sheba Medical Center, Tel HaShomer, Israel
| | - Gideon Rechavi
- The Wohl Institute for Translational Medicine, Sheba Medical Center, Tel HaShomer, Israel.,Sheba Cancer Research Center, Sheba Medical Center, Tel HaShomer, Israel
| | - Atar Lev
- Pediatric Department A, Pediatric Immunology Service, "Edmond and Lily Safra" Children's Hospital, Jeffrey Modell Foundation (JMF) Center, Tel HaShomer, Israel
| | - Ortal Barel
- The Wohl Institute for Translational Medicine, Sheba Medical Center, Tel HaShomer, Israel.,Sheba Cancer Research Center, Sheba Medical Center, Tel HaShomer, Israel
| | | | - Amos Toren
- Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel.,Pediatric Hemato/Oncology Division and Bone Marrow Transplantation Unit, Tel HaShomer, Israel
| | - Ginette Schiby
- The Wohl Institute for Translational Medicine, Sheba Medical Center, Tel HaShomer, Israel
| | - Hannah Tamary
- Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel.,Departments of Hematology-Oncology, Schneider Children's Medical Center of Israel, Petach Tivka, Israel
| | - Orna Steinberg-Shemer
- Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel.,Departments of Hematology-Oncology, Schneider Children's Medical Center of Israel, Petach Tivka, Israel
| | - Raz Somech
- Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel.,Pediatric Department A, Pediatric Immunology Service, "Edmond and Lily Safra" Children's Hospital, Jeffrey Modell Foundation (JMF) Center, Tel HaShomer, Israel.,The Wohl Institute for Translational Medicine, Sheba Medical Center, Tel HaShomer, Israel
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22
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Dukovski D, Villella A, Bastos C, King R, Finley D, Kelly JW, Morimoto RI, Hartl FU, Munoz B, Lee PS, Zecevic M, Miller JP. Amplifiers co-translationally enhance CFTR biosynthesis via PCBP1-mediated regulation of CFTR mRNA. J Cyst Fibros 2020; 19:733-741. [PMID: 32067958 DOI: 10.1016/j.jcf.2020.02.006] [Citation(s) in RCA: 32] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2019] [Revised: 02/01/2020] [Accepted: 02/06/2020] [Indexed: 12/21/2022]
Abstract
BACKGROUND Cystic fibrosis (CF) is a recessive disorder caused by mutations in the cystic fibrosis transmembrane conductance regulator (CFTR) gene. We previously described a first-in-class CFTR modulator that functions as an amplifier to selectively increase CFTR expression and function. The amplifier mechanism is distinct from and complementary to corrector and potentiator classes of CFTR modulators. Here we characterize the mechanism by which amplifiers increase CFTR mRNA, protein, and activity. METHODS Biochemical studies elucidated the action of amplifiers on CFTR mRNA abundance and translation and defined the role of an amplifier-binding protein that was identified using chemical proteomics. RESULTS Amplifiers stabilize CFTR mRNA through a process that requires only the translated sequence of CFTR and involves translational elongation. Amplifiers enrich ER-associated CFTR mRNA and increase its translational efficiency through increasing the fraction of CFTR mRNA associated with polysomes. Pulldowns identified the poly(rC)-binding protein 1 (PCBP1) as directly binding to amplifier. A PCBP1 consensus element was identified within the CFTR open reading frame that binds PCBP1. This sequence proved necessary for amplifier responsiveness. CONCLUSIONS Small molecule amplifiers co-translationally increase CFTR mRNA stability. They enhance translation through addressing the inherently inefficient membrane targeting of CFTR mRNA. Amplifiers bind directly to PCBP1, show enhanced affinity in the presence of bound RNA, and require a PCBP1 consensus element within CFTR mRNA to elicit translational effects. These modulators represent a promising new and mechanistically novel class of CFTR therapeutic. They may be useful as a monotherapy or in combination with other CFTR modulators.
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Affiliation(s)
- Danijela Dukovski
- Proteostasis Therapeutics, Inc., 80 Guest St, Suite 500, Boston, MA 02135, United States
| | - Adriana Villella
- Proteostasis Therapeutics, Inc., 80 Guest St, Suite 500, Boston, MA 02135, United States
| | - Cecilia Bastos
- Proteostasis Therapeutics, Inc., 80 Guest St, Suite 500, Boston, MA 02135, United States
| | - Randall King
- Department of Cell Biology, Harvard Medical School, Boston, MA 02115, United States
| | - Daniel Finley
- Department of Cell Biology, Harvard Medical School, Boston, MA 02115, United States
| | - Jeffery W Kelly
- Departments of Molecular Medicine and Chemistry, The Scripps Research Institute, La Jolla, CA 92037, United States
| | - Richard I Morimoto
- Department of Molecular Bioscience, Rice Institute for Biomedical Research, Northwestern University, Evanston, IL, United States
| | - F Ulrich Hartl
- Department of Cellular Biochemistry, Max Planck Institute of Biochemistry, Am Klopferspitz 18, D-82152 Martinsried, Germany
| | - Benito Munoz
- Proteostasis Therapeutics, Inc., 80 Guest St, Suite 500, Boston, MA 02135, United States
| | - Po-Shun Lee
- Proteostasis Therapeutics, Inc., 80 Guest St, Suite 500, Boston, MA 02135, United States
| | - Marija Zecevic
- Proteostasis Therapeutics, Inc., 80 Guest St, Suite 500, Boston, MA 02135, United States
| | - John Preston Miller
- Proteostasis Therapeutics, Inc., 80 Guest St, Suite 500, Boston, MA 02135, United States.
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23
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Principle and potential applications of the non-classical protein secretory pathway in bacteria. Appl Microbiol Biotechnol 2019; 104:953-965. [PMID: 31853566 DOI: 10.1007/s00253-019-10285-4] [Citation(s) in RCA: 26] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2019] [Revised: 10/22/2019] [Accepted: 10/27/2019] [Indexed: 12/15/2022]
Abstract
In addition to the extracellular proteins secreted by known secretory pathways, a number of cytoplasmic proteins without predicable or known signal sequences or secretory motifs have been found in the extracellular milieu, and were consequently classified as non-classically secreted proteins. Non-classical protein secretion is considered to be a general, conserved cellular phenomenon in both eukaryotes and prokaryotes. There are several research hotspots on the non-classical protein secretory pathway, and the most important two of them are the recognition principle of substrate proteins and possible secretory mechanisms. To date, researchers have made some progress in understanding the characteristics of these proteins. For example, it was discovered that many non-classically secreted proteins exist and are secreted in multimeric form. Some of these proteins prefer to be clustered and exported at the poles and the septum of the cell. The majority of these proteins play different functions when they are in the intra- and extracellular environments, and several of their functions are related to survival and pathogenicity. Furthermore, non-classically secreted proteins can be used as leading proteins to guide a POI (protein of interest) out of the cells, which provides a novel strategy for protein secretion with potential applications in the industry. Summarizing these findings, this review emphasizes the hot spots related to non-classically secreted proteins in bacteria, lists the most important hypotheses on the selection and secretion mechanisms of non-classically secreted proteins, and put forward their potential applications.
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24
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Wild K, Juaire KD, Soni K, Shanmuganathan V, Hendricks A, Segnitz B, Beckmann R, Sinning I. Reconstitution of the human SRP system and quantitative and systematic analysis of its ribosome interactions. Nucleic Acids Res 2019; 47:3184-3196. [PMID: 30649417 PMCID: PMC6451106 DOI: 10.1093/nar/gky1324] [Citation(s) in RCA: 23] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2018] [Revised: 12/20/2018] [Accepted: 01/02/2019] [Indexed: 12/22/2022] Open
Abstract
Co-translational protein targeting to membranes depends on the regulated interaction of two ribonucleoprotein particles (RNPs): the ribosome and the signal recognition particle (SRP). Human SRP is composed of an SRP RNA and six proteins with the SRP GTPase SRP54 forming the targeting complex with the heterodimeric SRP receptor (SRαβ) at the endoplasmic reticulum membrane. While detailed structural and functional data are available especially for the bacterial homologs, the analysis of human SRP was impeded by the unavailability of recombinant SRP. Here, we describe the large-scale production of all human SRP components and the reconstitution of homogeneous SRP and SR complexes. Binding to human ribosomes is determined by microscale thermophoresis for individual components, assembly intermediates and entire SRP, and binding affinities are correlated with structural information available for all ribosomal contacts. We show that SRP RNA does not bind to the ribosome, while SRP binds with nanomolar affinity involving a two-step mechanism of the key-player SRP54. Ultrasensitive binding of SRP68/72 indicates avidity by multiple binding sites that are dominated by the C-terminus of SRP72. Our data extend the experimental basis to understand the mechanistic principles of co-translational targeting in mammals and may guide analyses of complex RNP–RNP interactions in general.
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Affiliation(s)
- Klemens Wild
- Heidelberg University Biochemistry Center (BZH), INF 328, D-69120 Heidelberg, Germany
| | - Keven D Juaire
- Heidelberg University Biochemistry Center (BZH), INF 328, D-69120 Heidelberg, Germany
| | - Komal Soni
- Heidelberg University Biochemistry Center (BZH), INF 328, D-69120 Heidelberg, Germany
| | - Vivekanandan Shanmuganathan
- Gene Center and Center for Integrated Protein Science Munich, Department of Biochemistry, University of Munich, Feodor-Lynen-Str. 25, D-81377 Munich, Germany
| | - Astrid Hendricks
- Heidelberg University Biochemistry Center (BZH), INF 328, D-69120 Heidelberg, Germany
| | - Bernd Segnitz
- Heidelberg University Biochemistry Center (BZH), INF 328, D-69120 Heidelberg, Germany
| | - Roland Beckmann
- Gene Center and Center for Integrated Protein Science Munich, Department of Biochemistry, University of Munich, Feodor-Lynen-Str. 25, D-81377 Munich, Germany
| | - Irmgard Sinning
- Heidelberg University Biochemistry Center (BZH), INF 328, D-69120 Heidelberg, Germany
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25
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Wang S, Jomaa A, Jaskolowski M, Yang CI, Ban N, Shan SO. The molecular mechanism of cotranslational membrane protein recognition and targeting by SecA. Nat Struct Mol Biol 2019; 26:919-929. [PMID: 31570874 PMCID: PMC6858539 DOI: 10.1038/s41594-019-0297-8] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2019] [Accepted: 08/12/2019] [Indexed: 11/16/2022]
Abstract
Cotranslational protein targeting is a conserved process for membrane protein biogenesis. In Escherichia coli, the essential ATPase SecA was found to cotranslationally target a subset of nascent membrane proteins to the SecYEG translocase at the plasma membrane. The molecular mechanism of this pathway remains unclear. Here we use biochemical and cryoelectron microscopy analyses to show that the amino-terminal amphipathic helix of SecA and the ribosomal protein uL23 form a composite binding site for the transmembrane domain (TMD) on the nascent protein. This binding mode further enables recognition of charged residues flanking the nascent TMD and thus explains the specificity of SecA recognition. Finally, we show that membrane-embedded SecYEG promotes handover of the translating ribosome from SecA to the translocase via a concerted mechanism. Our work provides a molecular description of the SecA-mediated cotranslational targeting pathway and demonstrates an unprecedented role of the ribosome in shielding nascent TMDs.
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Affiliation(s)
- Shuai Wang
- Division of Chemistry and Chemical Engineering, California Institute of Technology, Pasadena, CA, USA
| | - Ahmad Jomaa
- Department of Biology, Institute of Molecular Biology and Biophysics, ETH Zurich, Zurich, Switzerland
| | - Mateusz Jaskolowski
- Department of Biology, Institute of Molecular Biology and Biophysics, ETH Zurich, Zurich, Switzerland
| | - Chien-I Yang
- Division of Chemistry and Chemical Engineering, California Institute of Technology, Pasadena, CA, USA
| | - Nenad Ban
- Department of Biology, Institute of Molecular Biology and Biophysics, ETH Zurich, Zurich, Switzerland.
| | - Shu-Ou Shan
- Division of Chemistry and Chemical Engineering, California Institute of Technology, Pasadena, CA, USA.
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26
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Wild K, Becker MM, Kempf G, Sinning I. Structure, dynamics and interactions of large SRP variants. Biol Chem 2019; 401:63-80. [DOI: 10.1515/hsz-2019-0282] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2019] [Accepted: 08/09/2019] [Indexed: 12/11/2022]
Abstract
Abstract
Co-translational protein targeting to membranes relies on the signal recognition particle (SRP) system consisting of a cytosolic ribonucleoprotein complex and its membrane-associated receptor. SRP recognizes N-terminal cleavable signals or signal anchor sequences, retards translation, and delivers ribosome-nascent chain complexes (RNCs) to vacant translocation channels in the target membrane. While our mechanistic understanding is well advanced for the small bacterial systems it lags behind for the large bacterial, archaeal and eukaryotic SRP variants including an Alu and an S domain. Here we describe recent advances on structural and functional insights in domain architecture, particle dynamics and interplay with RNCs and translocon and GTP-dependent regulation of co-translational protein targeting stimulated by SRP RNA.
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Affiliation(s)
- Klemens Wild
- Heidelberg University Biochemistry Center (BZH) , INF 328 , D-69120 Heidelberg , Germany
| | - Matthias M.M. Becker
- Heidelberg University Biochemistry Center (BZH) , INF 328 , D-69120 Heidelberg , Germany
| | - Georg Kempf
- Heidelberg University Biochemistry Center (BZH) , INF 328 , D-69120 Heidelberg , Germany
| | - Irmgard Sinning
- Heidelberg University Biochemistry Center (BZH) , INF 328 , D-69120 Heidelberg , Germany
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27
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Kramer G, Shiber A, Bukau B. Mechanisms of Cotranslational Maturation of Newly Synthesized Proteins. Annu Rev Biochem 2019; 88:337-364. [DOI: 10.1146/annurev-biochem-013118-111717] [Citation(s) in RCA: 98] [Impact Index Per Article: 19.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
The timely production of functional proteins is of critical importance for the biological activity of cells. To reach the functional state, newly synthesized polypeptides have to become enzymatically processed, folded, and assembled into oligomeric complexes and, for noncytosolic proteins, translocated across membranes. Key activities of these processes occur cotranslationally, assisted by a network of machineries that transiently engage nascent polypeptides at distinct phases of translation. The sequence of events is tuned by intrinsic features of the nascent polypeptides and timely association of factors with the translating ribosome. Considering the dynamics of translation, the heterogeneity of cellular proteins, and the diversity of interaction partners, it is a major cellular achievement that these processes are temporally and spatially so precisely coordinated, minimizing the generation of damaged proteins. This review summarizes the current progress we have made toward a comprehensive understanding of the cotranslational interactions of nascent chains, which pave the way to their functional state.
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Affiliation(s)
- Günter Kramer
- Center for Molecular Biology of Heidelberg University (ZMBH) and German Cancer Research Center (DKFZ), DKFZ-ZMBH Alliance, D-69120 Heidelberg, Germany;,
| | - Ayala Shiber
- Center for Molecular Biology of Heidelberg University (ZMBH) and German Cancer Research Center (DKFZ), DKFZ-ZMBH Alliance, D-69120 Heidelberg, Germany;,
| | - Bernd Bukau
- Center for Molecular Biology of Heidelberg University (ZMBH) and German Cancer Research Center (DKFZ), DKFZ-ZMBH Alliance, D-69120 Heidelberg, Germany;,
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28
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Peng C, Shi C, Cao X, Li Y, Liu F, Lu F. Factors Influencing Recombinant Protein Secretion Efficiency in Gram-Positive Bacteria: Signal Peptide and Beyond. Front Bioeng Biotechnol 2019; 7:139. [PMID: 31245367 PMCID: PMC6579943 DOI: 10.3389/fbioe.2019.00139] [Citation(s) in RCA: 31] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2019] [Accepted: 05/23/2019] [Indexed: 11/13/2022] Open
Abstract
Signal peptides are short peptides directing newly synthesized proteins toward the secretory pathway. These N-terminal signal sequences are ubiquitous to all prokaryotes and eukaryotes. Signal peptides play a significant role in recombinant protein production. Previous studies have demonstrated that the secretion amount of a given target protein varies significantly depending on the signal peptide that is fused to the protein. Signal peptide selection and signal peptide modification are the two main methods for the optimization of a recombinant protein secretion. However, the highly efficient signal peptide for a target protein with a specific bacterial expression host is not predictable so far. In this article, we collect several signal peptides that have previously performed well for recombinant protein secretion in gram-positive bacteria. We also discuss several factors influencing recombinant protein secretion efficiency in gram-positive bacteria. Signal peptides with a higher charge/length ratio in n-region, more consensus residues at the-3 and-1positions in c-region and a much higher proportion of coils are more likely to perform well in the secretion of recombinant proteins. These summaries can be utilized to the selection and directed modification of signal peptides for a given recombinant protein.
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Affiliation(s)
- Chong Peng
- Key Laboratory of Industrial Fermentation Microbiology, Education Ministry of China, Tianjin, China
- National Engineering Laboratory for Industrial Enzymes, Tianjin, China
- Tianjin Engineering Research Center of Microbial Metabolism and Fermentation Process Control, Tianjin, China
- College of Biotechnology, Tianjin University of Science and Technology, Tianjin, China
| | - Chaoshuo Shi
- College of Biotechnology, Tianjin University of Science and Technology, Tianjin, China
| | - Xue Cao
- College of Biotechnology, Tianjin University of Science and Technology, Tianjin, China
| | - Yu Li
- Key Laboratory of Industrial Fermentation Microbiology, Education Ministry of China, Tianjin, China
- National Engineering Laboratory for Industrial Enzymes, Tianjin, China
- Tianjin Engineering Research Center of Microbial Metabolism and Fermentation Process Control, Tianjin, China
- College of Biotechnology, Tianjin University of Science and Technology, Tianjin, China
| | - Fufeng Liu
- Key Laboratory of Industrial Fermentation Microbiology, Education Ministry of China, Tianjin, China
- National Engineering Laboratory for Industrial Enzymes, Tianjin, China
- Tianjin Engineering Research Center of Microbial Metabolism and Fermentation Process Control, Tianjin, China
- College of Biotechnology, Tianjin University of Science and Technology, Tianjin, China
| | - Fuping Lu
- Key Laboratory of Industrial Fermentation Microbiology, Education Ministry of China, Tianjin, China
- National Engineering Laboratory for Industrial Enzymes, Tianjin, China
- Tianjin Engineering Research Center of Microbial Metabolism and Fermentation Process Control, Tianjin, China
- College of Biotechnology, Tianjin University of Science and Technology, Tianjin, China
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29
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Two Old Dogs, One New Trick: A Review of RNA Polymerase and Ribosome Interactions during Transcription-Translation Coupling. Int J Mol Sci 2019; 20:ijms20102595. [PMID: 31137816 PMCID: PMC6566652 DOI: 10.3390/ijms20102595] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2019] [Revised: 05/22/2019] [Accepted: 05/24/2019] [Indexed: 12/14/2022] Open
Abstract
The coupling of transcription and translation is more than mere translation of an mRNA that is still being transcribed. The discovery of physical interactions between RNA polymerase and ribosomes has spurred renewed interest into this long-standing paradigm of bacterial molecular biology. Here, we provide a concise presentation of recent insights gained from super-resolution microscopy, biochemical, and structural work, including cryo-EM studies. Based on the presented data, we put forward a dynamic model for the interaction between RNA polymerase and ribosomes, in which the interactions are repeatedly formed and broken. Furthermore, we propose that long intervening nascent RNA will loop out and away during the forming the interactions between the RNA polymerase and ribosomes. By comparing the effect of the direct interactions between RNA polymerase and ribosomes with those that transcription factors NusG and RfaH mediate, we submit that two distinct modes of coupling exist: Factor-free and factor-mediated coupling. Finally, we provide a possible framework for transcription-translation coupling and elude to some open questions in the field.
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30
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Li J, Zhang X, Xu J, Pei X, Wu Z, Wang T, Yin S. iTRAQ analysis of liver immune-related proteins from darkbarbel catfish (Pelteobagrus vachelli) infected with Edwardsiella ictaluri. FISH & SHELLFISH IMMUNOLOGY 2019; 87:695-704. [PMID: 30703552 DOI: 10.1016/j.fsi.2019.01.036] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/07/2018] [Revised: 01/18/2019] [Accepted: 01/25/2019] [Indexed: 06/09/2023]
Abstract
Edwardsiella ictaluri causes enteric septicemia of catfish (ESC), a major disease occurring in these siluriform fish. As the liver is an important organ for defending against bacterial pathogens in fish, this study aimed to determine the liver immune response at the protein level. The differential proteomes of the darkbarbel catfish liver in response to E. ictaluri infection were identified with isobaric tags for relative and absolute quantitation (iTRAQ) labeling followed by liquid chromatography-tandem mass spectrometry (LC-MS/MS). Using a 1.2-fold change in expression as a physiologically significant benchmark, a total of 819 differentially expressed proteins were reliably quantified using iTRAQ analysis, including 6 up-regulated proteins and 813 down-regulated proteins. GO enrichment analysis indicated that the "complement activation, alternative pathway" and "complement activation, classical pathway" were significantly enriched. KEGG enrichment analysis indicated the "antigen processing and presentation" and "bacterial secretion system" were significantly enriched. We selected the 6 up-regulated proteins and 10 immune-related down-regulated proteins for validation using real-time PCR. The 10 immune-related proteins included complement component C1r, C3, C5, C7, and C9 and plasma protease C1 inhibitor (C1-INH), signal recognition particle 54 kDa protein (SRP54), SRP receptor, proteasome activator complex subunit 1 (PSME1) and major histocompatibility complex class I (MHC class I) were selected from the GO clusters and KEGG pathways. The variations in mRNA expression for these genes were similar to the results of iTRAQ. This is the first report detailing the proteome response in the darkbarbel catfish liver during E. ictaluri infection and markedly contributes to our understanding of the defense mechanisms in the livers of darkbarbel catfish.
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Affiliation(s)
- Jie Li
- College of Life Sciences, College of Marine Science and Engineering, Nanjing Normal University, Nanjing, Jiangsu 210023, China; Co-Innovation Center for Marine Bio-Industry Technology of Jiangsu Province, Lianyungang, Jiangsu, 222005, China
| | - Xinyu Zhang
- College of Life Sciences, College of Marine Science and Engineering, Nanjing Normal University, Nanjing, Jiangsu 210023, China; Co-Innovation Center for Marine Bio-Industry Technology of Jiangsu Province, Lianyungang, Jiangsu, 222005, China
| | - Jiejie Xu
- College of Life Sciences, College of Marine Science and Engineering, Nanjing Normal University, Nanjing, Jiangsu 210023, China; Co-Innovation Center for Marine Bio-Industry Technology of Jiangsu Province, Lianyungang, Jiangsu, 222005, China
| | - Xueyin Pei
- College of Life Sciences, College of Marine Science and Engineering, Nanjing Normal University, Nanjing, Jiangsu 210023, China; Co-Innovation Center for Marine Bio-Industry Technology of Jiangsu Province, Lianyungang, Jiangsu, 222005, China
| | - Zhaowen Wu
- College of Life Sciences, College of Marine Science and Engineering, Nanjing Normal University, Nanjing, Jiangsu 210023, China; Co-Innovation Center for Marine Bio-Industry Technology of Jiangsu Province, Lianyungang, Jiangsu, 222005, China
| | - Tao Wang
- College of Life Sciences, College of Marine Science and Engineering, Nanjing Normal University, Nanjing, Jiangsu 210023, China; Co-Innovation Center for Marine Bio-Industry Technology of Jiangsu Province, Lianyungang, Jiangsu, 222005, China.
| | - Shaowu Yin
- College of Life Sciences, College of Marine Science and Engineering, Nanjing Normal University, Nanjing, Jiangsu 210023, China; Co-Innovation Center for Marine Bio-Industry Technology of Jiangsu Province, Lianyungang, Jiangsu, 222005, China.
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31
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Bhakta S, Akbar S, Sengupta J. Cryo-EM Structures Reveal Relocalization of MetAP in the Presence of Other Protein Biogenesis Factors at the Ribosomal Tunnel Exit. J Mol Biol 2019; 431:1426-1439. [DOI: 10.1016/j.jmb.2019.02.002] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2018] [Revised: 02/01/2019] [Accepted: 02/01/2019] [Indexed: 11/30/2022]
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Samson J, Cronin S, Dean K. BC200 (BCYRN1) - The shortest, long, non-coding RNA associated with cancer. Noncoding RNA Res 2018; 3:131-143. [PMID: 30175286 PMCID: PMC6114260 DOI: 10.1016/j.ncrna.2018.05.003] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2017] [Revised: 05/14/2018] [Accepted: 05/17/2018] [Indexed: 12/22/2022] Open
Abstract
With the discovery that the level of RNA synthesis in human cells far exceeds what is required to express protein-coding genes, there has been a concerted scientific effort to identify, catalogue and uncover the biological functions of the non-coding transcriptome. Long, non-coding RNAs (lncRNAs) are a diverse group of RNAs with equally wide-ranging biological roles in the cell. An increasing number of studies have reported alterations in the expression of lncRNAs in various cancers, although unravelling how they contribute specifically to the disease is a bigger challenge. Originally described as a brain-specific, non-coding RNA, BC200 (BCYRN1) is a 200-nucleotide, predominantly cytoplasmic lncRNA that has been linked to neurodegenerative disease and several types of cancer. Here we summarise what is known about BC200, primarily from studies in neuronal systems, before turning to a review of recent work that aims to understand how this lncRNA contributes to cancer initiation, progression and metastasis, along with its possible clinical utility as a biomarker or therapeutic target.
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Affiliation(s)
| | | | - K. Dean
- School of Biochemistry and Cell Biology, Western Gateway Building, University College Cork, Cork, Ireland
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33
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Mutations in the SRP54 gene cause severe congenital neutropenia as well as Shwachman-Diamond-like syndrome. Blood 2018; 132:1318-1331. [PMID: 29914977 DOI: 10.1182/blood-2017-12-820308] [Citation(s) in RCA: 73] [Impact Index Per Article: 12.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2017] [Accepted: 06/02/2018] [Indexed: 01/04/2023] Open
Abstract
Congenital neutropenias (CNs) are rare heterogeneous genetic disorders, with about 25% of patients without known genetic defects. Using whole-exome sequencing, we identified a heterozygous mutation in the SRP54 gene, encoding the signal recognition particle (SRP) 54 GTPase protein, in 3 sporadic cases and 1 autosomal dominant family. We subsequently sequenced the SRP54 gene in 66 probands from the French CN registry. In total, we identified 23 mutated cases (16 sporadic, 7 familial) with 7 distinct germ line SRP54 mutations including a recurrent in-frame deletion (Thr117del) in 14 cases. In nearly all patients, neutropenia was chronic and profound with promyelocytic maturation arrest, occurring within the first months of life, and required long-term granulocyte colony-stimulating factor therapy with a poor response. Neutropenia was sometimes associated with a severe neurodevelopmental delay (n = 5) and/or an exocrine pancreatic insufficiency requiring enzyme supplementation (n = 3). The SRP54 protein is a key component of the ribonucleoprotein complex that mediates the co-translational targeting of secretory and membrane proteins to the endoplasmic reticulum (ER). We showed that SRP54 was specifically upregulated during the in vitro granulocytic differentiation, and that SRP54 mutations or knockdown led to a drastically reduced proliferation of granulocytic cells associated with an enhanced P53-dependent apoptosis. Bone marrow examination of SRP54-mutated patients revealed a major dysgranulopoiesis and features of cellular ER stress and autophagy that were confirmed using SRP54-mutated primary cells and SRP54 knockdown cells. In conclusion, we characterized a pathological pathway, which represents the second most common cause of CN with maturation arrest in the French CN registry.
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34
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Le Scornet A, Redder P. Post-transcriptional control of virulence gene expression in Staphylococcus aureus. BIOCHIMICA ET BIOPHYSICA ACTA-GENE REGULATORY MECHANISMS 2018; 1862:734-741. [PMID: 29705591 DOI: 10.1016/j.bbagrm.2018.04.004] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/15/2018] [Revised: 04/25/2018] [Accepted: 04/25/2018] [Indexed: 12/12/2022]
Abstract
Opportunistic pathogens have to be ready to change life-style whenever the occasion arises, and therefore need to keep tight control over the expression of their virulence factors. Doubly so for commensal bacteria, such as Staphylococcus aureus, which should avoid harming their hosts when they are in a state of peaceful co-existence. S. aureus carries very few sigma factors to help define the transcriptional programs, but instead uses a plethora of small RNA molecules and RNA-RNA interactions to regulate gene expression post-transcriptionally. The endoribonucleases RNase III and RNase Y contribute to this regulatory diversity, and provide a link to RNA-decay and intra-cellular spatiotemporal control of expression. In this review we describe some of these post-transcriptional mechanisms as well as some of the novel transcriptomic approaches that have been used to find and to study them.
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Affiliation(s)
- Alexandre Le Scornet
- LMGM, Centre de Biologie Integrative, Paul Sabatier University, 118, Route de Narbonne, 31062 Toulouse, France
| | - Peter Redder
- LMGM, Centre de Biologie Integrative, Paul Sabatier University, 118, Route de Narbonne, 31062 Toulouse, France.
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35
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Freudl R. Signal peptides for recombinant protein secretion in bacterial expression systems. Microb Cell Fact 2018; 17:52. [PMID: 29598818 PMCID: PMC5875014 DOI: 10.1186/s12934-018-0901-3] [Citation(s) in RCA: 141] [Impact Index Per Article: 23.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2017] [Accepted: 03/27/2018] [Indexed: 02/06/2023] Open
Abstract
The secretion of biotechnologically or pharmaceutically relevant recombinant proteins into the culture supernatant of a bacterial expression host greatly facilitates their downstream processing and significantly reduces the production costs. The first step during the secretion of a desired target protein into the growth medium is its transport across the cytoplasmic membrane. In bacteria, two major export pathways, the general secretion or Sec pathway and the twin-arginine translocation or Tat pathway, exist for the transport of proteins across the plasma membrane. The routing into one of these alternative protein export systems requires the fusion of a Sec- or Tat-specific signal peptide to the amino-terminal end of the desired target protein. Since signal peptides, besides being required for the targeting to and membrane translocation by the respective protein translocases, also have additional influences on the biosynthesis, the folding kinetics, and the stability of the respective target proteins, it is not possible so far to predict in advance which signal peptide will perform best in the context of a given target protein and a given bacterial expression host. As outlined in this review, the most promising way to find the optimal signal peptide for a desired protein is to screen the largest possible diversity of signal peptides, either generated by signal peptide variation using large signal peptide libraries or, alternatively, by optimization of a given signal peptide using site-directed or random mutagenesis strategies.
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Affiliation(s)
- Roland Freudl
- Institut für Bio- und Geowissenschaften 1, Biotechnologie, Forschungszentrum Jülich GmbH, 52425, Jülich, Germany. .,Bioeconomy Science Center (BioSC), Forschungszentrum Jülich GmbH, 52425, Jülich, Germany.
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36
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Guo H, Sun J, Li X, Xiong Y, Wang H, Shu H, Zhu R, Liu Q, Huang Y, Madley R, Wang Y, Cui J, Arvan P, Liu M. Positive charge in the n-region of the signal peptide contributes to efficient post-translational translocation of small secretory preproteins. J Biol Chem 2017; 293:1899-1907. [PMID: 29229776 DOI: 10.1074/jbc.ra117.000922] [Citation(s) in RCA: 31] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2017] [Revised: 11/30/2017] [Indexed: 12/17/2022] Open
Abstract
Increasing evidence indicates that many small secretory preproteins can undergo post-translational translocation across the membrane of the endoplasmic reticulum. Although the cellular machinery involved in post-translational translocation of small secretory preproteins has begun to be elucidated, the intrinsic signals contained within these small secretory preproteins that contribute to their efficient post-translational translocation remain unknown. Here, we analyzed the eukaryotic secretory proteome and discovered the small secretory preproteins tend to have a higher probability to harbor the positive charge in the n-region of the signal peptide (SP). Eliminating the positive charge of the n-region blocked post-translational translocation of newly synthesized preproteins and selectively impaired translocation efficiency of small secretory preproteins. The pathophysiological significance of the positive charge in the n-region of SP was underscored by recently identified preproinsulin SP mutations that impair translocation of preproinsulin and cause maturity onset diabetes of youth (MODY). Remarkably, we have found that slowing the polypeptide elongation rate of small secretory preproteins could alleviate the translocation defect caused by loss of the n-region positive charge of the signal peptide. Together, these data reveal not only a previously unrecognized role of the n-region's positive charge in ensuring efficient post-translational translocation of small secretory preproteins, but they also highlight the molecular contribution of defects in this process to the pathogenesis of genetic disorders such as MODY.
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Affiliation(s)
- Huan Guo
- From the Department of Endocrinology and Metabolism, Tianjin Medical University General Hospital, Tianjin 300052, China.,the Division of Metabolism, Endocrinology and Diabetes, University of Michigan Medical School, Ann Arbor, Michigan 48105, and
| | - Jinhong Sun
- From the Department of Endocrinology and Metabolism, Tianjin Medical University General Hospital, Tianjin 300052, China.,the Division of Metabolism, Endocrinology and Diabetes, University of Michigan Medical School, Ann Arbor, Michigan 48105, and
| | - Xin Li
- From the Department of Endocrinology and Metabolism, Tianjin Medical University General Hospital, Tianjin 300052, China
| | - Yi Xiong
- the Division of Metabolism, Endocrinology and Diabetes, University of Michigan Medical School, Ann Arbor, Michigan 48105, and
| | - Heting Wang
- From the Department of Endocrinology and Metabolism, Tianjin Medical University General Hospital, Tianjin 300052, China
| | - Hua Shu
- From the Department of Endocrinology and Metabolism, Tianjin Medical University General Hospital, Tianjin 300052, China
| | - Ruimin Zhu
- From the Department of Endocrinology and Metabolism, Tianjin Medical University General Hospital, Tianjin 300052, China
| | - Qi Liu
- From the Department of Endocrinology and Metabolism, Tianjin Medical University General Hospital, Tianjin 300052, China
| | - Yumeng Huang
- From the Department of Endocrinology and Metabolism, Tianjin Medical University General Hospital, Tianjin 300052, China
| | - Rachel Madley
- the Division of Metabolism, Endocrinology and Diabetes, University of Michigan Medical School, Ann Arbor, Michigan 48105, and
| | - Yulun Wang
- the Division of Endocrinology, Tianjin People's Hospital, Tianjin 300120, China
| | - Jingqiu Cui
- From the Department of Endocrinology and Metabolism, Tianjin Medical University General Hospital, Tianjin 300052, China
| | - Peter Arvan
- the Division of Metabolism, Endocrinology and Diabetes, University of Michigan Medical School, Ann Arbor, Michigan 48105, and
| | - Ming Liu
- From the Department of Endocrinology and Metabolism, Tianjin Medical University General Hospital, Tianjin 300052, China, .,the Division of Metabolism, Endocrinology and Diabetes, University of Michigan Medical School, Ann Arbor, Michigan 48105, and
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37
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Benhalevy D, Biran I, Bochkareva ES, Sorek R, Bibi E. Evidence for a cytoplasmic pool of ribosome-free mRNAs encoding inner membrane proteins in Escherichia coli. PLoS One 2017; 12:e0183862. [PMID: 28841711 PMCID: PMC5571963 DOI: 10.1371/journal.pone.0183862] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2017] [Accepted: 08/11/2017] [Indexed: 12/13/2022] Open
Abstract
Translation-independent mRNA localization represents an emerging concept in cell biology. In Escherichia coli, mRNAs encoding integral membrane proteins (MPRs) are targeted to the membrane where they are translated by membrane associated ribosomes and the produced proteins are inserted into the membrane co-translationally. In order to better understand aspects of the biogenesis and localization of MPRs, we investigated their subcellular distribution using cell fractionation, RNA-seq and qPCR. The results show that MPRs are overrepresented in the membrane fraction, as expected, and depletion of the signal recognition particle-receptor, FtsY reduced the amounts of all mRNAs on the membrane. Surprisingly, however, MPRs were also found relatively abundant in the soluble ribosome-free fraction and their amount in this fraction is increased upon overexpression of CspE, which was recently shown to interact with MPRs. CspE also conferred a positive effect on the membrane-expression of integral membrane proteins. We discuss the possibility that the effects of CspE overexpression may link the intriguing subcellular localization of MPRs to the cytosolic ribosome-free fraction with their translation into membrane proteins and that the ribosome-free pool of MPRs may represent a stage during their targeting to the membrane, which precedes translation.
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Affiliation(s)
- Daniel Benhalevy
- Department of Biological Chemistry, Weizmann Institute of Science, Rehovot, Israel
| | - Ido Biran
- Department of Biological Chemistry, Weizmann Institute of Science, Rehovot, Israel
| | - Elena S. Bochkareva
- Department of Biological Chemistry, Weizmann Institute of Science, Rehovot, Israel
| | - Rotem Sorek
- Department of Molecular Genetics, Weizmann Institute of Science, Rehovot, Israel
| | - Eitan Bibi
- Department of Biological Chemistry, Weizmann Institute of Science, Rehovot, Israel
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38
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Gold VA, Chroscicki P, Bragoszewski P, Chacinska A. Visualization of cytosolic ribosomes on the surface of mitochondria by electron cryo-tomography. EMBO Rep 2017; 18:1786-1800. [PMID: 28827470 PMCID: PMC5623831 DOI: 10.15252/embr.201744261] [Citation(s) in RCA: 98] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2017] [Revised: 07/11/2017] [Accepted: 07/14/2017] [Indexed: 12/31/2022] Open
Abstract
We employed electron cryo‐tomography to visualize cytosolic ribosomes on the surface of mitochondria. Translation‐arrested ribosomes reveal the clustered organization of the TOM complex, corroborating earlier reports of localized translation. Ribosomes are shown to interact specifically with the TOM complex, and nascent chain binding is crucial for ribosome recruitment and stabilization. Ribosomes are bound to the membrane in discrete clusters, often in the vicinity of the crista junctions. This interaction highlights how protein synthesis may be coupled with transport. Our work provides unique insights into the spatial organization of cytosolic ribosomes on mitochondria.
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Affiliation(s)
- Vicki Am Gold
- Department of Structural Biology, Max Planck Institute of Biophysics, Frankfurt am Main, Germany .,Living Systems Institute, University of Exeter, Exeter, UK.,College of Life and Environmental Sciences, Geoffrey Pope, University of Exeter, Exeter, UK
| | - Piotr Chroscicki
- The International Institute of Molecular and Cell Biology, Warsaw, Poland
| | - Piotr Bragoszewski
- The International Institute of Molecular and Cell Biology, Warsaw, Poland
| | - Agnieszka Chacinska
- The International Institute of Molecular and Cell Biology, Warsaw, Poland .,Centre of New Technologies, University of Warsaw, Warsaw, Poland
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39
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Marino J, Holzhüter K, Kuhn B, Geertsma ER. Efficient Screening and Optimization of Membrane Protein Production in Escherichia coli. Methods Enzymol 2017; 594:139-164. [PMID: 28779839 DOI: 10.1016/bs.mie.2017.05.011] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/06/2022]
Abstract
Escherichia coli is one of the most widely used expression hosts for membrane proteins. However, establishing conditions for its recombinant production of membrane proteins remains difficult. Attempts to produce membrane proteins frequently result in either no expression or expression as misfolded aggregates. We developed an efficient pipeline for improving membrane protein overexpression in E. coli that is based on two approaches. The first involves transcriptional fusions, small additional RNA sequences upstream of the target open reading frame, to overcome no or poor overall expression levels. The other is based on a tunable promoter in combination with a fusion to green fluorescent protein serving as a reporter for the folding state of the target membrane protein. The latter combination allows adjusting the membrane protein expression rate to the downstream folding capacity, in order to decrease the formation of protein aggregates. This pipeline has proven successful for the efficient and parallel optimization of a diverse set of membrane proteins.
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Affiliation(s)
| | | | - Benedikt Kuhn
- Goethe University Frankfurt, Frankfurt/Main, Germany
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40
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Abstract
Many proteins are translocated across the endoplasmic reticulum (ER) membrane in eukaryotes or the plasma membrane in prokaryotes. These proteins use hydrophobic signal sequences or transmembrane (TM) segments to trigger their translocation through the protein-conducting Sec61/SecY channel. Substrates are first directed to the channel by cytosolic targeting factors, which use hydrophobic pockets to bind diverse signal and TM sequences. Subsequently, these hydrophobic sequences insert into the channel, docking into a groove on the outside of the lateral gate of the channel, where they also interact with lipids. Structural data and biochemical experiments have elucidated how channel partners, the ribosome in cotranslational translocation, and the eukaryotic ER chaperone BiP or the prokaryotic cytosolic SecA ATPase in posttranslational translocation move polypeptides unidirectionally across the membrane. Structures of auxiliary components of the bacterial translocon, YidC and SecD/F, provide additional insight. Taken together, these recent advances result in mechanistic models of protein translocation.
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Affiliation(s)
- Tom A Rapoport
- Department of Cell Biology, Howard Hughes Medical Institute and Harvard Medical School, Boston, Massachusetts 02115; ,
| | - Long Li
- Department of Cell Biology, Howard Hughes Medical Institute and Harvard Medical School, Boston, Massachusetts 02115; ,
| | - Eunyong Park
- The Rockefeller University and Howard Hughes Medical Institute, New York, NY 10065;
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41
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Cellular Proteomes Drive Tissue-Specific Regulation of the Heat Shock Response. G3-GENES GENOMES GENETICS 2017; 7:1011-1018. [PMID: 28143946 PMCID: PMC5345702 DOI: 10.1534/g3.116.038232] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
Abstract
The heat shock response (HSR) is a cellular stress response that senses protein misfolding and restores protein folding homeostasis, or proteostasis. We previously identified an HSR regulatory network in Caenorhabditis elegans consisting of highly conserved genes that have important cellular roles in maintaining proteostasis. Unexpectedly, the effects of these genes on the HSR are distinctly tissue-specific. Here, we explore this apparent discrepancy and find that muscle-specific regulation of the HSR by the TRiC/CCT chaperonin is not driven by an enrichment of TRiC/CCT in muscle, but rather by the levels of one of its most abundant substrates, actin. Knockdown of actin subunits reduces induction of the HSR in muscle upon TRiC/CCT knockdown; conversely, overexpression of an actin subunit sensitizes the intestine so that it induces the HSR upon TRiC/CCT knockdown. Similarly, intestine-specific HSR regulation by the signal recognition particle (SRP), a component of the secretory pathway, is driven by the vitellogenins, some of the most abundant secretory proteins. Together, these data indicate that the specific protein folding requirements from the unique cellular proteomes sensitizes each tissue to disruption of distinct subsets of the proteostasis network. These findings are relevant for tissue-specific, HSR-associated human diseases such as cancer and neurodegenerative diseases. Additionally, we characterize organismal phenotypes of actin overexpression including a shortened lifespan, supporting a recent hypothesis that maintenance of the actin cytoskeleton is an important factor for longevity.
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42
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Becker MMM, Lapouge K, Segnitz B, Wild K, Sinning I. Structures of human SRP72 complexes provide insights into SRP RNA remodeling and ribosome interaction. Nucleic Acids Res 2016; 45:470-481. [PMID: 27899666 PMCID: PMC5224484 DOI: 10.1093/nar/gkw1124] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2016] [Revised: 10/21/2016] [Accepted: 10/28/2016] [Indexed: 12/30/2022] Open
Abstract
Co-translational protein targeting and membrane protein insertion is a fundamental process and depends on the signal recognition particle (SRP). In mammals, SRP is composed of the SRP RNA crucial for SRP assembly and function and six proteins. The two largest proteins SRP68 and SRP72 form a heterodimer and bind to a regulatory site of the SRP RNA. Despite their essential roles in the SRP pathway, structural information has been available only for the SRP68 RNA-binding domain (RBD). Here we present the crystal structures of the SRP68 protein-binding domain (PBD) in complex with SRP72-PBD and of the SRP72-RBD bound to the SRP S domain (SRP RNA, SRP19 and SRP68) detailing all interactions of SRP72 within SRP. The SRP72-PBD is a tetratricopeptide repeat, which binds an extended linear motif of SRP68 with high affinity. The SRP72-RBD is a flexible peptide crawling along the 5e- and 5f-loops of SRP RNA. A conserved tryptophan inserts into the 5e-loop forming a novel type of RNA kink-turn stabilized by a potassium ion, which we define as K+-turn. In addition, SRP72-RBD remodels the 5f-loop involved in ribosome binding and visualizes SRP RNA plasticity. Docking of the S domain structure into cryo-electron microscopy density maps reveals multiple contact sites between SRP68/72 and the ribosome, and explains the role of SRP72 in the SRP pathway.
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Affiliation(s)
- Matthias M M Becker
- Heidelberg University Biochemistry Center (BZH), Im Neuenheimer Feld 328, D-69120 Heidelberg, Germany
| | - Karine Lapouge
- Heidelberg University Biochemistry Center (BZH), Im Neuenheimer Feld 328, D-69120 Heidelberg, Germany
| | - Bernd Segnitz
- Heidelberg University Biochemistry Center (BZH), Im Neuenheimer Feld 328, D-69120 Heidelberg, Germany
| | - Klemens Wild
- Heidelberg University Biochemistry Center (BZH), Im Neuenheimer Feld 328, D-69120 Heidelberg, Germany
| | - Irmgard Sinning
- Heidelberg University Biochemistry Center (BZH), Im Neuenheimer Feld 328, D-69120 Heidelberg, Germany
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43
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Abstract
Bacterial toxin–antitoxin (TA) systems, in which a labile antitoxin binds and inhibits the toxin, can promote adaptation and persistence by modulating bacterial growth in response to stress. Some atypical TA systems, known as tripartite toxin–antitoxin–chaperone (TAC) modules, include a molecular chaperone that facilitates folding and protects the antitoxin from degradation. Here we use a TAC module from Mycobacterium tuberculosis as a model to investigate the molecular mechanisms by which classical TAs can become ‘chaperone-addicted'. The chaperone specifically binds the antitoxin at a short carboxy-terminal sequence (chaperone addiction sequence, ChAD) that is not present in chaperone-independent antitoxins. In the absence of chaperone, the ChAD sequence destabilizes the antitoxin, thus preventing toxin inhibition. Chaperone–ChAD pairs can be transferred to classical TA systems or to unrelated proteins and render them chaperone-dependent. This mechanism might be used to optimize the expression and folding of heterologous proteins in bacterial hosts for biotechnological or medical purposes. Some bacterial toxin-antitoxin systems consist of a labile antitoxin that inhibits a toxin, and a chaperone that stabilizes the antitoxin. Here, Bordes et al. identify a sequence within the antitoxin to which the chaperone binds and which can be transferred to other proteins to make them chaperone-dependent.
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44
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Arnold WK, Savage CR, Brissette CA, Seshu J, Livny J, Stevenson B. RNA-Seq of Borrelia burgdorferi in Multiple Phases of Growth Reveals Insights into the Dynamics of Gene Expression, Transcriptome Architecture, and Noncoding RNAs. PLoS One 2016; 11:e0164165. [PMID: 27706236 PMCID: PMC5051733 DOI: 10.1371/journal.pone.0164165] [Citation(s) in RCA: 40] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2016] [Accepted: 09/20/2016] [Indexed: 12/25/2022] Open
Abstract
Borrelia burgdorferi, the agent of Lyme disease, differentially expresses numerous genes and proteins as it cycles between mammalian hosts and tick vectors. Insights on regulatory mechanisms have been provided by earlier studies that examined B. burgdorferi gene expression patterns during cultivation. However, prior studies examined bacteria at only a single time point of cultivation, providing only a snapshot of what is likely a dynamic transcriptional program driving B. burgdorferi adaptations to changes during culture growth phases. To address that concern, we performed RNA sequencing (RNA-Seq) analysis of B. burgdorferi cultures at early-exponential, mid-exponential, and early-stationary phases of growth. We found that expression of nearly 18% of annotated B. burgdorferi genes changed significantly during culture maturation. Moreover, genome-wide mapping of the B. burgdorferi transcriptome in different growth phases enabled insight on transcript boundaries, operon structures, and identified numerous putative non-coding RNAs. These RNA-Seq data are discussed and presented as a resource for the community of researchers seeking to better understand B. burgdorferi biology and pathogenesis.
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Affiliation(s)
- William K Arnold
- Department of Microbiology, Immunology and Molecular Genetics, University of Kentucky School of Medicine, Lexington, KY, United States of America
| | - Christina R Savage
- Department of Microbiology, Immunology and Molecular Genetics, University of Kentucky School of Medicine, Lexington, KY, United States of America
| | - Catherine A Brissette
- Department of Biomedical Sciences, University of North Dakota School of Medicine and Health Sciences, Grand Forks, ND, United States of America
| | - Janakiram Seshu
- Department of Biology, University of Texas at San Antonio, San Antonio, TX, United States of America
| | - Jonathan Livny
- Broad Institute of MIT and Harvard, Cambridge, MA, United States of America
| | - Brian Stevenson
- Department of Microbiology, Immunology and Molecular Genetics, University of Kentucky School of Medicine, Lexington, KY, United States of America
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45
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Lee K, Sharma R, Shrestha OK, Bingman CA, Craig EA. Dual interaction of the Hsp70 J-protein cochaperone Zuotin with the 40S and 60S ribosomal subunits. Nat Struct Mol Biol 2016; 23:1003-1010. [PMID: 27669034 PMCID: PMC5097012 DOI: 10.1038/nsmb.3299] [Citation(s) in RCA: 33] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2016] [Accepted: 08/31/2016] [Indexed: 12/30/2022]
Abstract
Ribosome-associated J protein-Hsp70 chaperones promote nascent polypeptide folding and normal translational fidelity. Though known to span the ribosome subunits, understanding of J protein Zuo1 function is limited. New structural and crosslinking data allow more precise positioning of Saccharomyces cerevisiae Zuo1 near the 60S polypeptide exit site, pointing to interactions with ribosomal protein eL31 and 25S rRNA helix 24. The junction between the 60S-interacting and subunit-spanning helices is a hinge, positioning Zuo1 on the 40S, yet accommodating subunit rotation. Interaction between C-terminus of Zuo1 and 40S occurs via 18S rRNA expansion segment 12 (ES12) of helix 44, which originates at the decoding site. Deletions in either ES12 or C-terminus of Zuo1 alter stop codon readthrough and −1 frameshifting. Our study offers insight into how this cotranslational chaperone system may monitor decoding site activity and nascent polypeptide transit, thereby coordinating protein translation and folding.
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Affiliation(s)
- Kanghyun Lee
- Department of Biochemistry, University of Wisconsin-Madison, Madison, Wisconsin, USA
| | - Ruchika Sharma
- Department of Biochemistry, University of Wisconsin-Madison, Madison, Wisconsin, USA
| | - Om Kumar Shrestha
- Department of Biochemistry, University of Wisconsin-Madison, Madison, Wisconsin, USA
| | - Craig A Bingman
- Department of Biochemistry, University of Wisconsin-Madison, Madison, Wisconsin, USA
| | - Elizabeth A Craig
- Department of Biochemistry, University of Wisconsin-Madison, Madison, Wisconsin, USA
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46
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Telesnitsky A, Wolin SL. The Host RNAs in Retroviral Particles. Viruses 2016; 8:v8080235. [PMID: 27548206 PMCID: PMC4997597 DOI: 10.3390/v8080235] [Citation(s) in RCA: 38] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2016] [Revised: 08/15/2016] [Accepted: 08/16/2016] [Indexed: 12/15/2022] Open
Abstract
As they assemble, retroviruses encapsidate both their genomic RNAs and several types of host RNA. Whereas limited amounts of messenger RNA (mRNA) are detectable within virion populations, the predominant classes of encapsidated host RNAs do not encode proteins, but instead include endogenous retroelements and several classes of non-coding RNA (ncRNA), some of which are packaged in significant molar excess to the viral genome. Surprisingly, although the most abundant host RNAs in retroviruses are also abundant in cells, unusual forms of these RNAs are packaged preferentially, suggesting that these RNAs are recruited early in their biogenesis: before associating with their cognate protein partners, and/or from transient or rare RNA populations. These RNAs' packaging determinants differ from the viral genome's, and several of the abundantly packaged host ncRNAs serve cells as the scaffolds of ribonucleoprotein particles. Because virion assembly is equally efficient whether or not genomic RNA is available, yet RNA appears critical to the structural integrity of retroviral particles, it seems possible that the selectively encapsidated host ncRNAs might play roles in assembly. Indeed, some host ncRNAs appear to act during replication, as some transfer RNA (tRNA) species may contribute to nuclear import of human immunodeficiency virus 1 (HIV-1) reverse transcription complexes, and other tRNA interactions with the viral Gag protein aid correct trafficking to plasma membrane assembly sites. However, despite high conservation of packaging for certain host RNAs, replication roles for most of these selectively encapsidated RNAs-if any-have remained elusive.
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Affiliation(s)
- Alice Telesnitsky
- Department of Microbiology and Immunology, University of Michigan, Ann Arbor, MI 48109, USA.
| | - Sandra L Wolin
- Department of Cell Biology, Yale School of Medicine, New Haven, CT 06536, USA.
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47
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Chartron JW, Hunt KCL, Frydman J. Cotranslational signal-independent SRP preloading during membrane targeting. Nature 2016; 536:224-8. [PMID: 27487213 PMCID: PMC5120976 DOI: 10.1038/nature19309] [Citation(s) in RCA: 113] [Impact Index Per Article: 14.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2015] [Accepted: 07/18/2016] [Indexed: 12/24/2022]
Abstract
Ribosome-associated factors must faithfully decode the limited information available in nascent polypeptides to direct them to their correct cellular fate1. It is unclear how the low complexity information exposed by the nascent chain suffices for accurate recognition by the many factors competing for the limited surface near the ribosomal exit site2,3. Questions remain even for the well-studied cotranslational targeting cycle to the endoplasmic reticulum (ER), involving recognition of linear hydrophobic Signal Sequences (SS) or Transmembrane Domains (TMD) by the Signal Recognition Particle (SRP)4,5. Intriguingly, SRP is in low abundance relative to the large number of ribosome nascent chain complexes (RNCs), yet it accurately selects those destined to the ER6. Despite their overlapping specificities, SRP and the cotranslational Hsp70 SSB display exquisite mutually exclusive selectivity in vivo for their cognate RNCs7,8. To understand cotranslational nascent chain recognition in vivo, we interrogated the cotranslational membrane targeting cycle using ribosome profiling (herein Ribo-seq)9 coupled with biochemical fractionation of ribosome populations. Unexpectedly, SRP preferentially binds secretory RNCs before targeting signals are translated. We show non-coding mRNA elements can promote this signal-independent SRP pre-recruitment. Our study defines the complex kinetic interplay between elongation and determinants in the polypeptide and mRNA modulating SRP-substrate selection and membrane targeting.
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48
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Pfeffer S, Dudek J, Zimmermann R, Förster F. Organization of the native ribosome-translocon complex at the mammalian endoplasmic reticulum membrane. Biochim Biophys Acta Gen Subj 2016; 1860:2122-9. [PMID: 27373685 DOI: 10.1016/j.bbagen.2016.06.024] [Citation(s) in RCA: 36] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2016] [Revised: 06/24/2016] [Accepted: 06/28/2016] [Indexed: 11/17/2022]
Abstract
BACKGROUND In eukaryotic cells, many proteins have to be transported across or inserted into the endoplasmic reticulum membrane during their biogenesis on the ribosome. This process is facilitated by the protein translocon, a highly dynamic multi-subunit membrane protein complex. SCOPE OF REVIEW The aim of this review is to summarize the current structural knowledge about protein translocon components in mammals. MAJOR CONCLUSIONS Various structural biology approaches have been used in synergy to characterize the translocon in recent years. X-ray crystallography and cryoelectron microscopy single particle analysis have yielded highly detailed insights into the structure and functional mechanism of the protein-conducting channel Sec61, which constitutes the functional core of the translocon. Cryoelectron tomography and subtomogram analysis have advanced our understanding of the overall structure, molecular organization and compositional heterogeneity of the translocon in a native membrane environment. Tomography densities at subnanometer resolution revealed an intricate network of interactions between the ribosome, Sec61 and accessory translocon components that assist in protein transport, membrane insertion and maturation. GENERAL SIGNIFICANCE The protein translocon is a gateway for approximately one third of all synthesized proteins and numerous human diseases are associated with malfunctioning of its components. Thus, detailed insights into the structure and molecular organization of the translocon will not only advance our understanding of membrane protein biogenesis in general, but they can potentially pave the way for novel therapeutic approaches against human diseases.
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Affiliation(s)
- Stefan Pfeffer
- Max-Planck Institute of Biochemistry, Department of Molecular Structural Biology, D-82152 Martinsried, Germany
| | - Johanna Dudek
- Saarland University, Medical Biochemistry and Molecular Biology, D-66421 Homburg, Germany
| | - Richard Zimmermann
- Saarland University, Medical Biochemistry and Molecular Biology, D-66421 Homburg, Germany.
| | - Friedrich Förster
- Max-Planck Institute of Biochemistry, Department of Molecular Structural Biology, D-82152 Martinsried, Germany; Cryo-Electron Microscopy, Bijvoet Center for Biomolecular Research, Utrecht University, Padualaan 8, 3584 CH Utrecht, The Netherlands.
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49
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Wild K, Bange G, Motiejunas D, Kribelbauer J, Hendricks A, Segnitz B, Wade RC, Sinning I. Structural Basis for Conserved Regulation and Adaptation of the Signal Recognition Particle Targeting Complex. J Mol Biol 2016; 428:2880-97. [PMID: 27241309 DOI: 10.1016/j.jmb.2016.05.015] [Citation(s) in RCA: 37] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2016] [Revised: 05/13/2016] [Accepted: 05/18/2016] [Indexed: 12/25/2022]
Abstract
The signal recognition particle (SRP) is a ribonucleoprotein complex with a key role in targeting and insertion of membrane proteins. The two SRP GTPases, SRP54 (Ffh in bacteria) and FtsY (SRα in eukaryotes), form the core of the targeting complex (TC) regulating the SRP cycle. The architecture of the TC and its stimulation by RNA has been described for the bacterial SRP system while this information is lacking for other domains of life. Here, we present the crystal structures of the GTPase heterodimers of archaeal (Sulfolobus solfataricus), eukaryotic (Homo sapiens), and chloroplast (Arabidopsis thaliana) SRP systems. The comprehensive structural comparison combined with Brownian dynamics simulations of TC formation allows for the description of the general blueprint and of specific adaptations of the quasi-symmetric heterodimer. Our work defines conserved external nucleotide-binding sites for SRP GTPase activation by RNA. Structural analyses of the GDP-bound, post-hydrolysis states reveal a conserved, magnesium-sensitive switch within the I-box. Overall, we provide a general model for SRP cycle regulation by RNA.
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Affiliation(s)
- Klemens Wild
- Heidelberg University Biochemistry Center (BZH), INF 328, D-69120 Heidelberg, Germany
| | - Gert Bange
- Heidelberg University Biochemistry Center (BZH), INF 328, D-69120 Heidelberg, Germany
| | - Domantas Motiejunas
- Molecular and Cellular Modeling Group, Heidelberg Institute for Theoretical Studies (HITS), Schloss-Wolfsbrunnenweg 35, D-69118 Heidelberg, Germany
| | - Judith Kribelbauer
- Heidelberg University Biochemistry Center (BZH), INF 328, D-69120 Heidelberg, Germany
| | - Astrid Hendricks
- Heidelberg University Biochemistry Center (BZH), INF 328, D-69120 Heidelberg, Germany
| | - Bernd Segnitz
- Heidelberg University Biochemistry Center (BZH), INF 328, D-69120 Heidelberg, Germany
| | - Rebecca C Wade
- Molecular and Cellular Modeling Group, Heidelberg Institute for Theoretical Studies (HITS), Schloss-Wolfsbrunnenweg 35, D-69118 Heidelberg, Germany; Zentrum für Molekulare Biologie der Universität Heidelberg, DKFZ-ZMBH Alliance, INF 282, 69120 Heidelberg, Germany
| | - Irmgard Sinning
- Heidelberg University Biochemistry Center (BZH), INF 328, D-69120 Heidelberg, Germany.
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50
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Ishimura R, Nagy G, Dotu I, Chuang JH, Ackerman SL. Activation of GCN2 kinase by ribosome stalling links translation elongation with translation initiation. eLife 2016; 5. [PMID: 27085088 PMCID: PMC4917338 DOI: 10.7554/elife.14295] [Citation(s) in RCA: 121] [Impact Index Per Article: 15.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2016] [Accepted: 04/14/2016] [Indexed: 12/17/2022] Open
Abstract
Ribosome stalling during translation has recently been shown to cause neurodegeneration, yet the signaling pathways triggered by stalled elongation complexes are unknown. To investigate these pathways we analyzed the brain of C57BL/6J-Gtpbp2nmf205-/- mice in which neuronal elongation complexes are stalled at AGA codons due to deficiencies in a tRNAArgUCU tRNA and GTPBP2, a mammalian ribosome rescue factor. Increased levels of phosphorylation of eIF2α (Ser51) were detected prior to neurodegeneration in these mice and transcriptome analysis demonstrated activation of ATF4, a key transcription factor in the integrated stress response (ISR) pathway. Genetic experiments showed that this pathway was activated by the eIF2α kinase, GCN2, in an apparent deacylated tRNA-independent fashion. Further we found that the ISR attenuates neurodegeneration in C57BL/6J-Gtpbp2nmf205-/- mice, underscoring the importance of cellular and stress context on the outcome of activation of this pathway. These results demonstrate the critical interplay between translation elongation and initiation in regulating neuron survival during cellular stress. DOI:http://dx.doi.org/10.7554/eLife.14295.001 Information stored in DNA is used to make proteins in a two-step process. First, the DNA is copied to make molecules of messenger ribonucleic acid (or messenger RNA for short). Next, machines called ribosomes use the messenger RNAs as templates to assemble chains of amino acids – the building blocks of proteins – in a process called translation. Another type of RNA molecule called transfer RNA carries each amino acid to the ribosomes. If a specific transfer RNA is not available for translation at the right time, the ribosome might stall as it moves along the messenger RNA. At this point, the ribosome needs to be restarted or it will fall off the mRNA without finishing the protein. In 2014, a group of researchers reported that certain types of brain cells are very sensitive to ribosome stalling, and tend to die if translation does not continue. A protein called GTPBP2 was shown to play an important role in restarting stalled ribosomes in these cells. Here, Ishimura, Nagy et al. – including some of the researchers from the earlier work – investigated the molecular pathways that ribosome stalling triggers in brain cells using mutant mice that lacked the GTPBP2 protein. The experiments show that ribosome stalling activates an enzyme known as GCN2, which was already known to sense other types of malfunctions in cellular processes. Ishimura, Nagy et al. also show that GCN2 triggers stress responses in the cells by activating a communication system called the ATF4 pathway. This pathway protects the cells from damage, and its absence results in more rapid cell deterioration and death. The next challenges are to understand the exact mechanism by which GCN2 senses stalled ribosomes, and to find out how ribosome stalling causes the death of brain cells. DOI:http://dx.doi.org/10.7554/eLife.14295.002
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Affiliation(s)
- Ryuta Ishimura
- Howard Hughes Medical Institute, The Jackson Laboratory for Mammalian Genetics, Bar Harbor, United States
| | - Gabor Nagy
- Howard Hughes Medical Institute, The Jackson Laboratory for Mammalian Genetics, Bar Harbor, United States
| | - Ivan Dotu
- Research Programme on Biomedical Informatics, Department of Experimental and Health Sciences, Universitat Pompeu Fabra, Barcelona, Spain
| | - Jeffrey H Chuang
- The Jackson Laboratory for Genomic Medicine, Farmington, United States.,Department of Genetics and Genome Sciences, University of Connecticut Health Center, Farmington, United States
| | - Susan L Ackerman
- Howard Hughes Medical Institute, The Jackson Laboratory for Mammalian Genetics, Bar Harbor, United States.,Department of Cell and Molecular Medicine, University of California, San Diego School of Medicine, La Jolla, United States.,Section of Neurobiology, University of California, La Jolla, United States
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