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Kobayashi N, Nishikawa SI. Nuclear Fusion in Yeast and Plant Reproduction. PLANTS (BASEL, SWITZERLAND) 2023; 12:3608. [PMID: 37896071 PMCID: PMC10609895 DOI: 10.3390/plants12203608] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/20/2023] [Revised: 10/09/2023] [Accepted: 10/16/2023] [Indexed: 10/29/2023]
Abstract
Nuclear fusion is essential for the sexual reproduction of various organisms, including plants, animals, and fungi. During the life cycle of flowering plants, nuclear fusion occurs three times: once during female gametogenesis and twice during double fertilization, when two sperm cells fertilize the egg and the central cell. Haploid nuclei migrate in an actin filament-dependent manner to become in close contact and, then, two nuclei fuse. The nuclear fusion process in plant reproduction is achieved through sequential nuclear membrane fusion events. Recent molecular genetic analyses using Arabidopsis thaliana showed the conservation of nuclear membrane fusion machinery between plants and the budding yeast Saccharomyces cerevisiae. These include the heat-shock protein 70 in the endoplasmic reticulum and the conserved nuclear membrane proteins. Analyses of the A. thaliana mutants of these components show that the completion of the sperm nuclear fusion at fertilization is essential for proper embryo and endosperm development.
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Affiliation(s)
- Nanami Kobayashi
- Graduate School of Science and Technology, Niigata University, Niigata 950-2181, Japan;
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2
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Heasley LR, DeLuca JG, Markus SM. Effectors of the spindle assembly checkpoint are confined within the nucleus of Saccharomyces cerevisiae. Biol Open 2019; 8:bio.037424. [PMID: 31182632 PMCID: PMC6602339 DOI: 10.1242/bio.037424] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022] Open
Abstract
The spindle assembly checkpoint (SAC) prevents erroneous chromosome segregation by delaying mitotic progression when chromosomes are incorrectly attached to the mitotic spindle. This delay is mediated by mitotic checkpoint complexes (MCCs), which assemble at unattached kinetochores and repress the activity of the anaphase promoting complex/cyclosome (APC/C). The cellular localizations of MCCs are likely critical for proper SAC function, yet remain poorly defined. We recently demonstrated that in mammalian cells, in which the nuclear envelope disassembles during mitosis, MCCs diffuse throughout the spindle region and cytoplasm. Here, we employed an approach using binucleate yeast zygotes to examine the localization dynamics of SAC effectors required for MCC assembly and function in budding yeast, in which the nuclear envelope remains intact throughout mitosis. Our findings indicate that in yeast, MCCs are confined to the nuclear compartment and excluded from the cytoplasm during mitosis. Summary: The effectors of the spindle assembly checkpoint are confined with the nuclear compartment of budding yeast, and cannot exchange between nuclei in a binucleate zygote.
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Affiliation(s)
- Lydia R Heasley
- Department of Environmental and Radiological Health Sciences, Colorado State University, Fort Collins, Colorado 80523, USA
| | - Jennifer G DeLuca
- Department of Biochemistry and Molecular Biology, Colorado State University, Fort Collins, Colorado 80523, USA
| | - Steven M Markus
- Department of Biochemistry and Molecular Biology, Colorado State University, Fort Collins, Colorado 80523, USA
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3
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Garapati HS, Mishra K. Comparative genomics of nuclear envelope proteins. BMC Genomics 2018; 19:823. [PMID: 30445911 PMCID: PMC6240307 DOI: 10.1186/s12864-018-5218-4] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2018] [Accepted: 10/31/2018] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND The nuclear envelope (NE) that encapsulates the nuclear genome is a double lipid bilayer with several integral and peripherally associated proteins. It is a characteristic feature of the eukaryotes and acts as a hub for a number of important nuclear events including transcription, repair, and regulated gene expression. The proteins associated with the nuclear envelope mediate the NE functions and maintain its structural integrity, which is crucial for survival. In spite of the importance of this structure, knowledge of the protein composition of the nuclear envelope and their function, are limited to very few organisms belonging to Opisthokonta and Archaeplastida supergroups. The NE composition is largely unknown in organisms outside these two supergroups. RESULTS In this study, we have taken a comparative sequence analysis approach to identify the NE proteome that is present across all five eukaryotic supergroups. We identified 22 proteins involved in various nuclear functions to be part of the core NE proteome. The presence of these proteins across eukaryotes, suggests that they are traceable to the Last Eukaryotic Common Ancestor (LECA). Additionally, we also identified the NE proteins that have evolved in a lineage specific manner and those that have been preserved only in a subset of organisms. CONCLUSIONS Our study identifies the conserved features of the nuclear envelope across eukaryotes and provides insights into the potential composition and the functionalities that were constituents of the LECA NE.
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Affiliation(s)
- Hita Sony Garapati
- Department of Biochemistry, School of Life Sciences, University of Hyderabad, Hyderabad, 500046, India
| | - Krishnaveni Mishra
- Department of Biochemistry, School of Life Sciences, University of Hyderabad, Hyderabad, 500046, India.
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Tartakoff AM, Dulce D, Landis E. Delayed Encounter of Parental Genomes Can Lead to Aneuploidy in Saccharomyces cerevisiae. Genetics 2018; 208:139-151. [PMID: 29150427 PMCID: PMC5753854 DOI: 10.1534/genetics.117.300289] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2017] [Accepted: 10/31/2017] [Indexed: 11/18/2022] Open
Abstract
We have investigated an extreme deviation from the norm of genome unification that occurs during mating in the yeast, Saccharomyces cerevisiae This deviation is encountered when yeast that carry a mutation of the spindle pole body protein, Kar1, are mated with wildtype cells. In this case, nuclear fusion is delayed and the genotypes of a fraction of zygotic progeny suggest that chromosomes have "transferred" between the parental nuclei in zygotes. This classic, yet bizarre, occurrence is routinely used to generate aneuploid (disomic) yeast. [kar1 × wt] zygotes, like [wt × wt] zygotes, initially have a single spindle pole body per nucleus. Unlike [wt × wt] zygotes, in [kar1 × wt] zygotes, the number of spindle pole bodies per nucleus then can increase before nuclear fusion. When such nuclei fuse, the spindle pole bodies do not coalesce efficiently, and subsets of spindle pole bodies and centromeres can enter buds. The genotypes of corresponding biparental progeny show evidence of extensive haplotype-biased chromosome loss, and can also include heterotypic chromosomal markers. They thus allow rationalization of chromosome "transfer" as being due to an unanticipated yet plausible mechanism. Perturbation of the unification of genomes likely contributes to infertility in other organisms.
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Affiliation(s)
- Alan Michael Tartakoff
- Pathology Department and Cell Biology Program, Case Western Reserve University, Cleveland, Ohio 44106
| | - David Dulce
- Pathology Department and Cell Biology Program, Case Western Reserve University, Cleveland, Ohio 44106
| | - Elizabeth Landis
- Pathology Department and Cell Biology Program, Case Western Reserve University, Cleveland, Ohio 44106
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5
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Amini S, Holstege FCP, Kemmeren P. Growth condition dependency is the major cause of non-responsiveness upon genetic perturbation. PLoS One 2017; 12:e0173432. [PMID: 28257504 PMCID: PMC5336285 DOI: 10.1371/journal.pone.0173432] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2016] [Accepted: 02/10/2017] [Indexed: 11/29/2022] Open
Abstract
Investigating the role and interplay between individual proteins in biological processes is often performed by assessing the functional consequences of gene inactivation or removal. Depending on the sensitivity of the assay used for determining phenotype, between 66% (growth) and 53% (gene expression) of Saccharomyces cerevisiae gene deletion strains show no defect when analyzed under a single condition. Although it is well known that this non-responsive behavior is caused by different types of redundancy mechanisms or by growth condition/cell type dependency, it is not known what the relative contribution of these different causes is. Understanding the underlying causes of and their relative contribution to non-responsive behavior upon genetic perturbation is extremely important for designing efficient strategies aimed at elucidating gene function and unraveling complex cellular systems. Here, we provide a systematic classification of the underlying causes of and their relative contribution to non-responsive behavior upon gene deletion. The overall contribution of redundancy to non-responsive behavior is estimated at 29%, of which approximately 17% is due to homology-based redundancy and 12% is due to pathway-based redundancy. The major determinant of non-responsiveness is condition dependency (71%). For approximately 14% of protein complexes, just-in-time assembly can be put forward as a potential mechanistic explanation for how proteins can be regulated in a condition dependent manner. Taken together, the results underscore the large contribution of growth condition requirement to non-responsive behavior, which needs to be taken into account for strategies aimed at determining gene function. The classification provided here, can also be further harnessed in systematic analyses of complex cellular systems.
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Affiliation(s)
- Saman Amini
- Princess Máxima Center for Pediatric Oncology, Utrecht, The Netherlands
- Center for Molecular Medicine, University Medical Centre Utrecht, Utrecht, The Netherlands
| | | | - Patrick Kemmeren
- Princess Máxima Center for Pediatric Oncology, Utrecht, The Netherlands
- Center for Molecular Medicine, University Medical Centre Utrecht, Utrecht, The Netherlands
- * E-mail:
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6
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Falk JE, Tsuchiya D, Verdaasdonk J, Lacefield S, Bloom K, Amon A. Spatial signals link exit from mitosis to spindle position. eLife 2016; 5. [PMID: 27166637 PMCID: PMC4887205 DOI: 10.7554/elife.14036] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/24/2015] [Accepted: 04/07/2016] [Indexed: 12/20/2022] Open
Abstract
In budding yeast, if the spindle becomes mispositioned, cells prevent exit from mitosis by inhibiting the mitotic exit network (MEN). The MEN is a signaling cascade that localizes to spindle pole bodies (SPBs) and activates the phosphatase Cdc14. There are two competing models that explain MEN regulation by spindle position. In the 'zone model', exit from mitosis occurs when a MEN-bearing SPB enters the bud. The 'cMT-bud neck model' posits that cytoplasmic microtubule (cMT)-bud neck interactions prevent MEN activity. Here we find that 1) eliminating cMT– bud neck interactions does not trigger exit from mitosis and 2) loss of these interactions does not precede Cdc14 activation. Furthermore, using binucleate cells, we show that exit from mitosis occurs when one SPB enters the bud despite the presence of a mispositioned spindle. We conclude that exit from mitosis is triggered by a correctly positioned spindle rather than inhibited by improper spindle position. DOI:http://dx.doi.org/10.7554/eLife.14036.001 Most cells duplicate their genetic material and then separate the two copies before they divide. This is true for budding yeast cells, which divide in an unusual manner. New daughter cells grow as a bud on the side of a larger mother cell and are eventually pinched off. To make healthy daughter cells, yeast must share their chromosomes between the mother cell and the bud. This involves threading the chromosomes through a small opening called the bud neck, which connects the mother cell and the bud. A surveillance mechanism in budding yeast monitors the placement of the molecular machine (called the spindle) that separates the chromosomes before a cell divides. This mechanism stops the cell from dividing if the spindle is not positioned correctly. Two models could explain how an incorrectly positioned spindle prevents budding yeast from dividing. The first model proposes that yeast cells do not divide if protein filaments (called microtubules) touch the bud neck. This only occurs if the spindle is not properly threaded into the bud through the small opening of the bud neck. The second model proposes that specific proteins required for cell division (which are found at the ends of the spindle) are inhibited while they are inside the mother cell. This means that the cell cannot divide until one end of its spindle moves out of the mother cell and into the bud. Now, Falk et al. report the results of experiments that aimed to distinguish between these two models. First, a laser was used to cut the spindle filaments in live yeast cells. This stopped the filaments from touching the neck between the mother cell and the bud, but did not cause the cell to divide. Therefore, these results refute the first model. Next, Falk et al. generated yeast cells that had essentially been tricked into forming two separate spindles before they started to divide. As would be predicted by the second model, these cells could divide as long as an end from at least one of the spindles entered the bud. These findings strongly suggest that the second model provides the best explanation for how yeast cells sense spindle position to control cell division. The findings also lend further support to previous work that showed that activators of cell division are found in the bud, while inhibitors of cell division are found in the mother cell. Finally, in a related study, Gryaznova, Caydasi et al. identify a protein at the ends of the spindle that acts like a regulatory hub to coordinate cell division with spindle position. Their findings also suggest that the surveillance mechanism is switched off in the bud to allow the cell to divide. DOI:http://dx.doi.org/10.7554/eLife.14036.002
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Affiliation(s)
- Jill Elaine Falk
- David H Koch Institute for Integrative Cancer Research, Howard Hughes Medical Institute, Massachusetts Institute of Technology, Cambridge, United States
| | - Dai Tsuchiya
- Department of Biology, Indiana University, Bloomington, United States
| | - Jolien Verdaasdonk
- Department of Biology, The University of North Carolina at Chapel Hill, Chapel Hill, United States
| | - Soni Lacefield
- Department of Biology, Indiana University, Bloomington, United States
| | - Kerry Bloom
- Department of Biology, The University of North Carolina at Chapel Hill, Chapel Hill, United States
| | - Angelika Amon
- David H Koch Institute for Integrative Cancer Research, Howard Hughes Medical Institute, Massachusetts Institute of Technology, Cambridge, United States
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7
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Meseroll RA, Cohen-Fix O. The Malleable Nature of the Budding Yeast Nuclear Envelope: Flares, Fusion, and Fenestrations. J Cell Physiol 2016; 231:2353-60. [PMID: 26909870 DOI: 10.1002/jcp.25355] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2016] [Accepted: 02/19/2016] [Indexed: 11/10/2022]
Abstract
In eukaryotes, the nuclear envelope (NE) physically separates nuclear components and activities from rest of the cell. The NE also provides rigidity to the nucleus and contributes to chromosome organization. At the same time, the NE is highly dynamic; it must change shape and rearrange its components during development and throughout the cell cycle, and its morphology can be altered in response to mutation and disease. Here we focus on the NE of budding yeast, Saccharomyces cerevisiae, which has several unique features: it remains intact throughout the cell cycle, expands symmetrically during interphase, elongates during mitosis and, expands asymmetrically during mitotic delay. Moreover, its NE is safely breached during mating and when large structures, such as nuclear pore complexes and the spindle pole body, are embedded into its double membrane. The budding yeast NE lacks lamins and yet the nucleus is capable of maintaining a spherical shape throughout interphase. Despite these eccentricities, studies of the budding yeast NE have uncovered interesting, and likely conserved, processes that contribute to NE dynamics. In particular, we discuss the processes that drive and enable NE expansion and the dramatic changes in the NE that lead to extensions and fenestrations. J. Cell. Physiol. 231: 2353-2360, 2016. Published 2016. This article is a U.S. Government work and is in the public domain in the USA.
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Affiliation(s)
- Rebecca A Meseroll
- The Laboratory of Cell and Molecular Biology, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, Maryland
| | - Orna Cohen-Fix
- The Laboratory of Cell and Molecular Biology, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, Maryland
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8
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Alvaro CG, Thorner J. Heterotrimeric G Protein-coupled Receptor Signaling in Yeast Mating Pheromone Response. J Biol Chem 2016; 291:7788-95. [PMID: 26907689 PMCID: PMC4824985 DOI: 10.1074/jbc.r116.714980] [Citation(s) in RCA: 78] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
Abstract
The DNAs encoding the receptors that respond to the peptide mating pheromones of the budding yeast Saccharomyces cerevisiae were isolated in 1985, and were the very first genes for agonist-binding heterotrimeric G protein-coupled receptors (GPCRs) to be cloned in any organism. Now, over 30 years later, this yeast and its receptors continue to provide a pathfinding experimental paradigm for investigating GPCR-initiated signaling and its regulation, as described in this retrospective overview.
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Affiliation(s)
- Christopher G Alvaro
- From the Division of Biochemistry, Biophysics and Structural Biology, Department of Molecular and Cell Biology, University of California, Berkeley, California 94720-3202
| | - Jeremy Thorner
- From the Division of Biochemistry, Biophysics and Structural Biology, Department of Molecular and Cell Biology, University of California, Berkeley, California 94720-3202
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9
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Tartakoff AM. Cell biology of yeast zygotes, from genesis to budding. BIOCHIMICA ET BIOPHYSICA ACTA-MOLECULAR CELL RESEARCH 2015; 1853:1702-14. [PMID: 25862405 DOI: 10.1016/j.bbamcr.2015.03.018] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/17/2014] [Revised: 03/28/2015] [Accepted: 03/31/2015] [Indexed: 12/23/2022]
Abstract
The zygote is the essential intermediate that allows interchange of nuclear, mitochondrial and cytosolic determinants between cells. Zygote formation in Saccharomyces cerevisiae is accomplished by mechanisms that are not characteristic of mitotic cells. These include shifting the axis of growth away from classical cortical landmarks, dramatically reorganizing the cell cortex, remodeling the cell wall in preparation for cell fusion, fusing with an adjacent partner, accomplishing nuclear fusion, orchestrating two steps of septin morphogenesis that account for a delay in fusion of mitochondria, and implementing new norms for bud site selection. This essay emphasizes the sequence of dependent relationships that account for this progression from cell encounters through zygote budding. It briefly summarizes classical studies of signal transduction and polarity specification and then focuses on downstream events.
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Affiliation(s)
- Alan M Tartakoff
- Department of Pathology and Cell Biology Program, Case Western Reserve University, Cleveland, OH 44106, USA.
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10
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Kar5p is required for multiple functions in both inner and outer nuclear envelope fusion in Saccharomyces cerevisiae. G3-GENES GENOMES GENETICS 2014; 5:111-21. [PMID: 25467943 PMCID: PMC4291462 DOI: 10.1534/g3.114.015800] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
Abstract
During mating in the budding yeast Saccharomyces cerevisiae, two haploid nuclei fuse via two sequential membrane fusion steps. SNAREs (i.e., soluble N-ethylmaleimide–sensitive factor attachment protein receptors) and Prm3p mediate outer nuclear membrane fusion, but the inner membrane fusogen remains unknown. Kar5p is a highly conserved transmembrane protein that localizes adjacent to the spindle pole body (SPB), mediates nuclear envelope fusion, and recruits Prm3p adjacent to the SPB. To separate Kar5p’s functions, we tested localization, Prm3p recruitment, and nuclear fusion efficiency in various kar5 mutants. All domains and the conserved cysteine residues were essential for nuclear fusion. Several kar5 mutant proteins localized properly but did not mediate Prm3p recruitment; other kar5 mutant proteins localized and recruited Prm3p but were nevertheless defective for nuclear fusion, demonstrating additional functions beyond Prm3p recruitment. We identified one Kar5p domain required for SPB localization, which is dependent on the half-bridge protein Mps3p. Electron microscopy revealed a kar5 mutant that arrests with expanded nuclear envelope bridges, suggesting that Kar5p is required after outer nuclear envelope fusion. Finally, a split-GFP assay demonstrated that Kar5p localizes to both the inner and outer nuclear envelope. These insights suggest a mechanism by which Kar5p mediates inner nuclear membrane fusion.
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11
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Rogers JV, Arlow T, Inkellis ER, Koo TS, Rose MD. ER-associated SNAREs and Sey1p mediate nuclear fusion at two distinct steps during yeast mating. Mol Biol Cell 2013; 24:3896-908. [PMID: 24152736 PMCID: PMC3861085 DOI: 10.1091/mbc.e13-08-0441] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2013] [Revised: 10/07/2013] [Accepted: 10/16/2013] [Indexed: 11/28/2022] Open
Abstract
During yeast mating, two haploid nuclei fuse membranes to form a single diploid nucleus. However, the known proteins required for nuclear fusion are unlikely to function as direct fusogens (i.e., they are unlikely to directly catalyze lipid bilayer fusion) based on their predicted structure and localization. Therefore we screened known fusogens from vesicle trafficking (soluble N-ethylmaleimide-sensitive factor attachment protein receptors [SNAREs]) and homotypic endoplasmic reticulum (ER) fusion (Sey1p) for additional roles in nuclear fusion. Here we demonstrate that the ER-localized SNAREs Sec20p, Ufe1p, Use1p, and Bos1p are required for efficient nuclear fusion. In contrast, Sey1p is required indirectly for nuclear fusion; sey1Δ zygotes accumulate ER at the zone of cell fusion, causing a block in nuclear congression. However, double mutants of Sey1p and Sec20p, Ufe1p, or Use1p, but not Bos1p, display extreme ER morphology defects, worse than either single mutant, suggesting that retrograde SNAREs fuse ER in the absence of Sey1p. Together these data demonstrate that SNAREs mediate nuclear fusion, ER fusion after cell fusion is necessary to complete nuclear congression, and there exists a SNARE-mediated, Sey1p-independent ER fusion pathway.
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Affiliation(s)
- Jason V. Rogers
- Department of Molecular Biology, Princeton University, Princeton, NJ 08544-1014
| | - Tim Arlow
- Department of Molecular Biology, Princeton University, Princeton, NJ 08544-1014
| | | | - Timothy S. Koo
- Department of Molecular Biology, Princeton University, Princeton, NJ 08544-1014
| | - Mark D. Rose
- Department of Molecular Biology, Princeton University, Princeton, NJ 08544-1014
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12
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Abstract
Autophagy is a membrane trafficking pathway responsible for the breakdown of unwanted intracellular materials and crucial for the cell healthiness and survival. In the autophagic flux, various dynamic membrane rearrangements occurs starting with the elongation of the phagophore and its closure to build an autophagosome and ending with its fusion with late endosomes and lysosomes to form an autolysosome. Although Ca2+ is a well established regulator of membrane fusion events, little is known about its role in these processes during autophagy. Recent studies, based on proteomic analyses of lysosomal membranes, have provided new insights into this field of study. Thus, the levels on lysosomal membranes of annexin A1, annexin A5 and copine 1, three proteins that bind to phospholipid membranes in a Ca2+-dependent manner, increased under nutrient deprivation, a condition that promotes autophagic degradation. In addition, two different studies showed that annexin A5 and annexin A1 are involved in autophagosome maturation. Here, we discuss the molecular mechanisms by which the fusion of autophagosomes with endosomes and lysosomes could be regulated by these three proteins and Ca2+.
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Affiliation(s)
- Ghita Ghislat
- Laboratorio de Biología Celular; Centro de Investigación Príncipe; Valencia, Spain
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13
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Khmelinskii A, Meurer M, Duishoev N, Delhomme N, Knop M. Seamless gene tagging by endonuclease-driven homologous recombination. PLoS One 2011; 6:e23794. [PMID: 21915245 PMCID: PMC3161820 DOI: 10.1371/journal.pone.0023794] [Citation(s) in RCA: 49] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2011] [Accepted: 07/27/2011] [Indexed: 11/27/2022] Open
Abstract
Gene tagging facilitates systematic genomic and proteomic analyses but chromosomal tagging typically disrupts gene regulatory sequences. Here we describe a seamless gene tagging approach that preserves endogenous gene regulation and is potentially applicable in any species with efficient DNA double-strand break repair by homologous recombination. We implement seamless tagging in Saccharomyces cerevisiae and demonstrate its application for protein tagging while preserving simultaneously upstream and downstream gene regulatory elements. Seamless tagging is compatible with high-throughput strain construction using synthetic genetic arrays (SGA), enables functional analysis of transcription antisense to open reading frames and should facilitate systematic and minimally-invasive analysis of gene functions.
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Affiliation(s)
- Anton Khmelinskii
- Cell Biology and Biophysics Unit, European Molecular Biology Laboratory (EMBL), Heidelberg, Germany
| | - Matthias Meurer
- Cell Biology and Biophysics Unit, European Molecular Biology Laboratory (EMBL), Heidelberg, Germany
| | - Nurlanbek Duishoev
- Cell Biology and Biophysics Unit, European Molecular Biology Laboratory (EMBL), Heidelberg, Germany
| | - Nicolas Delhomme
- Genome Biology Unit, European Molecular Biology Laboratory (EMBL), Heidelberg, Germany
| | - Michael Knop
- Cell Biology and Biophysics Unit, European Molecular Biology Laboratory (EMBL), Heidelberg, Germany
- * E-mail:
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14
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Weidberg H, Shpilka T, Shvets E, Abada A, Shimron F, Elazar Z. LC3 and GATE-16 N termini mediate membrane fusion processes required for autophagosome biogenesis. Dev Cell 2011; 20:444-54. [PMID: 21497758 DOI: 10.1016/j.devcel.2011.02.006] [Citation(s) in RCA: 252] [Impact Index Per Article: 18.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2010] [Revised: 12/23/2010] [Accepted: 02/15/2011] [Indexed: 11/18/2022]
Abstract
Autophagy is a unique membrane trafficking pathway describing the formation and targeting of double membrane autophagosomes to the vacuole/lysosome. The biogenesis of autophagosomes and their delivery to the vacuole/lysosome depend on multiple membrane fusion events. Using a cell-free system, we have investigated the ability of LC3 and GATE-16, two mammalian Atg8 orthologs, to mediate membrane fusion. We found that both proteins promote tethering and membrane fusion, mediated by the proteins' N-terminal α helices. We further show that short, 10 amino acid long synthetic peptides derived from the N terminus of LC3 or GATE-16 are sufficient to promote membrane fusion. Our data indicate that the fusion activity of LC3 is mediated by positively charged amino acids, whereas the activity of GATE-16 is mediated by hydrophobic interactions. Finally, we demonstrate that LC3 and GATE-16 N termini in general and specific residues needed for the fusion activity are essential for the proteins role in autophagosome biogenesis.
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Affiliation(s)
- Hilla Weidberg
- Department of Biological Chemistry, The Weizmann Institute of Science, Rehovot 76100, Israel
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15
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Kreft SG, Hochstrasser M. An unusual transmembrane helix in the endoplasmic reticulum ubiquitin ligase Doa10 modulates degradation of its cognate E2 enzyme. J Biol Chem 2011; 286:20163-74. [PMID: 21467040 DOI: 10.1074/jbc.m110.196360] [Citation(s) in RCA: 34] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
In the endoplasmic reticulum (ER), nascent membrane and secreted proteins that are misfolded are retrotranslocated into the cytosol and degraded by the proteasome. For most ER-associated degradation (ERAD) substrates, ubiquitylation is essential for both their retrotranslocation and degradation. Yeast Doa10 is a polytopic membrane ubiquitin ligase (E3) that along with its cognate ubiquitin-conjugating enzymes (E2s), Ubc7 and the C-terminally membrane-anchored Ubc6, makes a major contribution to ER-associated degradation. Ubc6 is also a substrate of Doa10. One highly conserved Doa10 element, the uncharacterized ~130-residue TEB4-Doa10 domain, includes three transmembrane helices (TMs). We find that the first of these, TM5, includes an absolutely conserved ΦPΦXXG motif that is required for Doa10 function, as well as highly conserved negatively charged glutamate and aspartate residues. The conservative exchange of the TM5 glutamate to aspartate (doa10-E633D) results in complete stabilization of Ubc6 but has little if any effect on other substrates. Unexpectedly, mutating the glutamate to glutamine (doa10-E633Q) specifically accelerates Ubc6 degradation by ~5-fold. Other substrates are weakly stabilized in doa10-E633Q cells, consistent with reduced Ubc6 levels. Notably, catalytically inactive ubc6-C87A is degraded in doa10-E633Q but not wild-type cells, but an active version of Ubc6 is required in trans. Fusion of the Ubc6 TM to a soluble protein yields a protein that is degraded in a doa10-E633Q-dependent manner, whereas fusion of the C-terminal TM from an unrelated protein does not. These results suggest that the TEB4-Doa10 domain regulates Doa10 association with the Ubc6 membrane anchor, thereby controlling the degradation rate of the E2.
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Affiliation(s)
- Stefan G Kreft
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, Connecticut 06520-8114, USA.
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Rafikova ER, Melikov K, Chernomordik LV. Cytosol-dependent membrane fusion in ER, nuclear envelope and nuclear pore assembly: biological implications. Nucleus 2011; 1:487-91. [PMID: 21327091 DOI: 10.4161/nucl.1.6.13514] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2010] [Revised: 08/19/2010] [Accepted: 09/03/2010] [Indexed: 12/26/2022] Open
Abstract
Endoplasmic reticulum and nuclear envelope rearrangements after mitosis are often studied in the reconstitution system based on Xenopus egg extract. In our recent work we partially replaced the membrane vesicles in the reconstitution mix with protein-free liposomes to explore the relative contributions of cytosolic and transmembrane proteins. Here we discuss our finding that cytosolic proteins mediate fusion between membranes lacking functional transmembrane proteins and the role of membrane fusion in endoplasmic reticulum and nuclear envelope reorganization. Cytosol-dependent liposome fusion has allowed us to restore, without adding transmembrane nucleoporins, functionality of nuclear pores, their spatial distribution and chromatin decondensation in nuclei formed at insufficient amounts of membrane material and characterized by only partial decondensation of chromatin and lack of nuclear transport. Both the mechanisms and the biological implications of the discovered coupling between spatial distribution of nuclear pores, chromatin decondensation and nuclear transport are discussed.
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Affiliation(s)
- Elvira R Rafikova
- Department of Molecular, Cell and Developmental Biology, University of California Santa Cruz, Santa Cruz, CA, USA
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Kim CS, Epand RF, Leikina E, Epand RM, Chernomordik LV. The final conformation of the complete ectodomain of the HA2 subunit of influenza hemagglutinin can by itself drive low pH-dependent fusion. J Biol Chem 2011; 286:13226-34. [PMID: 21292763 DOI: 10.1074/jbc.m110.181297] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
One of the best characterized fusion proteins, the influenza virus hemagglutinin (HA), mediates fusion between the viral envelope and the endosomal membrane during viral entry into the cell. In the initial conformation of HA, its fusogenic subunit, the transmembrane protein HA2, is locked in a metastable conformation by the receptor-binding HA1 subunit of HA. Acidification in the endosome triggers HA2 refolding toward the final lowest energy conformation. Is the fusion process driven by this final conformation or, as often suggested, by the energy released by protein restructuring? Here we explored structural properties as well as the fusogenic activity of the full sized trimeric HA2(1-185) (here called HA2*) that presents the final conformation of the HA2 ectodomain. We found HA2* to mediate fusion between lipid bilayers and between biological membranes in a low pH-dependent manner. Two mutations known to inhibit HA-mediated fusion strongly inhibited the fusogenic activity of HA2*. At surface densities similar to those of HA in the influenza virus particle, HA2* formed small fusion pores but did not expand them. Our results confirm that the HA1 subunit responsible for receptor binding as well as the transmembrane and cytosolic domains of HA2 is not required for fusion pore opening and substantiate the hypothesis that the final form of HA2 is more important for fusion than the conformational change that generates this form.
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Affiliation(s)
- Chang Sup Kim
- Department of Biotechnology, Division of Applied Chemistry and Biotechnology, Hanbat National University, Daejeon 305-719, South Korea.
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18
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Chang YW, Chuang YC, Ho YC, Cheng MY, Sun YJ, Hsiao CD, Wang C. Crystal structure of Get4-Get5 complex and its interactions with Sgt2, Get3, and Ydj1. J Biol Chem 2010; 285:9962-9970. [PMID: 20106980 DOI: 10.1074/jbc.m109.087098] [Citation(s) in RCA: 71] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Get3, Get4, and Get5 in Saccharomyces cerevisiae participate in the insertion of tail-anchored proteins into the endoplasmic reticulum membrane. We elucidated the interaction between Get4 and Get5 and investigated their interaction with Get3 and a tetratricopeptide repeat-containing protein, Sgt2. Based on co-immunoprecipitation and crystallographic studies, Get4 and Get5 formed a tight complex, suggesting that they constitute subunits of a larger complex. In contrast, although Get3 interacted physically with the Get4-Get5 complex, low amounts of Get3 co-precipitated with Get5, implying a transient interaction between Get3 and Get4-Get5. Sgt2 also interacted with Get5, although the amount of Sgt2 that co-precipitated with Get5 varied. Moreover, GET3, GET4, and GET5 interacted genetically with molecular chaperone YDJ1, suggesting that chaperones might also be involved in the insertion of tail-anchored proteins.
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Affiliation(s)
- Yi-Wei Chang
- Institute of Molecular Biology, Academia Sinica, Taipei 115; Institute of Bioinformatics and Structural Biology, National Tsing Hua University, Hsinchu 300
| | | | - Yu-Chi Ho
- Institute of Molecular Biology, Academia Sinica, Taipei 115
| | - Ming-Yuan Cheng
- Institute of Genome Sciences, National Yang-Ming University, Taipei 112, Taiwan
| | - Yuh-Ju Sun
- Institute of Bioinformatics and Structural Biology, National Tsing Hua University, Hsinchu 300
| | | | - Chung Wang
- Institute of Molecular Biology, Academia Sinica, Taipei 115.
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Current awareness on yeast. Yeast 2009. [DOI: 10.1002/yea.1626] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022] Open
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Rafikova ER, Melikov K, Ramos C, Dye L, Chernomordik LV. Transmembrane protein-free membranes fuse into xenopus nuclear envelope and promote assembly of functional pores. J Biol Chem 2009; 284:29847-59. [PMID: 19696024 PMCID: PMC2785615 DOI: 10.1074/jbc.m109.044453] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2009] [Revised: 08/17/2009] [Indexed: 11/06/2022] Open
Abstract
Post-mitotic reassembly of nuclear envelope (NE) and the endoplasmic reticulum (ER) has been reconstituted in a cell-free system based on interphase Xenopus egg extract. To evaluate the relative contributions of cytosolic and transmembrane proteins in NE and ER assembly, we replaced a part of native membrane vesicles with ones either functionally impaired by trypsin or N-ethylmaleimide treatments or with protein-free liposomes. Although neither impaired membrane vesicles nor liposomes formed ER and nuclear membrane, they both supported assembly reactions by fusing with native membrane vesicles. At membrane concentrations insufficient to generate full-sized functional nuclei, addition of liposomes and their fusion with membrane vesicles resulted in an extensive expansion of NE, further chromatin decondensation, restoration of the functionality, and spatial distribution of the nuclear pore complexes (NPCs), and, absent newly delivered transmembrane proteins, an increase in NPC numbers. This rescue of the nuclear assembly by liposomes was inhibited by wheat germ agglutinin and thus required active nuclear transport, similarly to the assembly of full-sized functional NE with membrane vesicles. Mechanism of fusion between liposomes and between liposomes and membrane vesicles was investigated using lipid mixing assay. This fusion required interphase cytosol and, like fusion between native membrane vesicles, was inhibited by guanosine 5'-3-O-(thio)triphosphate, soluble N-ethylmaleimide-sensitive factor attachment protein, and N-ethylmaleimide. Our findings suggest that interphase cytosol contains proteins that mediate the fusion stage of ER and NE reassembly, emphasize an unexpected tolerance of nucleus assembly to changes in concentrations of transmembrane proteins, and reveal the existence of a feedback mechanism that couples NE expansion with NPC assembly.
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Affiliation(s)
- Elvira R. Rafikova
- From the Section on Membrane Biology, Laboratory of Cellular and Molecular Biophysics, Eunice Kennedy Shriver NICHD, National Institutes of Health, Bethesda, Maryland 20892-1855
| | - Kamran Melikov
- From the Section on Membrane Biology, Laboratory of Cellular and Molecular Biophysics, Eunice Kennedy Shriver NICHD, National Institutes of Health, Bethesda, Maryland 20892-1855
| | - Corinne Ramos
- the Section of Cell and Developmental Biology, Division of Biological Sciences, University of California, San Diego, La Jolla, California 92093-0347, and
| | - Louis Dye
- the Microscopy and Imaging Core, Eunice Kennedy Shriver NICHD, National Institutes of Health, Bethesda, Maryland 20892-1855
| | - Leonid V. Chernomordik
- From the Section on Membrane Biology, Laboratory of Cellular and Molecular Biophysics, Eunice Kennedy Shriver NICHD, National Institutes of Health, Bethesda, Maryland 20892-1855
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21
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Melloy P, Shen S, White E, Rose MD. Distinct roles for key karyogamy proteins during yeast nuclear fusion. Mol Biol Cell 2009; 20:3773-82. [PMID: 19570912 PMCID: PMC2735476 DOI: 10.1091/mbc.e09-02-0163] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2009] [Revised: 06/19/2009] [Accepted: 06/23/2009] [Indexed: 11/11/2022] Open
Abstract
During yeast mating, cell fusion is followed by the congression and fusion of the two nuclei. Proteins required for nuclear fusion are found at the surface (Prm3p) and within the lumen (Kar2p, Kar5p, and Kar8p) of the nuclear envelope (NE). Electron tomography (ET) of zygotes revealed that mutations in these proteins block nuclear fusion with different morphologies, suggesting that they act in different steps of fusion. Specifically, prm3 zygotes were blocked before formation of membrane bridges, whereas kar2, kar5, and kar8 zygotes frequently contained them. Membrane bridges were significantly larger and occurred more frequently in kar2 and kar8, than in kar5 mutant zygotes. The kinetics of NE fusion in prm3, kar5, and kar8 mutants, measured by live-cell fluorescence microscopy, were well correlated with the size and frequency of bridges observed by ET. However the kar2 mutant was defective for transfer of NE lumenal GFP, but not diffusion within the lumen, suggesting that transfer was blocked at the NE fusion junction. These observations suggest that Prm3p acts before initiation of outer NE fusion, Kar5p may help dilation of the initial fusion pore, and Kar2p and Kar8p act after outer NE fusion, during inner NE fusion.
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Affiliation(s)
- Patricia Melloy
- Department of Molecular Biology, Princeton University, Princeton, NJ 08544, USA.
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