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Neiman AM. Membrane and organelle rearrangement during ascospore formation in budding yeast. Microbiol Mol Biol Rev 2024; 88:e0001324. [PMID: 38899894 PMCID: PMC11426023 DOI: 10.1128/mmbr.00013-24] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/21/2024] Open
Abstract
SUMMARYIn ascomycete fungi, sexual spores, termed ascospores, are formed after meiosis. Ascospore formation is an unusual cell division in which daughter cells are created within the cytoplasm of the mother cell by de novo generation of membranes that encapsulate each of the haploid chromosome sets created by meiosis. This review describes the molecular events underlying the creation, expansion, and closure of these membranes in the budding yeast, Saccharomyces cerevisiae. Recent advances in our understanding of the regulation of gene expression and the dynamic behavior of different membrane-bound organelles during this process are detailed. While less is known about ascospore formation in other systems, comparison to the distantly related fission yeast suggests that the molecular events will be broadly similar throughout the ascomycetes.
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Affiliation(s)
- Aaron M Neiman
- Department of Biochemistry and Cell Biology, Stony Brook University, Stony Brook, New York, USA
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2
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Prokisch S, Büttner S. Partitioning into ER membrane microdomains impacts autophagic protein turnover during cellular aging. Sci Rep 2024; 14:13653. [PMID: 38871812 DOI: 10.1038/s41598-024-64493-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2023] [Accepted: 06/09/2024] [Indexed: 06/15/2024] Open
Abstract
Eukaryotic membranes are compartmentalized into distinct micro- and nanodomains that rearrange dynamically in response to external and internal cues. This lateral heterogeneity of the lipid bilayer and associated clustering of distinct membrane proteins contribute to the spatial organization of numerous cellular processes. Here, we show that membrane microdomains within the endoplasmic reticulum (ER) of yeast cells are reorganized during metabolic reprogramming and aging. Using biosensors with varying transmembrane domain length to map lipid bilayer thickness, we demonstrate that in young cells, microdomains of increased thickness mainly exist within the nuclear ER, while progressing cellular age drives the formation of numerous microdomains specifically in the cortical ER. Partitioning of biosensors with long transmembrane domains into these microdomains increased protein stability and prevented autophagic removal. In contrast, reporters with short transmembrane domains progressively accumulated at the membrane contact site between the nuclear ER and the vacuole, the so-called nucleus-vacuole junction (NVJ), and were subjected to turnover via selective microautophagy occurring specifically at these sites. Reporters with long transmembrane domains were excluded from the NVJ. Our data reveal age-dependent rearrangement of the lateral organization of the ER and establish transmembrane domain length as a determinant of membrane contact site localization and autophagic degradation.
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Affiliation(s)
- Simon Prokisch
- Department of Molecular Biosciences, The Wenner-Gren Institute, Stockholm University, 10691, Stockholm, Sweden
| | - Sabrina Büttner
- Department of Molecular Biosciences, The Wenner-Gren Institute, Stockholm University, 10691, Stockholm, Sweden.
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3
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Liu D, Yuan H, Chen S, Ferro-Novick S, Novick P. Different ER-plasma membrane tethers play opposing roles in autophagy of the cortical ER. Proc Natl Acad Sci U S A 2024; 121:e2321991121. [PMID: 38838012 PMCID: PMC11181077 DOI: 10.1073/pnas.2321991121] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2023] [Accepted: 05/08/2024] [Indexed: 06/07/2024] Open
Abstract
The endoplasmic reticulum (ER) undergoes degradation by selective macroautophagy (ER-phagy) in response to starvation or the accumulation of misfolded proteins within its lumen. In yeast, actin assembly at sites of contact between the cortical ER (cER) and endocytic pits acts to displace elements of the ER from their association with the plasma membrane (PM) so they can interact with the autophagosome assembly machinery near the vacuole. A collection of proteins tether the cER to the PM. Of these, Scs2/22 and Ist2 are required for cER-phagy, most likely through their roles in lipid transport, while deletion of the tricalbins, TCB1/2/3, bypasses those requirements. An artificial ER-PM tether blocks cER-phagy in both the wild type (WT) and a strain lacking endogenous tethers, supporting the importance of cER displacement from the PM. Scs2 and Ist2 can be cross-linked to the selective cER-phagy receptor, Atg40. The COPII cargo adaptor subunit, Lst1, associates with Atg40 and is required for cER-phagy. This requirement is also bypassed by deletion of the ER-PM tethers, suggesting a role for Lst1 prior to the displacement of the cER from the PM during cER-phagy. Although pexophagy and mitophagy also require actin assembly, deletion of ER-PM tethers does not bypass those requirements. We propose that within the context of rapamycin-induced cER-phagy, Scs2/22, Ist2, and Lst1 promote the local displacement of an element of the cER from the cortex, while Tcb1/2/3 act in opposition, anchoring the cER to the plasma membrane.
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Affiliation(s)
- Dongmei Liu
- Department of Cellular and Molecular Medicine, University of California San Diego, La Jolla, CA92093-0668
| | - Hua Yuan
- Department of Cellular and Molecular Medicine, University of California San Diego, La Jolla, CA92093-0668
| | - Shuliang Chen
- Department of Cellular and Molecular Medicine, University of California San Diego, La Jolla, CA92093-0668
| | - Susan Ferro-Novick
- Department of Cellular and Molecular Medicine, University of California San Diego, La Jolla, CA92093-0668
| | - Peter Novick
- Department of Cellular and Molecular Medicine, University of California San Diego, La Jolla, CA92093-0668
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4
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Reinhard J, Starke L, Klose C, Haberkant P, Hammarén H, Stein F, Klein O, Berhorst C, Stumpf H, Sáenz JP, Hub J, Schuldiner M, Ernst R. MemPrep, a new technology for isolating organellar membranes provides fingerprints of lipid bilayer stress. EMBO J 2024; 43:1653-1685. [PMID: 38491296 PMCID: PMC11021466 DOI: 10.1038/s44318-024-00063-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2022] [Revised: 02/16/2024] [Accepted: 02/26/2024] [Indexed: 03/18/2024] Open
Abstract
Biological membranes have a stunning ability to adapt their composition in response to physiological stress and metabolic challenges. Little is known how such perturbations affect individual organelles in eukaryotic cells. Pioneering work has provided insights into the subcellular distribution of lipids in the yeast Saccharomyces cerevisiae, but the composition of the endoplasmic reticulum (ER) membrane, which also crucially regulates lipid metabolism and the unfolded protein response, remains insufficiently characterized. Here, we describe a method for purifying organelle membranes from yeast, MemPrep. We demonstrate the purity of our ER membrane preparations by proteomics, and document the general utility of MemPrep by isolating vacuolar membranes. Quantitative lipidomics establishes the lipid composition of the ER and the vacuolar membrane. Our findings provide a baseline for studying membrane protein biogenesis and have important implications for understanding the role of lipids in regulating the unfolded protein response (UPR). The combined preparative and analytical MemPrep approach uncovers dynamic remodeling of ER membranes in stressed cells and establishes distinct molecular fingerprints of lipid bilayer stress.
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Affiliation(s)
- John Reinhard
- Saarland University, Medical Biochemistry and Molecular Biology, Homburg, Germany
- Saarland University, Preclinical Center for Molecular Signaling (PZMS), Homburg, Germany
| | - Leonhard Starke
- Saarland University, Theoretical Physics and Center for Biophysics, Saarbrücken, Germany
| | | | - Per Haberkant
- EMBL Heidelberg, Proteomics Core Facility, Heidelberg, Germany
| | | | - Frank Stein
- EMBL Heidelberg, Proteomics Core Facility, Heidelberg, Germany
| | - Ofir Klein
- Weizmann Institute of Science, Department of Molecular Genetics, Rehovot, Israel
| | - Charlotte Berhorst
- Saarland University, Medical Biochemistry and Molecular Biology, Homburg, Germany
- Saarland University, Preclinical Center for Molecular Signaling (PZMS), Homburg, Germany
| | - Heike Stumpf
- Saarland University, Medical Biochemistry and Molecular Biology, Homburg, Germany
- Saarland University, Preclinical Center for Molecular Signaling (PZMS), Homburg, Germany
| | - James P Sáenz
- Technische Universität Dresden, B CUBE, Dresden, Germany
| | - Jochen Hub
- Saarland University, Theoretical Physics and Center for Biophysics, Saarbrücken, Germany
| | - Maya Schuldiner
- Weizmann Institute of Science, Department of Molecular Genetics, Rehovot, Israel
| | - Robert Ernst
- Saarland University, Medical Biochemistry and Molecular Biology, Homburg, Germany.
- Saarland University, Preclinical Center for Molecular Signaling (PZMS), Homburg, Germany.
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5
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Piña F, Yan B, Hu J, Niwa M. Reticulons bind sphingolipids to activate the endoplasmic reticulum cell cycle checkpoint, the ER surveillance pathway. Cell Rep 2023; 42:113403. [PMID: 37979174 DOI: 10.1016/j.celrep.2023.113403] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2021] [Revised: 12/09/2022] [Accepted: 10/23/2023] [Indexed: 11/20/2023] Open
Abstract
The inheritance of a functional endoplasmic reticulum (ER) is ensured by the ER stress surveillance (ERSU) pathway. Here, we made the unexpected discovery that reticulon 1 (Rtn1) and Yop1, well-known ER-curvature-generating proteins, each possess two sphingolipid-binding motifs within their transmembrane domains and that these motifs recognize the ER-stress-induced sphingolipid phytosphingosine (PHS), resulting in an ER inheritance block. Upon binding PHS, Rtn1/Yop1 accumulate on the ER tubule, poised to enter the emerging daughter cell, and cause its misdirection to the bud scars (i.e., previous cell division sites). Amino acid changes in the conserved PHS-binding motifs preclude Rtn1 or Yop1 from binding PHS and diminish their enrichment on the tubular ER, ultimately preventing the ER-stress-induced inheritance block. Conservation of these sphingolipid-binding motifs in human reticulons suggests that sphingolipid binding to Rtn1 and Yop1 represents an evolutionarily conserved mechanism that enables cells to respond to ER stress.
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Affiliation(s)
- Francisco Piña
- Division of Biological Sciences, Molecular Biology Section, University of California, San Diego, NSB#1, Rm. 5328, 9500 Gilman Drive, San Diego, CA 92093-0377, USA
| | - Bing Yan
- Institute of Biophysics, Chinese Academy of Sciences, 15 Datun Road, Rm. 6210, Chaoyang District, Beijing 100101, China
| | - Junjie Hu
- Institute of Biophysics, Chinese Academy of Sciences, 15 Datun Road, Rm. 6210, Chaoyang District, Beijing 100101, China
| | - Maho Niwa
- Division of Biological Sciences, Molecular Biology Section, University of California, San Diego, NSB#1, Rm. 5328, 9500 Gilman Drive, San Diego, CA 92093-0377, USA.
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6
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Esch BM, Walter S, Schmidt O, Fröhlich F. Identification of distinct active pools of yeast serine palmitoyltransferase in sub-compartments of the ER. J Cell Sci 2023; 136:jcs261353. [PMID: 37982431 DOI: 10.1242/jcs.261353] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2023] [Accepted: 11/09/2023] [Indexed: 11/21/2023] Open
Abstract
Sphingolipids (SPs) are one of the three major lipid classes in eukaryotic cells and serve as structural components of the plasma membrane. The rate-limiting step in SP biosynthesis is catalyzed by the serine palmitoyltransferase (SPT). In budding yeast (Saccharomyces cerevisiae), SPT is negatively regulated by the two proteins, Orm1 and Orm2. Regulating SPT activity enables cells to adapt SP metabolism to changing environmental conditions. Therefore, the Orm proteins are phosphorylated by two signaling pathways originating from either the plasma membrane or the lysosome (or vacuole in yeast). Moreover, uptake of exogenous serine is necessary for the regulation of SP biosynthesis, which suggests the existence of differentially regulated SPT pools based on their intracellular localization. However, measuring lipid metabolic enzyme activity in different cellular sub-compartments has been challenging. Combining a nanobody recruitment approach with SP flux analysis, we show that the nuclear endoplasmic reticulum (ER)-localized SPT and the peripheral ER localized SPT pools are differentially active. Thus, our data add another layer to the complex network of SPT regulation. Moreover, combining lipid metabolic enzyme re-localization with flux analysis serves as versatile tool to measure lipid metabolism with subcellular resolution.
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Affiliation(s)
- Bianca M Esch
- Osnabrück University, Department of Biology-Chemistry, Bioanalytical Chemistry Section, Barbarastrasse 13, 49076 Osnabrück, Germany
- Osnabrück University, Center for Cellular Nanoanalytic Osnabrück (CellNanOs), Barbarastrasse 11, 49076 Osnabrück, Germany
| | - Stefan Walter
- Osnabrück University, Center for Cellular Nanoanalytic Osnabrück (CellNanOs), Barbarastrasse 11, 49076 Osnabrück, Germany
| | - Oliver Schmidt
- Institute of Cell Biology, Biocenter Innsbruck, Medical University of Innsbruck, Innrain 80, 6020 Innsbruck, Austria
| | - Florian Fröhlich
- Osnabrück University, Department of Biology-Chemistry, Bioanalytical Chemistry Section, Barbarastrasse 13, 49076 Osnabrück, Germany
- Osnabrück University, Center for Cellular Nanoanalytic Osnabrück (CellNanOs), Barbarastrasse 11, 49076 Osnabrück, Germany
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7
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Canonical and Noncanonical ER Stress-Mediated Autophagy Is a Bite the Bullet in View of Cancer Therapy. Cells 2022; 11:cells11233773. [PMID: 36497032 PMCID: PMC9738281 DOI: 10.3390/cells11233773] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2022] [Revised: 11/20/2022] [Accepted: 11/22/2022] [Indexed: 11/29/2022] Open
Abstract
Cancer cells adapt multiple mechanisms to counter intense stress on their way to growth. Tumor microenvironment stress leads to canonical and noncanonical endoplasmic stress (ER) responses, which mediate autophagy and are engaged during proteotoxic challenges to clear unfolded or misfolded proteins and damaged organelles to mitigate stress. In these conditions, autophagy functions as a cytoprotective mechanism in which malignant tumor cells reuse degraded materials to generate energy under adverse growing conditions. However, cellular protection by autophagy is thought to be complicated, contentious, and context-dependent; the stress response to autophagy is suggested to support tumorigenesis and drug resistance, which must be adequately addressed. This review describes significant findings that suggest accelerated autophagy in cancer, a novel obstacle for anticancer therapy, and discusses the UPR components that have been suggested to be untreatable. Thus, addressing the UPR or noncanonical ER stress components is the most effective approach to suppressing cytoprotective autophagy for better and more effective cancer treatment.
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8
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Castro IG, Shortill SP, Dziurdzik SK, Cadou A, Ganesan S, Valenti R, David Y, Davey M, Mattes C, Thomas FB, Avraham RE, Meyer H, Fadel A, Fenech EJ, Ernst R, Zaremberg V, Levine TP, Stefan C, Conibear E, Schuldiner M. Systematic analysis of membrane contact sites in Saccharomyces cerevisiae uncovers modulators of cellular lipid distribution. eLife 2022; 11:74602. [DOI: 10.7554/elife.74602] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2021] [Accepted: 10/19/2022] [Indexed: 11/11/2022] Open
Abstract
Actively maintained close appositions between organelle membranes, also known as contact sites, enable the efficient transfer of biomolecules between cellular compartments. Several such sites have been described as well as their tethering machineries. Despite these advances we are still far from a comprehensive understanding of the function and regulation of most contact sites. To systematically characterize contact site proteomes, we established a high-throughput screening approach in Saccharomyces cerevisiae based on co-localization imaging. We imaged split fluorescence reporters for six different contact sites, several of which are poorly characterized, on the background of 1165 strains expressing a mCherry-tagged yeast protein that has a cellular punctate distribution (a hallmark of contact sites), under regulation of the strong TEF2 promoter. By scoring both co-localization events and effects on reporter size and abundance, we discovered over 100 new potential contact site residents and effectors in yeast. Focusing on several of the newly identified residents, we identified three homologs of Vps13 and Atg2 that are residents of multiple contact sites. These proteins share their lipid transport domain, thus expanding this family of lipid transporters. Analysis of another candidate, Ypr097w, which we now call Lec1 (Lipid-droplet Ergosterol Cortex 1), revealed that this previously uncharacterized protein dynamically shifts between lipid droplets and the cell cortex, and plays a role in regulation of ergosterol distribution in the cell. Overall, our analysis expands the universe of contact site residents and effectors and creates a rich database to mine for new functions, tethers, and regulators.
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Affiliation(s)
| | - Shawn P Shortill
- Centre for Molecular Medicine and Therapeutics, British Columbia Children’s Hospital Research Institute, University of British Columbia
- Department of Medical Genetics, University of British Columbia
| | - Samantha Katarzyna Dziurdzik
- Centre for Molecular Medicine and Therapeutics, British Columbia Children’s Hospital Research Institute, University of British Columbia
- Department of Medical Genetics, University of British Columbia
| | - Angela Cadou
- Laboratory for Molecular Cell Biology, University College London
| | | | - Rosario Valenti
- Department of Molecular Genetics, Weizmann Institute of Science
| | - Yotam David
- Department of Molecular Genetics, Weizmann Institute of Science
| | - Michael Davey
- Centre for Molecular Medicine and Therapeutics, British Columbia Children’s Hospital Research Institute, University of British Columbia
| | - Carsten Mattes
- Medical Biochemistry and Molecular Biology, PZMS, Medical Faculty, Saarland University
| | - Ffion B Thomas
- Laboratory for Molecular Cell Biology, University College London
| | | | - Hadar Meyer
- Department of Molecular Genetics, Weizmann Institute of Science
| | - Amir Fadel
- Department of Molecular Genetics, Weizmann Institute of Science
| | - Emma J Fenech
- Department of Molecular Genetics, Weizmann Institute of Science
| | - Robert Ernst
- Medical Biochemistry and Molecular Biology, PZMS, Medical Faculty, Saarland University
| | | | - Tim P Levine
- UCL Institute of Ophthalmology, University College London
| | | | - Elizabeth Conibear
- Centre for Molecular Medicine and Therapeutics, British Columbia Children’s Hospital Research Institute, University of British Columbia
- Department of Medical Genetics, University of British Columbia
| | - Maya Schuldiner
- Department of Molecular Genetics, Weizmann Institute of Science
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9
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ER-phagy requires the assembly of actin at sites of contact between the cortical ER and endocytic pits. Proc Natl Acad Sci U S A 2022; 119:2117554119. [PMID: 35101986 PMCID: PMC8833162 DOI: 10.1073/pnas.2117554119] [Citation(s) in RCA: 15] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 12/24/2021] [Indexed: 01/03/2023] Open
Abstract
Portions of the endoplasmic reticulum (ER) are degraded by autophagy (ER-phagy) in response to starvation or the accumulation of misfolded proteins. We show that ER-phagy requires assembly of actin at sites of contact between the edges of ER sheets and endocytic pits on the plasma membrane. Actin assembly may help to bring an element of the ER carrying the selective autophagy receptor Atg40 into the cell interior, where it associates with Atg11, a scaffold needed to recruit components for autophagosome assembly. Understanding the mechanism by which regions of the ER are selected for degradation and sequestered within autophagosomes may help in the development of novel approaches to treat diseases that result from the accumulation of misfolded proteins within the ER. Fragments of the endoplasmic reticulum (ER) are selectively delivered to the lysosome (mammals) or vacuole (yeast) in response to starvation or the accumulation of misfolded proteins through an autophagic process known as ER-phagy. A screen of the Saccharomyces cerevisiae deletion library identified end3Δ as a candidate knockout strain that is defective in ER-phagy during starvation conditions, but not bulk autophagy. We find that loss of End3 and its stable binding partner Pan1, or inhibition of the Arp2/3 complex that is coupled by the End3-Pan1 complex to endocytic pits, blocks the association of the cortical ER autophagy receptor, Atg40, with the autophagosomal assembly scaffold protein Atg11. The membrane contact site module linking the rim of cortical ER sheets and endocytic pits, consisting of Scs2 or Scs22, Osh2 or Osh3, and Myo3 or Myo5, is also needed for ER-phagy. Both Atg40 and Scs2 are concentrated at the edges of ER sheets and can be cross-linked to each other. Our results are consistent with a model in which actin assembly at sites of contact between the cortical ER and endocytic pits contributes to ER sequestration into autophagosomes.
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10
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Spindle Dynamics during Meiotic Development of the Fungus Podospora anserina Requires the Endoplasmic Reticulum-Shaping Protein RTN1. mBio 2021; 12:e0161521. [PMID: 34607459 PMCID: PMC8546617 DOI: 10.1128/mbio.01615-21] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022] Open
Abstract
The endoplasmic reticulum (ER) is an elaborate organelle composed of distinct structural and functional domains. ER structure and dynamics involve membrane-shaping proteins of the reticulon and Yop1/DP1 families, which promote membrane curvature and regulate ER shaping and remodeling. Here, we analyzed the function of the reticulon (RTN1) and Yop1 proteins (YOP1 and YOP2) of the model fungus Podospora anserina and their contribution to sexual development. We found that RTN1 and YOP2 localize to the peripheral ER and are enriched in the dynamic apical ER domains of the polarized growing hyphal region. We discovered that the formation of these domains is diminished in the absence of RTN1 or YOP2 and abolished in the absence of YOP1 and that hyphal growth is moderately reduced when YOP1 is deleted in combination with RTN1 and/or YOP2. In addition, we found that RTN1 associates with the Spitzenkörper. Moreover, RTN1 localization is regulated during meiotic development, where it accumulates at the apex of growing asci (meiocytes) during their differentiation and at their middle region during the subsequent meiotic progression. Furthermore, we discovered that loss of RTN1 affects ascospore (meiotic spore) formation, in a process that does not involve YOP1 or YOP2. Finally, we show that the defects in ascospore formation of rtn1 mutants are associated with defective nuclear segregation and spindle dynamics throughout meiotic development. Our results show that sexual development in P. anserina involves a developmental remodeling of the ER that implicates the reticulon RTN1, which is required for meiotic nucleus segregation.
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11
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Gammons J, Halpage J, Mancarella S. Mapping the Proximity Interaction Network of STIM1 Reveals New Mechanisms of Cytoskeletal Regulation. Cells 2021; 10:2701. [PMID: 34685680 PMCID: PMC8535089 DOI: 10.3390/cells10102701] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2021] [Revised: 10/01/2021] [Accepted: 10/01/2021] [Indexed: 11/16/2022] Open
Abstract
Stromal interaction molecule 1 (STIM1) resides primarily in the sarco/endoplasmic reticulum, where it senses intraluminal Ca2+ levels and activates Orai channels on the plasma membrane to initiate Ca2+ influx. We have previously shown that STIM1 is involved in the dynamic remodeling of the actin cytoskeleton. However, the downstream effectors of STIM1 that lead to cytoskeletal remodeling are not known. The proximity-labeling technique (BioID) can capture weak and transient protein-protein interactions, including proteins that reside in the close vicinity of the bait, but that may not be direct binders. Hence, in the present study, we investigated the STIM1 interactome using the BioID technique. A promiscuous biotin ligase was fused to the cytoplasmic C-terminus of STIM1 and was stably expressed in a mouse embryonic fibroblast (MEF) cell line. Screening of biotinylated proteins identified several high confidence targets. Here, we report Gelsolin (GSN) as a new member of the STIM1 interactome. GSN is a Ca2+-dependent actin-severing protein that promotes actin filament assembly and disassembly. Results were validated using knockdown approaches and immunostaining. We tested our results in neonatal cardiomyocytes where STIM1 overexpression induced altered actin dynamics and cytoskeletal instability. This is the first time that BioID assay was used to investigate the STIM1 interactome. Our work highlights the role of STIM1/GSN in the structure and function of the cytoskeleton.
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Affiliation(s)
| | | | - Salvatore Mancarella
- Health Sciences Center, Department of Physiology, University of Tennessee, Memphis, TN 38163, USA; (J.G.); (J.H.)
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12
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Sun J, Harion R, Naito T, Saheki Y. INPP5K and Atlastin-1 maintain the nonuniform distribution of ER-plasma membrane contacts in neurons. Life Sci Alliance 2021; 4:4/11/e202101092. [PMID: 34556534 PMCID: PMC8507493 DOI: 10.26508/lsa.202101092] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2021] [Revised: 09/03/2021] [Accepted: 09/11/2021] [Indexed: 02/04/2023] Open
Abstract
In neurons, the ER extends throughout all cellular processes, forming multiple contacts with the plasma membrane (PM) to fine-tune neuronal physiology. However, the mechanisms that regulate the distribution of neuronal ER-PM contacts are not known. Here, we used the Caenorhabditis elegans DA9 motor neuron as our model system and found that neuronal ER-PM contacts are enriched in soma and dendrite and mostly absent in axons. Using forward genetic screen, we identified that the inositol 5-phosphatase, CIL-1 (human INPP5K), and the dynamin-like GTPase, ATLN-1 (human Atlastin-1), help to maintain the non-uniform, somatodendritic enrichment of neuronal ER-PM contacts. Mechanistically, CIL-1 acts upstream of ATLN-1 to maintain the balance between ER tubules and sheets. In mutants of CIL-1 or ATLN-1, ER sheets expand and invade into the axon. This is accompanied by the ectopic formation of axonal ER-PM contacts and defects in axon regeneration following laser-induced axotomy. As INPP5K and Atlastin-1 have been linked to neurological disorders, the unique distribution of neuronal ER-PM contacts maintained by these proteins may support neuronal resilience during the onset and progression of these diseases.
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Affiliation(s)
- Jingbo Sun
- Lee Kong Chian School of Medicine, Nanyang Technological University, Singapore
| | - Raihanah Harion
- Lee Kong Chian School of Medicine, Nanyang Technological University, Singapore
| | - Tomoki Naito
- Lee Kong Chian School of Medicine, Nanyang Technological University, Singapore
| | - Yasunori Saheki
- Lee Kong Chian School of Medicine, Nanyang Technological University, Singapore .,Department of Molecular Physiology, Faculty of Life Sciences, Kumamoto University, Kumamoto, Japan
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13
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Parashar S, Chidambaram R, Chen S, Liem CR, Griffis E, Lambert GG, Shaner NC, Wortham M, Hay JC, Ferro-Novick S. Endoplasmic reticulum tubules limit the size of misfolded protein condensates. eLife 2021; 10:e71642. [PMID: 34467852 PMCID: PMC8486381 DOI: 10.7554/elife.71642] [Citation(s) in RCA: 31] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2021] [Accepted: 08/31/2021] [Indexed: 12/19/2022] Open
Abstract
The endoplasmic reticulum (ER) is composed of sheets and tubules. Here we report that the COPII coat subunit, SEC24C, works with the long form of the tubular ER-phagy receptor, RTN3, to target dominant-interfering mutant proinsulin Akita puncta to lysosomes. When the delivery of Akita puncta to lysosomes was disrupted, large puncta accumulated in the ER. Unexpectedly, photobleach analysis indicated that Akita puncta behaved as condensates and not aggregates, as previously suggested. Akita puncta enlarged when either RTN3 or SEC24C were depleted, or when ER sheets were proliferated by either knocking out Lunapark or overexpressing CLIMP63. Other ER-phagy substrates that are segregated into tubules behaved like Akita, while a substrate (type I procollagen) that is degraded by the ER-phagy sheets receptor, FAM134B, did not. Conversely, when ER tubules were augmented in Lunapark knock-out cells by overexpressing reticulons, ER-phagy increased and the number of large Akita puncta was reduced. Our findings imply that segregating cargoes into tubules has two beneficial roles. First, it localizes mutant misfolded proteins, the receptor, and SEC24C to the same ER domain. Second, physically restraining condensates within tubules, before they undergo ER-phagy, prevents them from enlarging and impacting cell health.
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Affiliation(s)
- Smriti Parashar
- Department of Cellular and Molecular Medicine, University of California at San DiegoLa Jolla, CaliforniaUnited States
| | - Ravi Chidambaram
- Department of Cellular and Molecular Medicine, University of California at San DiegoLa Jolla, CaliforniaUnited States
| | - Shuliang Chen
- Department of Cellular and Molecular Medicine, University of California at San DiegoLa Jolla, CaliforniaUnited States
| | - Christina R Liem
- Division of Biological Sciences, University of California at San DiegoLa Jolla, CaliforniaUnited States
| | - Eric Griffis
- Nikon Imaging Center, University of California at San DiegoLa Jolla, CaliforniaUnited States
| | - Gerard G Lambert
- Department of Neurosciences, University of California at San DiegoLa Jolla, CaliforniaUnited States
| | - Nathan C Shaner
- Department of Neurosciences, University of California at San DiegoLa Jolla, CaliforniaUnited States
| | - Matthew Wortham
- Department of Pediatrics, Pediatric Diabetes Research Center, University of California at San DiegoLa Jolla, CaliforniaUnited States
| | - Jesse C Hay
- Division of Biological Sciences and Center for Structural & Functional Neuroscience, University of MontanaMissoulaUnited States
| | - Susan Ferro-Novick
- Department of Cellular and Molecular Medicine, University of California at San DiegoLa Jolla, CaliforniaUnited States
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14
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Tran PTH, Asghar N, Johansson M, Melik W. Roles of the Endogenous Lunapark Protein during Flavivirus Replication. Viruses 2021; 13:v13071198. [PMID: 34206552 PMCID: PMC8310331 DOI: 10.3390/v13071198] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2021] [Revised: 06/08/2021] [Accepted: 06/17/2021] [Indexed: 12/19/2022] Open
Abstract
The endoplasmic reticulum (ER) of eukaryotic cells is a dynamic organelle, which undergoes continuous remodeling. At the three-way tubular junctions of the ER, the lunapark (LNP) protein acts as a membrane remodeling factor to stabilize these highly curved membrane junctions. In addition, during flavivirus infection, the ER membrane is invaginated to form vesicles (Ve) for virus replication. Thus, LNP may have roles in the generation or maintenance of the Ve during flavivirus infection. In this study, our aim was to characterize the functions of LNP during flavivirus infection and investigate the underlying mechanisms of these functions. To specifically study virus replication, we generated cell lines expressing replicons of West Nile virus (Kunjin strain) or Langat virus. By using these replicon platforms and electron microscopy, we showed that depletion of LNP resulted in reduced virus replication, which is due to its role in the generation of the Ve. By using biochemical assays and high-resolution microscopy, we found that LNP is recruited to the Ve and the protein interacts with the nonstructural protein (NS) 4B. Therefore, these data shed new light on the interactions between flavivirus and host factors during viral replication.
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15
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Mioka T, Guo T, Wang S, Tsuji T, Kishimoto T, Fujimoto T, Tanaka K. Characterization of micron-scale protein-depleted plasma membrane domains in phosphatidylserine-deficient yeast cells. J Cell Sci 2021; 135:261783. [PMID: 34000034 DOI: 10.1242/jcs.256529] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2020] [Accepted: 03/16/2021] [Indexed: 12/30/2022] Open
Abstract
Membrane phase separation to form micron-scale domains of lipids and proteins occurs in artificial membranes; however, a similar large-scale phase separation has not been reported in the plasma membrane of the living cells. We show here that a stable micron-scale protein-depleted region is generated in the plasma membrane of yeast mutants lacking phosphatidylserine at high temperatures. We named this region the 'void zone'. Transmembrane proteins and certain peripheral membrane proteins and phospholipids are excluded from the void zone. The void zone is rich in ergosterol, and requires ergosterol and sphingolipids for its formation. Such properties are also found in the cholesterol-enriched domains of phase-separated artificial membranes, but the void zone is a novel membrane domain that requires energy and various cellular functions for its formation. The formation of the void zone indicates that the plasma membrane in living cells has the potential to undergo phase separation with certain lipid compositions. We also found that void zones were frequently in contact with vacuoles, in which a membrane domain was also formed at the contact site.
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Affiliation(s)
- Tetsuo Mioka
- Division of Molecular Interaction, Institute for Genetic Medicine, Hokkaido University Graduate School of Life Science, Sapporo, Hokkaido 060-0815, Japan
| | - Tian Guo
- Division of Molecular Interaction, Institute for Genetic Medicine, Hokkaido University Graduate School of Life Science, Sapporo, Hokkaido 060-0815, Japan
| | - Shiyao Wang
- Division of Molecular Interaction, Institute for Genetic Medicine, Hokkaido University Graduate School of Life Science, Sapporo, Hokkaido 060-0815, Japan
| | - Takuma Tsuji
- Laboratory of Molecular Cell Biology, Research Institute for Diseases of Old Age, Juntendo University Graduate School of Medicine, Tokyo 113-8421, Japan
| | - Takuma Kishimoto
- Division of Molecular Interaction, Institute for Genetic Medicine, Hokkaido University Graduate School of Life Science, Sapporo, Hokkaido 060-0815, Japan
| | - Toyoshi Fujimoto
- Laboratory of Molecular Cell Biology, Research Institute for Diseases of Old Age, Juntendo University Graduate School of Medicine, Tokyo 113-8421, Japan
| | - Kazuma Tanaka
- Division of Molecular Interaction, Institute for Genetic Medicine, Hokkaido University Graduate School of Life Science, Sapporo, Hokkaido 060-0815, Japan
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16
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He Y, Rashan EH, Linke V, Shishkova E, Hebert AS, Jochem A, Westphall MS, Pagliarini DJ, Overmyer KA, Coon JJ. Multi-Omic Single-Shot Technology for Integrated Proteome and Lipidome Analysis. Anal Chem 2021; 93:4217-4222. [PMID: 33617230 PMCID: PMC8028036 DOI: 10.1021/acs.analchem.0c04764] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
Mass spectrometry (MS) serves as the centerpiece technology for proteome, lipidome, and metabolome analysis. To gain a better understanding of the multifaceted networks of myriad regulatory layers in complex organisms, integration of different multiomic layers is increasingly performed, including joint extraction methods of diverse biomolecular classes and comprehensive data analyses of different omics. Despite the versatility of MS systems, fractured methodology drives nearly all MS laboratories to specialize in analysis of a single ome at the exclusion of the others. Although liquid chromatography-mass spectrometry (LC-MS) analysis is similar for different biomolecular classes, the integration on the instrument level is lagging behind. The recent advancements in high flow proteomics enable us to take a first step towards integration of protein and lipid analysis. Here, we describe a technology to achieve broad and deep coverage of multiple molecular classes simultaneously through multi-omic single-shot technology (MOST), requiring only one column, one LC-MS instrument, and a simplified workflow. MOST achieved great robustness and reproducibility. Its application to a Saccharomyces cerevisiae study consisting of 20 conditions revealed 2842 protein groups and 325 lipids and potential molecular relationships.
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Affiliation(s)
- Yuchen He
- Department of Biomolecular Chemistry, University of Wisconsin-Madison, Madison WI 53706, USA
| | - Edrees H. Rashan
- Department of Biochemistry, University of Wisconsin-Madison, Madison WI 53706, USA
| | - Vanessa Linke
- Department of Biomolecular Chemistry, University of Wisconsin-Madison, Madison WI 53706, USA
| | - Evgenia Shishkova
- Department of Biomolecular Chemistry, University of Wisconsin-Madison, Madison WI 53706, USA
| | - Alexander S. Hebert
- Department of Biomolecular Chemistry, University of Wisconsin-Madison, Madison WI 53706, USA
| | - Adam Jochem
- Morgridge Institute for Research, Madison, WI 53715, USA
| | - Michael S. Westphall
- Department of Biomolecular Chemistry, University of Wisconsin-Madison, Madison WI 53706, USA
| | - David J. Pagliarini
- Departments of Cell Biology and Physiology; Biochemistry and Molecular Biophysics; and Genetics, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Katherine A. Overmyer
- Department of Biomolecular Chemistry, University of Wisconsin-Madison, Madison WI 53706, USA
- Morgridge Institute for Research, Madison, WI 53715, USA
| | - Joshua J. Coon
- Department of Biomolecular Chemistry, University of Wisconsin-Madison, Madison WI 53706, USA
- Department of Chemistry, University of Wisconsin-Madison, Madison WI 53706, USA
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17
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Bruno SR, Anathy V. Lung epithelial endoplasmic reticulum and mitochondrial 3D ultrastructure: a new frontier in lung diseases. Histochem Cell Biol 2021; 155:291-300. [PMID: 33598824 PMCID: PMC7889473 DOI: 10.1007/s00418-020-01950-1] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 11/24/2020] [Indexed: 12/15/2022]
Abstract
It has long been appreciated that the endoplasmic reticulum (ER) and mitochondria, organelles important for regular cell function and survival, also play key roles in pathogenesis of various lung diseases, including asthma, fibrosis, and infections. Alterations in processes regulated within these organelles, including but not limited to protein folding in the ER and oxidative phosphorylation in the mitochondria, are important in disease pathogenesis. In recent years it has also become increasingly apparent that organelle structure dictates function. It is now clear that organelles must maintain precise organization and localization for proper function. Newer microscopy capabilities have allowed the scientific community to reveal, via 3D imaging, that the structure of these organelles and their interactions with each other are a main component of regulating function and, therefore, effects on the disease state. In this review, we will examine how 3D imaging through techniques could allow advancements in knowledge of how the ER and mitochondria function and the roles they may play in lung epithelia in progression of lung disease.
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Affiliation(s)
- Sierra R Bruno
- Department of Pathology and Laboratory Medicine, University of Vermont, Larner College of Medicine, 149 Beaumont Ave, Burlington, VT, 05405, USA
| | - Vikas Anathy
- Department of Pathology and Laboratory Medicine, University of Vermont, Larner College of Medicine, 149 Beaumont Ave, Burlington, VT, 05405, USA.
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18
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Kriechbaumer V, Brandizzi F. The plant endoplasmic reticulum: an organized chaos of tubules and sheets with multiple functions. J Microsc 2020; 280:122-133. [PMID: 32426862 PMCID: PMC10895883 DOI: 10.1111/jmi.12909] [Citation(s) in RCA: 22] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2020] [Revised: 05/08/2020] [Accepted: 05/14/2020] [Indexed: 12/14/2022]
Abstract
The endoplasmic reticulum is a fascinating organelle at the core of the secretory pathway. It is responsible for the synthesis of one third of the cellular proteome and, in plant cells, it produces receptors and transporters of hormones as well as the proteins responsible for the biosynthesis of critical components of a cellulosic cell wall. The endoplasmic reticulum structure resembles a spider-web network of interconnected tubules and cisternae that pervades the cell. The study of the dynamics and interaction of this organelles with other cellular structures such as the plasma membrane, the Golgi apparatus and the cytoskeleton, have been permitted by the implementation of fluorescent protein and advanced confocal imaging. In this review, we report on the findings that contributed towards the understanding of the endoplasmic reticulum morphology and function with the aid of fluorescent proteins, focusing on the contributions provided by pioneering work from the lab of the late Professor Chris Hawes.
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Affiliation(s)
- V Kriechbaumer
- Plant Cell Biology, Department of Biological and Medical Sciences, Oxford Brookes University, Oxford, U.K
| | - F Brandizzi
- MSU-DOE Plant Research Laboratory, Department of Plant Biology, Michigan State University, East Lansing, Michigan, U.S.A
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19
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Miyasaka M, Mioka T, Kishimoto T, Itoh E, Tanaka K. A complex genetic interaction implicates that phospholipid asymmetry and phosphate homeostasis regulate Golgi functions. PLoS One 2020; 15:e0236520. [PMID: 32730286 PMCID: PMC7392219 DOI: 10.1371/journal.pone.0236520] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2020] [Accepted: 07/07/2020] [Indexed: 11/24/2022] Open
Abstract
In eukaryotic cells, phospholipid flippases translocate phospholipids from the exoplasmic to the cytoplasmic leaflet of the lipid bilayer. Budding yeast contains five flippases, of which Cdc50p-Drs2p and Neo1p are primarily involved in membrane trafficking in endosomes and Golgi membranes. The ANY1/CFS1 gene was identified as a suppressor of growth defects in the neo1Δ and cdc50Δ mutants. Cfs1p is a membrane protein of the PQ-loop family and is localized to endosomal/Golgi membranes, but its relationship to phospholipid asymmetry remains unknown. The neo1Δ cfs1Δ mutant appears to function normally in membrane trafficking but may function abnormally in the regulation of phospholipid asymmetry. To identify a gene that is functionally relevant to NEO1 and CFS1, we isolated a mutation that is synthetically lethal with neo1Δ cfs1Δ and identified ERD1. Erd1p is a Golgi membrane protein that is involved in the transport of phosphate (Pi) from the Golgi lumen to the cytoplasm. The Neo1p-depleted cfs1Δ erd1Δ mutant accumulated plasma membrane proteins in the Golgi, perhaps due to a lack of phosphatidylinositol 4-phosphate. The Neo1p-depleted cfs1Δ erd1Δ mutant also exhibited abnormal structure of the endoplasmic reticulum (ER) and induced an unfolded protein response, likely due to defects in the retrieval pathway from the cis-Golgi region to the ER. Genetic analyses suggest that accumulation of Pi in the Golgi lumen is responsible for defects in Golgi functions in the Neo1p-depleted cfs1Δ erd1Δ mutant. Thus, the luminal ionic environment is functionally relevant to phospholipid asymmetry. Our results suggest that flippase-mediated phospholipid redistribution and luminal Pi concentration coordinately regulate Golgi membrane functions.
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Affiliation(s)
- Mamoru Miyasaka
- Division of Molecular Interaction, Institute for Genetic Medicine, Hokkaido University Graduate School of Life Science, Sapporo, Hokkaido, Japan
- Department of Gastroenterological Surgery II, Hokkaido University Faculty of Medicine, Sapporo, Hokkaido, Japan
| | - Tetsuo Mioka
- Division of Molecular Interaction, Institute for Genetic Medicine, Hokkaido University Graduate School of Life Science, Sapporo, Hokkaido, Japan
| | - Takuma Kishimoto
- Division of Molecular Interaction, Institute for Genetic Medicine, Hokkaido University Graduate School of Life Science, Sapporo, Hokkaido, Japan
| | - Eriko Itoh
- Division of Molecular Interaction, Institute for Genetic Medicine, Hokkaido University Graduate School of Life Science, Sapporo, Hokkaido, Japan
| | - Kazuma Tanaka
- Division of Molecular Interaction, Institute for Genetic Medicine, Hokkaido University Graduate School of Life Science, Sapporo, Hokkaido, Japan
- * E-mail:
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20
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Merech F, Soczewski E, Hauk V, Paparini D, Ramhorst R, Vota D, Pérez Leirós C. Vasoactive Intestinal Peptide induces glucose and neutral amino acid uptake through mTOR signalling in human cytotrophoblast cells. Sci Rep 2019; 9:17152. [PMID: 31748639 PMCID: PMC6868285 DOI: 10.1038/s41598-019-53676-3] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2019] [Accepted: 10/31/2019] [Indexed: 11/21/2022] Open
Abstract
The transport of nutrients across the placenta involves trophoblast cell specific transporters modulated through the mammalian target of rapamycin (mTOR). The vasoactive intestinal peptide (VIP) has embryotrophic effects in mice and regulates human cytotrophoblast cell migration and invasion. Here we explored the effect of VIP on glucose and System A amino acid uptake by human trophoblast-derived cells (Swan 71 and BeWo cell lines). VIP activated D-glucose specific uptake in single cytotrophoblast cells in a concentration-dependent manner through PKA, MAPK, PI3K and mTOR signalling pathways. Glucose uptake was reduced in VIP-knocked down cytotrophoblast cells. Also, VIP stimulated System A amino acid uptake and the expression of GLUT1 glucose transporter and SNAT1 neutral amino acid transporter. VIP increased mTOR expression and mTOR/S6 phosphorylation whereas VIP silencing reduced mTOR mRNA and protein expression. Inhibition of mTOR signalling with rapamycin reduced the expression of endogenous VIP and of VIP-induced S6 phosphorylation. Our findings support a role of VIP in the transport of glucose and neutral amino acids in cytotrophoblast cells through mTOR-regulated pathways and they are instrumental for understanding the physiological regulation of nutrient sensing by endogenous VIP at the maternal-foetal interface.
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Affiliation(s)
- Fatima Merech
- CONICET - Universidad de Buenos Aires. Instituto de Química Biológica de la Facultad de Ciencias Exactas y Naturales (IQUIBICEN), Buenos Aires, Argentina
| | - Elizabeth Soczewski
- CONICET - Universidad de Buenos Aires. Instituto de Química Biológica de la Facultad de Ciencias Exactas y Naturales (IQUIBICEN), Buenos Aires, Argentina
| | - Vanesa Hauk
- CONICET - Universidad de Buenos Aires. Instituto de Química Biológica de la Facultad de Ciencias Exactas y Naturales (IQUIBICEN), Buenos Aires, Argentina
| | - Daniel Paparini
- CONICET - Universidad de Buenos Aires. Instituto de Química Biológica de la Facultad de Ciencias Exactas y Naturales (IQUIBICEN), Buenos Aires, Argentina
| | - Rosanna Ramhorst
- CONICET - Universidad de Buenos Aires. Instituto de Química Biológica de la Facultad de Ciencias Exactas y Naturales (IQUIBICEN), Buenos Aires, Argentina
| | - Daiana Vota
- CONICET - Universidad de Buenos Aires. Instituto de Química Biológica de la Facultad de Ciencias Exactas y Naturales (IQUIBICEN), Buenos Aires, Argentina
| | - Claudia Pérez Leirós
- CONICET - Universidad de Buenos Aires. Instituto de Química Biológica de la Facultad de Ciencias Exactas y Naturales (IQUIBICEN), Buenos Aires, Argentina.
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21
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Napoli B, Gumeni S, Forgiarini A, Fantin M, De Filippis C, Panzeri E, Vantaggiato C, Orso G. Naringenin Ameliorates Drosophila ReepA Hereditary Spastic Paraplegia-Linked Phenotypes. Front Neurosci 2019; 13:1202. [PMID: 31803000 PMCID: PMC6877660 DOI: 10.3389/fnins.2019.01202] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2019] [Accepted: 10/23/2019] [Indexed: 12/11/2022] Open
Abstract
Defects in the endoplasmic reticulum (ER) membrane shaping and interaction with other organelles seem to be a crucial mechanism underlying Hereditary Spastic Paraplegia (HSP) neurodegeneration. REEP1, a transmembrane protein belonging to TB2/HVA22 family, is implicated in SPG31, an autosomal dominant form of HSP, and its interaction with Atlastin/SPG3A and Spastin/SPG4, the other two major HSP linked proteins, has been demonstrated to play a crucial role in modifying ER architecture. In addition, the Drosophila ortholog of REEP1, named ReepA, has been found to regulate the response to ER neuronal stress. Herein we investigated the role of ReepA in ER morphology and stress response. ReepA is upregulated under stress conditions and aging. Our data show that ReepA triggers a selective activation of Ire1 and Atf6 branches of Unfolded Protein Response (UPR) and modifies ER morphology. Drosophila lacking ReepA showed Atf6 and Ire1 activation, expansion of ER sheet-like structures, locomotor dysfunction and shortened lifespan. Furthermore, we found that naringenin, a flavonoid that possesses strong antioxidant and neuroprotective activity, can rescue the cellular phenotypes, the lifespan and locomotor disability associated with ReepA loss of function. Our data highlight the importance of ER homeostasis in nervous system functionality and HSP neurodegenerative mechanisms, opening new opportunities for HSP treatment.
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Affiliation(s)
- Barbara Napoli
- Scientific Institute, IRCCS Eugenio Medea, Laboratory of Molecular Biology, Bosisio Parini, Lecco, Italy
| | - Sentiljana Gumeni
- Department of Cell Biology and Biophysics, Faculty of Biology, National and Kapodistrian University of Athens, Athens, Greece
| | - Alessia Forgiarini
- Department of Pharmaceutical and Pharmacological Sciences, University of Padova, Padova, Italy
| | - Marianna Fantin
- Scientific Institute, IRCCS Eugenio Medea, Laboratory of Molecular Biology, Bosisio Parini, Lecco, Italy
| | - Concetta De Filippis
- Foundation Institute of Pediatric Research, “Città della Speranza”, Padova, Italy
| | - Elena Panzeri
- Scientific Institute, IRCCS Eugenio Medea, Laboratory of Molecular Biology, Bosisio Parini, Lecco, Italy
| | - Chiara Vantaggiato
- Scientific Institute, IRCCS Eugenio Medea, Laboratory of Molecular Biology, Bosisio Parini, Lecco, Italy
| | - Genny Orso
- Department of Pharmaceutical and Pharmacological Sciences, University of Padova, Padova, Italy
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22
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Kurokawa K, Nakano A. The ER exit sites are specialized ER zones for the transport of cargo proteins from the ER to the Golgi apparatus. J Biochem 2019; 165:109-114. [PMID: 30304445 DOI: 10.1093/jb/mvy080] [Citation(s) in RCA: 41] [Impact Index Per Article: 8.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2018] [Accepted: 10/05/2018] [Indexed: 12/29/2022] Open
Abstract
The endoplasmic reticulum (ER) is a multifunctional organelle, including secretory protein biogenesis, lipid synthesis, drug metabolism, Ca2+ signalling and so on. Since the ER is a single continuous membrane structure, it includes distinct zones responsible for its different functions. The export of newly synthesized proteins from the ER is facilitated via coat protein complex II (COPII)-coated vesicles, which form in specialized zones within the ER, called the ER exit sites (ERES) or transitional ER. In this review, we highlight recent advances in our understanding of the structural organization of ERES, the correlation between the ERES and Golgi organization, and the faithful cargo transport mechanism from the ERES to the Golgi.
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Affiliation(s)
- Kazuo Kurokawa
- Live Cell Super-Resolution Imaging Research Team, RIKEN Center for Advanced Photonics, 2-1 Hirosawa, Wako, Saitama 351-0198, Japan
| | - Akihiko Nakano
- Live Cell Super-Resolution Imaging Research Team, RIKEN Center for Advanced Photonics, 2-1 Hirosawa, Wako, Saitama 351-0198, Japan
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23
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Xie L, Song XJ, Liao ZF, Wu B, Yang J, Zhang H, Hong J. Endoplasmic reticulum remodeling induced by Wheat yellow mosaic virus infection studied by transmission electron microscopy. Micron 2019; 120:80-90. [PMID: 30807983 DOI: 10.1016/j.micron.2019.01.007] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2018] [Revised: 01/16/2019] [Accepted: 01/22/2019] [Indexed: 11/28/2022]
Abstract
Plant virus was a kind of organism lived depending on infecting viable host cell and propagated their posterity by replicating its hereditary nucleotide, transcripting into protein, assembling protein and nucleotide into virion (Ortín and Parra, 2006; Sanfaçon, 2005). Viral infection usually induces remodeling of host cell, especially endoplasmic reticulum (ER) for generating membrane packed viral factory. During the infection of Bymovirus, a kind of membranous body (MB) was generated in host cells, which is thought as an ER aggregate. In present study we performed a study on Wheat yellow mosaic virus (WYMV) induced MB by several transmission electron microscopy (TEM) based methods, including cytological observation, component analysis by immuno-gold labeling and structural analysis by electron tomography (ET). WYMV infection induced at least two morphologies of MB, including the lamella dominated morphology (lamella-MB) looked like sprawling cirrus, and the tubule dominated morphology (tubule-MB) looked like latticed network. MB was verified composing of ER as revealed by immuno-gold labeling by antibody against endoplasmic reticulum (ER) retention signal as well as by detailed observation of MB construction modules as double layer membrane. By immuno-gold labeling, both two MB morphologies (lamella-MB and tubule-MB) had same components in viral derived protein and membrane origination (from ER). Structural analysis by ET reconstruction revealed the organization of ER in MB. Lamella-MB was composed of cesER like structures arranged irregularly whereas tubule-MB was composed of tubER like structures arranged regularly. This study provided insights into the structural details in how Bymovirus utilizing host membrane system.
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Affiliation(s)
- Li Xie
- Analysis Center of Agrobiology and Environmental Sciences, Zhejiang University, Hangzhou 310058, China.
| | - Xi-Jiao Song
- State Key Laboratory Breeding Base for Zhejiang Sustainable Pest and Disease Control, Ministry of Agriculture Key Laboratory of Biotechnology in Plant Protection, Zhejiang Provincial Key Laboratory of Plant Virology, Institute of Virology and Biotechnology, Zhejiang Academy of Agricultural Sciences, Hangzhou 310021, China.
| | - Zhen-Feng Liao
- State Key Laboratory Breeding Base for Zhejiang Sustainable Pest and Disease Control, Ministry of Agriculture Key Laboratory of Biotechnology in Plant Protection, Zhejiang Provincial Key Laboratory of Plant Virology, Institute of Virology and Biotechnology, Zhejiang Academy of Agricultural Sciences, Hangzhou 310021, China.
| | - Bin Wu
- Institute of plant protection, Shandong Academy of Agricultural Sciences, Jinan 250100, China.
| | - Jian Yang
- State Key Laboratory Breeding Base for Zhejiang Sustainable Pest and Disease Control, Ministry of Agriculture Key Laboratory of Biotechnology in Plant Protection, Zhejiang Provincial Key Laboratory of Plant Virology, Institute of Virology and Biotechnology, Zhejiang Academy of Agricultural Sciences, Hangzhou 310021, China.
| | - Hengmu Zhang
- State Key Laboratory Breeding Base for Zhejiang Sustainable Pest and Disease Control, Ministry of Agriculture Key Laboratory of Biotechnology in Plant Protection, Zhejiang Provincial Key Laboratory of Plant Virology, Institute of Virology and Biotechnology, Zhejiang Academy of Agricultural Sciences, Hangzhou 310021, China.
| | - Jian Hong
- Analysis Center of Agrobiology and Environmental Sciences, Zhejiang University, Hangzhou 310058, China.
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24
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Avci D, Malchus NS, Heidasch R, Lorenz H, Richter K, Neßling M, Lemberg MK. The intramembrane protease SPP impacts morphology of the endoplasmic reticulum by triggering degradation of morphogenic proteins. J Biol Chem 2018; 294:2786-2800. [PMID: 30578301 DOI: 10.1074/jbc.ra118.005642] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2018] [Revised: 12/12/2018] [Indexed: 11/06/2022] Open
Abstract
The endoplasmic reticulum (ER), as a multifunctional organelle, plays crucial roles in lipid biosynthesis and calcium homeostasis as well as the synthesis and folding of secretory and membrane proteins. Therefore, it is of high importance to maintain ER homeostasis and to adapt ER function and morphology to cellular needs. Here, we show that signal peptide peptidase (SPP) modulates the ER shape through degradation of morphogenic proteins. Elevating SPP activity induces rapid rearrangement of the ER and formation of dynamic ER clusters. Inhibition of SPP activity rescues the phenotype without the need for new protein synthesis, and this rescue depends on a pre-existing pool of proteins in the Golgi. With the help of organelle proteomics, we identified certain membrane proteins to be diminished upon SPP expression and further show that the observed morphology changes depend on SPP-mediated cleavage of ER morphogenic proteins, including the SNARE protein syntaxin-18. Thus, we suggest that SPP-mediated protein abundance control by a regulatory branch of ER-associated degradation (ERAD-R) has a role in shaping the early secretory pathway.
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Affiliation(s)
- Dönem Avci
- From the Centre for Molecular Biology of Heidelberg University (ZMBH), DKFZ-ZMBH Alliance, 69120 Heidelberg, Germany and
| | - Nicole S Malchus
- From the Centre for Molecular Biology of Heidelberg University (ZMBH), DKFZ-ZMBH Alliance, 69120 Heidelberg, Germany and
| | - Ronny Heidasch
- From the Centre for Molecular Biology of Heidelberg University (ZMBH), DKFZ-ZMBH Alliance, 69120 Heidelberg, Germany and
| | - Holger Lorenz
- From the Centre for Molecular Biology of Heidelberg University (ZMBH), DKFZ-ZMBH Alliance, 69120 Heidelberg, Germany and
| | - Karsten Richter
- German Cancer Research Center (DKFZ), Central Unit Electron Microscopy, 69120 Heidelberg, Germany
| | - Michelle Neßling
- German Cancer Research Center (DKFZ), Central Unit Electron Microscopy, 69120 Heidelberg, Germany
| | - Marius K Lemberg
- From the Centre for Molecular Biology of Heidelberg University (ZMBH), DKFZ-ZMBH Alliance, 69120 Heidelberg, Germany and
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25
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Kriechbaumer V, Breeze E, Pain C, Tolmie F, Frigerio L, Hawes C. Arabidopsis Lunapark proteins are involved in ER cisternae formation. THE NEW PHYTOLOGIST 2018; 219:990-1004. [PMID: 29797722 PMCID: PMC6055799 DOI: 10.1111/nph.15228] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/26/2018] [Accepted: 04/17/2018] [Indexed: 05/04/2023]
Abstract
The plant endoplasmic reticulum (ER) is crucial to the maintenance of cellular homeostasis. The ER consists of a dynamic and continuously remodelling network of tubules and cisternae. Several conserved membrane proteins have been implicated in formation and maintenance of the ER network in plants, such as RHD3 and the reticulon proteins. Despite the recent work in mammalian and yeast cells, the detailed molecular mechanisms of ER network organization in plants remain largely unknown. Recently, novel ER network-shaping proteins called Lunapark (LNP) have been identified in yeast and mammalian cells. Here we identify two Arabidopsis LNP homologues and investigate their subcellular localization via confocal microscopy and potential function in shaping the ER network using protein-protein interaction assays and mutant analysis. We show that AtLNP1 overexpression in tobacco leaf epidermal cells mainly labels cisternae in the ER network, whereas AtLNP2 labels the whole ER. Overexpression of LNP proteins results in an increased abundance of ER cisternae and lnp1 and lnp1lnp2 amiRNA lines display a reduction in cisternae and larger polygonal areas. Thus, we hypothesize that AtLNP1 and AtLNP2 are involved in determining the network morphology of the plant ER, possibly by regulating the formation of ER cisternae.
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Affiliation(s)
- Verena Kriechbaumer
- Plant Cell Biology, Biological and Medical SciencesOxford Brookes UniversityOxfordOX3 0BPUK
| | - Emily Breeze
- School of Life SciencesUniversity of WarwickGibbet HillCoventryCV4 7ALUK
| | - Charlotte Pain
- Plant Cell Biology, Biological and Medical SciencesOxford Brookes UniversityOxfordOX3 0BPUK
| | - Frances Tolmie
- Plant Cell Biology, Biological and Medical SciencesOxford Brookes UniversityOxfordOX3 0BPUK
| | - Lorenzo Frigerio
- School of Life SciencesUniversity of WarwickGibbet HillCoventryCV4 7ALUK
| | - Chris Hawes
- Plant Cell Biology, Biological and Medical SciencesOxford Brookes UniversityOxfordOX3 0BPUK
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Chen S, Cui Y, Parashar S, Novick PJ, Ferro-Novick S. ER-phagy requires Lnp1, a protein that stabilizes rearrangements of the ER network. Proc Natl Acad Sci U S A 2018; 115:E6237-E6244. [PMID: 29915089 PMCID: PMC6142256 DOI: 10.1073/pnas.1805032115] [Citation(s) in RCA: 38] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
The endoplasmic reticulum (ER) forms a contiguous network of tubules and sheets that is predominantly associated with the cell cortex in yeast. Upon treatment with rapamycin, the ER undergoes degradation by selective autophagy. This process, termed ER-phagy, requires Atg40, a selective autophagy receptor that localizes to the cortical ER. Here we report that ER-phagy also requires Lnp1, an ER membrane protein that normally resides at the three-way junctions of the ER network, where it serves to stabilize the network as it is continually remodeled. Rapamycin treatment increases the expression of Atg40, driving ER domains marked by Atg40 puncta to associate with Atg11, a scaffold protein needed to form autophagosomes. Although Atg40 largely localizes to the cortical ER, the autophagy machinery resides in the cell interior. The localization of Atg40 to sites of autophagosome formation is blocked in an lnp1Δ mutant or upon treatment of wild-type cells with the actin-depolymerizing drug Latrunculin A. This prevents the association of Atg40 with Atg11 and the packaging of the ER into autophagosomes. We propose that Lnp1 is needed to stabilize the actin-dependent remodeling of the ER that is essential for ER-phagy.
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Affiliation(s)
- Shuliang Chen
- Department of Cellular and Molecular Medicine, University of California, San Diego, La Jolla, CA 92093-0668
| | - Yixian Cui
- Department of Cellular and Molecular Medicine, University of California, San Diego, La Jolla, CA 92093-0668
| | - Smriti Parashar
- Department of Cellular and Molecular Medicine, University of California, San Diego, La Jolla, CA 92093-0668
| | - Peter J Novick
- Department of Cellular and Molecular Medicine, University of California, San Diego, La Jolla, CA 92093-0668
| | - Susan Ferro-Novick
- Department of Cellular and Molecular Medicine, University of California, San Diego, La Jolla, CA 92093-0668
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27
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Ahmed R, Kodgire S, Santhakumari B, Patil R, Kulkarni M, Zore G. Serum responsive proteome reveals correlation between oxidative phosphorylation and morphogenesis in Candida albicans ATCC10231. J Proteomics 2018; 185:25-38. [PMID: 29959084 DOI: 10.1016/j.jprot.2018.06.018] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2018] [Revised: 06/05/2018] [Accepted: 06/18/2018] [Indexed: 12/17/2022]
Abstract
To understand the impact of fetal bovine serum (FBS) on metabolism and cellular architecture in addition to morphogenesis, we have identified FBS responsive proteome of Candida albicans. FBS induced 34% hyphae and 60% pseudohyphae in C. albicans at 30 °C while 98% hyphae at 37 °C. LC-MS/MS analysis revealed that 285 proteins modulated significantly in response to FBS at 30 °C and 37 °C. Out of which 152 were upregulated and 62 were downregulated at 30 °C while 18 were up and 53 were downregulated at 37 °C. Functional annotation suggests that FBS may inhibit glycolysis and fermentative pathway and enhance oxidative phosphorylation (OxPhos), TCA cycle, amino acid and fatty acid metabolism indicating a use of alternative energy source by C. albicans. OxPhos inhibition assay using sodium azide corroborated the correlation between inhibition of glycolysis and enhanced OxPhos with pseudohyphae formation. C. albicans induced hyphae in response to FBS irrespective of down regulation of Ras1,Asr1/Asr2, indicates the possible involvement of MAPK and cAMP-PKA independent pathway. The Cell wall of cells grown in presence of FBS at 30 °C was rich in mannan, Beta 1,3-glucan and chitin while membranes were rich in ergosterol compared to those grown at 37 °C. SIGNIFICANCE OF THE STUDY This is the first study suggesting a correlation between OxPhos and morphogenesis especially pseudohyphae formation in C. albicans. Our data also indicate that fetal bovine serum (FBS) induced morphogenesis is multifactorial and may involve MAPK and cAMP-PKA independent pathway. In addition to morphogenesis, our study provides an insight in to the modulation of metabolism and cellular architecture of C. albicans in response to FBS.
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Affiliation(s)
- Radfan Ahmed
- School of Life Sciences, Swami Ramanand Teerth Marathwada University, Nanded 431606, MS, India
| | - Santosh Kodgire
- School of Life Sciences, Swami Ramanand Teerth Marathwada University, Nanded 431606, MS, India
| | - B Santhakumari
- CSIR-National Chemical Laboratory, Dr. Homi Bhabha Road, Pune 411008, MS, India.
| | - Rajendra Patil
- Department of Biotechnology, Savitribai Phule Pune University, Ganeshkhind, Pune 411007, MS, India.
| | - Mahesh Kulkarni
- CSIR-National Chemical Laboratory, Dr. Homi Bhabha Road, Pune 411008, MS, India.
| | - Gajanan Zore
- School of Life Sciences, Swami Ramanand Teerth Marathwada University, Nanded 431606, MS, India.
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28
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Suda Y, Kurokawa K, Nakano A. Regulation of ER-Golgi Transport Dynamics by GTPases in Budding Yeast. Front Cell Dev Biol 2018; 5:122. [PMID: 29473037 PMCID: PMC5810278 DOI: 10.3389/fcell.2017.00122] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2017] [Accepted: 12/28/2017] [Indexed: 01/21/2023] Open
Abstract
A large number of proteins are synthesized de novo in the endoplasmic reticulum (ER). They are transported through the Golgi apparatus and then delivered to their proper destinations. The ER and the Golgi play a central role in protein processing and sorting and show dynamic features in their forms. Ras super family small GTPases mediate the protein transport through and between these organelles. The ER-localized GTPase, Sar1, facilitates the formation of COPII transport carriers at the ER exit sites (ERES) on the ER for the transport of cargo proteins from the ER to the Golgi. The Golgi-localized GTPase, Arf1, controls intra-Golgi, and Golgi-to-ER transport of cargo proteins by the formation of COPI carriers. Rab GTPases localized at the Golgi, which are responsible for fusion of membranes, are thought to establish the identities of compartments. Recent evidence suggests that these small GTPases regulate not only discrete sites for generation/fusion of transport carriers, but also membrane dynamics of the organelles where they locate to ensure the integrity of transport. Here we summarize the current understandings about the membrane traffic between these organelles and highlight the cutting-edge advances from super-resolution live imaging of budding yeast, Saccharomyces cerevisiae.
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Affiliation(s)
- Yasuyuki Suda
- Live Cell Super-Resolution Imaging Research Team, RIKEN Center for Advanced Photonics, Saitama, Japan.,Laboratory of Molecular Cell Biology, Faculty of Medicine, University of Tsukuba, Tsukuba, Japan
| | - Kazuo Kurokawa
- Live Cell Super-Resolution Imaging Research Team, RIKEN Center for Advanced Photonics, Saitama, Japan
| | - Akihiko Nakano
- Live Cell Super-Resolution Imaging Research Team, RIKEN Center for Advanced Photonics, Saitama, Japan.,Department of Biological Sciences, Graduate School of Science, The University of Tokyo, Tokyo, Japan
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29
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Jin X, Cao X, Wang X, Jiang J, Wan J, Laliberté JF, Zhang Y. Three-Dimensional Architecture and Biogenesis of Membrane Structures Associated with Plant Virus Replication. FRONTIERS IN PLANT SCIENCE 2018; 9:57. [PMID: 29441085 PMCID: PMC5797596 DOI: 10.3389/fpls.2018.00057] [Citation(s) in RCA: 37] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/03/2017] [Accepted: 01/11/2018] [Indexed: 05/20/2023]
Abstract
Positive-sense (+) RNA viruses represent the most abundant group of viruses and are dependent on the host cell machinery to replicate. One remarkable feature that occurs after (+) RNA virus entry into cells is the remodeling of host endomembranes, leading to the formation of viral replication factories. Recently, rapid progress in three-dimensional (3D) imaging technologies, such as electron tomography (ET) and focused ion beam-scanning electron microscopy (FIB-SEM), has enabled researchers to visualize the novel membrane structures induced by viruses at high resolution. These 3D imaging technologies provide new mechanistic insights into the viral infection cycle. In this review, we summarize the latest reports on the cellular remodeling that occurs during plant virus infection; in particular, we focus on studies that provide 3D architectural information on viral replication factories. We also outline the mechanisms underlying the formation of these membranous structures and discuss possible future research directions.
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Affiliation(s)
- Xuejiao Jin
- State Key Laboratory of Agro-Biotechnology and Ministry of Agriculture Key Laboratory of Soil Microbiology, College of Biological Sciences, China Agricultural University, Beijing, China
| | - Xiuling Cao
- State Key Laboratory of Agro-Biotechnology and Ministry of Agriculture Key Laboratory of Soil Microbiology, College of Biological Sciences, China Agricultural University, Beijing, China
| | - Xueting Wang
- State Key Laboratory of Agro-Biotechnology and Ministry of Agriculture Key Laboratory of Soil Microbiology, College of Biological Sciences, China Agricultural University, Beijing, China
| | - Jun Jiang
- Institut National de la Recherche Scientifique—Institut Armand-Frappier, Laval, QC, Canada
| | - Juan Wan
- Institut National de la Recherche Scientifique—Institut Armand-Frappier, Laval, QC, Canada
| | - Jean-François Laliberté
- Institut National de la Recherche Scientifique—Institut Armand-Frappier, Laval, QC, Canada
- *Correspondence: Jean-François Laliberté
| | - Yongliang Zhang
- State Key Laboratory of Agro-Biotechnology and Ministry of Agriculture Key Laboratory of Soil Microbiology, College of Biological Sciences, China Agricultural University, Beijing, China
- Yongliang Zhang
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30
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Encinar Del Dedo J, Idrissi FZ, Fernandez-Golbano IM, Garcia P, Rebollo E, Krzyzanowski MK, Grötsch H, Geli MI. ORP-Mediated ER Contact with Endocytic Sites Facilitates Actin Polymerization. Dev Cell 2017; 43:588-602.e6. [PMID: 29173820 DOI: 10.1016/j.devcel.2017.10.031] [Citation(s) in RCA: 34] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2016] [Revised: 09/11/2017] [Accepted: 10/27/2017] [Indexed: 11/18/2022]
Abstract
Oxysterol binding protein-related proteins (ORPs) are conserved lipid binding polypeptides, enriched at ER contacts sites. ORPs promote non-vesicular lipid transport and work as lipid sensors in the context of many cellular tasks, but the determinants of their distinct localization and function are not understood. Here, we demonstrate that the yeast endocytic invaginations associate with the ER and that this association specifically requires the ORPs Osh2 and Osh3, which bridge the endocytic myosin-I Myo5 to the ER integral-membrane VAMP-associated protein (VAP) Scs2. Disruption of the ER contact with endocytic sites using ORP, VAP, myosin-I, or reticulon mutants delays and weakens actin polymerization and interferes with vesicle scission. Finally, we provide evidence suggesting that ORP-dependent sterol transfer facilitates actin polymerization at endocytic sites.
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Affiliation(s)
- Javier Encinar Del Dedo
- Institute for Molecular Biology of Barcelona (CSIC), Baldiri Reixac 15, 08028 Barcelona, Spain
| | - Fatima-Zahra Idrissi
- Institute for Molecular Biology of Barcelona (CSIC), Baldiri Reixac 15, 08028 Barcelona, Spain
| | | | - Patricia Garcia
- Institute for Molecular Biology of Barcelona (CSIC), Baldiri Reixac 15, 08028 Barcelona, Spain
| | - Elena Rebollo
- Institute for Molecular Biology of Barcelona (CSIC), Baldiri Reixac 15, 08028 Barcelona, Spain
| | - Marek K Krzyzanowski
- Institute for Molecular Biology of Barcelona (CSIC), Baldiri Reixac 15, 08028 Barcelona, Spain
| | - Helga Grötsch
- Institute for Molecular Biology of Barcelona (CSIC), Baldiri Reixac 15, 08028 Barcelona, Spain
| | - Maria Isabel Geli
- Institute for Molecular Biology of Barcelona (CSIC), Baldiri Reixac 15, 08028 Barcelona, Spain.
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31
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Association of genetic variations in RTN4 3′-UTR with risk for clear cell renal cell carcinoma. Fam Cancer 2017; 17:129-134. [DOI: 10.1007/s10689-017-0005-y] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
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32
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Mast FD, Jamakhandi A, Saleem RA, Dilworth DJ, Rogers RS, Rachubinski RA, Aitchison JD. Peroxins Pex30 and Pex29 Dynamically Associate with Reticulons to Regulate Peroxisome Biogenesis from the Endoplasmic Reticulum. J Biol Chem 2016; 291:15408-27. [PMID: 27129769 DOI: 10.1074/jbc.m116.728154] [Citation(s) in RCA: 38] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2016] [Indexed: 12/11/2022] Open
Abstract
Peroxisome proliferation occurs by at least two routes, division of existing peroxisomes and de novo biogenesis from the endoplasmic reticulum (ER). The proteins and molecular mechanisms governing peroxisome emergence from the ER are poorly characterized. In this study, we report that two integral membrane peroxins (proteins required for peroxisome biogenesis) in Saccharomyces cerevisiae, Pex29 and Pex30, reside in distinct regions of the ER and associate with Rtn1 and Yop1, reticulon family members that contribute to ER morphology, to govern peroxisome emergence from the ER. In vivo and in vitro analyses reveal that peroxisome proliferation is therefore not restricted to the peroxisome but begins at the level of the ER.
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Affiliation(s)
- Fred D Mast
- From the Center for Infectious Disease Research and Institute for Systems Biology, Seattle, Washington 98109 and
| | - Arvind Jamakhandi
- From the Center for Infectious Disease Research and Institute for Systems Biology, Seattle, Washington 98109 and
| | - Ramsey A Saleem
- From the Center for Infectious Disease Research and Institute for Systems Biology, Seattle, Washington 98109 and
| | - David J Dilworth
- From the Center for Infectious Disease Research and Institute for Systems Biology, Seattle, Washington 98109 and
| | - Richard S Rogers
- From the Center for Infectious Disease Research and Institute for Systems Biology, Seattle, Washington 98109 and
| | - Richard A Rachubinski
- the Department of Cell Biology, University of Alberta, Edmonton, Alberta T6G 2H7, Canada
| | - John D Aitchison
- From the Center for Infectious Disease Research and Institute for Systems Biology, Seattle, Washington 98109 and
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33
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Piña FJ, Fleming T, Pogliano K, Niwa M. Reticulons Regulate the ER Inheritance Block during ER Stress. Dev Cell 2016; 37:279-88. [PMID: 27117666 DOI: 10.1016/j.devcel.2016.03.025] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2015] [Revised: 03/07/2016] [Accepted: 03/28/2016] [Indexed: 01/05/2023]
Abstract
Segregation of functional organelles during the cell cycle is crucial to generate healthy daughter cells. In Saccharomyces cerevisiae, ER stress causes an ER inheritance block to ensure cells inherit a functional ER. Here, we report that formation of tubular ER in the mother cell, the first step in ER inheritance, depends on functional symmetry between the cortical ER (cER) and perinuclear ER (pnER). ER stress induces functional asymmetry, blocking tubular ER formation and ER inheritance. Using fluorescence recovery after photobleaching, we show that the ER chaperone Kar2/BiP fused to GFP and an ER membrane reporter, Hmg1-GFP, behave differently in the cER and pnER. The functional asymmetry and tubular ER formation depend on Reticulons/Yop1, which maintain ER structure. LUNAPARK1 deletion in rtn1Δrtn2Δyop1Δ cells restores the pnER/cER functional asymmetry, tubular ER generation, and ER inheritance blocks. Thus, Reticulon/Yop1-dependent changes in ER structure are linked to ER inheritance during the yeast cell cycle.
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Affiliation(s)
- Francisco Javier Piña
- Section of Molecular Biology, Division of Biological Sciences, University of California, San Diego, NSB#1, Room 5328, La Jolla, CA 92093-0377, USA
| | - Tinya Fleming
- Section of Molecular Biology, Division of Biological Sciences, University of California, San Diego, NSB#1, Room 4113, La Jolla, CA 92093-0377, USA
| | - Kit Pogliano
- Section of Molecular Biology, Division of Biological Sciences, University of California, San Diego, NSB#1, Room 4113, La Jolla, CA 92093-0377, USA
| | - Maho Niwa
- Section of Molecular Biology, Division of Biological Sciences, University of California, San Diego, NSB#1, Room 5328, La Jolla, CA 92093-0377, USA.
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34
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Li H, Liang R, Lu Y, Wang M, Li Z. RTN3 Regulates the Expression Level of Chemokine Receptor CXCR4 and is Required for Migration of Primordial Germ Cells. Int J Mol Sci 2016; 17:382. [PMID: 27070582 PMCID: PMC4848882 DOI: 10.3390/ijms17040382] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2016] [Revised: 02/23/2016] [Accepted: 03/03/2016] [Indexed: 12/25/2022] Open
Abstract
CXCR4 is a crucial chemokine receptor that plays key roles in primordial germ cell (PGC) homing. To further characterize the CXCR4-mediated migration of PGCs, we screened CXCR4-interacting proteins using yeast two-hybrid screening. We identified reticulon3 (RTN3), a member of the reticulon family, and considered an apoptotic signal transducer, as able to interact directly with CXCR4. Furthermore, we discovered that the mRNA and protein expression levels of CXCR4 could be regulated by RTN3. We also found that RTN3 altered CXCR4 translocation and localization. Moreover, increasing the signaling of either CXCR4b or RTN3 produced similar PGC mislocalization phenotypes in zebrafish. These results suggested that RTN3 modulates PGC migration through interaction with, and regulation of, CXCR4.
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Affiliation(s)
- Haitao Li
- State Key Laboratory for Agrobiotechnology, College of Biological Sciences, China Agricultural University, No. 2 Yuan Ming Yuan West Road, Beijing 100193, China.
| | - Rong Liang
- State Key Laboratory for Agrobiotechnology, College of Biological Sciences, China Agricultural University, No. 2 Yuan Ming Yuan West Road, Beijing 100193, China.
| | - Yanan Lu
- State Key Laboratory for Agrobiotechnology, College of Biological Sciences, China Agricultural University, No. 2 Yuan Ming Yuan West Road, Beijing 100193, China.
| | - Mengxia Wang
- State Key Laboratory for Agrobiotechnology, College of Biological Sciences, China Agricultural University, No. 2 Yuan Ming Yuan West Road, Beijing 100193, China.
| | - Zandong Li
- State Key Laboratory for Agrobiotechnology, College of Biological Sciences, China Agricultural University, No. 2 Yuan Ming Yuan West Road, Beijing 100193, China.
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35
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Malcova I, Farkasovsky M, Senohrabkova L, Vasicova P, Hasek J. New integrative modules for multicolor-protein labeling and live-cell imaging in Saccharomyces cerevisiae. FEMS Yeast Res 2016; 16:fow027. [PMID: 26994102 DOI: 10.1093/femsyr/fow027] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 03/14/2016] [Indexed: 12/30/2022] Open
Abstract
Live-imaging analysis is performed in many laboratories all over the world. Various tools have been developed to enable protein labeling either in plasmid or genomic context in live yeast cells. Here, we introduce a set of nine integrative modules for the C-terminal gene tagging that combines three fluorescent proteins (FPs)-ymTagBFP, mCherry and yTagRFP-T with three dominant selection markers: geneticin, nourseothricin and hygromycin. In addition, the construction of two episomal modules for Saccharomyces cerevisiae with photostable yTagRFP-T is also referred to. Our cassettes with orange, red and blue FPs can be combined with other fluorescent probes like green fluorescent protein to prepare double- or triple-labeled strains for multicolor live-cell imaging. Primers for PCR amplification of the cassettes were designed in such a way as to be fully compatible with the existing PCR toolbox representing over 50 various integrative modules and also with deletion cassettes either for single or repeated usage to enable a cost-effective and an easy exchange of tags. New modules can also be used for biochemical analysis since antibodies are available for all three fluorescent probes.
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Affiliation(s)
- Ivana Malcova
- Laboratory of Cell Reproduction, Institute of Microbiology CAS, v.v.i., 142 20 Prague 4, Czech Republic
| | - Marian Farkasovsky
- Laboratory of Molecular Microbiology, Institute of Molecular Biology SAS, 845 51 Bratislava, Slovakia
| | - Lenka Senohrabkova
- Laboratory of Cell Reproduction, Institute of Microbiology CAS, v.v.i., 142 20 Prague 4, Czech Republic
| | - Pavla Vasicova
- Laboratory of Cell Reproduction, Institute of Microbiology CAS, v.v.i., 142 20 Prague 4, Czech Republic
| | - Jiri Hasek
- Laboratory of Cell Reproduction, Institute of Microbiology CAS, v.v.i., 142 20 Prague 4, Czech Republic
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36
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Zhang D, Bidone TC, Vavylonis D. ER-PM Contacts Define Actomyosin Kinetics for Proper Contractile Ring Assembly. Curr Biol 2016; 26:647-53. [PMID: 26877082 DOI: 10.1016/j.cub.2015.12.070] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2015] [Revised: 12/24/2015] [Accepted: 12/24/2015] [Indexed: 12/20/2022]
Abstract
The cortical endoplasmic reticulum (ER), an elaborate network of tubules and cisternae [1], establishes contact sites with the plasma membrane (PM) through tethering machinery involving a set of conserved integral ER proteins [2]. The physiological consequences of forming ER-PM contacts are not fully understood. Here, we reveal a kinetic restriction role of ER-PM contacts over ring compaction process for proper actomyosin ring assembly in Schizosaccharomyces pombe. We show that fission yeast cells deficient in ER-PM contacts exhibit aberrant equatorial clustering of actin cables during ring assembly and are particularly susceptible to compromised actin filament crosslinking activity. Using quantitative image analyses and computer simulation, we demonstrate that ER-PM contacts function to modulate the distribution of ring components and to constrain their compaction kinetics. We propose that ER-PM contacts have evolved as important physical modulators to ensure robust ring assembly.
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Affiliation(s)
- Dan Zhang
- Temasek Life Sciences Laboratory, 1 Research Link, Singapore 117604, Singapore.
| | - Tamara C Bidone
- Department of Physics, Lehigh University, Bethlehem, PA 18015, USA
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37
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Schwarz DS, Blower MD. The endoplasmic reticulum: structure, function and response to cellular signaling. Cell Mol Life Sci 2016; 73:79-94. [PMID: 26433683 PMCID: PMC4700099 DOI: 10.1007/s00018-015-2052-6] [Citation(s) in RCA: 889] [Impact Index Per Article: 111.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2015] [Revised: 09/21/2015] [Accepted: 09/22/2015] [Indexed: 02/06/2023]
Abstract
The endoplasmic reticulum (ER) is a large, dynamic structure that serves many roles in the cell including calcium storage, protein synthesis and lipid metabolism. The diverse functions of the ER are performed by distinct domains; consisting of tubules, sheets and the nuclear envelope. Several proteins that contribute to the overall architecture and dynamics of the ER have been identified, but many questions remain as to how the ER changes shape in response to cellular cues, cell type, cell cycle state and during development of the organism. Here we discuss what is known about the dynamics of the ER, what questions remain, and how coordinated responses add to the layers of regulation in this dynamic organelle.
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Affiliation(s)
- Dianne S Schwarz
- Department of Molecular Biology, Massachusetts General Hospital, Boston, MA, 02114, USA
- Department of Genetics, Harvard Medical School, Boston, MA, 02115, USA
- New England Biolabs, Ipswich, MA, 01938, USA
| | - Michael D Blower
- Department of Molecular Biology, Massachusetts General Hospital, Boston, MA, 02114, USA.
- Department of Genetics, Harvard Medical School, Boston, MA, 02115, USA.
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38
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Heider MR, Gu M, Duffy CM, Mirza AM, Marcotte LL, Walls AC, Farrall N, Hakhverdyan Z, Field MC, Rout MP, Frost A, Munson M. Subunit connectivity, assembly determinants and architecture of the yeast exocyst complex. Nat Struct Mol Biol 2016; 23:59-66. [PMID: 26656853 PMCID: PMC4752824 DOI: 10.1038/nsmb.3146] [Citation(s) in RCA: 87] [Impact Index Per Article: 10.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2015] [Accepted: 11/19/2015] [Indexed: 01/12/2023]
Abstract
The exocyst is a hetero-octameric complex that has been proposed to serve as the tethering complex for exocytosis, although it remains poorly understood at the molecular level. Here, we purified endogenous exocyst complexes from Saccharomyces cerevisiae and showed that they are stable and consist of all eight subunits with equal stoichiometry. Using a combination of biochemical and auxin induced-degradation experiments in yeast, we mapped the subunit connectivity, identified two stable four-subunit modules within the octamer and demonstrated that several known exocyst-binding partners are not necessary for exocyst assembly and stability. Furthermore, we visualized the structure of the yeast complex by using negative-stain electron microscopy; our results indicate that the exocyst exists predominantly as a stable, octameric complex with an elongated architecture that suggests that the subunits are contiguous helical bundles packed together into a bundle of long rods.
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Affiliation(s)
- Margaret R. Heider
- Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, Worcester, MA, USA
| | - Mingyu Gu
- Department of Biochemistry, University of Utah, Salt Lake City, UT, USA
| | - Caroline M. Duffy
- Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, Worcester, MA, USA
| | - Anne M. Mirza
- Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, Worcester, MA, USA
| | - Laura L. Marcotte
- Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, Worcester, MA, USA
| | - Alexandra C. Walls
- Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, Worcester, MA, USA
| | - Nicholas Farrall
- Department of Biochemistry, University of Utah, Salt Lake City, UT, USA
| | - Zhanna Hakhverdyan
- Laboratory of Cellular and Structural Biology, The Rockefeller University, New York, NY, USA
| | - Mark C. Field
- Division of Biological Chemistry and Drug Discovery, University of Dundee, Dundee, UK
| | - Michael P. Rout
- Laboratory of Cellular and Structural Biology, The Rockefeller University, New York, NY, USA
| | - Adam Frost
- Department of Biochemistry, University of Utah, Salt Lake City, UT, USA
- Department of Biochemistry and Biophysics, University of California San Francisco, San Francisco, CA, USA
| | - Mary Munson
- Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, Worcester, MA, USA
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39
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Hakhverdyan Z, Domanski M, Hough LE, Oroskar AA, Oroskar AR, Keegan S, Dilworth DJ, Molloy KR, Sherman V, Aitchison JD, Fenyö D, Chait BT, Jensen TH, Rout MP, LaCava J. Rapid, optimized interactomic screening. Nat Methods 2015; 12:553-60. [PMID: 25938370 PMCID: PMC4449307 DOI: 10.1038/nmeth.3395] [Citation(s) in RCA: 57] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2014] [Accepted: 03/03/2015] [Indexed: 12/25/2022]
Abstract
We must reliably map the interactomes of cellular macromolecular
complexes in order to fully explore and understand biological systems. However,
there are no methods to accurately predict how to capture a given macromolecular
complex with its physiological binding partners. Here, we present a screen that
comprehensively explores the parameters affecting the stability of interactions
in affinity-captured complexes, enabling the discovery of physiological binding
partners and the elucidation of their functional interactions in unparalleled
detail. We have implemented this screen on several macromolecular complexes from
a variety of organisms, revealing novel profiles even for well-studied proteins.
Our approach is robust, economical and automatable, providing an inroad to the
rigorous, systematic dissection of cellular interactomes.
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Affiliation(s)
- Zhanna Hakhverdyan
- Laboratory of Cellular and Structural Biology, The Rockefeller University, New York, New York, USA
| | - Michal Domanski
- 1] Laboratory of Cellular and Structural Biology, The Rockefeller University, New York, New York, USA. [2] Department of Molecular Biology and Genetics, Aarhus University, Aarhus, Denmark
| | - Loren E Hough
- Laboratory of Cellular and Structural Biology, The Rockefeller University, New York, New York, USA
| | | | | | - Sarah Keegan
- 1] Center for Health Informatics and Bioinformatics, New York University School of Medicine, New York, New York, USA. [2] Department of Biochemistry and Molecular Pharmacology, New York University School of Medicine, New York, New York, USA
| | - David J Dilworth
- 1] Institute for Systems Biology, Seattle, Washington, USA. [2] Seattle Biomedical Research Institute, Seattle, Washington, USA
| | - Kelly R Molloy
- Laboratory of Mass Spectrometry and Gaseous Ion Chemistry, The Rockefeller University, New York, New York, USA
| | - Vadim Sherman
- High Energy Physics Instrument Shop, The Rockefeller University, New York, New York, USA
| | - John D Aitchison
- 1] Institute for Systems Biology, Seattle, Washington, USA. [2] Seattle Biomedical Research Institute, Seattle, Washington, USA
| | - David Fenyö
- 1] Center for Health Informatics and Bioinformatics, New York University School of Medicine, New York, New York, USA. [2] Department of Biochemistry and Molecular Pharmacology, New York University School of Medicine, New York, New York, USA
| | - Brian T Chait
- Laboratory of Mass Spectrometry and Gaseous Ion Chemistry, The Rockefeller University, New York, New York, USA
| | - Torben Heick Jensen
- Department of Molecular Biology and Genetics, Aarhus University, Aarhus, Denmark
| | - Michael P Rout
- Laboratory of Cellular and Structural Biology, The Rockefeller University, New York, New York, USA
| | - John LaCava
- Laboratory of Cellular and Structural Biology, The Rockefeller University, New York, New York, USA
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40
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Liu D, Novick P. Bem1p contributes to secretory pathway polarization through a direct interaction with Exo70p. ACTA ACUST UNITED AC 2015; 207:59-72. [PMID: 25313406 PMCID: PMC4195821 DOI: 10.1083/jcb.201404122] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
The exocyst serves to tether secretory vesicles to cortical sites specified by polarity determinants, in preparation for fusion with the plasma membrane. Although most exocyst components are brought to these sites by riding on secretory vesicles as they are actively transported along actin cables, Exo70p displays actin-independent localization to these sites, implying an interaction with a polarity determinant. Here we show that Exo70p directly and specifically binds to the polarity determinant scaffold protein Bem1p. The interaction involves multiple domains of both Exo70p and Bem1p. Mutations in Exo70p that disrupt its interaction with Bem1, without impairing its interactions with other known binding partners, lead to the loss of actin-independent localization. Synthetic genetic interactions confirm the importance of the Exo70p-Bem1p interaction, although there is some possible redundancy with Sec3p and Sec15p, other exocyst components that also interact with polarity determinants. Similar to Sec3p, the actin-independent localization of Exo70p requires a synergistic interaction with the phosphoinositide PI(4,5)P2.
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Affiliation(s)
- Dongmei Liu
- Department of Cellular and Molecular Medicine, University of California, San Diego, La Jolla, CA 92130
| | - Peter Novick
- Department of Cellular and Molecular Medicine, University of California, San Diego, La Jolla, CA 92130
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41
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Hawes C, Kiviniemi P, Kriechbaumer V. The endoplasmic reticulum: a dynamic and well-connected organelle. JOURNAL OF INTEGRATIVE PLANT BIOLOGY 2015; 57:50-62. [PMID: 25319240 DOI: 10.1111/jipb.12297] [Citation(s) in RCA: 56] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/18/2014] [Accepted: 10/09/2014] [Indexed: 06/04/2023]
Abstract
The endoplasmic reticulum forms the first compartment in a series of organelles which comprise the secretory pathway. It takes the form of an extremely dynamic and pleomorphic membrane-bounded network of tubules and cisternae which have numerous different cellular functions. In this review, we discuss the nature of endoplasmic reticulum structure and dynamics, its relationship with closely associated organelles, and its possible function as a highway for the distribution and delivery of a diverse range of structures from metabolic complexes to viral particles.
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Affiliation(s)
- Chris Hawes
- Department of Biological and Medical Sciences, Oxford Brookes University, Oxford, OX3 0BP, UK
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42
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Lunapark stabilizes nascent three-way junctions in the endoplasmic reticulum. Proc Natl Acad Sci U S A 2014; 112:418-23. [PMID: 25548161 DOI: 10.1073/pnas.1423026112] [Citation(s) in RCA: 88] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022] Open
Abstract
The endoplasmic reticulum (ER) consists of a polygonal network of sheets and tubules interconnected by three-way junctions. This network undergoes continual remodeling through competing processes: the branching and fusion of tubules forms new three-way junctions and new polygons, and junction sliding and ring closure leads to polygon loss. However, little is known about the machinery required to generate and maintain junctions. We previously reported that yeast Lnp1 localizes to ER junctions, and that loss of Lnp1 leads to a collapsed, densely reticulated ER network. In mammalian cells, only approximately half the junctions contain Lnp1. Here we use live cell imaging to show that mammalian Lnp1 (mLnp1) affects ER junction mobility and hence network dynamics. Three-way junctions with mLnp1 are less mobile than junctions without mLnp1. Newly formed junctions that acquire mLnp1 remain stable within the ER network, whereas nascent junctions that fail to acquire mLnp1 undergo rapid ring closure. These findings imply that mLnp1 plays a key role in stabilizing nascent three-way ER junctions.
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43
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Rogers JV, McMahon C, Baryshnikova A, Hughson FM, Rose MD. ER-associated retrograde SNAREs and the Dsl1 complex mediate an alternative, Sey1p-independent homotypic ER fusion pathway. Mol Biol Cell 2014; 25:3401-12. [PMID: 25187651 PMCID: PMC4214786 DOI: 10.1091/mbc.e14-07-1220] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022] Open
Abstract
SNAREs and the Dsl1 complex mediate an alternative, Sey1p-independent homotypic endoplasmic reticulum (ER) fusion pathway in yeast. When both pathways and the reticulons are simultaneously disrupted, cells are inviable. This demonstrates that homotypic ER fusion is an essential process in yeast and that the Dsl1 complex has vesicle trafficking-independent functions. The peripheral endoplasmic reticulum (ER) network is dynamically maintained by homotypic (ER–ER) fusion. In Saccharomyces cerevisiae, the dynamin-like GTPase Sey1p can mediate ER–ER fusion, but sey1Δ cells have no growth defect and only slightly perturbed ER structure. Recent work suggested that ER-localized soluble N-ethylmaleimide–sensitive factor attachment protein receptors (SNAREs) mediate a Sey1p-independent ER–ER fusion pathway. However, an alternative explanation—that the observed phenotypes arose from perturbed vesicle trafficking—could not be ruled out. In this study, we used candidate and synthetic genetic array (SGA) approaches to more fully characterize SNARE-mediated ER–ER fusion. We found that Dsl1 complex mutations in sey1Δ cells cause strong synthetic growth and ER structure defects and delayed ER–ER fusion in vivo, additionally implicating the Dsl1 complex in SNARE-mediated ER–ER fusion. In contrast, cytosolic coat protein I (COPI) vesicle coat mutations in sey1Δ cells caused no synthetic defects, excluding perturbed retrograde trafficking as a cause for the previously observed synthetic defects. Finally, deleting the reticulons that help maintain ER architecture in cells disrupted for both ER–ER fusion pathways caused almost complete inviability. We conclude that the ER SNAREs and the Dsl1 complex directly mediate Sey1p-independent ER–ER fusion and that, in the absence of both pathways, cell viability depends upon membrane curvature–promoting reticulons.
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Affiliation(s)
- Jason V Rogers
- Department of Molecular Biology, Princeton University, Princeton, NJ 08544-1014
| | - Conor McMahon
- Department of Molecular Biology, Princeton University, Princeton, NJ 08544-1014
| | - Anastasia Baryshnikova
- Lewis-Sigler Institute for Integrative Genomics, Princeton University, Princeton, NJ 08544-1014
| | - Frederick M Hughson
- Department of Molecular Biology, Princeton University, Princeton, NJ 08544-1014
| | - Mark D Rose
- Department of Molecular Biology, Princeton University, Princeton, NJ 08544-1014
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44
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Jozsef L, Tashiro K, Kuo A, Park EJ, Skoura A, Albinsson S, Rivera-Molina F, Harrison KD, Iwakiri Y, Toomre D, Sessa WC. Reticulon 4 is necessary for endoplasmic reticulum tubulation, STIM1-Orai1 coupling, and store-operated calcium entry. J Biol Chem 2014; 289:9380-95. [PMID: 24558039 DOI: 10.1074/jbc.m114.548602] [Citation(s) in RCA: 52] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023] Open
Abstract
Despite recent advances in understanding store-operated calcium entry (SOCE) regulation, the fundamental question of how ER morphology affects this process remains unanswered. Here we show that the loss of RTN4, is sufficient to alter ER morphology and severely compromise SOCE. Mechanistically, we show this to be the result of defective STIM1-Orai1 coupling because of loss of ER tubulation and redistribution of STIM1 to ER sheets. As a functional consequence, RTN4-depleted cells fail to sustain elevated cytoplasmic Ca(2+) levels via SOCE and therefor are less susceptible to Ca(2+) overload induced apoptosis. Thus, for the first time, our results show a direct correlation between ER morphology and SOCE and highlight the importance of RTN4 in cellular Ca(2+) homeostasis.
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Affiliation(s)
- Levente Jozsef
- From the Vascular Biology and Therapeutics Program, Department of Pharmacology
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45
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Terasaki M, Shemesh T, Kasthuri N, Klemm RW, Schalek R, Hayworth KJ, Hand AR, Yankova M, Huber G, Lichtman JW, Rapoport TA, Kozlov MM. Stacked endoplasmic reticulum sheets are connected by helicoidal membrane motifs. Cell 2013; 154:285-96. [PMID: 23870120 PMCID: PMC3767119 DOI: 10.1016/j.cell.2013.06.031] [Citation(s) in RCA: 159] [Impact Index Per Article: 14.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2013] [Revised: 04/25/2013] [Accepted: 06/20/2013] [Indexed: 12/28/2022]
Abstract
The endoplasmic reticulum (ER) often forms stacked membrane sheets, an arrangement that is likely required to accommodate a maximum of membrane-bound polysomes for secretory protein synthesis. How sheets are stacked is unknown. Here, we used improved staining and automated ultrathin sectioning electron microscopy methods to analyze stacked ER sheets in neuronal cells and secretory salivary gland cells of mice. Our results show that stacked ER sheets form a continuous membrane system in which the sheets are connected by twisted membrane surfaces with helical edges of left- or right-handedness. The three-dimensional structure of tightly stacked ER sheets resembles a parking garage, in which the different levels are connected by helicoidal ramps. A theoretical model explains the experimental observations and indicates that the structure corresponds to a minimum of elastic energy of sheet edges and surfaces. The structure allows the dense packing of ER sheets in the restricted space of a cell.
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Affiliation(s)
- Mark Terasaki
- Department of Cell Biology, University of Connecticut Health Center, Farmington, CT 06030, USA
- Correspondence: (M.T.), (T.A.R.)
| | - Tom Shemesh
- Department of Chemical Engineering, Columbia University, New York, NY 10027, USA
| | - Narayanan Kasthuri
- Department of Molecular and Cellular Biology, Harvard University, Cambridge, MA, USA
| | - Robin W. Klemm
- Howard Hughes Medical Institute and Department of Cell Biology, Harvard Medical School, 240 Longwood Avenue, Boston, MA 02115, USA
| | - Richard Schalek
- Department of Molecular and Cellular Biology, Harvard University, Cambridge, MA, USA
| | - Kenneth J. Hayworth
- Department of Molecular and Cellular Biology, Harvard University, Cambridge, MA, USA
| | - Arthur R. Hand
- Departments of Craniofacial Sciences and Cell Biology, University of Connecticut School of Dental Medicine, Farmington, CT 06032, USA
| | - Maya Yankova
- Central Electron Microscopy Facility, University of Connecticut Health Center, Farmington, CT 06030, USA
| | - Greg Huber
- Department of Cell Biology, University of Connecticut Health Center, Farmington, CT 06030, USA
- Kavli Institute for Theoretical Physics, Kohn Hall, University of California, Santa Barbara, CA 93106-4030
| | - Jeff W. Lichtman
- Department of Molecular and Cellular Biology, Harvard University, Cambridge, MA, USA
| | - Tom A. Rapoport
- Howard Hughes Medical Institute and Department of Cell Biology, Harvard Medical School, 240 Longwood Avenue, Boston, MA 02115, USA
- Correspondence: (M.T.), (T.A.R.)
| | - Michael M. Kozlov
- Department of Physiology and Pharmacology, Sackler Faculty of Medicine, Tel Aviv University, Ramat Aviv, 69978 Tel Aviv, Israel
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46
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Teng FYH, Tang BL. Nogo/RTN4 isoforms and RTN3 expression protect SH-SY5Y cells against multiple death insults. Mol Cell Biochem 2013; 384:7-19. [PMID: 23955438 DOI: 10.1007/s11010-013-1776-6] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2013] [Accepted: 08/09/2013] [Indexed: 01/27/2023]
Abstract
Among the members of the reticulon (RTN) family, Nogo-A/RTN4A, a prominent myelin-associated neurite growth inhibitory protein, and RTN3 are highly expressed in neurons. However, neuronal cell-autonomous functions of Nogo-A, as well as other members of the RTN family, are unclear. We show here that SH-SY5Y neuroblastoma cells stably over-expressing either two of the three major isoforms of Nogo/RTN4 (Nogo-A and Nogo-B) or a major isoform of RTN3 were protected against cell death induced by a battery of apoptosis-inducing agents (including serum deprivation, staurosporine, etoposide, and H2O2) compared to vector-transfected control cells. Nogo-A, -B, and RTN3 are particularly effective in terms of protection against H2O2-induced increase in intracellular reactive oxygen species levels and ensuing apoptotic and autophagic cell death. Expression of these RTNs upregulated basal levels of Bax, activated Bax, and activated caspase 3, but did not exhibit an enhanced ER stress response. The protective effect of RTNs is also not dependent on classical survival-promoting signaling pathways such as Akt and Erk kinase pathways. Neuron-enriched Nogo-A/Rtn4A and RTN3 may, therefore, exert a protective effect on neuronal cells against death stimuli, and elevation of their levels during injury may have a cell-autonomous survival-promoting function.
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Affiliation(s)
- Felicia Yu Hsuan Teng
- Department of Biochemistry, National University of Singapore, MD7, 8 Medical Drive, Singapore, 117597, Republic of Singapore
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47
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Georgiev AG, Johansen J, Ramanathan VD, Sere YY, Beh CT, Menon AK. Arv1 regulates PM and ER membrane structure and homeostasis but is dispensable for intracellular sterol transport. Traffic 2013; 14:912-21. [PMID: 23668914 DOI: 10.1111/tra.12082] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2012] [Revised: 05/08/2013] [Accepted: 05/13/2013] [Indexed: 11/28/2022]
Abstract
The pan-eukaryotic endoplasmic reticulum (ER) membrane protein Arv1 has been suggested to play a role in intracellular sterol transport. We tested this proposal by comparing sterol traffic in wild-type and Arv1-deficient Saccharomyces cerevisiae. We used fluorescence microscopy to track the retrograde movement of exogenously supplied dehydroergosterol (DHE) from the plasma membrane (PM) to the ER and lipid droplets and high performance liquid chromatography to quantify, in parallel, the transport-coupled formation of DHE esters. Metabolic labeling and subcellular fractionation were used to assay anterograde transport of ergosterol from the ER to the PM. We report that sterol transport between the ER and PM is unaffected by Arv1 deficiency. Instead, our results indicate differences in ER morphology and the organization of the PM lipid bilayer between wild-type and arv1Δ cells suggesting a distinct role for Arv1 in membrane homeostasis. In arv1Δ cells, specific defects affecting single C-terminal transmembrane domain proteins suggest that Arv1 might regulate membrane insertion of tail-anchored proteins involved in membrane homoeostasis.
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48
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David C, Koch J, Oeljeklaus S, Laernsack A, Melchior S, Wiese S, Schummer A, Erdmann R, Warscheid B, Brocard C. A combined approach of quantitative interaction proteomics and live-cell imaging reveals a regulatory role for endoplasmic reticulum (ER) reticulon homology proteins in peroxisome biogenesis. Mol Cell Proteomics 2013; 12:2408-25. [PMID: 23689284 DOI: 10.1074/mcp.m112.017830] [Citation(s) in RCA: 64] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022] Open
Abstract
Peroxisome biogenesis initiates at the endoplasmic reticulum (ER) and maturation allows for the formation of metabolically active organelles. Yet, peroxisomes can also multiply by growth and division. Several proteins, called peroxins, are known to participate in these processes but little is known about their organization to orchestrate peroxisome proliferation. Here, we demonstrate that regulation of peroxisome proliferation relies on the integrity of the tubular ER network. Using a dual track SILAC-based quantitative interaction proteomics approach, we established a comprehensive network of stable as well as transient interactions of the peroxin Pex30p, an integral membrane protein. Through association with merely ER resident proteins, in particular with proteins containing a reticulon homology domain, and with other peroxins, Pex30p designates peroxisome contact sites at ER subdomains. We show that Pex30p traffics through the ER and segregates in punctae to which peroxisomes specifically append, and we ascertain its transient interaction with all subunits of the COPI coatomer complex suggesting the involvement of a vesicle-mediated transport. We establish that the membrane protein Pex30p facilitates the connection of peroxisomes to the ER. Taken together, our data indicate that Pex30p-containing protein complexes act as focal points from which peroxisomes can form and that the tubular ER architecture organized by the reticulon homology proteins Rtn1p, Rtn2p and Yop1p controls this process.
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Affiliation(s)
- Christine David
- University of Vienna, Max F. Perutz Laboratories, Center of Molecular Biology, Department of Biochemistry and Cell Biology, Dr. Bohr-Gasse 9, A-1030, Vienna, Austria
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49
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English AR, Voeltz GK. Endoplasmic reticulum structure and interconnections with other organelles. Cold Spring Harb Perspect Biol 2013; 5:a013227. [PMID: 23545422 DOI: 10.1101/cshperspect.a013227] [Citation(s) in RCA: 226] [Impact Index Per Article: 20.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
Abstract
The endoplasmic reticulum (ER) is a large, continuous membrane-bound organelle comprised of functionally and structurally distinct domains including the nuclear envelope, peripheral tubular ER, peripheral cisternae, and numerous membrane contact sites at the plasma membrane, mitochondria, Golgi, endosomes, and peroxisomes. These domains are required for multiple cellular processes, including synthesis of proteins and lipids, calcium level regulation, and exchange of macromolecules with various organelles at ER-membrane contact sites. The ER maintains its unique overall structure regardless of dynamics or transfer at ER-organelle contacts. In this review, we describe the numerous factors that contribute to the structure of the ER.
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Affiliation(s)
- Amber R English
- Department of Molecular, Cellular and Developmental Biology, University of Colorado, Boulder, CO 80309, USA
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50
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Chen S, Novick P, Ferro-Novick S. ER structure and function. Curr Opin Cell Biol 2013; 25:428-33. [PMID: 23478217 DOI: 10.1016/j.ceb.2013.02.006] [Citation(s) in RCA: 142] [Impact Index Per Article: 12.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2013] [Accepted: 02/13/2013] [Indexed: 12/31/2022]
Abstract
The ER forms a contiguous structure of interconnected sheets and tubules that spreads from the nuclear envelope to the cell cortex. Through its attachment to the cytoskeleton, the ER undergoes dynamic rearrangements, such as tubule extension and movement. ER shaping proteins (reticulons and DP1/Yop1p) play key roles in generating and maintaining the unique reticular morphology of the ER. Atlastin and its yeast homologue, Sey1p, mediate homotypic ER membrane fusion, which leads to the formation of new three-way junctions within the polygonal network. At these junctions, the Lunapark protein, Lnp1p, works in conjunction with the reticulons, DP1/Yop1p, and in antagonism to atlastin/Sey1p to maintain the network in a dynamic equilibrium. Defects in ER morphology have been linked to certain neurological disorders.
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Affiliation(s)
- Shuliang Chen
- Department of Cellular and Molecular Medicine, Howard Hughes, Medical Institute, University of California at San Diego, La Jolla, CA 92093-0668, USA
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