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Nabet BY, Qiu Y, Shabason JE, Wu TJ, Yoon T, Kim BC, Benci JL, DeMichele AM, Tchou J, Marcotrigiano J, Minn AJ. Exosome RNA Unshielding Couples Stromal Activation to Pattern Recognition Receptor Signaling in Cancer. Cell 2017; 170:352-366.e13. [PMID: 28709002 PMCID: PMC6611169 DOI: 10.1016/j.cell.2017.06.031] [Citation(s) in RCA: 297] [Impact Index Per Article: 42.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2016] [Revised: 04/26/2017] [Accepted: 06/20/2017] [Indexed: 12/24/2022]
Abstract
Interactions between stromal fibroblasts and cancer cells generate signals for cancer progression, therapy resistance, and inflammatory responses. Although endogenous RNAs acting as damage-associated molecular patterns (DAMPs) for pattern recognition receptors (PRRs) may represent one such signal, these RNAs must remain unrecognized under non-pathological conditions. We show that triggering of stromal NOTCH-MYC by breast cancer cells results in a POL3-driven increase in RN7SL1, an endogenous RNA normally shielded by RNA binding proteins SRP9/14. This increase in RN7SL1 alters its stoichiometry with SRP9/14 and generates unshielded RN7SL1 in stromal exosomes. After exosome transfer to immune cells, unshielded RN7SL1 drives an inflammatory response. Upon transfer to breast cancer cells, unshielded RN7SL1 activates the PRR RIG-I to enhance tumor growth, metastasis, and therapy resistance. Corroborated by evidence from patient tumors and blood, these results demonstrate that regulation of RNA unshielding couples stromal activation with deployment of RNA DAMPs that promote aggressive features of cancer. VIDEO ABSTRACT.
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Affiliation(s)
- Barzin Y Nabet
- Department of Radiation Oncology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA; Abramson Family Cancer Research Institute, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Yu Qiu
- Department of Radiation Oncology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA; Abramson Family Cancer Research Institute, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Jacob E Shabason
- Department of Radiation Oncology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA; Abramson Family Cancer Research Institute, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Tony J Wu
- Department of Radiation Oncology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA; Abramson Family Cancer Research Institute, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Taewon Yoon
- Department of Radiation Oncology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA; Abramson Family Cancer Research Institute, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Brian C Kim
- Department of Radiation Oncology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA; Abramson Family Cancer Research Institute, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Joseph L Benci
- Department of Radiation Oncology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA; Abramson Family Cancer Research Institute, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Angela M DeMichele
- Department of Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA; Basser Center for BRCA, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA; Abramson Cancer Center, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Julia Tchou
- Department of Surgery, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA; Abramson Cancer Center, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Joseph Marcotrigiano
- Department of Chemistry and Chemical Biology, Rutgers University, Piscataway, NJ, USA
| | - Andy J Minn
- Department of Radiation Oncology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA; Institute for Immunology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA; Parker Institute for Cancer Immunotherapy, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA; Basser Center for BRCA, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA; Abramson Cancer Center, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA; Abramson Family Cancer Research Institute, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA.
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202
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Abstract
Many proteins are translocated across the endoplasmic reticulum (ER) membrane in eukaryotes or the plasma membrane in prokaryotes. These proteins use hydrophobic signal sequences or transmembrane (TM) segments to trigger their translocation through the protein-conducting Sec61/SecY channel. Substrates are first directed to the channel by cytosolic targeting factors, which use hydrophobic pockets to bind diverse signal and TM sequences. Subsequently, these hydrophobic sequences insert into the channel, docking into a groove on the outside of the lateral gate of the channel, where they also interact with lipids. Structural data and biochemical experiments have elucidated how channel partners, the ribosome in cotranslational translocation, and the eukaryotic ER chaperone BiP or the prokaryotic cytosolic SecA ATPase in posttranslational translocation move polypeptides unidirectionally across the membrane. Structures of auxiliary components of the bacterial translocon, YidC and SecD/F, provide additional insight. Taken together, these recent advances result in mechanistic models of protein translocation.
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Affiliation(s)
- Tom A Rapoport
- Department of Cell Biology, Howard Hughes Medical Institute and Harvard Medical School, Boston, Massachusetts 02115; ,
| | - Long Li
- Department of Cell Biology, Howard Hughes Medical Institute and Harvard Medical School, Boston, Massachusetts 02115; ,
| | - Eunyong Park
- The Rockefeller University and Howard Hughes Medical Institute, New York, NY 10065;
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203
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Jomaa A, Fu YHH, Boehringer D, Leibundgut M, Shan SO, Ban N. Structure of the quaternary complex between SRP, SR, and translocon bound to the translating ribosome. Nat Commun 2017; 8:15470. [PMID: 28524878 PMCID: PMC5454536 DOI: 10.1038/ncomms15470] [Citation(s) in RCA: 43] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2017] [Accepted: 03/29/2017] [Indexed: 01/05/2023] Open
Abstract
During co-translational protein targeting, the signal recognition particle (SRP) binds to the translating ribosome displaying the signal sequence to deliver it to the SRP receptor (SR) on the membrane, where the signal peptide is transferred to the translocon. Using electron cryo-microscopy, we have determined the structure of a quaternary complex of the translating Escherichia coli ribosome, the SRP–SR in the ‘activated' state and the translocon. Our structure, supported by biochemical experiments, reveals that the SRP RNA adopts a kinked and untwisted conformation to allow repositioning of the ‘activated' SRP–SR complex on the ribosome. In addition, we observe the translocon positioned through interactions with the SR in the vicinity of the ribosome exit tunnel where the signal sequence is extending beyond its hydrophobic binding groove of the SRP M domain towards the translocon. Our study provides new insights into the mechanism of signal sequence transfer from the SRP to the translocon. Membrane proteins are inserted co-transnationally through the association between ribosome, the signal recognition particle and its receptor, and the membrane-bound translocon. Here the authors present a cryo-EM reconstruction of this quaternary complex in the activated state and propose a model for signal sequence transfer to the translocon.
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Affiliation(s)
- Ahmad Jomaa
- Department of Biology, Institute of Molecular Biology and Biophysics, Otto-Stern-Weg 5, ETH, Zurich CH-8093, Switzerland
| | - Yu-Hsien Hwang Fu
- Division of Chemistry and Chemical Engineering, California Institute of Technology, Pasadena, California 91125, USA
| | - Daniel Boehringer
- Department of Biology, Institute of Molecular Biology and Biophysics, Otto-Stern-Weg 5, ETH, Zurich CH-8093, Switzerland
| | - Marc Leibundgut
- Department of Biology, Institute of Molecular Biology and Biophysics, Otto-Stern-Weg 5, ETH, Zurich CH-8093, Switzerland
| | - Shu-Ou Shan
- Division of Chemistry and Chemical Engineering, California Institute of Technology, Pasadena, California 91125, USA
| | - Nenad Ban
- Department of Biology, Institute of Molecular Biology and Biophysics, Otto-Stern-Weg 5, ETH, Zurich CH-8093, Switzerland
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204
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Min KW, Davila S, Zealy RW, Lloyd LT, Lee IY, Lee R, Roh KH, Jung A, Jemielity J, Choi EJ, Chang JH, Yoon JH. eIF4E phosphorylation by MST1 reduces translation of a subset of mRNAs, but increases lncRNA translation. BIOCHIMICA ET BIOPHYSICA ACTA-GENE REGULATORY MECHANISMS 2017; 1860:761-772. [PMID: 28487214 DOI: 10.1016/j.bbagrm.2017.05.002] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Received: 10/03/2016] [Revised: 05/03/2017] [Accepted: 05/05/2017] [Indexed: 10/19/2022]
Abstract
Post-transcriptional gene regulation is an important step in eukaryotic gene expression. The last step to govern production of nascent peptides is during the process of mRNA translation. mRNA translation is controlled by many translation initiation factors that are susceptible to post-translational modifications. Here we report that one of the translation initiation factors, eIF4E, is phosphorylated by Mammalian Ste20-like kinase (MST1). Upon phosphorylation, eIF4E weakly interacts with the 5' CAP to inhibit mRNA translation. Simultaneously, active polyribosome is more associated with long noncoding RNAs (lncRNAs). Moreover, the linc00689-derived micropeptide, STORM (Stress- and TNF-α-activated ORF Micropeptide), is triggered by TNF-α-induced and MST1-mediated eIF4E phosphorylation, which exhibits molecular mimicry of SRP19 and, thus, competes for 7SL RNA. Our findings have uncovered a novel function of MST1 in mRNA and lncRNA translation by direct phosphorylation of eIF4E. This novel signaling pathway will provide new platforms for regulation of mRNA translation via post-translational protein modification.
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Affiliation(s)
- Kyung-Won Min
- Department of Biochemistry and Molecular Biology, Medical University of South Carolina, Charleston, SC 29425, USA
| | - Sylvia Davila
- Department of Biochemistry and Molecular Biology, Medical University of South Carolina, Charleston, SC 29425, USA
| | - Richard W Zealy
- Department of Biochemistry and Molecular Biology, Medical University of South Carolina, Charleston, SC 29425, USA
| | - Lawson T Lloyd
- Department of Biochemistry and Molecular Biology, Medical University of South Carolina, Charleston, SC 29425, USA
| | - In Young Lee
- Laboratory of Cell Death and Human Diseases, Department of Life Sciences, School of Life Sciences and Biotechnology, Korea University, Seoul, Republic of Korea
| | - Rumi Lee
- Laboratory of Cell Death and Human Diseases, Department of Life Sciences, School of Life Sciences and Biotechnology, Korea University, Seoul, Republic of Korea
| | - Kyung Hye Roh
- Laboratory of Cell Death and Human Diseases, Department of Life Sciences, School of Life Sciences and Biotechnology, Korea University, Seoul, Republic of Korea
| | - Ahjin Jung
- Department of Biology Education, Kyungpook National University, Daegu 41566, Republic of Korea
| | - Jacek Jemielity
- Centre of New Technologies, University of Warsaw, S. Banacha 2c, 02-097 Warsaw, Poland
| | - Eui-Ju Choi
- Laboratory of Cell Death and Human Diseases, Department of Life Sciences, School of Life Sciences and Biotechnology, Korea University, Seoul, Republic of Korea
| | - Jeong Ho Chang
- Department of Biology Education, Kyungpook National University, Daegu 41566, Republic of Korea.
| | - Je-Hyun Yoon
- Department of Biochemistry and Molecular Biology, Medical University of South Carolina, Charleston, SC 29425, USA; Laboratory of Genetics, National Institute on Aging-Intramural Research Program, NIH, Baltimore, MD 21224, USA.
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205
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Angelos E, Ruberti C, Kim SJ, Brandizzi F. Maintaining the factory: the roles of the unfolded protein response in cellular homeostasis in plants. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2017; 90:671-682. [PMID: 27943485 PMCID: PMC5415411 DOI: 10.1111/tpj.13449] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/05/2016] [Revised: 11/23/2016] [Accepted: 12/02/2016] [Indexed: 05/07/2023]
Abstract
Much like a factory, the endoplasmic reticulum (ER) assembles simple cellular building blocks into complex molecular machines known as proteins. In order to protect the delicate protein folding process and ensure the proper cellular delivery of protein products under environmental stresses, eukaryotes have evolved a set of signaling mechanisms known as the unfolded protein response (UPR) to increase the folding capacity of the ER. This process is particularly important in plants, because their sessile nature commands adaptation for survival rather than escape from stress. As such, plants make special use of the UPR, and evidence indicates that the master regulators and downstream effectors of the UPR have distinct roles in mediating cellular processes that affect organism growth and development as well as stress responses. In this review we outline recent developments in this field that support a strong relevance of the UPR to many areas of plant life.
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Affiliation(s)
- Evan Angelos
- MSU-DOE Plant Research Lab and Plant Biology Department, Michigan State University, East Lansing, MI 48824, USA
| | - Cristina Ruberti
- MSU-DOE Plant Research Lab and Plant Biology Department, Michigan State University, East Lansing, MI 48824, USA
| | - Sang-Jin Kim
- MSU-DOE Plant Research Lab and Plant Biology Department, Michigan State University, East Lansing, MI 48824, USA
- Great Lakes Bioenergy Research Center, Michigan State University, East Lansing, MI 48824, USA
| | - Federica Brandizzi
- MSU-DOE Plant Research Lab and Plant Biology Department, Michigan State University, East Lansing, MI 48824, USA
- Department of Plant Biology, Michigan State University, East Lansing, MI 48824, USA
- Great Lakes Bioenergy Research Center, Michigan State University, East Lansing, MI 48824, USA
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206
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Zhao G, Hou J, Xu G, Xiang A, Kang Y, Yan Y, Zhang X, Yang G, Xiao S, Sun S. Cellular microRNA miR-10a-5p inhibits replication of porcine reproductive and respiratory syndrome virus by targeting the host factor signal recognition particle 14. J Gen Virol 2017; 98:624-632. [PMID: 28086075 DOI: 10.1099/jgv.0.000708] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Porcine reproductive and respiratory syndrome virus (PRRSV) is one of the most economically important viruses affecting the swine industry worldwide. MicroRNAs have recently been demonstrated to play vital roles in virus-host interactions. Our previous research on small RNA deep sequencing showed that the expression level of miR-10a increased during the viral life cycle. The present study sought to determine the function of miR-10a and its molecular mechanism during PRRSV infection. In the current study, the result of PRRSV infection inducing miR-10a expression was validated by quantitative reverse transcriptase PCR. Overexpression of miR-10a-5p using its mimics markedly reduced the expression level of intracellular PRRSV ORF7 mRNA and N protein. Simultaneously, overexpression of miR-10a-5p also significantly decreased the expression level of extracellular viral RNA and virus titres in the supernatants. These results demonstrated that miR-10a-5p could suppress the replication of PRRSV. A direct interaction between miR-10a-5p and signal recognition particle 14 (SRP14) was confirmed using bioinformatic prediction and experimental verification. miR-10a-5p could directly target the 3'UTR of pig SRP14 mRNA in a sequence-specific manner and decrease SRP14 expression through translational repression but not mRNA degradation. Further, knockdown of SRP14 by small interfering RNA also inhibits the replication of PRRSV. Collectively, these results suggested that miR-10a-5p inhibits PRRSV replication through suppression of SRP14 expression, which not only provides new insights into virus-host interactions during PRRSV infection but also suggests potential new antiviral strategies against PRRSV infection.
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Affiliation(s)
- Guangwei Zhao
- College of Animal Science and Technology, Northwest A&F University, No. 22 Xinong Road, Yangling, Shaanxi 712100, PR China
| | - Jianye Hou
- Chuying Agro-Pastoral Group Co., Ltd, No. 1 Century Avenue, Zhengzhou Airport Development Zone, Zhengzhou, Henan 451162, PR China
| | - Gaoxiao Xu
- College of Animal Science and Technology, Northwest A&F University, No. 22 Xinong Road, Yangling, Shaanxi 712100, PR China
| | - Aoqi Xiang
- College of Animal Science and Technology, Northwest A&F University, No. 22 Xinong Road, Yangling, Shaanxi 712100, PR China
| | - Yanmei Kang
- Department of Animal Science and Technology, Guangdong Vocational College of Science and Trade, No. 388 Shiqing Road, Baiyun, Guangzhou, Guangdong 510640, PR China
| | - Yunhuan Yan
- College of Veterinary Medicine, Northwest A&F University, No. 22 Xinong Road, Yangling, Shaanxi 712100, PR China
| | - Xiaobin Zhang
- College of Veterinary Medicine, Northwest A&F University, No. 22 Xinong Road, Yangling, Shaanxi 712100, PR China
| | - Gongshe Yang
- College of Animal Science and Technology, Northwest A&F University, No. 22 Xinong Road, Yangling, Shaanxi 712100, PR China
| | - Shuqi Xiao
- College of Veterinary Medicine, Northwest A&F University, No. 22 Xinong Road, Yangling, Shaanxi 712100, PR China
| | - Shiduo Sun
- College of Animal Science and Technology, Northwest A&F University, No. 22 Xinong Road, Yangling, Shaanxi 712100, PR China
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207
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Maeda T, Tanaka Y, Wachi M, Inui M. Polynucleotide Phosphorylase, RNase E/G, and YbeY Are Involved in the Maturation of 4.5S RNA in Corynebacterium glutamicum. J Bacteriol 2017; 199:e00798-16. [PMID: 28031281 PMCID: PMC5309912 DOI: 10.1128/jb.00798-16] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2016] [Accepted: 12/20/2016] [Indexed: 12/13/2022] Open
Abstract
Corynebacterium glutamicum has been applied for the industrial production of various metabolites, such as amino acids. To understand the biosynthesis of the membrane protein in this bacterium, we investigated the process of signal recognition particle (SRP) assembly. SRP is found in all three domains of life and plays an important role in the membrane insertion of proteins. SRP RNA is initially transcribed as precursor molecules; however, relatively little is known about its maturation. In C. glutamicum, SRP consists of the Ffh protein and 4.5S RNA lacking an Alu domain. In this study, we found that 3'-to-5' exoribonuclease, polynucleotide phosphorylase (PNPase), and two endo-type RNases, RNase E/G and YbeY, are involved in the 3' maturation of 4.5S RNA in C. glutamicum The mature form of 4.5S RNA was inefficiently formed in ΔrneG Δpnp mutant cells, suggesting the existence of an alternative pathway for the 3' maturation of 4.5S RNA. Primer extension analysis also revealed that the 5' mature end of 4.5S RNA corresponds to that of the transcriptional start site. Immunoprecipitated Ffh protein contained immature 4.5S RNA in Δpnp, ΔrneG, and ΔybeY mutants, suggesting that 4.5S RNA precursors can interact with Ffh. These results imply that the maturation of 4.5S RNA can be performed in the 4.5S RNA-Ffh complex.IMPORTANCE Overproduction of a membrane protein, such as a transporter, is useful for engineering of strains of Corynebacterium glutamicum, which is a workhorse of amino acid production. To understand membrane protein biogenesis in this bacterium, we investigated the process of signal recognition particle (SRP) assembly. SRP contains the Ffh protein and SRP RNA and plays an important role in the membrane insertion of proteins. Although SRP RNA is highly conserved among the three domains of life, relatively little is known about its maturation. We show that PNPase, RNase E/G, and YbeY are involved in the 3' maturation of the SRP RNA (4.5S RNA) in this bacterium. This indicates that 3' end processing in this organism is different from that in other bacteria, such as Escherichia coli.
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Affiliation(s)
- Tomoya Maeda
- Research Institute of Innovative Technology for the Earth, Kyoto, Japan
- Department of Bioengineering, Tokyo Institute of Technology, Yokohama, Japan
| | - Yuya Tanaka
- Research Institute of Innovative Technology for the Earth, Kyoto, Japan
| | - Masaaki Wachi
- Department of Bioengineering, Tokyo Institute of Technology, Yokohama, Japan
| | - Masayuki Inui
- Research Institute of Innovative Technology for the Earth, Kyoto, Japan
- Graduate School of Biological Sciences, Nara Institute of Science and Technology, Nara, Japan
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208
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Abstract
The insertion and assembly of proteins into the inner membrane of bacteria are crucial for many cellular processes, including cellular respiration, signal transduction, and ion and pH homeostasis. This process requires efficient membrane targeting and insertion of proteins into the lipid bilayer in their correct orientation and proper conformation. Playing center stage in these events are the targeting components, signal recognition particle (SRP) and the SRP receptor FtsY, as well as the insertion components, the Sec translocon and the YidC insertase. Here, we will discuss new insights provided from the recent high-resolution structures of these proteins. In addition, we will review the mechanism by which a variety of proteins with different topologies are inserted into the inner membrane of Gram-negative bacteria. Finally, we report on the energetics of this process and provide information on how membrane insertion occurs in Gram-positive bacteria and Archaea. It should be noted that most of what we know about membrane protein assembly in bacteria is based on studies conducted in Escherichia coli.
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Affiliation(s)
- Andreas Kuhn
- Institute for Microbiology and Molecular Biology, University of Hohenheim, 70599 Stuttgart, Germany
| | - Hans-Georg Koch
- Institute for Biochemistry and Molecular Biology, Faculty of Medicine, Albert-Ludwigs-University of Freiburg, 79104, Freiburg, Germany
| | - Ross E Dalbey
- Department of Chemistry, The Ohio State University, Columbus, OH 43210
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209
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Russo J, Lee JE, López CM, Anderson J, Nguyen TMP, Heck AM, Wilusz J, Wilusz CJ. The CELF1 RNA-Binding Protein Regulates Decay of Signal Recognition Particle mRNAs and Limits Secretion in Mouse Myoblasts. PLoS One 2017; 12:e0170680. [PMID: 28129347 PMCID: PMC5271678 DOI: 10.1371/journal.pone.0170680] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2016] [Accepted: 01/09/2017] [Indexed: 02/06/2023] Open
Abstract
We previously identified several mRNAs encoding components of the secretory pathway, including signal recognition particle (SRP) subunit mRNAs, among transcripts associated with the RNA-binding protein CELF1. Through immunoprecipitation of RNAs crosslinked to CELF1 in myoblasts and in vitro binding assays using recombinant CELF1, we now provide evidence that CELF1 directly binds the mRNAs encoding each of the subunits of the SRP. Furthermore, we determined the half-lives of the Srp transcripts in control and CELF1 knockdown myoblasts. Our results indicate CELF1 is a destabilizer of at least five of the six Srp transcripts and that the relative abundance of the SRP proteins is out of balance when CELF1 is depleted. CELF1 knockdown myoblasts exhibit altered secretion of a luciferase reporter protein and are impaired in their ability to migrate and close a wound, consistent with a defect in the secreted extracellular matrix. Importantly, similar defects in wound healing are observed when SRP subunit imbalance is induced by over-expression of SRP68. Our studies support the existence of an RNA regulon containing Srp mRNAs that is controlled by CELF1. One implication is that altered function of CELF1 in myotonic dystrophy may contribute to changes in the extracellular matrix of affected muscle through defects in secretion.
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Affiliation(s)
- Joseph Russo
- Department of Microbiology, Immunology and Pathology, Colorado State University, Fort Collins, Colorado, United States of America
| | - Jerome E. Lee
- Department of Microbiology, Immunology and Pathology, Colorado State University, Fort Collins, Colorado, United States of America
- Program in Cell and Molecular Biology, Colorado State University, Fort Collins, Colorado, United States of America
| | - Carolina M. López
- Department of Microbiology, Immunology and Pathology, Colorado State University, Fort Collins, Colorado, United States of America
| | - John Anderson
- Department of Microbiology, Immunology and Pathology, Colorado State University, Fort Collins, Colorado, United States of America
| | - Thuy-mi P. Nguyen
- Department of Microbiology, Immunology and Pathology, Colorado State University, Fort Collins, Colorado, United States of America
| | - Adam M. Heck
- Department of Microbiology, Immunology and Pathology, Colorado State University, Fort Collins, Colorado, United States of America
- Program in Cell and Molecular Biology, Colorado State University, Fort Collins, Colorado, United States of America
| | - Jeffrey Wilusz
- Department of Microbiology, Immunology and Pathology, Colorado State University, Fort Collins, Colorado, United States of America
- Program in Cell and Molecular Biology, Colorado State University, Fort Collins, Colorado, United States of America
| | - Carol J. Wilusz
- Department of Microbiology, Immunology and Pathology, Colorado State University, Fort Collins, Colorado, United States of America
- Program in Cell and Molecular Biology, Colorado State University, Fort Collins, Colorado, United States of America
- * E-mail:
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210
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Lyu Z, Whitman WB. Evolution of the archaeal and mammalian information processing systems: towards an archaeal model for human disease. Cell Mol Life Sci 2017; 74:183-212. [PMID: 27261368 PMCID: PMC11107668 DOI: 10.1007/s00018-016-2286-y] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2016] [Revised: 05/05/2016] [Accepted: 05/27/2016] [Indexed: 12/22/2022]
Abstract
Current evolutionary models suggest that Eukaryotes originated from within Archaea instead of being a sister lineage. To test this model of ancient evolution, we review recent studies and compare the three major information processing subsystems of replication, transcription and translation in the Archaea and Eukaryotes. Our hypothesis is that if the Eukaryotes arose within the archaeal radiation, their information processing systems will appear to be one of kind and not wholly original. Within the Eukaryotes, the mammalian or human systems are emphasized because of their importance in understanding health. Biochemical as well as genetic studies provide strong evidence for the functional similarity of archaeal homologs to the mammalian information processing system and their dissimilarity to the bacterial systems. In many independent instances, a simple archaeal system is functionally equivalent to more elaborate eukaryotic homologs, suggesting that evolution of complexity is likely an central feature of the eukaryotic information processing system. Because fewer components are often involved, biochemical characterizations of the archaeal systems are often easier to interpret. Similarly, the archaeal cell provides a genetically and metabolically simpler background, enabling convenient studies on the complex information processing system. Therefore, Archaea could serve as a parsimonious and tractable host for studying human diseases that arise in the information processing systems.
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Affiliation(s)
- Zhe Lyu
- Department of Microbiology, University of Georgia, Athens, GA, 30602, USA
| | - William B Whitman
- Department of Microbiology, University of Georgia, Athens, GA, 30602, USA.
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211
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van Gijtenbeek LA, Robinson A, van Oijen AM, Poolman B, Kok J. On the Spatial Organization of mRNA, Plasmids, and Ribosomes in a Bacterial Host Overexpressing Membrane Proteins. PLoS Genet 2016; 12:e1006523. [PMID: 27977669 PMCID: PMC5201305 DOI: 10.1371/journal.pgen.1006523] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2016] [Revised: 12/30/2016] [Accepted: 12/06/2016] [Indexed: 01/03/2023] Open
Abstract
By using fluorescence imaging, we provide a time-resolved single-cell view on coupled defects in transcription, translation, and growth during expression of heterologous membrane proteins in Lactococcus lactis. Transcripts encoding poorly produced membrane proteins accumulate in mRNA-dense bodies at the cell poles, whereas transcripts of a well-expressed homologous membrane protein show membrane-proximal localization in a translation-dependent fashion. The presence of the aberrant polar mRNA foci correlates with cessation of cell division, which is restored once these bodies are cleared. In addition, activation of the heat-shock response and a loss of nucleoid-occluded ribosomes are observed. We show that the presence of a native-like N-terminal domain is key to SRP-dependent membrane localization and successful production of membrane proteins. The work presented gives new insights and detailed understanding of aberrant membrane protein biogenesis, which can be used for strategies to optimize membrane protein production.
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Affiliation(s)
- Lieke A. van Gijtenbeek
- Department of Molecular Genetics, University of Groningen, Groningen, The Netherlands
- * E-mail: (LAvG); (JK)
| | - Andrew Robinson
- Zernike Institute for Advanced Materials, University of Groningen, Groningen, The Netherlands
| | - Antoine M. van Oijen
- Zernike Institute for Advanced Materials, University of Groningen, Groningen, The Netherlands
| | - Bert Poolman
- Zernike Institute for Advanced Materials, University of Groningen, Groningen, The Netherlands
- Department of Biochemistry, University of Groningen, Groningen, The Netherlands
| | - Jan Kok
- Department of Molecular Genetics, University of Groningen, Groningen, The Netherlands
- * E-mail: (LAvG); (JK)
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212
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Chandrasekar S, Shan SO. Anionic Phospholipids and the Albino3 Translocase Activate Signal Recognition Particle-Receptor Interaction during Light-harvesting Chlorophyll a/b-binding Protein Targeting. J Biol Chem 2016; 292:397-406. [PMID: 27895124 DOI: 10.1074/jbc.m116.752956] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2016] [Revised: 10/14/2016] [Indexed: 01/12/2023] Open
Abstract
The universally conserved signal recognition particle (SRP) co-translationally delivers newly synthesized membrane and secretory proteins to the target cellular membrane. The only exception is found in the chloroplast of green plants, where the chloroplast SRP (cpSRP) post-translationally targets light-harvesting chlorophyll a/b-binding proteins (LHCP) to the thylakoid membrane. The mechanism and regulation of this post-translational mode of targeting by cpSRP remain unclear. Using biochemical and biophysical methods, here we show that anionic phospholipids activate the cpSRP receptor cpFtsY to promote rapid and stable cpSRP54·cpFtsY complex assembly. Furthermore, the stromal domain of the Alb3 translocase binds with high affinity to and regulates GTP hydrolysis in the cpSRP54·cpFtsY complex, suggesting that cpFtsY is primarily responsible for initial recruitment of the targeting complex to Alb3. These results suggest a new model for the sequential recruitment, remodeling, and unloading of the targeting complex at membrane translocase sites in the post-translational cpSRP pathway.
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Affiliation(s)
- Sowmya Chandrasekar
- From the Division of Chemistry and Chemical Engineering, California Institute of Technology, Pasadena, California 91125
| | - Shu-Ou Shan
- From the Division of Chemistry and Chemical Engineering, California Institute of Technology, Pasadena, California 91125
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213
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Chandrasekar S, Sweredoski MJ, Sohn CH, Hess S, Shan SO. Co-evolution of Two GTPases Enables Efficient Protein Targeting in an RNA-less Chloroplast Signal Recognition Particle Pathway. J Biol Chem 2016; 292:386-396. [PMID: 27895118 DOI: 10.1074/jbc.m116.752931] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2016] [Revised: 11/17/2016] [Indexed: 11/06/2022] Open
Abstract
The signal recognition particle (SRP) is an essential ribonucleoprotein particle that mediates the co-translational targeting of newly synthesized proteins to cellular membranes. The SRP RNA is a universally conserved component of SRP that mediates key interactions between two GTPases in SRP and its receptor, thus enabling rapid delivery of cargo to the target membrane. Notably, this essential RNA is bypassed in the chloroplast (cp) SRP of green plants. Previously, we showed that the cpSRP and cpSRP receptor GTPases (cpSRP54 and cpFtsY, respectively) interact efficiently by themselves without the SRP RNA. Here, we explore the molecular mechanism by which this is accomplished. Fluorescence analyses showed that, in the absence of SRP RNA, the M-domain of cpSRP54 both accelerates and stabilizes complex assembly between cpSRP54 and cpFtsY. Cross-linking coupled with mass spectrometry and mutational analyses identified a new interaction between complementarily charged residues on the cpFtsY G-domain and the vicinity of the cpSRP54 M-domain. These residues are specifically conserved in plastids, and their evolution coincides with the loss of SRP RNA in green plants. These results provide an example of how proteins replace the functions of RNA during evolution.
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Affiliation(s)
| | - Michael J Sweredoski
- the Proteome Exploration Laboratory, Division of Biology and Biological Engineering, Beckman Institute, California Institute of Technology, Pasadena, California 91125
| | - Chang Ho Sohn
- From the Division of Chemistry and Chemical Engineering and
| | - Sonja Hess
- the Proteome Exploration Laboratory, Division of Biology and Biological Engineering, Beckman Institute, California Institute of Technology, Pasadena, California 91125
| | - Shu-Ou Shan
- From the Division of Chemistry and Chemical Engineering and
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214
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215
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Effects of Glycosylation on the Enzymatic Activity and Mechanisms of Proteases. Int J Mol Sci 2016; 17:ijms17121969. [PMID: 27898009 PMCID: PMC5187769 DOI: 10.3390/ijms17121969] [Citation(s) in RCA: 73] [Impact Index Per Article: 9.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2016] [Revised: 11/07/2016] [Accepted: 11/10/2016] [Indexed: 02/06/2023] Open
Abstract
Posttranslational modifications are an important feature of most proteases in higher organisms, such as the conversion of inactive zymogens into active proteases. To date, little information is available on the role of glycosylation and functional implications for secreted proteases. Besides a stabilizing effect and protection against proteolysis, several proteases show a significant influence of glycosylation on the catalytic activity. Glycans can alter the substrate recognition, the specificity and binding affinity, as well as the turnover rates. However, there is currently no known general pattern, since glycosylation can have both stimulating and inhibiting effects on activity. Thus, a comparative analysis of individual cases with sufficient enzyme kinetic and structural data is a first approach to describe mechanistic principles that govern the effects of glycosylation on the function of proteases. The understanding of glycan functions becomes highly significant in proteomic and glycomic studies, which demonstrated that cancer-associated proteases, such as kallikrein-related peptidase 3, exhibit strongly altered glycosylation patterns in pathological cases. Such findings can contribute to a variety of future biomedical applications.
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216
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Ziehe D, Dünschede B, Zenker M, Funke S, Nowaczyk MM, Schünemann D. The Chloroplast SRP Systems of Chaetosphaeridium globosum and Physcomitrella patens as Intermediates in the Evolution of SRP-Dependent Protein Transport in Higher Plants. PLoS One 2016; 11:e0166818. [PMID: 27861610 PMCID: PMC5115805 DOI: 10.1371/journal.pone.0166818] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2016] [Accepted: 11/05/2016] [Indexed: 11/19/2022] Open
Abstract
The bacterial signal recognition particle (SRP) mediates the cotranslational targeting of membrane proteins and is a high affinity complex consisting of a SRP54 protein subunit (Ffh) and an SRP RNA. The chloroplast SRP (cpSRP) pathway has adapted throughout evolution to enable the posttranslational targeting of the light harvesting chlorophyll a/b binding proteins (LHCPs) to the thylakoid membrane. In spermatophytes (seed plants), the cpSRP lacks the SRP RNA and is instead formed by a high affinity interaction of the conserved 54-kD subunit (cpSRP54) with the chloroplast-specific cpSRP43 protein. This heterodimeric cpSRP recognizes LHCP and delivers it to the thylakoid membrane. However, in contrast to spermatophytes, plastid SRP RNAs were identified within all streptophyte lineages and in all chlorophyte branches. Furthermore, it was shown that cpSRP43 does not interact with cpSRP54 in chlorophytes (e.g., Chlamydomonas reinhardtii). In this study, we biochemically characterized the cpSRP system of the charophyte Chaetosphaeridium globosum and the bryophyte Physcomitrella patens. Interaction studies demonstrate low affinity binding of cpSRP54 to cpSRP43 (Kd ~10 μM) in Chaetosphaeridium globosum and Physcomitrella patens as well as relatively low affinity binding of cpSRP54 to cpSRP RNA (Kd ~1 μM) in Physcomitrella patens. CpSRP54/cpSRP43 complex formation in charophytes is supported by the finding that specific alterations in the second chromodomain of cpSRP43, that are conserved within charophytes and absent in land plants, do not interfere with cpSRP54 binding. Furthermore, our data show that the elongated apical loop structure of the Physcomitrella patens cpSRP RNA contributes to the low binding affinity between cpSRP54 and the cpSRP RNA.
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Affiliation(s)
- Dominik Ziehe
- Molecular Biology of Plant Organelles, Ruhr-University Bochum, 44780, Bochum, Germany
| | - Beatrix Dünschede
- Molecular Biology of Plant Organelles, Ruhr-University Bochum, 44780, Bochum, Germany
| | - Mira Zenker
- Molecular Biology of Plant Organelles, Ruhr-University Bochum, 44780, Bochum, Germany
| | - Silke Funke
- Molecular Biology of Plant Organelles, Ruhr-University Bochum, 44780, Bochum, Germany
| | - Marc M. Nowaczyk
- Cyanobacterial Membrane Protein Complexes, Ruhr-University Bochum, 44780, Bochum, Germany
| | - Danja Schünemann
- Molecular Biology of Plant Organelles, Ruhr-University Bochum, 44780, Bochum, Germany
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217
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Regulation of Srpr Expression by miR-330-5p Controls Proliferation of Mouse Epidermal Keratinocyte. PLoS One 2016; 11:e0164896. [PMID: 27768721 PMCID: PMC5074476 DOI: 10.1371/journal.pone.0164896] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2016] [Accepted: 10/03/2016] [Indexed: 01/10/2023] Open
Abstract
Srpr is a gene encoding α subunit of the signal recognition particle receptor which is involved in the targeting and translocation of nascent secretory and membrane proteins to the endoplasmic reticulum. Previous studies showed aberrant expression of Srpr in several cell types with abnormal growth rate. Although Srpr is expressed in various tissues including skin, the role of Srpr in keratinocytes and regulation of its expression by miRNAs have not been studied. In this study, we investigated the role of SRPR and regulation of its expression by miRNA in skin keratinocytes. We found that SRPR was highly expressed in epidermal keratinocytes and regulated keratinocyte proliferation by affecting cell cycle progression. We also demonstrated that miR-330-5p directly inhibits Srpr expression. These data suggest that miR-330-5p-mediated regulation of the SRPR level is needed for the regulation of proliferation of epidermal keratinocytes.
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218
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Mazzantini D, Celandroni F, Salvetti S, Gueye SA, Lupetti A, Senesi S, Ghelardi E. FlhF Is Required for Swarming Motility and Full Pathogenicity of Bacillus cereus. Front Microbiol 2016; 7:1644. [PMID: 27807433 PMCID: PMC5069341 DOI: 10.3389/fmicb.2016.01644] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2016] [Accepted: 10/03/2016] [Indexed: 11/13/2022] Open
Abstract
Besides sporulation, Bacillus cereus can undergo a differentiation process in which short swimmer cells become elongated and hyperflagellated swarmer cells that favor migration of the bacterial community on a surface. The functionally enigmatic flagellar protein FlhF, which is the third paralog of the signal recognition particle (SRP) GTPases Ffh and FtsY, is required for swarming in many bacteria. Previous data showed that FlhF is involved in the control of the number and positioning of flagella in B. cereus. In this study, in silico analysis of B. cereus FlhF revealed that this protein presents conserved domains that are typical of SRPs in many organisms and a peculiar N-terminal basic domain. By proteomic analysis, a significant effect of FlhF depletion on the amount of secreted proteins was found with some proteins increased (e.g., B component of the non-hemolytic enterotoxin, cereolysin O, enolase) and others reduced (e.g., flagellin, L2 component of hemolysin BL, bacillolysin, sphingomyelinase, PC-PLC, PI-PLC, cytotoxin K) in the extracellular proteome of a ΔflhF mutant. Deprivation of FlhF also resulted in significant attenuation in the pathogenicity of this strain in an experimental model of infection in Galleria mellonella larvae. Our work highlights the multifunctional role of FlhF in B. cereus, being this protein involved in bacterial flagellation, swarming, protein secretion, and pathogenicity.
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Affiliation(s)
- Diletta Mazzantini
- Department of Translational Research and New Technologies in Medicine and Surgery, University of Pisa Pisa, Italy
| | - Francesco Celandroni
- Department of Translational Research and New Technologies in Medicine and Surgery, University of Pisa Pisa, Italy
| | - Sara Salvetti
- Department of Translational Research and New Technologies in Medicine and Surgery, University of Pisa Pisa, Italy
| | - Sokhna A Gueye
- Department of Translational Research and New Technologies in Medicine and Surgery, University of Pisa Pisa, Italy
| | - Antonella Lupetti
- Department of Translational Research and New Technologies in Medicine and Surgery, University of Pisa Pisa, Italy
| | - Sonia Senesi
- Department of Biology, University of Pisa Pisa, Italy
| | - Emilia Ghelardi
- Department of Translational Research and New Technologies in Medicine and Surgery, University of PisaPisa, Italy; Research Center Nutraceuticals and Food for Health-Nutrafood, University of PisaPisa, Italy
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219
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Chen Y, Shen K, Shan SO, Kou SC. Analyzing Single-Molecule Protein Transportation Experiments via Hierarchical Hidden Markov Models. J Am Stat Assoc 2016; 111:951-966. [PMID: 28943680 PMCID: PMC5606165 DOI: 10.1080/01621459.2016.1140050] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2014] [Revised: 12/01/2015] [Indexed: 01/10/2023]
Abstract
To maintain proper cellular functions, over 50% of proteins encoded in the genome need to be transported to cellular membranes. The molecular mechanism behind such a process, often referred to as protein targeting, is not well understood. Single-molecule experiments are designed to unveil the detailed mechanisms and reveal the functions of different molecular machineries involved in the process. The experimental data consist of hundreds of stochastic time traces from the fluorescence recordings of the experimental system. We introduce a Bayesian hierarchical model on top of hidden Markov models (HMMs) to analyze these data and use the statistical results to answer the biological questions. In addition to resolving the biological puzzles and delineating the regulating roles of different molecular complexes, our statistical results enable us to propose a more detailed mechanism for the late stages of the protein targeting process.
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Affiliation(s)
- Yang Chen
- Ph.D. candidate, Department of Statistics, Harvard University, Cambridge, MA 02138
| | - Kuang Shen
- Pfizer fellow of the Life Sciences Research Foundation, Whitehead Institute for Biomedical Research, Cambridge, MA 02142
| | - Shu-Ou Shan
- Professor, Division of Chemistry and Chemical Engineering, California Institute of Technology, Pasadena, CA 91125
| | - S C Kou
- Professor, Department of Statistics, Harvard University, Cambridge, MA 02138
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220
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Henderson RC, Gao F, Jayanthi S, Kight A, Sharma P, Goforth RL, Heyes CD, Henry RL, Suresh Kumar TK. Domain Organization in the 54-kDa Subunit of the Chloroplast Signal Recognition Particle. Biophys J 2016; 111:1151-1162. [PMID: 27653474 PMCID: PMC5034345 DOI: 10.1016/j.bpj.2016.08.004] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2016] [Revised: 07/29/2016] [Accepted: 08/02/2016] [Indexed: 10/21/2022] Open
Abstract
Chloroplast signal recognition particle (cpSRP) is a heterodimer composed of an evolutionarily conserved 54-kDa GTPase (cpSRP54) and a unique 43-kDa subunit (cpSRP43) responsible for delivering light-harvesting chlorophyll binding protein to the thylakoid membrane. While a nearly complete three-dimensional structure of cpSRP43 has been determined, no high-resolution structure is yet available for cpSRP54. In this study, we developed and examined an in silico three-dimensional model of the structure of cpSRP54 by homology modeling using cytosolic homologs. Model selection was guided by single-molecule Förster resonance energy transfer experiments, which revealed the presence of at least two distinct conformations. Small angle x-ray scattering showed that the linking region among the GTPase (G-domain) and methionine-rich (M-domain) domains, an M-domain loop, and the cpSRP43 binding C-terminal extension of cpSRP54 are predominantly disordered. Interestingly, the linker and loop segments were observed to play an important role in organizing the domain arrangement of cpSRP54. Further, deletion of the finger loop abolished loading of the cpSRP cargo, light-harvesting chlorophyll binding protein. These data highlight important structural dynamics relevant to cpSRP54's role in the post- and cotranslational signaling processes.
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Affiliation(s)
- Rory C Henderson
- Department of Chemistry and Biochemistry, University of Arkansas, Fayetteville, Arkansas
| | - Feng Gao
- Department of Chemistry and Biochemistry, University of Arkansas, Fayetteville, Arkansas
| | - Srinivas Jayanthi
- Department of Chemistry and Biochemistry, University of Arkansas, Fayetteville, Arkansas
| | - Alicia Kight
- Department of Biological Sciences, University of Arkansas, Fayetteville, Arkansas
| | - Priyanka Sharma
- Department of Biological Sciences, University of Arkansas, Fayetteville, Arkansas
| | - Robyn L Goforth
- Department of Biological Sciences, University of Arkansas, Fayetteville, Arkansas
| | - Colin D Heyes
- Department of Chemistry and Biochemistry, University of Arkansas, Fayetteville, Arkansas
| | - Ralph L Henry
- Department of Biological Sciences, University of Arkansas, Fayetteville, Arkansas
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221
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Autonomous translational pausing is required for XBP1u mRNA recruitment to the ER via the SRP pathway. Proc Natl Acad Sci U S A 2016; 113:E5886-E5895. [PMID: 27651490 DOI: 10.1073/pnas.1604435113] [Citation(s) in RCA: 44] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Unconventional mRNA splicing on the endoplasmic reticulum (ER) membrane is the sole conserved mechanism in eukaryotes to transmit information regarding misfolded protein accumulation to the nucleus to activate the stress response. In metazoans, the unspliced form of X-box-binding protein 1 (XBP1u) mRNA is recruited to membranes as a ribosome nascent chain (RNC) complex for efficient splicing. We previously reported that both hydrophobic (HR2) and translational pausing regions of XBP1u are important for the recruitment of its own mRNA to membranes. However, its precise location and the molecular mechanism of translocation are unclear. We show that XBP1u-RNC is specifically recruited to the ER membrane in an HR2- and translational pausing-dependent manner by immunostaining, fluorescent recovery after photobleaching, and biochemical analyses. Notably, translational pausing during XBP1u synthesis is indispensable for the recognition of HR2 by the signal recognition particle (SRP), resulting in efficient ER-specific targeting of the complex, similar to secretory protein targeting to the ER. On the ER, the XBP1u nascent chain is transferred from the SRP to the translocon; however, it cannot pass through the translocon or insert into the membrane. Therefore, our results support a noncanonical mechanism by which mRNA substrates are recruited to the ER for unconventional splicing.
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222
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ATPase and GTPase Tangos Drive Intracellular Protein Transport. Trends Biochem Sci 2016; 41:1050-1060. [PMID: 27658684 DOI: 10.1016/j.tibs.2016.08.012] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2016] [Revised: 08/18/2016] [Accepted: 08/23/2016] [Indexed: 11/24/2022]
Abstract
The GTPase superfamily of proteins provides molecular switches to regulate numerous cellular processes. The 'GTPase switch' paradigm, in which external regulatory factors control the switch of a GTPase between 'on' and 'off' states, has been used to interpret the regulatory mechanism of many GTPases. However, recent work unveiled a class of nucleotide hydrolases that do not adhere to this classical paradigm. Instead, they use nucleotide-dependent dimerization cycles to regulate key cellular processes. In this review article, recent studies of dimeric GTPases and ATPases involved in intracellular protein targeting are summarized. It is suggested that these proteins can use the conformational plasticity at their dimer interface to generate multiple points of regulation, thereby providing the driving force and spatiotemporal coordination of complex cellular pathways.
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223
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Kallehauge TB, Kol S, Rørdam Andersen M, Kroun Damgaard C, Lee GM, Faustrup Kildegaard H. Endoplasmic reticulum-directed recombinant mRNA displays subcellular localization equal to endogenous mRNA during transient expression in CHO cells. Biotechnol J 2016; 11:1362-1367. [PMID: 27624596 DOI: 10.1002/biot.201600347] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2016] [Revised: 08/12/2016] [Accepted: 08/15/2016] [Indexed: 12/13/2022]
Abstract
When expressing pharmaceutical recombinant proteins in mammalian cells, the protein is commonly directed through the secretory pathway, in a signal peptide-dependent manner, to acquire specific post-translational modifications and to facilitate secretion into the culture medium. One key premise for this is the direction of the mRNA encoding the recombinant protein to the surface of the endoplasmic reticulum (ER) for subsequent protein translocation into the secretory pathway. To evaluate the efficiency of this process in Chinese hamster ovary (CHO) cells, the subcellular localization of recombinant mRNA encoding the therapeutic proteins, erythropoietin (EPO) and Rituximab, was determined. The results show that ER-directed recombinant mRNAs exhibited an efficient recruitment to the ER when compared to an endogenous ER-directed mRNA, with no cytoplasmic translation of ER-directed recombinant proteins observed. These observations indicate that the recombinant mRNA, encoding ER-directed proteins, follows the same distribution pattern as endogenous mRNA directed towards the ER. Furthermore, the previous established fractionation method proves to be an efficient tool to study not only recombinant mRNA localization, but also recombinant protein trafficking between the ER and cytosol in CHO cells.
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Affiliation(s)
- Thomas Beuchert Kallehauge
- The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Hørsholm, Denmark.
| | - Stefan Kol
- The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Hørsholm, Denmark
| | | | | | - Gyun Min Lee
- The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Hørsholm, Denmark
- Department of Biological Sciences, KAIST, Daejeon, Korea
| | - Helene Faustrup Kildegaard
- The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Hørsholm, Denmark.
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224
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Global profiling of SRP interaction with nascent polypeptides. Nature 2016; 536:219-23. [PMID: 27487212 DOI: 10.1038/nature19070] [Citation(s) in RCA: 98] [Impact Index Per Article: 12.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2016] [Accepted: 06/29/2016] [Indexed: 12/23/2022]
Abstract
Signal recognition particle (SRP) is a universally conserved protein-RNA complex that mediates co-translational protein translocation and membrane insertion by targeting translating ribosomes to membrane translocons. The existence of parallel co- and post-translational transport pathways, however, raises the question of the cellular substrate pool of SRP and the molecular basis of substrate selection. Here we determine the binding sites of bacterial SRP within the nascent proteome of Escherichia coli at amino acid resolution, by sequencing messenger RNA footprints of ribosome-nascent-chain complexes associated with SRP. SRP, on the basis of its strong preference for hydrophobic transmembrane domains (TMDs), constitutes a compartment-specific targeting factor for nascent inner membrane proteins (IMPs) that efficiently excludes signal-sequence-containing precursors of periplasmic and outer membrane proteins. SRP associates with hydrophobic TMDs enriched in consecutive stretches of hydrophobic and bulky aromatic amino acids immediately on their emergence from the ribosomal exit tunnel. By contrast with current models, N-terminal TMDs are frequently skipped and TMDs internal to the polypeptide sequence are selectively recognized. Furthermore, SRP binds several TMDs in many multi-spanning membrane proteins, suggesting cycles of SRP-mediated membrane targeting. SRP-mediated targeting is not accompanied by a transient slowdown of translation and is not influenced by the ribosome-associated chaperone trigger factor (TF), which has a distinct substrate pool and acts at different stages during translation. Overall, our proteome-wide data set of SRP-binding sites reveals the underlying principles of pathway decisions for nascent chains in bacteria, with SRP acting as the dominant triaging factor, sufficient to separate IMPs from substrates of the SecA-SecB post-translational translocation and TF-assisted cytosolic protein folding pathways.
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225
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Chartron JW, Hunt KCL, Frydman J. Cotranslational signal-independent SRP preloading during membrane targeting. Nature 2016; 536:224-8. [PMID: 27487213 PMCID: PMC5120976 DOI: 10.1038/nature19309] [Citation(s) in RCA: 119] [Impact Index Per Article: 14.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2015] [Accepted: 07/18/2016] [Indexed: 12/24/2022]
Abstract
Ribosome-associated factors must faithfully decode the limited information available in nascent polypeptides to direct them to their correct cellular fate1. It is unclear how the low complexity information exposed by the nascent chain suffices for accurate recognition by the many factors competing for the limited surface near the ribosomal exit site2,3. Questions remain even for the well-studied cotranslational targeting cycle to the endoplasmic reticulum (ER), involving recognition of linear hydrophobic Signal Sequences (SS) or Transmembrane Domains (TMD) by the Signal Recognition Particle (SRP)4,5. Intriguingly, SRP is in low abundance relative to the large number of ribosome nascent chain complexes (RNCs), yet it accurately selects those destined to the ER6. Despite their overlapping specificities, SRP and the cotranslational Hsp70 SSB display exquisite mutually exclusive selectivity in vivo for their cognate RNCs7,8. To understand cotranslational nascent chain recognition in vivo, we interrogated the cotranslational membrane targeting cycle using ribosome profiling (herein Ribo-seq)9 coupled with biochemical fractionation of ribosome populations. Unexpectedly, SRP preferentially binds secretory RNCs before targeting signals are translated. We show non-coding mRNA elements can promote this signal-independent SRP pre-recruitment. Our study defines the complex kinetic interplay between elongation and determinants in the polypeptide and mRNA modulating SRP-substrate selection and membrane targeting.
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226
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Abstract
The endoplasmic reticulum is the port of entry for proteins into the secretory pathway and the site of synthesis for several important lipids, including cholesterol, triacylglycerol, and phospholipids. Protein production within the endoplasmic reticulum is tightly regulated by a cohort of resident machinery that coordinates the folding, modification, and deployment of secreted and integral membrane proteins. Proteins failing to attain their native conformation are degraded through the endoplasmic reticulum-associated degradation (ERAD) pathway via a series of tightly coupled steps: substrate recognition, dislocation, and ubiquitin-dependent proteasomal destruction. The same ERAD machinery also controls the flux through various metabolic pathways by coupling the turnover of metabolic enzymes to the levels of key metabolites. We review the current understanding and biological significance of ERAD-mediated regulation of lipid metabolism in mammalian cells.
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Affiliation(s)
- Julian Stevenson
- Program in Metabolic Biology, Department of Nutritional Sciences and Toxicology, University of California, Berkeley, California 94720;
| | - Edmond Y Huang
- Program in Metabolic Biology, Department of Nutritional Sciences and Toxicology, University of California, Berkeley, California 94720;
| | - James A Olzmann
- Program in Metabolic Biology, Department of Nutritional Sciences and Toxicology, University of California, Berkeley, California 94720;
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227
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Nilsson RH, Alm Rosenblad M, Martín MP, Tedersoo L, Ryberg MK, Larsson E, Wurzbacher C, Abarenkov K. Detection of signal recognition particle (SRP) RNAs in the nuclear ribosomal internal transcribed spacer 1 (ITS1) of three lineages of ectomycorrhizal fungi (Agaricomycetes, Basidiomycota). MycoKeys 2016. [DOI: 10.3897/mycokeys.13.8579] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023] Open
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228
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Nyathi Y, Pool MR. Analysis of the interplay of protein biogenesis factors at the ribosome exit site reveals new role for NAC. J Cell Biol 2016. [PMID: 26195668 PMCID: PMC4508901 DOI: 10.1083/jcb.201410086] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022] Open
Abstract
The protein biogenesis factor NAC regulates the access of the enzyme MetAP and the signal recognition particle (SRP) to the ribosome, functions in SRP-dependent targeting, and can act to protect substrates from aggregation before translocation The ribosome exit site is a focal point for the interaction of protein-biogenesis factors that guide the fate of nascent polypeptides. These factors include chaperones such as NAC, N-terminal-modifying enzymes like Methionine aminopeptidase (MetAP), and the signal recognition particle (SRP), which targets secretory and membrane proteins to the ER. These factors potentially compete with one another in the short time-window when the nascent chain first emerges at the exit site, suggesting a need for regulation. Here, we show that MetAP contacts the ribosome at the universal adaptor site where it is adjacent to the α subunit of NAC. SRP is also known to contact the ribosome at this site. In the absence of NAC, MetAP and SRP antagonize each other, indicating a novel role for NAC in regulating the access of MetAP and SRP to the ribosome. NAC also functions in SRP-dependent targeting and helps to protect substrates from aggregation before translocation.
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Affiliation(s)
- Yvonne Nyathi
- Faculty of Life Sciences, University of Manchester, Manchester M13 9PT, England, UK
| | - Martin R Pool
- Faculty of Life Sciences, University of Manchester, Manchester M13 9PT, England, UK
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Suzuki R, Kawahara H. UBQLN4 recognizes mislocalized transmembrane domain proteins and targets these to proteasomal degradation. EMBO Rep 2016; 17:842-57. [PMID: 27113755 DOI: 10.15252/embr.201541402] [Citation(s) in RCA: 50] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2015] [Accepted: 03/24/2016] [Indexed: 12/21/2022] Open
Abstract
The majority of transmembrane proteins are integrated into the endoplasmic reticulum (ER) by virtue of a signal sequence-mediated co-translational process. However, a substantial portion of transmembrane proteins fails to reach the ER, leading to mislocalized cytosolic polypeptides. Their appropriate recognition and removal are of the utmost importance to avoid proteotoxic stress. Here, we identified UBQLN4 as a BAG6-binding factor that eliminates newly synthesized defective polypeptides. Using a truncated transmembrane domain protein whose degradation occurs during a pre-ER incorporation process as a model, we show that UBQLN4 recognizes misassembled proteins in the cytoplasm and targets these to the proteasome. We suggest that the exposed transmembrane segment of the defective polypeptides is essential for the UBQLN4-mediated substrate discrimination. Importantly, UBQLN4 recognizes not only the defective model substrate but also a pool of endogenous defective proteins that were induced by the depletion of the SRP54 subunit of the signal recognition particle. This study identifies a novel quality control mechanism for newly synthesized and defective transmembrane domain polypeptides that fail to reach their correct destination at the ER membrane.
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Affiliation(s)
- Rigel Suzuki
- Laboratory of Cell Biology and Biochemistry, Department of Biological Sciences, Tokyo Metropolitan University, Tokyo, Japan
| | - Hiroyuki Kawahara
- Laboratory of Cell Biology and Biochemistry, Department of Biological Sciences, Tokyo Metropolitan University, Tokyo, Japan
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230
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A Novel SRP Recognition Sequence in the Homeostatic Control Region of Heat Shock Transcription Factor σ32. Sci Rep 2016; 6:24147. [PMID: 27052372 PMCID: PMC4823717 DOI: 10.1038/srep24147] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2016] [Accepted: 03/21/2016] [Indexed: 12/29/2022] Open
Abstract
Heat shock response (HSR) generally plays a major role in sustaining protein homeostasis. In Escherichia coli, the activity and amount of the dedicated transcription factor σ32 transiently increase upon heat shock. The initial induction is followed by chaperone-mediated negative feedback to inactivate and degrade σ32. Previous work reported that signal recognition particle (SRP)-dependent targeting of σ32 to the membrane is essential for feedback control, though how SRP recognizes σ32 remained unknown. Extensive photo- and disulfide cross-linking studies in vivo now reveal that the highly conserved regulatory region of σ32 that lacks a consecutive hydrophobic stretch interacts with the signal peptide-binding site of Ffh (the protein subunit of SRP). Importantly, the σ32–Ffh interaction observed was significantly affected by mutations in this region that compromise the feedback regulation, but not by deleting the DnaK/DnaJ chaperones. Homeostatic regulation of HSR thus requires a novel type of SRP recognition mechanism.
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231
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Zhang Y, Stefanovic B. LARP6 Meets Collagen mRNA: Specific Regulation of Type I Collagen Expression. Int J Mol Sci 2016; 17:419. [PMID: 27011170 PMCID: PMC4813270 DOI: 10.3390/ijms17030419] [Citation(s) in RCA: 55] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2016] [Revised: 03/15/2016] [Accepted: 03/17/2016] [Indexed: 01/15/2023] Open
Abstract
Type I collagen is the most abundant structural protein in all vertebrates, but its constitutive rate of synthesis is low due to long half-life of the protein (60-70 days). However, several hundred fold increased production of type I collagen is often seen in reparative or reactive fibrosis. The mechanism which is responsible for this dramatic upregulation is complex, including multiple levels of regulation. However, posttranscriptional regulation evidently plays a predominant role. Posttranscriptional regulation comprises processing, transport, stabilization and translation of mRNAs and is executed by RNA binding proteins. There are about 800 RNA binding proteins, but only one, La ribonucleoprotein domain family member 6 (LARP6), is specifically involved in type I collagen regulation. In the 5'untranslated region (5'UTR) of mRNAs encoding for type I and type III collagens there is an evolutionally conserved stem-loop (SL) structure; this structure is not found in any other mRNA, including any other collagen mRNA. LARP6 binds to the 5'SL in sequence specific manner to regulate stability of collagen mRNAs and their translatability. Here, we will review current understanding of how is LARP6 involved in posttranscriptional regulation of collagen mRNAs. We will also discuss how other proteins recruited by LARP6, including nonmuscle myosin, vimentin, serine threonine kinase receptor associated protein (STRAP), 25 kD FK506 binding protein (FKBP25) and RNA helicase A (RHA), contribute to this process.
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Affiliation(s)
- Yujie Zhang
- Department of Biomedical Sciences, College of Medicine, Florida State University, Tallahassee, FL 32306, USA.
| | - Branko Stefanovic
- Department of Biomedical Sciences, College of Medicine, Florida State University, Tallahassee, FL 32306, USA.
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232
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Kida Y, Ishihara Y, Fujita H, Onishi Y, Sakaguchi M. Stability and flexibility of marginally hydrophobic-segment stalling at the endoplasmic reticulum translocon. Mol Biol Cell 2016; 27:930-40. [PMID: 26823014 PMCID: PMC4791137 DOI: 10.1091/mbc.e15-09-0672] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2015] [Accepted: 01/19/2016] [Indexed: 01/10/2023] Open
Abstract
Many membrane proteins are integrated into the endoplasmic reticulum membrane through the protein-conducting channel, the translocon. Transmembrane segments with insufficient hydrophobicity for membrane integration are frequently found in multispanning membrane proteins, and such marginally hydrophobic (mH) segments should be accommodated, at least transiently, at the membrane. Here we investigated how mH-segments stall at the membrane and their stability. Our findings show that mH-segments can be retained at the membrane without moving into the lipid phase and that such segments flank Sec61α, the core channel of the translocon, in the translational intermediate state. The mH-segments are gradually transferred from the Sec61 channel to the lipid environment in a hydrophobicity-dependent manner, and this lateral movement may be affected by the ribosome. In addition, stalling mH-segments allow for insertion of the following transmembrane segment, forming an Ncytosol/Clumen orientation, suggesting that mH-segments can move laterally to accommodate the next transmembrane segment. These findings suggest that mH-segments may be accommodated at the ER membrane with lateral fluctuation between the Sec61 channel and the lipid phase.
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Affiliation(s)
- Yuichiro Kida
- Graduate School of Life Science, University of Hyogo, Kamigori, Hyogo 678-1297, Japan
| | - Yudai Ishihara
- Graduate School of Life Science, University of Hyogo, Kamigori, Hyogo 678-1297, Japan
| | - Hidenobu Fujita
- Graduate School of Life Science, University of Hyogo, Kamigori, Hyogo 678-1297, Japan
| | - Yukiko Onishi
- Graduate School of Life Science, University of Hyogo, Kamigori, Hyogo 678-1297, Japan
| | - Masao Sakaguchi
- Graduate School of Life Science, University of Hyogo, Kamigori, Hyogo 678-1297, Japan
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233
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Shi X, Huang L, Lilley DMJ, Harbury PB, Herschlag D. The solution structural ensembles of RNA kink-turn motifs and their protein complexes. Nat Chem Biol 2016; 12:146-52. [PMID: 26727239 PMCID: PMC4755865 DOI: 10.1038/nchembio.1997] [Citation(s) in RCA: 33] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2015] [Accepted: 11/04/2015] [Indexed: 12/22/2022]
Abstract
With the growing number of crystal structures of RNA and RNA-protein complexes, a critical next step is understanding the dynamic solution behavior of these entities in terms of conformational ensembles and energy landscapes. To this end, we have used X-ray scattering interferometry (XSI) to probe the ubiquitous RNA kink-turn motif and its complexes with the canonical kink-turn binding protein L7Ae. XSI revealed that the folded kink-turn is best described as a restricted conformational ensemble. The ions present in solution alter the nature of this ensemble, and protein binding can perturb the kink-turn ensemble without collapsing it to a unique state. This study demonstrates how XSI can reveal structural and ensemble properties of RNAs and RNA-protein complexes and uncovers the behavior of an important RNA-protein motif. This type of information will be necessary to understand, predict and engineer the behavior and function of RNAs and their protein complexes.
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Affiliation(s)
- Xuesong Shi
- Department of Biochemistry, Stanford University, Stanford, California, USA
| | - Lin Huang
- Nucleic Acid Structure Research Group, School of Life Sciences, University of Dundee, Dundee, UK
| | - David M J Lilley
- Nucleic Acid Structure Research Group, School of Life Sciences, University of Dundee, Dundee, UK
| | - Pehr B Harbury
- Department of Biochemistry, Stanford University, Stanford, California, USA
- ChEM-H, Stanford University, Stanford, California, USA
| | - Daniel Herschlag
- Department of Biochemistry, Stanford University, Stanford, California, USA
- ChEM-H, Stanford University, Stanford, California, USA
- Department of Chemistry, Stanford University, Stanford, California, USA
- Department of Chemical Engineering, Stanford University, Stanford, California, USA
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234
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Klasek L, Inoue K. Dual Protein Localization to the Envelope and Thylakoid Membranes Within the Chloroplast. INTERNATIONAL REVIEW OF CELL AND MOLECULAR BIOLOGY 2016; 323:231-63. [PMID: 26944623 DOI: 10.1016/bs.ircmb.2015.12.008] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Indexed: 01/13/2023]
Abstract
The chloroplast houses various metabolic processes essential for plant viability. This organelle originated from an ancestral cyanobacterium via endosymbiosis and maintains the three membranes of its progenitor. Among them, the outer envelope membrane functions mainly in communication with cytoplasmic components while the inner envelope membrane houses selective transport of various metabolites and the biosynthesis of several compounds, including membrane lipids. These two envelope membranes also play essential roles in import of nuclear-encoded proteins and in organelle division. The third membrane, the internal membrane system known as the thylakoid, houses photosynthetic electron transport and chemiosmotic phosphorylation. The inner envelope and thylakoid membranes share similar lipid composition. Specific targeting pathways determine their defined proteomes and, thus, their distinct functions. Nonetheless, several proteins have been shown to exist in both the envelope and thylakoid membranes. These proteins include those that play roles in protein transport, tetrapyrrole biosynthesis, membrane dynamics, or transport of nucleotides or inorganic phosphate. In this review, we summarize the current knowledge about proteins localized to both the envelope and thylakoid membranes in the chloroplast, discussing their roles in each membrane and potential mechanisms of their dual localization. Addressing the unanswered questions about these dual-localized proteins should help advance our understanding of chloroplast development, protein transport, and metabolic regulation.
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Affiliation(s)
- Laura Klasek
- Department of Plant Sciences, University of California at Davis, Davis, CA, United States of America
| | - Kentaro Inoue
- Department of Plant Sciences, University of California at Davis, Davis, CA, United States of America.
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235
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Kariithi HM, İnce İA, Boeren S, Murungi EK, Meki IK, Otieno EA, Nyanjom SRG, van Oers MM, Vlak JM, Abd-Alla AMM. Comparative Analysis of Salivary Gland Proteomes of Two Glossina Species that Exhibit Differential Hytrosavirus Pathologies. Front Microbiol 2016; 7:89. [PMID: 26903969 PMCID: PMC4746320 DOI: 10.3389/fmicb.2016.00089] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2015] [Accepted: 01/18/2016] [Indexed: 01/19/2023] Open
Abstract
Glossina pallidipes salivary gland hypertrophy virus (GpSGHV; family Hytrosaviridae) is a dsDNA virus exclusively pathogenic to tsetse flies (Diptera; Glossinidae). The 190 kb GpSGHV genome contains 160 open reading frames and encodes more than 60 confirmed proteins. The asymptomatic GpSGHV infection in flies can convert to symptomatic infection that is characterized by overt salivary gland hypertrophy (SGH). Flies with SGH show reduced general fitness and reproductive dysfunction. Although the occurrence of SGH is an exception rather than the rule, G. pallidipes is thought to be the most susceptible to expression of overt SGH symptoms compared to other Glossina species that are largely asymptomatic. Although Glossina salivary glands (SGs) play an essential role in GpSGHV transmission, the functions of the salivary components during the virus infection are poorly understood. In this study, we used mass spectrometry to study SG proteomes of G. pallidipes and G. m. morsitans, two Glossina model species that exhibit differential GpSGHV pathologies (high and low incidence of SGH, respectively). A total of 540 host proteins were identified, of which 23 and 9 proteins were significantly up- and down-regulated, respectively, in G. pallidipes compared to G. m. morsitans. Whereas 58 GpSGHV proteins were detected in G. pallidipes F1 progenies, only 5 viral proteins were detected in G. m. morsitans. Unlike in G. pallidipes, qPCR assay did not show any significant increase in virus titers in G. m. morsitans F1 progenies, confirming that G. m. morsitans is less susceptible to GpSGHV infection and replication compared to G. pallidipes. Based on our results, we speculate that in the case of G. pallidipes, GpSGHV employs a repertoire of host intracellular signaling pathways for successful infection. In the case of G. m. morsitans, antiviral responses appeared to be dominant. These results are useful for designing additional tools to investigate the Glossina-GpSGHV interactions.
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Affiliation(s)
- Henry M Kariithi
- Biotechnology Research Institute, Kenya Agricultural and Livestock Research OrganizationNairobi, Kenya; Insect Pest Control Laboratory, Joint FAO/IAEA Programme of Nuclear Techniques in Food and Agriculture, International Atomic Energy AgencyVienna, Austria; Laboratory of Virology, Wageningen UniversityWageningen, Netherlands
| | - İkbal Agah İnce
- Department of Medical Microbiology, Acıbadem University İstanbul, Turkey
| | - Sjef Boeren
- Laboratory of Biochemistry, Wageningen University Wageningen, Netherlands
| | - Edwin K Murungi
- South African National Bioinformatics Institute, University of the Western Cape Cape Town, South Africa
| | - Irene K Meki
- Insect Pest Control Laboratory, Joint FAO/IAEA Programme of Nuclear Techniques in Food and Agriculture, International Atomic Energy AgencyVienna, Austria; Laboratory of Virology, Wageningen UniversityWageningen, Netherlands
| | - Everlyne A Otieno
- Department of Biochemistry, Jomo Kenyatta University of Agriculture and Technology Nairobi, Kenya
| | - Steven R G Nyanjom
- Department of Biochemistry, Jomo Kenyatta University of Agriculture and Technology Nairobi, Kenya
| | | | - Just M Vlak
- Laboratory of Virology, Wageningen University Wageningen, Netherlands
| | - Adly M M Abd-Alla
- Insect Pest Control Laboratory, Joint FAO/IAEA Programme of Nuclear Techniques in Food and Agriculture, International Atomic Energy Agency Vienna, Austria
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236
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Abstract
A fascinating aspect of retroviruses is their tendency to nonrandomly incorporate host cell RNAs into virions. In addition to the specific tRNAs that prime reverse transcription, all examined retroviruses selectively package multiple host cell noncoding RNAs (ncRNAs). Many of these ncRNAs appear to be encapsidated shortly after synthesis, before assembling with their normal protein partners. Remarkably, although some packaged ncRNAs, such as pre-tRNAs and the spliceosomal U6 small nuclear RNA (snRNA), were believed to reside exclusively within mammalian nuclei, it was demonstrated recently that the model retrovirus murine leukemia virus (MLV) packages these ncRNAs from a novel pathway in which unneeded nascent ncRNAs are exported to the cytoplasm for degradation. The finding that retroviruses package forms of ncRNAs that are rare in cells suggests several hypotheses for how these RNAs could assist retrovirus assembly and infectivity. Moreover, recent experiments in several laboratories have identified additional ways in which cellular ncRNAs may contribute to the retrovirus life cycle. This review focuses on the ncRNAs that are packaged by retroviruses and the ways in which both encapsidated ncRNAs and other cellular ncRNAs may contribute to retrovirus replication.
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237
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Kuhn P, Draycheva A, Vogt A, Petriman NA, Sturm L, Drepper F, Warscheid B, Wintermeyer W, Koch HG. Ribosome binding induces repositioning of the signal recognition particle receptor on the translocon. J Cell Biol 2016; 211:91-104. [PMID: 26459600 PMCID: PMC4602035 DOI: 10.1083/jcb.201502103] [Citation(s) in RCA: 37] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023] Open
Abstract
The cotranslational transfer of nascent membrane proteins to the SecYEG translocon is facilitated by a reorientation of the SecY-bound signal recognition particle (SRP) receptor, FtsY, which accompanies the formation of a quaternary targeting complex consisting of SecYEG, FtsY, SRP, and the ribosome. Cotranslational protein targeting delivers proteins to the bacterial cytoplasmic membrane or to the eukaryotic endoplasmic reticulum membrane. The signal recognition particle (SRP) binds to signal sequences emerging from the ribosomal tunnel and targets the ribosome-nascent-chain complex (RNC) to the SRP receptor, termed FtsY in bacteria. FtsY interacts with the fifth cytosolic loop of SecY in the SecYEG translocon, but the functional role of the interaction is unclear. By using photo-cross-linking and fluorescence resonance energy transfer measurements, we show that FtsY–SecY complex formation is guanosine triphosphate independent but requires a phospholipid environment. Binding of an SRP–RNC complex exposing a hydrophobic transmembrane segment induces a rearrangement of the SecY–FtsY complex, which allows the subsequent contact between SecY and ribosomal protein uL23. These results suggest that direct RNC transfer to the translocon is guided by the interaction between SRP and translocon-bound FtsY in a quaternary targeting complex.
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Affiliation(s)
- Patrick Kuhn
- Institute of Biochemistry and Molecular Biology, Albert-Ludwigs-University Freiburg, 79104 Freiburg, Germany Faculty of Biology, Albert-Ludwigs-University Freiburg, 79104 Freiburg, Germany
| | - Albena Draycheva
- Department of Physical Biochemistry, Max Planck Institute for Biophysical Chemistry, 37077 Göttingen, Germany
| | - Andreas Vogt
- Institute of Biochemistry and Molecular Biology, Albert-Ludwigs-University Freiburg, 79104 Freiburg, Germany Faculty of Biology, Albert-Ludwigs-University Freiburg, 79104 Freiburg, Germany Spemann Graduate School of Biology and Medicine, Albert-Ludwigs-University Freiburg, 79104 Freiburg, Germany
| | - Narcis-Adrian Petriman
- Institute of Biochemistry and Molecular Biology, Albert-Ludwigs-University Freiburg, 79104 Freiburg, Germany Faculty of Biology, Albert-Ludwigs-University Freiburg, 79104 Freiburg, Germany
| | - Lukas Sturm
- Institute of Biochemistry and Molecular Biology, Albert-Ludwigs-University Freiburg, 79104 Freiburg, Germany
| | - Friedel Drepper
- Department of Biochemistry and Functional Proteomics, Faculty of Biology and BIOSS Centre for Biological Signalling Studies, Albert-Ludwigs-University Freiburg, 79104 Freiburg, Germany
| | - Bettina Warscheid
- Spemann Graduate School of Biology and Medicine, Albert-Ludwigs-University Freiburg, 79104 Freiburg, Germany Department of Biochemistry and Functional Proteomics, Faculty of Biology and BIOSS Centre for Biological Signalling Studies, Albert-Ludwigs-University Freiburg, 79104 Freiburg, Germany
| | - Wolfgang Wintermeyer
- Department of Physical Biochemistry, Max Planck Institute for Biophysical Chemistry, 37077 Göttingen, Germany
| | - Hans-Georg Koch
- Institute of Biochemistry and Molecular Biology, Albert-Ludwigs-University Freiburg, 79104 Freiburg, Germany Spemann Graduate School of Biology and Medicine, Albert-Ludwigs-University Freiburg, 79104 Freiburg, Germany
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238
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Probing the kinetic and thermodynamic consequences of the tetraloop/tetraloop receptor monovalent ion-binding site in P4-P6 RNA by smFRET. Biochem Soc Trans 2016; 43:172-8. [PMID: 25849913 DOI: 10.1042/bst20140268] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
Abstract
Structured RNA molecules play roles in central biological processes and understanding the basic forces and features that govern RNA folding kinetics and thermodynamics can help elucidate principles that underlie biological function. Here we investigate one such feature, the specific interaction of monovalent cations with a structured RNA, the P4-P6 domain of the Tetrahymena ribozyme. We employ single molecule FRET (smFRET) approaches as these allow determination of folding equilibrium and rate constants over a wide range of stabilities and thus allow direct comparisons without the need for extrapolation. These experiments provide additional evidence for specific binding of monovalent cations, Na+ and K+, to the RNA tetraloop-tetraloop receptor (TL-TLR) tertiary motif. These ions facilitate both folding and unfolding, consistent with an ability to help order the TLR for binding and further stabilize the tertiary contact subsequent to attainment of the folding transition state.
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239
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Mammalian SRP receptor switches the Sec61 translocase from Sec62 to SRP-dependent translocation. Nat Commun 2015; 6:10133. [PMID: 26634806 PMCID: PMC4686813 DOI: 10.1038/ncomms10133] [Citation(s) in RCA: 41] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2015] [Accepted: 11/05/2015] [Indexed: 02/07/2023] Open
Abstract
Two distinct pathways deliver secretory proteins to the Sec61 protein translocase in the endoplasmic reticulum membrane. The canonical pathway requires the signal recognition particle (SRP) and its cognate receptor (SR), and targets ribosome-associated proteins to the Sec translocase. The SRP-independent pathway requires the Sec translocase-associated ER membrane protein Sec62 and can be uncoupled from translation. Here we show that SR switches translocons to SRP-dependent translocation by displacing Sec62. This activity localizes to the charged linker region between the longin and GTPase domains of SRα. Using truncation variants, crosslinking and translocation assays reveals two elements with distinct functions as follows: one rearranges the translocon, displacing Sec62 from Sec61. A second promotes ribosome binding and is conserved between all eukaryotes. These specific regions in SRα reprogramme the Sec translocon and facilitate recruitment of ribosome-nascent chain complexes. Overall, our study identifies an important function of SR, which mechanistically links two seemingly independent modes of translocation.
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240
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Fernández-Boo S, Villalba A, Cao A. Variable protein profiles in extracellular products of the protistan parasite Perkinsus olseni among regions of the Spanish coast. J Invertebr Pathol 2015; 132:233-241. [DOI: 10.1016/j.jip.2015.11.003] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2015] [Revised: 11/02/2015] [Accepted: 11/06/2015] [Indexed: 10/22/2022]
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241
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Elvekrog MM, Walter P. Dynamics of co-translational protein targeting. Curr Opin Chem Biol 2015; 29:79-86. [PMID: 26517565 DOI: 10.1016/j.cbpa.2015.09.016] [Citation(s) in RCA: 41] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2015] [Accepted: 09/15/2015] [Indexed: 12/20/2022]
Abstract
Most membrane and secretory proteins are delivered co-translationally to protein translocation channels in their destination membrane by the signal recognition particle (SRP) and its receptor. This co-translational molecular machinery is conserved across all kingdoms of life, though it varies in composition and function. Here we report recent progress towards understanding the mechanism of SRP function, focusing on findings about Escherichia coli SRP's conformational dynamics throughout the targeting process. These insights shed light on a key checkpoint in the targeting cycle: how SRP regulates engagement of an actively translating ribosome with the translocation machinery at the membrane.
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Affiliation(s)
- Margaret M Elvekrog
- The Howard Hughes Medical Institute, Department of Biochemistry and Biophysics, University of California, San Francisco, San Francisco, CA 94143, United States
| | - Peter Walter
- The Howard Hughes Medical Institute, Department of Biochemistry and Biophysics, University of California, San Francisco, San Francisco, CA 94143, United States.
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242
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Abstract
More than one third of the cellular proteome is destined for incorporation into cell membranes or export from the cell. In all domains of life, the signal recognition particle (SRP) delivers these proteins to the membrane and protein traffic falls apart without SRP logistics. With the aid of a topogenic transport signal, SRP retrieves its cargo right at the ribosome, from where they are sorted to the translocation channel. Mammalian SRP is a ribonucleoprotein complex consisting of an SRP RNA of 300 nucleotides and 6 proteins bound to it. Assembly occurs in a hierarchical manner mainly in the nucleolus and only SRP54, which recognizes the signal sequence and regulates the targeting process, is added as the last component in the cytosol. Here we present an update on recent insights in the structure, function and dynamics of SRP RNA in SRP assembly with focus on the S domain, and present SRP as an example for the complex biogenesis of a rather small ribonucleoprotein particle.
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Affiliation(s)
- Klemens Wild
- a Heidelberg University Biochemistry Center (BZH) ; Heidelberg , Germany
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243
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Abstract
Accumulating recent evidence identified the ribosome as binding target for numerous small and long non-protein-coding RNAs (ncRNAs) in various organisms of all 3 domains of life. Therefore it appears that ribosome-associated ncRNAs (rancRNAs) are a prevalent, yet poorly understood class of cellular transcripts. Since rancRNAs are associated with the arguable most central enzyme of the cell it seems plausible to propose a role in translation control. Indeed first experimental evidence on small rancRNAs has been presented, linking ribosome association with fine-tuning the rate of protein biosynthesis in a stress-dependent manner.
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Affiliation(s)
- Andreas Pircher
- a Department of Chemistry and Biochemistry ; University of Bern ; Bern , Switzerland
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244
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Eckwahl MJ, Sim S, Smith D, Telesnitsky A, Wolin SL. A retrovirus packages nascent host noncoding RNAs from a novel surveillance pathway. Genes Dev 2015; 29:646-57. [PMID: 25792599 PMCID: PMC4378196 DOI: 10.1101/gad.258731.115] [Citation(s) in RCA: 39] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
Abstract
Eckwahl et al. used high-throughput sequencing to obtain a comprehensive description of the RNAs packaged by a model retrovirus, murine leukemia virus. The major encapsidated host RNAs are noncoding RNAs (ncRNAs) and members of the VL30 class of endogenous retroviruses. Packaging of both pre-tRNAs and U6 snRNA requires the nuclear export receptor Exportin-5. Adenylated and uridylated forms of these RNAs accumulate in cells and virions when the cytoplasmic exoribonuclease DIS3L2 and subunits of the RNA exosome are depleted. Although all retroviruses recruit host cell RNAs into virions, both the spectrum of RNAs encapsidated and the mechanisms by which they are recruited remain largely unknown. Here, we used high-throughput sequencing to obtain a comprehensive description of the RNAs packaged by a model retrovirus, murine leukemia virus. The major encapsidated host RNAs are noncoding RNAs (ncRNAs) and members of the VL30 class of endogenous retroviruses. Remarkably, although Moloney leukemia virus (MLV) assembles in the cytoplasm, precursors to specific tRNAs, small nuclear RNAs (snRNAs), and small nucleolar RNAs (snoRNAs) are all enriched in virions. Consistent with their cytoplasmic recruitment, packaging of both pre-tRNAs and U6 snRNA requires the nuclear export receptor Exportin-5. Adenylated and uridylated forms of these RNAs accumulate in cells and virions when the cytoplasmic exoribonuclease DIS3L2 and subunits of the RNA exosome are depleted. Together, our data reveal that MLV recruits RNAs from a novel host cell surveillance pathway in which unprocessed and unneeded nuclear ncRNAs are exported to the cytoplasm for degradation.
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Affiliation(s)
- Matthew J Eckwahl
- Department of Cell Biology, Yale School of Medicine, New Haven, Connecticut 06536, USA
| | - Soyeong Sim
- Department of Cell Biology, Yale School of Medicine, New Haven, Connecticut 06536, USA
| | - Derek Smith
- Department of Molecular Biophysics and Biochemistry, Yale School of Medicine, New Haven, Connecticut 06536, USA
| | - Alice Telesnitsky
- Department of Microbiology and Immunology, University of Michigan, Ann Arbor, Michigan, 48109, USA
| | - Sandra L Wolin
- Department of Cell Biology, Yale School of Medicine, New Haven, Connecticut 06536, USA Department of Molecular Biophysics and Biochemistry, Yale School of Medicine, New Haven, Connecticut 06536, USA Yale Cancer Center, New Haven, Connecticut 06520
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245
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Doris SM, Smith DR, Beamesderfer JN, Raphael BJ, Nathanson JA, Gerbi SA. Universal and domain-specific sequences in 23S-28S ribosomal RNA identified by computational phylogenetics. RNA (NEW YORK, N.Y.) 2015; 21:1719-1730. [PMID: 26283689 PMCID: PMC4574749 DOI: 10.1261/rna.051144.115] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/30/2015] [Accepted: 07/07/2015] [Indexed: 06/01/2023]
Abstract
Comparative analysis of ribosomal RNA (rRNA) sequences has elucidated phylogenetic relationships. However, this powerful approach has not been fully exploited to address ribosome function. Here we identify stretches of evolutionarily conserved sequences, which correspond with regions of high functional importance. For this, we developed a structurally aligned database, FLORA (full-length organismal rRNA alignment) to identify highly conserved nucleotide elements (CNEs) in 23S-28S rRNA from each phylogenetic domain (Eukarya, Bacteria, and Archaea). Universal CNEs (uCNEs) are conserved in sequence and structural position in all three domains. Those in regions known to be essential for translation validate our approach. Importantly, some uCNEs reside in areas of unknown function, thus identifying novel sequences of likely great importance. In contrast to uCNEs, domain-specific CNEs (dsCNEs) are conserved in just one phylogenetic domain. This is the first report of conserved sequence elements in rRNA that are domain-specific; they are largely a eukaryotic phenomenon. The locations of the eukaryotic dsCNEs within the structure of the ribosome suggest they may function in nascent polypeptide transit through the ribosome tunnel and in tRNA exit from the ribosome. Our findings provide insights and a resource for ribosome function studies.
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Affiliation(s)
- Stephen M Doris
- Department of Molecular Biology, Cell Biology and Biochemistry, Brown University Division of Biology and Medicine, Providence, Rhode Island 02912, USA
| | - Deborah R Smith
- Department of Molecular Biology, Cell Biology and Biochemistry, Brown University Division of Biology and Medicine, Providence, Rhode Island 02912, USA
| | - Julia N Beamesderfer
- Department of Molecular Biology, Cell Biology and Biochemistry, Brown University Division of Biology and Medicine, Providence, Rhode Island 02912, USA
| | - Benjamin J Raphael
- Department of Computer Science and Center for Computational Molecular Biology, Brown University Division of Biology and Medicine, Providence, Rhode Island 02912, USA
| | - Judith A Nathanson
- Department of Molecular Biology, Cell Biology and Biochemistry, Brown University Division of Biology and Medicine, Providence, Rhode Island 02912, USA
| | - Susan A Gerbi
- Department of Molecular Biology, Cell Biology and Biochemistry, Brown University Division of Biology and Medicine, Providence, Rhode Island 02912, USA
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246
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Kunze M, Berger J. The similarity between N-terminal targeting signals for protein import into different organelles and its evolutionary relevance. Front Physiol 2015; 6:259. [PMID: 26441678 PMCID: PMC4585086 DOI: 10.3389/fphys.2015.00259] [Citation(s) in RCA: 73] [Impact Index Per Article: 8.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2015] [Accepted: 09/04/2015] [Indexed: 12/04/2022] Open
Abstract
The proper distribution of proteins between the cytosol and various membrane-bound compartments is crucial for the functionality of eukaryotic cells. This requires the cooperation between protein transport machineries that translocate diverse proteins from the cytosol into these compartments and targeting signal(s) encoded within the primary sequence of these proteins that define their cellular destination. The mechanisms exerting protein translocation differ remarkably between the compartments, but the predominant targeting signals for mitochondria, chloroplasts and the ER share the N-terminal position, an α-helical structural element and the removal from the core protein by intraorganellar cleavage. Interestingly, similar properties have been described for the peroxisomal targeting signal type 2 mediating the import of a fraction of soluble peroxisomal proteins, whereas other peroxisomal matrix proteins encode the type 1 targeting signal residing at the extreme C-terminus. The structural similarity of N-terminal targeting signals poses a challenge to the specificity of protein transport, but allows the generation of ambiguous targeting signals that mediate dual targeting of proteins into different compartments. Dual targeting might represent an advantage for adaptation processes that involve a redistribution of proteins, because it circumvents the hierarchy of targeting signals. Thus, the co-existence of two equally functional import pathways into peroxisomes might reflect a balance between evolutionary constant and flexible transport routes.
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Affiliation(s)
- Markus Kunze
- Department of Pathobiology of the Nervous System, Center for Brain Research, Medical University of Vienna Vienna, Austria
| | - Johannes Berger
- Department of Pathobiology of the Nervous System, Center for Brain Research, Medical University of Vienna Vienna, Austria
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247
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Fung HYJ, Fu SC, Brautigam CA, Chook YM. Structural determinants of nuclear export signal orientation in binding to exportin CRM1. eLife 2015; 4:e10034. [PMID: 26349033 PMCID: PMC4596688 DOI: 10.7554/elife.10034] [Citation(s) in RCA: 58] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2015] [Accepted: 09/08/2015] [Indexed: 12/03/2022] Open
Abstract
The Chromosome Region of Maintenance 1 (CRM1) protein mediates nuclear export of hundreds of proteins through recognition of their nuclear export signals (NESs), which are highly variable in sequence and structure. The plasticity of the CRM1-NES interaction is not well understood, as there are many NES sequences that seem incompatible with structures of the NES-bound CRM1 groove. Crystal structures of CRM1 bound to two different NESs with unusual sequences showed the NES peptides binding the CRM1 groove in the opposite orientation (minus) to that of previously studied NESs (plus). Comparison of minus and plus NESs identified structural and sequence determinants for NES orientation. The binding of NESs to CRM1 in both orientations results in a large expansion in NES consensus patterns and therefore a corresponding expansion of potential NESs in the proteome.
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Affiliation(s)
- Ho Yee Joyce Fung
- Department of Pharmacology, University of Texas Southwestern Medical Center, Dallas, United States
| | - Szu-Chin Fu
- Department of Pharmacology, University of Texas Southwestern Medical Center, Dallas, United States
| | - Chad A Brautigam
- Department of Biophysics, University of Texas Southwestern Medical Center, Dallas, United States
| | - Yuh Min Chook
- Department of Pharmacology, University of Texas Southwestern Medical Center, Dallas, United States
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248
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Translational arrest by a prokaryotic signal recognition particle is mediated by RNA interactions. Nat Struct Mol Biol 2015; 22:767-73. [PMID: 26344568 DOI: 10.1038/nsmb.3086] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2014] [Accepted: 08/13/2015] [Indexed: 12/25/2022]
Abstract
The signal recognition particle (SRP) recognizes signal sequences of nascent polypeptides and targets ribosome-nascent chain complexes to membrane translocation sites. In eukaryotes, translating ribosomes are slowed down by the Alu domain of SRP to allow efficient targeting. In prokaryotes, however, little is known about the structure and function of Alu domain-containing SRPs. Here, we report a complete molecular model of SRP from the Gram-positive bacterium Bacillus subtilis, based on cryo-EM. The SRP comprises two subunits, 6S RNA and SRP54 or Ffh, and it facilitates elongation slowdown similarly to its eukaryotic counterpart. However, protein contacts with the small ribosomal subunit observed for the mammalian Alu domain are substituted in bacteria by RNA-RNA interactions of 6S RNA with the α-sarcin-ricin loop and helices H43 and H44 of 23S rRNA. Our findings provide a structural basis for cotranslational targeting and RNA-driven elongation arrest in prokaryotes.
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249
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Borowska MT, Dominik PK, Anghel SA, Kossiakoff AA, Keenan RJ. A YidC-like Protein in the Archaeal Plasma Membrane. Structure 2015; 23:1715-1724. [PMID: 26256539 PMCID: PMC4558205 DOI: 10.1016/j.str.2015.06.025] [Citation(s) in RCA: 51] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2015] [Revised: 05/29/2015] [Accepted: 06/21/2015] [Indexed: 01/08/2023]
Abstract
Cells possess specialized machinery to direct the insertion of membrane proteins into the lipid bilayer. In bacteria, the essential protein YidC inserts certain proteins into the plasma membrane, and eukaryotic orthologs are present in the mitochondrial inner membrane and the chloroplast thylakoid membrane. The existence of homologous insertases in archaea has been proposed based on phylogenetic analysis. However, limited sequence identity, distinct architecture, and the absence of experimental data have made this assignment ambiguous. Here we describe the 3.5-Å crystal structure of an archaeal DUF106 protein from Methanocaldococcus jannaschii (Mj0480), revealing a lipid-exposed hydrophilic surface presented by a conserved YidC-like fold. Functional analysis reveals selective binding of Mj0480 to ribosomes displaying a stalled YidC substrate, and a direct interaction between the buried hydrophilic surface of Mj0480 and the nascent chain. These data provide direct experimental evidence that the archaeal DUF106 proteins are YidC/Oxa1/Alb3-like insertases of the archaeal plasma membrane.
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Affiliation(s)
- Marta T Borowska
- Department of Biochemistry and Molecular Biology, The University of Chicago, 929 East 57(th) Street, Chicago, IL 60637, USA
| | - Pawel K Dominik
- Department of Biochemistry and Molecular Biology, The University of Chicago, 929 East 57(th) Street, Chicago, IL 60637, USA
| | - S Andrei Anghel
- Department of Biochemistry and Molecular Biology, The University of Chicago, 929 East 57(th) Street, Chicago, IL 60637, USA
| | - Anthony A Kossiakoff
- Department of Biochemistry and Molecular Biology, The University of Chicago, 929 East 57(th) Street, Chicago, IL 60637, USA
| | - Robert J Keenan
- Department of Biochemistry and Molecular Biology, The University of Chicago, 929 East 57(th) Street, Chicago, IL 60637, USA.
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250
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Dumesic PA, Rosenblad MA, Samuelsson T, Nguyen T, Moresco JJ, Yates JR, Madhani HD. Noncanoncial signal recognition particle RNAs in a major eukaryotic phylum revealed by purification of SRP from the human pathogen Cryptococcus neoformans. Nucleic Acids Res 2015; 43:9017-27. [PMID: 26275773 PMCID: PMC4605306 DOI: 10.1093/nar/gkv819] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2015] [Accepted: 08/01/2015] [Indexed: 12/21/2022] Open
Abstract
Despite conservation of the signal recognition particle (SRP) from bacteria to man, computational approaches have failed to identify SRP components from genomes of many lower eukaryotes, raising the possibility that they have been lost or altered in those lineages. We report purification and analysis of SRP in the human pathogen Cryptococcus neoformans, providing the first description of SRP in basidiomycetous yeast. The C. neoformans SRP RNA displays a predicted structure in which the universally conserved helix 8 contains an unprecedented stem-loop insertion. Guided by this sequence, we computationally identified 152 SRP RNAs throughout the phylum Basidiomycota. This analysis revealed additional helix 8 alterations including single and double stem-loop insertions as well as loop diminutions affecting RNA structural elements that are otherwise conserved from bacteria to man. Strikingly, these SRP RNA features in Basidiomycota are accompanied by phylum-specific alterations in the RNA-binding domain of Srp54, the SRP protein subunit that directly interacts with helix 8. Our findings reveal unexpected fungal SRP diversity and suggest coevolution of the two most conserved SRP features-SRP RNA helix 8 and Srp54-in basidiomycetes. Because members of this phylum include important human and plant pathogens, these noncanonical features provide new targets for antifungal compound development.
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Affiliation(s)
- Phillip A Dumesic
- Department of Biochemistry and Biophysics, University of California, San Francisco, CA 94158, USA
| | - Magnus A Rosenblad
- Department of Chemistry and Molecular Biology, University of Gothenburg, Gothenburg, SE-405 30, Sweden
| | - Tore Samuelsson
- Department of Medical Biochemistry and Cell Biology, Institute of Biomedicine, The Sahlgrenska Academy, University of Gothenburg, Gothenburg, SE-405 30, Sweden
| | - Tiffany Nguyen
- Department of Biochemistry and Biophysics, University of California, San Francisco, CA 94158, USA
| | - James J Moresco
- Department of Chemical Physiology, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - John R Yates
- Department of Chemical Physiology, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Hiten D Madhani
- Department of Biochemistry and Biophysics, University of California, San Francisco, CA 94158, USA
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