151
|
Carvalho Barbosa C, Calhoun SH, Wieden HJ. Non-coding RNAs: what are we missing? Biochem Cell Biol 2020; 98:23-30. [DOI: 10.1139/bcb-2019-0037] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
Over the past two decades, the importance of small non-coding RNAs (sncRNAs) as regulatory molecules has become apparent in all three domains of life (archaea, bacteria, eukaryotes). In fact, sncRNAs play an important role in the control of gene expression at both the transcriptional and the post-transcriptional level, with crucial roles in fine-tuning cell responses during internal and external stress. Multiple pathways for sncRNA biogenesis and diverse mechanisms of regulation have been reported, and although biogenesis and mechanisms of sncRNAs in prokaryotes and eukaryotes are different, remarkable similarities exist. Here, we briefly review and compare the major sncRNA classes that act post-transcriptionally, and focus on recent discoveries regarding the ribosome as a target of regulation and the conservation of these mechanisms between prokaryotes and eukaryotes.
Collapse
Affiliation(s)
- Cristina Carvalho Barbosa
- Alberta RNA Research and Training Institute, Department of Chemistry and Biochemistry, University of Lethbridge, Lethbridge, AB T1K 3M4, Canada
- Alberta RNA Research and Training Institute, Department of Chemistry and Biochemistry, University of Lethbridge, Lethbridge, AB T1K 3M4, Canada
| | - Sydnee H. Calhoun
- Alberta RNA Research and Training Institute, Department of Chemistry and Biochemistry, University of Lethbridge, Lethbridge, AB T1K 3M4, Canada
- Alberta RNA Research and Training Institute, Department of Chemistry and Biochemistry, University of Lethbridge, Lethbridge, AB T1K 3M4, Canada
| | - Hans-Joachim Wieden
- Alberta RNA Research and Training Institute, Department of Chemistry and Biochemistry, University of Lethbridge, Lethbridge, AB T1K 3M4, Canada
| |
Collapse
|
152
|
Baysal C, Pérez-González A, Eseverri Á, Jiang X, Medina V, Caro E, Rubio L, Christou P, Zhu C. Recognition motifs rather than phylogenetic origin influence the ability of targeting peptides to import nuclear-encoded recombinant proteins into rice mitochondria. Transgenic Res 2020; 29:37-52. [PMID: 31598902 PMCID: PMC7000509 DOI: 10.1007/s11248-019-00176-9] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2019] [Accepted: 10/01/2019] [Indexed: 10/30/2022]
Abstract
Mitochondria fulfil essential functions in respiration and metabolism as well as regulating stress responses and apoptosis. Most native mitochondrial proteins are encoded by nuclear genes and are imported into mitochondria via one of several receptors that recognize N-terminal signal peptides. The targeting of recombinant proteins to mitochondria therefore requires the presence of an appropriate N-terminal peptide, but little is known about mitochondrial import in monocotyledonous plants such as rice (Oryza sativa). To gain insight into this phenomenon, we targeted nuclear-encoded enhanced green fluorescent protein (eGFP) to rice mitochondria using six mitochondrial pre-sequences with diverse phylogenetic origins, and investigated their effectiveness by immunoblot analysis as well as confocal and electron microscopy. We found that the ATPA and COX4 (Saccharomyces cerevisiae), SU9 (Neurospora crassa), pFA (Arabidopsis thaliana) and OsSCSb (Oryza sativa) peptides successfully directed most of the eGFP to the mitochondria, whereas the MTS2 peptide (Nicotiana plumbaginifolia) showed little or no evidence of targeting ability even though it is a native plant sequence. Our data therefore indicate that the presence of particular recognition motifs may be required for mitochondrial targeting, whereas the phylogenetic origin of the pre-sequences probably does not play a key role in the success of mitochondrial targeting in dedifferentiated rice callus and plants.
Collapse
Affiliation(s)
- Can Baysal
- Department of Plant Production and Forestry Science, University of Lleida-Agrotecnio Center, Av. Alcalde Rovira Roure, 191, 25198, Lleida, Spain
| | - Ana Pérez-González
- Centre for Plant Biotechnology and Genomics, Universidad Politécnica de Madrid (UPM) - Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria (INIA), Campus Montegancedo UPM, 28223, Pozuelo de Alarcón, Madrid, Spain
| | - Álvaro Eseverri
- Centre for Plant Biotechnology and Genomics, Universidad Politécnica de Madrid (UPM) - Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria (INIA), Campus Montegancedo UPM, 28223, Pozuelo de Alarcón, Madrid, Spain
| | - Xi Jiang
- Centre for Plant Biotechnology and Genomics, Universidad Politécnica de Madrid (UPM) - Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria (INIA), Campus Montegancedo UPM, 28223, Pozuelo de Alarcón, Madrid, Spain
| | - Vicente Medina
- Department of Plant Production and Forestry Science, University of Lleida-Agrotecnio Center, Av. Alcalde Rovira Roure, 191, 25198, Lleida, Spain
| | - Elena Caro
- Centre for Plant Biotechnology and Genomics, Universidad Politécnica de Madrid (UPM) - Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria (INIA), Campus Montegancedo UPM, 28223, Pozuelo de Alarcón, Madrid, Spain
| | - Luis Rubio
- Centre for Plant Biotechnology and Genomics, Universidad Politécnica de Madrid (UPM) - Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria (INIA), Campus Montegancedo UPM, 28223, Pozuelo de Alarcón, Madrid, Spain
| | - Paul Christou
- Department of Plant Production and Forestry Science, University of Lleida-Agrotecnio Center, Av. Alcalde Rovira Roure, 191, 25198, Lleida, Spain
- ICREA, Catalan Institute for Research and Advanced Studies, Passeig Lluís Companys 23, 08010, Barcelona, Spain
| | - Changfu Zhu
- Department of Plant Production and Forestry Science, University of Lleida-Agrotecnio Center, Av. Alcalde Rovira Roure, 191, 25198, Lleida, Spain.
| |
Collapse
|
153
|
Tsukazaki T. Structural Basis of the Sec Translocon and YidC Revealed Through X-ray Crystallography. Protein J 2020; 38:249-261. [PMID: 30972527 DOI: 10.1007/s10930-019-09830-x] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023]
Abstract
Protein translocation and membrane integration are fundamental, conserved processes. After or during ribosomal protein synthesis, precursor proteins containing an N-terminal signal sequence are directed to a conserved membrane protein complex called the Sec translocon (also known as the Sec translocase) in the endoplasmic reticulum membrane in eukaryotic cells, or the cytoplasmic membrane in bacteria. The Sec translocon comprises the Sec61 complex in eukaryotic cells, or the SecY complex in bacteria, and mediates translocation of substrate proteins across/into the membrane. Several membrane proteins are associated with the Sec translocon. In Escherichia coli, the membrane protein YidC functions not only as a chaperone for membrane protein biogenesis along with the Sec translocon, but also as an independent membrane protein insertase. To understand the molecular mechanism underlying these dynamic processes at the membrane, high-resolution structural models of these proteins are needed. This review focuses on X-ray crystallographic analyses of the Sec translocon and YidC and discusses the structural basis for protein translocation and integration.
Collapse
Affiliation(s)
- Tomoya Tsukazaki
- Nara Institute of Science and Technology, Ikoma, Nara, 630-0192, Japan.
| |
Collapse
|
154
|
Abstract
The past several decades have witnessed tremendous growth in the protein targeting, transport and translocation field. Major advances were made during this time period. Now the molecular details of the targeting factors, receptors and the membrane channels that were envisioned in Blobel's Signal Hypothesis in the 1970s have been revealed by powerful structural methods. It is evident that there is a myriad of cytosolic and membrane associated systems that accurately sort and target newly synthesized proteins to their correct membrane translocases for membrane insertion or protein translocation. Here we will describe the common principles for protein transport in prokaryotes and eukaryotes.
Collapse
|
155
|
Morishita Y, Arvan P. Lessons from animal models of endocrine disorders caused by defects of protein folding in the secretory pathway. Mol Cell Endocrinol 2020; 499:110613. [PMID: 31605742 PMCID: PMC6886696 DOI: 10.1016/j.mce.2019.110613] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/24/2019] [Revised: 09/26/2019] [Accepted: 10/04/2019] [Indexed: 02/06/2023]
Abstract
Most peptide hormones originate from secretory protein precursors synthesized within the endoplasmic reticulum (ER). In this specialized organelle, the newly-made prohormones must fold to their native state. Completion of prohormone folding usually occurs prior to migration through the secretory pathway, as unfolded/misfolded prohormones are retained by mechanisms collectively known as ER quality control. Not only do most monomeric prohormones need to fold properly, but many also dimerize or oligomerize within the ER. If oligomerization occurs before completion of monomer folding then when a poorly folded peptide prohormone is retained by quality control mechanisms, it may confer ER retention upon its oligomerization partners. Conversely, oligomerization between well-folded and improperly folded partners might help to override ER quality control, resulting in rescue of misfolded forms. Both scenarios appear to be possible in different animal models of endocrine disorders caused by genetic defects of protein folding in the secretory pathway. In this paper, we briefly review three such conditions, including familial neurohypophyseal diabetes insipidus, insulin-deficient diabetes mellitus, and hypothyroidism with defective thyroglobulin.
Collapse
Affiliation(s)
- Yoshiaki Morishita
- Division of Diabetes, Department of Internal Medicine, Aichi Medical University, 1-1 Yazakokarimata, Nagakute, Aichi, 480-1195, Japan.
| | - Peter Arvan
- Division of Metabolism, Endocrinology & Diabetes, University of Michigan School of Medicine, Brehm Tower Room 5112, 1000, Wall St., Ann Arbor, MI, USA.
| |
Collapse
|
156
|
The functional diversity of structural disorder in plant proteins. Arch Biochem Biophys 2019; 680:108229. [PMID: 31870661 DOI: 10.1016/j.abb.2019.108229] [Citation(s) in RCA: 22] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2019] [Revised: 12/05/2019] [Accepted: 12/17/2019] [Indexed: 12/29/2022]
Abstract
Structural disorder in proteins is a widespread feature distributed in all domains of life, particularly abundant in eukaryotes, including plants. In these organisms, intrinsically disordered proteins (IDPs) perform a diversity of functions, participating as integrators of signaling networks, in transcriptional and post-transcriptional regulation, in metabolic control, in stress responses and in the formation of biomolecular condensates by liquid-liquid phase separation. Their roles impact the perception, propagation and control of various developmental and environmental cues, as well as the plant defense against abiotic and biotic adverse conditions. In this review, we focus on primary processes to exhibit a broad perspective of the relevance of IDPs in plant cell functions. The information here might help to incorporate this knowledge into a more dynamic view of plant cells, as well as open more questions and promote new ideas for a better understanding of plant life.
Collapse
|
157
|
Langlete P, Krabberød AK, Winther-Larsen HC. Vesicles From Vibrio cholerae Contain AT-Rich DNA and Shorter mRNAs That Do Not Correlate With Their Protein Products. Front Microbiol 2019; 10:2708. [PMID: 31824470 PMCID: PMC6883915 DOI: 10.3389/fmicb.2019.02708] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2019] [Accepted: 11/08/2019] [Indexed: 12/29/2022] Open
Abstract
Extracellular vesicles secreted by Gram-negative bacteria have proven to be important in bacterial defense, communication and host–pathogen relationships. They resemble smaller versions of the bacterial mother cell, with similar contents of proteins, LPS, DNA, and RNA. Vesicles can elicit a protective immune response in a range of hosts, and as vaccine candidates, it is of interest to properly characterize their cargo. Genetic sequencing data is already available for vesicles from several bacterial strains, but it is not yet clear how the genetic makeup of vesicles differ from that of their parent cells, and which properties may characterize enriched genetic material. The present study provides evidence for DNA inside vesicles from Vibrio cholerae O395, and key characteristics of their genetic and proteomic content are compared to that of whole cells. DNA analysis reveals enrichment of fragments containing ToxR binding sites, as well as a positive correlation between AT-content and enrichment. Some mRNAs were highly enriched in the vesicle fraction, such as membrane protein genes ompV, ompK, and ompU, DNA-binding protein genes hupA, hupB, ihfB, fis, and ssb, and a negative correlation was found between mRNA enrichment and transcript length, suggesting mRNA inclusion in vesicles may be a size-dependent process. Certain non-coding and functional RNAs were found to be enriched, such as VrrA, GcvB, tmRNA, RNase P, CsrB2, and CsrB3. Mass spectrometry revealed enrichment of outer membrane proteins, known virulence factors, phage components, flagella and extracellular proteins in the vesicle fraction, and a low, negative correlation was found between transcript-, and protein enrichment. This result opposes the hypothesis that a significant degree of protein translation occurs in vesicles after budding. The abundance of viral-, and flagellar proteins in the vesicle fraction underlines the importance of purification during vesicle isolation.
Collapse
Affiliation(s)
- Petter Langlete
- Section for Pharmacology and Pharmaceutical Biosciences, Department of Pharmacy, University of Oslo, Oslo, Norway.,Centre for Integrative Microbial Evolution (CIME), Department of Biosciences, University of Oslo, Oslo, Norway
| | - Anders Kristian Krabberød
- Centre for Integrative Microbial Evolution (CIME), Department of Biosciences, University of Oslo, Oslo, Norway.,Section for Genetics and Evolutionary Biology (EVOGENE), Department of Biosciences, University of Oslo, Oslo, Norway
| | - Hanne Cecilie Winther-Larsen
- Section for Pharmacology and Pharmaceutical Biosciences, Department of Pharmacy, University of Oslo, Oslo, Norway.,Centre for Integrative Microbial Evolution (CIME), Department of Biosciences, University of Oslo, Oslo, Norway
| |
Collapse
|
158
|
Yang CI, Hsieh HH, Shan SO. Timing and specificity of cotranslational nascent protein modification in bacteria. Proc Natl Acad Sci U S A 2019; 116:23050-23060. [PMID: 31666319 PMCID: PMC6859321 DOI: 10.1073/pnas.1912264116] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022] Open
Abstract
The nascent polypeptide exit site of the ribosome is a crowded environment where multiple ribosome-associated protein biogenesis factors (RPBs) compete for the nascent polypeptide to influence their localization, folding, or quality control. Here we address how N-terminal methionine excision (NME), a ubiquitous process crucial for the maturation of over 50% of the bacterial proteome, occurs in a timely and selective manner in this crowded environment. In bacteria, NME is mediated by 2 essential enzymes, peptide deformylase (PDF) and methionine aminopeptidase (MAP). We show that the reaction of MAP on ribosome-bound nascent chains approaches diffusion-limited rates, allowing immediate methionine excision of optimal substrates after deformylation. Specificity is achieved by kinetic competition of NME with translation elongation and by regulation from other RPBs, which selectively narrow the processing time window for suboptimal substrates. A mathematical model derived from the data accurately predicts cotranslational NME efficiency in the cytosol. Our results demonstrate how a fundamental enzymatic activity is reshaped by its associated macromolecular environment to optimize both efficiency and selectivity, and provides a platform to study other cotranslational protein biogenesis pathways.
Collapse
Affiliation(s)
- Chien-I Yang
- Division of Chemistry and Chemical Engineering, California Institute of Technology, Pasadena, CA 91125
| | - Hao-Hsuan Hsieh
- Division of Chemistry and Chemical Engineering, California Institute of Technology, Pasadena, CA 91125
| | - Shu-Ou Shan
- Division of Chemistry and Chemical Engineering, California Institute of Technology, Pasadena, CA 91125
| |
Collapse
|
159
|
Fukuda S, Yan S, Komi Y, Sun M, Gabizon R, Bustamante C. The Biogenesis of SRP RNA Is Modulated by an RNA Folding Intermediate Attained during Transcription. Mol Cell 2019; 77:241-250.e8. [PMID: 31706702 DOI: 10.1016/j.molcel.2019.10.006] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2018] [Revised: 08/29/2019] [Accepted: 10/04/2019] [Indexed: 11/16/2022]
Abstract
The signal recognition particle (SRP), responsible for co-translational protein targeting and delivery to cellular membranes, depends on the native long-hairpin fold of its RNA to confer functionality. Since RNA initiates folding during its synthesis, we used high-resolution optical tweezers to follow in real time the co-transcriptional folding of SRP RNA. Surprisingly, SRP RNA folding is robust to transcription rate changes and the presence or absence of its 5'-precursor sequence. The folding pathway also reveals the obligatory attainment of a non-native hairpin intermediate (H1) that eventually rearranges into the native fold. Furthermore, H1 provides a structural platform alternative to the native fold for RNase P to bind and mature SRP RNA co-transcriptionally. Delays in attaining the final native fold are detrimental to the cell, altogether showing that a co-transcriptional folding pathway underpins the proper biogenesis of function-essential SRP RNA.
Collapse
Affiliation(s)
- Shingo Fukuda
- Institute for Quantitative Biosciences-QB3, University of California, Berkeley, Berkeley, CA, USA; Okazaki Institute for Integrative Bioscience and Institute for Molecular Science, National Institutes of Natural Science, Tokyo, Japan; Nano Life Science Institute (WPI-NanoLSI), Kanazawa University, Kanazawa 920-1192, Japan.
| | - Shannon Yan
- Institute for Quantitative Biosciences-QB3, University of California, Berkeley, Berkeley, CA, USA; Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, CA, USA.
| | - Yusuke Komi
- Institute for Quantitative Biosciences-QB3, University of California, Berkeley, Berkeley, CA, USA; Laboratory for Protein Conformation Diseases, RIKEN Center for Brain Science, Wako, Saitama, Japan
| | - Mingxuan Sun
- Institute for Quantitative Biosciences-QB3, University of California, Berkeley, Berkeley, CA, USA; Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, CA, USA
| | - Ronen Gabizon
- Institute for Quantitative Biosciences-QB3, University of California, Berkeley, Berkeley, CA, USA
| | - Carlos Bustamante
- Institute for Quantitative Biosciences-QB3, University of California, Berkeley, Berkeley, CA, USA; Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, CA, USA; Jason L. Choy Laboratory of Single-Molecule Biophysics, University of California, Berkeley, Berkeley, CA, USA; Biophysics Graduate Group, University of California, Berkeley, Berkeley, CA, USA; Department of Chemistry, University of California, Berkeley, Berkeley, CA, USA; Department of Physics, University of California, Berkeley, Berkeley, CA, USA; Howard Hughes Medical Institute, University of California, Berkeley, Berkeley, CA, USA; Kavli Energy Nanoscience Institute, University of California, Berkeley, Berkeley, CA, USA.
| |
Collapse
|
160
|
Hristou A, Gerlach I, Stolle DS, Neumann J, Bischoff A, Dünschede B, Nowaczyk MM, Zoschke R, Schünemann D. Ribosome-Associated Chloroplast SRP54 Enables Efficient Cotranslational Membrane Insertion of Key Photosynthetic Proteins. THE PLANT CELL 2019; 31:2734-2750. [PMID: 31444312 PMCID: PMC6881123 DOI: 10.1105/tpc.19.00169] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/02/2019] [Revised: 07/12/2019] [Accepted: 08/22/2019] [Indexed: 05/20/2023]
Abstract
Key proteins of the photosynthetic complexes are encoded in the chloroplast genome and cotranslationally inserted into the thylakoid membrane. However, the molecular details of this process are largely unknown. Here, we demonstrate by ribosome profiling that the conserved chloroplast signal recognition particle subunit (cpSRP54) is required for efficient cotranslational targeting of several central photosynthetic proteins, such as the PSII PsbA (D1) subunit, in Arabidopsis (Arabidopsis thaliana). High-resolution analysis of membrane-associated and soluble ribosome footprints revealed that the SRP-dependent membrane targeting of PsbA is already initiated at an early translation step before exposure of the nascent chain from the ribosome. In contrast to cytosolic SRP, which contacts the ribosome close to the peptide tunnel exit site, analysis of the cpSRP54/ribosome binding interface revealed a direct interaction of cpSRP54 and the ribosomal subunit uL4, which is not located at the tunnel exit site but forms a part of the internal peptide tunnel wall by a loop domain. The plastid-specific C-terminal tail region of cpSRP54 plays a crucial role in uL4 binding. Our data indicate a novel mechanism of SRP-dependent membrane protein transport with the cpSRP54/uL4 interaction as a central element in early initiation of cotranslational membrane targeting.
Collapse
Affiliation(s)
- Athina Hristou
- Molecular Biology of Plant Organelles, Faculty of Biology and Biotechnology, Ruhr University Bochum, 44780 Bochum, Germany
| | - Ines Gerlach
- Max Planck Institute of Molecular Plant Physiology, 14476 Potsdam-Golm, Germany
| | - Dominique S Stolle
- Molecular Biology of Plant Organelles, Faculty of Biology and Biotechnology, Ruhr University Bochum, 44780 Bochum, Germany
| | - Jennifer Neumann
- Molecular Biology of Plant Organelles, Faculty of Biology and Biotechnology, Ruhr University Bochum, 44780 Bochum, Germany
| | - Annika Bischoff
- Molecular Biology of Plant Organelles, Faculty of Biology and Biotechnology, Ruhr University Bochum, 44780 Bochum, Germany
| | - Beatrix Dünschede
- Molecular Biology of Plant Organelles, Faculty of Biology and Biotechnology, Ruhr University Bochum, 44780 Bochum, Germany
| | - Marc M Nowaczyk
- Plant Biochemistry, Faculty of Biology and Biotechnology, Ruhr University Bochum, 44780 Bochum, Germany
| | - Reimo Zoschke
- Max Planck Institute of Molecular Plant Physiology, 14476 Potsdam-Golm, Germany
| | - Danja Schünemann
- Molecular Biology of Plant Organelles, Faculty of Biology and Biotechnology, Ruhr University Bochum, 44780 Bochum, Germany
| |
Collapse
|
161
|
Sanguinetti M, Iriarte A, Amillis S, Marín M, Musto H, Ramón A. A pair of non-optimal codons are necessary for the correct biosynthesis of the Aspergillus nidulans urea transporter, UreA. ROYAL SOCIETY OPEN SCIENCE 2019; 6:190773. [PMID: 31827830 PMCID: PMC6894576 DOI: 10.1098/rsos.190773] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 05/10/2019] [Accepted: 10/07/2019] [Indexed: 06/10/2023]
Abstract
In both prokaryotic and eukaryotic genomes, synonymous codons are unevenly used. Such differential usage of optimal or non-optimal codons has been suggested to play a role in the control of translation initiation and elongation, as well as at the level of transcription and mRNA stability. In the case of membrane proteins, codon usage has been proposed to assist in the establishment of a pause necessary for the correct targeting of the nascent chains to the translocon. By using as a model UreA, the Aspergillus nidulans urea transporter, we revealed that a pair of non-optimal codons encoding amino acids situated at the boundary between the N-terminus and the first transmembrane segment are necessary for proper biogenesis of the protein at 37°C. These codons presumably regulate the translation rate in a previously undescribed fashion, possibly contributing to the correct interaction of ureA-translating ribosome-nascent chain complexes with the signal recognition particle and/or other factors, while the polypeptide has not yet emerged from the ribosomal tunnel. Our results suggest that the presence of the pair of non-optimal codons would not be functionally important in all cellular conditions. Whether this mechanism would affect other proteins remains to be determined.
Collapse
Affiliation(s)
- Manuel Sanguinetti
- Sección Bioquímica, Departamento de Biología Celular y Molecular, Facultad de Ciencias, Universidad de la República (UdelaR), Montevideo, Uruguay
| | - Andrés Iriarte
- Laboratorio de Biología Computacional, Departamento de Desarrollo Biotecnológico, Instituto de Higiene, Facultad de Medicina, UdelaR, Montevideo, Uruguay
- Laboratorio de Organización y Evolución del Genoma, Unidad de Genómica Evolutiva, Departamento de Evolución, Facultad de Ciencias, UdelaR, Montevideo, Uruguay
| | - Sotiris Amillis
- Department of Biology, National and Kapodistrian University of Athens, Athens, Hellas, Greece
| | - Mónica Marín
- Sección Bioquímica, Departamento de Biología Celular y Molecular, Facultad de Ciencias, Universidad de la República (UdelaR), Montevideo, Uruguay
| | - Héctor Musto
- Laboratorio de Organización y Evolución del Genoma, Unidad de Genómica Evolutiva, Departamento de Evolución, Facultad de Ciencias, UdelaR, Montevideo, Uruguay
| | - Ana Ramón
- Sección Bioquímica, Departamento de Biología Celular y Molecular, Facultad de Ciencias, Universidad de la República (UdelaR), Montevideo, Uruguay
| |
Collapse
|
162
|
Abstract
One-fourth of eukaryotic genes code for integral membrane proteins, nearly all of which are inserted and assembled at the endoplasmic reticulum (ER). The defining feature of membrane proteins is one or more transmembrane domains (TMDs). During membrane protein biogenesis, TMDs are selectively recognized, shielded, and chaperoned into the lipid bilayer, where they often assemble with other TMDs. If maturation fails, exposed TMDs serve as a cue for engagement of degradation pathways. Thus, TMD-recognition factors in the cytosol and ER are essential for membrane protein biogenesis and quality control. Here, we discuss the growing assortment of cytosolic and membrane-embedded TMD-recognition factors, the pathways within which they operate, and mechanistic principles of recognition.
Collapse
|
163
|
Das T, Eliezer D. Membrane interactions of intrinsically disordered proteins: The example of alpha-synuclein. BIOCHIMICA ET BIOPHYSICA ACTA. PROTEINS AND PROTEOMICS 2019; 1867:879-889. [PMID: 31096049 PMCID: PMC6661188 DOI: 10.1016/j.bbapap.2019.05.001] [Citation(s) in RCA: 32] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/08/2019] [Revised: 05/03/2019] [Accepted: 05/08/2019] [Indexed: 12/11/2022]
Abstract
Peripheral membrane proteins associate reversibly with biological membranes that, compared to protein binding partners, are structurally labile and devoid of specific binding pockets. Membranes in different subcellular compartments vary primarily in their chemical composition and physical properties, and recognition of these features is therefore critical for allowing such proteins to engage their proper membrane targets. Intrinsically disordered proteins (IDPs) are well-suited to accomplish this task using highly specific and low- to moderate-affinity interactions governed by recognition principles that are both similar to and different from those that mediate the membrane interactions of rigid proteins. IDPs have also evolved multiple mechanisms to regulate membrane (and other) interactions and achieve their impressive functional diversity. Moreover, IDP-membrane interactions may have a kinetic advantage in fast processes requiring rapid control of such interactions, such as synaptic transmission or signaling. Herein we review the biophysics, regulation and functional implications of IDP-membrane interactions and include a brief overview of some of the methods that can be used to study such interactions. At each step, we use the example of alpha-synuclein, a protein involved in the pathogenesis of Parkinson's disease and one of the best characterized membrane-binding IDP, to illustrate some of the principles discussed.
Collapse
Affiliation(s)
- Tapojyoti Das
- Department of Biochemistry, Weill Cornell Medicine, New York, NY, United States of America
| | - David Eliezer
- Department of Biochemistry, Weill Cornell Medicine, New York, NY, United States of America.
| |
Collapse
|
164
|
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.
Collapse
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.
| |
Collapse
|
165
|
Phan TH, Houben ENG. Bacterial secretion chaperones: the mycobacterial type VII case. FEMS Microbiol Lett 2019; 365:5067300. [PMID: 30085058 PMCID: PMC6109436 DOI: 10.1093/femsle/fny197] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2018] [Accepted: 08/04/2018] [Indexed: 12/13/2022] Open
Abstract
Chaperones are central players in maintaining the proteostasis in all living cells. Besides highly conserved generic chaperones that assist protein folding and assembly in the cytosol, additional more specific chaperones have evolved to ensure the successful trafficking of proteins with extra-cytoplasmic locations. Associated with the distinctive secretion systems present in bacteria, different dedicated chaperones have been described that not only keep secretory proteins in a translocation competent state, but often are also involved in substrate targeting to the specific translocation channel. Recently, a new class of such chaperones has been identified that are involved in the specific recognition of substrates transported via the type VII secretion pathway in mycobacteria. In this minireview, we provide an overview of the different bacterial chaperones with a focus on their roles in protein secretion and will discuss in detail the roles of mycobacterial type VII secretion chaperones in substrate recognition and targeting.
Collapse
Affiliation(s)
- Trang H Phan
- Section Molecular Microbiology, Amsterdam Institute for Molecules, Medicines and Systems, Vrije Universiteit, Amsterdam, The Netherlands
| | - Edith N G Houben
- Section Molecular Microbiology, Amsterdam Institute for Molecules, Medicines and Systems, Vrije Universiteit, Amsterdam, The Netherlands
| |
Collapse
|
166
|
Hwang Fu YH, Chandrasekar S, Lee JH, Shan SO. A molecular recognition feature mediates ribosome-induced SRP-receptor assembly during protein targeting. J Cell Biol 2019; 218:3307-3319. [PMID: 31537711 PMCID: PMC6781444 DOI: 10.1083/jcb.201901001] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/01/2019] [Revised: 06/28/2019] [Accepted: 08/26/2019] [Indexed: 12/21/2022] Open
Abstract
Molecular recognition features (MoRFs) provide interaction motifs in intrinsically disordered protein regions to mediate diverse cellular functions. Here we report that a MoRF element, located in the disordered linker domain of the mammalian signal recognition particle (SRP) receptor and conserved among eukaryotes, plays an essential role in sensing the ribosome during cotranslational protein targeting to the endoplasmic reticulum. Loss of the MoRF in the SRP receptor (SR) largely abolishes the ability of the ribosome to activate SRP-SR assembly and impairs cotranslational protein targeting. These results demonstrate a novel role for MoRF elements and provide a mechanism for the ribosome-induced activation of the mammalian SRP pathway. Kinetic analyses and comparison with the bacterial SRP further suggest that the SR MoRF functionally replaces the essential GNRA tetraloop in the bacterial SRP RNA, providing an example for the replacement of RNA function by proteins during the evolution of ancient ribonucleoprotein particles.
Collapse
Affiliation(s)
- Yu-Hsien Hwang Fu
- Division of Chemistry and Chemical Engineering, California Institute of Technology, Pasadena, CA
| | - Sowmya Chandrasekar
- Division of Chemistry and Chemical Engineering, California Institute of Technology, Pasadena, CA
| | - Jae Ho Lee
- Division of Chemistry and Chemical Engineering, California Institute of Technology, Pasadena, CA
| | - Shu-Ou Shan
- Division of Chemistry and Chemical Engineering, California Institute of Technology, Pasadena, CA
| |
Collapse
|
167
|
Faoro C, Ataide SF. Structural insights into the G-loop dynamics of E. coli FtsY NG domain. J Struct Biol 2019; 208:107387. [PMID: 31520694 DOI: 10.1016/j.jsb.2019.09.004] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2019] [Revised: 08/27/2019] [Accepted: 09/10/2019] [Indexed: 10/26/2022]
Abstract
The bacterial signal recognition particle (SRP) receptor, FtsY, participates with the SRP in co-translation targeting of proteins. Multiple crystal structures of the NG domain of E. coli FtsYNG have been determined at high-resolution (1.22-1.88 Å), in the nucleotide-free (apo) form as well as bound to GDP and non-hydrolysable GTP analogues. The combination of high-resolution and multiple solved structures of FtsYNG in different states revealed a new sensor-relay system of this unique GTPase receptor. A nucleotide sensing function of the P-loop assists FtsYNG in nucleotide-binding and contributes to modulate nucleotide binding properties in SRP GTPases. A reorganization of the other G-loops and the insertion binding domain (IBD) is observed only upon transition from a diphosphate to a triphosphate nucleotide. The role of a magnesium ion during the GDP and GTP-bound states has also been observed. The binding of magnesium in the nucleotide site causes the reorientation of the β- and γ- phosphate groups toward the jaws of the P-loop and stabilizes the binding of the nucleotide, creating a network of hydrogen and water-bridge interactions.
Collapse
Affiliation(s)
- Camilla Faoro
- School of Life and Environmental Sciences, The University of Sydney, Sydney 2006, Australia
| | - Sandro F Ataide
- School of Life and Environmental Sciences, The University of Sydney, Sydney 2006, Australia.
| |
Collapse
|
168
|
Steinberg R, Knüpffer L, Origi A, Asti R, Koch HG. Co-translational protein targeting in bacteria. FEMS Microbiol Lett 2019; 365:4966980. [PMID: 29790984 DOI: 10.1093/femsle/fny095] [Citation(s) in RCA: 57] [Impact Index Per Article: 11.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2018] [Accepted: 04/09/2018] [Indexed: 01/16/2023] Open
Abstract
About 30% of all bacterial proteins execute their function outside of the cytosol and have to be transported into or across the cytoplasmic membrane. Bacteria use multiple protein transport systems in parallel, but the majority of proteins engage two distinct targeting systems. One is the co-translational targeting by two universally conserved GTPases, the signal recognition particle (SRP) and its receptor FtsY, which deliver inner membrane proteins to either the SecYEG translocon or the YidC insertase for membrane insertion. The other targeting system depends on the ATPase SecA, which targets secretory proteins, i.e. periplasmic and outer membrane proteins, to SecYEG for their subsequent ATP-dependent translocation. While SRP selects its substrates already very early during their synthesis, the recognition of secretory proteins by SecA is believed to occur primarily after translation termination, i.e. post-translationally. In this review we highlight recent progress on how SRP recognizes its substrates at the ribosome and how the fidelity of the targeting reaction to SecYEG is maintained. We furthermore discuss similarities and differences in the SRP-dependent targeting to either SecYEG or YidC and summarize recent results that suggest that some membrane proteins are co-translationally targeted by SecA.
Collapse
Affiliation(s)
- Ruth Steinberg
- Institute of Biochemistry and Molecular Biology, Faculty of Medicine, Albert-Ludwigs University Freiburg, Stefan Meier Str. 17, Freiburg D-79104, Germany
| | - Lara Knüpffer
- Institute of Biochemistry and Molecular Biology, Faculty of Medicine, Albert-Ludwigs University Freiburg, Stefan Meier Str. 17, Freiburg D-79104, Germany
| | - Andrea Origi
- Institute of Biochemistry and Molecular Biology, Faculty of Medicine, Albert-Ludwigs University Freiburg, Stefan Meier Str. 17, Freiburg D-79104, Germany.,Faculty of Biology, Albert-Ludwigs-University Freiburg, Schänzlestr. 1, Freiburg D-79104, Germany
| | - Rossella Asti
- Institute of Biochemistry and Molecular Biology, Faculty of Medicine, Albert-Ludwigs University Freiburg, Stefan Meier Str. 17, Freiburg D-79104, Germany
| | - Hans-Georg Koch
- Institute of Biochemistry and Molecular Biology, Faculty of Medicine, Albert-Ludwigs University Freiburg, Stefan Meier Str. 17, Freiburg D-79104, Germany
| |
Collapse
|
169
|
Kang T, Boland BB, Alarcon C, Grimsby JS, Rhodes CJ, Larsen MR. Proteomic Analysis of Restored Insulin Production and Trafficking in Obese Diabetic Mouse Pancreatic Islets Following Euglycemia. J Proteome Res 2019; 18:3245-3258. [PMID: 31317746 DOI: 10.1021/acs.jproteome.9b00160] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
Abstract
For the treatment of patients with prediabetes or diabetes, clinical evidence has emerged that β-cell function can be restored by glucose-lowering therapeutic strategies. However, little is known about the molecular mechanisms underlying this functional adaptive behavior of the pancreatic β-cell. This study examines the dynamic changes in protein expression and phosphorylation state associated with (pro)insulin production and secretory pathway function mediated by euglycemia to induce β-cell rest in obese/diabetic db/db islet β-cells. Unbiased quantitative profiling of the protein expression and phosphorylation events that occur upon β-cell adaption during the transition from hyperglycemia to euglycemia was assessed in isolated pancreatic islets from obese diabetic db/db and wild-type (WT) mice using quantitative proteomics and phosphoproteomics together with bioinformatics analysis. Dynamic changes in the expression and phosphorylation of proteins associated with pancreatic β-cell (pro)insulin production and complementary regulated-secretory pathway regulation were observed in obese diabetic db/db islets in a hyperglycemic environment, relative to WT mouse islets in a normal euglycemic environment, that resolved when isolated db/db islets were exposed to euglycemia for 12 h in vitro. By similarly treating WT islets in parallel, the effects of tissue culture could be mostly eliminated and only those changes associated with resolution by euglycemia were assessed. Among such regulated protein phosphorylation-dependent signaling events were those associated with COPII-coated vesicle-dependent ER exit, ER-to-Golgi trafficking, clathrin-coat disassembly, and a particular association for the luminal Golgi protein kinase, FAM20C, in control of distal secretory pathway trafficking, sorting, and granule biogenesis. Protein expression and especially phosphorylation play key roles in the regulation of (pro)insulin production, correlative secretory pathway trafficking, and the restoration of β-cell secretory capacity in the adaptive functional β-cell response to metabolic demand, especially that mediated by glucose.
Collapse
Affiliation(s)
- Taewook Kang
- Protein Research Group, Department of Biochemistry and Molecular Biology , University of Southern Denmark , DK-5230 Odense M , Denmark.,The Danish Diabetes Academy , 5000 Odense , Denmark
| | - Brandon B Boland
- The Kovler Diabetes Center, Department of Medicine Section of Endocrinology, Diabetes & Metabolism , University of Chicago , Chicago , Illinois 60637 , United States.,Cardiovascular, Renal and Metabolic Disease Research , MedImmune LLC , Gaithersburg , Maryland 20878 , United States
| | - Cristina Alarcon
- The Kovler Diabetes Center, Department of Medicine Section of Endocrinology, Diabetes & Metabolism , University of Chicago , Chicago , Illinois 60637 , United States
| | - Joseph S Grimsby
- Cardiovascular, Renal and Metabolic Disease Research , MedImmune LLC , Gaithersburg , Maryland 20878 , United States
| | - Christopher J Rhodes
- The Kovler Diabetes Center, Department of Medicine Section of Endocrinology, Diabetes & Metabolism , University of Chicago , Chicago , Illinois 60637 , United States.,Cardiovascular, Renal and Metabolic Disease Research , MedImmune LLC , Gaithersburg , Maryland 20878 , United States
| | - Martin R Larsen
- Protein Research Group, Department of Biochemistry and Molecular Biology , University of Southern Denmark , DK-5230 Odense M , Denmark
| |
Collapse
|
170
|
Silencing of Aberrant Secretory Protein Expression by Disease-Associated Mutations. J Mol Biol 2019; 431:2567-2580. [PMID: 31100385 DOI: 10.1016/j.jmb.2019.05.011] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2019] [Revised: 05/04/2019] [Accepted: 05/07/2019] [Indexed: 11/23/2022]
Abstract
Signal recognition particle (SRP) recognizes signal sequences of secretory proteins and targets them to the endoplasmic reticulum membrane for translocation. Many human diseases are connected with defects in signal sequences. The current dogma states that the molecular basis of the disease-associated mutations in the secretory proteins is connected with defects in their transport. Here, we demonstrate for several secretory proteins with disease-associated mutations that the molecular mechanism is different from the dogma. Positively charged or helix-breaking mutations in the signal sequence hydrophobic core prevent synthesis of the aberrant proteins and lead to degradation of their mRNAs. The degree of mRNA depletion depends on the location and severity of the mutation in the signal sequence and correlates with inhibition of SRP interaction. Thus, SRP protects secretory protein mRNAs from degradation. The data demonstrate that if disease-associated mutations obstruct SRP interaction, they lead to silencing of the mutated protein expression.
Collapse
|
171
|
Mutagenesis of DsbAss is Crucial for the Signal Recognition Particle Mechanism in Escherichia coli: Insights from Molecular Dynamics Simulations. Biomolecules 2019; 9:biom9040133. [PMID: 30987187 PMCID: PMC6523802 DOI: 10.3390/biom9040133] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2019] [Revised: 03/17/2019] [Accepted: 03/20/2019] [Indexed: 12/11/2022] Open
Abstract
The disulfide bond signal sequence (DsbAss) protein is characterized as an important virulence factor in gram-negative bacteria. This study aimed to analyze the "alanine" alteration in the hydrophobic (H) region of DsbAss and to understand the conformational DsbAss alteration(s) inside the fifty-four homolog (Ffh)-binding groove which were revealed to be crucial for translocation of ovine growth hormone (OGH) to the periplasmic space in Escherichia coli via the secretory (Sec) pathway. An experimental design was used to explore the hydrophobicity and alteration of alanine (Ala) to isoleucine (Ile) in the tripartite structure of DsbAss. As a result, two DsbAss mutants (Ala at positions -11 and -13) with same hydrophobicity of 1.539 led to the conflicting translocation of the active OGH gene. We performed molecular dynamics (MD) simulations and molecular mechanics generalized born surface area (MM-GBSA) binding free energy calculations to examine the interaction energetic and dynamic aspects of DsbAss/signal repetition particle 54 (SRP54) binding, which has a principle role in Escherichia coli Sec pathways. Although both DsbAss mutants retained helicity, the MD simulation analysis evidenced that altering Ala-13 changed the orientation of the signal peptide in the Ffh M binding domain groove, favored more stable interaction energies (MM-GBSA ΔGtotal = -140.62 kcal mol-1), and hampered the process of OGH translocation, while Ala-11 pointed outward due to unstable conformation and less binding energy (ΔGtotal = -124.24 kcal mol-1). Here we report the dynamic behavior of change of "alanine" in the H-domain of DsbAss which affects the process of translocation of OGH, where MD simulation and MM-GBSA can be useful initial tools to investigate the virulence of bacteria.
Collapse
|
172
|
Malik S, Zafar Paracha R, Khalid M, Nisar M, Siddiqa A, Hussain Z, Nawaz R, Ali A, Ahmad J. MicroRNAs and their target mRNAs as potential biomarkers among smokers and non-smokers with lung adenocarcinoma. IET Syst Biol 2019; 13:69-76. [PMID: 33444474 PMCID: PMC8687273 DOI: 10.1049/iet-syb.2018.5040] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2018] [Revised: 07/17/2018] [Accepted: 08/06/2018] [Indexed: 01/09/2023] Open
Abstract
Lung adenocarcinoma is one of the major causes of mortality. Current methods of diagnosis can be improved through identification of disease specific biomarkers. MicroRNAs are small non-coding regulators of gene expression, which can be potential biomarkers in various diseases. Thus, the main objective of this study was to gain mechanistic insights into genetic abnormalities occurring in lung adenocarcinoma by implementing an integrative analysis of miRNAs and mRNAs expression profiles in the case of both smokers and non-smokers. Differential expression was analysed by comparing publicly available lung adenocarcinoma samples with controls. Furthermore, weighted gene co-expression network analysis is performed which revealed mRNAs and miRNAs significantly correlated with lung adenocarcinoma. Moreover, an integrative analysis resulted in identification of several miRNA-mRNA pairs which were significantly dysregulated in non-smokers with lung adenocarcinoma. Also two pairs (miR-133b/Protein Kinase C Zeta (PRKCZ) and miR-557/STEAP3) were found specifically dysregulated in smokers. Pathway analysis further revealed their role in important signalling pathways including cell cycle. This analysis has not only increased the authors' understanding about lung adenocarcinoma but also proposed potential biomarkers. However, further wet laboratory studies are required for the validation of these potential biomarkers which can be used to diagnose lung adenocarcinoma.
Collapse
Affiliation(s)
- Sumaria Malik
- Research Center For Modeling & Simulation (RCMS)National University of Sciences and Technology (NUST)Sector H‐12IslamabadPakistan
| | - Rehan Zafar Paracha
- Research Center For Modeling & Simulation (RCMS)National University of Sciences and Technology (NUST)Sector H‐12IslamabadPakistan
| | - Maryam Khalid
- Research Center For Modeling & Simulation (RCMS)National University of Sciences and Technology (NUST)Sector H‐12IslamabadPakistan
| | - Maryum Nisar
- Research Center For Modeling & Simulation (RCMS)National University of Sciences and Technology (NUST)Sector H‐12IslamabadPakistan
| | - Amnah Siddiqa
- Research Center For Modeling & Simulation (RCMS)National University of Sciences and Technology (NUST)Sector H‐12IslamabadPakistan
| | - Zamir Hussain
- Research Center For Modeling & Simulation (RCMS)National University of Sciences and Technology (NUST)Sector H‐12IslamabadPakistan
| | - Raheel Nawaz
- School of ComputingMathematics and Digital Technology, Manchester Metropolitan UniversityGM459 Geoffrey Manton BuildingManchesterEngland
| | - Amjad Ali
- Atta‐ur‐Rahman School of Applied Biosciences – ASABNational University of Sciences and Technology (NUST)Sector H‐ 12IslamabadPakistan
| | - Jamil Ahmad
- Research Center For Modeling & Simulation (RCMS)National University of Sciences and Technology (NUST)Sector H‐12IslamabadPakistan
| |
Collapse
|
173
|
Stav S, Atilho RM, Mirihana Arachchilage G, Nguyen G, Higgs G, Breaker RR. Genome-wide discovery of structured noncoding RNAs in bacteria. BMC Microbiol 2019; 19:66. [PMID: 30902049 PMCID: PMC6429828 DOI: 10.1186/s12866-019-1433-7] [Citation(s) in RCA: 33] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2018] [Accepted: 03/07/2019] [Indexed: 12/15/2022] Open
Abstract
Background Structured noncoding RNAs (ncRNAs) play essential roles in many biological processes such as gene regulation, signaling, RNA processing, and protein synthesis. Among the most common groups of ncRNAs in bacteria are riboswitches. These cis-regulatory, metabolite-binding RNAs are present in many species where they regulate various metabolic and signaling pathways. Collectively, there are likely to be hundreds of novel riboswitch classes that remain hidden in the bacterial genomes that have already been sequenced, and potentially thousands of classes distributed among various other species in the biosphere. The vast majority of these undiscovered classes are proposed to be exceedingly rare, and so current bioinformatics search techniques are reaching their limits for differentiating between true riboswitch candidates and false positives. Results Herein, we exploit a computational search pipeline that can efficiently identify intergenic regions most likely to encode structured ncRNAs. Application of this method to five bacterial genomes yielded nearly 70 novel genetic elements including 30 novel candidate ncRNA motifs. Among the riboswitch candidates identified is an RNA motif involved in the regulation of thiamin biosynthesis. Conclusions Analysis of other genomes will undoubtedly lead to the discovery of many additional novel structured ncRNAs, and provide insight into the range of riboswitches and other kinds of ncRNAs remaining to be discovered in bacteria and archaea. Electronic supplementary material The online version of this article (10.1186/s12866-019-1433-7) contains supplementary material, which is available to authorized users.
Collapse
Affiliation(s)
- Shira Stav
- Department of Molecular, Cellular and Developmental Biology, Yale University, New Haven, USA
| | - Ruben M Atilho
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, USA
| | | | - Giahoa Nguyen
- Department of Molecular, Cellular and Developmental Biology, Yale University, New Haven, USA
| | - Gadareth Higgs
- Department of Molecular, Cellular and Developmental Biology, Yale University, New Haven, USA
| | - Ronald R Breaker
- Department of Molecular, Cellular and Developmental Biology, Yale University, New Haven, USA. .,Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, USA. .,Howard Hughes Medical Institute, Yale University, New Haven, CT, 06520, USA.
| |
Collapse
|
174
|
Biever A, Donlin-Asp PG, Schuman EM. Local translation in neuronal processes. Curr Opin Neurobiol 2019; 57:141-148. [PMID: 30861464 DOI: 10.1016/j.conb.2019.02.008] [Citation(s) in RCA: 82] [Impact Index Per Article: 16.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2019] [Accepted: 02/07/2019] [Indexed: 12/19/2022]
Abstract
Neurons exhibit a unique degree of spatial compartmentalization and are able to maintain and remodel their proteomes independently from the cell body. While much effort has been devoted to understanding the capacity and role for local protein synthesis in dendrites and spines, local mRNA translation in mature axons, projecting over distances up to a meter, has received much less attention. Also, little is known about the spatio-temporal dynamics of axonal and dendritic gene expression as function of mRNA abundance, protein synthesis and degradation. Here, we summarize key recent findings that have shaped our knowledge of the precise location of local protein production and discuss unique strategies used by neurons to shape presynaptic and postsynaptic proteomes.
Collapse
Affiliation(s)
- Anne Biever
- Max Planck Institute for Brain Research, Frankfurt am Main, Germany
| | | | - Erin M Schuman
- Max Planck Institute for Brain Research, Frankfurt am Main, Germany.
| |
Collapse
|
175
|
Cai D, Rao Y, Zhan Y, Wang Q, Chen S. EngineeringBacillusfor efficient production of heterologous protein: current progress, challenge and prospect. J Appl Microbiol 2019; 126:1632-1642. [DOI: 10.1111/jam.14192] [Citation(s) in RCA: 42] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2018] [Revised: 12/13/2018] [Accepted: 12/28/2018] [Indexed: 12/18/2022]
Affiliation(s)
- D. Cai
- State Key Laboratory of Biocatalysis and Enzyme Engineering, Environmental Microbial Technology Center of Hubei Province Hubei Collaborative Innovation Center for Green Transformation of Bio‐Resources, College of Life Sciences, Hubei University Wuhan PR China
| | - Y. Rao
- State Key Laboratory of Biocatalysis and Enzyme Engineering, Environmental Microbial Technology Center of Hubei Province Hubei Collaborative Innovation Center for Green Transformation of Bio‐Resources, College of Life Sciences, Hubei University Wuhan PR China
| | - Y. Zhan
- State Key Laboratory of Biocatalysis and Enzyme Engineering, Environmental Microbial Technology Center of Hubei Province Hubei Collaborative Innovation Center for Green Transformation of Bio‐Resources, College of Life Sciences, Hubei University Wuhan PR China
| | - Q. Wang
- State Key Laboratory of Biocatalysis and Enzyme Engineering, Environmental Microbial Technology Center of Hubei Province Hubei Collaborative Innovation Center for Green Transformation of Bio‐Resources, College of Life Sciences, Hubei University Wuhan PR China
| | - S. Chen
- State Key Laboratory of Biocatalysis and Enzyme Engineering, Environmental Microbial Technology Center of Hubei Province Hubei Collaborative Innovation Center for Green Transformation of Bio‐Resources, College of Life Sciences, Hubei University Wuhan PR China
| |
Collapse
|
176
|
Streptococcus mutans yidC1
and
yidC2
Impact Cell Envelope Biogenesis, the Biofilm Matrix, and Biofilm Biophysical Properties. J Bacteriol 2019; 201:JB.00396-18. [DOI: 10.1128/jb.00396-18] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2018] [Accepted: 09/28/2018] [Indexed: 01/25/2023] Open
Abstract
YidC proteins are membrane-localized chaperone insertases that are universally conserved in all bacteria and are traditionally studied in the context of membrane protein insertion and assembly. Both YidC paralogs of the cariogenic pathogen
Streptococcus mutans
are required for proper envelope biogenesis and full virulence, indicating that these proteins may also contribute to optimal biofilm formation in streptococci. Here, we show that the deletion of either
yidC
results in changes to the structure and physical properties of the EPS matrix produced by
S. mutans
, ultimately impairing optimal biofilm development, diminishing its mechanical stability, and facilitating its removal. Importantly, the universal conservation of bacterial
yidC
orthologs, combined with our findings, provide a rationale for YidC as a possible drug target for antibiofilm therapies.
Collapse
|
177
|
Abstract
The inner membrane of Gram-negative bacteria is a ~6 nm thick phospholipid bilayer. It forms a semi-permeable barrier between the cytoplasm and periplasm allowing only regulated export and import of ions, sugar polymers, DNA and proteins. Inner membrane proteins, embedded via hydrophobic transmembrane α-helices, play an essential role in this regulated trafficking: they mediate insertion into the membrane (insertases) or complete crossing of the membrane (translocases) or both. The Gram-negative inner membrane is equipped with a variety of different insertases and translocases. Many of them are specialized, taking care of the export of only a few protein substrates, while others have more general roles. Here, we focus on the three general export/insertion pathways, the secretory (Sec) pathway, YidC and the twin-arginine translocation (TAT) pathway, focusing closely on the Escherichia coli (E. coli) paradigm. We only briefly mention dedicated export pathways found in different Gram-negative bacteria. The Sec system deals with the majority of exported proteins and functions both as a translocase for secretory proteins and an insertase for membrane proteins. The insertase YidC assists the Sec system or operates independently on membrane protein clients. Sec and YidC, in common with most export pathways, require their protein clients to be in soluble non-folded states to fit through the translocation channels and grooves. The TAT pathway is an exception, as it translocates folded proteins, some loaded with prosthetic groups.
Collapse
Affiliation(s)
- Jozefien De Geyter
- Laboratory of Molecular Bacteriology, Department of Microbiology and Immunology, Rega Institute for Medical Research, KU Leuven - University of Leuven, Herestraat 49, 3000, Leuven, Belgium
| | - Dries Smets
- Laboratory of Molecular Bacteriology, Department of Microbiology and Immunology, Rega Institute for Medical Research, KU Leuven - University of Leuven, Herestraat 49, 3000, Leuven, Belgium
| | - Spyridoula Karamanou
- Laboratory of Molecular Bacteriology, Department of Microbiology and Immunology, Rega Institute for Medical Research, KU Leuven - University of Leuven, Herestraat 49, 3000, Leuven, Belgium
| | - Anastassios Economou
- Laboratory of Molecular Bacteriology, Department of Microbiology and Immunology, Rega Institute for Medical Research, KU Leuven - University of Leuven, Herestraat 49, 3000, Leuven, Belgium.
| |
Collapse
|
178
|
Pohlschroder M, Pfeiffer F, Schulze S, Abdul Halim MF. Archaeal cell surface biogenesis. FEMS Microbiol Rev 2018; 42:694-717. [PMID: 29912330 PMCID: PMC6098224 DOI: 10.1093/femsre/fuy027] [Citation(s) in RCA: 39] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2018] [Accepted: 06/12/2018] [Indexed: 12/13/2022] Open
Abstract
Cell surfaces are critical for diverse functions across all domains of life, from cell-cell communication and nutrient uptake to cell stability and surface attachment. While certain aspects of the mechanisms supporting the biosynthesis of the archaeal cell surface are unique, likely due to important differences in cell surface compositions between domains, others are shared with bacteria or eukaryotes or both. Based on recent studies completed on a phylogenetically diverse array of archaea, from a wide variety of habitats, here we discuss advances in the characterization of mechanisms underpinning archaeal cell surface biogenesis. These include those facilitating co- and post-translational protein targeting to the cell surface, transport into and across the archaeal lipid membrane, and protein anchoring strategies. We also discuss, in some detail, the assembly of specific cell surface structures, such as the archaeal S-layer and the type IV pili. We will highlight the importance of post-translational protein modifications, such as lipid attachment and glycosylation, in the biosynthesis as well as the regulation of the functions of these cell surface structures and present the differences and similarities in the biogenesis of type IV pili across prokaryotic domains.
Collapse
Affiliation(s)
| | - Friedhelm Pfeiffer
- Computational Biology Group, Max Planck Institute of Biochemistry, 82152 Martinsried, Germany
| | - Stefan Schulze
- Department of Biology, University of Pennsylvania, Philadelphia, PA 19104, USA
| | | |
Collapse
|
179
|
Weill U, Krieger G, Avihou Z, Milo R, Schuldiner M, Davidi D. Assessment of GFP Tag Position on Protein Localization and Growth Fitness in Yeast. J Mol Biol 2018; 431:636-641. [PMID: 30550779 DOI: 10.1016/j.jmb.2018.12.004] [Citation(s) in RCA: 37] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2018] [Revised: 11/05/2018] [Accepted: 12/05/2018] [Indexed: 11/30/2022]
Abstract
While protein tags are ubiquitously utilized in molecular biology, they harbor the potential to interfere with functional traits of their fusion counterparts. Systematic evaluation of the effect of protein tags on function would promote accurate use of tags in experimental setups. Here we examine the effect of green fluorescent protein tagging at either the N or C terminus of budding yeast proteins on subcellular localization and functionality. We use a competition-based approach to decipher the relative fitness of two strains tagged on the same protein but on opposite termini and from that infer the correct, physiological localization for each protein and the optimal position for tagging. Our study provides a first of a kind systematic assessment of the effect of tags on the functionality of proteins and provides a step toward broad investigation of protein fusion libraries.
Collapse
Affiliation(s)
- Uri Weill
- Department of Molecular Genetics, Weizmann Institute of Science, Rehovot 7610001, Israel
| | - Gat Krieger
- Department of Molecular Genetics, Weizmann Institute of Science, Rehovot 7610001, Israel
| | - Zohar Avihou
- Department of Molecular Genetics, Weizmann Institute of Science, Rehovot 7610001, Israel
| | - Ron Milo
- Department of Plant and Environmental Sciences, Weizmann Institute of Science, Rehovot 7610001, Israel
| | - Maya Schuldiner
- Department of Molecular Genetics, Weizmann Institute of Science, Rehovot 7610001, Israel.
| | - Dan Davidi
- Department of Plant and Environmental Sciences, Weizmann Institute of Science, Rehovot 7610001, Israel.
| |
Collapse
|
180
|
Ziehe D, Dünschede B, Schünemann D. Molecular mechanism of SRP-dependent light-harvesting protein transport to the thylakoid membrane in plants. PHOTOSYNTHESIS RESEARCH 2018; 138:303-313. [PMID: 29956039 PMCID: PMC6244792 DOI: 10.1007/s11120-018-0544-6] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/30/2017] [Accepted: 06/20/2018] [Indexed: 05/26/2023]
Abstract
The light-harvesting chlorophyll a/b binding proteins (LHCP) belong to a large family of membrane proteins. They form the antenna complexes of photosystem I and II and function in light absorption and transfer of the excitation energy to the photosystems. As nuclear-encoded proteins, the LHCPs are imported into the chloroplast and further targeted to their final destination-the thylakoid membrane. Due to their hydrophobicity, the formation of the so-called 'transit complex' in the stroma is important to prevent their aggregation in this aqueous environment. The posttranslational LHCP targeting mechanism is well regulated through the interaction of various soluble and membrane-associated protein components and includes several steps: the binding of the LHCP to the heterodimeric cpSRP43/cpSRP54 complex to form the soluble transit complex; the docking of the transit complex to the SRP receptor cpFtsY and the Alb3 translocase at the membrane followed by the release and integration of the LHCP into the thylakoid membrane in a GTP-dependent manner. This review summarizes the molecular mechanisms and dynamics behind the posttranslational LHCP targeting to the thylakoid membrane of Arabidopsis thaliana.
Collapse
Affiliation(s)
- Dominik Ziehe
- Molecular Biology of Plant Organelles, Ruhr-University Bochum, Universitätsstraße 150, 44780, Bochum, Germany
| | - Beatrix Dünschede
- Molecular Biology of Plant Organelles, Ruhr-University Bochum, Universitätsstraße 150, 44780, Bochum, Germany
| | - Danja Schünemann
- Molecular Biology of Plant Organelles, Ruhr-University Bochum, Universitätsstraße 150, 44780, Bochum, Germany.
| |
Collapse
|
181
|
Cho H, Chio US, Shan SO. In vitro Assays for Targeting and Insertion of Tail-Anchored Proteins Into the ER Membrane. ACTA ACUST UNITED AC 2018; 81:e63. [PMID: 30253068 DOI: 10.1002/cpcb.63] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Abstract
Membrane proteins mediate numerous essential cellular functions. Due to the aggregation propensity of hydrophobic transmembrane domains in aqueous environments, the targeting and insertion of membrane proteins pose major challenges to cells. In the Guided Entry of Tail-anchored protein (GET) pathway, an essential class of newly synthesized tail-anchored proteins (TAs) are chaperoned and guided by multiple targeting factors to the endoplasmic reticulum (ER) membrane. Deciphering the molecular mechanism of this cellular process has benefitted from successful in vitro reconstitution of individual molecular events in the GET pathway with purified components. Here we describe recently developed protocols for in vitro reconstitution of functional complexes of TA substrates with their targeting factors, for monitoring the transfer of TAs between targeting factors, and for the insertion of TA into the microsomal membrane. These procedures are generally applicable to the interrogation of other post-translational membrane protein targeting pathways. © 2018 by John Wiley & Sons, Inc.
Collapse
Affiliation(s)
- Hyunju Cho
- Division of Chemistry and Chemical Engineering, California Institute of Technology, Pasadena, California
| | - Un Seng Chio
- Division of Chemistry and Chemical Engineering, California Institute of Technology, Pasadena, California
| | - Shu-Ou Shan
- Division of Chemistry and Chemical Engineering, California Institute of Technology, Pasadena, California
| |
Collapse
|
182
|
Lipids modulate the insertion and folding of the nascent chains of alpha helical membrane proteins. Biochem Soc Trans 2018; 46:1355-1366. [PMID: 30190329 DOI: 10.1042/bst20170424] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2018] [Revised: 07/18/2018] [Accepted: 07/31/2018] [Indexed: 02/08/2023]
Abstract
Membrane proteins must be inserted into a membrane and folded into their correct structure to function correctly. This insertion occurs during translation and synthesis by the ribosome for most α-helical membrane proteins. Precisely how this co-translational insertion and folding occurs, and the role played by the surrounding lipids, is still not understood. Most of the work on the influence of the lipid environment on folding and insertion has focussed on denatured, fully translated proteins, and thus does not replicate folding during unidirectional elongation of nascent chains that occurs in the cell. This review aims to highlight recent advances in elucidating lipid composition and bilayer properties optimal for insertion and folding of nascent chains in the membrane and in the assembly of oligomeric proteins.
Collapse
|
183
|
Liu M, Weiss MA, Arunagiri A, Yong J, Rege N, Sun J, Haataja L, Kaufman RJ, Arvan P. Biosynthesis, structure, and folding of the insulin precursor protein. Diabetes Obes Metab 2018; 20 Suppl 2:28-50. [PMID: 30230185 PMCID: PMC6463291 DOI: 10.1111/dom.13378] [Citation(s) in RCA: 126] [Impact Index Per Article: 21.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/25/2018] [Revised: 05/04/2018] [Accepted: 05/23/2018] [Indexed: 02/06/2023]
Abstract
Insulin synthesis in pancreatic β-cells is initiated as preproinsulin. Prevailing glucose concentrations, which oscillate pre- and postprandially, exert major dynamic variation in preproinsulin biosynthesis. Accompanying upregulated translation of the insulin precursor includes elements of the endoplasmic reticulum (ER) translocation apparatus linked to successful orientation of the signal peptide, translocation and signal peptide cleavage of preproinsulin-all of which are necessary to initiate the pathway of proper proinsulin folding. Evolutionary pressures on the primary structure of proinsulin itself have preserved the efficiency of folding ("foldability"), and remarkably, these evolutionary pressures are distinct from those protecting the ultimate biological activity of insulin. Proinsulin foldability is manifest in the ER, in which the local environment is designed to assist in the overall load of proinsulin folding and to favour its disulphide bond formation (while limiting misfolding), all of which is closely tuned to ER stress response pathways that have complex (beneficial, as well as potentially damaging) effects on pancreatic β-cells. Proinsulin misfolding may occur as a consequence of exuberant proinsulin biosynthetic load in the ER, proinsulin coding sequence mutations, or genetic predispositions that lead to an altered ER folding environment. Proinsulin misfolding is a phenotype that is very much linked to deficient insulin production and diabetes, as is seen in a variety of contexts: rodent models bearing proinsulin-misfolding mutants, human patients with Mutant INS-gene-induced Diabetes of Youth (MIDY), animal models and human patients bearing mutations in critical ER resident proteins, and, quite possibly, in more common variety type 2 diabetes.
Collapse
Affiliation(s)
- Ming Liu
- Department of Endocrinology and Metabolism, Tianjin Medical University General Hospital, Tianjin, China 300052
- Division of Metabolism, Endocrinology & Diabetes, University of Michigan Medical School, Ann Arbor 48105 MI USA
| | - Michael A. Weiss
- Department of Biochemistry and Molecular Biology, Indiana University School of Medicine, Indianapolis 46202 IN USA
- Department of Biochemistry, Case-Western Reserve University, Cleveland 44016 OH USA
| | - Anoop Arunagiri
- Division of Metabolism, Endocrinology & Diabetes, University of Michigan Medical School, Ann Arbor 48105 MI USA
| | - Jing Yong
- Degenerative Diseases Program, Sanford Burnham Prebys Medical Discovery Institute, La Jolla, CA 92307 USA
| | - Nischay Rege
- Department of Biochemistry, Case-Western Reserve University, Cleveland 44016 OH USA
| | - Jinhong Sun
- Department of Endocrinology and Metabolism, Tianjin Medical University General Hospital, Tianjin, China 300052
- Division of Metabolism, Endocrinology & Diabetes, University of Michigan Medical School, Ann Arbor 48105 MI USA
| | - Leena Haataja
- Division of Metabolism, Endocrinology & Diabetes, University of Michigan Medical School, Ann Arbor 48105 MI USA
| | - Randal J. Kaufman
- Degenerative Diseases Program, Sanford Burnham Prebys Medical Discovery Institute, La Jolla, CA 92307 USA
| | - Peter Arvan
- Division of Metabolism, Endocrinology & Diabetes, University of Michigan Medical School, Ann Arbor 48105 MI USA
| |
Collapse
|
184
|
Kempf G, Stjepanovic G, Sloan J, Hendricks A, Lapouge K, Sinning I. The Escherichia coli SRP Receptor Forms a Homodimer at the Membrane. Structure 2018; 26:1440-1450.e5. [PMID: 30146170 DOI: 10.1016/j.str.2018.07.008] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2018] [Revised: 06/14/2018] [Accepted: 07/22/2018] [Indexed: 01/19/2023]
Abstract
The Escherichia coli signal recognition particle (SRP) receptor, FtsY, plays a fundamental role in co-translational targeting of membrane proteins via the SRP pathway. Efficient targeting relies on membrane interaction of FtsY and heterodimerization with the SRP protein Ffh, which is driven by detachment of α helix (αN1) in FtsY. Here we show that apart from the heterodimer, FtsY forms a nucleotide-dependent homodimer on the membrane, and upon αN1 removal also in solution. Homodimerization triggers reciprocal stimulation of GTP hydrolysis and occurs in vivo. Biochemical characterization together with integrative modeling suggests that the homodimer employs the same interface as the heterodimer. Structure determination of FtsY NG+1 with GMPPNP shows that a dimerization-induced conformational switch of the γ-phosphate is conserved in Escherichia coli, filling an important gap in SRP GTPase activation. Our findings add to the current understanding of SRP GTPases and may challenge previous studies that did not consider homodimerization of FtsY.
Collapse
Affiliation(s)
- Georg Kempf
- Heidelberg University Biochemistry Centre, Heidelberg 69120, Germany
| | - Goran Stjepanovic
- Heidelberg University Biochemistry Centre, Heidelberg 69120, Germany
| | - Jeremy Sloan
- Heidelberg University Biochemistry Centre, Heidelberg 69120, Germany
| | - Astrid Hendricks
- Heidelberg University Biochemistry Centre, Heidelberg 69120, Germany
| | - Karine Lapouge
- Heidelberg University Biochemistry Centre, Heidelberg 69120, Germany
| | - Irmgard Sinning
- Heidelberg University Biochemistry Centre, Heidelberg 69120, Germany.
| |
Collapse
|
185
|
Ghosh S, Saini S, Saraogi I. Peptide nucleic acid mediated inhibition of the bacterial signal recognition particle. Chem Commun (Camb) 2018; 54:8257-8260. [PMID: 29989112 DOI: 10.1039/c8cc04715d] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023]
Abstract
We have identified the bacterial signal recognition particle (SRP) as a novel antibacterial target. As a proof of principle, we used an antisense peptide nucleic acid to target a key SRP RNA. The PNA molecules showed efficient inhibition of SRP function and bacterial cell growth, thereby validating our hypothesis.
Collapse
Affiliation(s)
- Sudipta Ghosh
- Department of Chemistry, Indian Institute of Science Education and Research Bhopal, Bhopal Bypass Road, Bhauri, Bhopal 462066, MP, India.
| | | | | |
Collapse
|
186
|
Fujiwara K, Ito K, Chiba S. MifM-instructed translation arrest involves nascent chain interactions with the exterior as well as the interior of the ribosome. Sci Rep 2018; 8:10311. [PMID: 29985442 PMCID: PMC6037786 DOI: 10.1038/s41598-018-28628-y] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2018] [Accepted: 06/25/2018] [Indexed: 11/09/2022] Open
Abstract
Bacillus subtilis MifM is a monitoring substrate of the YidC pathways of protein integration into the membrane and controls the expression of the YidC2 (YqjG) homolog by undergoing regulated translational elongation arrest. The elongation arrest requires interactions between the MifM nascent polypeptide and the ribosomal components near the peptidyl transferase center (PTC) as well as at the constriction site of the ribosomal exit tunnel. Here, we addressed the roles played by more N-terminal regions of MifM and found that, in addition to the previously-identified arrest-provoking elements, the MifM residues 41-60 likely located at the tunnel exit and outside the ribosome contribute to the full induction of elongation arrest. Mutational effects of the cytosolically exposed part of the ribosomal protein uL23 suggested its involvement in the elongation arrest, presumably by interacting with the extra-ribosomal portion of MifM. In vitro translation with reconstituted translation components recapitulated the effects of the mutations at the 41-60 segment, reinforcing the importance of direct molecular interactions between the nascent chain and the ribosome. These results indicate that the nascent MifM polypeptide interacts extensively with the ribosome both from within and without to direct the elongation halt and consequent up-regulation of YidC2.
Collapse
Affiliation(s)
- Keigo Fujiwara
- Faculty of Life Sciences and Institute for Protein Dynamics, Kyoto Sangyo University, Motoyama, Kamigamo, Kita-Ku, Kyoto, 603-8555, Japan
| | - Koreaki Ito
- Faculty of Life Sciences and Institute for Protein Dynamics, Kyoto Sangyo University, Motoyama, Kamigamo, Kita-Ku, Kyoto, 603-8555, Japan
| | - Shinobu Chiba
- Faculty of Life Sciences and Institute for Protein Dynamics, Kyoto Sangyo University, Motoyama, Kamigamo, Kita-Ku, Kyoto, 603-8555, Japan.
| |
Collapse
|
187
|
Boivin V, Deschamps-Francoeur G, Couture S, Nottingham RM, Bouchard-Bourelle P, Lambowitz AM, Scott MS, Abou-Elela S. Simultaneous sequencing of coding and noncoding RNA reveals a human transcriptome dominated by a small number of highly expressed noncoding genes. RNA (NEW YORK, N.Y.) 2018; 24:950-965. [PMID: 29703781 PMCID: PMC6004057 DOI: 10.1261/rna.064493.117] [Citation(s) in RCA: 49] [Impact Index Per Article: 8.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/16/2017] [Accepted: 04/24/2018] [Indexed: 06/01/2023]
Abstract
Comparing the abundance of one RNA molecule to another is crucial for understanding cellular functions but most sequencing techniques can target only specific subsets of RNA. In this study, we used a new fragmented ribodepleted TGIRT sequencing method that uses a thermostable group II intron reverse transcriptase (TGIRT) to generate a portrait of the human transcriptome depicting the quantitative relationship of all classes of nonribosomal RNA longer than 60 nt. Comparison between different sequencing methods indicated that FRT is more accurate in ranking both mRNA and noncoding RNA than viral reverse transcriptase-based sequencing methods, even those that specifically target these species. Measurements of RNA abundance in different cell lines using this method correlate with biochemical estimates, confirming tRNA as the most abundant nonribosomal RNA biotype. However, the single most abundant transcript is 7SL RNA, a component of the signal recognition particle. Structured noncoding RNAs (sncRNAs) associated with the same biological process are expressed at similar levels, with the exception of RNAs with multiple functions like U1 snRNA. In general, sncRNAs forming RNPs are hundreds to thousands of times more abundant than their mRNA counterparts. Surprisingly, only 50 sncRNA genes produce half of the non-rRNA transcripts detected in two different cell lines. Together the results indicate that the human transcriptome is dominated by a small number of highly expressed sncRNAs specializing in functions related to translation and splicing.
Collapse
Affiliation(s)
- Vincent Boivin
- Département de biochimie, Faculté de médecine et des sciences de la santé, Université de Sherbrooke, Sherbrooke, Québec J1E 4K8, Canada
| | - Gabrielle Deschamps-Francoeur
- Département de biochimie, Faculté de médecine et des sciences de la santé, Université de Sherbrooke, Sherbrooke, Québec J1E 4K8, Canada
| | - Sonia Couture
- Département de microbiologie et d'infectiologie, Faculté de médecine et des sciences de la santé, Université de Sherbrooke, Sherbrooke, Québec J1E 4K8, Canada
| | - Ryan M Nottingham
- Institute for Cellular and Molecular Biology and Department of Molecular Biosciences, University of Texas at Austin, Austin, Texas 78712, USA
| | - Philia Bouchard-Bourelle
- Département de biochimie, Faculté de médecine et des sciences de la santé, Université de Sherbrooke, Sherbrooke, Québec J1E 4K8, Canada
| | - Alan M Lambowitz
- Institute for Cellular and Molecular Biology and Department of Molecular Biosciences, University of Texas at Austin, Austin, Texas 78712, USA
| | - Michelle S Scott
- Département de biochimie, Faculté de médecine et des sciences de la santé, Université de Sherbrooke, Sherbrooke, Québec J1E 4K8, Canada
| | - Sherif Abou-Elela
- Département de microbiologie et d'infectiologie, Faculté de médecine et des sciences de la santé, Université de Sherbrooke, Sherbrooke, Québec J1E 4K8, Canada
| |
Collapse
|
188
|
Sequential activation of human signal recognition particle by the ribosome and signal sequence drives efficient protein targeting. Proc Natl Acad Sci U S A 2018; 115:E5487-E5496. [PMID: 29848629 DOI: 10.1073/pnas.1802252115] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023] Open
Abstract
Signal recognition particle (SRP) is a universally conserved targeting machine that mediates the targeted delivery of ∼30% of the proteome. The molecular mechanism by which eukaryotic SRP achieves efficient and selective protein targeting remains elusive. Here, we describe quantitative analyses of completely reconstituted human SRP (hSRP) and SRP receptor (SR). Enzymatic and fluorescence analyses showed that the ribosome, together with a functional signal sequence on the nascent polypeptide, are required to activate SRP for rapid recruitment of the SR, thereby delivering translating ribosomes to the endoplasmic reticulum. Single-molecule fluorescence spectroscopy combined with cross-complementation analyses reveal a sequential mechanism of activation whereby the ribosome unlocks the hSRP from an autoinhibited state and primes SRP to sample a variety of conformations. The signal sequence further preorganizes the mammalian SRP into the optimal conformation for efficient recruitment of the SR. Finally, the use of a signal sequence to activate SRP for receptor recruitment is a universally conserved feature to enable efficient and selective protein targeting, and the eukaryote-specific components confer upon the mammalian SRP the ability to sense and respond to ribosomes.
Collapse
|
189
|
Abstract
Proper localization of membrane proteins is essential for the function of biological membranes and for the establishment of organelle identity within a cell. Molecular machineries that mediate membrane protein biogenesis need to not only achieve a high degree of efficiency and accuracy, but also prevent off-pathway aggregation events that can be detrimental to cells. The posttranslational targeting of tail-anchored proteins (TAs) provides tractable model systems to probe these fundamental issues. Recent advances in understanding TA-targeting pathways reveal sophisticated molecular machineries that drive and regulate these processes. These findings also suggest how an interconnected network of targeting factors, cochaperones, and quality control machineries together ensures robust membrane protein biogenesis.
Collapse
Affiliation(s)
- Un Seng Chio
- Division of Chemistry and Chemical Engineering, California Institute of Technology, Pasadena, California 91125; , ,
| | - Hyunju Cho
- Division of Chemistry and Chemical Engineering, California Institute of Technology, Pasadena, California 91125; , ,
| | - Shu-Ou Shan
- Division of Chemistry and Chemical Engineering, California Institute of Technology, Pasadena, California 91125; , ,
| |
Collapse
|
190
|
Martins MP, Gomes EV, Sanches PR, Pedersoli WR, Martinez-Rossi NM, Rossi A. mus-52 disruption and metabolic regulation in Neurospora crassa: Transcriptional responses to extracellular phosphate availability. PLoS One 2018; 13:e0195871. [PMID: 29668735 PMCID: PMC5905970 DOI: 10.1371/journal.pone.0195871] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2017] [Accepted: 03/30/2018] [Indexed: 12/01/2022] Open
Abstract
Advances in the understanding of molecular systems depend on specific tools like the disruption of genes to produce strains with the desired characteristics. The disruption of any mutagen sensitive (mus) genes in the model fungus Neurospora crassa, i.e. mus-51, mus-52, or mus-53, orthologous to the human genes KU70, KU80, and LIG4, respectively, provides efficient tools for gene targeting. Accordingly, we used RNA-sequencing and reverse transcription-quantitative polymerase chain reaction amplification techniques to evaluate the effects of mus-52 deletion in N. crassa gene transcriptional modulation, and thus, infer its influence regarding metabolic response to extracellular availability of inorganic phosphate (Pi). Notably, the absence of MUS-52 affected the transcription of a vast number of genes, highlighting the expression of those coding for transcription factors, kinases, circadian clocks, oxi-reduction balance, and membrane- and nucleolus-related proteins. These findings may provide insights toward the KU molecular mechanisms, which have been related to telomere maintenance, apoptosis, DNA replication, and gene transcription regulation, as well as associated human conditions including immune system disorders, cancer, and aging.
Collapse
Affiliation(s)
- Maíra P. Martins
- Department of Genetics, Ribeirão Preto Medical School, São Paulo University, Ribeirão Preto, São Paulo, Brazil
| | - Eriston V. Gomes
- Department of Genetics, Ribeirão Preto Medical School, São Paulo University, Ribeirão Preto, São Paulo, Brazil
| | - Pablo R. Sanches
- Department of Genetics, Ribeirão Preto Medical School, São Paulo University, Ribeirão Preto, São Paulo, Brazil
| | - Wellington R. Pedersoli
- Department of Genetics, Ribeirão Preto Medical School, São Paulo University, Ribeirão Preto, São Paulo, Brazil
| | - Nilce M. Martinez-Rossi
- Department of Genetics, Ribeirão Preto Medical School, São Paulo University, Ribeirão Preto, São Paulo, Brazil
| | - Antonio Rossi
- Department of Genetics, Ribeirão Preto Medical School, São Paulo University, Ribeirão Preto, São Paulo, Brazil
| |
Collapse
|
191
|
A statistical analysis on transcriptome sequences: The enrichment of Alu-element is associated with subcellular location. Biochem Biophys Res Commun 2018. [PMID: 29524415 DOI: 10.1016/j.bbrc.2018.03.024] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Abstract
The Alu-element plays important roles in mediating alternative splicing, RNA editing and translation regulation. However, the distribution and function of the Alu-element are never analysed at the transcriptome level. This study presents a statistical analysis of the Alu-element on human transcriptome. We found that mRNAs and lncRNAs share the same sequence form for the Alu-element. The Alu-element covers 5.8% of the coding transcripts and 17.1% of the coding genes for mRNAs, and covers 9.3% of the transcripts and 13.6% of the genes for lncRNAs. The Alu-element is preferentially located at the 3' end. Statistical analysis demonstrates that the enrichment of Alu-element is associated with subcellular location. For instance, Alu-inclusive transcripts are overexpressed in nucleus, mitochondrion and Golgi apparatus membrane while under-expressed in cell membrane and extracellular space. We found that genes contain both Alu-element and S- domains of 7SL RNA are all associated with cellular activities carried out in mitochondrion.
Collapse
|
192
|
Gao Y, Zhang Q, Lang Y, Liu Y, Dong X, Chen Z, Tian W, Tang J, Wu W, Tong Y, Chen Z. Human apo-SRP72 and SRP68/72 complex structures reveal the molecular basis of protein translocation. J Mol Cell Biol 2018; 9:220-230. [PMID: 28369529 PMCID: PMC5907831 DOI: 10.1093/jmcb/mjx010] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2016] [Accepted: 03/15/2017] [Indexed: 02/04/2023] Open
Abstract
The co-translational targeting or insertion of secretory and membrane proteins into the endoplasmic reticulum (ER) is a key biological process mediated by the signal recognition particle (SRP). In eukaryotes, the SRP68–SRP72 (SRP68/72) heterodimer plays an essential role in protein translocation. However, structural information on the two largest SRP proteins, SRP68 and SRP72, is limited, especially regarding their interaction. Herein, we report the first crystal structures of human apo-SRP72 and the SRP68/72 complex at 2.91Å and 1.7Å resolution, respectively. The SRP68-binding domain of SRP72 contains four atypical tetratricopeptide repeats (TPR) and a flexible C-terminal cap. Apo-SRP72 exists mainly as dimers in solution. To bind to SRP68, the SRP72 homodimer disassociates, and the indispensable C-terminal cap undergoes a pronounced conformational change to assist formation of the SRP68/72 heterodimer. A 23-residue polypeptide of SRP68 is sufficient for tight binding to SRP72 through its unusually hydrophobic and extended surface. Structural, biophysical, and mutagenesis analyses revealed that cancer-associated mutations disrupt the SRP68–SRP72 interaction and their co-localization with ER in mammalian cells. The results highlight the essential role of the SRP68–SRP72 interaction in SRP-mediated protein translocation and provide a structural basis for disease diagnosis, pathophysiology, and drug design.
Collapse
Affiliation(s)
- Yina Gao
- Beijing Advanced Innovation Center for Food Nutrition and Human Health, State Key Laboratory of Agrobiotechnology, China Agricultural University, Beijing 100193, China
| | - Qi Zhang
- Structural Genomics Consortium, Toronto, Ontario M5G 1L7, Canada
| | - Yue Lang
- College of Veterinary Medicine, China Agricultural University, Beijing 100193, China
| | - Yang Liu
- Beijing Advanced Innovation Center for Food Nutrition and Human Health, State Key Laboratory of Agrobiotechnology, China Agricultural University, Beijing 100193, China
| | - Xiaofei Dong
- Beijing Advanced Innovation Center for Food Nutrition and Human Health, State Key Laboratory of Agrobiotechnology, China Agricultural University, Beijing 100193, China
| | - Zhenhang Chen
- Beijing Advanced Innovation Center for Food Nutrition and Human Health, State Key Laboratory of Agrobiotechnology, China Agricultural University, Beijing 100193, China
| | - Wenli Tian
- Institute of Apicultural Research, Chinese Academy of Agricultural Sciences, Beijing 100093, China
| | - Jun Tang
- Beijing Advanced Innovation Center for Food Nutrition and Human Health, State Key Laboratory of Agrobiotechnology, China Agricultural University, Beijing 100193, China.,College of Veterinary Medicine, China Agricultural University, Beijing 100193, China
| | - Wei Wu
- Beijing Advanced Innovation Center for Food Nutrition and Human Health, State Key Laboratory of Agrobiotechnology, China Agricultural University, Beijing 100193, China
| | - Yufeng Tong
- Structural Genomics Consortium, Toronto, Ontario M5G 1L7, Canada.,Department of Pharmacology and Toxicology, University of Toronto, Toronto, Ontario M5G 1L7, Canada
| | - Zhongzhou Chen
- Beijing Advanced Innovation Center for Food Nutrition and Human Health, State Key Laboratory of Agrobiotechnology, China Agricultural University, Beijing 100193, China
| |
Collapse
|
193
|
Chloroplast SRP43 acts as a chaperone for glutamyl-tRNA reductase, the rate-limiting enzyme in tetrapyrrole biosynthesis. Proc Natl Acad Sci U S A 2018; 115:E3588-E3596. [PMID: 29581280 DOI: 10.1073/pnas.1719645115] [Citation(s) in RCA: 30] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022] Open
Abstract
Assembly of light-harvesting complexes requires synchronization of chlorophyll (Chl) biosynthesis with biogenesis of light-harvesting Chl a/b-binding proteins (LHCPs). The chloroplast signal recognition particle (cpSRP) pathway is responsible for transport of nucleus-encoded LHCPs in the stroma of the plastid and their integration into the thylakoid membranes. Correct folding and assembly of LHCPs require the incorporation of Chls, whose biosynthesis must therefore be precisely coordinated with membrane insertion of LHCPs. How the spatiotemporal coordination between the cpSRP machinery and Chl biosynthesis is achieved is poorly understood. In this work, we demonstrate a direct interaction between cpSRP43, the chaperone that mediates LHCP targeting and insertion, and glutamyl-tRNA reductase (GluTR), a rate-limiting enzyme in tetrapyrrole biosynthesis. Concurrent deficiency for cpSRP43 and the GluTR-binding protein (GBP) additively reduces GluTR levels, indicating that cpSRP43 and GBP act nonredundantly to stabilize GluTR. The substrate-binding domain of cpSRP43 binds to the N-terminal region of GluTR, which harbors aggregation-prone motifs, and the chaperone activity of cpSRP43 efficiently prevents aggregation of these regions. Our work thus reveals a function of cpSRP43 in Chl biosynthesis and suggests a striking mechanism for posttranslational coordination of LHCP insertion with Chl biosynthesis.
Collapse
|
194
|
Flores JK, Ataide SF. Structural Changes of RNA in Complex with Proteins in the SRP. Front Mol Biosci 2018; 5:7. [PMID: 29459899 PMCID: PMC5807370 DOI: 10.3389/fmolb.2018.00007] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2017] [Accepted: 01/17/2018] [Indexed: 12/18/2022] Open
Abstract
The structural flexibility of RNA allows it to exist in several shapes and sizes. Thus, RNA is functionally diverse and is known to be involved in processes such as catalysis, ligand binding, and most importantly, protein recognition. RNA can adopt different structures, which can often dictate its functionality. When RNA binds onto protein to form a ribonucleoprotein complex (RNP), multiple interactions and conformational changes occur with the RNA and protein. However, there is the question of whether there is a specific pattern for these changes to occur upon recognition. In particular when RNP complexity increases with the addition of multiple proteins/RNA, it becomes difficult to structurally characterize the overall changes using the current structural determination techniques. Hence, there is a need to use a combination of biochemical, structural and computational modeling to achieve a better understanding of the processes that RNPs are involved. Nevertheless, there are well-characterized systems that are evolutionarily conserved [such as the signal recognition particle (SRP)] that give us important information on the structural changes of RNA and protein upon complex formation.
Collapse
Affiliation(s)
- Janine K Flores
- Ataide Lab, School of Life and Environmental Sciences, University of Sydney, Sydney, NSW, Australia
| | - Sandro F Ataide
- Ataide Lab, School of Life and Environmental Sciences, University of Sydney, Sydney, NSW, Australia
| |
Collapse
|
195
|
Di W, Fujita A, Hamaguchi K, Delannoy P, Sato C, Kitajima K. Diverse subcellular localizations of the insect CMP-sialic acid synthetases. Glycobiology 2018; 27:329-341. [PMID: 27986833 DOI: 10.1093/glycob/cww128] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2016] [Accepted: 12/07/2016] [Indexed: 11/12/2022] Open
Abstract
The occurrence and biological importance of sialic acid (Sia) and its metabolic enzymes in insects have been studied using Drosophila melanogaster. The most prominent feature of D. melanogaster CMP-Sia synthetase (DmCSS) is its Golgi-localization, contrasted with nuclear localization of vertebrate CSSs. However, it remains unclear if the Golgi-localization is common to other insect CSSs and why it happens. To answer these questions, Aedes aegypti (mosquito) CSS (AaCSS) and Tribolium castaneum (beetle) CSS (TcCSS) were cloned and characterized for their activity and subcellular localization. Our new findings show: (1) AaCSS and TcCSS share a common overall structure with DmCSS in terms of evolutionarily conserved motifs and the absence of the C-terminal domain typical to vertebrate CSSs; (2) when expressed in mammalian and insect cells, AaCSS and TcCSS showed in vivo and in vitro CSS activities, similar to DmCSS. In contrast, when expressed in bacteria, they lacked CSS activity because the N-terminal hydrophobic region appeared to induce protein aggregation; (3) when expressed in Drosophila S2 cells, AaCSS and TcCSS were predominantly localized in the ER, but not in the Golgi. Surprisingly, DmCSS was mainly secreted into the culture medium, although partially detected in Golgi. Consistent with these results, the N-terminal hydrophobic regions of AaCSS and TcCSS functioned as a signal peptide to render them soluble in the ER, while the N-terminus of DmCSS functioned as a membrane-spanning region of type II transmembrane proteins whose cytosolic KLK sequence functioned as an ER export signal. Accordingly, the differential subcellular localization of insect CSSs are distinctively more diverse than previously recognized.
Collapse
Affiliation(s)
- Wu Di
- Bioscience and Biotechnology Center, and Graduate School of Bioagricultural Sciences, Nagoya University, Nagoya, Japan.,Program for Leading Graduate Schools, Integrative Graduate Education and Research Program in Green Natural Sciences, Nagoya University, Nagoya, Japan
| | - Akiko Fujita
- Bioscience and Biotechnology Center, and Graduate School of Bioagricultural Sciences, Nagoya University, Nagoya, Japan
| | - Kayo Hamaguchi
- Bioscience and Biotechnology Center, and Graduate School of Bioagricultural Sciences, Nagoya University, Nagoya, Japan
| | - Philippe Delannoy
- University of Lille, CNRS, UMR 8576-UGS-Unité de Glycobiologie Structurale et Fonctionnelle, Lille, France
| | - Chihiro Sato
- Bioscience and Biotechnology Center, and Graduate School of Bioagricultural Sciences, Nagoya University, Nagoya, Japan.,Program for Leading Graduate Schools, Integrative Graduate Education and Research Program in Green Natural Sciences, Nagoya University, Nagoya, Japan
| | - Ken Kitajima
- Bioscience and Biotechnology Center, and Graduate School of Bioagricultural Sciences, Nagoya University, Nagoya, Japan.,Program for Leading Graduate Schools, Integrative Graduate Education and Research Program in Green Natural Sciences, Nagoya University, Nagoya, Japan
| |
Collapse
|
196
|
Influenza A Virus M2 Protein: Roles from Ingress to Egress. Int J Mol Sci 2017; 18:ijms18122649. [PMID: 29215568 PMCID: PMC5751251 DOI: 10.3390/ijms18122649] [Citation(s) in RCA: 52] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2017] [Revised: 12/04/2017] [Accepted: 12/05/2017] [Indexed: 11/17/2022] Open
Abstract
Influenza A virus (IAV) matrix protein 2 (M2) is among the smallest bona fide, hence extensively studied, ion channel proteins. The M2 ion channel activity is not only essential for virus replication, but also involved in modulation of cellular homeostasis in a variety of ways. It is also the target for ion channel inhibitors, i.e., anti-influenza drugs. Thus far, several studies have been conducted to elucidate its biophysical characteristics, structure-function relationships of the ion channel, and the M2-host interactome. In this review, we discuss M2 protein synthesis and assembly into an ion channel, its roles in IAV replication, and the pathophysiological impact on the host cell.
Collapse
|
197
|
Morgan GJ, Burkhardt DH, Kelly JW, Powers ET. Translation efficiency is maintained at elevated temperature in Escherichia coli. J Biol Chem 2017; 293:777-793. [PMID: 29183994 DOI: 10.1074/jbc.ra117.000284] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2017] [Revised: 11/22/2017] [Indexed: 01/30/2023] Open
Abstract
Cellular protein levels are dictated by the balance between gene transcription, mRNA translation, and protein degradation, among other factors. Translation requires the interplay of several RNA hybridization processes, which are expected to be temperature-sensitive. We used ribosome profiling to monitor translation in Escherichia coli at 30 °C and to investigate how this changes after 10-20 min of heat shock at 42 °C. Translation efficiencies are robustly maintained after thermal heat shock and after mimicking the heat-shock response transcriptional program at 30 °C by overexpressing the heat shock σ factor encoded by the rpoH gene. We compared translation efficiency, the ratio of ribosome footprint reads to mRNA reads for each gene, to parameters derived from gene sequences. Genes with stable mRNA structures, non-optimal codon use, and those whose gene product is cotranslationally translocated into the inner membrane are generally less highly translated than other genes. Comparison with other published datasets suggests a role for translational elongation in coupling mRNA structures to translation initiation. Genome-wide calculations of the temperature dependence of mRNA structure predict that relatively few mRNAs show a melting transition between 30 and 42 °C, consistent with the observed lack of changes in translation efficiency. We developed a linear model with six parameters that can predict 38% of the variation in translation efficiency between genes, which may be useful in interpreting transcriptome data.
Collapse
Affiliation(s)
- Gareth J Morgan
- From the Departments of Chemistry and Molecular Medicine and
| | - David H Burkhardt
- California Institute of Quantitative Biosciences and Department of Microbiology and Immunology, University of California, San Francisco, San Francisco, California 94158
| | - Jeffery W Kelly
- From the Departments of Chemistry and Molecular Medicine and.,Skaggs Institute for Chemical Biology, The Scripps Research Institute, La, Jolla, California 92037, and
| | - Evan T Powers
- From the Departments of Chemistry and Molecular Medicine and
| |
Collapse
|
198
|
Elimination of a signal sequence-uncleaved form of defective HLA protein through BAG6. Sci Rep 2017; 7:14545. [PMID: 29109525 PMCID: PMC5674028 DOI: 10.1038/s41598-017-14975-9] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2017] [Accepted: 10/16/2017] [Indexed: 12/15/2022] Open
Abstract
A portion of newly synthesized transmembrane domain proteins tend to fail to assemble correctly in the lumen of the endoplasmic reticulum, thus resulting in the production of a signal sequence-uncleaved form of the defective species. Although the efficient degradation of these mistargeted polypeptides is crucial, the molecular mechanism of their elimination pathway has not been adequately characterized. In this study, we focused on one such cryptic portion of a defective transmembrane domain protein, HLA-A, and show that a part of HLA-A is produced as a signal sequence-uncleaved labile species that is immediately targeted to the degradation pathway. We found that both BAG6 and proteasomes are indispensable for elimination of mislocalized HLA-A species. Furthermore, defective HLA-A is subjected to BAG6-dependent solubilization in the cytoplasm. These observations suggest that BAG6 acts as a critical factor for proteasome-mediated degradation of mislocalized HLA-A with a non-cleaved signal sequence at its N-terminus.
Collapse
|
199
|
Magin RS, Deng S, Zhang H, Cooperman B, Marmorstein R. Probing the interaction between NatA and the ribosome for co-translational protein acetylation. PLoS One 2017; 12:e0186278. [PMID: 29016658 PMCID: PMC5634638 DOI: 10.1371/journal.pone.0186278] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2017] [Accepted: 09/28/2017] [Indexed: 01/02/2023] Open
Abstract
N-terminal acetylation is among the most abundant protein modifications in eukaryotic cells. Over the last decade, significant progress has been made in elucidating the function of N-terminal acetylation for a number of diverse systems, involved in a wide variety of biological processes. The enzymes responsible for the modification are the N-terminal acetyltransferases (NATs). The NATs are a highly conserved group of enzymes in eukaryotes, which are responsible for acetylating over 80% of the soluble proteome in human cells. Importantly, many of these NATs act co-translationally; they interact with the ribosome near the exit tunnel and acetylate the nascent protein chain as it is being translated. While the structures of many of the NATs have been determined, the molecular basis for the interaction with ribosome is not known. Here, using purified ribosomes and NatA, a very well-studied NAT, we show that NatA forms a stable complex with the ribosome in the absence of other stabilizing factors and through two conserved regions; primarily through an N-terminal domain and an internal basic helix. These regions may orient the active site of the NatA to face the peptide emerging from the exit tunnel. This work provides a framework for understanding how NatA and potentially other NATs interact with the ribosome for co-translational protein acetylation and sets the foundation for future studies to decouple N-terminal acetyltransferase activity from ribosome association.
Collapse
Affiliation(s)
- Robert S. Magin
- Department of Biochemistry and Biophysics, Abramson Family Cancer Research Institute, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, United States of America
- Graduate Group in Biochemistry and Biophysics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, United States of America
| | - Sunbin Deng
- Department of Biochemistry and Biophysics, Abramson Family Cancer Research Institute, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, United States of America
- Department of Chemistry, University of Pennsylvania, Philadelphia, Pennsylvania, United States of America
| | - Haibo Zhang
- Department of Chemistry, University of Pennsylvania, Philadelphia, Pennsylvania, United States of America
| | - Barry Cooperman
- Department of Chemistry, University of Pennsylvania, Philadelphia, Pennsylvania, United States of America
| | - Ronen Marmorstein
- Department of Biochemistry and Biophysics, Abramson Family Cancer Research Institute, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, United States of America
- Department of Chemistry, University of Pennsylvania, Philadelphia, Pennsylvania, United States of America
| |
Collapse
|
200
|
Carapito R, Konantz M, Paillard C, Miao Z, Pichot A, Leduc MS, Yang Y, Bergstrom KL, Mahoney DH, Shardy DL, Alsaleh G, Naegely L, Kolmer A, Paul N, Hanauer A, Rolli V, Müller JS, Alghisi E, Sauteur L, Macquin C, Morlon A, Sancho CS, Amati-Bonneau P, Procaccio V, Mosca-Boidron AL, Marle N, Osmani N, Lefebvre O, Goetz JG, Unal S, Akarsu NA, Radosavljevic M, Chenard MP, Rialland F, Grain A, Béné MC, Eveillard M, Vincent M, Guy J, Faivre L, Thauvin-Robinet C, Thevenon J, Myers K, Fleming MD, Shimamura A, Bottollier-Lemallaz E, Westhof E, Lengerke C, Isidor B, Bahram S. Mutations in signal recognition particle SRP54 cause syndromic neutropenia with Shwachman-Diamond-like features. J Clin Invest 2017; 127:4090-4103. [PMID: 28972538 DOI: 10.1172/jci92876] [Citation(s) in RCA: 107] [Impact Index Per Article: 15.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2017] [Accepted: 08/10/2017] [Indexed: 12/12/2022] Open
Abstract
Shwachman-Diamond syndrome (SDS) (OMIM #260400) is a rare inherited bone marrow failure syndrome (IBMFS) that is primarily characterized by neutropenia and exocrine pancreatic insufficiency. Seventy-five to ninety percent of patients have compound heterozygous loss-of-function mutations in the Shwachman-Bodian-Diamond syndrome (sbds) gene. Using trio whole-exome sequencing (WES) in an sbds-negative SDS family and candidate gene sequencing in additional SBDS-negative SDS cases or molecularly undiagnosed IBMFS cases, we identified 3 independent patients, each of whom carried a de novo missense variant in srp54 (encoding signal recognition particle 54 kDa). These 3 patients shared congenital neutropenia linked with various other SDS phenotypes. 3D protein modeling revealed that the 3 variants affect highly conserved amino acids within the GTPase domain of the protein that are critical for GTP and receptor binding. Indeed, we observed that the GTPase activity of the mutated proteins was impaired. The level of SRP54 mRNA in the bone marrow was 3.6-fold lower in patients with SRP54-mutations than in healthy controls. Profound reductions in neutrophil counts and chemotaxis as well as a diminished exocrine pancreas size in a SRP54-knockdown zebrafish model faithfully recapitulated the human phenotype. In conclusion, autosomal dominant mutations in SRP54, a key member of the cotranslation protein-targeting pathway, lead to syndromic neutropenia with a Shwachman-Diamond-like phenotype.
Collapse
Affiliation(s)
- Raphael Carapito
- Laboratoire d'ImmunoRhumatologie Moléculaire, Plateforme GENOMAX, INSERM UMR - S1109, Faculté de Médecine, Fédération Hospitalo-Universitaire OMICARE, Fédération de Médecine Translationnelle de Strasbourg (FMTS), Université de Strasbourg, Strasbourg, France.,LabEx TRANSPLANTEX, Faculté de Médecine, Université de Strasbourg, Strasbourg, France.,Service d'Immunologie Biologique, Plateau Technique de Biologie, Pôle de Biologie, Nouvel Hôpital Civil, Strasbourg, France
| | - Martina Konantz
- Department of Biomedicine, University Hospital Basel, University of Basel, Basel, Switzerland
| | - Catherine Paillard
- Laboratoire d'ImmunoRhumatologie Moléculaire, Plateforme GENOMAX, INSERM UMR - S1109, Faculté de Médecine, Fédération Hospitalo-Universitaire OMICARE, Fédération de Médecine Translationnelle de Strasbourg (FMTS), Université de Strasbourg, Strasbourg, France.,LabEx TRANSPLANTEX, Faculté de Médecine, Université de Strasbourg, Strasbourg, France.,Service d'Onco-hématologie Pédiatrique, Hôpital de Hautepierre, Hôpitaux Universitaires de Strasbourg, Strasbourg, France
| | - Zhichao Miao
- Architecture et Réactivité de l'ARN, CNRS UPR 9002, LabEx NetRNA, Institut de Biologie Moléculaire et Cellulaire, Université de Strasbourg, Strasbourg, France
| | - Angélique Pichot
- Laboratoire d'ImmunoRhumatologie Moléculaire, Plateforme GENOMAX, INSERM UMR - S1109, Faculté de Médecine, Fédération Hospitalo-Universitaire OMICARE, Fédération de Médecine Translationnelle de Strasbourg (FMTS), Université de Strasbourg, Strasbourg, France.,LabEx TRANSPLANTEX, Faculté de Médecine, Université de Strasbourg, Strasbourg, France
| | - Magalie S Leduc
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas, USA.,Baylor Genetics, Holcombe, Houston, Texas, USA
| | - Yaping Yang
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas, USA
| | - Katie L Bergstrom
- Department of Pediatrics, Hematology-Oncology Section, Texas Children's Hematology and Cancer Centers, Baylor College of Medicine, Houston, Texas, USA
| | - Donald H Mahoney
- Department of Pediatrics, Hematology-Oncology Section, Texas Children's Hematology and Cancer Centers, Baylor College of Medicine, Houston, Texas, USA
| | - Deborah L Shardy
- Department of Pediatrics, Hematology-Oncology Section, Texas Children's Hematology and Cancer Centers, Baylor College of Medicine, Houston, Texas, USA
| | - Ghada Alsaleh
- Laboratoire d'ImmunoRhumatologie Moléculaire, Plateforme GENOMAX, INSERM UMR - S1109, Faculté de Médecine, Fédération Hospitalo-Universitaire OMICARE, Fédération de Médecine Translationnelle de Strasbourg (FMTS), Université de Strasbourg, Strasbourg, France.,LabEx TRANSPLANTEX, Faculté de Médecine, Université de Strasbourg, Strasbourg, France
| | - Lydie Naegely
- Laboratoire d'ImmunoRhumatologie Moléculaire, Plateforme GENOMAX, INSERM UMR - S1109, Faculté de Médecine, Fédération Hospitalo-Universitaire OMICARE, Fédération de Médecine Translationnelle de Strasbourg (FMTS), Université de Strasbourg, Strasbourg, France.,LabEx TRANSPLANTEX, Faculté de Médecine, Université de Strasbourg, Strasbourg, France
| | - Aline Kolmer
- Laboratoire d'ImmunoRhumatologie Moléculaire, Plateforme GENOMAX, INSERM UMR - S1109, Faculté de Médecine, Fédération Hospitalo-Universitaire OMICARE, Fédération de Médecine Translationnelle de Strasbourg (FMTS), Université de Strasbourg, Strasbourg, France.,LabEx TRANSPLANTEX, Faculté de Médecine, Université de Strasbourg, Strasbourg, France
| | - Nicodème Paul
- Laboratoire d'ImmunoRhumatologie Moléculaire, Plateforme GENOMAX, INSERM UMR - S1109, Faculté de Médecine, Fédération Hospitalo-Universitaire OMICARE, Fédération de Médecine Translationnelle de Strasbourg (FMTS), Université de Strasbourg, Strasbourg, France.,LabEx TRANSPLANTEX, Faculté de Médecine, Université de Strasbourg, Strasbourg, France
| | - Antoine Hanauer
- Laboratoire d'ImmunoRhumatologie Moléculaire, Plateforme GENOMAX, INSERM UMR - S1109, Faculté de Médecine, Fédération Hospitalo-Universitaire OMICARE, Fédération de Médecine Translationnelle de Strasbourg (FMTS), Université de Strasbourg, Strasbourg, France.,LabEx TRANSPLANTEX, Faculté de Médecine, Université de Strasbourg, Strasbourg, France
| | - Véronique Rolli
- Laboratoire d'ImmunoRhumatologie Moléculaire, Plateforme GENOMAX, INSERM UMR - S1109, Faculté de Médecine, Fédération Hospitalo-Universitaire OMICARE, Fédération de Médecine Translationnelle de Strasbourg (FMTS), Université de Strasbourg, Strasbourg, France.,LabEx TRANSPLANTEX, Faculté de Médecine, Université de Strasbourg, Strasbourg, France.,Service d'Immunologie Biologique, Plateau Technique de Biologie, Pôle de Biologie, Nouvel Hôpital Civil, Strasbourg, France
| | - Joëlle S Müller
- Department of Biomedicine, University Hospital Basel, University of Basel, Basel, Switzerland
| | - Elisa Alghisi
- Department of Biomedicine, University Hospital Basel, University of Basel, Basel, Switzerland
| | - Loïc Sauteur
- Department of Biomedicine, University Hospital Basel, University of Basel, Basel, Switzerland
| | - Cécile Macquin
- Laboratoire d'ImmunoRhumatologie Moléculaire, Plateforme GENOMAX, INSERM UMR - S1109, Faculté de Médecine, Fédération Hospitalo-Universitaire OMICARE, Fédération de Médecine Translationnelle de Strasbourg (FMTS), Université de Strasbourg, Strasbourg, France.,LabEx TRANSPLANTEX, Faculté de Médecine, Université de Strasbourg, Strasbourg, France
| | | | - Consuelo Sebastia Sancho
- Service de Radiologie Pédiatrique, Hôpital de Hautepierre, Hôpitaux Universitaires de Strasbourg, Strasbourg, France
| | - Patrizia Amati-Bonneau
- CNRS UMR 6015, INSERM UMR - S1083, MitoVasc Institute, Angers University, Angers, France.,Department of Biochemistry and Genetics, Angers Hospital, Angers, France
| | - Vincent Procaccio
- CNRS UMR 6015, INSERM UMR - S1083, MitoVasc Institute, Angers University, Angers, France.,Department of Biochemistry and Genetics, Angers Hospital, Angers, France
| | - Anne-Laure Mosca-Boidron
- Laboratoire de Cytogénétique, Pôle de Biologie, Centre Hospitalier Universitaire (CHU) de Dijon, Dijon, France
| | - Nathalie Marle
- Laboratoire de Cytogénétique, Pôle de Biologie, Centre Hospitalier Universitaire (CHU) de Dijon, Dijon, France
| | - Naël Osmani
- Laboratoire d'ImmunoRhumatologie Moléculaire, Plateforme GENOMAX, INSERM UMR - S1109, Faculté de Médecine, Fédération Hospitalo-Universitaire OMICARE, Fédération de Médecine Translationnelle de Strasbourg (FMTS), Université de Strasbourg, Strasbourg, France
| | - Olivier Lefebvre
- Laboratoire d'ImmunoRhumatologie Moléculaire, Plateforme GENOMAX, INSERM UMR - S1109, Faculté de Médecine, Fédération Hospitalo-Universitaire OMICARE, Fédération de Médecine Translationnelle de Strasbourg (FMTS), Université de Strasbourg, Strasbourg, France
| | - Jacky G Goetz
- Laboratoire d'ImmunoRhumatologie Moléculaire, Plateforme GENOMAX, INSERM UMR - S1109, Faculté de Médecine, Fédération Hospitalo-Universitaire OMICARE, Fédération de Médecine Translationnelle de Strasbourg (FMTS), Université de Strasbourg, Strasbourg, France
| | - Sule Unal
- Division of Pediatric Hematology, Hacettepe University Medical Faculty, Sihhiye, Ankara, Turkey
| | - Nurten A Akarsu
- Gene Mapping Laboratory, Department of Medical Genetics, Hacettepe University Medical Faculty, Sihhiye, Ankara, Turkey
| | - Mirjana Radosavljevic
- Laboratoire d'ImmunoRhumatologie Moléculaire, Plateforme GENOMAX, INSERM UMR - S1109, Faculté de Médecine, Fédération Hospitalo-Universitaire OMICARE, Fédération de Médecine Translationnelle de Strasbourg (FMTS), Université de Strasbourg, Strasbourg, France.,LabEx TRANSPLANTEX, Faculté de Médecine, Université de Strasbourg, Strasbourg, France.,Service d'Immunologie Biologique, Plateau Technique de Biologie, Pôle de Biologie, Nouvel Hôpital Civil, Strasbourg, France
| | - Marie-Pierre Chenard
- Département de Pathologie, Hôpitaux Universitaires de Strasbourg, Strasbourg, France
| | - Fanny Rialland
- Service d'Oncologie et Hématologie Pédiatrique, Hôpital Femmes-enfants-adolescents, CHU de Nantes, Nantes, France
| | - Audrey Grain
- Service d'Oncologie et Hématologie Pédiatrique, Hôpital Femmes-enfants-adolescents, CHU de Nantes, Nantes, France
| | | | | | - Marie Vincent
- Service de Génétique Médicale, Hôpital Femmes-enfants-adolescents, CHU de Nantes, Nantes, France
| | - Julien Guy
- Service d'Hématologie Biologique, Pôle Biologie, CHU de Dijon, Dijon, France
| | - Laurence Faivre
- Service de Génétique, Hôpital d'enfants, CHU de Dijon, Dijon, France
| | | | - Julien Thevenon
- Service de Génétique, Hôpital d'enfants, CHU de Dijon, Dijon, France
| | - Kasiani Myers
- Division of Blood and Marrow Transplantation and Immune Deficiency, The Cancer and Blood Diseases Institute, Cincinnati Children's Hospital Medical Center, Cincinnati, Ohio, USA
| | - Mark D Fleming
- Department of Pathology, Boston Children's Hospital, and
| | - Akiko Shimamura
- Dana-Farber/Boston Children's Cancer and Blood Disorders Center, Harvard Medical School, Boston, Massachusetts, USA
| | | | - Eric Westhof
- Architecture et Réactivité de l'ARN, CNRS UPR 9002, LabEx NetRNA, Institut de Biologie Moléculaire et Cellulaire, Université de Strasbourg, Strasbourg, France
| | - Claudia Lengerke
- Department of Biomedicine, University Hospital Basel, University of Basel, Basel, Switzerland.,Division of Hematology, University Hospital Basel, University of Basel, Basel, Switzerland
| | - Bertrand Isidor
- Service de Génétique Médicale, Hôpital Femmes-enfants-adolescents, CHU de Nantes, Nantes, France.,Laboratoire de Physiopathologie de la Résorption Osseuse et Thérapie des Tumeurs Osseuses Primitives, INSERM UMR - S957, Faculté de Médecine, Nantes, France
| | - Seiamak Bahram
- Laboratoire d'ImmunoRhumatologie Moléculaire, Plateforme GENOMAX, INSERM UMR - S1109, Faculté de Médecine, Fédération Hospitalo-Universitaire OMICARE, Fédération de Médecine Translationnelle de Strasbourg (FMTS), Université de Strasbourg, Strasbourg, France.,LabEx TRANSPLANTEX, Faculté de Médecine, Université de Strasbourg, Strasbourg, France.,Service d'Immunologie Biologique, Plateau Technique de Biologie, Pôle de Biologie, Nouvel Hôpital Civil, Strasbourg, France
| |
Collapse
|