1
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Duan M, Plemel RL, Takenaka T, Lin A, Delgado BM, Nattermann U, Nickerson DP, Mima J, Miller EA, Merz AJ. SNARE chaperone Sly1 directly mediates close-range vesicle tethering. J Cell Biol 2024; 223:e202001032. [PMID: 38478018 PMCID: PMC10943277 DOI: 10.1083/jcb.202001032] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2020] [Revised: 12/20/2023] [Accepted: 02/22/2024] [Indexed: 03/17/2024] Open
Abstract
The essential Golgi protein Sly1 is a member of the Sec1/mammalian Unc-18 (SM) family of SNARE chaperones. Sly1 was originally identified through remarkable gain-of-function alleles that bypass requirements for diverse vesicle tethering factors. Employing genetic analyses and chemically defined reconstitutions of ER-Golgi fusion, we discovered that a loop conserved among Sly1 family members is not only autoinhibitory but also acts as a positive effector. An amphipathic lipid packing sensor (ALPS)-like helix within the loop directly binds high-curvature membranes. Membrane binding is required for relief of Sly1 autoinhibition and also allows Sly1 to directly tether incoming vesicles to the Qa-SNARE on the target organelle. The SLY1-20 mutation bypasses requirements for diverse tethering factors but loses this ability if the tethering activity is impaired. We propose that long-range tethers, including Golgins and multisubunit tethering complexes, hand off vesicles to Sly1, which then tethers at close range to initiate trans-SNARE complex assembly and fusion in the early secretory pathway.
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Affiliation(s)
- Mengtong Duan
- Department of Biochemistry, University of Washington, Seattle, WA, USA
| | - Rachael L. Plemel
- Department of Biochemistry, University of Washington, Seattle, WA, USA
| | | | - Ariel Lin
- Department of Biochemistry, University of Washington, Seattle, WA, USA
- Department of Biology, California State University, San Bernardino, CA, USA
| | | | - Una Nattermann
- Department of Biochemistry, University of Washington, Seattle, WA, USA
- Biophysics, Structure, and Design Graduate Program, University of Washington, Seattle, WA, USA
- Institute for Protein Design, University of Washington, Seattle, WA, USA
| | | | - Joji Mima
- Institute for Protein Research, Osaka University, Osaka, Japan
| | | | - Alexey J. Merz
- Department of Biochemistry, University of Washington, Seattle, WA, USA
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2
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Reddien PW. The purpose and ubiquity of turnover. Cell 2024; 187:2657-2681. [PMID: 38788689 DOI: 10.1016/j.cell.2024.04.034] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2024] [Revised: 03/19/2024] [Accepted: 04/24/2024] [Indexed: 05/26/2024]
Abstract
Turnover-constant component production and destruction-is ubiquitous in biology. Turnover occurs across organisms and scales, including for RNAs, proteins, membranes, macromolecular structures, organelles, cells, hair, feathers, nails, antlers, and teeth. For many systems, turnover might seem wasteful when degraded components are often fully functional. Some components turn over with shockingly high rates and others do not turn over at all, further making this process enigmatic. However, turnover can address fundamental problems by yielding powerful properties, including regeneration, rapid repair onset, clearance of unpredictable damage and errors, maintenance of low constitutive levels of disrepair, prevention of stable hazards, and transitions. I argue that trade-offs between turnover benefits and metabolic costs, combined with constraints on turnover, determine its presence and rates across distinct contexts. I suggest that the limits of turnover help explain aging and that turnover properties and the basis for its levels underlie this fundamental component of life.
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Affiliation(s)
- Peter W Reddien
- Whitehead Institute for Biomedical Research, Cambridge, MA 02142, USA; Department of Biology, MIT, Cambridge, MA 02139, USA; Howard Hughes Medical Institute, MIT, Cambridge, MA 02139, USA.
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3
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Marshall WF. The flagellar length control system: exploring the physical biology of organelle size. Phys Biol 2023; 20:10.1088/1478-3975/acb18d. [PMID: 36623317 PMCID: PMC9877179 DOI: 10.1088/1478-3975/acb18d] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2022] [Accepted: 01/09/2023] [Indexed: 01/11/2023]
Abstract
How cells build and maintain dynamic structures of defined size is currently an important unsolved problem in quantitative cell biology. The flagella of the unicellular green algaChlamydomonasprovide a highly tractable model system to investigate this general question, but while the powerful genetics of this organism have revealed numerous genes required for proper flagellar length, in most cases we do not understand their mechanistic role in length control. Flagellar length can be viewed as the steady state solution of a dynamical system involving assembly and disassembly of axonemal microtubules, with assembly depending on an active transport process known as intraflagellar transport (IFT). The inherent length dependence of IFT gives rise to a family of simple models for length regulation that can account for many previously described phenomena such as the ability of flagella to maintain equal lengths. But these models requires that the cell has a way to measure flagellar length in order to adjust IFT rates accordingly. Several models for length sensing have been modeled theoretically and evaluated experimentally, allowing them to be ruled out. Current data support a model in which the diffusive return of the kinesin motor driving IFT provides a length dependence that ultimately is the basis for length regulation. By combining models of length sensing with a more detailed representation of cargo transport and availability, it is now becoming possible to formulate concrete hypotheses to explain length altering mutants.
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Affiliation(s)
- Wallace F Marshall
- Department Biochemistry & Biophysics, University of California San Francisco, San Francisco, CA, United States of America
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4
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Chen P, Levy DL. Regulation of organelle size and organization during development. Semin Cell Dev Biol 2023; 133:53-64. [PMID: 35148938 PMCID: PMC9357868 DOI: 10.1016/j.semcdb.2022.02.002] [Citation(s) in RCA: 9] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2021] [Revised: 01/20/2022] [Accepted: 02/01/2022] [Indexed: 12/11/2022]
Abstract
During early embryogenesis, as cells divide in the developing embryo, the size of intracellular organelles generally decreases to scale with the decrease in overall cell size. Organelle size scaling is thought to be important to establish and maintain proper cellular function, and defective scaling may lead to impaired development and disease. However, how the cell regulates organelle size and organization are largely unanswered questions. In this review, we summarize the process of size scaling at both the cell and organelle levels and discuss recently discovered mechanisms that regulate this process during early embryogenesis. In addition, we describe how some recently developed techniques and Xenopus as an animal model can be used to investigate the underlying mechanisms of size regulation and to uncover the significance of proper organelle size scaling and organization.
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Affiliation(s)
- Pan Chen
- Institute of Biochemistry and Molecular Biology, School of Medicine, Ningbo University, Ningbo, Zhejiang 315211, China.
| | - Daniel L Levy
- Department of Molecular Biology, University of Wyoming, Laramie, WY 82071, USA.
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5
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Amiri KP, Kalish A, Mukherji S. Robustness and Universality in Organelle Size Control. PHYSICAL REVIEW LETTERS 2023; 130:018401. [PMID: 36669211 PMCID: PMC10316456 DOI: 10.1103/physrevlett.130.018401] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/11/2021] [Accepted: 11/07/2022] [Indexed: 06/15/2023]
Abstract
One of the grand challenges in cellular biophysics is understanding the precision with which cells assemble and maintain subcellular structures. Organelle sizes, for example, must be flexible enough to allow cells to grow or shrink them as environments demand yet be maintained within homeostatic limits. Despite identification of molecular factors that regulate organelle sizes we lack insight into the quantitative principles underlying organelle size control. Here we show experimentally that cells can robustly control average fluctuations in organelle size. By demonstrating that organelle sizes obey a universal scaling relationship we predict theoretically, our framework suggests that organelles grow in random bursts from a limiting pool of building blocks. Burstlike growth provides a general biophysical mechanism by which cells can maintain on average reliable yet plastic organelle sizes.
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Affiliation(s)
| | - Asa Kalish
- Department of Physics, Washington University in St. Louis
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6
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Kinase Hog1 and Adr1 Opposingly Regulate Haploid Cell Morphology by Controlling Vacuole Size in Sporisorium scitamineum. J Fungi (Basel) 2022; 8:jof8080865. [PMID: 36012854 PMCID: PMC9410113 DOI: 10.3390/jof8080865] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2022] [Revised: 08/13/2022] [Accepted: 08/15/2022] [Indexed: 11/16/2022] Open
Abstract
Morphogenesis is a strictly regulated efficient system in eukaryotes for adapting to environmental changes. However, the morphogenesis regulatory mechanism in smut fungi is not clear. This study reports a relationship between MAP kinase Hog1 and cAMP-dependent protein kinase A catalytic subunit (Adr1) for the morphological regulation in the sugarcane pathogen Sporisorium scitamineum. The results demonstrated that MAP kinase Hog1 and cAMP/PKA signaling pathways are essential for the morphological development of S. scitamineum. Interestingly, MAP kinase Hog1 and cAMP/PKA signaling pathways’ defective mutants exhibit an opposite morphological phenotype. The morphology of cAMP/PKA defective mutants is recovered by deleting the SsHOG1 gene. However, MAP kinase Hog1 and cAMP-dependent protein kinase catalytic subunit Adr1 do not interfere with each other. Further investigations showed that kinase Hog1 and Adr1 antagonistically regulates the vacuolar size, which contributes to the cell size and determines the cellular elongation rates. Kinase Hog1 and Adr1 also antagonistically balanced the cell wall integrity and permeability. Taken together, kinase Hog1- and Adr1-based opposing morphogenesis regulation of S. scitamineum by controlling the vacuolar size and cell wall permeability is established during the study.
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7
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Potassium and Sodium Salt Stress Characterization in the Yeasts Saccharomyces cerevisiae, Kluyveromyces marxianus, and Rhodotorula toruloides. Appl Environ Microbiol 2021; 87:e0310020. [PMID: 33893111 DOI: 10.1128/aem.03100-20] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Biotechnology requires efficient microbial cell factories. The budding yeast Saccharomyces cerevisiae is a vital cell factory, but more diverse cell factories are essential for the sustainable use of natural resources. Here, we benchmarked nonconventional yeasts Kluyveromyces marxianus and Rhodotorula toruloides against S. cerevisiae strains CEN.PK and W303 for their responses to potassium and sodium salt stress. We found an inverse relationship between the maximum growth rate and the median cell volume that was responsive to salt stress. The supplementation of K+ to CEN.PK cultures reduced Na+ toxicity and increased the specific growth rate 4-fold. The higher K+ and Na+ concentrations impaired ethanol and acetate metabolism in CEN.PK and acetate metabolism in W303. In R. toruloides cultures, these salt supplementations induced a trade-off between glucose utilization and cellular aggregate formation. Their combined use increased the beta-carotene yield by 60% compared with that of the reference. Neural network-based image analysis of exponential-phase cultures showed that the vacuole-to-cell volume ratio increased with increased cell volume for W303 and K. marxianus but not for CEN.PK and R. toruloides in response to salt stress. Our results provide insights into common salt stress responses in yeasts and will help design efficient bioprocesses. IMPORTANCE Characterization of microbial cell factories under industrially relevant conditions is crucial for designing efficient bioprocesses. Salt stress, typical in industrial bioprocesses, impinges upon cell volume and affects productivity. This study presents an open-source neural network-based analysis method to evaluate volumetric changes using yeast optical microscopy images. It allows quantification of cell and vacuole volumes relevant to cellular physiology. On applying salt stress in yeasts, we found that the combined use of K+ and Na+ improves the cellular fitness of Saccharomyces cerevisiae strain CEN.PK and increases the beta-carotene productivity in Rhodotorula toruloides, a commercially important antioxidant and a valuable additive in foods.
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8
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Chadwick WL, Biswas SK, Bianco S, Chan YHM. Non-random distribution of vacuoles in Schizosaccharomyces pombe. Phys Biol 2020; 17:065004. [PMID: 33035200 DOI: 10.1088/1478-3975/aba510] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
A central question in eukaryotic cell biology asks, during cell division, how is the growth and distribution of organelles regulated to ensure each daughter cell receives an appropriate amount. For vacuoles in budding yeast, there are well described organelle-to-cell size scaling trends as well as inheritance mechanisms involving highly coordinated movements. It is unclear whether such mechanisms are necessary in the symmetrically dividing fission yeast, Schizosaccharomyces pombe, in which random partitioning may be utilized to distribute vacuoles to daughter cells. To address the increasing need for high-throughput analysis, we are augmenting existing semi-automated image processing by developing fully automated machine learning methods for locating vacuoles and segmenting fission yeast cells from brightfield and fluorescence micrographs. All strains studied show qualitative correlations in vacuole-to-cell size scaling trends, i.e. vacuole volume, surface area, and number all increase with cell size. Furthermore, increasing vacuole number was found to be a consistent mechanism for the increase in total vacuole size in the cell. Vacuoles are not distributed evenly throughout the cell with respect to available cytoplasm. Rather, vacuoles show distinct peaks in distribution close to the nucleus, and this preferential localization was confirmed in mutants in which nucleus position is perturbed. Disruption of microtubules leads to quantitative changes in both vacuole size scaling trends and distribution patterns, indicating the microtubule cytoskeleton is a key mechanism for maintaining vacuole structure.
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Affiliation(s)
- William L Chadwick
- Department of Biology, San Francisco State University, San Francisco, CA, United States of America. Center for Cellular Construction, San Francisco Bay Area, CA, United States of America
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9
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Abstract
As cells grow, the size and number of their internal organelles increase in order to keep up with increased metabolic requirements. Abnormal size of organelles is a hallmark of cancer and an important aspect of diagnosis in cytopathology. Most organelles vary in either size or number, or both, as a function of cell size, but the mechanisms that create this variation remain unclear. In some cases, organelle size appears to scale with cell size through processes of relative growth, but in others the size may be set by either active measurement systems or genetic programs that instruct organelle biosynthetic activities to create organelles of a size appropriate to a given cell type.
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Affiliation(s)
- Wallace F Marshall
- Department of Biochemistry and Biophysics, University of California, San Francisco, California 94143, USA;
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10
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Tsuboi T, Viana MP, Xu F, Yu J, Chanchani R, Arceo XG, Tutucci E, Choi J, Chen YS, Singer RH, Rafelski SM, Zid BM. Mitochondrial volume fraction and translation duration impact mitochondrial mRNA localization and protein synthesis. eLife 2020; 9:e57814. [PMID: 32762840 PMCID: PMC7413667 DOI: 10.7554/elife.57814] [Citation(s) in RCA: 27] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2020] [Accepted: 07/23/2020] [Indexed: 12/31/2022] Open
Abstract
Mitochondria are dynamic organelles that must precisely control their protein composition according to cellular energy demand. Although nuclear-encoded mRNAs can be localized to the mitochondrial surface, the importance of this localization is unclear. As yeast switch to respiratory metabolism, there is an increase in the fraction of the cytoplasm that is mitochondrial. Our data point to this change in mitochondrial volume fraction increasing the localization of certain nuclear-encoded mRNAs to the surface of the mitochondria. We show that mitochondrial mRNA localization is necessary and sufficient to increase protein production to levels required during respiratory growth. Furthermore, we find that ribosome stalling impacts mRNA sensitivity to mitochondrial volume fraction and counterintuitively leads to enhanced protein synthesis by increasing mRNA localization to mitochondria. This points to a mechanism by which cells are able to use translation elongation and the geometric constraints of the cell to fine-tune organelle-specific gene expression through mRNA localization.
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Affiliation(s)
- Tatsuhisa Tsuboi
- Department of Chemistry and Biochemistry, University of California San DiegoLa JollaUnited States
- Department of Developmental and Cell Biology and Center for Complex Biological Systems, University of California IrvineIrvineUnited States
- Division of Biological Science, Graduate School of Science, Nagoya UniversityNagoyaJapan
| | - Matheus P Viana
- Department of Developmental and Cell Biology and Center for Complex Biological Systems, University of California IrvineIrvineUnited States
| | - Fan Xu
- Department of Chemistry and Biochemistry, University of California San DiegoLa JollaUnited States
| | - Jingwen Yu
- Department of Chemistry and Biochemistry, University of California San DiegoLa JollaUnited States
| | - Raghav Chanchani
- Department of Chemistry and Biochemistry, University of California San DiegoLa JollaUnited States
| | - Ximena G Arceo
- Department of Chemistry and Biochemistry, University of California San DiegoLa JollaUnited States
| | - Evelina Tutucci
- Department of Anatomy and Structural Biology, Albert Einstein College of MedicineBronxUnited States
| | - Joonhyuk Choi
- Department of Chemistry and Biochemistry, University of California San DiegoLa JollaUnited States
| | - Yang S Chen
- Department of Chemistry and Biochemistry, University of California San DiegoLa JollaUnited States
| | - Robert H Singer
- Department of Anatomy and Structural Biology, Albert Einstein College of MedicineBronxUnited States
- Gruss-Lipper Biophotonics Center, Albert Einstein College of MedicineBronxUnited States
- Department of Neuroscience, Albert Einstein College of MedicineBronxUnited States
- Janelia Research Campus, Howard Hughes Medical InstituteAshburnUnited States
| | - Susanne M Rafelski
- Department of Developmental and Cell Biology and Center for Complex Biological Systems, University of California IrvineIrvineUnited States
| | - Brian M Zid
- Department of Chemistry and Biochemistry, University of California San DiegoLa JollaUnited States
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11
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Mołoń M, Molestak E, Kula-Maximenko M, Grela P, Tchórzewski M. Ribosomal Protein uL11 as a Regulator of Metabolic Circuits Related to Aging and Cell Cycle. Cells 2020; 9:cells9071745. [PMID: 32708309 PMCID: PMC7409069 DOI: 10.3390/cells9071745] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2020] [Revised: 07/06/2020] [Accepted: 07/16/2020] [Indexed: 11/16/2022] Open
Abstract
Aging is a biological phenomenon common to all living organisms. It is thought that the rate of aging is influenced by diverse factors, in many cases related to the control of energy metabolism, i.e., the so-called pro-longevity effects of starvation. Translation, regarded as the main energy consumption process, lies at the center of interest, as it has a significant impact on the longevity phenomenon. It has been shown that perturbations in the translational apparatus may lead to a lower rate of aging. Therefore, the main aim of this study was to investigate aging in relation to the protein biosynthesis circuit, taking into account the uL11 ribosomal protein as a vital ribosomal element. To this end, we used set of yeast mutants with deleted single uL11A or uL11B genes and a double disruptant uL11AB mutant. We applied an integrated approach analyzing a broad range of biological parameters of yeast mutant cells, especially the longevity phenomenon, supplemented with biochemical and high throughput transcriptomic and metobolomic approaches. The analysis showed that the longevity phenomenon is not fully related to the commonly considered energy restriction effect, thus the slow-down of translation does not represent the sole source of aging. Additionally, we showed that uL11 can be classified as a moonlighting protein with extra-ribosomal function having cell-cycle regulatory potential.
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Affiliation(s)
- Mateusz Mołoń
- Department of Biochemistry and Cell Biology, University of Rzeszów, 35-601 Rzeszów, Poland
- Correspondence: (M.M.); (M.T.); Tel.: +48-17-7855407 (M.M.); +48-81-5375956 (M.T.)
| | - Eliza Molestak
- Department of Molecular Biology, Maria Curie-Skłodowska University, 20-033 Lublin, Poland; (E.M.); (P.G.)
| | - Monika Kula-Maximenko
- The Franciszek Górski Institute of Plant Physiology, Polish Academy of Sciences, 30-239 Krakow, Poland;
| | - Przemysław Grela
- Department of Molecular Biology, Maria Curie-Skłodowska University, 20-033 Lublin, Poland; (E.M.); (P.G.)
| | - Marek Tchórzewski
- Department of Molecular Biology, Maria Curie-Skłodowska University, 20-033 Lublin, Poland; (E.M.); (P.G.)
- Correspondence: (M.M.); (M.T.); Tel.: +48-17-7855407 (M.M.); +48-81-5375956 (M.T.)
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12
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Abstract
Cells are complex machines with tremendous potential for applications in medicine and biotechnology. Although much effort has been devoted to engineering the metabolic, genetic, and signaling pathways of cells, methods for systematically engineering the physical structure of cells are less developed. Here we consider how coarse-grained models for cellular geometry at the organelle level can be used to build computer-aided design (CAD) tools for cellular structure.
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Affiliation(s)
- Simone Bianco
- Center for Cellular Construction, San Francisco, CA, United States of America. IBM Almaden Research Center, San Jose, CA, United States of America
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13
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Wesley CC, Mishra S, Levy DL. Organelle size scaling over embryonic development. WILEY INTERDISCIPLINARY REVIEWS-DEVELOPMENTAL BIOLOGY 2020; 9:e376. [PMID: 32003549 DOI: 10.1002/wdev.376] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/26/2019] [Revised: 12/19/2019] [Accepted: 01/08/2020] [Indexed: 12/13/2022]
Abstract
Cell division without growth results in progressive cell size reductions during early embryonic development. How do the sizes of intracellular structures and organelles scale with cell size and what are the functional implications of such scaling relationships? Model organisms, in particular Caenorhabditis elegans worms, Drosophila melanogaster flies, Xenopus laevis frogs, and Mus musculus mice, have provided insights into developmental size scaling of the nucleus, mitotic spindle, and chromosomes. Nuclear size is regulated by nucleocytoplasmic transport, nuclear envelope proteins, and the cytoskeleton. Regulators of microtubule dynamics and chromatin compaction modulate spindle and mitotic chromosome size scaling, respectively. Developmental scaling relationships for membrane-bound organelles, like the endoplasmic reticulum, Golgi, mitochondria, and lysosomes, have been less studied, although new imaging approaches promise to rectify this deficiency. While models that invoke limiting components and dynamic regulation of assembly and disassembly can account for some size scaling relationships in early embryos, it will be exciting to investigate the contribution of newer concepts in cell biology such as phase separation and interorganellar contacts. With a growing understanding of the underlying mechanisms of organelle size scaling, future studies promise to uncover the significance of proper scaling for cell function and embryonic development, as well as how aberrant scaling contributes to disease. This article is categorized under: Establishment of Spatial and Temporal Patterns > Regulation of Size, Proportion, and Timing Early Embryonic Development > Fertilization to Gastrulation Comparative Development and Evolution > Model Systems.
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Affiliation(s)
- Chase C Wesley
- Department of Molecular Biology, University of Wyoming, Laramie, Wyoming
| | - Sampada Mishra
- Department of Molecular Biology, University of Wyoming, Laramie, Wyoming
| | - Daniel L Levy
- Department of Molecular Biology, University of Wyoming, Laramie, Wyoming
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14
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Hipolito VEB, Diaz JA, Tandoc KV, Oertlin C, Ristau J, Chauhan N, Saric A, Mclaughlan S, Larsson O, Topisirovic I, Botelho RJ. Enhanced translation expands the endo-lysosome size and promotes antigen presentation during phagocyte activation. PLoS Biol 2019; 17:e3000535. [PMID: 31800587 PMCID: PMC6913987 DOI: 10.1371/journal.pbio.3000535] [Citation(s) in RCA: 38] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2018] [Revised: 12/16/2019] [Accepted: 11/04/2019] [Indexed: 02/06/2023] Open
Abstract
The mechanisms that govern organelle adaptation and remodelling remain poorly defined. The endo-lysosomal system degrades cargo from various routes, including endocytosis, phagocytosis, and autophagy. For phagocytes, endosomes and lysosomes (endo-lysosomes) are kingpin organelles because they are essential to kill pathogens and process and present antigens. During phagocyte activation, endo-lysosomes undergo a morphological transformation, going from a collection of dozens of globular structures to a tubular network in a process that requires the phosphatidylinositol-3-kinase-AKT-mechanistic target of rapamycin (mTOR) signalling pathway. Here, we show that the endo-lysosomal system undergoes an expansion in volume and holding capacity during phagocyte activation within 2 h of lipopolysaccharides (LPS) stimulation. Endo-lysosomal expansion was paralleled by an increase in lysosomal protein levels, but this was unexpectedly largely independent of the transcription factor EB (TFEB) and transcription factor E3 (TFE3), which are known to scale up lysosome biogenesis. Instead, we demonstrate a hitherto unappreciated mechanism of acute organelle expansion via mTOR Complex 1 (mTORC1)-dependent increase in translation, which appears to be mediated by both S6Ks and 4E-BPs. Moreover, we show that stimulation of RAW 264.7 macrophage cell line with LPS alters translation of a subset but not all of mRNAs encoding endo-lysosomal proteins, thereby suggesting that endo-lysosome expansion is accompanied by functional remodelling. Importantly, mTORC1-dependent increase in translation activity was necessary for efficient and rapid antigen presentation by dendritic cells. Collectively, we identified a previously unknown and functionally relevant mechanism for endo-lysosome expansion that relies on mTORC1-dependent translation to stimulate endo-lysosome biogenesis in response to an infection signal. Activation of phagocytes rapidly expands the endo-lysosomal system and promotes antigen presentation. Endo-lysosome expansion was driven by mTORC1-dependent enhanced translation, revealing regulated translation as a mechanism to remodel membrane organelles in response to external signals and stresses.
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Affiliation(s)
- Victoria E. B. Hipolito
- Graduate Program in Molecular Science, Ryerson University, Toronto, Ontario, Canada
- Department of Chemistry and Biology, Ryerson University, Toronto, Ontario, Canada
| | - Jacqueline A. Diaz
- Department of Chemistry and Biology, Ryerson University, Toronto, Ontario, Canada
| | - Kristofferson V. Tandoc
- Department of Experimental Medicine, McGill University, Montréal, Quebec, Canada
- The Lady Davis Institute, Jewish General Hospital, Montréal, Quebec, Canada
| | - Christian Oertlin
- Department of Oncology-Pathology, Science for Life Laboratory, Karolinska Institutet, Stockholm, Sweden
| | - Johannes Ristau
- Department of Oncology-Pathology, Science for Life Laboratory, Karolinska Institutet, Stockholm, Sweden
| | - Neha Chauhan
- Department of Chemistry and Biology, Ryerson University, Toronto, Ontario, Canada
| | - Amra Saric
- Graduate Program in Molecular Science, Ryerson University, Toronto, Ontario, Canada
- Department of Chemistry and Biology, Ryerson University, Toronto, Ontario, Canada
| | - Shannon Mclaughlan
- The Lady Davis Institute, Jewish General Hospital, Montréal, Quebec, Canada
| | - Ola Larsson
- Department of Oncology-Pathology, Science for Life Laboratory, Karolinska Institutet, Stockholm, Sweden
| | - Ivan Topisirovic
- Department of Experimental Medicine, McGill University, Montréal, Quebec, Canada
- The Lady Davis Institute, Jewish General Hospital, Montréal, Quebec, Canada
- Gerald Bronfman Department of Oncology, McGill University, Montréal, Quebec, Canada
- Department of Biochemistry, McGill University, Montréal, Quebec, Canada
| | - Roberto J. Botelho
- Graduate Program in Molecular Science, Ryerson University, Toronto, Ontario, Canada
- Department of Chemistry and Biology, Ryerson University, Toronto, Ontario, Canada
- * E-mail:
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15
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Choy CH, Saffi G, Gray MA, Wallace C, Dayam RM, Ou ZYA, Lenk G, Puertollano R, Watkins SC, Botelho RJ. Lysosome enlargement during inhibition of the lipid kinase PIKfyve proceeds through lysosome coalescence. J Cell Sci 2018; 131:jcs.213587. [PMID: 29661845 DOI: 10.1242/jcs.213587] [Citation(s) in RCA: 66] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2017] [Accepted: 04/10/2018] [Indexed: 01/07/2023] Open
Abstract
Lysosomes receive and degrade cargo from endocytosis, phagocytosis and autophagy. They also play an important role in sensing and instructing cells on their metabolic state. The lipid kinase PIKfyve generates phosphatidylinositol-3,5-bisphosphate to modulate lysosome function. PIKfyve inhibition leads to impaired degradative capacity, ion dysregulation, abated autophagic flux and a massive enlargement of lysosomes. Collectively, this leads to various physiological defects, including embryonic lethality, neurodegeneration and overt inflammation. The reasons for such drastic lysosome enlargement remain unclear. Here, we examined whether biosynthesis and/or fusion-fission dynamics contribute to swelling. First, we show that PIKfyve inhibition activates TFEB, TFE3 and MITF, enhancing lysosome gene expression. However, this did not augment lysosomal protein levels during acute PIKfyve inhibition, and deletion of TFEB and/or related proteins did not impair lysosome swelling. Instead, PIKfyve inhibition led to fewer but enlarged lysosomes, suggesting that an imbalance favouring lysosome fusion over fission causes lysosome enlargement. Indeed, conditions that abated fusion curtailed lysosome swelling in PIKfyve-inhibited cells.
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Affiliation(s)
- Christopher H Choy
- Department of Chemistry and Biology, Ryerson University, Toronto, ON, Canada, M5B2K3.,The Graduate Program in Molecular Science, Ryerson University, Toronto, ON, Canada, M5B2K3
| | - Golam Saffi
- Department of Chemistry and Biology, Ryerson University, Toronto, ON, Canada, M5B2K3.,The Graduate Program in Molecular Science, Ryerson University, Toronto, ON, Canada, M5B2K3
| | - Matthew A Gray
- Department of Chemistry and Biology, Ryerson University, Toronto, ON, Canada, M5B2K3
| | - Callen Wallace
- Department of Cell Biology, University of Pittsburgh, Pittsburgh, PA 15261, USA
| | - Roya M Dayam
- Department of Chemistry and Biology, Ryerson University, Toronto, ON, Canada, M5B2K3.,The Graduate Program in Molecular Science, Ryerson University, Toronto, ON, Canada, M5B2K3
| | - Zhen-Yi A Ou
- Department of Chemistry and Biology, Ryerson University, Toronto, ON, Canada, M5B2K3
| | - Guy Lenk
- Department of Human Genetics, University of Michigan, Ann Arbor, MI 48109, USA
| | - Rosa Puertollano
- Cell Biology and Physiology Center, National Heart, Lung, and Blood Institute, National Institutes of Health, 50 South Drive, Building 50, Room 3537, Bethesda, MD 20892, USA
| | - Simon C Watkins
- Department of Cell Biology, University of Pittsburgh, Pittsburgh, PA 15261, USA
| | - Roberto J Botelho
- Department of Chemistry and Biology, Ryerson University, Toronto, ON, Canada, M5B2K3 .,The Graduate Program in Molecular Science, Ryerson University, Toronto, ON, Canada, M5B2K3
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Tang SKY, Marshall WF. Self-repairing cells: How single cells heal membrane ruptures and restore lost structures. Science 2018; 356:1022-1025. [PMID: 28596334 DOI: 10.1126/science.aam6496] [Citation(s) in RCA: 72] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
Abstract
Many organisms and tissues display the ability to heal and regenerate as needed for normal physiology and as a result of pathogenesis. However, these repair activities can also be observed at the single-cell level. The physical and molecular mechanisms by which a cell can heal membrane ruptures and rebuild damaged or missing cellular structures remain poorly understood. This Review presents current understanding in wound healing and regeneration as two distinct aspects of cellular self-repair by examining a few model organisms that have displayed robust repair capacity, including Xenopus oocytes, Chlamydomonas, and Stentor coeruleus Although many open questions remain, elucidating how cells repair themselves is important for our mechanistic understanding of cell biology. It also holds the potential for new applications and therapeutic approaches for treating human disease.
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Affiliation(s)
- Sindy K Y Tang
- Department of Mechanical Engineering, Stanford University, Stanford, CA, USA.
| | - Wallace F Marshall
- Department of Biochemistry and Biophysics, University of California-San Francisco, San Francisco, CA, USA.
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17
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Chang AY, Marshall WF. Organelles - understanding noise and heterogeneity in cell biology at an intermediate scale. J Cell Sci 2017; 130:819-826. [PMID: 28183729 DOI: 10.1242/jcs.181024] [Citation(s) in RCA: 30] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022] Open
Abstract
Many studies over the years have shown that non-genetic mechanisms for producing cell-to-cell variation can lead to highly variable behaviors across genetically identical populations of cells. Most work to date has focused on gene expression noise as the primary source of phenotypic heterogeneity, yet other sources may also contribute. In this Commentary, we explore organelle-level heterogeneity as a potential secondary source of cellular 'noise' that contributes to phenotypic heterogeneity. We explore mechanisms for generating organelle heterogeneity and present evidence of functional links between organelle morphology and cellular behavior. Given the many instances in which molecular-level heterogeneity has been linked to phenotypic heterogeneity, we posit that organelle heterogeneity may similarly contribute to overall phenotypic heterogeneity and underline the importance of studying organelle heterogeneity to develop a more comprehensive understanding of phenotypic heterogeneity. Finally, we conclude with a discussion of the medical challenges associated with phenotypic heterogeneity and outline how improved methods for characterizing and controlling this heterogeneity may lead to improved therapeutic strategies and outcomes for patients.
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Affiliation(s)
- Amy Y Chang
- Department of Biochemistry and Biophysics, Center for Cellular Construction, University of California, San Francisco, CA 94158, USA
| | - Wallace F Marshall
- Department of Biochemistry and Biophysics, Center for Cellular Construction, University of California, San Francisco, CA 94158, USA
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