151
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Bec N, Bonhoure A, Henry L, Berry L, Larroque C, Coux O, Stoebner P, Vidal M. Proteasome 19S RP and translation preinitiation complexes are secreted within exosomes upon serum starvation. Traffic 2019; 20:516-536. [DOI: 10.1111/tra.12653] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2018] [Revised: 04/29/2019] [Accepted: 04/30/2019] [Indexed: 12/23/2022]
Affiliation(s)
- Nicole Bec
- PP2IUniversity of Montpellier, IRCM Montpellier France
- IRBMUniversity of Montpellier CNRS, Montpellier France
| | - Anne Bonhoure
- DIMNPUniversity of Montpellier, CNRS Montpellier France
| | - Laurent Henry
- IBMMUniversity of Montpellier, CNRS Montpellier France
| | | | - Christian Larroque
- PP2IUniversity of Montpellier, IRCM Montpellier France
- ICMInstitut du Cancer de Montpellier Montpellier France
| | - Olivier Coux
- CRBMUniversity of Montpellier, CNRS Montpellier France
| | | | - Michel Vidal
- DIMNPUniversity of Montpellier, CNRS Montpellier France
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152
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Batista-Silva W, Heinemann B, Rugen N, Nunes-Nesi A, Araújo WL, Braun HP, Hildebrandt TM. The role of amino acid metabolism during abiotic stress release. PLANT, CELL & ENVIRONMENT 2019; 42:1630-1644. [PMID: 30632176 DOI: 10.1111/pce.13518] [Citation(s) in RCA: 189] [Impact Index Per Article: 37.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/06/2018] [Revised: 12/21/2018] [Accepted: 12/22/2018] [Indexed: 05/08/2023]
Abstract
Plant responses to abiotic stress include various modifications in amino acid metabolism. By using a hydroponic culture system, we systematically investigate modification in amino acid profiles and the proteome of Arabidopsis thaliana leaves during initial recovery from low water potential or high salinity. Both treatments elicited oxidative stress leading to a biphasic stress response during recovery. Degradation of highly abundant proteins such as subunits of photosystems and ribosomes contributed to an accumulation of free amino acids. Catabolic pathways for several low abundant amino acids were induced indicating their usage as an alternative respiratory substrate to compensate for the decreased photosynthesis. Our results demonstrate that rapid detoxification of potentially detrimental amino acids such as Lys is a priority during the initial stress recovery period. The content of Pro, which acts as a compatible osmolyte during stress, was adjusted by balancing its synthesis and catabolism both of which were induced both during and after stress treatments. The production of amino acid derived secondary metabolites was up-regulated specifically during the recovery period, and our dataset also indicates increased synthesis rates of the precursor amino acids. Overall, our results support a tight relationship between amino acid metabolism and stress responses.
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Affiliation(s)
- Willian Batista-Silva
- Max-Planck Partner Group at the Departamento de Biologia Vegetal, Universidade Federal de Viçosa, Viçosa, Brazil
- Institut für Pflanzengenetik, Leibniz Universität Hannover, Hannover, Germany
| | - Björn Heinemann
- Institut für Pflanzengenetik, Leibniz Universität Hannover, Hannover, Germany
| | - Nils Rugen
- Institut für Pflanzengenetik, Leibniz Universität Hannover, Hannover, Germany
| | - Adriano Nunes-Nesi
- Max-Planck Partner Group at the Departamento de Biologia Vegetal, Universidade Federal de Viçosa, Viçosa, Brazil
| | - Wagner L Araújo
- Max-Planck Partner Group at the Departamento de Biologia Vegetal, Universidade Federal de Viçosa, Viçosa, Brazil
| | - Hans-Peter Braun
- Institut für Pflanzengenetik, Leibniz Universität Hannover, Hannover, Germany
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153
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Ferretti MB, Karbstein K. Does functional specialization of ribosomes really exist? RNA (NEW YORK, N.Y.) 2019; 25:521-538. [PMID: 30733326 PMCID: PMC6467006 DOI: 10.1261/rna.069823.118] [Citation(s) in RCA: 79] [Impact Index Per Article: 15.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/21/2023]
Abstract
It has recently become clear that ribosomes are much more heterogeneous than previously thought, with diversity arising from rRNA sequence and modifications, ribosomal protein (RP) content and posttranslational modifications (PTMs), as well as bound nonribosomal proteins. In some cases, the existence of these diverse ribosome populations has been verified by biochemical or structural methods. Furthermore, knockout or knockdown of RPs can diversify ribosome populations, while also affecting the translation of some mRNAs (but not others) with biological consequences. However, the effects on translation arising from depletion of diverse proteins can be highly similar, suggesting that there may be a more general defect in ribosome function or stability, perhaps arising from reduced ribosome numbers. Consistently, overall reduced ribosome numbers can differentially affect subclasses of mRNAs, necessitating controls for specificity. Moreover, in order to study the functional consequences of ribosome diversity, perturbations including affinity tags and knockouts are introduced, which can also affect the outcome of the experiment. Here we review the available literature to carefully evaluate whether the published data support functional diversification, defined as diverse ribosome populations differentially affecting translation of distinct mRNA (classes). Based on these observations and the commonly observed cellular responses to perturbations in the system, we suggest a set of important controls to validate functional diversity, which should include gain-of-function assays and the demonstration of inducibility under physiological conditions.
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Affiliation(s)
- Max B Ferretti
- Department of Integrative Structural and Molecular Biology, The Scripps Research Institute, Jupiter, Florida 33458, USA
- The Skaggs Graduate School of Chemical and Biological Sciences, The Scripps Research Institute, Jupiter, Florida 33458, USA
| | - Katrin Karbstein
- Department of Integrative Structural and Molecular Biology, The Scripps Research Institute, Jupiter, Florida 33458, USA
- The Skaggs Graduate School of Chemical and Biological Sciences, The Scripps Research Institute, Jupiter, Florida 33458, USA
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154
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Yoon SH, Chung T. Protein and RNA Quality Control by Autophagy in Plant Cells. Mol Cells 2019; 42:285-291. [PMID: 31091554 PMCID: PMC6530645 DOI: 10.14348/molcells.2019.0011] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2019] [Revised: 03/03/2019] [Accepted: 03/19/2019] [Indexed: 11/27/2022] Open
Abstract
Eukaryotic cells use conserved quality control mechanisms to repair or degrade defective proteins, which are synthesized at a high rate during proteotoxic stress. Quality control mechanisms include molecular chaperones, the ubiquitin-proteasome system, and autophagic machinery. Recent research reveals that during autophagy, membrane-bound organelles are selectively sequestered and degraded. Selective autophagy is also critical for the clearance of excess or damaged protein complexes (e.g., proteasomes and ribosomes) and membrane-less compartments (e.g., protein aggregates and ribonucleoprotein granules). As sessile organisms, plants rely on quality control mechanisms for their adaptation to fluctuating environments. In this mini-review, we highlight recent work elucidating the roles of selective autophagy in the quality control of proteins and RNA in plant cells. Emphasis will be placed on selective degradation of membrane-less compartments and protein complexes in the cytoplasm. We also propose possible mechanisms by which defective proteins are selectively recognized by autophagic machinery.
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Affiliation(s)
- Seok Ho Yoon
- Department of Biological Sciences, Pusan National University, Busan 46241,
Korea
| | - Taijoon Chung
- Department of Biological Sciences, Pusan National University, Busan 46241,
Korea
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155
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156
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Watch What You (Self-) Eat: Autophagic Mechanisms that Modulate Metabolism. Cell Metab 2019; 29:803-826. [PMID: 30943392 PMCID: PMC6450419 DOI: 10.1016/j.cmet.2019.03.003] [Citation(s) in RCA: 188] [Impact Index Per Article: 37.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/15/2019] [Revised: 02/07/2019] [Accepted: 03/04/2019] [Indexed: 02/07/2023]
Abstract
Autophagy is an evolutionarily conserved lysosome- or vacuole-dependent catabolic pathway in eukaryotes. Autophagy functions basally for cellular quality control and is induced to act as an alternative source of basic metabolites during nutrient deprivation. These functions of autophagy are intimately connected to the regulation of metabolism, and the metabolic status of the cell in turn controls the nature and extent of autophagic induction. Here, we highlight the co-regulation of autophagy and metabolism with a special focus on selective autophagy that, along with bulk autophagy, plays a central role in regulating and rewiring metabolic circuits. We outline the metabolic signals that activate these pathways, the mechanisms involved, and the downstream effects and implications while recognizing yet unanswered questions. We also discuss the role of autophagy in the development and maintenance of adipose tissue, an emerging player in systemic metabolic homeostasis, and describe what is currently known about the complex relationship between autophagy and cancer.
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157
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Wiegering A, Rüther U, Gerhardt C. The Role of Primary Cilia in the Crosstalk between the Ubiquitin⁻Proteasome System and Autophagy. Cells 2019; 8:cells8030241. [PMID: 30875746 PMCID: PMC6468794 DOI: 10.3390/cells8030241] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2018] [Revised: 03/06/2019] [Accepted: 03/11/2019] [Indexed: 12/22/2022] Open
Abstract
Protein degradation is a pivotal process for eukaryotic development and homeostasis. The majority of proteins are degraded by the ubiquitin⁻proteasome system and by autophagy. Recent studies describe a crosstalk between these two main eukaryotic degradation systems which allows for establishing a kind of safety mechanism. If one of these degradation systems is hampered, the other compensates for this defect. The mechanism behind this crosstalk is poorly understood. Novel studies suggest that primary cilia, little cellular protrusions, are involved in the regulation of the crosstalk between the two degradation systems. In this review article, we summarise the current knowledge about the association between cilia, the ubiquitin⁻proteasome system and autophagy.
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Affiliation(s)
- Antonia Wiegering
- Institute for Animal Developmental and Molecular Biology, Heinrich Heine University, 40225 Düsseldorf, Germany.
| | - Ulrich Rüther
- Institute for Animal Developmental and Molecular Biology, Heinrich Heine University, 40225 Düsseldorf, Germany.
| | - Christoph Gerhardt
- Institute for Animal Developmental and Molecular Biology, Heinrich Heine University, 40225 Düsseldorf, Germany.
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158
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Abstract
The ribosome, a ribonucleoprotein machine for protein synthesis, can also serve as an abundant nutrient source under starvation conditions. In a recent issue of Science, Wyant et al. (2018) discovered a specialized "spoon" to "scoop up" more ribosomes for degradation by autophagy.
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Affiliation(s)
- Hitoshi Nakatogawa
- School of Life Science and Technology, Tokyo Institute of Technology, Yokohama 226-8501, Japan.
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159
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Horos R, Büscher M, Kleinendorst R, Alleaume AM, Tarafder AK, Schwarzl T, Dziuba D, Tischer C, Zielonka EM, Adak A, Castello A, Huber W, Sachse C, Hentze MW. The Small Non-coding Vault RNA1-1 Acts as a Riboregulator of Autophagy. Cell 2019; 176:1054-1067.e12. [PMID: 30773316 DOI: 10.1016/j.cell.2019.01.030] [Citation(s) in RCA: 106] [Impact Index Per Article: 21.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2018] [Revised: 10/15/2018] [Accepted: 01/16/2019] [Indexed: 12/11/2022]
Abstract
Vault RNAs (vtRNA) are small non-coding RNAs transcribed by RNA polymerase III found in many eukaryotes. Although they have been linked to drug resistance, apoptosis, and viral replication, their molecular functions remain unclear. Here, we show that vault RNAs directly bind the autophagy receptor sequestosome-1/p62 in human and murine cells. Overexpression of human vtRNA1-1 inhibits, while its antisense LNA-mediated knockdown enhances p62-dependent autophagy. Starvation of cells reduces the steady-state and p62-bound levels of vault RNA1-1 and induces autophagy. Mechanistically, p62 mutants that fail to bind vtRNAs display increased p62 homo-oligomerization and augmented interaction with autophagic effectors. Thus, vtRNA1-1 directly regulates selective autophagy by binding p62 and interference with oligomerization, a critical step of p62 function. Our data uncover a striking example of the potential of RNA to control protein functions directly, as previously recognized for protein-protein interactions and post-translational modifications.
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Affiliation(s)
- Rastislav Horos
- European Molecular Biology Laboratory, Meyerhofstrasse 1, 69117 Heidelberg, Germany.
| | - Magdalena Büscher
- European Molecular Biology Laboratory, Meyerhofstrasse 1, 69117 Heidelberg, Germany
| | | | - Anne-Marie Alleaume
- European Molecular Biology Laboratory, Meyerhofstrasse 1, 69117 Heidelberg, Germany
| | - Abul K Tarafder
- European Molecular Biology Laboratory, Meyerhofstrasse 1, 69117 Heidelberg, Germany
| | - Thomas Schwarzl
- European Molecular Biology Laboratory, Meyerhofstrasse 1, 69117 Heidelberg, Germany
| | - Dmytro Dziuba
- European Molecular Biology Laboratory, Meyerhofstrasse 1, 69117 Heidelberg, Germany
| | - Christian Tischer
- European Molecular Biology Laboratory, Meyerhofstrasse 1, 69117 Heidelberg, Germany
| | - Elisabeth M Zielonka
- European Molecular Biology Laboratory, Meyerhofstrasse 1, 69117 Heidelberg, Germany
| | - Asli Adak
- European Molecular Biology Laboratory, Meyerhofstrasse 1, 69117 Heidelberg, Germany
| | - Alfredo Castello
- Department of Biochemistry, University of Oxford, South Parks Road, Oxford OX1 3QU, UK
| | - Wolfgang Huber
- European Molecular Biology Laboratory, Meyerhofstrasse 1, 69117 Heidelberg, Germany
| | - Carsten Sachse
- European Molecular Biology Laboratory, Meyerhofstrasse 1, 69117 Heidelberg, Germany; Ernst Ruska-Centre for Microscopy and Spectroscopy with Electrons/ER-C3 Structural Biology, Wilhem-Johnen-Straße, 52425 Jülich, Germany
| | - Matthias W Hentze
- European Molecular Biology Laboratory, Meyerhofstrasse 1, 69117 Heidelberg, Germany.
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160
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Trendel J, Schwarzl T, Horos R, Prakash A, Bateman A, Hentze MW, Krijgsveld J. The Human RNA-Binding Proteome and Its Dynamics during Translational Arrest. Cell 2019; 176:391-403.e19. [PMID: 30528433 DOI: 10.1016/j.cell.2018.11.004] [Citation(s) in RCA: 238] [Impact Index Per Article: 47.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2018] [Revised: 09/21/2018] [Accepted: 10/31/2018] [Indexed: 12/21/2022]
Abstract
Proteins and RNA functionally and physically intersect in multiple biological processes, however, currently no universal method is available to purify protein-RNA complexes. Here, we introduce XRNAX, a method for the generic purification of protein-crosslinked RNA, and demonstrate its versatility to study the composition and dynamics of protein-RNA interactions by various transcriptomic and proteomic approaches. We show that XRNAX captures all RNA biotypes and use this to characterize the sub-proteomes that interact with coding and non-coding RNAs (ncRNAs) and to identify hundreds of protein-RNA interfaces. Exploiting the quantitative nature of XRNAX, we observe drastic remodeling of the RNA-bound proteome during arsenite-induced stress, distinct from autophagy-related changes in the total proteome. In addition, we combine XRNAX with crosslinking immunoprecipitation sequencing (CLIP-seq) to validate the interaction of ncRNA with lamin B1 and EXOSC2. Thus, XRNAX is a resourceful approach to study structural and compositional aspects of protein-RNA interactions to address fundamental questions in RNA-biology.
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Affiliation(s)
- Jakob Trendel
- German Cancer Research Center (DKFZ), Im Neuenheimer Feld 581, Heidelberg, Germany; European Molecular Biology Laboratory (EMBL), Meyerhofstrasse 1, Heidelberg, Germany; Collaboration for joint PhD degree between EMBL and Heidelberg University, Faculty of Biosciences
| | - Thomas Schwarzl
- European Molecular Biology Laboratory (EMBL), Meyerhofstrasse 1, Heidelberg, Germany
| | - Rastislav Horos
- European Molecular Biology Laboratory (EMBL), Meyerhofstrasse 1, Heidelberg, Germany
| | - Ananth Prakash
- European Molecular Biology Laboratory, European Bioinformatics Institute (EBI), Wellcome Genome Campus, Hinxton, Cambridge, UK
| | - Alex Bateman
- European Molecular Biology Laboratory, European Bioinformatics Institute (EBI), Wellcome Genome Campus, Hinxton, Cambridge, UK
| | - Matthias W Hentze
- European Molecular Biology Laboratory (EMBL), Meyerhofstrasse 1, Heidelberg, Germany
| | - Jeroen Krijgsveld
- German Cancer Research Center (DKFZ), Im Neuenheimer Feld 581, Heidelberg, Germany; Heidelberg University, Medical Faculty, Im Neuenheimer Feld 672, Heidelberg, Germany.
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161
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Rodrigues RAL, Arantes TS, Oliveira GP, dos Santos Silva LK, Abrahão JS. The Complex Nature of Tupanviruses. Adv Virus Res 2019; 103:135-166. [PMID: 30635075 DOI: 10.1016/bs.aivir.2018.09.001] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
The discovery of giant viruses revealed a new level of complexity in the virosphere, raising important questions about the diversity, ecology, and evolution of these viruses. The family Mimiviridae was the first group of amoebal giant viruses to be discovered (by Bernard La Scola and Didier Raoult team), containing viruses with structural and genetic features that challenged many concepts of classic virology. The tupanviruses are among the newest members of this family and exhibit structural, biological, and genetic features never previously observed in other giant viruses. The complexity of these viruses has put us one step forward toward the comprehension of giant virus biology and evolution, but also has raised important questions that still need to be addressed. In this chapter, we tell the history behind the discovery of one of the most complex viruses isolated to date, highlighting the unique features exhibited by tupanviruses, and discuss how these giant viruses have contributed to redefining limits for the virosphere.
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162
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Lamming DW, Bar-Peled L. Lysosome: The metabolic signaling hub. Traffic 2019; 20:27-38. [PMID: 30306667 PMCID: PMC6294686 DOI: 10.1111/tra.12617] [Citation(s) in RCA: 92] [Impact Index Per Article: 18.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2018] [Revised: 09/17/2018] [Accepted: 10/07/2018] [Indexed: 12/27/2022]
Abstract
For the past five decades, the lysosome has been characterized as an unglamorous cellular recycling center. This notion has undergone a radical shift in the last 10 years, with new research revealing that this organelle serves as a major hub for metabolic signaling pathways. The discovery that master growth regulators, including the protein kinase mTOR (mechanistic target of rapamycin), make their home at the lysosomal surface has generated intense interest in the lysosome's key role in nutrient sensing and cellular homeostasis. The transcriptional networks required for lysosomal maintenance and function are just being unraveled and their connection to lysosome-based signaling pathways revealed. The catabolic and anabolic pathways that converge on the lysosome connect this organelle with multiple facets of cellular function; when these pathways are deregulated they underlie multiple human diseases, and promote cellular and organismal aging. Thus, understanding how lysosome-based signaling pathways function will not only illuminate the fascinating biology of this organelle but will also be critical in unlocking its therapeutic potentials.
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Affiliation(s)
- Dudley W. Lamming
- William S. Middleton Memorial Veterans Hospital, Madison, WI, USA
- Department of Medicine, University of Wisconsin-Madison, Madison, WI, USA
| | - Liron Bar-Peled
- Department of Molecular Medicine, The Scripps Research Institute, La Jolla, CA, USA
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163
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Delorme-Axford E, Klionsky DJ. On the edge of degradation: Autophagy regulation by RNA decay. WILEY INTERDISCIPLINARY REVIEWS-RNA 2018; 10:e1522. [PMID: 30560575 DOI: 10.1002/wrna.1522] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/20/2018] [Revised: 11/21/2018] [Accepted: 11/27/2018] [Indexed: 12/21/2022]
Abstract
Cells must dynamically adapt to altered environmental conditions, particularly during times of stress, to ensure their ability to function effectively and survive. The macroautophagy/autophagy pathway is highly conserved across eukaryotic cells and promotes cell survival during stressful conditions. In general, basal autophagy occurs at a low level to sustain cellular homeostasis and metabolism. However, autophagy is robustly upregulated in response to nutrient deprivation, pathogen infection and increased accumulation of potentially toxic protein aggregates and superfluous organelles. Within the cell, RNA decay maintains quality control to remove aberrant transcripts and regulate appropriate levels of gene expression. Recent evidence has identified components of the cellular mRNA decay machinery as novel regulators of autophagy. Here, we review current findings that demonstrate how autophagy is modulated through RNA decay. This article is categorized under: RNA Turnover and Surveillance > Turnover/Surveillance Mechanisms RNA Turnover and Surveillance > Regulation of RNA Stability.
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Affiliation(s)
| | - Daniel J Klionsky
- Life Sciences Institute, University of Michigan, Ann Arbor, Michigan
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164
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Wang C, Fu J, Wang M, Cai Y, Hua X, Du Y, Yang Z, Li Y, Wang Z, Sheng H, Yin N, Liu X, Koehler JE, Yuan C. Bartonella quintana type IV secretion effector BepE-induced selective autophagy by conjugation with K63 polyubiquitin chain. Cell Microbiol 2018; 21:e12984. [PMID: 30463105 DOI: 10.1111/cmi.12984] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2018] [Revised: 11/08/2018] [Accepted: 11/14/2018] [Indexed: 12/20/2022]
Abstract
Bartonella effector proteins (named Beps) are substrates of VirB type IV secretion system for translocation into host cells evolved in Bartonella spp. Among these, BepE has been shown to protect cells from fragmentation effects triggered by other Beps and to promote in vivo dissemination of bacteria from the dermal site of inoculation to the bloodstream. Bacterial pathogens secreted effectors to modulate the interplay with host autophagy, either to combat autophagy to escape its bactericidal effect or to exploit autophagy to benefit intracellular replication. Here, we reported a distinct phenotype that selective autophagy in host cells is activated as a countermeasure, to attack BepE via conjugation with K63 polyubiquitin chain on BepE. We found that ectopic expression of Bartonella quintana BepE specifically induced punctate structures that colocalised with an autophagy marker (LC3-II) in host cells, in addition to filopodia and membrane ruffle formation. Two tandemly arranged Bartonella Intracellular Delivery (BID) domains in the BepE C-terminus, where ubiquitination of sister pairs of lysine residues was confirmed, were essential to activate host cell autophagy. Multiple polyubiquitin chain linkages of K27, K29, K33, and K63 were found to be conjugated at sites of K222 and K365 on BepE, of which K63 polyubiquitination on BepE K365 determined the selective autophagy (p62/SQSTM1 positive autophagy) independent of the PI3K pathway. Colocalisation of BepE with LAMP1 confirmed the maturation of BepE-induced autophagosomes in which BepE were targeted for degradation. Moreover, host cells employed selective autophagy to counter-attack BepE to rescue cells from BepE-induced endocytosis deficiency.
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Affiliation(s)
- Chunyan Wang
- School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai, China
| | - Jiaqi Fu
- Institute of Analytical Chemistry and Synthetic and Functional Biomolecules Center, College of Chemistry and Molecular Engineering, Peking University, Beijing, China
| | - Meng Wang
- School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai, China
| | - Yuhao Cai
- School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai, China
| | - Xiuguo Hua
- School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai, China
| | - Yuming Du
- School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai, China
| | - Zhibiao Yang
- School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai, China
| | - Yan Li
- Shanghai General Hospital, Shanghai Jiao Tong University, Shanghai, China
| | - Zhenxia Wang
- Shanghai General Hospital, Shanghai Jiao Tong University, Shanghai, China
| | - Huiming Sheng
- Tongren hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, China
| | - Na Yin
- Xinhua hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, China
| | - Xiaoyun Liu
- Institute of Analytical Chemistry and Synthetic and Functional Biomolecules Center, College of Chemistry and Molecular Engineering, Peking University, Beijing, China
| | - Jane E Koehler
- Department of Medicine, Division of Infectious Diseases, and the Microbial Pathogenesis and Host Defense Program, University of California, San Francisco, California, USA
| | - Congli Yuan
- School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai, China.,Shanghai Key Laboratory of Veterinary Medicine, Shanghai Jiao Tong University, Shanghai, China
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165
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Melino VJ, Casartelli A, George J, Rupasinghe T, Roessner U, Okamoto M, Heuer S. RNA Catabolites Contribute to the Nitrogen Pool and Support Growth Recovery of Wheat. FRONTIERS IN PLANT SCIENCE 2018; 9:1539. [PMID: 30455708 PMCID: PMC6230992 DOI: 10.3389/fpls.2018.01539] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/31/2018] [Accepted: 10/01/2018] [Indexed: 05/23/2023]
Abstract
Turn-over of RNA and catabolism of nucleotides releases one to four ammonia molecules; the released nutrients being reassimilated into primary metabolism. Preliminary evidence indicates that monocots store high levels of free nucleotides and nucleosides but their potential as a source of internal organic nitrogen for use and remobilization is uncharted. Early tillering wheat plants were therefore starved of N over a 5-day time-course with examination of nucleic acid yields in whole shoots, young and old leaves and roots. Nucleic acids constituted ∼4% of the total N pool of N starved wheat plants, which was comparable with the N available from nitrate (NO3 -) and greater than that available from the sum of 20 proteinogenic amino acids. Methods were optimized to detect nucleotide (purine and pyrimidine) metabolites, and wheat orthologs of RNA degradation (TaRNS), nucleoside transport (TaENT1, TaENT3) and salvage (TaADK) were identified. It was found that N starved wheat roots actively catabolised RNA and specific purines but accumulated pyrimidines. Reduced levels of RNA corresponded with induction of TaRNS2, TaENT1, TaENT3, and TaADK in the roots. Reduced levels of GMP, guanine, xanthine, allantoin, allantoate and glyoxylate in N starved roots correlated with accumulation of allantoate and glyoxylate in the oldest leaf, suggesting translocation of allantoin. Furthermore, N starved wheat plants exogenously supplied with N in the form of purine catabolites grew and photosynthesized as well as those plants re-supplied with NO3 -. These results support the hypothesis that the nitrogen and carbon recovered from purine metabolism can support wheat growth.
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Affiliation(s)
- Vanessa Jane Melino
- Waite Research Institute, University of Adelaide, Glen Osmond, SA, Australia
- School of Agriculture and Food, University of Melbourne, Parkville, VIC, Australia
| | - Alberto Casartelli
- Waite Research Institute, University of Adelaide, Glen Osmond, SA, Australia
| | - Jessey George
- Waite Research Institute, University of Adelaide, Glen Osmond, SA, Australia
| | - Thusitha Rupasinghe
- Metabolomics Australia, School of Biosciences, The University of Melbourne, Parkville, VIC, Australia
| | - Ute Roessner
- Metabolomics Australia, School of Biosciences, The University of Melbourne, Parkville, VIC, Australia
| | - Mamoru Okamoto
- Waite Research Institute, University of Adelaide, Glen Osmond, SA, Australia
| | - Sigrid Heuer
- Waite Research Institute, University of Adelaide, Glen Osmond, SA, Australia
- Department of Plant Biology and Crop Science, Rothamsted Research, Harpenden, United Kingdom
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166
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Kocaturk NM, Gozuacik D. Crosstalk Between Mammalian Autophagy and the Ubiquitin-Proteasome System. Front Cell Dev Biol 2018; 6:128. [PMID: 30333975 PMCID: PMC6175981 DOI: 10.3389/fcell.2018.00128] [Citation(s) in RCA: 271] [Impact Index Per Article: 45.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2018] [Accepted: 09/13/2018] [Indexed: 12/16/2022] Open
Abstract
Autophagy and the ubiquitin-proteasome system (UPS) are the two major intracellular quality control and recycling mechanisms that are responsible for cellular homeostasis in eukaryotes. Ubiquitylation is utilized as a degradation signal by both systems, yet, different mechanisms are in play. The UPS is responsible for the degradation of short-lived proteins and soluble misfolded proteins whereas autophagy eliminates long-lived proteins, insoluble protein aggregates and even whole organelles (e.g., mitochondria, peroxisomes) and intracellular parasites (e.g., bacteria). Both the UPS and selective autophagy recognize their targets through their ubiquitin tags. In addition to an indirect connection between the two systems through ubiquitylated proteins, recent data indicate the presence of connections and reciprocal regulation mechanisms between these degradation pathways. In this review, we summarize these direct and indirect interactions and crosstalks between autophagy and the UPS, and their implications for cellular stress responses and homeostasis.
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Affiliation(s)
- Nur Mehpare Kocaturk
- Molecular Biology, Genetics and Bioengineering Program, Faculty of Engineering and Natural Sciences, Sabanci University, Istanbul, Turkey
| | - Devrim Gozuacik
- Molecular Biology, Genetics and Bioengineering Program, Faculty of Engineering and Natural Sciences, Sabanci University, Istanbul, Turkey
- Center of Excellence for Functional Surfaces and Interfaces for Nano Diagnostics (EFSUN), Sabanci University, Istanbul, Turkey
- Nanotechnology Research and Application Center (SUNUM), Sabanci University, Istanbul, Turkey
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167
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Bas L, Papinski D, Licheva M, Torggler R, Rohringer S, Schuschnig M, Kraft C. Reconstitution reveals Ykt6 as the autophagosomal SNARE in autophagosome-vacuole fusion. J Cell Biol 2018; 217:3656-3669. [PMID: 30097514 PMCID: PMC6168255 DOI: 10.1083/jcb.201804028] [Citation(s) in RCA: 85] [Impact Index Per Article: 14.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2018] [Revised: 06/12/2018] [Accepted: 07/05/2018] [Indexed: 11/22/2022] Open
Abstract
Autophagy mediates the bulk degradation of cytoplasmic material, particularly during starvation. Upon the induction of autophagy, autophagosomes form a sealed membrane around cargo, fuse with a lytic compartment, and release the cargo for degradation. The mechanism of autophagosome-vacuole fusion is poorly understood, although factors that mediate other cellular fusion events have been implicated. In this study, we developed an in vitro reconstitution assay that enables systematic discovery and dissection of the players involved in autophagosome-vacuole fusion. We found that this process requires the Atg14-Vps34 complex to generate PI3P and thus recruit the Ypt7 module to autophagosomes. The HOPS-tethering complex, recruited by Ypt7, is required to prepare SNARE proteins for fusion. Furthermore, we discovered that fusion requires the R-SNARE Ykt6 on the autophagosome, together with the Q-SNAREs Vam3, Vam7, and Vti1 on the vacuole. These findings shed new light on the mechanism of autophagosome-vacuole fusion and reveal that the R-SNARE Ykt6 is required for this process.
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Affiliation(s)
- Levent Bas
- Max F. Perutz Laboratories, Vienna Biocenter, University of Vienna, Vienna, Austria
| | - Daniel Papinski
- Max F. Perutz Laboratories, Vienna Biocenter, University of Vienna, Vienna, Austria
| | - Mariya Licheva
- Institute of Biochemistry and Molecular Biology, Centre for Biochemistry and Molecular Cell Research , Faculty of Medicine, University of Freiburg, Freiburg, Germany
- Faculty of Biology, University of Freiburg, Freiburg, Germany
| | - Raffaela Torggler
- Max F. Perutz Laboratories, Vienna Biocenter, University of Vienna, Vienna, Austria
- Institute of Biochemistry and Molecular Biology, Centre for Biochemistry and Molecular Cell Research , Faculty of Medicine, University of Freiburg, Freiburg, Germany
- Faculty of Biology, University of Freiburg, Freiburg, Germany
| | - Sabrina Rohringer
- Max F. Perutz Laboratories, Vienna Biocenter, University of Vienna, Vienna, Austria
| | - Martina Schuschnig
- Max F. Perutz Laboratories, Vienna Biocenter, University of Vienna, Vienna, Austria
| | - Claudine Kraft
- Max F. Perutz Laboratories, Vienna Biocenter, University of Vienna, Vienna, Austria
- Institute of Biochemistry and Molecular Biology, Centre for Biochemistry and Molecular Cell Research , Faculty of Medicine, University of Freiburg, Freiburg, Germany
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168
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Paul S, McDonald WH, Moye-Rowley WS. Negative regulation of Candida glabrata Pdr1 by the deubiquitinase subunit Bre5 occurs in a ubiquitin independent manner. Mol Microbiol 2018; 110:309-323. [PMID: 30137659 DOI: 10.1111/mmi.14109] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 08/20/2018] [Indexed: 12/24/2022]
Abstract
The primary route for development of azole resistance in the fungal pathogen Candida glabrata is acquisition of a point mutation in the PDR1 gene. This locus encodes a transcription factor that upon mutation drives high level expression of a range of genes including the ATP-binding cassette transporter-encoding gene CDR1. Pdr1 activity is also elevated in cells that lack the mitochondrial genome (ρ° cells), with associated high expression of CDR1 driving azole resistance. To gain insight into the mechanisms controlling activity of Pdr1, we expressed a tandem affinity purification (TAP)-tagged form of Pdr1 in both wild-type (ρ+ ) and ρ° cells. Purified proteins were analyzed by multidimensional protein identification technology mass spectrometry identifying a protein called Bre5 as a factor that co-purified with TAP-Pdr1. In Saccharomyces cerevisiae, Bre5 is part of a deubiquitinase complex formed by association with the ubiquitin-specific protease Ubp3. Genetic analyses in C. glabrata revealed that loss of BRE5, but not UBP3, led to an increase in expression of PDR1 and CDR1 at the transcriptional level. These studies support the view that Bre5 acts as a negative regulator of Pdr1 transcriptional activity and behaves as a C. glabrata-specific modulator of azole resistance.
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Affiliation(s)
- Sanjoy Paul
- Department of Molecular Physiology and Biophysics, Carver College of Medicine, University of Iowa, Iowa City, IA, 52242, USA
| | - W Hayes McDonald
- Department of Biochemistry, Vanderbilt University Medical Center, Nashville, TN, 37232, USA
| | - W Scott Moye-Rowley
- Department of Molecular Physiology and Biophysics, Carver College of Medicine, University of Iowa, Iowa City, IA, 52242, USA
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169
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Freeman SA, Grinstein S. Resolution of macropinosomes, phagosomes and autolysosomes: Osmotically driven shrinkage enables tubulation and vesiculation. Traffic 2018; 19:965-974. [DOI: 10.1111/tra.12614] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2018] [Revised: 08/15/2018] [Accepted: 08/16/2018] [Indexed: 12/14/2022]
Affiliation(s)
- Spencer A. Freeman
- Program in Cell Biology; Peter Gilgan Centre for Research and Learning, Hospital for Sick Children; Toronto Ontario Canada
| | - Sergio Grinstein
- Program in Cell Biology; Peter Gilgan Centre for Research and Learning, Hospital for Sick Children; Toronto Ontario Canada
- Keenan Research Centre of the Li Ka Shing Knowledge Institute, St. Michael's Hospital; Toronto Ontario Canada
- Department of Biochemistry; University of Toronto; Toronto Ontario Canada
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170
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Thomas RE, Vincow ES, Merrihew GE, MacCoss MJ, Davis MY, Pallanck LJ. Glucocerebrosidase deficiency promotes protein aggregation through dysregulation of extracellular vesicles. PLoS Genet 2018; 14:e1007694. [PMID: 30256786 PMCID: PMC6175534 DOI: 10.1371/journal.pgen.1007694] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2018] [Revised: 10/08/2018] [Accepted: 09/13/2018] [Indexed: 12/21/2022] Open
Abstract
Mutations in the glucosylceramidase beta (GBA) gene are strongly associated with neurodegenerative diseases marked by protein aggregation. GBA encodes the lysosomal enzyme glucocerebrosidase, which breaks down glucosylceramide. A common explanation for the link between GBA mutations and protein aggregation is that lysosomal accumulation of glucosylceramide causes impaired autophagy. We tested this hypothesis directly by measuring protein turnover and abundance in Drosophila mutants with deletions in the GBA ortholog Gba1b. Proteomic analyses revealed that known autophagy substrates, which had severely impaired turnover in autophagy-deficient Atg7 mutants, showed little to no overall slowing of turnover or increase in abundance in Gba1b mutants. Likewise, Gba1b mutants did not have the marked impairment of mitochondrial protein turnover seen in mitophagy-deficient parkin mutants. Proteasome activity, microautophagy, and endocytic degradation also appeared unaffected in Gba1b mutants. However, we found striking changes in the turnover and abundance of proteins associated with extracellular vesicles (EVs), which have been proposed as vehicles for the spread of protein aggregates in neurodegenerative disease. These changes were specific to Gba1b mutants and did not represent an acceleration of normal aging. Western blotting of isolated EVs confirmed the increased abundance of EV proteins in Gba1b mutants, and nanoparticle tracking analysis revealed that Gba1b mutants had six times as many EVs as controls. Genetic perturbations of EV production in Gba1b mutants suppressed protein aggregation, demonstrating that the increase in EV abundance contributed to the accumulation of protein aggregates. Together, our findings indicate that glucocerebrosidase deficiency causes pathogenic changes in EV metabolism and may promote the spread of protein aggregates through extracellular vesicles.
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Affiliation(s)
- Ruth E. Thomas
- Department of Genome Sciences, University of Washington, Seattle, WA, United States of America
| | - Evelyn S. Vincow
- Department of Genome Sciences, University of Washington, Seattle, WA, United States of America
| | - Gennifer E. Merrihew
- Department of Genome Sciences, University of Washington, Seattle, WA, United States of America
| | - Michael J. MacCoss
- Department of Genome Sciences, University of Washington, Seattle, WA, United States of America
| | - Marie Y. Davis
- Department of Neurology, University of Washington, Seattle, WA, United States of America
- Department of Neurology, Veterans Affairs Puget Sound Health Care System, Seattle, WA, United States of America
| | - Leo J. Pallanck
- Department of Genome Sciences, University of Washington, Seattle, WA, United States of America
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171
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Pigna E, Sanna K, Coletti D, Li Z, Parlakian A, Adamo S, Moresi V. Increasing autophagy does not affect neurogenic muscle atrophy. Eur J Transl Myol 2018; 28:7687. [PMID: 30344980 PMCID: PMC6176397 DOI: 10.4081/ejtm.2018.7687] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2018] [Revised: 08/11/2018] [Accepted: 08/10/2018] [Indexed: 11/23/2022] Open
Abstract
Physiological autophagy plays a crucial role in the regulation of muscle mass and metabolism, while the excessive induction or the inhibition of the autophagic flux contributes to the progression of several diseases. Autophagy can be activated by different stimuli, including cancer, exercise, caloric restriction and denervation. The latter leads to muscle atrophy through the activation of catabolic pathways, i.e. the ubiquitin-proteasome system and autophagy. However, the kinetics of autophagy activation and the upstream molecular pathways in denervated skeletal muscle have not been reported yet. In this study, we characterized the kinetics of autophagic induction, quickly triggered by denervation, and report the Akt/mTOR axis activation. Besides, with the aim to assess the relative contribution of autophagy in neurogenic muscle atrophy, we triggered autophagy with different stimuli along with denervation, and observed that four week-long autophagic induction, by either intermitted fasting or rapamycin treatment, did not significantly affect muscle mass loss. We conclude that: i) autophagy does not play a major role in inducing muscle loss following denervation; ii) nonetheless, autophagy may have a regulatory role in denervation induced muscle atrophy, since it is significantly upregulated as early as eight hours after denervation; iii) Akt/mTOR axis, AMPK and FoxO3a are activated consistently with the progression of muscle atrophy, further highlighting the complexity of the signaling response to the atrophying stimulus deriving from denervation.
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Affiliation(s)
- Eva Pigna
- Department of Anatomy, Histology, Forensic Medicine & Orthopedics, Histology & Medical Embryology Section, Sapienza University of Rome, Italy
| | - Krizia Sanna
- Department of Anatomy, Histology, Forensic Medicine & Orthopedics, Histology & Medical Embryology Section, Sapienza University of Rome, Italy
| | - Dario Coletti
- Department of Anatomy, Histology, Forensic Medicine & Orthopedics, Histology & Medical Embryology Section, Sapienza University of Rome, Italy.,Interuniversity Institute of Myology, Italy.,Sorbonne Université, CNRS UMR 8256-INSERM ERL U1164, IBPS B2A Department of Biological Adaptation and Aging, Paris, France
| | - Zhenlin Li
- Sorbonne Université, CNRS UMR 8256-INSERM ERL U1164, IBPS B2A Department of Biological Adaptation and Aging, Paris, France
| | - Ara Parlakian
- Sorbonne Université, CNRS UMR 8256-INSERM ERL U1164, IBPS B2A Department of Biological Adaptation and Aging, Paris, France
| | | | - Viviana Moresi
- Department of Anatomy, Histology, Forensic Medicine & Orthopedics, Histology & Medical Embryology Section, Sapienza University of Rome, Italy.,Interuniversity Institute of Myology, Italy
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172
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Liu Y, Zou W, Yang P, Wang L, Ma Y, Zhang H, Wang X. Autophagy-dependent ribosomal RNA degradation is essential for maintaining nucleotide homeostasis during C. elegans development. eLife 2018; 7:36588. [PMID: 30102152 PMCID: PMC6101943 DOI: 10.7554/elife.36588] [Citation(s) in RCA: 37] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2018] [Accepted: 08/12/2018] [Indexed: 12/24/2022] Open
Abstract
Ribosome degradation through the autophagy-lysosome pathway is crucial for cell survival during nutrient starvation, but whether it occurs under normal growth conditions and contributes to animal physiology remains unaddressed. In this study, we identified RNST-2, a C. elegans T2 family endoribonuclease, as the key enzyme that degrades ribosomal RNA in lysosomes. We found that loss of rnst-2 causes accumulation of rRNA and ribosomal proteins in enlarged lysosomes and both phenotypes are suppressed by blocking autophagy, which indicates that RNST-2 mediates autophagic degradation of ribosomal RNA in lysosomes. rnst-2(lf) mutants are defective in embryonic and larval development and are short-lived. Remarkably, simultaneous loss of RNST-2 and de novo synthesis of pyrimidine nucleotides leads to complete embryonic lethality, which is suppressed by supplements of uridine or cytidine. Our study reveals an essential role of autophagy-dependent degradation of ribosomal RNA in maintaining nucleotide homeostasis during animal development.
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Affiliation(s)
- Yubing Liu
- Peking University-Tsinghua University-National Institute of Biological Joint Graduate Program, School of Life Sciences, Peking University, Beijing, China.,National Institute of Biological Science, Beijing, China.,National Laboratory of Biomacromolecules, CAS Center for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing, China
| | - Wei Zou
- National Institute of Biological Science, Beijing, China
| | - Peiguo Yang
- National Laboratory of Biomacromolecules, CAS Center for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing, China
| | - Li Wang
- National Laboratory of Biomacromolecules, CAS Center for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing, China.,College of Life Sciences, University of Chinese Academy of Sciences, Beijing, China
| | - Yan Ma
- National Institute of Biological Science, Beijing, China
| | - Hong Zhang
- National Laboratory of Biomacromolecules, CAS Center for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing, China.,College of Life Sciences, University of Chinese Academy of Sciences, Beijing, China
| | - Xiaochen Wang
- National Laboratory of Biomacromolecules, CAS Center for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing, China.,College of Life Sciences, University of Chinese Academy of Sciences, Beijing, China
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173
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Tang M, Chen Z, Wu D, Chen L. Ferritinophagy/ferroptosis: Iron-related newcomers in human diseases. J Cell Physiol 2018; 233:9179-9190. [PMID: 30076709 DOI: 10.1002/jcp.26954] [Citation(s) in RCA: 181] [Impact Index Per Article: 30.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2018] [Accepted: 06/12/2018] [Indexed: 02/06/2023]
Abstract
Nuclear receptor coactivator 4 mediated ferritinophagy is an autophagic phenomenon that specifically involves ferritin to release intracellular free iron. Ferritinophagy is implicated in maintaining efficient erythropoiesis. Notably, ferritinophagy also plays a central role in driving some pathological processes, including Parkinson's disease (PD) and urinary tract infections. Some evidence has demonstrated that ferritinophagy is critical to induce ferroptosis. Ferroptosis is a newly nonapoptotic form of cell death, characterized by the accumulation of iron-based lipid reactive oxygen species. Ferroptosis plays an important role in inhibiting some types of cancers, such as hepatocellular carcinoma, pancreatic carcinoma, prostate cancer, and breast cancer. Conversely, the activation of ferroptosis accelerates neurodegeneration diseases, including PD and Alzheimer's disease. Therefore, in this review, we summarize the regulatory mechanisms related to ferritinophagy and ferroptosis. Moreover, the distinctive effects of ferritinophagy in human erythropoiesis and some pathologies, coupled with the promotive or inhibitory role of tumorous and neurodegenerative diseases mediated by ferroptosis, are elucidated. Obviously, activating or inhibiting ferroptosis could be exploited to achieve desirable therapeutic effects on diverse cancers and neurodegeneration diseases. Interrupting ferritinophagy to control iron level might provide a potentially therapeutic avenue to suppress urinary tract infections.
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Affiliation(s)
- Mingzhu Tang
- Institute of Pharmacy and Pharmacology, Learning Key Laboratory for Pharmacoproteomics, Hunan Province Cooperative Innovation Center for Molecular Target New Drug Study, University of South China, Hengyang, China
| | - Zhe Chen
- Institute of Pharmacy and Pharmacology, Learning Key Laboratory for Pharmacoproteomics, Hunan Province Cooperative Innovation Center for Molecular Target New Drug Study, University of South China, Hengyang, China
| | - Di Wu
- Institute of Pharmacy and Pharmacology, Learning Key Laboratory for Pharmacoproteomics, Hunan Province Cooperative Innovation Center for Molecular Target New Drug Study, University of South China, Hengyang, China
| | - Linxi Chen
- Institute of Pharmacy and Pharmacology, Learning Key Laboratory for Pharmacoproteomics, Hunan Province Cooperative Innovation Center for Molecular Target New Drug Study, University of South China, Hengyang, China
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174
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Moon LDF. Chromatolysis: Do injured axons regenerate poorly when ribonucleases attack rough endoplasmic reticulum, ribosomes and RNA? Dev Neurobiol 2018; 78:1011-1024. [PMID: 30027624 PMCID: PMC6334169 DOI: 10.1002/dneu.22625] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2018] [Revised: 05/31/2018] [Accepted: 06/04/2018] [Indexed: 02/06/2023]
Abstract
After axonal injury, chromatolysis (fragmentation of Nissl substance) can occur in the soma. Electron microscopy shows that chromatolysis involves fission of the rough endoplasmic reticulum. In CNS neurons (which do not regenerate axons back to their original targets) or in motor neurons or dorsal root ganglion neurons denied axon regeneration (e.g., by transection and ligation), chromatolysis is often accompanied by degranulation (loss of ribosomes from rough endoplasmic reticulum), disaggregation of polyribosomes and degradation of monoribosomes into dust‐like particles. Ribosomes and rough endoplasmic reticulum may also be degraded in autophagic vacuoles by ribophagy and reticulophagy, respectively. In other words, chromatolysis is disruption of parts of the protein synthesis infrastructure. Whereas some neurons may show transient or no chromatolysis, severely injured neurons can remain chromatolytic and never again synthesize normal levels of protein; some may atrophy or die. Ribonuclease(s) might cause the following features of chromatolysis: fragmentation and degranulation of rough endoplasmic reticulum, disaggregation of polyribosomes and degradation of monoribosomes. For example, ribonucleases in the EndoU/PP11 family can modify rough endoplasmic reticulum; many ribonucleases can degrade mRNA causing polyribosomes to unchain and disperse, and they can disassemble monoribosomes; Ribonuclease 5 can control rRNA synthesis and degrade tRNA; Ribonuclease T2 can degrade ribosomes, endoplasmic reticulum and RNA within autophagic vacuoles; and Ribonuclease IRE1α acts as a stress sensor within the endoplasmic reticulum. Regeneration might be improved after axonal injury by protecting the protein synthesis machinery from catabolism; targeting ribonucleases using inhibitors can enhance neurite outgrowth and could be a profitable strategy in vivo. © 2018 Wiley Periodicals, Inc. Develop Neurobiol, 2018
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Affiliation(s)
- Lawrence David Falcon Moon
- Neurorestoration Group, Wolfson Centre for Age-Related Diseases, 16-20 Newcomen Street, London, SE1 1UL, United Kingdom
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175
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Abstract
Although ribophagy was demonstrated in budding yeast a decade ago, a specific receptor for this process has been unknown. Recently, a study revealed that NUFIP1 (nuclear FMR1 interacting protein 1) functions as a receptor for the selective degradation of ribosomes by starvation-induced autophagy in cultured mammalian cells. In addition to the identification of a selective autophagy receptor, this study suggests a strategy that can be adapted to the identification of additional novel receptor proteins.
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Affiliation(s)
- Meiyan Jin
- a Department of Molecular & Cell Biology , University of California , Berkeley , CA , USA
| | - Daniel J Klionsky
- b Life Sciences Institute and Department of Molecular, Cellular and Developmental Biology , University of Michigan , Ann Arbor , MI , USA
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176
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Becker AC, Gannagé M, Giese S, Hu Z, Abou-Eid S, Roubaty C, Paul P, Bühler L, Gretzmeier C, Dumit VI, Kaeser-Pebernard S, Schwemmle M, Münz C, Dengjel J. Influenza A Virus Induces Autophagosomal Targeting of Ribosomal Proteins. Mol Cell Proteomics 2018; 17:1909-1921. [PMID: 29980615 PMCID: PMC6166674 DOI: 10.1074/mcp.ra117.000364] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2017] [Revised: 07/04/2018] [Indexed: 12/24/2022] Open
Abstract
Seasonal epidemics of influenza A virus are a major cause of severe illness and are of high socio-economic relevance. For the design of effective antiviral therapies, a detailed knowledge of pathways perturbed by virus infection is critical. We performed comprehensive expression and organellar proteomics experiments to study the cellular consequences of influenza A virus infection using three human epithelial cell lines derived from human lung carcinomas: A549, Calu-1 and NCI-H1299. As a common response, the type I interferon pathway was up-regulated upon infection. Interestingly, influenza A virus infection led to numerous cell line-specific responses affecting both protein abundance as well as subcellular localization. In A549 cells, the vesicular compartment appeared expanded after virus infection. The composition of autophagsomes was altered by targeting of ribosomes, viral mRNA and proteins to these double membrane vesicles. Thus, autophagy may support viral protein translation by promoting the clustering of the respective molecular machinery in autophagosomes in a cell line-dependent manner.
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Affiliation(s)
- Andrea C Becker
- From the ‡Department of Dermatology, Medical Center University of Freiburg, Hauptstr. 7, 79104 Freiburg, Germany.,§Faculty of Medicine, University of Freiburg, Breisacher Strasse 153, 79110 Freiburg, Germany
| | - Monique Gannagé
- ¶Department of Pathology and Immunology, School of Medicine, University of Geneva, 1 rue Michel Servet, 1211 Geneva, Switzerland
| | - Sebastian Giese
- §Faculty of Medicine, University of Freiburg, Breisacher Strasse 153, 79110 Freiburg, Germany.,‖Institute for Virology, Medical Center, University of Freiburg, Hermann-Herder-Strasse 11, 79104 Freiburg, Germany
| | - Zehan Hu
- From the ‡Department of Dermatology, Medical Center University of Freiburg, Hauptstr. 7, 79104 Freiburg, Germany.,§Faculty of Medicine, University of Freiburg, Breisacher Strasse 153, 79110 Freiburg, Germany.,§§Department of Biology, University of Fribourg, Chemin du Musée 10, 1700 Fribourg, Switzerland
| | - Shadi Abou-Eid
- §§Department of Biology, University of Fribourg, Chemin du Musée 10, 1700 Fribourg, Switzerland
| | - Carole Roubaty
- §§Department of Biology, University of Fribourg, Chemin du Musée 10, 1700 Fribourg, Switzerland
| | - Petra Paul
- **Viral Immunobiology, Institute of Experimental Immunology, University of Zurich, Winterthurerstrasse 190, 8057 Zürich, Switzerland
| | - Lea Bühler
- From the ‡Department of Dermatology, Medical Center University of Freiburg, Hauptstr. 7, 79104 Freiburg, Germany.,§Faculty of Medicine, University of Freiburg, Breisacher Strasse 153, 79110 Freiburg, Germany
| | - Christine Gretzmeier
- From the ‡Department of Dermatology, Medical Center University of Freiburg, Hauptstr. 7, 79104 Freiburg, Germany.,§Faculty of Medicine, University of Freiburg, Breisacher Strasse 153, 79110 Freiburg, Germany
| | - Veronica I Dumit
- ‡‡Core Facility Proteomics, Center for Biological Systems Analysis (ZBSA), University of Freiburg, Habsburgerstr. 49, 79104 Freiburg, Germany
| | | | - Martin Schwemmle
- §Faculty of Medicine, University of Freiburg, Breisacher Strasse 153, 79110 Freiburg, Germany.,‖Institute for Virology, Medical Center, University of Freiburg, Hermann-Herder-Strasse 11, 79104 Freiburg, Germany
| | - Christian Münz
- **Viral Immunobiology, Institute of Experimental Immunology, University of Zurich, Winterthurerstrasse 190, 8057 Zürich, Switzerland
| | - Jörn Dengjel
- From the ‡Department of Dermatology, Medical Center University of Freiburg, Hauptstr. 7, 79104 Freiburg, Germany; .,§Faculty of Medicine, University of Freiburg, Breisacher Strasse 153, 79110 Freiburg, Germany.,§§Department of Biology, University of Fribourg, Chemin du Musée 10, 1700 Fribourg, Switzerland
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177
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Dissanayaka DMSB, Plaxton WC, Lambers H, Siebers M, Marambe B, Wasaki J. Molecular mechanisms underpinning phosphorus-use efficiency in rice. PLANT, CELL & ENVIRONMENT 2018; 41:1483-1496. [PMID: 29520969 DOI: 10.1111/pce.13191] [Citation(s) in RCA: 43] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/10/2017] [Revised: 02/27/2018] [Accepted: 03/03/2018] [Indexed: 05/18/2023]
Abstract
Orthophosphate (H2 PO4- , Pi) is an essential macronutrient integral to energy metabolism as well as a component of membrane lipids, nucleic acids, including ribosomal RNA, and therefore essential for protein synthesis. The Pi concentration in the solution of most soils worldwide is usually far too low for maximum growth of crops, including rice. This has prompted the massive use of inefficient, polluting, and nonrenewable phosphorus (P) fertilizers in agriculture. We urgently need alternative and more sustainable approaches to decrease agriculture's dependence on Pi fertilizers. These include manipulating crops by (a) enhancing the ability of their roots to acquire limiting Pi from the soil (i.e. increased P-acquisition efficiency) and/or (b) increasing the total biomass/yield produced per molecule of Pi acquired from the soil (i.e. increased P-use efficiency). Improved P-use efficiency may be achieved by producing high-yielding plants with lower P concentrations or by improving the remobilization of acquired P within the plant so as to maximize growth and biomass allocation to developing organs. Membrane lipid remodelling coupled with hydrolysis of RNA and smaller P-esters in senescing organs fuels P remobilization in rice, the world's most important cereal crop.
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Affiliation(s)
- D M S B Dissanayaka
- Graduate School of Biosphere Science, Hiroshima University, Kagamiyama 1-7-1, Higashi-, Hiroshima, 739-8521, Japan
- Department of Crop Science, Faculty of Agriculture, University of Peradeniya, Peradeniya, 20400, Sri Lanka
| | - William C Plaxton
- Department of Biology and Department of Biomedical and Molecular Sciences, Queen's University, Kingston, Ontario, K7L3N6, Canada
| | - Hans Lambers
- School of Biological Sciences and Institute of Agriculture, The University of Western Australia, 35 Stirling Highway, Crawley (Perth), Western Australia, 6009, Australia
| | - Meike Siebers
- Max-Planck-Institute for Plant Breeding Research, Carl-von-Linné-Weg 10, 50829, Cologne, Germany
| | - Buddhi Marambe
- Department of Crop Science, Faculty of Agriculture, University of Peradeniya, Peradeniya, 20400, Sri Lanka
| | - Jun Wasaki
- Graduate School of Biosphere Science, Hiroshima University, Kagamiyama 1-7-1, Higashi-, Hiroshima, 739-8521, Japan
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178
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Abstract
Translation is a key step in the regulation of gene expression and one of the most energy-consuming processes in the cell. In response to various stimuli, multiple signaling pathways converge on the translational machinery to regulate its function. To date, the roles of phosphoinositide 3-kinase (PI3K)/AKT and the mitogen-activated protein kinase (MAPK) pathways in the regulation of translation are among the best understood. Both pathways engage the mechanistic target of rapamycin (mTOR) to regulate a variety of components of the translational machinery. While these pathways regulate protein synthesis in homeostasis, their dysregulation results in aberrant translation leading to human diseases, including diabetes, neurological disorders, and cancer. Here we review the roles of the PI3K/AKT and MAPK pathways in the regulation of mRNA translation. We also highlight additional signaling mechanisms that have recently emerged as regulators of the translational apparatus.
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179
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Piekarski A, Nagarajan G, Ishola P, Flees J, Greene ES, Kuenzel WJ, Ohkubo T, Maier H, Bottje WG, Cline MA, Dridi S. AMP-Activated Protein Kinase Mediates the Effect of Leptin on Avian Autophagy in a Tissue-Specific Manner. Front Physiol 2018; 9:541. [PMID: 29867578 PMCID: PMC5963154 DOI: 10.3389/fphys.2018.00541] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2018] [Accepted: 04/26/2018] [Indexed: 12/23/2022] Open
Abstract
Autophagy, a highly conserved intracellular self-digestion process, plays an integral role in maintaining cellular homeostasis. Although emerging evidence indicate that the endocrine system regulates autophagy in mammals, there is still a scarcity of information on autophagy in avian (non-mammalian) species. Here, we show that intracerebroventricular administration of leptin reduces feed intake, modulates the expression of feeding-related hypothalamic neuropeptides, activates leptin receptor and signal transducer and activator of transcription (Ob-Rb/STAT) pathway, and significantly increases the expression of autophagy-related proteins (Atg3, Atg5, Atg7, beclin1, and LC3B) in chicken hypothalamus, liver, and muscle. Similarly, leptin treatment activates Ob-Rb/STAT pathway and increased the expression of autophagy-related markers in chicken hypothalamic organotypic cultures, muscle (QM7) and hepatocyte (Sim-CEL) cell cultures as well as in Chinese Hamster Ovary (CHO-K1) cells-overexpressing chicken Ob-Rb and STAT3. To define the downstream mediator(s) of leptin's effects on autophagy, we determined the role of the master energy sensor AMP-activated protein kinase (AMPK). Leptin treatment significantly increased the phosphorylated levels of AMPKα1/2 at Thr172 site in chicken hypothalamus and liver, but not in muscle. Likewise, AMPKα1/2 was activated by leptin in chicken hypothalamic organotypic culture and Sim-CEL, but not in QM7 cells. Blocking AMPK activity by compound C reverses the autophagy-inducing effect of leptin. Together, these findings indicate that AMPK mediates the effect of leptin on chicken autophagy in a tissue-specific manner.
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Affiliation(s)
- Alissa Piekarski
- Center of Excellence for Poultry Science, University of Arkansas, Fayetteville, AR, United States
| | - Gurueswar Nagarajan
- Center of Excellence for Poultry Science, University of Arkansas, Fayetteville, AR, United States
| | - Peter Ishola
- Center of Excellence for Poultry Science, University of Arkansas, Fayetteville, AR, United States
| | - Joshua Flees
- Center of Excellence for Poultry Science, University of Arkansas, Fayetteville, AR, United States
| | - Elizabeth S. Greene
- Center of Excellence for Poultry Science, University of Arkansas, Fayetteville, AR, United States
| | - Wayne J. Kuenzel
- Center of Excellence for Poultry Science, University of Arkansas, Fayetteville, AR, United States
| | - Takeshi Ohkubo
- College of Agriculture, Ibaraki University, Ibaraki, Japan
| | - Helena Maier
- Nidovirus-Cell Interactions Group, The Pirbright Institute, Woking, United Kingdom
| | - Walter G. Bottje
- Center of Excellence for Poultry Science, University of Arkansas, Fayetteville, AR, United States
| | - Mark A. Cline
- Department of Animal and Poultry Sciences, Virginia Tech, Blacksburg, VA, United States
| | - Sami Dridi
- Center of Excellence for Poultry Science, University of Arkansas, Fayetteville, AR, United States
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180
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Abstract
Plants have evolved sophisticated mechanisms to recycle intracellular constituents, which are essential for developmental and metabolic transitions; for efficient nutrient reuse; and for the proper disposal of proteins, protein complexes, and even entire organelles that become obsolete or dysfunctional. One major route is autophagy, which employs specialized vesicles to encapsulate and deliver cytoplasmic material to the vacuole for breakdown. In the past decade, the mechanics of autophagy and the scores of components involved in autophagic vesicle assembly have been documented. Now emerging is the importance of dedicated receptors that help recruit appropriate cargo, which in many cases exploit ubiquitylation as a signal. Although operating at a low constitutive level in all plant cells, autophagy is upregulated during senescence and various environmental challenges and is essential for proper nutrient allocation. Its importance to plant metabolism and energy balance in particular places autophagy at the nexus of robust crop performance, especially under suboptimal conditions.
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Affiliation(s)
| | - Richard D Vierstra
- Department of Biology, Washington University in St. Louis, St. Louis, Missouri 63130, USA;
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181
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Wyant GA, Abu-Remaileh M, Frenkel EM, Laqtom NN, Dharamdasani V, Lewis CA, Chan SH, Heinze I, Ori A, Sabatini DM. NUFIP1 is a ribosome receptor for starvation-induced ribophagy. Science 2018; 360:751-758. [PMID: 29700228 DOI: 10.1126/science.aar2663] [Citation(s) in RCA: 241] [Impact Index Per Article: 40.2] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2017] [Accepted: 03/19/2018] [Indexed: 12/11/2022]
Abstract
The lysosome degrades and recycles macromolecules, signals to the master growth regulator mTORC1 [mechanistic target of rapamycin (mTOR) complex 1], and is associated with human disease. We performed quantitative proteomic analyses of rapidly isolated lysosomes and found that nutrient levels and mTOR dynamically modulate the lysosomal proteome. Upon mTORC1 inhibition, NUFIP1 (nuclear fragile X mental retardation-interacting protein 1) redistributes from the nucleus to autophagosomes and lysosomes. Upon these conditions, NUFIP1 interacts with ribosomes and delivers them to autophagosomes by directly binding to microtubule-associated proteins 1A/1B light chain 3B (LC3B). The starvation-induced degradation of ribosomes via autophagy (ribophagy) depends on the capacity of NUFIP1 to bind LC3B and promotes cell survival. We propose that NUFIP1 is a receptor for the selective autophagy of ribosomes.
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Affiliation(s)
- Gregory A Wyant
- Whitehead Institute for Biomedical Research and Department of Biology, Massachusetts Institute of Technology, Cambridge, MA 02142, USA.,Howard Hughes Medical Institute, Department of Biology, Massachusetts Institute of Technology, Cambridge, MA 02139, USA.,Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA 02142, USA.,Broad Institute of Harvard and MIT, Cambridge, MA 02142, USA
| | - Monther Abu-Remaileh
- Whitehead Institute for Biomedical Research and Department of Biology, Massachusetts Institute of Technology, Cambridge, MA 02142, USA.,Howard Hughes Medical Institute, Department of Biology, Massachusetts Institute of Technology, Cambridge, MA 02139, USA.,Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA 02142, USA.,Broad Institute of Harvard and MIT, Cambridge, MA 02142, USA
| | - Evgeni M Frenkel
- Whitehead Institute for Biomedical Research and Department of Biology, Massachusetts Institute of Technology, Cambridge, MA 02142, USA.,Howard Hughes Medical Institute, Department of Biology, Massachusetts Institute of Technology, Cambridge, MA 02139, USA.,Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA 02142, USA.,Broad Institute of Harvard and MIT, Cambridge, MA 02142, USA
| | - Nouf N Laqtom
- Whitehead Institute for Biomedical Research and Department of Biology, Massachusetts Institute of Technology, Cambridge, MA 02142, USA.,Howard Hughes Medical Institute, Department of Biology, Massachusetts Institute of Technology, Cambridge, MA 02139, USA.,Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA 02142, USA.,Broad Institute of Harvard and MIT, Cambridge, MA 02142, USA
| | - Vimisha Dharamdasani
- Whitehead Institute for Biomedical Research and Department of Biology, Massachusetts Institute of Technology, Cambridge, MA 02142, USA.,Howard Hughes Medical Institute, Department of Biology, Massachusetts Institute of Technology, Cambridge, MA 02139, USA.,Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA 02142, USA.,Broad Institute of Harvard and MIT, Cambridge, MA 02142, USA
| | - Caroline A Lewis
- Whitehead Institute for Biomedical Research and Department of Biology, Massachusetts Institute of Technology, Cambridge, MA 02142, USA
| | - Sze Ham Chan
- Whitehead Institute for Biomedical Research and Department of Biology, Massachusetts Institute of Technology, Cambridge, MA 02142, USA
| | - Ivonne Heinze
- Leibniz Institute on Aging-Fritz Lipmann Institute, 07745 Jena, Germany
| | - Alessandro Ori
- Leibniz Institute on Aging-Fritz Lipmann Institute, 07745 Jena, Germany.
| | - David M Sabatini
- Whitehead Institute for Biomedical Research and Department of Biology, Massachusetts Institute of Technology, Cambridge, MA 02142, USA. .,Howard Hughes Medical Institute, Department of Biology, Massachusetts Institute of Technology, Cambridge, MA 02139, USA.,Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA 02142, USA.,Broad Institute of Harvard and MIT, Cambridge, MA 02142, USA
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182
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Marshall RS, Vierstra RD. Proteasome storage granules protect proteasomes from autophagic degradation upon carbon starvation. eLife 2018; 7:34532. [PMID: 29624167 PMCID: PMC5947986 DOI: 10.7554/elife.34532] [Citation(s) in RCA: 72] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2017] [Accepted: 04/05/2018] [Indexed: 12/14/2022] Open
Abstract
26S proteasome abundance is tightly regulated at multiple levels, including the elimination of excess or inactive particles by autophagy. In yeast, this proteaphagy occurs upon nitrogen starvation but not carbon starvation, which instead stimulates the rapid sequestration of proteasomes into cytoplasmic puncta termed proteasome storage granules (PSGs). Here, we show that PSGs help protect proteasomes from autophagic degradation. Both the core protease and regulatory particle sub-complexes are sequestered separately into PSGs via pathways dependent on the accessory proteins Blm10 and Spg5, respectively. Modulating PSG formation, either by perturbing cellular energy status or pH, or by genetically eliminating factors required for granule assembly, not only influences the rate of proteasome degradation, but also impacts cell viability upon recovery from carbon starvation. PSG formation and concomitant protection against proteaphagy also occurs in Arabidopsis, suggesting that PSGs represent an evolutionarily conserved cache of proteasomes that can be rapidly re-mobilized based on energy availability. Proteins perform many jobs within an organism, including providing structure and support, and protecting against infection. The levels of the many proteins in a cell need to be carefully controlled so that the correct amounts are present at the right place and time to perform these tasks. This control can be achieved by balancing the production of new proteins with the break down (or degradation) of proteins that are no longer required or become dysfunctional. Most cells have two pathways for degrading proteins. One pathway breaks down individual proteins specifically marked for elimination; this causes them to be recognized by a structure called the proteasome, which chops proteins into smaller pieces. Larger protein assemblies – including the proteasome itself – are to big for the proteasome and thus need to be degraded by another pathway called autophagy. This process engulfs and delivers parts of a cell to a membrane-bound compartment called the vacuole, which ‘digests’ and recycles these larger constituents. Proteasomes are degraded by autophagy when they are not working correctly and when nitrogen (a crucial nutrient) is in short supply. However, proteasomes are not degraded when cells lack carbon, even though this starvation is known to activate autophagy in the same way that an absence of nitrogen does. So how do proteasomes escape degradation when cells are starved for carbon? Marshall and Vierstra now show that upon carbon starvation, proteasomes rapidly exit the cell nucleus and cluster together in the main part of the cell (termed the cytosol). These clusters are known as proteasome storage granules (PSGs). In fungi and plants, mutations or conditions inside the cell that make it difficult for PSGs to assemble cause proteasomes to instead be broken down in the vacuole when carbon availability is low. Clustering into PSGs therefore protects proteasomes from autophagy. This clustering appears advantageous to cells; yeast cells that could form PSGs were better able to start growing again when their nutrient supply improved. Protein clustering (also known as aggregation) is an important strategy that cells use to survive stressful conditions. However, it can also be harmful when proteins aggregate inappropriately, such as occurs in Alzheimer’s disease. Researchers may be able to use PSG assembly as a convenient model to study the causes and consequences of protein aggregation; this knowledge could ultimately be applied to improve human health and crop productivity.
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Affiliation(s)
- Richard S Marshall
- Department of Biology, Washington University in St. Louis, St. Louis, United States
| | - Richard D Vierstra
- Department of Biology, Washington University in St. Louis, St. Louis, United States
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183
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Couso I, Pérez-Pérez ME, Martínez-Force E, Kim HS, He Y, Umen JG, Crespo JL. Autophagic flux is required for the synthesis of triacylglycerols and ribosomal protein turnover in Chlamydomonas. JOURNAL OF EXPERIMENTAL BOTANY 2018; 69:1355-1367. [PMID: 29053817 PMCID: PMC6018900 DOI: 10.1093/jxb/erx372] [Citation(s) in RCA: 66] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/12/2017] [Accepted: 09/28/2017] [Indexed: 05/19/2023]
Abstract
Autophagy is an intracellular catabolic process that allows cells to recycle unneeded or damaged material to maintain cellular homeostasis. This highly dynamic process is characterized by the formation of double-membrane vesicles called autophagosomes, which engulf and deliver the cargo to the vacuole. Flow of material through the autophagy pathway and its degradation in the vacuole is known as autophagic flux, and reflects the autophagic degradation activity. A number of assays have been developed to determine autophagic flux in yeasts, mammals, and plants, but it has not been examined yet in algae. Here we analyzed autophagic flux in the model green alga Chlamydomonas reinhardtii. By monitoring specific autophagy markers such as ATG8 lipidation and using immunofluorescence and electron microscopy techniques, we show that concanamycin A, a vacuolar ATPase inhibitor, blocks autophagic flux in Chlamydomonas. Our results revealed that vacuolar lytic function is needed for the synthesis of triacylglycerols and the formation of lipid bodies in nitrogen- or phosphate-starved cells. Moreover, we found that concanamycin A treatment prevented the degradation of ribosomal proteins RPS6 and RPL37 under nitrogen or phosphate deprivation. These results indicate that autophagy might play an important role in the regulation of lipid metabolism and the recycling of ribosomal proteins under nutrient limitation in Chlamydomonas.
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Affiliation(s)
- Inmaculada Couso
- Instituto de Bioquímica Vegetal y Fotosíntesis, Consejo Superior de Investigaciones Científicas (CSIC)-Universidad de Sevilla, Seville, Spain
| | - María Esther Pérez-Pérez
- Instituto de Bioquímica Vegetal y Fotosíntesis, Consejo Superior de Investigaciones Científicas (CSIC)-Universidad de Sevilla, Seville, Spain
| | - Enrique Martínez-Force
- Instituto de la Grasa (CSIC), Edificio 46, Campus Universitario Pablo de Olavide, Seville, Spain
| | - Hee-Sik Kim
- Korea Research Institute of Bioscience and Biotechnology (KRIBB), Daejeon, Korea
| | - Yonghua He
- Donald Danforth Plant Science Center, St. Louis, MO, USA
| | - James G Umen
- Donald Danforth Plant Science Center, St. Louis, MO, USA
| | - José L Crespo
- Instituto de Bioquímica Vegetal y Fotosíntesis, Consejo Superior de Investigaciones Científicas (CSIC)-Universidad de Sevilla, Seville, Spain
- Correspondence:
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184
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Avin-Wittenberg T, Baluška F, Bozhkov PV, Elander PH, Fernie AR, Galili G, Hassan A, Hofius D, Isono E, Le Bars R, Masclaux-Daubresse C, Minina EA, Peled-Zehavi H, Coll NS, Sandalio LM, Satiat-Jeunemaitre B, Sirko A, Testillano PS, Batoko H. Autophagy-related approaches for improving nutrient use efficiency and crop yield protection. JOURNAL OF EXPERIMENTAL BOTANY 2018; 69:1335-1353. [PMID: 29474677 DOI: 10.1093/jxb/ery069] [Citation(s) in RCA: 62] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/20/2017] [Accepted: 02/16/2018] [Indexed: 05/18/2023]
Abstract
Autophagy is a eukaryotic catabolic pathway essential for growth and development. In plants, it is activated in response to environmental cues or developmental stimuli. However, in contrast to other eukaryotic systems, we know relatively little regarding the molecular players involved in autophagy and the regulation of this complex pathway. In the framework of the COST (European Cooperation in Science and Technology) action TRANSAUTOPHAGY (2016-2020), we decided to review our current knowledge of autophagy responses in higher plants, with emphasis on knowledge gaps. We also assess here the potential of translating the acquired knowledge to improve crop plant growth and development in a context of growing social and environmental challenges for agriculture in the near future.
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Affiliation(s)
- Tamar Avin-Wittenberg
- Department of Plant and Environmental Sciences, Alexander Silberman Institute of Life Sciences, Hebrew University of Jerusalem, Givat Ram, Jerusalem, Israel
| | - Frantisek Baluška
- Institute of Cellular and Molecular Botany, University of Bonn, Kirschallee, Bonn, Germany
| | - Peter V Bozhkov
- Department of Molecular Sciences, Uppsala BioCenter, Swedish University of Agricultural Sciences and Linnean Center for Plant Biology, Uppsala, Sweden
| | - Pernilla H Elander
- Department of Molecular Sciences, Uppsala BioCenter, Swedish University of Agricultural Sciences and Linnean Center for Plant Biology, Uppsala, Sweden
| | - Alisdair R Fernie
- Max-Planck-Institute of Molecular Plant Physiology, Am Mühlenberg, Potsdam-Golm, Germany
| | - Gad Galili
- Department of Plant and Environmental Sciences, Weizmann Institute of Science, Rehovot Israel
| | - Ammar Hassan
- Institute of Cellular and Molecular Botany, University of Bonn, Kirschallee, Bonn, Germany
| | - Daniel Hofius
- Department of Plant Biology, Uppsala BioCenter, Swedish University of Agricultural Sciences and Linnean Center of Plant Biology, Uppsala, Sweden
| | - Erika Isono
- Department of Biology, University of Konstanz, Universitätsstrasse, Konstanz, Germany
| | - Romain Le Bars
- Cell Biology Pôle Imagerie-Gif, Institute of Integrative Biology of the Cell (I2BC), CEA, CNRS, Université Paris-Sud, Université Paris-Saclay, Gif-sur-Yvette, France
| | - Céline Masclaux-Daubresse
- INRA-AgroParisTech, Institut Jean-Pierre Bourgin, UMR1318, ERL CNRS 3559, Saclay Plant Sciences, Versailles, France
| | - Elena A Minina
- Department of Molecular Sciences, Uppsala BioCenter, Swedish University of Agricultural Sciences and Linnean Center for Plant Biology, Uppsala, Sweden
| | - Hadas Peled-Zehavi
- Department of Plant and Environmental Sciences, Weizmann Institute of Science, Rehovot Israel
| | - Núria S Coll
- Centre for Research in Agricultural Genomics (CSIC-IRTA-UAB-UB), Bellaterra-Cerdanyola del Valles, Catalonia, Spain
| | - Luisa M Sandalio
- Departmento de Bioquímica, Biología Celular y Molecular de Plantas Experimental del Zaidín, CSIC, Granada, Spain
| | - Béatrice Satiat-Jeunemaitre
- Cell Biology Pôle Imagerie-Gif, Institute of Integrative Biology of the Cell (I2BC), CEA, CNRS, Université Paris-Sud, Université Paris-Saclay, Gif-sur-Yvette, France
| | - Agnieszka Sirko
- Institute of Biochemistry and Biophysics Polish Academy of Sciences, ul. Pawinskiego, Warsaw, Poland
| | - Pilar S Testillano
- Pollen Biotechnology of Crop Plants group, Centro de Investigaciones Biológicas, Biological Research Centre (CIB), CSIC, Ramiro de Maeztu, Madrid, Spain
| | - Henri Batoko
- Université Catholique de Louvain, Institute of Life Sciences, Croix du Sud, Louvain-la-Neuve, Belgium
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185
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Kalinowska K, Isono E. All roads lead to the vacuole-autophagic transport as part of the endomembrane trafficking network in plants. JOURNAL OF EXPERIMENTAL BOTANY 2018; 69:1313-1324. [PMID: 29165603 DOI: 10.1093/jxb/erx395] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/18/2017] [Accepted: 10/14/2017] [Indexed: 05/10/2023]
Abstract
Plants regulate their development and response to the changing environment by sensing and interpreting environmental signals. Intracellular trafficking pathways including endocytic-, vacuolar-, and autophagic trafficking are important for the various aspects of responses in plants. Studies in the last decade have shown that the autophagic transport pathway uses common key components of endomembrane trafficking as well as specific regulators. A number of factors previously described for their function in endosomal trafficking have been discovered to be involved in the regulation of autophagy in plants. These include conserved endocytic machineries, such as the endosomal sorting complex required for transport (ESCRT), subunits of the HOPS and exocyst complexes, SNAREs, and RAB GTPases as well as plant-specific proteins. Defects in these factors have been shown to cause impairment of autophagosome formation, transport, fusion, and degradation, suggesting crosstalk between autophagy and other intracellular trafficking processes. In this review, we focus mainly on possible functions of endosomal trafficking components in autophagy.
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186
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Affiliation(s)
- Peter V Bozhkov
- Department of Molecular Sciences, Uppsala BioCenter, Swedish University of Agricultural Sciences and Linnean Center for Plant Biology, Uppsala, Sweden
- Correspondence:
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187
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Neuronal Proteomic Analysis of the Ubiquitinated Substrates of the Disease-Linked E3 Ligases Parkin and Ube3a. BIOMED RESEARCH INTERNATIONAL 2018; 2018:3180413. [PMID: 29693004 PMCID: PMC5859835 DOI: 10.1155/2018/3180413] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/23/2017] [Accepted: 01/15/2018] [Indexed: 01/09/2023]
Abstract
Both Parkin and UBE3A are E3 ubiquitin ligases whose mutations result in severe brain dysfunction. Several of their substrates have been identified using cell culture models in combination with proteasome inhibitors, but not in more physiological settings. We recently developed the bioUb strategy to isolate ubiquitinated proteins in flies and have now identified by mass spectrometry analysis the neuronal proteins differentially ubiquitinated by those ligases. This is an example of how flies can be used to provide biological material in order to reveal steady state substrates of disease causing genes. Collectively our results provide new leads to the possible physiological functions of the activity of those two disease causing E3 ligases. Particularly, in the case of Parkin the novelty of our data originates from the experimental setup, which is not overtly biased by acute mitochondrial depolarisation. In the case of UBE3A, it is the first time that a nonbiased screen for its neuronal substrates has been reported.
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188
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Williams JA, Ding WX. Mechanisms, pathophysiological roles and methods for analyzing mitophagy - recent insights. Biol Chem 2018; 399:147-178. [PMID: 28976892 DOI: 10.1515/hsz-2017-0228] [Citation(s) in RCA: 63] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2017] [Accepted: 09/13/2017] [Indexed: 12/17/2022]
Abstract
In 2012, we briefly summarized the mechanisms, pathophysiological roles and methods for analyzing mitophagy. As then, the mitophagy field has continued to grow rapidly, and many new molecular mechanisms regulating mitophagy and molecular tools for monitoring mitophagy have been discovered and developed. Therefore, the purpose of this review is to update information regarding these advances in mitophagy while focusing on basic molecular mechanisms of mitophagy in different organisms and its pathophysiological roles. We also discuss the advantage and limitations of current methods to monitor and quantify mitophagy in cultured cells and in vivo mouse tissues.
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Affiliation(s)
- Jessica A Williams
- Department of Pharmacology, Toxicology and Therapeutics, University of Kansas Medical Center, 3901 Rainbow Blvd., Kansas City, KS 66160, USA
| | - Wen-Xing Ding
- Department of Pharmacology, Toxicology and Therapeutics, University of Kansas Medical Center, Kansas City, KS 66160, USA
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189
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Fukuda T, Kanki T. Mechanisms and Physiological Roles of Mitophagy in Yeast. Mol Cells 2018; 41:35-44. [PMID: 29370687 PMCID: PMC5792711 DOI: 10.14348/molcells.2018.2214] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2017] [Revised: 11/08/2017] [Accepted: 12/05/2017] [Indexed: 12/20/2022] Open
Abstract
Mitochondria are responsible for supplying of most of the cell's energy via oxidative phosphorylation. However, mitochondria also can be deleterious for a cell because they are the primary source of reactive oxygen species, which are generated as a byproduct of respiration. Accumulation of mitochondrial and cellular oxidative damage leads to diverse pathologies. Thus, it is important to maintain a population of healthy and functional mitochondria for normal cellular metabolism. Eukaryotes have developed defense mechanisms to cope with aberrant mitochondria. Mitochondria autophagy (known as mitophagy) is thought to be one such process that selectively sequesters dysfunctional or excess mitochondria within double-membrane autophagosomes and carries them into lysosomes/vacuoles for degradation. The power of genetics and conservation of fundamental cellular processes among eukaryotes make yeast an excellent model for understanding the general mechanisms, regulation, and function of mitophagy. In budding yeast, a mitochondrial surface protein, Atg32, serves as a mitochondrial receptor for selective autophagy that interacts with Atg11, an adaptor protein for selective types of autophagy, and Atg8, a ubiquitin-like protein localized to the isolation membrane. Atg32 is regulated transcriptionally and post-translationally to control mitophagy. Moreover, because Atg32 is a mitophagy-specific protein, analysis of its deficient mutant enables investigation of the physiological roles of mitophagy. Here, we review recent progress in the understanding of the molecular mechanisms and functional importance of mitophagy in yeast at multiple levels.
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Affiliation(s)
- Tomoyuki Fukuda
- Department of Cellular Physiology, Niigata University Graduate School of Medical and Dental Sciences, Niigata 951-8510,
Japan
| | - Tomotake Kanki
- Department of Cellular Physiology, Niigata University Graduate School of Medical and Dental Sciences, Niigata 951-8510,
Japan
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190
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191
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Delorme-Axford E, Klionsky DJ. Transcriptional and post-transcriptional regulation of autophagy in the yeast Saccharomyces cerevisiae. J Biol Chem 2018; 293:5396-5403. [PMID: 29371397 DOI: 10.1074/jbc.r117.804641] [Citation(s) in RCA: 44] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/23/2023] Open
Abstract
Autophagy is a highly conserved catabolic pathway that is vital for development, cell survival, and the degradation of dysfunctional organelles and potentially toxic aggregates. Dysregulation of autophagy is associated with cancer, neurodegeneration, and lysosomal storage diseases. Accordingly, autophagy is precisely regulated at multiple levels (transcriptional, post-transcriptional, translational, and post-translational) to prevent aberrant activity. Various model organisms are used to study autophagy, but the baker's yeast Saccharomyces cerevisiae continues to be advantageous for genetic and biochemical analysis of non-selective and selective autophagy. In this Minireview, we focus on the cellular mechanisms that regulate autophagy transcriptionally and post-transcriptionally in S. cerevisiae.
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Affiliation(s)
| | - Daniel J Klionsky
- From the Life Sciences Institute, University of Michigan, Ann Arbor, Michigan 48109
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192
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Tesnière C, Pradal M, Bessière C, Sanchez I, Blondin B, Bigey F. Relief from nitrogen starvation triggers transient destabilization of glycolytic mRNAs in Saccharomyces cerevisiae cells. Mol Biol Cell 2017; 29:490-498. [PMID: 29282283 PMCID: PMC6014168 DOI: 10.1091/mbc.e17-01-0061] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2017] [Revised: 11/21/2017] [Accepted: 12/11/2017] [Indexed: 11/11/2022] Open
Abstract
Nitrogen replenishment of nitrogen-starved yeast cells resulted in substantial transcriptome changes. There was an unexplained rapid, transient down-regulation of glycolytic genes. This unexpected result prompted us to search for the factors controlling these changes, among which is the possible involvement of different nutrient-sensing pathways such as the TORC1 and cAMP/PKA pathways. To that end, the effects of various gene deletions or chemical blocking agents were tested by investigating the expression of PGK1, one of the glycolytic genes most affected after nitrogen replenishment. We report here that several factors affected glycolytic mRNA stability, among which were glucose sensing, protein elongation, nitrogen metabolism, and TOR signaling. Ammonium sensing was not involved in the response, but ammonium metabolism was required. Thus, our results suggest that, in the presence of glucose, carbon/nitrogen cross-talk is likely involved in the response to nitrogen upshift. Our data suggest that posttranscriptional control of glycolytic gene expression may be an important response to nitrogen replenishment.
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Affiliation(s)
- Catherine Tesnière
- SPO, Université Montpellier, INRA, Montpellier SupAgro, 34060 Montpellier, France
| | - Martine Pradal
- SPO, Université Montpellier, INRA, Montpellier SupAgro, 34060 Montpellier, France
| | - Chloé Bessière
- SPO, Université Montpellier, INRA, Montpellier SupAgro, 34060 Montpellier, France
| | - Isabelle Sanchez
- SPO, Université Montpellier, INRA, Montpellier SupAgro, 34060 Montpellier, France
| | - Bruno Blondin
- SPO, Université Montpellier, INRA, Montpellier SupAgro, 34060 Montpellier, France
| | - Frédéric Bigey
- SPO, Université Montpellier, INRA, Montpellier SupAgro, 34060 Montpellier, France
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193
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Smestad J, Hamidi O, Wang L, Holte MN, Khazal FA, Erber L, Chen Y, Maher LJ. Characterization and metabolic synthetic lethal testing in a new model of SDH-loss familial pheochromocytoma and paraganglioma. Oncotarget 2017; 9:6109-6127. [PMID: 29464059 PMCID: PMC5814199 DOI: 10.18632/oncotarget.23639] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2017] [Accepted: 11/20/2017] [Indexed: 12/26/2022] Open
Abstract
Succinate dehydrogenase (SDH)-loss pheochromocytoma and paraganglioma (PPGL) are tumors driven by metabolic derangement. SDH loss leads to accumulation of intracellular succinate, which competitively inhibits dioxygenase enzymes, causing activation of pseudohypoxic signaling and hypermethylation of histones and DNA. The mechanisms by which these alterations lead to tumorigenesis are unclear, however. In an effort to fundamentally understand how SDH loss reprograms cell biology, we developed an immortalized mouse embryonic fibroblast cell line with conditional disruption of Sdhc and characterize the kinetics of Sdhc gene rearrangement, SDHC protein loss, succinate accumulation, and the resultant hypoproliferative phenotype. We further perform global transcriptomic, epigenomic, and proteomic characterization of changes resulting from SDHC loss, identifying specific perturbations at each biological level. We compare the observed patterns of epigenomic derangement to another previously-described immortalized mouse chromaffin cell model of SDHB loss, and compare both models to human SDH-loss tumors. Finally, we perform analysis of SDHC synthetic lethality with lactate dehydrogenase A (LDHA) and pyruvate carboxylase (PCX), which are important for regeneration of NAD+ and aspartate biosynthesis, respectively. Our data show that SDH-loss cells are selectively vulnerable to LDH genetic knock-down or chemical inhibition, suggesting that LDH inhibition may be an effective therapeutic strategy for SDH-loss PPGL.
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Affiliation(s)
- John Smestad
- Mayo Clinic Medical Scientist Training Program, Mayo Clinic College of Medicine and Science, Rochester, MN, USA.,Department of Biochemistry and Molecular Biology, Mayo Clinic, Rochester, MN, USA
| | - Oksana Hamidi
- Division of Endocrinology, Diabetes, and Nutrition, Mayo Clinic, Rochester, MN, USA
| | - Lin Wang
- Department of Pediatric and Adolescent Medicine, Mayo Clinic College of Medicine and Science, Rochester, MN, USA
| | - Molly Nelson Holte
- Department of Biochemistry and Molecular Biology, Mayo Clinic, Rochester, MN, USA
| | - Fatimah Al Khazal
- Department of Biochemistry and Molecular Biology, Mayo Clinic, Rochester, MN, USA
| | - Luke Erber
- Department of Biochemistry, Molecular Biology and Biophysics, University of Minnesota at Twin Cities, Minneapolis, MN, USA
| | - Yue Chen
- Department of Biochemistry, Molecular Biology and Biophysics, University of Minnesota at Twin Cities, Minneapolis, MN, USA
| | - L James Maher
- Department of Biochemistry and Molecular Biology, Mayo Clinic, Rochester, MN, USA
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194
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Huseinovic A, van Dijk M, Vermeulen NPE, van Leeuwen F, Kooter JM, Vos JC. Drug toxicity profiling of a Saccharomyces cerevisiae deubiquitinase deletion panel shows that acetaminophen mimics tyrosine. Toxicol In Vitro 2017; 47:259-268. [PMID: 29258884 DOI: 10.1016/j.tiv.2017.12.007] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2017] [Revised: 12/05/2017] [Accepted: 12/13/2017] [Indexed: 10/18/2022]
Abstract
Post-translational protein modification by addition or removal of the small polypeptide ubiquitin is involved in a range of critical cellular processes, like proteasomal protein degradation, DNA repair, gene expression, internalization of membrane proteins, and drug sensitivity. We recently identified genes important for acetaminophen (APAP) toxicity in a comprehensive screen and our findings suggested that a small set of yeast strains carrying deletions of ubiquitin-related genes can be informative for drug toxicity profiling. In yeast, approximately 20 different deubiquitinating enzymes (DUBs) have been identified, of which only one is essential for viability. We investigated whether the toxicity profile of DUB deletion yeast strains would be informative about the toxicological mode of action of APAP. A set of DUB deletion strains was tested for sensitivity and resistance to a diverse series of compounds, including APAP, quinine, ibuprofen, rapamycin, cycloheximide, cadmium, peroxide and amino acids and a cluster analysis was performed. Most DUB deletion strains showed an altered growth pattern when exposed to these compounds by being either more sensitive or more resistant than WT. Toxicity profiling of the DUB strains revealed a remarkable overlap between the amino acid tyrosine and acetaminophen (APAP), but not its stereoisomer AMAP. Furthermore, co-exposure of cells to both APAP and tyrosine showed an enhancement of the cellular growth inhibition, suggesting that APAP and tyrosine have a similar mode of action.
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Affiliation(s)
- Angelina Huseinovic
- AIMMS, Division of Molecular Toxicology, Department of Chemistry and Pharmaceutical Sciences, VU University Amsterdam, 1081 HZ Amsterdam, The Netherlands
| | - Marc van Dijk
- AIMMS, Division of Molecular Toxicology, Department of Chemistry and Pharmaceutical Sciences, VU University Amsterdam, 1081 HZ Amsterdam, The Netherlands
| | - Nico P E Vermeulen
- AIMMS, Division of Molecular Toxicology, Department of Chemistry and Pharmaceutical Sciences, VU University Amsterdam, 1081 HZ Amsterdam, The Netherlands
| | - Fred van Leeuwen
- Division of Gene Regulation, Netherlands Cancer Institute, Amsterdam 1066 CX, The Netherlands
| | - Jan M Kooter
- AIMMS, Department of Molecular Cell Biology, Section Genetics, VU University Amsterdam, 1081 HZ Amsterdam, The Netherlands
| | - J Chris Vos
- AIMMS, Division of Molecular Toxicology, Department of Chemistry and Pharmaceutical Sciences, VU University Amsterdam, 1081 HZ Amsterdam, The Netherlands.
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195
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Sarkar S, Chakravorty S, Mukherjee A, Bhattacharya D, Bhattacharya S, Gachhui R. De novo RNA-Seq based transcriptome analysis of Papiliotrema laurentii strain RY1 under nitrogen starvation. Gene 2017; 645:146-156. [PMID: 29247800 DOI: 10.1016/j.gene.2017.12.014] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2017] [Revised: 11/20/2017] [Accepted: 12/11/2017] [Indexed: 02/07/2023]
Abstract
Nitrogen is a key nutrient for all cell forms. Most organisms respond to nitrogen scarcity by slowing down their growth rate. On the contrary, our previous studies have shown that Papiliotrema laurentii strain RY1 has a robust growth under nitrogen starvation. To understand the global regulation that leads to such an extraordinary response, we undertook a de novo approach for transcriptome analysis of the yeast. Close to 33 million sequence reads of high quality for nitrogen limited and enriched condition were generated using Illumina NextSeq500. Trinity analysis and clustered transcripts annotation of the reads produced 17,611 unigenes, out of which 14,157 could be annotated. Gene Ontology term analysis generated 44.92% cellular component terms, 39.81% molecular function terms and 15.24% biological process terms. The most over represented pathways in general were translation, carbohydrate metabolism, amino acid metabolism, general metabolism, folding, sorting, degradation followed by transport and catabolism, nucleotide metabolism, replication and repair, transcription and lipid metabolism. A total of 4256 Single Sequence Repeats were identified. Differential gene expression analysis detected 996 P-significant transcripts to reveal transmembrane transport, lipid homeostasis, fatty acid catabolism and translation as the enriched terms which could be essential for Papiliotrema laurentii strain RY1 to adapt during nitrogen deprivation. Transcriptome data was validated by quantitative real-time PCR analysis of twelve transcripts. To the best of our knowledge, this is the first report of Papiliotrema laurentii strain RY1 transcriptome which would play a pivotal role in understanding the biochemistry of the yeast under acute nitrogen stress and this study would be encouraging to initiate extensive investigations into this Papiliotrema system.
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Affiliation(s)
- Soumyadev Sarkar
- Department of Life Science & Biotechnology, Jadavpur University, India
| | - Somnath Chakravorty
- Department of Biochemistry and Molecular Biophysics, Kansas State University, Manhattan, KS, USA
| | - Avishek Mukherjee
- Department of Life Science & Biotechnology, Jadavpur University, India
| | | | | | - Ratan Gachhui
- Department of Life Science & Biotechnology, Jadavpur University, India.
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196
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Systematic analysis of ribophagy in human cells reveals bystander flux during selective autophagy. Nat Cell Biol 2017; 20:135-143. [PMID: 29230017 PMCID: PMC5786475 DOI: 10.1038/s41556-017-0007-x] [Citation(s) in RCA: 123] [Impact Index Per Article: 17.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2017] [Accepted: 11/14/2017] [Indexed: 12/17/2022]
Abstract
Ribosomes are abundant cellular machines1,2
regulated by assembly, supernumerary subunit turnover, and nascent chain quality
control mechanisms1–5. Moreover, nitrogen starvation
in yeast has been reported to promote selective ribosome delivery to the vacuole
in an autophagy conjugation system-dependent manner, a process called
“ribophagy”6,7. However,
whether ribophagy in mammals is selective or regulated is unclear. Using
Ribo-Keima flux reporters, we find that starvation or mTOR inhibition promotes
VPS34-dependent ribophagic flux, which unlike yeast, is largely ATG8 conjugation
independent and occurs concomitantly with other cytosolic protein autophagic
flux reporters8,9. Ribophagic flux was not induced upon
inhibition of translational elongation or nascent chain uncoupling, but was
induced in a comparatively selective manner upon proteotoxic stress via
arsenite10 or
chromosome mis-segregation11
dependent upon VPS34 and ATG8 conjugation. Unexpectedly, agents typically used
to induce selective autophagy also promoted increased ribosome and cytosolic
protein reporter flux, suggesting significant bulk or
“by-stander” autophagy during what is often considered selective
autophagy12,13. These results emphasize the importance
of monitoring non-specific cargo flux when assessing selective autophagy
pathways.
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197
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Morriss SC, Liu X, Floyd BE, Bassham DC, MacIntosh GC. Cell growth and homeostasis are disrupted in arabidopsis rns2-2 mutants missing the main vacuolar RNase activity. ANNALS OF BOTANY 2017; 120:911-922. [PMID: 28961890 PMCID: PMC5710523 DOI: 10.1093/aob/mcx099] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/10/2017] [Accepted: 08/01/2017] [Indexed: 05/17/2023]
Abstract
BACKGROUND AND AIMS Enzymes belonging to the RNase T2 family are essential for normal rRNA turnover in eukaryotes. In Arabidopsis thaliana, this function is performed by RNS2. The null mutant rns2-2 has increased rRNA half-life and constitutive autophagy. The aim of this work was to determine the molecular changes that take place in the rns2-2 mutant that may lead to altered cellular homeostasis, manifested by the observed cellular phenotype. METHODS To determine the effect of defective rRNA turnover on cellular homeostasis, comparative transcriptome and metabolome analyses of 10-day-old wild-type and rns2-2 seedlings were used to identify molecular processes affected in the mutant. Bioinformatics analyses suggested additional phenotypes that were confirmed through direct plant size measurements and microscopy. KEY RESULTS Few genes were differentially expressed in the rns2-2 mutant, indicating that control of autophagy in this genotype is mainly achieved at the post-transcriptional level. Among differentially expressed genes, transcripts related to carbon flux processes, particularly the pentose phosphate pathway (PPP), were identified. Metabolite analyses confirmed changes in the levels of PPP intermediates. Genes related to cell wall loosening were also differentially expressed in the mutant, and a decrease in monosaccharide components of cell wall hemicellulose were found. As a potential effect of weaker cell walls, rns2-2 plants are larger than wild-type controls, due to larger cells and increased water content. Elevated levels of reactive oxygen species (ROS) were also measured in rns2-2, and the constitutive autophagy phenotype was blocked by preventing ROS production via NADPH oxidase. CONCLUSIONS Lack of rRNA recycling in rns2-2 cells triggers a change in carbon flux, which is redirected through the PPP to produce ribose-5-phosphate for de novo nucleoside synthesis. rRNA or ribosome turnover is thus essential for cellular homeostasis, probably through maintenance of nucleoside levels as part of the salvage pathway.
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Affiliation(s)
- Stephanie C Morriss
- Roy J. Carver Department of Biochemistry, Biophysics and Molecular Biology, Iowa State University, Ames, IA, USA
| | - Xiaoyi Liu
- Department of Genetics, Development and Cell Biology, Iowa State University, Ames, IA, USA
| | - Brice E Floyd
- Department of Genetics, Development and Cell Biology, Iowa State University, Ames, IA, USA
| | - Diane C Bassham
- Department of Genetics, Development and Cell Biology, Iowa State University, Ames, IA, USA
| | - Gustavo C MacIntosh
- Roy J. Carver Department of Biochemistry, Biophysics and Molecular Biology, Iowa State University, Ames, IA, USA
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198
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Konstantakou EG, Velentzas AD, Anagnostopoulos AK, Giannopoulou AF, Anastasiadou E, Papassideri IS, Voutsinas GE, Tsangaris GT, Stravopodis DJ. Unraveling the human protein atlas of metastatic melanoma in the course of ultraviolet radiation-derived photo-therapy. J Proteomics 2017; 188:119-138. [PMID: 29180045 DOI: 10.1016/j.jprot.2017.11.015] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2017] [Revised: 11/09/2017] [Accepted: 11/21/2017] [Indexed: 02/06/2023]
Abstract
To explore the photo-therapeutic capacity of UV radiation in solid tumors, we herein employed an nLC-MS/MS technology to profile the proteomic landscape of irradiated WM-266-4 human metastatic-melanoma cells. Obtained data resulted in proteomic catalogues of 5982 and 7280 proteins for UVB- and UVC-radiation conditions, respectively, and indicated the ability of UVB/C-radiation forms to eliminate metastatic-melanoma cells through induction of synergistically operating programs of apoptosis and necroptosis. However, it seems that one or more WM-266-4 cell sub-populations may escape from UV-radiation's photo-damaging activity, acquiring, besides apoptosis tolerance, an EMT phenotype that likely offers them the advantage of developing resistance to certain chemotherapeutic drugs. Low levels of autophagy may also critically contribute to the selective survival and growth of UV-irradiated melanoma-cell escapers. These are the cells that must be systemically targeted with novel therapeutic schemes, like the one of UV radiation and Irinotecan herein suggested to be holding strong promise for the effective treatment of metastatic-melanoma patients. Given the dual nature of UV radiation to serve as both anti-tumorigenic and tumorigenic agent, all individuals being subjected to risk factors for melanoma development have to be appropriately informed and educated, in order to integrate the innovative PPPM concept in their healthcare-sector management. SIGNIFICANCE This study reports the application of nLC-MS/MS technology to deeply map the proteomic landscape of UV-irradiated human metastatic-melanoma cells. Data bioinformatics processing led to molecular-network reconstructions that unearthed the dual nature of UV radiation to serve as both anti-tumorigenic and tumorigenic factor in metastatic-melanoma cellular environments. Our UV radiation-derived "photo-proteomic" atlas may prove valuable for the identification of new biomarkers and development of novel therapies for the disease. Given that UV radiation represents a major risk factor causing melanoma, a PPPM-based life style and clinical practice must be embraced by all individuals being prone to disease's appearance and expansion.
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Affiliation(s)
- Eumorphia G Konstantakou
- Section of Cell Biology and Biophysics, Department of Biology, School of Science, National and Kapodistrian University of Athens, Athens, Greece
| | - Athanassios D Velentzas
- Section of Cell Biology and Biophysics, Department of Biology, School of Science, National and Kapodistrian University of Athens, Athens, Greece
| | - Athanasios K Anagnostopoulos
- Proteomics Core Facility, Systems Biology Center, Biomedical Research Foundation of the Academy of Athens, Athens, Greece
| | - Aikaterini F Giannopoulou
- Section of Cell Biology and Biophysics, Department of Biology, School of Science, National and Kapodistrian University of Athens, Athens, Greece
| | - Ema Anastasiadou
- Basic Research Center, Biomedical Research Foundation of the Academy of Athens, Athens, Greece
| | - Issidora S Papassideri
- Section of Cell Biology and Biophysics, Department of Biology, School of Science, National and Kapodistrian University of Athens, Athens, Greece
| | - Gerassimos E Voutsinas
- Laboratory of Environmental Mutagenesis and Carcinogenesis, Institute of Biosciences and Applications, National Center for Scientific Research "Demokritos", Athens, Greece
| | - George Th Tsangaris
- Proteomics Core Facility, Systems Biology Center, Biomedical Research Foundation of the Academy of Athens, Athens, Greece.
| | - Dimitrios J Stravopodis
- Section of Cell Biology and Biophysics, Department of Biology, School of Science, National and Kapodistrian University of Athens, Athens, Greece.
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199
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Jung Y, Kim HD, Yang HW, Kim HJ, Jang CY, Kim J. Modulating cellular balance of Rps3 mono-ubiquitination by both Hel2 E3 ligase and Ubp3 deubiquitinase regulates protein quality control. Exp Mol Med 2017; 49:e390. [PMID: 29147007 PMCID: PMC5704183 DOI: 10.1038/emm.2017.128] [Citation(s) in RCA: 31] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2017] [Revised: 03/25/2017] [Accepted: 03/27/2017] [Indexed: 12/14/2022] Open
Abstract
When a ribosome complex is stalled during the translation elongation process in eukaryotes, the mono-ubiquitination of Rps3 has recently been shown to be critical to ribosome quality control. We have discovered that the regulatory role of Rps3 mono-ubiquitination is controlled by a deubiquitinase. We also showed that an autophagic signal appears to be coupled to the mono-ubiquitination of Rps3p through the entrance of Ubp3p into the autophagosome in yeasts. The mono-ubiquitination of the Rps3 protein is tightly modulated by reciprocal action between the Hel2p E3 ligase and the Ubp3p deubiquitinase in yeasts and the reciprocal action between the RNF123 E3 ligase and the USP10 deubiquitinase in mammalian cells. We also found that the Ubp3p/USP10 deubiquitinases critically modulate Hel2p/RNF123-mediated Rps3p mono-ubiquitination. In addition, we found that Hel2p/RNF123 and Ubp3p/USP10 appeared to be differently localized in the ribosome complex after ultraviolet irradiation. Together, our results support a model in which coordinated ubiquitination and deubiquitination activities can finely balance the level of regulatory Rps3p mono-ubiquitination in ribosome-associated quality control and autophagy processes.
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Affiliation(s)
- Youjin Jung
- Laboratory of Biochemistry, Division of Life Sciences, Korea University, Seoul, Republic of Korea
| | - Hag Dong Kim
- Laboratory of Biochemistry, Division of Life Sciences, Korea University, Seoul, Republic of Korea.,HAEL Lab, TechnoComplex Building 603-3, Korea University, Seoul, Republic of Korea
| | - Hee Woong Yang
- Laboratory of Biochemistry, Division of Life Sciences, Korea University, Seoul, Republic of Korea
| | - Hye Jin Kim
- Laboratory of Biochemistry, Division of Life Sciences, Korea University, Seoul, Republic of Korea
| | - Chang-Young Jang
- Laboratory of Cell Biology, Research Center for Cell Fate Control, College of Pharmacy, Sookmyung Women's University, Seoul, Republic of Korea
| | - Joon Kim
- Laboratory of Biochemistry, Division of Life Sciences, Korea University, Seoul, Republic of Korea.,HAEL Lab, TechnoComplex Building 603-3, Korea University, Seoul, Republic of Korea
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200
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Nemec AA, Howell LA, Peterson AK, Murray MA, Tomko RJ. Autophagic clearance of proteasomes in yeast requires the conserved sorting nexin Snx4. J Biol Chem 2017; 292:21466-21480. [PMID: 29109144 DOI: 10.1074/jbc.m117.817999] [Citation(s) in RCA: 54] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2017] [Revised: 11/03/2017] [Indexed: 11/06/2022] Open
Abstract
Turnover of the 26S proteasome by autophagy is an evolutionarily conserved process that governs cellular proteolytic capacity and eliminates inactive particles. In most organisms, proteasomes are located in both the nucleus and cytoplasm. However, the specific autophagy routes for nuclear and cytoplasmic proteasomes are unclear. Here, we investigate the spatial control of autophagic proteasome turnover in budding yeast (Saccharomyces cerevisiae). We found that nitrogen starvation-induced proteasome autophagy is independent of known nucleophagy pathways but is compromised when nuclear protein export is blocked. Furthermore, via pharmacological tethering of proteasomes to chromatin or the plasma membrane, we provide evidence that nuclear proteasomes at least partially disassemble before autophagic turnover, whereas cytoplasmic proteasomes remain largely intact. A targeted screen of autophagy genes identified a requirement for the conserved sorting nexin Snx4 in the autophagic turnover of proteasomes and several other large multisubunit complexes. We demonstrate that Snx4 cooperates with sorting nexins Snx41 and Snx42 to mediate proteasome turnover and is required for the formation of cytoplasmic proteasome puncta that accumulate when autophagosome formation is blocked. Together, our results support distinct mechanistic paths in the turnover of nuclear versus cytoplasmic proteasomes and point to a critical role for Snx4 in cytoplasmic agglomeration of proteasomes en route to autophagic destruction.
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Affiliation(s)
- Antonia A Nemec
- From the Department of Biomedical Sciences, College of Medicine, Florida State University, Tallahassee, Florida 32306
| | - Lauren A Howell
- From the Department of Biomedical Sciences, College of Medicine, Florida State University, Tallahassee, Florida 32306
| | - Anna K Peterson
- From the Department of Biomedical Sciences, College of Medicine, Florida State University, Tallahassee, Florida 32306
| | - Matthew A Murray
- From the Department of Biomedical Sciences, College of Medicine, Florida State University, Tallahassee, Florida 32306
| | - Robert J Tomko
- From the Department of Biomedical Sciences, College of Medicine, Florida State University, Tallahassee, Florida 32306
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