1
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Wilson ZN, Balasubramaniam SS, Wong S, Schuler MH, Wopat MJ, Hughes AL. Mitochondrial-derived compartments remove surplus proteins from the outer mitochondrial membrane. J Cell Biol 2024; 223:e202307036. [PMID: 39136938 PMCID: PMC11320589 DOI: 10.1083/jcb.202307036] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2023] [Revised: 05/24/2024] [Accepted: 07/18/2024] [Indexed: 09/13/2024] Open
Abstract
The outer mitochondrial membrane (OMM) creates a boundary that imports most of the mitochondrial proteome while removing extraneous or damaged proteins. How the OMM senses aberrant proteins and remodels to maintain OMM integrity remains unresolved. Previously, we identified a mitochondrial remodeling mechanism called the mitochondrial-derived compartment (MDC) that removes a subset of the mitochondrial proteome. Here, we show that MDCs specifically sequester proteins localized only at the OMM, providing an explanation for how select mitochondrial proteins are incorporated into MDCs. Remarkably, selective sorting into MDCs also occurs within the OMM, as subunits of the translocase of the outer membrane (TOM) complex are excluded from MDCs unless assembly of the TOM complex is impaired. Considering that overloading the OMM with mitochondrial membrane proteins or mistargeted tail-anchored membrane proteins induces MDCs to form and sequester these proteins, we propose that one functional role of MDCs is to create an OMM-enriched trap that segregates and sequesters excess proteins from the mitochondrial surface.
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Affiliation(s)
- Zachary N Wilson
- Department of Biochemistry, University of Utah School of Medicine, Salt Lake City, UT, USA
| | | | - Sara Wong
- Department of Biochemistry, University of Utah School of Medicine, Salt Lake City, UT, USA
| | - Max-Hinderk Schuler
- Department of Biochemistry, University of Utah School of Medicine, Salt Lake City, UT, USA
| | - Mitchell J Wopat
- Department of Biochemistry, University of Utah School of Medicine, Salt Lake City, UT, USA
| | - Adam L Hughes
- Department of Biochemistry, University of Utah School of Medicine, Salt Lake City, UT, USA
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2
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Wilson ZN, West M, English AM, Odorizzi G, Hughes AL. Mitochondrial-derived compartments are multilamellar domains that encase membrane cargo and cytosol. J Cell Biol 2024; 223:e202307035. [PMID: 39136939 PMCID: PMC11320809 DOI: 10.1083/jcb.202307035] [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: 07/07/2023] [Revised: 05/24/2024] [Accepted: 07/17/2024] [Indexed: 08/21/2024] Open
Abstract
Preserving the health of the mitochondrial network is critical to cell viability and longevity. To do so, mitochondria employ several membrane remodeling mechanisms, including the formation of mitochondrial-derived vesicles (MDVs) and compartments (MDCs) to selectively remove portions of the organelle. In contrast to well-characterized MDVs, the distinguishing features of MDC formation and composition remain unclear. Here, we used electron tomography to observe that MDCs form as large, multilamellar domains that generate concentric spherical compartments emerging from mitochondrial tubules at ER-mitochondria contact sites. Time-lapse fluorescence microscopy of MDC biogenesis revealed that mitochondrial membrane extensions repeatedly elongate, coalesce, and invaginate to form these compartments that encase multiple layers of membrane. As such, MDCs strongly sequester portions of the outer mitochondrial membrane, securing membrane cargo into a protected domain, while also enclosing cytosolic material within the MDC lumen. Collectively, our results provide a model for MDC formation and describe key features that distinguish MDCs from other previously identified mitochondrial structures and cargo-sorting domains.
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Affiliation(s)
- Zachary N Wilson
- Department of Biochemistry, University of Utah School of Medicine, Salt Lake City, UT, USA
| | - Matt West
- Department of Molecular, Cellular, and Developmental Biology, University of Colorado Boulder, Boulder, CO, USA
| | - Alyssa M English
- Department of Biochemistry, University of Utah School of Medicine, Salt Lake City, UT, USA
| | - Greg Odorizzi
- Department of Molecular, Cellular, and Developmental Biology, University of Colorado Boulder, Boulder, CO, USA
| | - Adam L Hughes
- Department of Biochemistry, University of Utah School of Medicine, Salt Lake City, UT, USA
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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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Zhang Y, Lin C. Lipid osmosis, membrane tension, and other mechanochemical driving forces of lipid flow. Curr Opin Cell Biol 2024; 88:102377. [PMID: 38823338 PMCID: PMC11193448 DOI: 10.1016/j.ceb.2024.102377] [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: 01/10/2024] [Revised: 05/12/2024] [Accepted: 05/13/2024] [Indexed: 06/03/2024]
Abstract
Nonvesicular lipid transport among different membranes or membrane domains plays crucial roles in lipid homeostasis and organelle biogenesis. However, the forces that drive such lipid transport are not well understood. We propose that lipids tend to flow towards the membrane area with a higher membrane protein density in a process termed lipid osmosis. This process lowers the membrane tension in the area, resulting in a membrane tension difference called osmotic membrane tension. We examine the thermodynamic basis and experimental evidence of lipid osmosis and osmotic membrane tension. We predict that lipid osmosis can drive bulk lipid flows between different membrane regions through lipid transfer proteins, scramblases, or similar barriers that selectively pass lipids but not membrane proteins. We also speculate on the biological functions of lipid osmosis. Finally, we explore other driving forces for lipid transfer and describe potential methods and systems to further test our theory.
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Affiliation(s)
- Yongli Zhang
- Department of Cell Biology, Yale University School of Medicine, New Haven, CT 06510, USA; Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT 06511, USA.
| | - Chenxiang Lin
- Department of Cell Biology, Yale University School of Medicine, New Haven, CT 06510, USA; Nanobiology Institute, Yale University, West Haven, CT 06516, USA; Department of Biomedical Engineering, Yale University, New Haven, CT 06520, USA.
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5
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Zhang Y, Lin C. Lipid osmosis, membrane tension, and other mechanochemical driving forces of lipid flow. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.01.08.574656. [PMID: 38260424 PMCID: PMC10802412 DOI: 10.1101/2024.01.08.574656] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/24/2024]
Abstract
Nonvesicular lipid transport among different membranes or membrane domains plays crucial roles in lipid homeostasis and organelle biogenesis. However, the forces that drive such lipid transport are not well understood. We propose that lipids tend to flow towards the membrane area with a higher membrane protein density in a process termed lipid osmosis. This process lowers the membrane tension in the area, resulting in a membrane tension difference called osmotic membrane tension. We examine the thermodynamic basis and experimental evidence of lipid osmosis and osmotic membrane tension. We predict that lipid osmosis can drive bulk lipid flows between different membrane regions through lipid transfer proteins, scramblases, or other similar barriers that selectively pass lipids but not membrane proteins. We also speculate on the biological functions of lipid osmosis. Finally, we explore other driving forces for lipid transfer and describe potential methods and systems to further test our theory.
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Affiliation(s)
- Yongli Zhang
- Department of Cell Biology, Yale University School of Medicine, New Haven, CT 06510, USA
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT 06511, USA
| | - Chenxiang Lin
- Department of Cell Biology, Yale University School of Medicine, New Haven, CT 06510, USA
- Nanobiology Institute, Yale University, West Haven, CT 06516, USA
- Department of Biomedical Engineering, Yale University, New Haven, CT 06520, USA
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6
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Wang S, Meng D, Feng M, Li C, Wang Y. Efficient Plant Triterpenoids Synthesis in Saccharomyces cerevisiae: from Mechanisms to Engineering Strategies. ACS Synth Biol 2024; 13:1059-1076. [PMID: 38546129 DOI: 10.1021/acssynbio.4c00061] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/20/2024]
Abstract
Triterpenoids possess a range of biological activities and are extensively utilized in the pharmaceutical, food, cosmetic, and chemical industries. Traditionally, they are acquired through chemical synthesis and plant extraction. However, these methods have drawbacks, including high energy consumption, environmental pollution, and being time-consuming. Recently, the de novo synthesis of triterpenoids in microbial cell factories has been achieved. This represents a promising and environmentally friendly alternative to traditional supply methods. Saccharomyces cerevisiae, known for its robustness, safety, and ample precursor supply, stands out as an ideal candidate for triterpenoid biosynthesis. However, challenges persist in industrial production and economic feasibility of triterpenoid biosynthesis. Consequently, metabolic engineering approaches have been applied to improve the triterpenoid yield, leading to substantial progress. This review explores triterpenoids biosynthesis mechanisms in S. cerevisiae and strategies for efficient production. Finally, the review also discusses current challenges and proposes potential solutions, offering insights for future engineering.
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Affiliation(s)
- Shuai Wang
- Key Laboratory of Medical Molecule Science and Pharmaceutical Engineering, Ministry of Industry and Information Technology, Institute of Biochemical Engineering, School of Chemistry and Chemical Engineering, Beijing Institute of Technology, Beijing 100081, China
| | - Dong Meng
- Key Laboratory of Medical Molecule Science and Pharmaceutical Engineering, Ministry of Industry and Information Technology, Institute of Biochemical Engineering, School of Chemistry and Chemical Engineering, Beijing Institute of Technology, Beijing 100081, China
| | - Meilin Feng
- Key Laboratory of Medical Molecule Science and Pharmaceutical Engineering, Ministry of Industry and Information Technology, Institute of Biochemical Engineering, School of Chemistry and Chemical Engineering, Beijing Institute of Technology, Beijing 100081, China
| | - Chun Li
- Key Laboratory for Industrial Biocatalysis, Ministry of Education, Department of Chemical Engineering, Tsinghua University, Beijing 100084, China
| | - Ying Wang
- Key Laboratory of Medical Molecule Science and Pharmaceutical Engineering, Ministry of Industry and Information Technology, Institute of Biochemical Engineering, School of Chemistry and Chemical Engineering, Beijing Institute of Technology, Beijing 100081, China
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7
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Wang M, Wu N, Wang H, Liu C, Chen Q, Xu T, Chen Y, Zhao Y, Ma Z. Overproduction of mycotoxin biosynthetic enzymes triggers Fusarium toxisome-shaped structure formation via endoplasmic reticulum remodeling. PLoS Pathog 2024; 20:e1011913. [PMID: 38166144 PMCID: PMC10786393 DOI: 10.1371/journal.ppat.1011913] [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: 07/04/2023] [Revised: 01/12/2024] [Accepted: 12/19/2023] [Indexed: 01/04/2024] Open
Abstract
Mycotoxin deoxynivalenol (DON) produced by the Fusarium graminearum complex is highly toxic to animal and human health. During DON synthesis, the endoplasmic reticulum (ER) of F. graminearum is intensively reorganized, from thin reticular structure to thickened spherical and crescent structure, which was referred to as "DON toxisome". However, the underlying mechanism of how the ER is reorganized into toxisome remains unknown. In this study, we discovered that overproduction of ER-localized DON biosynthetic enzyme Tri4 or Tri1, or intrinsic ER-resident membrane proteins FgHmr1 and FgCnx was sufficient to induce toxisome-shaped structure (TSS) formation under non-toxin-inducing conditions. Moreover, heterologous overexpression of Tri1 and Tri4 proteins in non-DON-producing fungi F. oxysporum f. sp. lycopersici and F. fujikuroi also led to TSS formation. In addition, we found that the high osmolarity glycerol (HOG), but not the unfolded protein response (UPR) signaling pathway was involved in the assembly of ER into TSS. By using toxisome as a biomarker, we screened and identified a novel chemical which exhibited high inhibitory activity against toxisome formation and DON biosynthesis, and inhibited Fusarium growth species-specifically. Taken together, this study demonstrated that the essence of ER remodeling into toxisome structure is a response to the overproduction of ER-localized DON biosynthetic enzymes, providing a novel pathway for management of mycotoxin contamination.
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Affiliation(s)
- Minhui Wang
- State Key Laboratory of Rice Biology, Key Laboratory of Biology of Crop Pathogens and Insects, Institute of Biotechnology, Zhejiang University, Hangzhou, People’s Republic of China
| | - Ningjie Wu
- Zhejiang Research Institute of Chemical Industry, Hangzhou, People’s Republic of China
| | - Huiyuan Wang
- State Key Laboratory of Rice Biology, Key Laboratory of Biology of Crop Pathogens and Insects, Institute of Biotechnology, Zhejiang University, Hangzhou, People’s Republic of China
| | - Chang Liu
- State Key Laboratory of Rice Biology, Key Laboratory of Biology of Crop Pathogens and Insects, Institute of Biotechnology, Zhejiang University, Hangzhou, People’s Republic of China
| | - Qiaowan Chen
- State Key Laboratory of Rice Biology, Key Laboratory of Biology of Crop Pathogens and Insects, Institute of Biotechnology, Zhejiang University, Hangzhou, People’s Republic of China
| | - Tianming Xu
- Zhejiang Research Institute of Chemical Industry, Hangzhou, People’s Republic of China
| | - Yun Chen
- State Key Laboratory of Rice Biology, Key Laboratory of Biology of Crop Pathogens and Insects, Institute of Biotechnology, Zhejiang University, Hangzhou, People’s Republic of China
| | - Youfu Zhao
- Irrigated Agriculture Research and Extension Center, Department of Plant Pathology, Washington State University, Prosser, Washington, United States of America
| | - Zhonghua Ma
- State Key Laboratory of Rice Biology, Key Laboratory of Biology of Crop Pathogens and Insects, Institute of Biotechnology, Zhejiang University, Hangzhou, People’s Republic of China
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8
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Nenadic A, Zaman MF, Johansen J, Volpiana MW, Beh CT. Increased Phospholipid Flux Bypasses Overlapping Essential Requirements for the Yeast Sac1p Phosphoinositide Phosphatase and ER-PM Membrane Contact Sites. J Biol Chem 2023; 299:105092. [PMID: 37507017 PMCID: PMC10470028 DOI: 10.1016/j.jbc.2023.105092] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2022] [Revised: 07/13/2023] [Accepted: 07/17/2023] [Indexed: 07/30/2023] Open
Abstract
In budding yeast cells, much of the inner surface of the plasma membrane (PM) is covered with the endoplasmic reticulum (ER). This association is mediated by seven ER membrane proteins that confer cortical ER-PM association at membrane contact sites (MCSs). Several of these membrane "tether" proteins are known to physically interact with the phosphoinositide phosphatase Sac1p. However, it is unclear how or if these interactions are necessary for their interdependent functions. We find that SAC1 inactivation in cells lacking the homologous synaptojanin-like genes INP52 and INP53 results in a significant increase in cortical ER-PM MCSs. We show in sac1Δ, sac1tsinp52Δ inp53Δ, or Δ-super-tether (Δ-s-tether) cells lacking all seven ER-PM tethering genes that phospholipid biosynthesis is disrupted and phosphoinositide distribution is altered. Furthermore, SAC1 deletion in Δ-s-tether cells results in lethality, indicating a functional overlap between SAC1 and ER-PM tethering genes. Transcriptomic profiling indicates that SAC1 inactivation in either Δ-s-tether or inp52Δ inp53Δ cells induces an ER membrane stress response and elicits phosphoinositide-dependent changes in expression of autophagy genes. In addition, by isolating high-copy suppressors that rescue sac1Δ Δ-s-tether lethality, we find that key phospholipid biosynthesis genes bypass the overlapping function of SAC1 and ER-PM tethers and that overexpression of the phosphatidylserine/phosphatidylinositol-4-phosphate transfer protein Osh6 also provides limited suppression. Combined with lipidomic analysis and determinations of intracellular phospholipid distributions, these results suggest that Sac1p and ER phospholipid flux controls lipid distribution to drive Osh6p-dependent phosphatidylserine/phosphatidylinositol-4-phosphate counter-exchange at ER-PM MCSs.
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Affiliation(s)
- Aleksa Nenadic
- Department of Molecular Biology and Biochemistry, Simon Fraser University, Burnaby, British Columbia, Canada
| | - Mohammad F Zaman
- Department of Molecular Biology and Biochemistry, Simon Fraser University, Burnaby, British Columbia, Canada
| | - Jesper Johansen
- Department of Molecular Biology and Biochemistry, Simon Fraser University, Burnaby, British Columbia, Canada
| | - Matthew W Volpiana
- Department of Molecular Biology and Biochemistry, Simon Fraser University, Burnaby, British Columbia, Canada
| | - Christopher T Beh
- Department of Molecular Biology and Biochemistry, Simon Fraser University, Burnaby, British Columbia, Canada; Centre for Cell Biology, Development, and Disease, Simon Fraser University, Burnaby, British Columbia, Canada.
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9
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Wilson ZN, West M, English AM, Odorizzi G, Hughes AL. Mitochondrial-Derived Compartments are Multilamellar Domains that Encase Membrane Cargo and Cytosol. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.07.07.548169. [PMID: 37461645 PMCID: PMC10350034 DOI: 10.1101/2023.07.07.548169] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 07/24/2023]
Abstract
Preserving the health of the mitochondrial network is critical to cell viability and longevity. To do so, mitochondria employ several membrane remodeling mechanisms, including the formation of mitochondrial-derived vesicles (MDVs) and compartments (MDCs) to selectively remove portions of the organelle. In contrast to well-characterized MDVs, the distinguishing features of MDC formation and composition remain unclear. Here we used electron tomography to observe that MDCs form as large, multilamellar domains that generate concentric spherical compartments emerging from mitochondrial tubules at ER-mitochondria contact sites. Time-lapse fluorescence microscopy of MDC biogenesis revealed that mitochondrial membrane extensions repeatedly elongate, coalesce, and invaginate to form these compartments that encase multiple layers of membrane. As such, MDCs strongly sequester portions of the outer mitochondrial membrane, securing membrane cargo into a protected domain, while also enclosing cytosolic material within the MDC lumen. Collectively, our results provide a model for MDC formation and describe key features that distinguish MDCs from other previously identified mitochondrial structures and cargo-sorting domains.
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Affiliation(s)
- Zachary N. Wilson
- Department of Biochemistry, University of Utah School of Medicine, Salt Lake City, UT 84112, USA
| | - Matt West
- Department of Molecular, Cellular, and Developmental Biology, University of Colorado Boulder, Boulder, CO 80309
| | - Alyssa M. English
- Department of Biochemistry, University of Utah School of Medicine, Salt Lake City, UT 84112, USA
| | - Greg Odorizzi
- Department of Molecular, Cellular, and Developmental Biology, University of Colorado Boulder, Boulder, CO 80309
| | - Adam L. Hughes
- Department of Biochemistry, University of Utah School of Medicine, Salt Lake City, UT 84112, USA
- Lead contact
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10
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Santana-Sosa S, Matos-Perdomo E, Ayra-Plasencia J, Machín F. A Yeast Mitotic Tale for the Nucleus and the Vacuoles to Embrace. Int J Mol Sci 2023; 24:9829. [PMID: 37372977 DOI: 10.3390/ijms24129829] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2023] [Revised: 06/02/2023] [Accepted: 06/03/2023] [Indexed: 06/29/2023] Open
Abstract
The morphology of the nucleus is roughly spherical in most eukaryotic cells. However, this organelle shape needs to change as the cell travels through narrow intercellular spaces during cell migration and during cell division in organisms that undergo closed mitosis, i.e., without dismantling the nuclear envelope, such as yeast. In addition, the nuclear morphology is often modified under stress and in pathological conditions, being a hallmark of cancer and senescent cells. Thus, understanding nuclear morphological dynamics is of uttermost importance, as pathways and proteins involved in nuclear shaping can be targeted in anticancer, antiaging, and antifungal therapies. Here, we review how and why the nuclear shape changes during mitotic blocks in yeast, introducing novel data that associate these changes with both the nucleolus and the vacuole. Altogether, these findings suggest a close relationship between the nucleolar domain of the nucleus and the autophagic organelle, which we also discuss here. Encouragingly, recent evidence in tumor cell lines has linked aberrant nuclear morphology to defects in lysosomal function.
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Affiliation(s)
- Silvia Santana-Sosa
- Research Unit, University Hospital Ntra Sra de Candelaria, Ctra del Rosario 145, 38010 Santa Cruz de Tenerife, Spain
- Institute of Biomedical Technologies, University of La Laguna, 38200 San Cristóbal de La Laguna, Spain
| | - Emiliano Matos-Perdomo
- Research Unit, University Hospital Ntra Sra de Candelaria, Ctra del Rosario 145, 38010 Santa Cruz de Tenerife, Spain
- Institute of Biomedical Technologies, University of La Laguna, 38200 San Cristóbal de La Laguna, Spain
| | - Jessel Ayra-Plasencia
- Research Unit, University Hospital Ntra Sra de Candelaria, Ctra del Rosario 145, 38010 Santa Cruz de Tenerife, Spain
- Institute of Biomedical Technologies, University of La Laguna, 38200 San Cristóbal de La Laguna, Spain
| | - Félix Machín
- Research Unit, University Hospital Ntra Sra de Candelaria, Ctra del Rosario 145, 38010 Santa Cruz de Tenerife, Spain
- Institute of Biomedical Technologies, University of La Laguna, 38200 San Cristóbal de La Laguna, Spain
- Faculty of Health Sciences, Fernando Pessoa Canarias University, 35450 Santa María de Guía, Spain
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11
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Amm I, Weberruss M, Hellwig A, Schwarz J, Tatarek-Nossol M, Lüchtenborg C, Kallas M, Brügger B, Hurt E, Antonin W. Distinct domains in Ndc1 mediate its interaction with the Nup84 complex and the nuclear membrane. J Cell Biol 2023; 222:e202210059. [PMID: 37154843 PMCID: PMC10165475 DOI: 10.1083/jcb.202210059] [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: 10/13/2022] [Revised: 01/31/2023] [Accepted: 03/17/2023] [Indexed: 05/10/2023] Open
Abstract
Nuclear pore complexes (NPCs) are embedded in the nuclear envelope and built from ∼30 different nucleoporins (Nups) in multiple copies, few are integral membrane proteins. One of these transmembrane nucleoporins, Ndc1, is thought to function in NPC assembly at the fused inner and outer nuclear membranes. Here, we show a direct interaction of Ndc1's transmembrane domain with Nup120 and Nup133, members of the pore membrane coating Y-complex. We identify an amphipathic helix in Ndc1's C-terminal domain binding highly curved liposomes. Upon overexpression, this amphipathic motif is toxic and dramatically alters the intracellular membrane organization in yeast. Ndc1's amphipathic motif functionally interacts with related motifs in the C-terminus of the nucleoporins Nup53 and Nup59, important for pore membrane binding and interconnecting NPC modules. The essential function of Ndc1 can be suppressed by deleting the amphipathic helix from Nup53. Our data indicate that nuclear membrane and presumably NPC biogenesis depends on a balanced ratio between amphipathic motifs in diverse nucleoporins.
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Affiliation(s)
- Ingo Amm
- Heidelberg University Biochemistry Center (BZH), University of Heidelberg, Heidelberg, Germany
| | - Marion Weberruss
- Institute of Biochemistry and Molecular Cell Biology, Medical School, RWTH Aachen University, Aachen, Germany
| | - Andrea Hellwig
- Department of Neurobiology, Interdisciplinary Center for Neurosciences (IZN), University of Heidelberg, Heidelberg, Germany
| | - Johannes Schwarz
- Heidelberg University Biochemistry Center (BZH), University of Heidelberg, Heidelberg, Germany
| | - Marianna Tatarek-Nossol
- Institute of Biochemistry and Molecular Cell Biology, Medical School, RWTH Aachen University, Aachen, Germany
| | - Christian Lüchtenborg
- Heidelberg University Biochemistry Center (BZH), University of Heidelberg, Heidelberg, Germany
| | - Martina Kallas
- Heidelberg University Biochemistry Center (BZH), University of Heidelberg, Heidelberg, Germany
| | - Britta Brügger
- Heidelberg University Biochemistry Center (BZH), University of Heidelberg, Heidelberg, Germany
| | - Ed Hurt
- Heidelberg University Biochemistry Center (BZH), University of Heidelberg, Heidelberg, Germany
| | - Wolfram Antonin
- Institute of Biochemistry and Molecular Cell Biology, Medical School, RWTH Aachen University, Aachen, Germany
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12
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Kralt A, Wojtynek M, Fischer JS, Agote-Aran A, Mancini R, Dultz E, Noor E, Uliana F, Tatarek-Nossol M, Antonin W, Onischenko E, Medalia O, Weis K. An amphipathic helix in Brl1 is required for nuclear pore complex biogenesis in S. cerevisiae. eLife 2022; 11:78385. [PMID: 36000978 PMCID: PMC9402233 DOI: 10.7554/elife.78385] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2022] [Accepted: 08/03/2022] [Indexed: 12/28/2022] Open
Abstract
The nuclear pore complex (NPC) is the central portal for macromolecular exchange between the nucleus and cytoplasm. In all eukaryotes, NPCs assemble into an intact nuclear envelope (NE) during interphase, but the process of NPC biogenesis remains poorly characterized. Furthermore, little is known about how NPC assembly leads to the fusion of the outer and inner NE, and no factors have been identified that could trigger this event. Here, we characterize the transmembrane protein Brl1 as an NPC assembly factor required for NE fusion in budding yeast. Brl1 preferentially associates with NPC assembly intermediates and its depletion halts NPC biogenesis, leading to NE herniations that contain inner and outer ring nucleoporins but lack the cytoplasmic export platform. Furthermore, we identify an essential amphipathic helix in the luminal domain of Brl1 that mediates interactions with lipid bilayers. Mutations in this amphipathic helix lead to NPC assembly defects, and cryo-electron tomography analyses reveal multilayered herniations of the inner nuclear membrane with NPC-like structures at the neck, indicating a failure in NE fusion. Taken together, our results identify a role for Brl1 in NPC assembly and suggest a function of its amphipathic helix in mediating the fusion of the inner and outer nuclear membranes.
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Affiliation(s)
- Annemarie Kralt
- Institute of Biochemistry, Department of Biology, ETH Zurich, Zurich, Switzerland
| | - Matthias Wojtynek
- Institute of Biochemistry, Department of Biology, ETH Zurich, Zurich, Switzerland.,Department of Biochemistry, University of Zurich, Zürich, Switzerland
| | - Jonas S Fischer
- Institute of Biochemistry, Department of Biology, ETH Zurich, Zurich, Switzerland
| | - Arantxa Agote-Aran
- Institute of Biochemistry, Department of Biology, ETH Zurich, Zurich, Switzerland
| | - Roberta Mancini
- Institute of Biochemistry, Department of Biology, ETH Zurich, Zurich, Switzerland
| | - Elisa Dultz
- Institute of Biochemistry, Department of Biology, ETH Zurich, Zurich, Switzerland
| | - Elad Noor
- Department of Plant and Environmental Sciences, Weizmann Institute of Science, Rehovot, Israel
| | - Federico Uliana
- Institute of Biochemistry, Department of Biology, ETH Zurich, Zurich, Switzerland
| | - Marianna Tatarek-Nossol
- Institute of Biochemistry and Molecular Cell Biology, Medical School, RWTH Aachen University, Aachen, Germany
| | - Wolfram Antonin
- Institute of Biochemistry and Molecular Cell Biology, Medical School, RWTH Aachen University, Aachen, Germany
| | - Evgeny Onischenko
- Department of Biological Sciences, University of Bergen, Bergen, Norway
| | - Ohad Medalia
- Department of Biochemistry, University of Zurich, Zürich, Switzerland
| | - Karsten Weis
- Institute of Biochemistry, Department of Biology, ETH Zurich, Zurich, Switzerland
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Recent advances in the microbial production of squalene. World J Microbiol Biotechnol 2022; 38:91. [PMID: 35426523 PMCID: PMC9010451 DOI: 10.1007/s11274-022-03273-w] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2022] [Accepted: 03/30/2022] [Indexed: 11/06/2022]
Abstract
Squalene is a triterpene hydrocarbon, a biochemical precursor for all steroids in plants and animals. It is a principal component of human surface lipids, in particular of sebum. Squalene has several applications in the food, pharmaceutical, and medical sectors. It is essentially used as a dietary supplement, vaccine adjuvant, moisturizer, cardio-protective agent, anti-tumor agent and natural antioxidant. With the increased demand for squalene along with regulations on shark-derived squalene, there is a need to find alternatives for squalene production which are low-cost as well as sustainable. Microbial platforms are being considered as a potential option to meet such challenges. Considerable progress has been made using both wild-type and engineered microbial strains for improved productivity and yields of squalene. Native strains for squalene production are usually limited by low growth rates and lesser titers. Metabolic engineering, which is a rational strain engineering tool, has enabled the development of microbial strains such as Saccharomyces cerevisiae and Yarrowia lipolytica, to overproduce the squalene in high titers. This review focuses on key strain engineering strategies involving both in-silico and in-vitro techniques. Emphasis is made on gene manipulations for improved precursor pool, enzyme modifications, cofactor regeneration, up-regulation of limiting reactions, and downregulation of competing reactions during squalene production. Process strategies and challenges related to both upstream and downstream during mass cultivation are detailed.
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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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Chandra S, Mannino PJ, Thaller DJ, Ader NR, King MC, Melia TJ, Lusk CP. Atg39 selectively captures inner nuclear membrane into lumenal vesicles for delivery to the autophagosome. J Cell Biol 2021; 220:e202103030. [PMID: 34714326 PMCID: PMC8575018 DOI: 10.1083/jcb.202103030] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2021] [Revised: 08/26/2021] [Accepted: 09/29/2021] [Indexed: 12/26/2022] Open
Abstract
Mechanisms that turn over components of the nucleus and inner nuclear membrane (INM) remain to be fully defined. We explore how components of the INM are selected by a cytosolic autophagy apparatus through a transmembrane nuclear envelope-localized cargo adaptor, Atg39. A split-GFP reporter showed that Atg39 localizes to the outer nuclear membrane (ONM) and thus targets the INM across the nuclear envelope lumen. Consistent with this, sequence elements that confer both nuclear envelope localization and a membrane remodeling activity are mapped to the Atg39 lumenal domain; these lumenal motifs are required for the autophagy-mediated degradation of integral INM proteins. Interestingly, correlative light and electron microscopy shows that the overexpression of Atg39 leads to the expansion of the ONM and the enclosure of a network of INM-derived vesicles in the nuclear envelope lumen. Thus, we propose an outside-in model of nucleophagy where INM is delivered into vesicles in the nuclear envelope lumen, which can be targeted by the autophagosome.
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Affiliation(s)
| | | | | | | | | | - Thomas J. Melia
- Department of Cell Biology, Yale School of Medicine, New Haven, CT
| | - C. Patrick Lusk
- Department of Cell Biology, Yale School of Medicine, New Haven, CT
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16
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Grados-Torrez RE, López-Iglesias C, Ferrer JC, Campos N. Loose Morphology and High Dynamism of OSER Structures Induced by the Membrane Domain of HMG-CoA Reductase. Int J Mol Sci 2021; 22:ijms22179132. [PMID: 34502042 PMCID: PMC8430881 DOI: 10.3390/ijms22179132] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2021] [Revised: 08/18/2021] [Accepted: 08/21/2021] [Indexed: 11/16/2022] Open
Abstract
The membrane domain of eukaryotic HMG-CoA reductase (HMGR) has the conserved capacity to induce endoplasmic reticulum (ER) proliferation and membrane association into Organized Smooth Endoplasmic Reticulum (OSER) structures. These formations develop in response to overexpression of particular proteins, but also occur naturally in cells of the three eukaryotic kingdoms. Here, we characterize OSER structures induced by the membrane domain of Arabidopsis HMGR (1S domain). Immunochemical confocal and electron microscopy studies demonstrate that the 1S:GFP chimera co-localizes with high levels of endogenous HMGR in several ER compartments, such as the ER network, the nuclear envelope, the outer and internal membranes of HMGR vesicles and the OSER structures, which we name ER-HMGR domains. After high-pressure freezing, ER-HMGR domains show typical crystalloid, whorled and lamellar ultrastructural patterns, but with wide heterogeneous luminal spaces, indicating that the native OSER is looser and more flexible than previously reported. The formation of ER-HMGR domains is reversible. OSER structures grow by incorporation of ER membranes on their periphery and progressive compaction to the inside. The ER-HMGR domains are highly dynamic in their formation versus their disassembly, their variable spherical-ovoid shape, their fluctuating borders and their rapid intracellular movement, indicating that they are not mere ER membrane aggregates, but active components of the eukaryotic cell.
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Affiliation(s)
- Ricardo Enrique Grados-Torrez
- Centre for Research in Agricultural Genomics (CRAG) CSIC-IRTA-UAB-UB, Department of Molecular Genetics, Campus UAB, Bellaterra (Cerdanyola del Vallès), 08193 Barcelona, Spain;
| | - Carmen López-Iglesias
- Scientific and Technological Centers, University of Barcelona, 08028 Barcelona, Spain;
- Microscopy CORE Lab, Maastricht Multimodal Molecular Imaging Institute, Maastricht University, 6229 ER Maastricht, The Netherlands
| | - Joan Carles Ferrer
- Department of Biochemistry and Molecular Biomedicine, Faculty of Biology, University of Barcelona, 08028 Barcelona, Spain;
| | - Narciso Campos
- Centre for Research in Agricultural Genomics (CRAG) CSIC-IRTA-UAB-UB, Department of Molecular Genetics, Campus UAB, Bellaterra (Cerdanyola del Vallès), 08193 Barcelona, Spain;
- Department of Biochemistry and Molecular Biomedicine, Faculty of Biology, University of Barcelona, 08028 Barcelona, Spain;
- Correspondence:
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Ni X, Jin C, Liu A, Chen Y, Hu Y. Physiological and transcriptomic analyses to reveal underlying phenolic acid action in consecutive monoculture problem of Polygonatum odoratum. BMC PLANT BIOLOGY 2021; 21:362. [PMID: 34364388 PMCID: PMC8349006 DOI: 10.1186/s12870-021-03135-x] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 03/23/2021] [Accepted: 07/25/2021] [Indexed: 06/13/2023]
Abstract
BACKGROUND The root rot of fragrant solomonseal (Polygonatum odoratum) has occurred frequently in the traditional P. odoratum cultivating areas in recent years, causing a heavy loss in yield and quality. The phenolic acids in soil, which are the exudates from the P. odoratum root, act as allelochemicals that contribute to the consecutive monoculture problem (CMP) of the medicinal plant. The aim of this study was to get a better understanding of P. odoratum CMP. RESULTS The phenolic acid contents, the nutrient chemical contents, and the enzyme activities related to the soil nutrient metabolism in the first cropping (FC) soil and continuous cropping (CC) soil were determined, and the differentially expressed genes (DEGs) related to the regulation of the phenolic acids in roots were analyzed. The results showed that five low-molecule-weight phenolic acids were detected both in the CC soil and FC soil, but the phenolic acid contents in the CC soil were significantly higher than those in the FC soil except vanillic acid. The contents of the available nitrogen, available phosphorus, and available potassium in the CC soil were significantly decreased, and the activities of urease and sucrase in the CC soil were significantly decreased. The genomic analysis showed that the phenolic acid anabolism in P. odoratum in the CC soil was promoted. These results indicated that the phenolic acids were accumulated in the CC soil, the nutrient condition in the CC soil deteriorated, and the nitrogen metabolism and sugar catabolism of the CC soil were lowered. Meantime, the anabolism of phenolic acids was increased in the CC plant. CONCLUSIONS The CC system promoted the phenolic acid anabolism in P. odoratum and made phenolic acids accumulate in the soil.
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Affiliation(s)
- Xianzhi Ni
- Collaborative Innovation Center for Field Weeds Control of Hunan Province, Hunan University of Humanities, Science and Technology, Loudi, 417000, China
| | - Chenzhong Jin
- Collaborative Innovation Center for Field Weeds Control of Hunan Province, Hunan University of Humanities, Science and Technology, Loudi, 417000, China
| | - Aiyu Liu
- College of Agronomy, Hunan Agricultural University, Changsha, 410128, China
| | - Yong Chen
- Collaborative Innovation Center for Field Weeds Control of Hunan Province, Hunan University of Humanities, Science and Technology, Loudi, 417000, China.
| | - Yihong Hu
- Collaborative Innovation Center for Field Weeds Control of Hunan Province, Hunan University of Humanities, Science and Technology, Loudi, 417000, China.
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Deolal P, Mishra K. Regulation of diverse nuclear shapes: pathways working independently, together. Commun Integr Biol 2021; 14:158-175. [PMID: 34262635 PMCID: PMC8259725 DOI: 10.1080/19420889.2021.1939942] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2021] [Revised: 06/02/2021] [Accepted: 06/03/2021] [Indexed: 12/16/2022] Open
Abstract
Membrane-bound organelles provide physical and functional compartmentalization of biological processes in eukaryotic cells. The characteristic shape and internal organization of these organelles is determined by a combination of multiple internal and external factors. The maintenance of the shape of nucleus, which houses the genetic material within a double membrane bilayer, is crucial for a seamless spatio-temporal control over nuclear and cellular functions. Dynamic morphological changes in the shape of nucleus facilitate various biological processes. Chromatin packaging, nuclear and cytosolic protein organization, and nuclear membrane lipid homeostasis are critical determinants of overall nuclear morphology. As such, a multitude of molecular players and pathways act together to regulate the nuclear shape. Here, we review the known mechanisms governing nuclear shape in various unicellular and multicellular organisms, including the non-spherical nuclei and non-lamin-related structural determinants. The review also touches upon cellular consequences of aberrant nuclear morphologies.
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Affiliation(s)
- Pallavi Deolal
- Department of Biochemistry, School of Life Sciences, University of Hyderabad, Hyderabad, India
| | - Krishnaveni Mishra
- Department of Biochemistry, School of Life Sciences, University of Hyderabad, Hyderabad, India
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19
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Mechanism of Nuclear Lamina Disruption and the Role of pUS3 in HSV-1 Nuclear Egress. J Virol 2021; 95:JVI.02432-20. [PMID: 33658339 PMCID: PMC8139644 DOI: 10.1128/jvi.02432-20] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Herpes simplex virus capsid envelopment at the nuclear membrane is coordinated by nuclear egress complex (NEC) proteins, pUL34 and pUL31, and is accompanied by alteration in the nuclear architecture and local disruption of nuclear lamina. Here, we examined the role of capsid envelopment in the changes of the nuclear architecture by characterizing HSV-1 recombinants that do not form capsids. Typical changes in nuclear architecture and disruption of the lamina were observed in the absence of capsids, suggesting that disruption of the nuclear lamina occurs prior to capsid envelopment. Surprisingly, in the absence of capsid envelopment, lamin A/C becomes concentrated at the nuclear envelope in a pUL34-independent and cell type-specific manner, suggesting that ongoing nuclear egress may be required for the dispersal of lamins observed in wild-type infection. Mutation of virus-encoded protein kinase, pUS3, on a wild-type virus background has been shown to cause accumulation of perinuclear enveloped capsids, formation of NEC aggregates, and exacerbated lamina disruption. We observed that mutation of US3 in the absence of capsids results in identical NEC aggregation and lamina disruption phenotypes, suggesting that they do not result from accumulation of perinuclear virions. TEM analysis revealed that, in the absence of capsids, NEC aggregates correspond to multi-folded nuclear membrane structures, suggesting that pUS3 may control NEC self-association and membrane deformation. To determine the significance of the pUS3 nuclear egress function for virus growth, the replication of single and double UL34 and US3 mutants was measured, showing that the significance of pUS3 nuclear egress function is cell-type specific.ImportanceThe nuclear lamina is an important player in infection by viruses that replicate in the nucleus. Herpesviruses alter the structure of the nuclear lamina to facilitate transport of capsids from the nucleus to the cytoplasm and use both viral and cellular effectors to disrupt the protein-protein interactions that maintain the lamina. Here we explore the role of capsid envelopment and the virus-encoded protein kinase, pUS3, in the disruption of lamina structure. We show that capsid envelopment is not necessary for the lamina disruption, or for US3 mutant phenotypes, including exaggerated lamina disruption, that accompany nuclear egress. These results clarify the mechanisms behind alteration of nuclear lamina structure and support a function for pUS3 in regulating the aggregation state of the nuclear egress machinery.
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20
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Royes J, Biou V, Dautin N, Tribet C, Miroux B. Inducible intracellular membranes: molecular aspects and emerging applications. Microb Cell Fact 2020; 19:176. [PMID: 32887610 PMCID: PMC7650269 DOI: 10.1186/s12934-020-01433-x] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2020] [Accepted: 08/27/2020] [Indexed: 02/08/2023] Open
Abstract
Membrane remodeling and phospholipid biosynthesis are normally tightly regulated to maintain the shape and function of cells. Indeed, different physiological mechanisms ensure a precise coordination between de novo phospholipid biosynthesis and modulation of membrane morphology. Interestingly, the overproduction of certain membrane proteins hijack these regulation networks, leading to the formation of impressive intracellular membrane structures in both prokaryotic and eukaryotic cells. The proteins triggering an abnormal accumulation of membrane structures inside the cells (or membrane proliferation) share two major common features: (1) they promote the formation of highly curved membrane domains and (2) they lead to an enrichment in anionic, cone-shaped phospholipids (cardiolipin or phosphatidic acid) in the newly formed membranes. Taking into account the available examples of membrane proliferation upon protein overproduction, together with the latest biochemical, biophysical and structural data, we explore the relationship between protein synthesis and membrane biogenesis. We propose a mechanism for the formation of these non-physiological intracellular membranes that shares similarities with natural inner membrane structures found in α-proteobacteria, mitochondria and some viruses-infected cells, pointing towards a conserved feature through evolution. We hope that the information discussed in this review will give a better grasp of the biophysical mechanisms behind physiological and induced intracellular membrane proliferation, and inspire new applications, either for academia (high-yield membrane protein production and nanovesicle production) or industry (biofuel production and vaccine preparation).
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Affiliation(s)
- Jorge Royes
- Laboratoire de Biologie Physico-Chimique des Protéines Membranaires, Université de Paris, LBPC-PM, CNRS, UMR7099, 75005, Paris, France. .,Institut de Biologie Physico-Chimique, Fondation Edmond de Rothschild pour le Développement de la Recherche Scientifique, 75005, Paris, France. .,Département de Chimie, École Normale Supérieure, PASTEUR, PSL University, CNRS, Sorbonne Université, 24 Rue Lhomond, 75005, Paris, France.
| | - Valérie Biou
- Laboratoire de Biologie Physico-Chimique des Protéines Membranaires, Université de Paris, LBPC-PM, CNRS, UMR7099, 75005, Paris, France.,Institut de Biologie Physico-Chimique, Fondation Edmond de Rothschild pour le Développement de la Recherche Scientifique, 75005, Paris, France
| | - Nathalie Dautin
- Laboratoire de Biologie Physico-Chimique des Protéines Membranaires, Université de Paris, LBPC-PM, CNRS, UMR7099, 75005, Paris, France.,Institut de Biologie Physico-Chimique, Fondation Edmond de Rothschild pour le Développement de la Recherche Scientifique, 75005, Paris, France
| | - Christophe Tribet
- Département de Chimie, École Normale Supérieure, PASTEUR, PSL University, CNRS, Sorbonne Université, 24 Rue Lhomond, 75005, Paris, France
| | - Bruno Miroux
- Laboratoire de Biologie Physico-Chimique des Protéines Membranaires, Université de Paris, LBPC-PM, CNRS, UMR7099, 75005, Paris, France. .,Institut de Biologie Physico-Chimique, Fondation Edmond de Rothschild pour le Développement de la Recherche Scientifique, 75005, Paris, France.
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Schäfer JA, Schessner JP, Bircham PW, Tsuji T, Funaya C, Pajonk O, Schaeff K, Ruffini G, Papagiannidis D, Knop M, Fujimoto T, Schuck S. ESCRT machinery mediates selective microautophagy of endoplasmic reticulum in yeast. EMBO J 2020; 39:e102586. [PMID: 31802527 PMCID: PMC6960443 DOI: 10.15252/embj.2019102586] [Citation(s) in RCA: 71] [Impact Index Per Article: 17.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2019] [Revised: 10/30/2019] [Accepted: 11/11/2019] [Indexed: 01/14/2023] Open
Abstract
ER-phagy, the selective autophagy of endoplasmic reticulum (ER), safeguards organelle homeostasis by eliminating misfolded proteins and regulating ER size. ER-phagy can occur by macroautophagic and microautophagic mechanisms. While dedicated machinery for macro-ER-phagy has been discovered, the molecules and mechanisms mediating micro-ER-phagy remain unknown. Here, we first show that micro-ER-phagy in yeast involves the conversion of stacked cisternal ER into multilamellar ER whorls during microautophagic uptake into lysosomes. Second, we identify the conserved Nem1-Spo7 phosphatase complex and the ESCRT machinery as key components for micro-ER-phagy. Third, we demonstrate that macro- and micro-ER-phagy are parallel pathways with distinct molecular requirements. Finally, we provide evidence that the ESCRT machinery directly functions in scission of the lysosomal membrane to complete the microautophagic uptake of ER. These findings establish a framework for a mechanistic understanding of micro-ER-phagy and, thus, a comprehensive appreciation of the role of autophagy in ER homeostasis.
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Affiliation(s)
- Jasmin A Schäfer
- DKFZ‐ZMBH Alliance and CellNetworks Cluster of ExcellenceCenter for Molecular Biology of Heidelberg University (ZMBH)HeidelbergGermany
| | - Julia P Schessner
- DKFZ‐ZMBH Alliance and CellNetworks Cluster of ExcellenceCenter for Molecular Biology of Heidelberg University (ZMBH)HeidelbergGermany
- Present address:
Department of Proteomics and Signal TransductionMax Planck Institute of BiochemistryMartinsriedGermany
| | - Peter W Bircham
- DKFZ‐ZMBH Alliance and CellNetworks Cluster of ExcellenceCenter for Molecular Biology of Heidelberg University (ZMBH)HeidelbergGermany
- Present address:
Laboratory of Systems BiologyVIB Center for Microbiology/Laboratory of Genetics and GenomicsCMPGKU LeuvenLeuvenBelgium
| | - Takuma Tsuji
- Research Institute for Diseases of Old AgeJuntendo University Graduate School of MedicineTokyoJapan
| | - Charlotta Funaya
- Electron Microscopy Core FacilityHeidelberg UniversityHeidelbergGermany
| | - Oliver Pajonk
- DKFZ‐ZMBH Alliance and CellNetworks Cluster of ExcellenceCenter for Molecular Biology of Heidelberg University (ZMBH)HeidelbergGermany
| | - Katharina Schaeff
- DKFZ‐ZMBH Alliance and CellNetworks Cluster of ExcellenceCenter for Molecular Biology of Heidelberg University (ZMBH)HeidelbergGermany
| | - Giulia Ruffini
- DKFZ‐ZMBH Alliance and CellNetworks Cluster of ExcellenceCenter for Molecular Biology of Heidelberg University (ZMBH)HeidelbergGermany
| | - Dimitrios Papagiannidis
- DKFZ‐ZMBH Alliance and CellNetworks Cluster of ExcellenceCenter for Molecular Biology of Heidelberg University (ZMBH)HeidelbergGermany
| | - Michael Knop
- DKFZ‐ZMBH Alliance and CellNetworks Cluster of ExcellenceCenter for Molecular Biology of Heidelberg University (ZMBH)HeidelbergGermany
| | - Toyoshi Fujimoto
- Research Institute for Diseases of Old AgeJuntendo University Graduate School of MedicineTokyoJapan
| | - Sebastian Schuck
- DKFZ‐ZMBH Alliance and CellNetworks Cluster of ExcellenceCenter for Molecular Biology of Heidelberg University (ZMBH)HeidelbergGermany
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Kim JE, Jang IS, Son SH, Ko YJ, Cho BK, Kim SC, Lee JY. Tailoring the Saccharomyces cerevisiae endoplasmic reticulum for functional assembly of terpene synthesis pathway. Metab Eng 2019; 56:50-59. [DOI: 10.1016/j.ymben.2019.08.013] [Citation(s) in RCA: 55] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2019] [Revised: 07/17/2019] [Accepted: 08/17/2019] [Indexed: 10/26/2022]
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Arhar S, Natter K. Common aspects in the engineering of yeasts for fatty acid- and isoprene-based products. Biochim Biophys Acta Mol Cell Biol Lipids 2019; 1864:158513. [PMID: 31465888 DOI: 10.1016/j.bbalip.2019.08.009] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2019] [Revised: 06/26/2019] [Accepted: 08/20/2019] [Indexed: 11/18/2022]
Abstract
The biosynthetic pathways for most lipophilic metabolites share several common principles. These substances are built almost exclusively from acetyl-CoA as the donor for the carbon scaffold and NADPH is required for the reductive steps during biosynthesis. Due to their hydrophobicity, the end products are sequestered into the same cellular compartment, the lipid droplet. In this review, we will summarize the efforts in the metabolic engineering of yeasts for the production of two major hydrophobic substance classes, fatty acid-based lipids and isoprenoids, with regard to these common aspects. We will compare and discuss the results of genetic engineering strategies to construct strains with enhanced synthesis of the precursor acetyl-CoA and with modified redox metabolism for improved NADPH supply. We will also discuss the role of the lipid droplet in the storage of the hydrophobic product and review the strategies to either optimize this organelle for higher capacity or to achieve excretion of the product into the medium.
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Affiliation(s)
- Simon Arhar
- Institute of Molecular Biosciences, NAWI Graz, University of Graz, Humboldtstrasse 50/II, 8010 Graz, Austria
| | - Klaus Natter
- Institute of Molecular Biosciences, NAWI Graz, University of Graz, Humboldtstrasse 50/II, 8010 Graz, Austria.
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Garapati HS, Mishra K. Comparative genomics of nuclear envelope proteins. BMC Genomics 2018; 19:823. [PMID: 30445911 PMCID: PMC6240307 DOI: 10.1186/s12864-018-5218-4] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2018] [Accepted: 10/31/2018] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND The nuclear envelope (NE) that encapsulates the nuclear genome is a double lipid bilayer with several integral and peripherally associated proteins. It is a characteristic feature of the eukaryotes and acts as a hub for a number of important nuclear events including transcription, repair, and regulated gene expression. The proteins associated with the nuclear envelope mediate the NE functions and maintain its structural integrity, which is crucial for survival. In spite of the importance of this structure, knowledge of the protein composition of the nuclear envelope and their function, are limited to very few organisms belonging to Opisthokonta and Archaeplastida supergroups. The NE composition is largely unknown in organisms outside these two supergroups. RESULTS In this study, we have taken a comparative sequence analysis approach to identify the NE proteome that is present across all five eukaryotic supergroups. We identified 22 proteins involved in various nuclear functions to be part of the core NE proteome. The presence of these proteins across eukaryotes, suggests that they are traceable to the Last Eukaryotic Common Ancestor (LECA). Additionally, we also identified the NE proteins that have evolved in a lineage specific manner and those that have been preserved only in a subset of organisms. CONCLUSIONS Our study identifies the conserved features of the nuclear envelope across eukaryotes and provides insights into the potential composition and the functionalities that were constituents of the LECA NE.
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Affiliation(s)
- Hita Sony Garapati
- Department of Biochemistry, School of Life Sciences, University of Hyderabad, Hyderabad, 500046, India
| | - Krishnaveni Mishra
- Department of Biochemistry, School of Life Sciences, University of Hyderabad, Hyderabad, 500046, India.
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Pichler H, Emmerstorfer-Augustin A. Modification of membrane lipid compositions in single-celled organisms – From basics to applications. Methods 2018; 147:50-65. [DOI: 10.1016/j.ymeth.2018.06.009] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2018] [Revised: 05/18/2018] [Accepted: 06/16/2018] [Indexed: 12/12/2022] Open
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Paramasivan K, Rajagopal K, Mutturi S. Studies on Squalene Biosynthesis and the Standardization of Its Extraction Methodology from Saccharomyces cerevisiae. Appl Biochem Biotechnol 2018; 187:691-707. [DOI: 10.1007/s12010-018-2845-9] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2018] [Accepted: 07/16/2018] [Indexed: 10/28/2022]
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Strunov A, Boldyreva LV, Andreyeva EN, Pavlova GA, Popova JV, Razuvaeva AV, Anders AF, Renda F, Pindyurin AV, Gatti M, Kiseleva E. Ultrastructural analysis of mitotic Drosophila S2 cells identifies distinctive microtubule and intracellular membrane behaviors. BMC Biol 2018; 16:68. [PMID: 29907103 PMCID: PMC6003134 DOI: 10.1186/s12915-018-0528-1] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2018] [Accepted: 05/08/2018] [Indexed: 12/31/2022] Open
Abstract
BACKGROUND S2 cells are one of the most widely used Drosophila melanogaster cell lines. A series of studies has shown that they are particularly suitable for RNAi-based screens aimed at the dissection of cellular pathways, including those controlling cell shape and motility, cell metabolism, and host-pathogen interactions. In addition, RNAi in S2 cells has been successfully used to identify many new mitotic genes that are conserved in the higher eukaryotes, and for the analysis of several aspects of the mitotic process. However, no detailed and complete description of S2 cell mitosis at the ultrastructural level has been done. Here, we provide a detailed characterization of all phases of S2 cell mitosis visualized by transmission electron microscopy (TEM). RESULTS We analyzed by TEM a random sample of 144 cells undergoing mitosis, focusing on intracellular membrane and microtubule (MT) behaviors. This unbiased approach provided a comprehensive ultrastructural view of the dividing cells, and allowed us to discover that S2 cells exhibit a previously uncharacterized behavior of intracellular membranes, involving the formation of a quadruple nuclear membrane in early prometaphase and its disassembly during late prometaphase. After nuclear envelope disassembly, the mitotic apparatus becomes encased by a discontinuous network of endoplasmic reticulum membranes, which associate with mitochondria, presumably to prevent their diffusion into the spindle area. We also observed a peculiar metaphase spindle organization. We found that kinetochores with attached k-fibers are almost invariably associated with lateral MT bundles that can be either interpolar bundles or k-fibers connected to a different kinetochore. This spindle organization is likely to favor chromosome alignment at metaphase and subsequent segregation during anaphase. CONCLUSIONS We discovered several previously unknown features of membrane and MT organization during S2 cell mitosis. The genetic determinants of these mitotic features can now be investigated, for instance by using an RNAi-based approach, which is particularly easy and efficient in S2 cells.
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Affiliation(s)
- Anton Strunov
- Institute of Molecular and Cellular Biology, Siberian Branch of RAS, Novosibirsk, 630090, Russia.
- Institute of Cytology and Genetics, Siberian Branch of RAS, Novosibirsk, 630090, Russia.
| | - Lidiya V Boldyreva
- Institute of Molecular and Cellular Biology, Siberian Branch of RAS, Novosibirsk, 630090, Russia
| | - Evgeniya N Andreyeva
- Institute of Molecular and Cellular Biology, Siberian Branch of RAS, Novosibirsk, 630090, Russia
| | - Gera A Pavlova
- Institute of Molecular and Cellular Biology, Siberian Branch of RAS, Novosibirsk, 630090, Russia
| | - Julia V Popova
- Institute of Molecular and Cellular Biology, Siberian Branch of RAS, Novosibirsk, 630090, Russia
- Institute of Cytology and Genetics, Siberian Branch of RAS, Novosibirsk, 630090, Russia
| | - Alena V Razuvaeva
- Institute of Molecular and Cellular Biology, Siberian Branch of RAS, Novosibirsk, 630090, Russia
- Novosibirsk State University, Novosibirsk, 630090, Russia
| | - Alina F Anders
- Institute of Molecular and Cellular Biology, Siberian Branch of RAS, Novosibirsk, 630090, Russia
- Novosibirsk State University, Novosibirsk, 630090, Russia
| | - Fioranna Renda
- IBPM CNR and Department of Biology and Biotechnology, Sapienza University of Rome, 00185, Rome, Italy
- Present address: Wadsworth Center, New York State Department of Health, Albany, NY, 12201, USA
| | - Alexey V Pindyurin
- Institute of Molecular and Cellular Biology, Siberian Branch of RAS, Novosibirsk, 630090, Russia
- Institute of Cytology and Genetics, Siberian Branch of RAS, Novosibirsk, 630090, Russia
- Novosibirsk State University, Novosibirsk, 630090, Russia
| | - Maurizio Gatti
- Institute of Molecular and Cellular Biology, Siberian Branch of RAS, Novosibirsk, 630090, Russia.
- IBPM CNR and Department of Biology and Biotechnology, Sapienza University of Rome, 00185, Rome, Italy.
| | - Elena Kiseleva
- Institute of Molecular and Cellular Biology, Siberian Branch of RAS, Novosibirsk, 630090, Russia
- Institute of Cytology and Genetics, Siberian Branch of RAS, Novosibirsk, 630090, Russia
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Paramasivan K, Mutturi S. Regeneration of NADPH Coupled with HMG-CoA Reductase Activity Increases Squalene Synthesis in Saccharomyces cerevisiae. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2017; 65:8162-8170. [PMID: 28845666 DOI: 10.1021/acs.jafc.7b02945] [Citation(s) in RCA: 52] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/07/2023]
Abstract
Although overexpression of the tHMG1 gene is a well-known strategy for terpene synthesis in Saccharomyces cerevisiae, the optimal level for tHMG1p has not been established. In the present study, it was observed that two copies of the tHMG1 gene on a dual gene expression cassette improved squalene synthesis in laboratory strain by 16.8-fold in comparison to single-copy expression. It was also observed that tHMG1p is limited by its cofactor (NADPH), as the overexpression of NADPH regenerating genes', viz., ZWF1 and POS5 (full length and without mitochondrial presequence), has led to its increased enzyme activity. Further, it was demonstrated that overexpression of full-length POS5 has improved squalene synthesis in cytosol. Finally, when tHMG1 and full-length POS5 were co-overexpressed there was a net 27.5-fold increase in squalene when compared to control strain. These results suggest novel strategies to increase squalene accumulation in S. cerevisiae.
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Affiliation(s)
- Kalaivani Paramasivan
- Microbiology and Fermentation Technology Department, CSIR-Central Food Technological Research Institute , Mysore, India
- Academy of Scientific and Innovative Research , Mysore, New Delhi, India
| | - Sarma Mutturi
- Microbiology and Fermentation Technology Department, CSIR-Central Food Technological Research Institute , Mysore, India
- Academy of Scientific and Innovative Research , Mysore, New Delhi, India
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29
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Qu S, Chapman N, Xia Z, Feng M, Feng S, Wang Z, Liu L. Ultramicroscopy reveals a layer of multiply folded membranes around the tannin-accumulating vacuole in honeysuckle petal trichomes. Micron 2017; 99:1-8. [PMID: 28395186 DOI: 10.1016/j.micron.2017.03.013] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2017] [Revised: 03/23/2017] [Accepted: 03/24/2017] [Indexed: 12/17/2022]
Abstract
Transmission electron microscopy was used to reveal a layer of multiply folded membranes that closely surrounded the tannin-accumulating vacuole in cells of honeysuckle petal trichomes. A huge amount of tannins were deposited in the peripheral region and the center of the vacuole. The prolific membranes extended to the tannins deposited along the vacuole periphery. It was difficult to distinguish the vacuole membrane, and it seemed as if it was the layer of multiply folded membranes that separated the vacuole lumen from the cytoplasm. In addition, there were also membrane assemblies in the cytoplasm away from the vacuole, which were continuous with the proliferated membranes bordering the vacuole. Therefore, the tannin-accumulating vacuole was in close association with a very large network of proliferated membranes. The occurrence of such a layer of multiply folded membranes around the tannin-accumulating vacuole might be a structural strategy for improvement of the efficiency of vacuolar accumulation of tannins.
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Affiliation(s)
- Shengnan Qu
- College of Pharmacy, Linyi University, Linyi 276000, China
| | - Navid Chapman
- Department of Chemistry, University of Rhode Island, Kingston, RI 02881, USA
| | - Zhengyan Xia
- College of Pharmacy, Linyi University, Linyi 276000, China
| | - Mingxiao Feng
- Department of Life Science, Linyi University, Linyi 276000, China; Department of Biological Sciences, University of South Carolina, Columbia, SC 29208, USA(1)
| | - Shangcai Feng
- College of Pharmacy, Linyi University, Linyi 276000, China
| | - Zhen Wang
- College of Pharmacy, Linyi University, Linyi 276000, China
| | - Lin Liu
- College of Pharmacy, Linyi University, Linyi 276000, China.
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30
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Boenisch MJ, Broz KL, Purvine SO, Chrisler WB, Nicora CD, Connolly LR, Freitag M, Baker SE, Kistler HC. Structural reorganization of the fungal endoplasmic reticulum upon induction of mycotoxin biosynthesis. Sci Rep 2017; 7:44296. [PMID: 28287158 PMCID: PMC5347122 DOI: 10.1038/srep44296] [Citation(s) in RCA: 61] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2016] [Accepted: 02/06/2017] [Indexed: 12/29/2022] Open
Abstract
Compartmentalization of metabolic pathways to particular organelles is a hallmark of eukaryotic cells. Knowledge of the development of organelles and attendant pathways under different metabolic states has been advanced by live cell imaging and organelle specific analysis. Nevertheless, relatively few studies have addressed the cellular localization of pathways for synthesis of fungal secondary metabolites, despite their importance as bioactive compounds with significance to medicine and agriculture. When triggered to produce sesquiterpene (trichothecene) mycotoxins, the endoplasmic reticulum (ER) of the phytopathogenic fungus Fusarium graminearum is reorganized both in vitro and in planta. Trichothecene biosynthetic enzymes accumulate in organized smooth ER with pronounced expansion at perinuclear- and peripheral positions. Fluorescence tagged trichothecene biosynthetic proteins co-localize with the modified ER as confirmed by co-fluorescence and co-purification with known ER proteins. We hypothesize that changes to the fungal ER represent a conserved process in specialized eukaryotic cells such as in mammalian hepatocytes and B-cells.
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Affiliation(s)
| | | | | | | | | | - Lanelle Reine Connolly
- Department of Biochemistry and Biophysics, Oregon State University, Corvallis, OR 97331, USA
| | - Michael Freitag
- Department of Biochemistry and Biophysics, Oregon State University, Corvallis, OR 97331, USA
| | | | - Harold Corby Kistler
- USDA ARS Cereal Disease Laboratory, St. Paul, MN 55108, USA.,Department of Plant Pathology, University of Minnesota, St. Paul, MN 55108, USA
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31
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Reider Apel A, d'Espaux L, Wehrs M, Sachs D, Li RA, Tong GJ, Garber M, Nnadi O, Zhuang W, Hillson NJ, Keasling JD, Mukhopadhyay A. A Cas9-based toolkit to program gene expression in Saccharomyces cerevisiae. Nucleic Acids Res 2017; 45:496-508. [PMID: 27899650 PMCID: PMC5224472 DOI: 10.1093/nar/gkw1023] [Citation(s) in RCA: 168] [Impact Index Per Article: 24.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2016] [Revised: 10/12/2016] [Accepted: 10/18/2016] [Indexed: 01/08/2023] Open
Abstract
Despite the extensive use of Saccharomyces cerevisiae as a platform for synthetic biology, strain engineering remains slow and laborious. Here, we employ CRISPR/Cas9 technology to build a cloning-free toolkit that addresses commonly encountered obstacles in metabolic engineering, including chromosomal integration locus and promoter selection, as well as protein localization and solubility. The toolkit includes 23 Cas9-sgRNA plasmids, 37 promoters of various strengths and temporal expression profiles, and 10 protein-localization, degradation and solubility tags. We facilitated the use of these parts via a web-based tool, that automates the generation of DNA fragments for integration. Our system builds upon existing gene editing methods in the thoroughness with which the parts are standardized and characterized, the types and number of parts available and the ease with which our methodology can be used to perform genetic edits in yeast. We demonstrated the applicability of this toolkit by optimizing the expression of a challenging but industrially important enzyme, taxadiene synthase (TXS). This approach enabled us to diagnose an issue with TXS solubility, the resolution of which yielded a 25-fold improvement in taxadiene production.
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Affiliation(s)
- Amanda Reider Apel
- DOE Joint BioEnergy Institute, Emeryville, California, CA 94608, USA
- Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, California, CA 94720, USA
| | - Leo d'Espaux
- DOE Joint BioEnergy Institute, Emeryville, California, CA 94608, USA
- Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, California, CA 94720, USA
| | - Maren Wehrs
- DOE Joint BioEnergy Institute, Emeryville, California, CA 94608, USA
- Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, California, CA 94720, USA
| | - Daniel Sachs
- DOE Joint BioEnergy Institute, Emeryville, California, CA 94608, USA
- Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, California, CA 94720, USA
| | - Rachel A Li
- DOE Joint BioEnergy Institute, Emeryville, California, CA 94608, USA
- Department of Plant and Microbial Biology, University of California, Berkeley, California, CA 94720, USA
| | - Gary J Tong
- DOE Joint BioEnergy Institute, Emeryville, California, CA 94608, USA
- Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, California, CA 94720, USA
| | - Megan Garber
- DOE Joint BioEnergy Institute, Emeryville, California, CA 94608, USA
- Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, California, CA 94720, USA
| | - Oge Nnadi
- DOE Joint BioEnergy Institute, Emeryville, California, CA 94608, USA
- Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, California, CA 94720, USA
| | - William Zhuang
- Department of Chemical and Biomolecular Engineering, University of California, Berkeley, California, CA 94720, USA
| | - Nathan J Hillson
- DOE Joint BioEnergy Institute, Emeryville, California, CA 94608, USA
- Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, California, CA 94720, USA
- DOE Joint Genome Institute, Walnut Creek, California, CA 94598, USA
| | - Jay D Keasling
- DOE Joint BioEnergy Institute, Emeryville, California, CA 94608, USA
- Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, California, CA 94720, USA
- Department of Chemical and Biomolecular Engineering, University of California, Berkeley, California, CA 94720, USA
- DOE Joint Genome Institute, Walnut Creek, California, CA 94598, USA
- The Novo Nordisk Foundation Center for Sustainability, Technical University of Denmark, 2800 Kgs. Lyngby, Denmark
| | - Aindrila Mukhopadhyay
- DOE Joint BioEnergy Institute, Emeryville, California, CA 94608, USA
- Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, California, CA 94720, USA
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Abstract
Squalene is a precursor in the eukaryotic sterol biosynthesis. It is a valuable compound with several human health-related applications. Since the traditional natural resources of squalene are limited, alternatives for the production of squalene on industrial scale have been intensively explored during past years. The yeast Saccharomyces cerevisiae represents an attractive option due to elaborated techniques of genetic and metabolic engineering that can be applied to improve squalene yields. We discuss in this chapter some theoretical aspects of genetic manipulations of the ergosterol biosynthesis pathway aimed at increased squalene production and describe analytical methods for squalene purification and determination of its content in yeast cells.
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Affiliation(s)
- Martin Valachovič
- Institute of Animal Biochemistry and Genetics, Slovak Academy of Sciences, Moyzesova 61, 90028, Ivanka pri Dunaji, Slovakia
| | - Ivan Hapala
- Institute of Animal Biochemistry and Genetics, Slovak Academy of Sciences, Moyzesova 61, 90028, Ivanka pri Dunaji, Slovakia.
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33
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Chemudupati M, Osmani AH, Osmani SA. A mitotic nuclear envelope tether for Gle1 also impacts nuclear and nucleolar architecture. Mol Biol Cell 2016; 27:mbc.E16-07-0544. [PMID: 27630260 PMCID: PMC5170558 DOI: 10.1091/mbc.e16-07-0544] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2016] [Revised: 09/06/2016] [Accepted: 09/08/2016] [Indexed: 01/16/2023] Open
Abstract
During Aspergillus nidulans mitosis peripheral nuclear pore complex (NPC) proteins (Nups) disperse from the core NPC structure. Unexpectedly, one predicted peripheral Nup, Gle1, remains at the mitotic NE via an unknown mechanism. Gle1 affinity purification identified MtgA ( M: itotic T: ether for G: le1), which tethers Gle1 to the NE during mitosis, but not during interphase when Gle1 is at NPCs. MtgA is the ortholog of the Schizosaccharomyces pombe telomere-anchoring inner nuclear membrane protein Bqt4. Like Bqt4, MtgA has meiotic roles but is functionally distinct from Bqt4 as MtgA is not required for tethering telomeres to the NE. Domain analyses revealed MtgA targeting to the NE requires its C-terminal transmembrane domain and a nuclear localization signal. Importantly, MtgA functions beyond Gle1 mitotic targeting and meiosis and impacts nuclear and nucleolar architecture when deleted or overexpressed. Deletion of MtgA generates small, round nuclei whereas overexpressing MtgA generates larger nuclei with altered nuclear compartmentalization resulting from NE expansion around the nucleolus. The accumulation of MtgA around the nucleolus promotes a similar accumulation of the endoplasmic reticulum (ER) protein Erg24 lowering its levels in the ER. This study extends the functions of Bqt4-like proteins to include mitotic Gle1 targeting and modulation of nuclear and nucleolar architecture.
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Affiliation(s)
- Mahesh Chemudupati
- Ohio State Biochemistry Program, Ohio State University, Columbus, Ohio 43210 Department of Molecular Genetics, Ohio State University, Columbus, Ohio 43210
| | - Aysha H Osmani
- Department of Molecular Genetics, Ohio State University, Columbus, Ohio 43210
| | - Stephen A Osmani
- Ohio State Biochemistry Program, Ohio State University, Columbus, Ohio 43210 Department of Molecular Genetics, Ohio State University, Columbus, Ohio 43210
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Masuda M, Oshima A, Noguchi T, Kagiwada S. Induction of intranuclear membranes by overproduction of Opi1p and Scs2p, regulators for yeast phospholipid biosynthesis, suggests a mechanism for Opi1p nuclear translocation. J Biochem 2015; 159:351-61. [PMID: 26590299 DOI: 10.1093/jb/mvv105] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2015] [Accepted: 09/24/2015] [Indexed: 12/17/2022] Open
Abstract
In the yeast Saccharomyces cerevisiae, the expression of phospholipid biosynthetic genes is suppressed by the Opi1p negative regulator. Opi1p enters into the nucleoplasm from the nuclear membrane to suppress the gene expression under repressing conditions. The binding of Opi1p to the nuclear membrane requires an integral membrane protein, Scs2p and phosphatidic acid (PA). Although it is demonstrated that the association of Opi1p with membranes is affected by PA levels, how Opi1p dissociates from Scs2p is unknown. Here, we found that fluorescently labelled Opi1p accumulated on a perinuclear region in an Scs2p-dependent manner. Electron microscopic analyses indicated that the perinuclear region consists of intranuclear membranes, which may be formed by the invagination of the nuclear membrane due to the accumulation of Opi1p and Scs2p in a restricted area. As expected, localization of Opi1p and Scs2p in the intranuclear membranes was detected by immunoelectron microscopy. Biochemical analysis showed that Opi1p recovered in the membrane fraction was detergent insoluble while Scs2p was soluble, implying that Opi1p behaves differently from Scs2p in the fraction. We hypothesize that Opi1p dissociates from Scs2p after targeting to the nuclear membrane, making it possible to be released from the membrane quickly when PA levels decrease.
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Affiliation(s)
- Miki Masuda
- Department of Biological Sciences, Faculty of Science, Nara Women's University, Nara 630-8506, Japan
| | - Ayaka Oshima
- Department of Biological Sciences, Faculty of Science, Nara Women's University, Nara 630-8506, Japan
| | - Tetsuko Noguchi
- Department of Biological Sciences, Faculty of Science, Nara Women's University, Nara 630-8506, Japan
| | - Satoshi Kagiwada
- Department of Biological Sciences, Faculty of Science, Nara Women's University, Nara 630-8506, Japan
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Evidence for a Nonendosomal Function of the Saccharomyces cerevisiae ESCRT-III-Like Protein Chm7. Genetics 2015; 201:1439-52. [PMID: 26510789 DOI: 10.1534/genetics.115.178939] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2015] [Accepted: 10/15/2015] [Indexed: 11/18/2022] Open
Abstract
Endosomal sorting complex required for transport (ESCRT) proteins are involved in a number of cellular processes, such as endosomal protein sorting, HIV budding, cytokinesis, plasma membrane repair, and resealing of the nuclear envelope during mitosis. Here we explored the function of a noncanonical member of the ESCRT-III protein family, the Saccharomyces cerevisiae ortholog of human CHMP7. Very little is known about this protein. In silico analysis predicted that Chm7 (yeast ORF YJL049w) is a fusion of an ESCRT-II and ESCRT-III-like domain, which would suggest a role in endosomal protein sorting. However, our data argue against a role of Chm7 in endosomal protein sorting. The turnover of the endocytic cargo protein Ste6 and the vacuolar protein sorting of carboxypeptidase S (CPS) were not affected by CHM7 deletion, and Chm7 also responded very differently to a loss in Vps4 function compared to a canonical ESCRT-III protein. Our data indicate that the Chm7 function could be connected to the endoplasmic reticulum (ER). In line with a function at the ER, we observed a strong negative genetic interaction between the deletion of a gene function (APQ12) implicated in nuclear pore complex assembly and messenger RNA (mRNA) export and the CHM7 deletion. The patterns of genetic interactions between the APQ12 deletion and deletions of ESCRT-III genes, two-hybrid interactions, and the specific localization of mCherry fusion proteins are consistent with the notion that Chm7 performs a novel function at the ER as part of an alternative ESCRT-III complex.
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Frankl A, Mari M, Reggiori F. Electron microscopy for ultrastructural analysis and protein localization in Saccharomyces cerevisiae. MICROBIAL CELL 2015; 2:412-428. [PMID: 28357267 PMCID: PMC5349205 DOI: 10.15698/mic2015.11.237] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
Abstract
The yeast Saccharomyces cerevisiae is a key model system for studying of a multitude of cellular processes because of its amenability to genetics, molecular biology and biochemical procedures. Ultrastructural examinations of this organism, though, are traditionally difficult because of the presence of a thick cell wall and the high density of cytoplasmic proteins. A series of recent methodological and technical developments, however, has revived interest in morphological analyses of yeast (e.g. 123). Here we present a review of established and new methods, from sample preparation to imaging, for the ultrastructural analysis of S. cerevisiae. We include information for the use of different fixation methods, embedding procedures, approaches for contrast enhancement, and sample visualization techniques, with references to successful examples. The goal of this review is to guide researchers that want to investigate a particular process at the ultrastructural level in yeast by aiding in the selection of the most appropriate approach to visualize a specific structure or subcellular compartment.
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Affiliation(s)
- Andri Frankl
- Department of Cell Biology, University Medical Center Groningen, University of Groningen, Groningen, The Netherlands
| | - Muriel Mari
- Department of Cell Biology, University Medical Center Groningen, University of Groningen, Groningen, The Netherlands
| | - Fulvio Reggiori
- Department of Cell Biology, University Medical Center Groningen, University of Groningen, Groningen, The Netherlands
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37
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Ferrero S, Grados-Torrez RE, Leivar P, Antolín-Llovera M, López-Iglesias C, Cortadellas N, Ferrer JC, Campos N. Proliferation and Morphogenesis of the Endoplasmic Reticulum Driven by the Membrane Domain of 3-Hydroxy-3-Methylglutaryl Coenzyme A Reductase in Plant Cells. PLANT PHYSIOLOGY 2015; 168:899-914. [PMID: 26015445 PMCID: PMC4741317 DOI: 10.1104/pp.15.00597] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/22/2015] [Accepted: 05/23/2015] [Indexed: 05/07/2023]
Abstract
The enzyme 3-hydroxy-3-methylglutaryl coenzyme A reductase (HMGR) has a key regulatory role in the mevalonate pathway for isoprenoid biosynthesis and is composed of an endoplasmic reticulum (ER)-anchoring membrane domain with low sequence similarity among eukaryotic kingdoms and a conserved cytosolic catalytic domain. Organized smooth endoplasmic reticulum (OSER) structures are common formations of hypertrophied tightly packed ER membranes devoted to specific biosynthetic and secretory functions, the biogenesis of which remains largely unexplored. We show that the membrane domain of plant HMGR suffices to trigger ER proliferation and OSER biogenesis. The proliferating membranes become highly enriched in HMGR protein, but they do not accumulate sterols, indicating a morphogenetic rather than a metabolic role for HMGR. The N-terminal MDVRRRPP motif present in most plant HMGR isoforms is not required for retention in the ER, which was previously proposed, but functions as an ER morphogenic signal. Plant OSER structures are morphologically similar to those of animal cells, emerge from tripartite ER junctions, and mainly build up beside the nuclear envelope, indicating conserved OSER biogenesis in high eukaryotes. Factors other than the OSER-inducing HMGR construct mediate the tight apposition of the proliferating membranes, implying separate ER proliferation and membrane association steps. Overexpression of the membrane domain of Arabidopsis (Arabidopsis thaliana) HMGR leads to ER hypertrophy in every tested cell type and plant species, whereas the knockout of the HMG1 gene from Arabidopsis, encoding its major HMGR isoform, causes ER aggregation at the nuclear envelope. Our results show that the membrane domain of HMGR contributes to ER morphogenesis in plant cells.
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Affiliation(s)
- Sergi Ferrero
- Departament de Bioquímica i Biologia Molecular, Facultat de Biologia, Universitat de Barcelona, 08028 Barcelona, Spain (S.F., P.L., M.A.-L., J.C.F., N.Ca.);Departament de Genètica Molecular, Centre de Recerca en Agrigenòmica (Consejo Superior de Investigaciones Científicas-Institut de Recerca i Tecnologia Agroalimentàries-Universitat Autònoma de Barcelona-Universitat de Barcelona), Bellaterra (Cerdanyola del Vallès), 08193 Barcelona, Spain (R.E.G.-T., N.Ca.);Crio-Microscopia Electrònica, Centres Científics i Tecnològics, Campus Pedralbes, Universitat de Barcelona, 08028 Barcelona, Spain (C.L.-I.); andUnitat de Microscopia Electrònica, Centres Científics i Tecnològics, Campus Casanova, Universitat de Barcelona, 08036 Barcelona, Spain (N.Co.)
| | - Ricardo Enrique Grados-Torrez
- Departament de Bioquímica i Biologia Molecular, Facultat de Biologia, Universitat de Barcelona, 08028 Barcelona, Spain (S.F., P.L., M.A.-L., J.C.F., N.Ca.);Departament de Genètica Molecular, Centre de Recerca en Agrigenòmica (Consejo Superior de Investigaciones Científicas-Institut de Recerca i Tecnologia Agroalimentàries-Universitat Autònoma de Barcelona-Universitat de Barcelona), Bellaterra (Cerdanyola del Vallès), 08193 Barcelona, Spain (R.E.G.-T., N.Ca.);Crio-Microscopia Electrònica, Centres Científics i Tecnològics, Campus Pedralbes, Universitat de Barcelona, 08028 Barcelona, Spain (C.L.-I.); andUnitat de Microscopia Electrònica, Centres Científics i Tecnològics, Campus Casanova, Universitat de Barcelona, 08036 Barcelona, Spain (N.Co.)
| | - Pablo Leivar
- Departament de Bioquímica i Biologia Molecular, Facultat de Biologia, Universitat de Barcelona, 08028 Barcelona, Spain (S.F., P.L., M.A.-L., J.C.F., N.Ca.);Departament de Genètica Molecular, Centre de Recerca en Agrigenòmica (Consejo Superior de Investigaciones Científicas-Institut de Recerca i Tecnologia Agroalimentàries-Universitat Autònoma de Barcelona-Universitat de Barcelona), Bellaterra (Cerdanyola del Vallès), 08193 Barcelona, Spain (R.E.G.-T., N.Ca.);Crio-Microscopia Electrònica, Centres Científics i Tecnològics, Campus Pedralbes, Universitat de Barcelona, 08028 Barcelona, Spain (C.L.-I.); andUnitat de Microscopia Electrònica, Centres Científics i Tecnològics, Campus Casanova, Universitat de Barcelona, 08036 Barcelona, Spain (N.Co.)
| | - Meritxell Antolín-Llovera
- Departament de Bioquímica i Biologia Molecular, Facultat de Biologia, Universitat de Barcelona, 08028 Barcelona, Spain (S.F., P.L., M.A.-L., J.C.F., N.Ca.);Departament de Genètica Molecular, Centre de Recerca en Agrigenòmica (Consejo Superior de Investigaciones Científicas-Institut de Recerca i Tecnologia Agroalimentàries-Universitat Autònoma de Barcelona-Universitat de Barcelona), Bellaterra (Cerdanyola del Vallès), 08193 Barcelona, Spain (R.E.G.-T., N.Ca.);Crio-Microscopia Electrònica, Centres Científics i Tecnològics, Campus Pedralbes, Universitat de Barcelona, 08028 Barcelona, Spain (C.L.-I.); andUnitat de Microscopia Electrònica, Centres Científics i Tecnològics, Campus Casanova, Universitat de Barcelona, 08036 Barcelona, Spain (N.Co.)
| | - Carmen López-Iglesias
- Departament de Bioquímica i Biologia Molecular, Facultat de Biologia, Universitat de Barcelona, 08028 Barcelona, Spain (S.F., P.L., M.A.-L., J.C.F., N.Ca.);Departament de Genètica Molecular, Centre de Recerca en Agrigenòmica (Consejo Superior de Investigaciones Científicas-Institut de Recerca i Tecnologia Agroalimentàries-Universitat Autònoma de Barcelona-Universitat de Barcelona), Bellaterra (Cerdanyola del Vallès), 08193 Barcelona, Spain (R.E.G.-T., N.Ca.);Crio-Microscopia Electrònica, Centres Científics i Tecnològics, Campus Pedralbes, Universitat de Barcelona, 08028 Barcelona, Spain (C.L.-I.); andUnitat de Microscopia Electrònica, Centres Científics i Tecnològics, Campus Casanova, Universitat de Barcelona, 08036 Barcelona, Spain (N.Co.)
| | - Nuria Cortadellas
- Departament de Bioquímica i Biologia Molecular, Facultat de Biologia, Universitat de Barcelona, 08028 Barcelona, Spain (S.F., P.L., M.A.-L., J.C.F., N.Ca.);Departament de Genètica Molecular, Centre de Recerca en Agrigenòmica (Consejo Superior de Investigaciones Científicas-Institut de Recerca i Tecnologia Agroalimentàries-Universitat Autònoma de Barcelona-Universitat de Barcelona), Bellaterra (Cerdanyola del Vallès), 08193 Barcelona, Spain (R.E.G.-T., N.Ca.);Crio-Microscopia Electrònica, Centres Científics i Tecnològics, Campus Pedralbes, Universitat de Barcelona, 08028 Barcelona, Spain (C.L.-I.); andUnitat de Microscopia Electrònica, Centres Científics i Tecnològics, Campus Casanova, Universitat de Barcelona, 08036 Barcelona, Spain (N.Co.)
| | - Joan Carles Ferrer
- Departament de Bioquímica i Biologia Molecular, Facultat de Biologia, Universitat de Barcelona, 08028 Barcelona, Spain (S.F., P.L., M.A.-L., J.C.F., N.Ca.);Departament de Genètica Molecular, Centre de Recerca en Agrigenòmica (Consejo Superior de Investigaciones Científicas-Institut de Recerca i Tecnologia Agroalimentàries-Universitat Autònoma de Barcelona-Universitat de Barcelona), Bellaterra (Cerdanyola del Vallès), 08193 Barcelona, Spain (R.E.G.-T., N.Ca.);Crio-Microscopia Electrònica, Centres Científics i Tecnològics, Campus Pedralbes, Universitat de Barcelona, 08028 Barcelona, Spain (C.L.-I.); andUnitat de Microscopia Electrònica, Centres Científics i Tecnològics, Campus Casanova, Universitat de Barcelona, 08036 Barcelona, Spain (N.Co.)
| | - Narciso Campos
- Departament de Bioquímica i Biologia Molecular, Facultat de Biologia, Universitat de Barcelona, 08028 Barcelona, Spain (S.F., P.L., M.A.-L., J.C.F., N.Ca.);Departament de Genètica Molecular, Centre de Recerca en Agrigenòmica (Consejo Superior de Investigaciones Científicas-Institut de Recerca i Tecnologia Agroalimentàries-Universitat Autònoma de Barcelona-Universitat de Barcelona), Bellaterra (Cerdanyola del Vallès), 08193 Barcelona, Spain (R.E.G.-T., N.Ca.);Crio-Microscopia Electrònica, Centres Científics i Tecnològics, Campus Pedralbes, Universitat de Barcelona, 08028 Barcelona, Spain (C.L.-I.); andUnitat de Microscopia Electrònica, Centres Científics i Tecnològics, Campus Casanova, Universitat de Barcelona, 08036 Barcelona, Spain (N.Co.)
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Luu O, Damm EW, Parent SE, Barua D, Smith THL, Wen JWH, Lepage SE, Nagel M, Ibrahim-Gawel H, Huang Y, Bruce AEE, Winklbauer R. PAPC mediates self/non-self-distinction during Snail1-dependent tissue separation. ACTA ACUST UNITED AC 2015; 208:839-56. [PMID: 25778923 PMCID: PMC4362454 DOI: 10.1083/jcb.201409026] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
In Xenopus and zebrafish gastrulae, PAPC attenuates planar cell polarity signaling and controls formation of an adhesive, yet flexible, contact at the ectoderm–mesoderm boundary. Cleft-like boundaries represent a type of cell sorting boundary characterized by the presence of a physical gap between tissues. We studied the cleft-like ectoderm–mesoderm boundary in Xenopus laevis and zebrafish gastrulae. We identified the transcription factor Snail1 as being essential for tissue separation, showed that its expression in the mesoderm depends on noncanonical Wnt signaling, and demonstrated that it enables paraxial protocadherin (PAPC) to promote tissue separation through two novel functions. First, PAPC attenuates planar cell polarity signaling at the ectoderm–mesoderm boundary to lower cell adhesion and facilitate cleft formation. Second, PAPC controls formation of a distinct type of adhesive contact between mesoderm and ectoderm cells that shows properties of a cleft-like boundary at the single-cell level. It consists of short stretches of adherens junction–like contacts inserted between intermediate-sized contacts and large intercellular gaps. These roles of PAPC constitute a self/non–self-recognition mechanism that determines the site of boundary formation at the interface between PAPC-expressing and -nonexpressing cells.
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Affiliation(s)
- Olivia Luu
- Department of Cell and Systems Biology, University of Toronto, Toronto, Ontario, Canada M5S 3G5
| | - Erich W Damm
- Department of Cell and Systems Biology, University of Toronto, Toronto, Ontario, Canada M5S 3G5
| | - Serge E Parent
- Department of Cell and Systems Biology, University of Toronto, Toronto, Ontario, Canada M5S 3G5
| | - Debanjan Barua
- Department of Cell and Systems Biology, University of Toronto, Toronto, Ontario, Canada M5S 3G5
| | - Tamara H L Smith
- Department of Cell and Systems Biology, University of Toronto, Toronto, Ontario, Canada M5S 3G5
| | - Jason W H Wen
- Department of Cell and Systems Biology, University of Toronto, Toronto, Ontario, Canada M5S 3G5
| | - Stephanie E Lepage
- Department of Cell and Systems Biology, University of Toronto, Toronto, Ontario, Canada M5S 3G5
| | - Martina Nagel
- Department of Cell and Systems Biology, University of Toronto, Toronto, Ontario, Canada M5S 3G5
| | | | - Yunyun Huang
- Department of Cell and Systems Biology, University of Toronto, Toronto, Ontario, Canada M5S 3G5
| | - Ashley E E Bruce
- Department of Cell and Systems Biology, University of Toronto, Toronto, Ontario, Canada M5S 3G5
| | - Rudolf Winklbauer
- Department of Cell and Systems Biology, University of Toronto, Toronto, Ontario, Canada M5S 3G5
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39
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Emmerstorfer A, Wimmer-Teubenbacher M, Wriessnegger T, Leitner E, Müller M, Kaluzna I, Schürmann M, Mink D, Zellnig G, Schwab H, Pichler H. Over-expression ofICE2stabilizes cytochrome P450 reductase inSaccharomyces cerevisiaeandPichia pastoris. Biotechnol J 2015; 10:623-35. [DOI: 10.1002/biot.201400780] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2014] [Revised: 12/17/2014] [Accepted: 01/09/2015] [Indexed: 01/15/2023]
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40
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Alexaki A, Gupta SD, Majumder S, Kono M, Tuymetova G, Harmon JM, Dunn TM, Proia RL. Autophagy regulates sphingolipid levels in the liver. J Lipid Res 2014; 55:2521-31. [PMID: 25332431 DOI: 10.1194/jlr.m051862] [Citation(s) in RCA: 37] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022] Open
Abstract
Sphingolipid levels are tightly regulated to maintain cellular homeostasis. During pathologic conditions such as in aging, inflammation, and metabolic and neurodegenerative diseases, levels of some sphingolipids, including the bioactive metabolite ceramide, are elevated. Sphingolipid metabolism has been linked to autophagy, a critical catabolic process in both normal cell function and disease; however, the in vivo relevance of the interaction is not well-understood. Here, we show that blocking autophagy in the liver by deletion of the Atg7 gene, which is essential for autophagosome formation, causes an increase in sphingolipid metabolites including ceramide. We also show that overexpression of serine palmitoyltransferase to elevate de novo sphingolipid biosynthesis induces autophagy in the liver. The results reveal autophagy as a process that limits excessive ceramide levels and that is induced by excessive elevation of de novo sphingolipid synthesis in the liver. Dysfunctional autophagy may be an underlying mechanism causing elevations in ceramide that may contribute to pathogenesis in diseases.
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Affiliation(s)
- Aikaterini Alexaki
- Genetics of Development and Disease Branch, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, MD 20892
| | - Sita D Gupta
- Departments of Biochemistry Uniformed Services University of the Health Sciences, Bethesda, MD 20184
| | - Saurav Majumder
- Genetics of Development and Disease Branch, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, MD 20892
| | - Mari Kono
- Genetics of Development and Disease Branch, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, MD 20892
| | - Galina Tuymetova
- Genetics of Development and Disease Branch, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, MD 20892
| | - Jeffrey M Harmon
- Molecular Biology and Pharmacology, Uniformed Services University of the Health Sciences, Bethesda, MD 20184
| | - Teresa M Dunn
- Departments of Biochemistry Uniformed Services University of the Health Sciences, Bethesda, MD 20184
| | - Richard L Proia
- Genetics of Development and Disease Branch, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, MD 20892
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41
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Emmerstorfer A, Wriessnegger T, Hirz M, Pichler H. Overexpression of membrane proteins from higher eukaryotes in yeasts. Appl Microbiol Biotechnol 2014; 98:7671-98. [PMID: 25070595 DOI: 10.1007/s00253-014-5948-4] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2014] [Revised: 07/08/2014] [Accepted: 07/09/2014] [Indexed: 02/08/2023]
Abstract
Heterologous expression and characterisation of the membrane proteins of higher eukaryotes is of paramount interest in fundamental and applied research. Due to the rather simple and well-established methods for their genetic modification and cultivation, yeast cells are attractive host systems for recombinant protein production. This review provides an overview on the remarkable progress, and discusses pitfalls, in applying various yeast host strains for high-level expression of eukaryotic membrane proteins. In contrast to the cell lines of higher eukaryotes, yeasts permit efficient library screening methods. Modified yeasts are used as high-throughput screening tools for heterologous membrane protein functions or as benchmark for analysing drug-target relationships, e.g., by using yeasts as sensors. Furthermore, yeasts are powerful hosts for revealing interactions stabilising and/or activating membrane proteins. We also discuss the stress responses of yeasts upon heterologous expression of membrane proteins. Through co-expression of chaperones and/or optimising yeast cultivation and expression strategies, yield-optimised hosts have been created for membrane protein crystallography or efficient whole-cell production of fine chemicals.
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Affiliation(s)
- Anita Emmerstorfer
- ACIB-Austrian Centre of Industrial Biotechnology, Petersgasse 14, 8010, Graz, Austria
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42
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Production of the sesquiterpenoid (+)-nootkatone by metabolic engineering of Pichia pastoris. Metab Eng 2014; 24:18-29. [DOI: 10.1016/j.ymben.2014.04.001] [Citation(s) in RCA: 117] [Impact Index Per Article: 11.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2013] [Revised: 04/02/2014] [Accepted: 04/08/2014] [Indexed: 11/18/2022]
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Vogl T, Thallinger GG, Zellnig G, Drew D, Cregg JM, Glieder A, Freigassner M. Towards improved membrane protein production in Pichia pastoris: general and specific transcriptional response to membrane protein overexpression. N Biotechnol 2014; 31:538-52. [PMID: 24594271 DOI: 10.1016/j.nbt.2014.02.009] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2013] [Revised: 02/20/2014] [Accepted: 02/23/2014] [Indexed: 01/13/2023]
Abstract
Membrane proteins are the largest group of human drug targets and are also used as biocatalysts. However, due to their complexity, efficient expression remains a bottleneck for high level production. In recent years, the methylotrophic yeast Pichia pastoris has emerged as one of the most commonly used expression systems for membrane protein production. Here, we have analysed the transcriptomes of P. pastoris strains producing different classes of membrane proteins (mitochondrial, ER/Golgi and plasma membrane localized) to understand the cellular response and to identify targets to engineer P. pastoris towards an improved chassis for membrane protein production. Microarray experiments revealed varying transcriptional responses depending on the enzymatic activity, subcellular localization and physiological role of the membrane proteins. While an alternative oxidase evoked primarily a response within the mitochondria, the overexpression of transporters entering the secretory pathway had a wide effect on lipid metabolism and induced the upregulation of the UPR (unfolded protein response) transcription factor Hac1p. Coexpression of P. pastoris endogenous HAC1 increased the levels of ER-resident membrane proteins 1.5- to 2.1-fold. Subsequent transcriptome analysis of HAC1 coexpression revealed an upregulation of the folding machinery correlating with an expansion of the ER membrane capacity, thus boosting membrane protein production. Hence, our study has helped to elucidate the cellular response of P. pastoris to the expression of different classes of membrane proteins and led specifically to new insights into the effect of PpHac1p on membrane proteins entering the secretory pathway.
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Affiliation(s)
- Thomas Vogl
- Institute for Molecular Biotechnology, Graz University of Technology, Petersgasse 14/2, 8010 Graz, Austria
| | - Gerhard G Thallinger
- Institute for Genomics and Bioinformatics, Graz University of Technology, Petersgasse 14/5, 8010 Graz, Austria; Omics Center Graz, Stiftingtalstrasse 24, 8036 Graz, Austria; Austrian Centre of Industrial Biotechnology (ACIB GmbH), Petersgasse 14/5, 8010 Graz, Austria
| | - Guenther Zellnig
- Institute of Plant Sciences, University of Graz, Schubertstrasse 51, 8010 Graz, Austria
| | - David Drew
- Division of Molecular Biosciences, Imperial College London, London SW7 2AZ, United Kingdom
| | - James M Cregg
- Keck Graduate Institute of Applied Life Sciences, 535 Watson Drive, Claremont, CA 91711, USA
| | - Anton Glieder
- Austrian Centre of Industrial Biotechnology (ACIB GmbH), Petersgasse 14/5, 8010 Graz, Austria
| | - Maria Freigassner
- Institute for Molecular Biotechnology, Graz University of Technology, Petersgasse 14/2, 8010 Graz, Austria.
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Escusa-Toret S, Vonk WIM, Frydman J. Spatial sequestration of misfolded proteins by a dynamic chaperone pathway enhances cellular fitness during stress. Nat Cell Biol 2013; 15:1231-43. [PMID: 24036477 PMCID: PMC4121856 DOI: 10.1038/ncb2838] [Citation(s) in RCA: 247] [Impact Index Per Article: 22.5] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2012] [Accepted: 08/07/2013] [Indexed: 02/06/2023]
Abstract
The extensive links between proteotoxic stress, protein aggregation and pathologies ranging from ageing to neurodegeneration underscore the importance of understanding how cells manage protein misfolding. Using live-cell imaging, we determine the fate of stress-induced misfolded proteins from their initial appearance until their elimination. Upon denaturation, misfolded proteins are sequestered from the bulk cytoplasm into dynamic endoplasmic reticulum (ER)-associated puncta that move and coalesce into larger structures in an energy-dependent but cytoskeleton-independent manner. These puncta, which we name Q-bodies, concentrate different misfolded and stress-denatured proteins en route to degradation, but do not contain amyloid aggregates, which localize instead to the insoluble protein deposit compartment. Q-body formation and clearance depends on an intact cortical ER and a complex chaperone network that is affected by rapamycin and impaired during chronological ageing. Importantly, Q-body formation enhances cellular fitness during stress. We conclude that spatial sequestration of misfolded proteins in Q-bodies is an early quality control strategy occurring synchronously with degradation to clear the cytoplasm of potentially toxic species.
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45
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Wriessnegger T, Pichler H. Yeast metabolic engineering – Targeting sterol metabolism and terpenoid formation. Prog Lipid Res 2013; 52:277-93. [DOI: 10.1016/j.plipres.2013.03.001] [Citation(s) in RCA: 63] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2012] [Revised: 03/26/2013] [Accepted: 03/27/2013] [Indexed: 12/28/2022]
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Abstract
Take a look at a textbook illustration of a cell and you will immediately be able to locate the nucleus, which is often drawn as a spherical or ovoid shaped structure. But not all cells have such nuclei. In fact, some disease states are diagnosed by the presence of nuclei that have an abnormal shape or size. What defines nuclear shape and nuclear size, and how does nuclear geometry affect nuclear function? While the answer to the latter question remains largely unknown, significant progress has been made towards understanding the former. In this review, we provide an overview of the factors and forces that affect nuclear shape and size, discuss the relationship between ER structure and nuclear morphology, and speculate on the possible connection between nuclear size and its shape. We also note the many interesting questions that remain to be explored.
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Affiliation(s)
- Alison D. Walters
- The Laboratory of Cell and Molecular Biology, NIDDK, NIH, Bethesda, Maryland 20892
| | - Ananth Bommakanti
- The Laboratory of Cell and Molecular Biology, NIDDK, NIH, Bethesda, Maryland 20892
| | - Orna Cohen-Fix
- The Laboratory of Cell and Molecular Biology, NIDDK, NIH, Bethesda, Maryland 20892
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Abstract
The classical genetic approach for exploring biological pathways typically begins by identifying mutations that cause a phenotype of interest. Overexpression or misexpression of a wild-type gene product, however, can also cause mutant phenotypes, providing geneticists with an alternative yet powerful tool to identify pathway components that might remain undetected using traditional loss-of-function analysis. This review describes the history of overexpression, the mechanisms that are responsible for overexpression phenotypes, tests that begin to distinguish between those mechanisms, the varied ways in which overexpression is used, the methods and reagents available in several organisms, and the relevance of overexpression to human disease.
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48
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Costantini LM, Fossati M, Francolini M, Snapp EL. Assessing the tendency of fluorescent proteins to oligomerize under physiologic conditions. Traffic 2012; 13:643-9. [PMID: 22289035 DOI: 10.1111/j.1600-0854.2012.01336.x] [Citation(s) in RCA: 155] [Impact Index Per Article: 12.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2011] [Revised: 01/27/2012] [Accepted: 01/30/2012] [Indexed: 11/28/2022]
Abstract
Several fluorescent proteins (FPs) are prone to forming low-affinity oligomers. This undesirable tendency is exacerbated when FPs are confined to membranes or when fused to naturally oligomeric proteins. Oligomerization of FPs limits their suitability for creating fusions with proteins of interest. Unfortunately, no standardized method evaluates the biologically relevant oligomeric state of FPs. Here, we describe a quantitative visual assay for assessing whether FPs are sufficiently monomeric under physiologic conditions. Membrane-associated FP-fusion proteins, by virtue of their constrained planar geometry, achieve high effective concentrations. We exploited this propensity to develop an assay to measure FP tendencies to oligomerize in cells. FPs were fused on the cytoplasmic end of an endoplasmic reticulum (ER) signal-anchor membrane protein (CytERM) and expressed in cells. Cells were scored based on the ability of CytERM to homo-oligomerize with proteins on apposing membranes and restructure the ER from a tubular network into organized smooth ER (OSER) whorl structures. The ratio of nuclear envelope and OSER structures mean fluorescent intensities for cells expressing enhanced green fluorescent protein (EGFP) or monomeric green fluorescent protein (mGFP) CytERM established standards for comparison of uncharacterized FPs. We tested three FPs and identified two as sufficiently monomeric, while a third previously reported as monomeric was found to strongly oligomerize.
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Affiliation(s)
- Lindsey M Costantini
- Department of Anatomy and Structural Biology, Albert Einstein College of Medicine of Yeshiva University, 1300 Morris Park Avenue, Bronx, NY 10461, USA
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49
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Host acyl coenzyme A binding protein regulates replication complex assembly and activity of a positive-strand RNA virus. J Virol 2012; 86:5110-21. [PMID: 22345450 DOI: 10.1128/jvi.06701-11] [Citation(s) in RCA: 34] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023] Open
Abstract
All positive-strand RNA viruses reorganize host intracellular membranes to assemble their replication complexes. Similarly, brome mosaic virus (BMV) induces two alternate forms of membrane-bound RNA replication complexes: vesicular spherules and stacks of appressed double-membrane layers. The mechanisms by which these membrane rearrangements are induced, however, remain unclear. We report here that host ACB1-encoded acyl coenzyme A (acyl-CoA) binding protein (ACBP) is required for the assembly and activity of both BMV RNA replication complexes. ACBP is highly conserved among eukaryotes, specifically binds to long-chain fatty acyl-CoA, and promotes general lipid synthesis. Deleting ACB1 inhibited BMV RNA replication up to 30-fold and resulted in formation of spherules that were ∼50% smaller but ∼4-fold more abundant than those in wild-type (wt) cells, consistent with the idea that BMV 1a invaginates and maintains viral spherules by coating the inner spherule membrane. Furthermore, smaller and more frequent spherules were preferentially formed under conditions that induce layer formation in wt cells. Conversely, cellular karmella structures, which are arrays of endoplasmic reticulum (ER) membranes formed upon overexpression of certain cellular ER membrane proteins, were formed normally, indicating a selective inhibition of 1a-induced membrane rearrangements. Restoring altered lipid composition largely complemented the BMV RNA replication defect, suggesting that ACBP was required for maintaining lipid homeostasis. Smaller and more frequent spherules are also induced by 1a mutants with specific substitutions in a membrane-anchoring amphipathic α-helix, implying that the 1a-lipid interactions play critical roles in viral replication complex assembly.
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50
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Machettira AB, Groß LE, Tillmann B, Weis BL, Englich G, Sommer MS, Königer M, Schleiff E. Protein-induced modulation of chloroplast membrane morphology. FRONTIERS IN PLANT SCIENCE 2012; 2:118. [PMID: 22639631 PMCID: PMC3355639 DOI: 10.3389/fpls.2011.00118] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/23/2011] [Accepted: 12/29/2011] [Indexed: 05/24/2023]
Abstract
Organelles are surrounded by membranes with a distinct lipid and protein composition. While it is well established that lipids affect protein functioning and vice versa, it has been only recently suggested that elevated membrane protein concentrations may affect the shape and organization of membranes. We therefore analyzed the effects of high chloroplast envelope protein concentrations on membrane structures using an in vivo approach with protoplasts. Transient expression of outer envelope proteins or protein domains such as CHUP1-TM-GFP, outer envelope protein of 7 kDa-GFP, or outer envelope protein of 24 kDa-GFP at high levels led to the formation of punctate, circular, and tubular membrane protrusions. Expression of inner membrane proteins such as translocase of inner chloroplast membrane 20, isoform II (Tic20-II)-GFP led to membrane protrusions including invaginations. Using increasing amounts of DNA for transfection, we could show that the frequency, size, and intensity of these protrusions increased with protein concentration. The membrane deformations were absent after cycloheximide treatment. Co-expression of CHUP1-TM-Cherry and Tic20-II-GFP led to membrane protrusions of various shapes and sizes including some stromule-like structures, for which several functions have been proposed. Interestingly, some structures seemed to contain both proteins, while others seem to contain one protein exclusively, indicating that outer and inner envelope dynamics might be regulated independently. While it was more difficult to investigate the effects of high expression levels of membrane proteins on mitochondrial membrane shapes using confocal imaging, it was striking that the expression of the outer membrane protein Tom20 led to more elongate mitochondria. We discuss that the effect of protein concentrations on membrane structure is possibly caused by an imbalance in the lipid to protein ratio and may be involved in a signaling pathway regulating membrane biogenesis. Finally, the observed phenomenon provides a valuable experimental approach to investigate the relationship between lipid synthesis and membrane protein expression in future studies.
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Affiliation(s)
- Anu B. Machettira
- Molecular Cell Biology of Plants, Johann-Wolfgang-Goethe University FrankfurtFrankfurt am Main, Germany
| | - Lucia E. Groß
- Molecular Cell Biology of Plants, Johann-Wolfgang-Goethe University FrankfurtFrankfurt am Main, Germany
| | - Bodo Tillmann
- Molecular Cell Biology of Plants, Johann-Wolfgang-Goethe University FrankfurtFrankfurt am Main, Germany
| | - Benjamin L. Weis
- Molecular Cell Biology of Plants, Johann-Wolfgang-Goethe University FrankfurtFrankfurt am Main, Germany
| | - Gisela Englich
- Molecular Cell Biology of Plants, Johann-Wolfgang-Goethe University FrankfurtFrankfurt am Main, Germany
| | - Maik S. Sommer
- Molecular Cell Biology of Plants, Johann-Wolfgang-Goethe University FrankfurtFrankfurt am Main, Germany
| | - Martina Königer
- Department of Biological Sciences, Wellesley CollegeWellesley, MA, USA
| | - Enrico Schleiff
- Molecular Cell Biology of Plants, Johann-Wolfgang-Goethe University FrankfurtFrankfurt am Main, Germany
- Cluster of Excellence “Macromolecular Complexes”, Johann-Wolfgang-Goethe University FrankfurtFrankfurt am Main, Germany
- Department of Biosciences, Center of Membrane Proteomics, Johann-Wolfgang-Goethe University FrankfurtFrankfurt am Main, Germany
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