151
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Alamos S, Reimer A, Niyogi KK, Garcia HG. Quantitative imaging of RNA polymerase II activity in plants reveals the single-cell basis of tissue-wide transcriptional dynamics. NATURE PLANTS 2021; 7:1037-1049. [PMID: 34373604 PMCID: PMC8616715 DOI: 10.1038/s41477-021-00976-0] [Citation(s) in RCA: 26] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/15/2020] [Accepted: 06/22/2021] [Indexed: 05/18/2023]
Abstract
The responses of plants to their environment are often dependent on the spatiotemporal dynamics of transcriptional regulation. While live-imaging tools have been used extensively to quantitatively capture rapid transcriptional dynamics in living animal cells, the lack of implementation of these technologies in plants has limited concomitant quantitative studies in this kingdom. Here, we applied the PP7 and MS2 RNA-labelling technologies for the quantitative imaging of RNA polymerase II activity dynamics in single cells of living plants as they respond to experimental treatments. Using this technology, we counted nascent RNA transcripts in real time in Nicotiana benthamiana (tobacco) and Arabidopsis thaliana. Examination of heat shock reporters revealed that plant tissues respond to external signals by modulating the proportion of cells that switch from an undetectable basal state to a high-transcription state, instead of modulating the rate of transcription across all cells in a graded fashion. This switch-like behaviour, combined with cell-to-cell variability in transcription rate, results in mRNA production variability spanning three orders of magnitude. We determined that cellular heterogeneity stems mainly from stochasticity intrinsic to individual alleles instead of variability in cellular composition. Together, our results demonstrate that it is now possible to quantitatively study the dynamics of transcriptional programs in single cells of living plants.
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Affiliation(s)
- Simon Alamos
- Department of Plant and Microbial Biology, University of California Berkeley, Berkeley, CA, USA
| | - Armando Reimer
- Biophysics Graduate Group, University of California Berkeley, Berkeley, CA, USA
| | - Krishna K Niyogi
- Department of Plant and Microbial Biology, University of California Berkeley, Berkeley, CA, USA.
- Howard Hughes Medical Institute, University of California Berkeley, Berkeley, CA, USA.
- Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA.
| | - Hernan G Garcia
- Biophysics Graduate Group, University of California Berkeley, Berkeley, CA, USA.
- Department of Molecular and Cell Biology, University of California Berkeley, Berkeley, CA, USA.
- Department of Physics, University of California Berkeley, Berkeley, CA, USA.
- Institute for Quantitative Biosciences-QB3, University of California Berkeley, Berkeley, CA, USA.
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152
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Diaz-Muñoz MD, Osma-Garcia IC. The RNA regulatory programs that govern lymphocyte development and function. WILEY INTERDISCIPLINARY REVIEWS-RNA 2021; 13:e1683. [PMID: 34327847 DOI: 10.1002/wrna.1683] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/03/2021] [Revised: 05/25/2021] [Accepted: 07/08/2021] [Indexed: 12/16/2022]
Abstract
Lymphocytes require of constant and dynamic changes in their transcriptome for timely activation and production of effector molecules to combat external pathogens. Synthesis and translation of messenger (m)RNAs into these effector proteins is controlled both quantitatively and qualitatively by RNA binding proteins (RBPs). RBP-dependent regulation of RNA editing, subcellular location, stability, and translation shapes immune cell development and immunity. Extensive evidences have now been gathered from few model RBPs, HuR, PTBP1, ZFP36, and Roquin. However, recently developed methodologies for global characterization of protein:RNA interactions suggest the existence of complex RNA regulatory networks in which RBPs co-ordinately regulate the fate of sets of RNAs controlling cellular pathways and functions. In turn, RNA can also act as scaffolding of functionally related proteins modulating their activation and function. Here we review current knowledge about how RBP-dependent regulation of RNA shapes our immune system and discuss about the existence of a hidden immune cell epitranscriptome. This article is categorized under: RNA Interactions with Proteins and Other Molecules > Protein-RNA Interactions: Functional Implications.
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Affiliation(s)
- Manuel D Diaz-Muñoz
- Toulouse Institute for Infectious and Inflammatory Diseases, Inserm UMR1291, CNRS UMR5051, University Paul Sabatier, Toulouse, France
| | - Ines C Osma-Garcia
- Toulouse Institute for Infectious and Inflammatory Diseases, Inserm UMR1291, CNRS UMR5051, University Paul Sabatier, Toulouse, France
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153
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Metastable biomolecular condensates of interferon-inducible antiviral Mx-family GTPases: A paradigm shift in the last three years. J Biosci 2021. [PMID: 34323222 PMCID: PMC8319588 DOI: 10.1007/s12038-021-00187-x] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/04/2022]
Abstract
Membraneless organelles (MLOs) in the cytoplasm and nucleus in the form of phase-separated biomolecular condensates are increasingly viewed as critical in regulating diverse cellular functions. We summarize a paradigm shift over the last 3 years in the field of interferon (IFN)-inducible antiviral Mx-family GTPases. Expression of the ‘myxovirus resistance proteins’ MxA in human cells and its ortholog Mx1 in murine cells is increased 50- to 100-fold by Type I (IFN-α and -β) and III IFNs (IFN-λ). Human MxA forms cytoplasmic structures, while murine Mx1 forms nuclear bodies. Since 2002, it has been widely thought that human (Hu) MxA is associated with the membraneous smooth endoplasmic reticulum (ER). In a paradigm shift, our recent data showed that HuMxA formed membraneless phase-separated biomolecular condensates in the cytoplasm. Some of the HuMxA condensates adhered to intermediate filaments generating a reticular pattern. Murine (Mu) Mx1, which was predominantly nuclear, was also confirmed to be in phase-separated nuclear biomolecular condensates. A subset of Huh7 cells showed association of GFP-MuMx1 with intermediate filaments in the cytoplasm. While cells with cytoplasmic GFP-HuMxA condensates and cytoplasmic GFP-MuMx1 filaments showed an antiviral phenotype towards vesicular stomatitis virus (VSV), those with only nuclear GFP-MuMx1 bodies did not. The new data bring forward the paradigm that both human MxA and murine Mx1 give rise to phase-separated biomolecular condensates, albeit in different subcellular compartments, and that differences in the subcellular localization of condensates of different Mx proteins determines the spectrum of their antiviral activity.
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154
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Busche M, Scarpin MR, Hnasko R, Brunkard JO. TOR coordinates nucleotide availability with ribosome biogenesis in plants. THE PLANT CELL 2021; 33:1615-1632. [PMID: 33793860 PMCID: PMC8254494 DOI: 10.1093/plcell/koab043] [Citation(s) in RCA: 32] [Impact Index Per Article: 10.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/03/2020] [Accepted: 01/29/2021] [Indexed: 05/10/2023]
Abstract
TARGET OF RAPAMYCIN (TOR) is a conserved eukaryotic Ser/Thr protein kinase that coordinates growth and metabolism with nutrient availability. We conducted a medium-throughput functional genetic screen to discover essential genes that promote TOR activity in plants, and identified a critical regulatory enzyme, cytosolic phosphoribosyl pyrophosphate (PRPP) synthetase (PRS4). PRS4 synthesizes cytosolic PRPP, a key upstream metabolite in nucleotide synthesis and salvage pathways. We found that prs4 knockouts are embryo-lethal in Arabidopsis thaliana, and that silencing PRS4 expression in Nicotiana benthamiana causes pleiotropic developmental phenotypes, including dwarfism, aberrant leaf shape, and delayed flowering. Transcriptomic analysis revealed that ribosome biogenesis is among the most strongly repressed processes in prs4 knockdowns. Building on these results, we discovered that TOR activity is inhibited by chemical or genetic disruption of nucleotide biosynthesis, but that this effect can be reversed by supplying plants with nucleobases. Finally, we show that TOR transcriptionally promotes nucleotide biosynthesis to support the demands of ribosomal RNA synthesis. We propose that TOR coordinates ribosome biogenesis with nucleotide availability in plants to maintain metabolic homeostasis and support growth.
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Affiliation(s)
- Michael Busche
- Department of Plant and Microbial Biology, University of California, Berkeley, CA 94720, USA
- Plant Gene Expression Center, USDA Agricultural Research Service, Albany, CA 94710, USA
| | - M Regina Scarpin
- Department of Plant and Microbial Biology, University of California, Berkeley, CA 94720, USA
- Plant Gene Expression Center, USDA Agricultural Research Service, Albany, CA 94710, USA
| | - Robert Hnasko
- Produce Safety and Microbiology Research Unit, Western Regional Research Center, Pacific West Area, USDA Agricultural Research Service, Albany, CA 94710,USA
| | - Jacob O Brunkard
- Department of Plant and Microbial Biology, University of California, Berkeley, CA 94720, USA
- Plant Gene Expression Center, USDA Agricultural Research Service, Albany, CA 94710, USA
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155
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Chang BJ, Manton JD, Sapoznik E, Pohlkamp T, Terrones TS, Welf ES, Murali VS, Roudot P, Hake K, Whitehead L, York AG, Dean KM, Fiolka R. Real-time multi-angle projection imaging of biological dynamics. Nat Methods 2021; 18:829-834. [PMID: 34183831 PMCID: PMC9206531 DOI: 10.1038/s41592-021-01175-7] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2020] [Accepted: 05/05/2021] [Indexed: 02/03/2023]
Abstract
We introduce a cost-effective and easily implementable scan unit that converts any camera-based microscope with optical sectioning capability into a multi-angle projection imaging system. Projection imaging reduces data overhead and accelerates imaging by a factor of >100, while also allowing users to readily view biological phenomena of interest from multiple perspectives on the fly. By rapidly interrogating the sample from just two perspectives, our method also enables real-time stereoscopic imaging and three-dimensional particle localization. We demonstrate projection imaging with spinning disk confocal, lattice light-sheet, multidirectional illumination light-sheet and oblique plane microscopes on specimens that range from organelles in single cells to the vasculature of a zebrafish embryo. Furthermore, we leverage our projection method to rapidly image cancer cell morphodynamics and calcium signaling in cultured neurons at rates up to 119 Hz as well as to simultaneously image orthogonal views of a beating embryonic zebrafish heart.
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Affiliation(s)
- Bo-Jui Chang
- Department of Cell Biology, University of Texas Southwestern Medical Center, Dallas, TX, USA
| | | | - Etai Sapoznik
- Department of Cell Biology, University of Texas Southwestern Medical Center, Dallas, TX, USA
| | - Theresa Pohlkamp
- Department of Molecular Genetics, UT Southwestern Medical Center, Dallas, TX, USA
| | - Tamara S Terrones
- Department of Molecular Genetics, UT Southwestern Medical Center, Dallas, TX, USA
| | - Erik S Welf
- Department of Cell Biology, University of Texas Southwestern Medical Center, Dallas, TX, USA
- Lyda Hill Department of Bioinformatics, University of Texas Southwestern Medical Center, Dallas, TX, USA
| | - Vasanth S Murali
- Department of Cell Biology, University of Texas Southwestern Medical Center, Dallas, TX, USA
- Lyda Hill Department of Bioinformatics, University of Texas Southwestern Medical Center, Dallas, TX, USA
| | - Philippe Roudot
- Lyda Hill Department of Bioinformatics, University of Texas Southwestern Medical Center, Dallas, TX, USA
| | - Kayley Hake
- Calico Life Sciences LLC, South San Francisco, CA, USA
| | - Lachlan Whitehead
- Walter and Eliza Hall Institute of Medical Research, Parkville, Victoria, Australia
- Department of Medical Biology, University of Melbourne, Parkville, Victoria, Australia
| | - Andrew G York
- Calico Life Sciences LLC, South San Francisco, CA, USA
| | - Kevin M Dean
- Department of Cell Biology, University of Texas Southwestern Medical Center, Dallas, TX, USA
- Lyda Hill Department of Bioinformatics, University of Texas Southwestern Medical Center, Dallas, TX, USA
| | - Reto Fiolka
- Department of Cell Biology, University of Texas Southwestern Medical Center, Dallas, TX, USA.
- Lyda Hill Department of Bioinformatics, University of Texas Southwestern Medical Center, Dallas, TX, USA.
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156
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Vweza AO, Song CG, Chong KT. Liquid-Liquid Phase Separation in the Presence of Macromolecular Crowding and State-dependent Kinetics. Int J Mol Sci 2021; 22:6675. [PMID: 34206440 PMCID: PMC8268629 DOI: 10.3390/ijms22136675] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2021] [Revised: 06/13/2021] [Accepted: 06/14/2021] [Indexed: 12/27/2022] Open
Abstract
Biomolecular condensates formed via liquid-liquid phase separation (LLPS) are increasingly being shown to play major roles in cellular self-organization dynamics in health and disease. It is well established that macromolecular crowding has a profound impact on protein interactions, particularly those that lead to LLPS. Although synthetic crowding agents are used during in vitro LLPS experiments, they are considerably different from the highly crowded nucleo-/cytoplasm and the effects of in vivo crowding remain poorly understood. In this work, we applied computational modeling to investigate the effects of macromolecular crowding on LLPS. To include biologically relevant LLPS dynamics, we extended the conventional Cahn-Hilliard model for phase separation by coupling it to experimentally derived macromolecular crowding dynamics and state-dependent reaction kinetics. Through extensive field-theoretic computer simulations, we show that the inclusion of macromolecular crowding results in late-stage coarsening and the stabilization of relatively smaller condensates. At a high crowding concentration, there is an accelerated growth and late-stage arrest of droplet formation, effectively resulting in anomalous labyrinthine morphologies akin to protein gelation observed in experiments. These results not only elucidate the crowder effects observed in experiments, but also highlight the importance of including state-dependent kinetics in LLPS models, and may help in designing further experiments to probe the intricate roles played by LLPS in self-organization dynamics of cells.
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Affiliation(s)
- Alick-O. Vweza
- Department of Electronics and Information Engineering, Jeonbuk National University, Jeonju 54896, Korea; (A.-O.V.); (C.-G.S.)
| | - Chul-Gyu Song
- Department of Electronics and Information Engineering, Jeonbuk National University, Jeonju 54896, Korea; (A.-O.V.); (C.-G.S.)
- Advanced Biomedical Imaging Center, Jeonbuk National University, Jeonju 54896, Korea
| | - Kil-To Chong
- Department of Electronics and Information Engineering, Jeonbuk National University, Jeonju 54896, Korea; (A.-O.V.); (C.-G.S.)
- Advanced Electronics and Information Research Center, Jeonbuk National University, Jeonju 54896, Korea
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157
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Di-Luoffo M, Ben-Meriem Z, Lefebvre P, Delarue M, Guillermet-Guibert J. PI3K functions as a hub in mechanotransduction. Trends Biochem Sci 2021; 46:878-888. [PMID: 34112586 DOI: 10.1016/j.tibs.2021.05.005] [Citation(s) in RCA: 21] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2021] [Revised: 04/22/2021] [Accepted: 05/12/2021] [Indexed: 01/18/2023]
Abstract
Mammalian cells integrate different types of stimuli that govern their fate. These stimuli encompass biochemical as well as biomechanical cues (shear, tensile, and compressive stresses) that are usually studied separately. The phosphatidylinositol 3-kinase (PI3K) enzymes, producing signaling phosphoinositides at plasma and intracellular membranes, are key in intracellular signaling and vesicular trafficking pathways. Recent evidence in cancer research demonstrates that these enzymes are essential in mechanotransduction. Despite this, the importance of the integration of biomechanical cues and PI3K-driven biochemical signals is underestimated. In this opinion article, we make the hypothesis that modeling of biomechanical cues is critical to understand PI3K oncogenicity. We also identify known/missing knowledge in terms of isoform specificity and molecular pathways of activation, knowledge that is needed for clinical applications.
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Affiliation(s)
- M Di-Luoffo
- Centre de Recherches en Cancérologie de Toulouse (CRCT), Université de Toulouse, Institut National de la Santé et de la Recherche Médicale (Inserm) U1037, Centre National de la Recherche Scientifique (CNRS) U5071, Toulouse, France; Laboratoire D'analyse et D'architectures Des Systems (LAAS)-CNRS (Centre National de la Recherche Scientifique), Toulouse, France
| | - Z Ben-Meriem
- Centre de Recherches en Cancérologie de Toulouse (CRCT), Université de Toulouse, Institut National de la Santé et de la Recherche Médicale (Inserm) U1037, Centre National de la Recherche Scientifique (CNRS) U5071, Toulouse, France; Laboratoire D'analyse et D'architectures Des Systems (LAAS)-CNRS (Centre National de la Recherche Scientifique), Toulouse, France
| | - P Lefebvre
- Centre de Recherches en Cancérologie de Toulouse (CRCT), Université de Toulouse, Institut National de la Santé et de la Recherche Médicale (Inserm) U1037, Centre National de la Recherche Scientifique (CNRS) U5071, Toulouse, France; Laboratoire D'analyse et D'architectures Des Systems (LAAS)-CNRS (Centre National de la Recherche Scientifique), Toulouse, France
| | - M Delarue
- Centre de Recherches en Cancérologie de Toulouse (CRCT), Université de Toulouse, Institut National de la Santé et de la Recherche Médicale (Inserm) U1037, Centre National de la Recherche Scientifique (CNRS) U5071, Toulouse, France; Laboratoire D'analyse et D'architectures Des Systems (LAAS)-CNRS (Centre National de la Recherche Scientifique), Toulouse, France
| | - J Guillermet-Guibert
- Centre de Recherches en Cancérologie de Toulouse (CRCT), Université de Toulouse, Institut National de la Santé et de la Recherche Médicale (Inserm) U1037, Centre National de la Recherche Scientifique (CNRS) U5071, Toulouse, France; TouCAN (Laboratoire d'Excellence Toulouse Cancer), Toulouse, France.
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158
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Li Y, Tang W, Guo M. The Cell as Matter: Connecting Molecular Biology to Cellular Functions. MATTER 2021; 4:1863-1891. [PMID: 35495565 PMCID: PMC9053450 DOI: 10.1016/j.matt.2021.03.013] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/12/2023]
Abstract
Viewing cell as matter to understand the intracellular biomolecular processes and multicellular tissue behavior represents an emerging research area at the interface of physics and biology. Cellular material displays various physical and mechanical properties, which can strongly affect both intracellular and multicellular biological events. This review provides a summary of how cells, as matter, connect molecular biology to cellular and multicellular scale functions. As an impact in molecular biology, we review recent progresses in utilizing cellular material properties to direct cell fate decisions in the communities of immune cells, neurons, stem cells, and cancer cells. Finally, we provide an outlook on how to integrate cellular material properties in developing biophysical methods for engineered living systems, regenerative medicine, and disease treatments.
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Affiliation(s)
- Yiwei Li
- Department of Mechanical Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Wenhui Tang
- Department of Mechanical Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Ming Guo
- Department of Mechanical Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
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159
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Iwakawa HO, Lam AYW, Mine A, Fujita T, Kiyokawa K, Yoshikawa M, Takeda A, Iwasaki S, Tomari Y. Ribosome stalling caused by the Argonaute-microRNA-SGS3 complex regulates the production of secondary siRNAs in plants. Cell Rep 2021; 35:109300. [PMID: 34192539 DOI: 10.1016/j.celrep.2021.109300] [Citation(s) in RCA: 28] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2021] [Revised: 04/10/2021] [Accepted: 06/03/2021] [Indexed: 12/31/2022] Open
Abstract
The path of ribosomes on mRNAs can be impeded by various obstacles. One such example is halting of ribosome movement by microRNAs, but the exact mechanism and physiological role remain unclear. Here, we find that ribosome stalling caused by the Argonaute-microRNA-SGS3 complex regulates production of secondary small interfering RNAs (siRNAs) in plants. We show that the double-stranded RNA-binding protein SGS3 interacts directly with the 3' end of the microRNA in an Argonaute protein, resulting in ribosome stalling. Importantly, microRNA-mediated ribosome stalling correlates positively with efficient production of secondary siRNAs from target mRNAs. Our results illustrate a role of paused ribosomes in regulation of small RNA function that may have broad biological implications across the plant kingdom.
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Affiliation(s)
- Hiro-Oki Iwakawa
- Laboratory of RNA Function, Institute for Quantitative Biosciences, The University of Tokyo, Bunkyo-ku, Tokyo 113-0032, Japan; JST, PRESTO, Kawaguchi, Saitama 332-0012, Japan.
| | - Andy Y W Lam
- Laboratory of RNA Function, Institute for Quantitative Biosciences, The University of Tokyo, Bunkyo-ku, Tokyo 113-0032, Japan; Department of Computational Biology and Medical Sciences, Graduate School of Frontier Sciences, The University of Tokyo, Bunkyo-ku, Tokyo 113-0032, Japan
| | - Akira Mine
- JST, PRESTO, Kawaguchi, Saitama 332-0012, Japan; Department of Biotechnology, Graduate School of Life Sciences, Ritsumeikan University, Kusatsu, Shiga 525-8577, Japan
| | - Tomoya Fujita
- RNA Systems Biochemistry Laboratory, RIKEN Cluster for Pioneering Research, Wako, Saitama 351-0198, Japan; School of Life Science and Technology, Tokyo Institute of Technology, Midori-ku, Kanagawa 226-8503, Japan
| | - Kaori Kiyokawa
- Laboratory of RNA Function, Institute for Quantitative Biosciences, The University of Tokyo, Bunkyo-ku, Tokyo 113-0032, Japan
| | - Manabu Yoshikawa
- Division of Crop Growth Mechanism, Research Institute of Agrobiological Sciences, National Agriculture and Food Research Organization, Tsukuba, Ibaraki 305-8518, Japan
| | - Atsushi Takeda
- Department of Biotechnology, Graduate School of Life Sciences, Ritsumeikan University, Kusatsu, Shiga 525-8577, Japan
| | - Shintaro Iwasaki
- Department of Computational Biology and Medical Sciences, Graduate School of Frontier Sciences, The University of Tokyo, Bunkyo-ku, Tokyo 113-0032, Japan; RNA Systems Biochemistry Laboratory, RIKEN Cluster for Pioneering Research, Wako, Saitama 351-0198, Japan
| | - Yukihide Tomari
- Laboratory of RNA Function, Institute for Quantitative Biosciences, The University of Tokyo, Bunkyo-ku, Tokyo 113-0032, Japan; Department of Computational Biology and Medical Sciences, Graduate School of Frontier Sciences, The University of Tokyo, Bunkyo-ku, Tokyo 113-0032, Japan
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160
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Self-assembly of protein superstructures by physical interactions under cytoplasm-like conditions. Biophys J 2021; 120:2701-2709. [PMID: 34022233 DOI: 10.1016/j.bpj.2021.05.007] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2021] [Revised: 04/20/2021] [Accepted: 05/13/2021] [Indexed: 11/21/2022] Open
Abstract
The structure-driven assembly of multimeric protein complexes and the formation of intracellular phase-like protein condensates have been the subject of intense research. However, the assembly of larger superstructures comprising cellular components, such as protein nanoparticles driven by general physical rather than specific biochemical interactions, remains relatively uncharacterized. Here, we use gas vesicles (GVs)-genetically encoded protein nanoparticles that form ordered intracellular clusters-as a model system to study the forces driving multiparticle assembly under cytoplasm-like conditions. Our calculations and experimental results show that the ordered assembly of GVs can be achieved by screening their mutual electrostatic repulsion with electrolytes and creating a crowding force with dissolved macromolecules. The precise balance of these forces results in different packing configurations. Biomacromolecules such as polylysine and DNA are capable of driving GV clustering. These results provide basic insights into how physically driven interactions affect the formation of protein superstructures, offer guidance for manipulating nanoparticle assembly in cellular environments through synthetic biology methods, and inform research on the biotechnology applications of GVs.
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161
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Vajrala VS, Alric B, Laborde A, Colin C, Suraniti E, Temple-Boyer P, Arbault S, Delarue M, Launay J. Microwell Array Based Opto-Electrochemical Detections Revealing Co-Adaptation of Rheological Properties and Oxygen Metabolism in Budding Yeast. Adv Biol (Weinh) 2021; 5:e2100484. [PMID: 33969641 DOI: 10.1002/adbi.202100484] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2021] [Revised: 03/29/2021] [Indexed: 11/08/2022]
Abstract
Microdevices composed of microwell arrays integrating nanoelectrodes (OptoElecWell) are developed to achieve dual high-resolution optical and electrochemical detections on single Saccharomyces cerevisiae yeast cells. Each array consists of 1.6 × 105 microwells measuring 8 µm in diameter and 5 µm height, with a platinum nanoring electrode for in situ electrochemistry, all integrated on a transparent thin wafer for further high-resolution live-cell imaging. After optimizing the filling rate, 32% of cells are effectively trapped within microwells. This allows to analyse S. cerevisiae metabolism associated with basal respiration while simultaneously measuring optically other cellular parameters. In this study, the impact of glucose concentration on respiration and intracellular rheology is focused. It is found that while the oxygen uptake rate decreases with increasing glucose concentration, diffusion of tracer nanoparticles increases. The OptoElecWell-based respiration methodology provides similar results compared to the commercial gold-standard Seahorse XF analyzer, while using 20 times fewer biological samples, paving the way to achieve single cell metabolomics. In addition, it facilitates an optical route to monitor the contents within single cells. The proposed device, in combination with the dual detection analysis, opens up new avenues for measuring cellular metabolism, and relating it to cellular physiological indicators at single cell level.
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Affiliation(s)
| | - Baptiste Alric
- CNRS, LAAS, 7 avenue du colonel Roche, Toulouse, F-31400, France.,Université de Toulouse, UPS, LAAS, Toulouse, F-31400, France
| | - Adrian Laborde
- CNRS, LAAS, 7 avenue du colonel Roche, Toulouse, F-31400, France.,Université de Toulouse, UPS, LAAS, Toulouse, F-31400, France
| | - Camille Colin
- Univ. Bordeaux, ISM, CNRS UMR 5255, INP Bordeaux, Pessac, 33607, France
| | - Emmanuel Suraniti
- Univ. Bordeaux, ISM, CNRS UMR 5255, INP Bordeaux, Pessac, 33607, France
| | | | - Stephane Arbault
- Univ. Bordeaux, ISM, CNRS UMR 5255, INP Bordeaux, Pessac, 33607, France
| | - Morgan Delarue
- CNRS, LAAS, 7 avenue du colonel Roche, Toulouse, F-31400, France
| | - Jérôme Launay
- CNRS, LAAS, 7 avenue du colonel Roche, Toulouse, F-31400, France.,Université de Toulouse, UPS, LAAS, Toulouse, F-31400, France
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162
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Lenne PF, Munro E, Heemskerk I, Warmflash A, Bocanegra-Moreno L, Kishi K, Kicheva A, Long Y, Fruleux A, Boudaoud A, Saunders TE, Caldarelli P, Michaut A, Gros J, Maroudas-Sacks Y, Keren K, Hannezo E, Gartner ZJ, Stormo B, Gladfelter A, Rodrigues A, Shyer A, Minc N, Maître JL, Di Talia S, Khamaisi B, Sprinzak D, Tlili S. Roadmap for the multiscale coupling of biochemical and mechanical signals during development. Phys Biol 2021; 18. [PMID: 33276350 PMCID: PMC8380410 DOI: 10.1088/1478-3975/abd0db] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2020] [Accepted: 12/04/2020] [Indexed: 12/12/2022]
Abstract
The way in which interactions between mechanics and biochemistry lead to the emergence of complex cell and tissue organization is an old question that has recently attracted renewed interest from biologists, physicists, mathematicians and computer scientists. Rapid advances in optical physics, microscopy and computational image analysis have greatly enhanced our ability to observe and quantify spatiotemporal patterns of signalling, force generation, deformation, and flow in living cells and tissues. Powerful new tools for genetic, biophysical and optogenetic manipulation are allowing us to perturb the underlying machinery that generates these patterns in increasingly sophisticated ways. Rapid advances in theory and computing have made it possible to construct predictive models that describe how cell and tissue organization and dynamics emerge from the local coupling of biochemistry and mechanics. Together, these advances have opened up a wealth of new opportunities to explore how mechanochemical patterning shapes organismal development. In this roadmap, we present a series of forward-looking case studies on mechanochemical patterning in development, written by scientists working at the interface between the physical and biological sciences, and covering a wide range of spatial and temporal scales, organisms, and modes of development. Together, these contributions highlight the many ways in which the dynamic coupling of mechanics and biochemistry shapes biological dynamics: from mechanoenzymes that sense force to tune their activity and motor output, to collectives of cells in tissues that flow and redistribute biochemical signals during development.
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Affiliation(s)
- Pierre-François Lenne
- Aix-Marseille University, CNRS, IBDM, Turing Center for Living Systems, Marseille, France
| | - Edwin Munro
- Department of Molecular Genetics and Cell Biology, University of Chicago, Chicago, IL 60637, United States of America
| | - Idse Heemskerk
- Department of Cell & Developmental Biology, University of Michigan Medical School, Ann Arbor, MI 48109, United States of America
| | - Aryeh Warmflash
- Department of Biosciences and Bioengineering, Rice University, Houston, TX, 77005, United States of America
| | | | - Kasumi Kishi
- IST Austria, Am Campus 1, 3400 Klosterneuburg, Austria
| | - Anna Kicheva
- IST Austria, Am Campus 1, 3400 Klosterneuburg, Austria
| | - Yuchen Long
- Reproduction et Dévelopement des Plantes, Université de Lyon, École normale supérieure de Lyon, Université Claude Bernard Lyon 1, INRAe, CNRS, 69364 Lyon Cedex 07, France
| | - Antoine Fruleux
- Reproduction et Dévelopement des Plantes, Université de Lyon, École normale supérieure de Lyon, Université Claude Bernard Lyon 1, INRAe, CNRS, 69364 Lyon Cedex 07, France.,LadHyX, CNRS, Ecole polytechnique, Institut Polytechnique de Paris, 91128 Palaiseau Cedex, France
| | - Arezki Boudaoud
- Reproduction et Dévelopement des Plantes, Université de Lyon, École normale supérieure de Lyon, Université Claude Bernard Lyon 1, INRAe, CNRS, 69364 Lyon Cedex 07, France.,LadHyX, CNRS, Ecole polytechnique, Institut Polytechnique de Paris, 91128 Palaiseau Cedex, France
| | - Timothy E Saunders
- Mechanobiology Institute, National University of Singapore, 117411, Singapore
| | - Paolo Caldarelli
- Cellule Pasteur UPMC, Sorbonne Université, rue du Dr Roux, 75015 Paris, France.,Department of Developmental and Stem Cell Biology Institut Pasteur, 75724 Paris, Cedex 15, France.,CNRS UMR3738, 75015 Paris, France
| | - Arthur Michaut
- Department of Developmental and Stem Cell Biology Institut Pasteur, 75724 Paris, Cedex 15, France.,CNRS UMR3738, 75015 Paris, France
| | - Jerome Gros
- Department of Developmental and Stem Cell Biology Institut Pasteur, 75724 Paris, Cedex 15, France.,CNRS UMR3738, 75015 Paris, France
| | - Yonit Maroudas-Sacks
- Department of Physics, Technion-Israel Institute of Technology, Haifa 32000, Israel
| | - Kinneret Keren
- Department of Physics, Technion-Israel Institute of Technology, Haifa 32000, Israel.,Network Biology Research Laboratories and The Russell Berrie Nanotechnology Institute, Technion-Israel Institute of Technology, Haifa 32000, Israel
| | - Edouard Hannezo
- Institute of Science and Technology Austria, Am Campus 1, 3400 Klosterneuburg, Austria
| | - Zev J Gartner
- Department of Pharmaceutical Chemistry, University of California, San Francisco, 600 16th St. Box 2280, San Francisco, CA 94158, United States of America
| | - Benjamin Stormo
- Department of Biology, University of North Carolina-Chapel Hill, Chapel Hill, NC 27599 United States of America
| | - Amy Gladfelter
- Department of Biology, University of North Carolina-Chapel Hill, Chapel Hill, NC 27599 United States of America
| | - Alan Rodrigues
- Laboratory of Morphogenesis, The Rockefeller University, 1230 York Avenue, New York, NY 10065, United States of America
| | - Amy Shyer
- Laboratory of Morphogenesis, The Rockefeller University, 1230 York Avenue, New York, NY 10065, United States of America
| | - Nicolas Minc
- Institut Jacques Monod, Université de Paris, CNRS UMR7592, 15 rue Hélène Brion, 75205 Paris Cedex 13, France
| | - Jean-Léon Maître
- Institut Curie, PSL Research University, Sorbonne Université, CNRS UMR3215, INSERM U934, Paris, France
| | - Stefano Di Talia
- Department of Cell Biology, Duke University Medical Center, Durham NC 27710, United States of America
| | - Bassma Khamaisi
- School of Neurobiology, Biochemistry and Biophysics, George S. Wise Faculty of Life Sciences, Tel Aviv University, Tel Aviv 6997801, Israel
| | - David Sprinzak
- School of Neurobiology, Biochemistry and Biophysics, George S. Wise Faculty of Life Sciences, Tel Aviv University, Tel Aviv 6997801, Israel
| | - Sham Tlili
- Aix-Marseille University, CNRS, IBDM, Turing Center for Living Systems, Marseille, France
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163
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Evers TMJ, Holt LJ, Alberti S, Mashaghi A. Reciprocal regulation of cellular mechanics and metabolism. Nat Metab 2021; 3:456-468. [PMID: 33875882 PMCID: PMC8863344 DOI: 10.1038/s42255-021-00384-w] [Citation(s) in RCA: 36] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/24/2020] [Accepted: 03/12/2021] [Indexed: 12/12/2022]
Abstract
Metabolism and mechanics are intrinsically intertwined. External forces, sensed through the cytoskeleton or distortion of the cell and organelles, induce metabolic changes in the cell. The resulting changes in metabolism, in turn, feed back to regulate every level of cell biology, including the mechanical properties of cells and tissues. Here we examine the links between metabolism and mechanics, highlighting signalling pathways involved in the regulation and response to cellular mechanosensing. We consider how forces and metabolism regulate one another through nanoscale molecular sensors, micrometre-scale cytoskeletal networks, organelles and dynamic biomolecular condensates. Understanding this cross-talk will create diagnostic and therapeutic opportunities for metabolic disorders such as cancer, cardiovascular pathologies and obesity.
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Affiliation(s)
- Tom M J Evers
- Medical Systems Biophysics and Bioengineering, Leiden Academic Centre for Drug Research, Faculty of Science, Leiden University, Leiden, the Netherlands
| | - Liam J Holt
- Institute for Systems Genetics, New York University Langone Health, New York, NY, USA
| | - Simon Alberti
- Max Planck Institute of Molecular Cell Biology and Genetics, Dresden, Germany
| | - Alireza Mashaghi
- Medical Systems Biophysics and Bioengineering, Leiden Academic Centre for Drug Research, Faculty of Science, Leiden University, Leiden, the Netherlands.
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164
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Schuster BS, Regy RM, Dolan EM, Kanchi Ranganath A, Jovic N, Khare SD, Shi Z, Mittal J. Biomolecular Condensates: Sequence Determinants of Phase Separation, Microstructural Organization, Enzymatic Activity, and Material Properties. J Phys Chem B 2021; 125:3441-3451. [PMID: 33661634 DOI: 10.1021/acs.jpcb.0c11606] [Citation(s) in RCA: 37] [Impact Index Per Article: 12.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
This perspective article highlights recent progress and emerging challenges in understanding the formation and function of membraneless organelles (MLOs). A long-term goal in the MLO field is to identify the sequence-encoded rules that dictate the formation of compositionally controlled biomolecular condensates, which cells utilize to perform a wide variety of functions. The molecular organization of the different components within a condensate can vary significantly, ranging from a homogeneous mixture to core-shell droplet structures. We provide many examples to highlight the richness of the observed behavior and potential research directions for improving our mechanistic understanding. The tunable environment within condensates can, in principle, alter enzymatic activity significantly. We examine recent examples where this was demonstrated, including applications in synthetic biology. An important question about MLOs is the role of liquid-like material properties in biological function. We discuss the need for improved quantitative characterization tools and the development of sequence-structure-dynamics relationships.
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Affiliation(s)
- Benjamin S Schuster
- Department of Chemical and Biochemical Engineering, Rutgers University, Piscataway, New Jersey 08854, United States
| | - Roshan Mammen Regy
- Department of Chemical and Biomolecular Engineering, Lehigh University, Bethlehem, Pennsylvania 18015, United States
| | - Elliott M Dolan
- Department of Chemistry and Chemical Biology, Rutgers University, Piscataway, New Jersey 08854, United States.,Institute for Quantitative Biomedicine, Rutgers University, Piscataway, New Jersey 08854, United States
| | - Aishwarya Kanchi Ranganath
- Department of Chemical and Biochemical Engineering, Rutgers University, Piscataway, New Jersey 08854, United States
| | - Nina Jovic
- Department of Chemical and Biomolecular Engineering, Lehigh University, Bethlehem, Pennsylvania 18015, United States
| | - Sagar D Khare
- Department of Chemistry and Chemical Biology, Rutgers University, Piscataway, New Jersey 08854, United States.,Institute for Quantitative Biomedicine, Rutgers University, Piscataway, New Jersey 08854, United States
| | - Zheng Shi
- Department of Chemistry and Chemical Biology, Rutgers University, Piscataway, New Jersey 08854, United States
| | - Jeetain Mittal
- Department of Chemical and Biomolecular Engineering, Lehigh University, Bethlehem, Pennsylvania 18015, United States
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165
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Watanabe K, Morishita K, Zhou X, Shiizaki S, Uchiyama Y, Koike M, Naguro I, Ichijo H. Cells recognize osmotic stress through liquid-liquid phase separation lubricated with poly(ADP-ribose). Nat Commun 2021; 12:1353. [PMID: 33649309 PMCID: PMC7921423 DOI: 10.1038/s41467-021-21614-5] [Citation(s) in RCA: 53] [Impact Index Per Article: 17.7] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2020] [Accepted: 02/02/2021] [Indexed: 12/17/2022] Open
Abstract
Cells are under threat of osmotic perturbation; cell volume maintenance is critical in cerebral edema, inflammation and aging, in which prominent changes in intracellular or extracellular osmolality emerge. After osmotic stress-enforced cell swelling or shrinkage, the cells regulate intracellular osmolality to recover their volume. However, the mechanisms recognizing osmotic stress remain obscured. We previously clarified that apoptosis signal-regulating kinase 3 (ASK3) bidirectionally responds to osmotic stress and regulates cell volume recovery. Here, we show that macromolecular crowding induces liquid-demixing condensates of ASK3 under hyperosmotic stress, which transduce osmosensing signal into ASK3 inactivation. A genome-wide small interfering RNA (siRNA) screen identifies an ASK3 inactivation regulator, nicotinamide phosphoribosyltransferase (NAMPT), related to poly(ADP-ribose) signaling. Furthermore, we clarify that poly(ADP-ribose) keeps ASK3 condensates in the liquid phase and enables ASK3 to become inactivated under hyperosmotic stress. Our findings demonstrate that cells rationally incorporate physicochemical phase separation into their osmosensing systems.
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Affiliation(s)
- Kengo Watanabe
- Laboratory of Cell Signaling, Graduate School of Pharmaceutical Sciences, The University of Tokyo, Tokyo, 113-0033, Japan.
| | - Kazuhiro Morishita
- Laboratory of Cell Signaling, Graduate School of Pharmaceutical Sciences, The University of Tokyo, Tokyo, 113-0033, Japan
| | - Xiangyu Zhou
- Laboratory of Cell Signaling, Graduate School of Pharmaceutical Sciences, The University of Tokyo, Tokyo, 113-0033, Japan
| | - Shigeru Shiizaki
- Laboratory of Cell Signaling, Graduate School of Pharmaceutical Sciences, The University of Tokyo, Tokyo, 113-0033, Japan
| | - Yasuo Uchiyama
- Department of Cellular and Molecular Neuropathology, Juntendo University Graduate School of Medicine, Tokyo, 113-8421, Japan
| | - Masato Koike
- Department of Cell Biology and Neuroscience, Juntendo University Graduate School of Medicine, Tokyo, 113-8421, Japan
| | - Isao Naguro
- Laboratory of Cell Signaling, Graduate School of Pharmaceutical Sciences, The University of Tokyo, Tokyo, 113-0033, Japan
| | - Hidenori Ichijo
- Laboratory of Cell Signaling, Graduate School of Pharmaceutical Sciences, The University of Tokyo, Tokyo, 113-0033, Japan.
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166
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Sun S, Gresham D. Cellular quiescence in budding yeast. Yeast 2021; 38:12-29. [PMID: 33350503 DOI: 10.1002/yea.3545] [Citation(s) in RCA: 31] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2020] [Revised: 12/11/2020] [Accepted: 12/14/2020] [Indexed: 12/20/2022] Open
Abstract
Cellular quiescence, the temporary and reversible exit from proliferative growth, is the predominant state of all cells. However, our understanding of the biological processes and molecular mechanisms that underlie cell quiescence remains incomplete. As with the mitotic cell cycle, budding and fission yeast are preeminent model systems for studying cellular quiescence owing to their rich experimental toolboxes and the evolutionary conservation across eukaryotes of pathways and processes that control quiescence. Here, we review current knowledge of cell quiescence in budding yeast and how it pertains to cellular quiescence in other organisms, including multicellular animals. Quiescence entails large-scale remodeling of virtually every cellular process, organelle, gene expression, and metabolic state that is executed dynamically as cells undergo the initiation, maintenance, and exit from quiescence. We review these major transitions, our current understanding of their molecular bases, and highlight unresolved questions. We summarize the primary methods employed for quiescence studies in yeast and discuss their relative merits. Understanding cell quiescence has important consequences for human disease as quiescent single-celled microbes are notoriously difficult to kill and quiescent human cells play important roles in diseases such as cancer. We argue that research on cellular quiescence will be accelerated through the adoption of common criteria, and methods, for defining cell quiescence. An integrated approach to studying cell quiescence, and a focus on the behavior of individual cells, will yield new insights into the pathways and processes that underlie cell quiescence leading to a more complete understanding of the life cycle of cells. TAKE AWAY: Quiescent cells are viable cells that have reversibly exited the cell cycle Quiescence is induced in response to a variety of nutrient starvation signals Quiescence is executed dynamically through three phases: initiation, maintenance, and exit Quiescence entails large-scale remodeling of gene expression, organelles, and metabolism Single-cell approaches are required to address heterogeneity among quiescent cells.
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Affiliation(s)
- Siyu Sun
- Center for Genomics and Systems Biology, New York University, New York, New York, 10003, USA.,Department of Biology, New York University, New York, New York, 10003, USA
| | - David Gresham
- Center for Genomics and Systems Biology, New York University, New York, New York, 10003, USA.,Department of Biology, New York University, New York, New York, 10003, USA
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167
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Shimizu T, Masuda T. The Role of Tetrapyrrole- and GUN1-Dependent Signaling on Chloroplast Biogenesis. PLANTS 2021; 10:plants10020196. [PMID: 33494334 PMCID: PMC7911674 DOI: 10.3390/plants10020196] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/15/2020] [Revised: 01/15/2021] [Accepted: 01/18/2021] [Indexed: 12/14/2022]
Abstract
Chloroplast biogenesis requires the coordinated expression of the chloroplast and nuclear genomes, which is achieved by communication between the developing chloroplasts and the nucleus. Signals emitted from the plastids, so-called retrograde signals, control nuclear gene expression depending on plastid development and functionality. Genetic analysis of this pathway identified a set of mutants defective in retrograde signaling and designated genomes uncoupled (gun) mutants. Subsequent research has pointed to a significant role of tetrapyrrole biosynthesis in retrograde signaling. Meanwhile, the molecular functions of GUN1, the proposed integrator of multiple retrograde signals, have not been identified yet. However, based on the interactions of GUN1, some working hypotheses have been proposed. Interestingly, GUN1 contributes to important biological processes, including plastid protein homeostasis, through transcription, translation, and protein import. Furthermore, the interactions of GUN1 with tetrapyrroles and their biosynthetic enzymes have been revealed. This review focuses on our current understanding of the function of tetrapyrrole retrograde signaling on chloroplast biogenesis.
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168
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Nosella ML, Forman-Kay JD. Phosphorylation-dependent regulation of messenger RNA transcription, processing and translation within biomolecular condensates. Curr Opin Cell Biol 2021; 69:30-40. [PMID: 33450720 DOI: 10.1016/j.ceb.2020.12.007] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2020] [Revised: 12/09/2020] [Accepted: 12/13/2020] [Indexed: 12/29/2022]
Abstract
Regulation of messenger RNA (mRNA) transcription, processing and translation occurs in the context of biomolecular condensates. How the physical properties of condensates connect with their biological regulatory functions is an ongoing area of interest, particularly for RNA metabolic pathways. Phosphorylation has emerged as an important mechanism for regulating protein phase separation propensities and localization patterns into different condensates, affecting compositions and dynamics. Key factors in transcription, mRNA processing and translation exhibit such phosphorylation-dependent changes in their roles within condensates, including their catalytic activities. Phosphorylation is increasingly understood to regulate the exchange of proteins through functionally linked condensates to fulfil their mRNA metabolic functions.
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Affiliation(s)
- Michael L Nosella
- Molecular Medicine Program, The Hospital for Sick Children, Toronto, ON, M5G 0A4, Canada; Department of Biochemistry, University of Toronto, Toronto, ON, M5S 1A8, Canada
| | - Julie D Forman-Kay
- Molecular Medicine Program, The Hospital for Sick Children, Toronto, ON, M5G 0A4, Canada; Department of Biochemistry, University of Toronto, Toronto, ON, M5S 1A8, Canada.
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169
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Xie Y, Miao Y. Polarisome assembly mediates actin remodeling during polarized yeast and fungal growth. J Cell Sci 2021; 134:134/1/jcs247916. [PMID: 33419950 DOI: 10.1242/jcs.247916] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022] Open
Abstract
Dynamic assembly and remodeling of actin is critical for many cellular processes during development and stress adaptation. In filamentous fungi and budding yeast, actin cables align in a polarized manner along the mother-to-daughter cell axis, and are essential for the establishment and maintenance of polarity; moreover, they rapidly remodel in response to environmental cues to achieve an optimal system response. A formin at the tip region within a macromolecular complex, called the polarisome, is responsible for driving actin cable polymerization during polarity establishment. This polarisome undergoes dynamic assembly through spatial and temporally regulated interactions between its components. Understanding this process is important to comprehend the tuneable activities of the formin-centered nucleation core, which are regulated through divergent molecular interactions and assembly modes within the polarisome. In this Review, we focus on how intrinsically disordered regions (IDRs) orchestrate the condensation of the polarisome components and the dynamic assembly of the complex. In addition, we address how these components are dynamically distributed in and out of the assembly zone, thereby regulating polarized growth. We also discuss the potential mechanical feedback mechanisms by which the force-induced actin polymerization at the tip of the budding yeast regulates the assembly and function of the polarisome.
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Affiliation(s)
- Ying Xie
- School of Biological Sciences, Nanyang Technological University, Singapore 637551, Singapore
| | - Yansong Miao
- School of Biological Sciences, Nanyang Technological University, Singapore 637551, Singapore
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170
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Chauhan G, Simpson ML, Abel SM. Crowding-induced interactions of ring polymers. SOFT MATTER 2021; 17:16-23. [PMID: 33155586 DOI: 10.1039/d0sm01847c] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/11/2023]
Abstract
Macromolecular crowding and the presence of surfaces can significantly impact the spatial organization of biopolymers. While the importance of crowding-induced depletion interactions in biology has been recognized, much remains to be understood about the effect of crowding on biopolymers such as DNA plasmids. A fundamental problem highlighted by recent experiments is to characterize the impact of crowding on polymer-polymer and polymer-surface interactions. Motivated by the need for quantitative insight, we studied flexible ring polymers in crowded environments using Langevin dynamics simulations. The simulations demonstrated that crowding can lead to compaction of isolated ring polymers and enhanced interactions between two otherwise repulsive polymers. Using umbrella sampling, we determined the potential of mean force (PMF) between two ring polymers as a function of their separation distance at different volume fractions of crowding particles, φ. An effective attraction emerged at φ≈ 0.4, which is similar to the degree of crowding in cells. Analogous simulations showed that crowding can lead to strong adsorption of a ring polymer to a wall, with an effective attraction to the wall emerging at a smaller volume fraction of crowders (φ≈ 0.2). Our results reveal the magnitude of depletion interactions in a biologically-inspired model and highlight how crowding can be used to tune interactions in both cellular and cell-free systems.
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Affiliation(s)
- Gaurav Chauhan
- Department of Chemical and Biomolecular Engineering, University of Tennessee, Knoxville, Tennessee 37996, USA.
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171
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Jalihal AP, Schmidt A, Gao G, Little SR, Pitchiaya S, Walter NG. Hyperosmotic phase separation: Condensates beyond inclusions, granules and organelles. J Biol Chem 2021; 296:100044. [PMID: 33168632 PMCID: PMC7948973 DOI: 10.1074/jbc.rev120.010899] [Citation(s) in RCA: 24] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2020] [Revised: 11/06/2020] [Accepted: 11/09/2020] [Indexed: 01/09/2023] Open
Abstract
Biological liquid-liquid phase separation has gained considerable attention in recent years as a driving force for the assembly of subcellular compartments termed membraneless organelles. The field has made great strides in elucidating the molecular basis of biomolecular phase separation in various disease, stress response, and developmental contexts. Many important biological consequences of such "condensation" are now emerging from in vivo studies. Here we review recent work from our group and others showing that many proteins undergo rapid, reversible condensation in the cellular response to ubiquitous environmental fluctuations such as osmotic changes. We discuss molecular crowding as an important driver of condensation in these responses and suggest that a significant fraction of the proteome is poised to undergo phase separation under physiological conditions. In addition, we review methods currently emerging to visualize, quantify, and modulate the dynamics of intracellular condensates in live cells. Finally, we propose a metaphor for rapid phase separation based on cloud formation, reasoning that our familiar experiences with the readily reversible condensation of water droplets help understand the principle of phase separation. Overall, we provide an account of how biological phase separation supports the highly intertwined relationship between the composition and dynamic internal organization of cells, thus facilitating extremely rapid reorganization in response to internal and external fluctuations.
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Affiliation(s)
- Ameya P Jalihal
- Single Molecule Analysis Group and Center for RNA Biomedicine, Department of Chemistry, University of Michigan, Ann Arbor, Michigan, USA; Cell and Molecular Biology Graduate Program, University of Michigan, Ann Arbor, Michigan, USA
| | - Andreas Schmidt
- Single Molecule Analysis Group and Center for RNA Biomedicine, Department of Chemistry, University of Michigan, Ann Arbor, Michigan, USA
| | - Guoming Gao
- Single Molecule Analysis Group and Center for RNA Biomedicine, Department of Chemistry, University of Michigan, Ann Arbor, Michigan, USA; Biophysics Graduate Program, University of Michigan, Ann Arbor, Michigan, USA
| | - Saffron R Little
- Single Molecule Analysis Group and Center for RNA Biomedicine, Department of Chemistry, University of Michigan, Ann Arbor, Michigan, USA; Program in Chemical Biology, University of Michigan, Ann Arbor, Michigan, USA
| | - Sethuramasundaram Pitchiaya
- Michigan Center for Translational Pathology, University of Michigan Medical School, Ann Arbor, Michigan, USA; Department of Pathology, University of Michigan, Ann Arbor, Michigan, USA
| | - Nils G Walter
- Single Molecule Analysis Group and Center for RNA Biomedicine, Department of Chemistry, University of Michigan, Ann Arbor, Michigan, USA.
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172
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Protein Synthesis in the Developing Neocortex at Near-Atomic Resolution Reveals Ebp1-Mediated Neuronal Proteostasis at the 60S Tunnel Exit. Mol Cell 2020; 81:304-322.e16. [PMID: 33357414 DOI: 10.1016/j.molcel.2020.11.037] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2019] [Revised: 09/04/2020] [Accepted: 11/19/2020] [Indexed: 02/07/2023]
Abstract
Protein synthesis must be finely tuned in the developing nervous system as the final essential step of gene expression. This study investigates the architecture of ribosomes from the neocortex during neurogenesis, revealing Ebp1 as a high-occupancy 60S peptide tunnel exit (TE) factor during protein synthesis at near-atomic resolution by cryoelectron microscopy (cryo-EM). Ribosome profiling demonstrated Ebp1-60S binding is highest during start codon initiation and N-terminal peptide elongation, regulating ribosome occupancy of these codons. Membrane-targeting domains emerging from the 60S tunnel, which recruit SRP/Sec61 to the shared binding site, displace Ebp1. Ebp1 is particularly abundant in the early-born neural stem cell (NSC) lineage and regulates neuronal morphology. Ebp1 especially impacts the synthesis of membrane-targeted cell adhesion molecules (CAMs), measured by pulsed stable isotope labeling by amino acids in cell culture (pSILAC)/bioorthogonal noncanonical amino acid tagging (BONCAT) mass spectrometry (MS). Therefore, Ebp1 is a central component of protein synthesis, and the ribosome TE is a focal point of gene expression control in the molecular specification of neuronal morphology during development.
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173
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Sankaranarayanan M, Weil TT. Granule regulation by phase separation during Drosophila oogenesis. Emerg Top Life Sci 2020; 4:343-352. [PMID: 32573699 PMCID: PMC7733668 DOI: 10.1042/etls20190155] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2020] [Revised: 05/29/2020] [Accepted: 06/02/2020] [Indexed: 12/13/2022]
Abstract
Drosophila eggs are highly polarised cells that use RNA-protein complexes to regulate storage and translational control of maternal RNAs. Ribonucleoprotein granules are a class of biological condensates that form predominantly by intracellular phase separation. Despite extensive in vitro studies testing the physical principles regulating condensates, how phase separation translates to biological function remains largely unanswered. In this perspective, we discuss granules in Drosophila oogenesis as a model system for investigating the physiological role of phase separation. We review key maternal granules and their properties while highlighting ribonucleoprotein phase separation behaviours observed during development. Finally, we discuss how concepts and models from liquid-liquid phase separation could be used to test mechanisms underlying granule assembly, regulation and function in Drosophila oogenesis.
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Affiliation(s)
- M Sankaranarayanan
- Department of Zoology, University of Cambridge, Downing Street, Cambridge CB2 3EJ, U.K
| | - Timothy T Weil
- Department of Zoology, University of Cambridge, Downing Street, Cambridge CB2 3EJ, U.K
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174
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Garcia-Seisdedos H, Heidenreich M, Levy ED. Not Going with the Flow: How Cells Adapt Internal Physics. Cell 2020; 183:1462-1463. [PMID: 33306951 DOI: 10.1016/j.cell.2020.11.021] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Defining the principles underlying the organization of biomolecules within cells is a key challenge of current cell biology research. Persson et al. now identify a powerful layer of regulation that allows cells to decouple diffusion from temperature by modulating their intracellular viscosity. This so-called viscoadaptation is mediated through trehalose and glycogen activities, which alter diffusion dynamics and self-assembly propensity inside the cell globally.
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Affiliation(s)
| | - Meta Heidenreich
- Department of Structural Biology, Weizmann Institute of Science, Rehovot, 7610001, Israel
| | - Emmanuel D Levy
- Department of Structural Biology, Weizmann Institute of Science, Rehovot, 7610001, Israel.
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175
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Sapoznik E, Chang BJ, Huh J, Ju RJ, Azarova EV, Pohlkamp T, Welf ES, Broadbent D, Carisey AF, Stehbens SJ, Lee KM, Marín A, Hanker AB, Schmidt JC, Arteaga CL, Yang B, Kobayashi Y, Tata PR, Kruithoff R, Doubrovinski K, Shepherd DP, Millett-Sikking A, York AG, Dean KM, Fiolka RP. A versatile oblique plane microscope for large-scale and high-resolution imaging of subcellular dynamics. eLife 2020; 9:e57681. [PMID: 33179596 PMCID: PMC7707824 DOI: 10.7554/elife.57681] [Citation(s) in RCA: 90] [Impact Index Per Article: 22.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2020] [Accepted: 11/09/2020] [Indexed: 12/31/2022] Open
Abstract
We present an oblique plane microscope (OPM) that uses a bespoke glass-tipped tertiary objective to improve the resolution, field of view, and usability over previous variants. Owing to its high numerical aperture optics, this microscope achieves lateral and axial resolutions that are comparable to the square illumination mode of lattice light-sheet microscopy, but in a user friendly and versatile format. Given this performance, we demonstrate high-resolution imaging of clathrin-mediated endocytosis, vimentin, the endoplasmic reticulum, membrane dynamics, and Natural Killer-mediated cytotoxicity. Furthermore, we image biological phenomena that would be otherwise challenging or impossible to perform in a traditional light-sheet microscope geometry, including cell migration through confined spaces within a microfluidic device, subcellular photoactivation of Rac1, diffusion of cytoplasmic rheological tracers at a volumetric rate of 14 Hz, and large field of view imaging of neurons, developing embryos, and centimeter-scale tissue sections.
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Affiliation(s)
- Etai Sapoznik
- Department of Cell Biology, University of Texas Southwestern Medical CenterDallasUnited States
- Lyda Hill Department of Bioinformatics, University of Texas Southwestern Medical CenterDallasUnited States
| | - Bo-Jui Chang
- Department of Cell Biology, University of Texas Southwestern Medical CenterDallasUnited States
| | - Jaewon Huh
- Department of Cell Biology, University of Texas Southwestern Medical CenterDallasUnited States
- Lyda Hill Department of Bioinformatics, University of Texas Southwestern Medical CenterDallasUnited States
| | - Robert J Ju
- Institute for Molecular Bioscience, University of QueenslandQueenslandAustralia
| | - Evgenia V Azarova
- Department of Cell Biology, University of Texas Southwestern Medical CenterDallasUnited States
| | - Theresa Pohlkamp
- Department of Molecular Genetics, University of Texas Southwestern Medical CenterDallasUnited States
| | - Erik S Welf
- Department of Cell Biology, University of Texas Southwestern Medical CenterDallasUnited States
- Lyda Hill Department of Bioinformatics, University of Texas Southwestern Medical CenterDallasUnited States
| | - David Broadbent
- Institute for Quantitative Health Sciences and Engineering, Michigan State UniversityEast LansingUnited States
| | - Alexandre F Carisey
- William T. Shearer Center for Human Immunobiology, Baylor College of Medicine and Texas Children’s HospitalHoustonUnited States
| | - Samantha J Stehbens
- Institute for Molecular Bioscience, University of QueenslandQueenslandAustralia
| | - Kyung-Min Lee
- Harold C. Simmons Comprehensive Cancer Center and the Department of Internal Medicine, University of Texas Southwestern Medical CenterDallasUnited States
| | - Arnaldo Marín
- Harold C. Simmons Comprehensive Cancer Center and the Department of Internal Medicine, University of Texas Southwestern Medical CenterDallasUnited States
- Department of Basic and Clinical Oncology, Faculty of Medicine, University of ChileSantiagoChile
| | - Ariella B Hanker
- Harold C. Simmons Comprehensive Cancer Center and the Department of Internal Medicine, University of Texas Southwestern Medical CenterDallasUnited States
| | - Jens C Schmidt
- Institute for Quantitative Health Sciences and Engineering, Michigan State UniversityEast LansingUnited States
- Department of Obstetrics, Gynecology, and Reproductive Biology, Michigan State UniversityEast LansingUnited States
| | - Carlos L Arteaga
- Harold C. Simmons Comprehensive Cancer Center and the Department of Internal Medicine, University of Texas Southwestern Medical CenterDallasUnited States
| | - Bin Yang
- Chan Zuckerberg BiohubSan FranciscoUnited States
| | - Yoshihiko Kobayashi
- Department of Cell Biology, Duke University School of MedicineDurhamUnited States
| | | | - Rory Kruithoff
- Center for Biological Physics and Department of Physics, Arizona State UniversityTempeUnited States
| | - Konstantin Doubrovinski
- Department of Cell Biology, University of Texas Southwestern Medical CenterDallasUnited States
- Cecil H. and Ida Green Comprehensive Center for Molecular, Computational and Systems Biology, University of Texas Southwestern Medical CenterDallasUnited States
| | - Douglas P Shepherd
- Center for Biological Physics and Department of Physics, Arizona State UniversityTempeUnited States
| | | | - Andrew G York
- Calico Life Sciences LLCSouth San FranciscoUnited States
| | - Kevin M Dean
- Department of Cell Biology, University of Texas Southwestern Medical CenterDallasUnited States
| | - Reto P Fiolka
- Department of Cell Biology, University of Texas Southwestern Medical CenterDallasUnited States
- Lyda Hill Department of Bioinformatics, University of Texas Southwestern Medical CenterDallasUnited States
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176
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A framework for understanding the functions of biomolecular condensates across scales. Nat Rev Mol Cell Biol 2020; 22:215-235. [PMID: 33169001 DOI: 10.1038/s41580-020-00303-z] [Citation(s) in RCA: 378] [Impact Index Per Article: 94.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 10/01/2020] [Indexed: 02/07/2023]
Abstract
Biomolecular condensates are found throughout eukaryotic cells, including in the nucleus, in the cytoplasm and on membranes. They are also implicated in a wide range of cellular functions, organizing molecules that act in processes ranging from RNA metabolism to signalling to gene regulation. Early work in the field focused on identifying condensates and understanding how their physical properties and regulation arise from molecular constituents. Recent years have brought a focus on understanding condensate functions. Studies have revealed functions that span different length scales: from molecular (modulating the rates of chemical reactions) to mesoscale (organizing large structures within cells) to cellular (facilitating localization of cellular materials and homeostatic responses). In this Roadmap, we discuss representative examples of biochemical and cellular functions of biomolecular condensates from the recent literature and organize these functions into a series of non-exclusive classes across the different length scales. We conclude with a discussion of areas of current interest and challenges in the field, and thoughts about how progress may be made to further our understanding of the widespread roles of condensates in cell biology.
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177
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Persson LB, Ambati VS, Brandman O. Cellular Control of Viscosity Counters Changes in Temperature and Energy Availability. Cell 2020; 183:1572-1585.e16. [PMID: 33157040 DOI: 10.1016/j.cell.2020.10.017] [Citation(s) in RCA: 76] [Impact Index Per Article: 19.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2019] [Revised: 02/26/2020] [Accepted: 10/08/2020] [Indexed: 11/18/2022]
Abstract
Cellular functioning requires the orchestration of thousands of molecular interactions in time and space. Yet most molecules in a cell move by diffusion, which is sensitive to external factors like temperature. How cells sustain complex, diffusion-based systems across wide temperature ranges is unknown. Here, we uncover a mechanism by which budding yeast modulate viscosity in response to temperature and energy availability. This "viscoadaptation" uses regulated synthesis of glycogen and trehalose to vary the viscosity of the cytosol. Viscoadaptation functions as a stress response and a homeostatic mechanism, allowing cells to maintain invariant diffusion across a 20°C temperature range. Perturbations to viscoadaptation affect solubility and phase separation, suggesting that viscoadaptation may have implications for multiple biophysical processes in the cell. Conditions that lower ATP trigger viscoadaptation, linking energy availability to rate regulation of diffusion-controlled processes. Viscoadaptation reveals viscosity to be a tunable property for regulating diffusion-controlled processes in a changing environment.
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Affiliation(s)
- Laura B Persson
- Department of Biology, Stanford University, Stanford, CA 94305, USA
| | - Vardhaan S Ambati
- Department of Biology, Stanford University, Stanford, CA 94305, USA; Department of Biochemistry, Stanford University, Stanford, CA 94305, USA
| | - Onn Brandman
- Department of Biochemistry, Stanford University, Stanford, CA 94305, USA.
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178
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Liu X, Oh S, Peshkin L, Kirschner MW. Computationally enhanced quantitative phase microscopy reveals autonomous oscillations in mammalian cell growth. Proc Natl Acad Sci U S A 2020; 117:27388-27399. [PMID: 33087574 PMCID: PMC7959529 DOI: 10.1073/pnas.2002152117] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023] Open
Abstract
The fine balance of growth and division is a fundamental property of the physiology of cells, and one of the least understood. Its study has been thwarted by difficulties in the accurate measurement of cell size and the even greater challenges of measuring growth of a single cell over time. We address these limitations by demonstrating a computationally enhanced methodology for quantitative phase microscopy for adherent cells, using improved image processing algorithms and automated cell-tracking software. Accuracy has been improved more than twofold and this improvement is sufficient to establish the dynamics of cell growth and adherence to simple growth laws. It is also sufficient to reveal unknown features of cell growth, previously unmeasurable. With these methodological and analytical improvements, in several cell lines we document a remarkable oscillation in growth rate, occurring throughout the cell cycle, coupled to cell division or birth yet independent of cell cycle progression. We expect that further exploration with this advanced tool will provide a better understanding of growth rate regulation in mammalian cells.
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Affiliation(s)
- Xili Liu
- Department of Systems Biology, Harvard Medical School, Boston, MA 02115
| | - Seungeun Oh
- Department of Systems Biology, Harvard Medical School, Boston, MA 02115
| | - Leonid Peshkin
- Department of Systems Biology, Harvard Medical School, Boston, MA 02115
| | - Marc W Kirschner
- Department of Systems Biology, Harvard Medical School, Boston, MA 02115
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179
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Vogel K, Greinert T, Reichard M, Held C, Harms H, Maskow T. Thermodynamics and Kinetics of Glycolytic Reactions. Part II: Influence of Cytosolic Conditions on Thermodynamic State Variables and Kinetic Parameters. Int J Mol Sci 2020; 21:ijms21217921. [PMID: 33113841 PMCID: PMC7663428 DOI: 10.3390/ijms21217921] [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: 08/30/2020] [Revised: 10/18/2020] [Accepted: 10/20/2020] [Indexed: 01/22/2023] Open
Abstract
For systems biology, it is important to describe the kinetic and thermodynamic properties of enzyme-catalyzed reactions and reaction cascades quantitatively under conditions prevailing in the cytoplasm. While in part I kinetic models based on irreversible thermodynamics were tested, here in part II, the influence of the presumably most important cytosolic factors was investigated using two glycolytic reactions (i.e., the phosphoglucose isomerase reaction (PGI) with a uni-uni-mechanism and the enolase reaction with an uni-bi-mechanism) as examples. Crowding by macromolecules was simulated using polyethylene glycol (PEG) and bovine serum albumin (BSA). The reactions were monitored calorimetrically and the equilibrium concentrations were evaluated using the equation of state ePC-SAFT. The pH and the crowding agents had the greatest influence on the reaction enthalpy change. Two kinetic models based on irreversible thermodynamics (i.e., single parameter flux-force and two-parameter Noor model) were applied to investigate the influence of cytosolic conditions. The flux-force model describes the influence of cytosolic conditions on reaction kinetics best. Concentrations of magnesium ions and crowding agents had the greatest influence, while temperature and pH-value had a medium influence on the kinetic parameters. With this contribution, we show that the interplay of thermodynamic modeling and calorimetric process monitoring allows a fast and reliable quantification of the influence of cytosolic conditions on kinetic and thermodynamic parameters.
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Affiliation(s)
- Kristina Vogel
- UFZ - Helmholtz Centre for Environmental Research, Department Environmental Microbiology, Leipzig, Permoserstr. 15, D-04318 Leipzig, Germany; (K.V.); (M.R.); (H.H.)
- Institute for Drug Development, Leipzig University Medical School, Leipzig University, Bruederstr. 34, 04103 Leipzig, Germany
| | - Thorsten Greinert
- Laboratory of Thermodynamics, Department of Biochemical and Chemical Engineering, Technische Universitaet Dortmund, Emil-Figge-Str. 70, 44227 Dortmund, Germany;
| | - Monique Reichard
- UFZ - Helmholtz Centre for Environmental Research, Department Environmental Microbiology, Leipzig, Permoserstr. 15, D-04318 Leipzig, Germany; (K.V.); (M.R.); (H.H.)
| | - Christoph Held
- Laboratory of Thermodynamics, Department of Biochemical and Chemical Engineering, Technische Universitaet Dortmund, Emil-Figge-Str. 70, 44227 Dortmund, Germany;
- Correspondence: (C.H.); (T.M.)
| | - Hauke Harms
- UFZ - Helmholtz Centre for Environmental Research, Department Environmental Microbiology, Leipzig, Permoserstr. 15, D-04318 Leipzig, Germany; (K.V.); (M.R.); (H.H.)
| | - Thomas Maskow
- UFZ - Helmholtz Centre for Environmental Research, Department Environmental Microbiology, Leipzig, Permoserstr. 15, D-04318 Leipzig, Germany; (K.V.); (M.R.); (H.H.)
- Correspondence: (C.H.); (T.M.)
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180
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Wlodarski M, Mancini L, Raciti B, Sclavi B, Lagomarsino MC, Cicuta P. Cytosolic Crowding Drives the Dynamics of Both Genome and Cytosol in Escherichia coli Challenged with Sub-lethal Antibiotic Treatments. iScience 2020; 23:101560. [PMID: 33083729 PMCID: PMC7522891 DOI: 10.1016/j.isci.2020.101560] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2019] [Revised: 05/22/2020] [Accepted: 09/10/2020] [Indexed: 11/28/2022] Open
Abstract
In contrast to their molecular mode of action, the system-level effect of antibiotics on cells is only beginning to be quantified. Molecular crowding is expected to be a relevant global regulator, which we explore here through the dynamic response phenotypes in Escherichia coli, at single-cell resolution, under sub-lethal regimes of different classes of clinically relevant antibiotics, acting at very different levels in the cell. We measure chromosomal mobility through tracking of fast (<15 s timescale) fluctuations of fluorescently tagged chromosomal loci, and we probe the fluidity of the cytoplasm by tracking cytosolic aggregates. Measuring cellular density, we show how the overall levels of macromolecular crowding affect both quantities, regardless of antibiotic-specific effects. The dominant trend is a strong correlation between the effects in different parts of the chromosome and between the chromosome and cytosol, supporting the concept of an overall global role of molecular crowding in cellular physiology.
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Affiliation(s)
- Michal Wlodarski
- Biological and Soft Systems, Cavendish Laboratory, University of Cambridge, Cambridge, UK
- Dipartimento di Fisica and I.N.F.N., Università degli Studi di Milano, Via Celoria 16, 20133 Milano, Italy
| | - Leonardo Mancini
- Biological and Soft Systems, Cavendish Laboratory, University of Cambridge, Cambridge, UK
| | - Bianca Raciti
- Biological and Soft Systems, Cavendish Laboratory, University of Cambridge, Cambridge, UK
| | - Bianca Sclavi
- Laboratory of Biology and Applied Pharmacology (UMR 8113 CNRS), École Normale Supérieure, Paris-Saclay, France
| | | | - Pietro Cicuta
- IFOM Foundation FIRC Institute of Molecular Oncology Foundation, Milan 20139, Italy
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181
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Danlasky BM, Panzica MT, McNally KP, Vargas E, Bailey C, Li W, Gong T, Fishman ES, Jiang X, McNally FJ. Evidence for anaphase pulling forces during C. elegans meiosis. J Cell Biol 2020; 219:211469. [PMID: 33064834 PMCID: PMC7577052 DOI: 10.1083/jcb.202005179] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2020] [Revised: 07/20/2020] [Accepted: 09/16/2020] [Indexed: 02/06/2023] Open
Abstract
Anaphase chromosome movement is thought to be mediated by pulling forces generated by end-on attachment of microtubules to the outer face of kinetochores. However, it has been suggested that during C. elegans female meiosis, anaphase is mediated by a kinetochore-independent pushing mechanism with microtubules only attached to the inner face of segregating chromosomes. We found that the kinetochore proteins KNL-1 and KNL-3 are required for preanaphase chromosome stretching, suggesting a role in pulling forces. In the absence of KNL-1,3, pairs of homologous chromosomes did not separate and did not move toward a spindle pole. Instead, each homolog pair moved together with the same spindle pole during anaphase B spindle elongation. Two masses of chromatin thus ended up at opposite spindle poles, giving the appearance of successful anaphase.
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182
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Li Y, Chen M, Hu J, Sheng R, Lin Q, He X, Guo M. Volumetric Compression Induces Intracellular Crowding to Control Intestinal Organoid Growth via Wnt/β-Catenin Signaling. Cell Stem Cell 2020; 28:63-78.e7. [PMID: 33053374 DOI: 10.1016/j.stem.2020.09.012] [Citation(s) in RCA: 58] [Impact Index Per Article: 14.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2019] [Revised: 02/26/2020] [Accepted: 09/14/2020] [Indexed: 12/14/2022]
Abstract
Enormous amounts of essential intracellular events are crowdedly packed inside picoliter-sized cellular space. However, the significance of the physical properties of cells remains underappreciated because of a lack of evidence of how they affect cellular functionalities. Here, we show that volumetric compression regulates the growth of intestinal organoids by modifying intracellular crowding and elevating Wnt/β-catenin signaling. Intracellular crowding varies upon stimulation by different types of extracellular physical/mechanical cues and leads to significant enhancement of Wnt/β-catenin signaling by stabilizing the LRP6 signalosome. By enhancing intracellular crowding using osmotic and mechanical compression, we show that expansion of intestinal organoids was facilitated through elevated Wnt/β-catenin signaling and greater intestinal stem cell (ISC) self-renewal. Our results provide an entry point for understanding how intracellular crowdedness functions as a physical regulator linking extracellular physical cues with intracellular signaling and potentially facilitate the design of engineering approaches for expansion of stem cells and organoids.
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Affiliation(s)
- Yiwei Li
- Department of Mechanical Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Maorong Chen
- F. M. Kirby Center, Boston Children's Hospital, Harvard Medical School, Boston, MA 02115, USA
| | - Jiliang Hu
- Department of Mechanical Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Ren Sheng
- F. M. Kirby Center, Boston Children's Hospital, Harvard Medical School, Boston, MA 02115, USA; College of Life and Health Science, Northeastern University, Shenyang, Liaoning, 110004, China
| | - Qirong Lin
- Department of Mechanical Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Xi He
- F. M. Kirby Center, Boston Children's Hospital, Harvard Medical School, Boston, MA 02115, USA
| | - Ming Guo
- Department of Mechanical Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139, USA.
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183
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Mouton SN, Thaller DJ, Crane MM, Rempel IL, Terpstra OT, Steen A, Kaeberlein M, Lusk CP, Boersma AJ, Veenhoff LM. A physicochemical perspective of aging from single-cell analysis of pH, macromolecular and organellar crowding in yeast. eLife 2020; 9:e54707. [PMID: 32990592 PMCID: PMC7556870 DOI: 10.7554/elife.54707] [Citation(s) in RCA: 24] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2019] [Accepted: 09/28/2020] [Indexed: 01/03/2023] Open
Abstract
Cellular aging is a multifactorial process that is characterized by a decline in homeostatic capacity, best described at the molecular level. Physicochemical properties such as pH and macromolecular crowding are essential to all molecular processes in cells and require maintenance. Whether a drift in physicochemical properties contributes to the overall decline of homeostasis in aging is not known. Here, we show that the cytosol of yeast cells acidifies modestly in early aging and sharply after senescence. Using a macromolecular crowding sensor optimized for long-term FRET measurements, we show that crowding is rather stable and that the stability of crowding is a stronger predictor for lifespan than the absolute crowding levels. Additionally, in aged cells, we observe drastic changes in organellar volume, leading to crowding on the micrometer scale, which we term organellar crowding. Our measurements provide an initial framework of physicochemical parameters of replicatively aged yeast cells.
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Affiliation(s)
- Sara N Mouton
- European Research Institute for the Biology of Ageing, University of Groningen, University Medical Center GroningenGroningenNetherlands
| | - David J Thaller
- Department of Cell Biology, Yale School of MedicineNew HavenUnited States
| | - Matthew M Crane
- Department of Pathology, School of Medicine, University of WashingtonSeattleUnited States
| | - Irina L Rempel
- European Research Institute for the Biology of Ageing, University of Groningen, University Medical Center GroningenGroningenNetherlands
| | - Owen T Terpstra
- European Research Institute for the Biology of Ageing, University of Groningen, University Medical Center GroningenGroningenNetherlands
| | - Anton Steen
- European Research Institute for the Biology of Ageing, University of Groningen, University Medical Center GroningenGroningenNetherlands
| | - Matt Kaeberlein
- Department of Pathology, School of Medicine, University of WashingtonSeattleUnited States
| | - C Patrick Lusk
- Department of Cell Biology, Yale School of MedicineNew HavenUnited States
| | | | - Liesbeth M Veenhoff
- European Research Institute for the Biology of Ageing, University of Groningen, University Medical Center GroningenGroningenNetherlands
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184
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O' Neill JS, Hoyle NP, Robertson JB, Edgar RS, Beale AD, Peak-Chew SY, Day J, Costa ASH, Frezza C, Causton HC. Eukaryotic cell biology is temporally coordinated to support the energetic demands of protein homeostasis. Nat Commun 2020; 11:4706. [PMID: 32943618 PMCID: PMC7499178 DOI: 10.1038/s41467-020-18330-x] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2020] [Accepted: 08/13/2020] [Indexed: 12/17/2022] Open
Abstract
Yeast physiology is temporally regulated, this becomes apparent under nutrient-limited conditions and results in respiratory oscillations (YROs). YROs share features with circadian rhythms and interact with, but are independent of, the cell division cycle. Here, we show that YROs minimise energy expenditure by restricting protein synthesis until sufficient resources are stored, while maintaining osmotic homeostasis and protein quality control. Although nutrient supply is constant, cells sequester and store metabolic resources via increased transport, autophagy and biomolecular condensation. Replete stores trigger increased H+ export which stimulates TORC1 and liberates proteasomes, ribosomes, chaperones and metabolic enzymes from non-membrane bound compartments. This facilitates translational bursting, liquidation of storage carbohydrates, increased ATP turnover, and the export of osmolytes. We propose that dynamic regulation of ion transport and metabolic plasticity are required to maintain osmotic and protein homeostasis during remodelling of eukaryotic proteomes, and that bioenergetic constraints selected for temporal organisation that promotes oscillatory behaviour.
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Affiliation(s)
- John S O' Neill
- MRC Laboratory of Molecular Biology, Cambridge, CB2 0QH, UK.
| | | | | | - Rachel S Edgar
- Molecular Virology, Department of Medicine, Imperial College, London, W2 1NY, UK
| | - Andrew D Beale
- MRC Laboratory of Molecular Biology, Cambridge, CB2 0QH, UK
| | | | - Jason Day
- Department of Earth Sciences, University of Cambridge, Cambridge, CB2 3EQ, UK
| | - Ana S H Costa
- MRC Cancer Unit, University of Cambridge, Cambridge, CB2 0XZ, UK.,Cold Spring Harbor Laboratory, Cold Spring Harbor, NY, 11724, USA
| | - Christian Frezza
- MRC Cancer Unit, University of Cambridge, Cambridge, CB2 0XZ, UK
| | - Helen C Causton
- Columbia University Medical Center, New York, NY, 10032, USA.
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185
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Jalihal AP, Pitchiaya S, Xiao L, Bawa P, Jiang X, Bedi K, Parolia A, Cieslik M, Ljungman M, Chinnaiyan AM, Walter NG. Multivalent Proteins Rapidly and Reversibly Phase-Separate upon Osmotic Cell Volume Change. Mol Cell 2020; 79:978-990.e5. [PMID: 32857953 PMCID: PMC7502480 DOI: 10.1016/j.molcel.2020.08.004] [Citation(s) in RCA: 68] [Impact Index Per Article: 17.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2019] [Revised: 06/11/2020] [Accepted: 08/05/2020] [Indexed: 12/12/2022]
Abstract
Processing bodies (PBs) and stress granules (SGs) are prominent examples of subcellular, membraneless compartments that are observed under physiological and stress conditions, respectively. We observe that the trimeric PB protein DCP1A rapidly (within ∼10 s) phase-separates in mammalian cells during hyperosmotic stress and dissolves upon isosmotic rescue (over ∼100 s) with minimal effect on cell viability even after multiple cycles of osmotic perturbation. Strikingly, this rapid intracellular hyperosmotic phase separation (HOPS) correlates with the degree of cell volume compression, distinct from SG assembly, and is exhibited broadly by homo-multimeric (valency ≥ 2) proteins across several cell types. Notably, HOPS sequesters pre-mRNA cleavage factor components from actively transcribing genomic loci, providing a mechanism for hyperosmolarity-induced global impairment of transcription termination. Our data suggest that the multimeric proteome rapidly responds to changes in hydration and molecular crowding, revealing an unexpected mode of globally programmed phase separation and sequestration.
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Affiliation(s)
- Ameya P Jalihal
- Single Molecule Analysis Group, Department of Chemistry, University of Michigan, Ann Arbor, MI 48109-1055, USA; Cell and Molecular Biology Graduate Program, University of Michigan, Ann Arbor, MI 48109, USA
| | - Sethuramasundaram Pitchiaya
- Michigan Center for Translational Pathology, University of Michigan Medical School, Ann Arbor, MI 48109-1055, USA; Department of Pathology, University of Michigan, Ann Arbor, MI 48109, USA; Center for RNA Biomedicine, University of Michigan, Ann Arbor, MI 48109, USA.
| | - Lanbo Xiao
- Michigan Center for Translational Pathology, University of Michigan Medical School, Ann Arbor, MI 48109-1055, USA; Department of Pathology, University of Michigan, Ann Arbor, MI 48109, USA
| | - Pushpinder Bawa
- Michigan Center for Translational Pathology, University of Michigan Medical School, Ann Arbor, MI 48109-1055, USA
| | - Xia Jiang
- Michigan Center for Translational Pathology, University of Michigan Medical School, Ann Arbor, MI 48109-1055, USA
| | - Karan Bedi
- Department of Radiation Oncology, University of Michigan, Ann Arbor, MI 48109, USA
| | - Abhijit Parolia
- Michigan Center for Translational Pathology, University of Michigan Medical School, Ann Arbor, MI 48109-1055, USA; Department of Pathology, University of Michigan, Ann Arbor, MI 48109, USA
| | - Marcin Cieslik
- Michigan Center for Translational Pathology, University of Michigan Medical School, Ann Arbor, MI 48109-1055, USA; Department of Pathology, University of Michigan, Ann Arbor, MI 48109, USA; Department of Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, MI 48109, USA
| | - Mats Ljungman
- Department of Radiation Oncology, University of Michigan, Ann Arbor, MI 48109, USA; Rogel Cancer Center, University of Michigan, Ann Arbor, MI 48109, USA; Center for RNA Biomedicine, University of Michigan, Ann Arbor, MI 48109, USA; Department of Environmental Health Sciences, University of Michigan, Ann Arbor, MI 48109, USA
| | - Arul M Chinnaiyan
- Michigan Center for Translational Pathology, University of Michigan Medical School, Ann Arbor, MI 48109-1055, USA; Department of Pathology, University of Michigan, Ann Arbor, MI 48109, USA; Howard Hughes Medical Institute, University of Michigan, Ann Arbor, MI 48109, USA; Department of Urology, University of Michigan, Ann Arbor, MI 48109, USA; Rogel Cancer Center, University of Michigan, Ann Arbor, MI 48109, USA; Center for RNA Biomedicine, University of Michigan, Ann Arbor, MI 48109, USA.
| | - Nils G Walter
- Single Molecule Analysis Group, Department of Chemistry, University of Michigan, Ann Arbor, MI 48109-1055, USA; Rogel Cancer Center, University of Michigan, Ann Arbor, MI 48109, USA; Center for RNA Biomedicine, University of Michigan, Ann Arbor, MI 48109, USA.
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186
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Carlini L, Brittingham GP, Holt LJ, Kapoor TM. Microtubules Enhance Mesoscale Effective Diffusivity in the Crowded Metaphase Cytoplasm. Dev Cell 2020; 54:574-582.e4. [PMID: 32818469 PMCID: PMC7685229 DOI: 10.1016/j.devcel.2020.07.020] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2020] [Revised: 06/10/2020] [Accepted: 07/24/2020] [Indexed: 12/12/2022]
Abstract
Mesoscale macromolecular complexes and organelles, tens to hundreds of nanometers in size, crowd the eukaryotic cytoplasm. It is therefore unclear how mesoscale particles remain sufficiently mobile to regulate dynamic processes such as cell division. Here, we study mobility across dividing cells that contain densely packed, dynamic microtubules, comprising the metaphase spindle. In dividing human cells, we tracked 40 nm genetically encoded multimeric nanoparticles (GEMs), whose sizes are commensurate with the inter-filament spacing in metaphase spindles. Unexpectedly, the effective diffusivity of GEMs was similar inside the dense metaphase spindle and the surrounding cytoplasm. Eliminating microtubules or perturbing their polymerization dynamics decreased diffusivity by ~30%, suggesting that microtubule polymerization enhances random displacements to amplify diffusive-like motion. Our results suggest that microtubules effectively fluidize the mitotic cytoplasm to equalize mesoscale mobility across a densely packed, dynamic, non-uniform environment, thus spatially maintaining a key biophysical parameter that impacts biochemistry, ranging from metabolism to the nucleation of cytoskeletal filaments.
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Affiliation(s)
- Lina Carlini
- Laboratory of Chemistry and Cell Biology, The Rockefeller University, New York, NY 10065, USA
| | - Gregory P Brittingham
- Institute for Systems Genetics, New York University Langone Health, New York, NY 10016, USA
| | - Liam J Holt
- Institute for Systems Genetics, New York University Langone Health, New York, NY 10016, USA
| | - Tarun M Kapoor
- Laboratory of Chemistry and Cell Biology, The Rockefeller University, New York, NY 10065, USA.
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187
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GABAergic Interneuron and Neurotransmission Are mTOR-Dependently Disturbed in Experimental Focal Cortical Dysplasia. Mol Neurobiol 2020; 58:156-169. [PMID: 32909150 DOI: 10.1007/s12035-020-02086-y] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2020] [Accepted: 08/21/2020] [Indexed: 01/13/2023]
Abstract
Focal cortical dysplasia (FCD) is a major cause for drug-resistant epilepsies. The molecular and cellular mechanisms of epileptogenesis in FCD are still poorly understood. Some studies have suggested that deficiencies of γ-aminobutyric acid (GABA) system may play an important role in type II FCD, but it remains controversial. In order to examine whether and how GABAergic interneurons and synaptic function are affected, we generated a somatic mTOR hyperactivation-based mouse model of type II FCD by in utero electroporation, quantified densities of interneurons in the malformed cortices, and recorded miniature inhibitory postsynaptic currents in dysmorphic neurons. We detected 20-25% reduction of GABAergic interneurons within malformed cortices, independent of cortical regions and cell subtypes but proportionate to the decrease of global neuron counts. GABAergic synaptic transmission from interneurons to mTOR hyperactivated dysmorphic neurons was dramatically disrupted, outweighing the decrease of interneuron counts. Postnatal mTOR inhibition partially rescued these alterations of GABAergic system. We also quantified the expression of GABAA receptor, GABA transporter, and chloridion transporter encoding genes and found that their expression was relatively intact within the malformed cortices. Taken together, these results confirmed that GABAergic interneuron and synapse transmission are disturbed profoundly in an mTOR-dependent manner in type II FCD. Our study suggests that postsynaptic mechanisms independent of interneuron reduction or altered expression of GABA synapse genes might be accountable for the impaired GABAergic neurotransmission in type II FCD as well as other mTOR-related epilepsies.
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188
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Chromosome clustering by Ki-67 excludes cytoplasm during nuclear assembly. Nature 2020; 587:285-290. [PMID: 32879492 PMCID: PMC7666080 DOI: 10.1038/s41586-020-2672-3] [Citation(s) in RCA: 59] [Impact Index Per Article: 14.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2019] [Accepted: 06/08/2020] [Indexed: 12/31/2022]
Abstract
Gene expression in eukaryotes requires the effective separation of nuclear transcription and RNA processing from cytosolic translation1. This separation is achieved by the nuclear envelope, which controls the exchange of macromolecules through nuclear pores2. During mitosis, however, the nuclear envelope in animal and plant cells disassembles, allowing cytoplasmic and nuclear components to intermix3. When the nuclear envelope is reformed, cytoplasmic components are removed from the nucleus by receptor-mediated transport through nuclear pores2. These pores have a size limit of 39 nanometres4-7, which raises the question of how larger cytoplasmic molecules are cleared from the nucleus. Here we show in HeLa cells that large cytoplasmic components are displaced before nuclear envelope assembly by the movement of chromosomes to a dense cluster. This clustering occurs when chromosomes approach the poles of anaphase spindles, and is mediated by a microtubule-independent mechanism that involves the surfactant-like protein Ki-67. Ki-67 forms repulsive molecular brushes during the early stages of mitosis8, but during mitotic exit the brushes collapse and Ki-67 promotes chromosome clustering. We show that the exclusion of mature ribosomes from the nucleus after mitosis depends on Ki-67-regulated chromosome clustering. Thus, our study reveals that chromosome mechanics help to re-establish the compartmentalization of eukaryotic cells after open mitosis.
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189
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Heidenreich M, Georgeson JM, Locatelli E, Rovigatti L, Nandi SK, Steinberg A, Nadav Y, Shimoni E, Safran SA, Doye JPK, Levy ED. Designer protein assemblies with tunable phase diagrams in living cells. Nat Chem Biol 2020; 16:939-945. [PMID: 32661377 DOI: 10.1038/s41589-020-0576-z] [Citation(s) in RCA: 50] [Impact Index Per Article: 12.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2019] [Accepted: 05/22/2020] [Indexed: 12/14/2022]
Abstract
Protein self-organization is a hallmark of biological systems. Although the physicochemical principles governing protein-protein interactions have long been known, the principles by which such nanoscale interactions generate diverse phenotypes of mesoscale assemblies, including phase-separated compartments, remain challenging to characterize. To illuminate such principles, we create a system of two proteins designed to interact and form mesh-like assemblies. We devise a new strategy to map high-resolution phase diagrams in living cells, which provide self-assembly signatures of this system. The structural modularity of the two protein components allows straightforward modification of their molecular properties, enabling us to characterize how interaction affinity impacts the phase diagram and material state of the assemblies in vivo. The phase diagrams and their dependence on interaction affinity were captured by theory and simulations, including out-of-equilibrium effects seen in growing cells. Finally, we find that cotranslational protein binding suffices to recruit a messenger RNA to the designed micron-scale structures.
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Affiliation(s)
- Meta Heidenreich
- Department of Structural Biology, Weizmann Institute of Science, Rehovot, Israel
| | - Joseph M Georgeson
- Department of Structural Biology, Weizmann Institute of Science, Rehovot, Israel
| | | | - Lorenzo Rovigatti
- Physical & Theoretical Chemistry Laboratory, Department of Chemistry, University of Oxford, Oxford, UK.
- Department of Physics, Sapienza Università di Roma, Rome, Italy.
| | - Saroj Kumar Nandi
- Department of Chemical and Biological Physics, Weizmann Institute of Science, Rehovot, Israel
- TIFR Centre for Interdisciplinary Sciences, Tata Institute of Fundamental Research, Hyderabad, India
| | - Avital Steinberg
- Department of Structural Biology, Weizmann Institute of Science, Rehovot, Israel
| | - Yotam Nadav
- Department of Structural Biology, Weizmann Institute of Science, Rehovot, Israel
| | - Eyal Shimoni
- Department of Chemical Research Support, Weizmann Institute of Science, Rehovot, Israel
| | - Samuel A Safran
- Department of Chemical and Biological Physics, Weizmann Institute of Science, Rehovot, Israel.
| | - Jonathan P K Doye
- Physical & Theoretical Chemistry Laboratory, Department of Chemistry, University of Oxford, Oxford, UK.
| | - Emmanuel D Levy
- Department of Structural Biology, Weizmann Institute of Science, Rehovot, Israel.
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190
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Jeong S, Kim IK, Kim H, Choi MJ, Lee J, Jo YS. Liver X Receptor β Related to Tumor Progression and Ribosome Gene Expression in Papillary Thyroid Cancer. Endocrinol Metab (Seoul) 2020; 35:656-668. [PMID: 32814418 PMCID: PMC7520597 DOI: 10.3803/enm.2020.667] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/02/2020] [Revised: 06/15/2020] [Accepted: 06/26/2020] [Indexed: 01/06/2023] Open
Abstract
BACKGROUND Intracellular lipid deposition has been reported in thyroid glands in obese animal and human. To understand the regulatory mechanism of lipid metabolism in thyroid cancer, we investigated the expression status of liver X receptor (LXR) and analyzed its clinicopathological characteristics and molecular biological features. METHODS Expression status of LXR and its transcriptional targets in human cancers were analyzed using The Cancer Genome Atlas (TCGA). The gene-sets related to high LXRβ expression was investigated by gene set enrichment analysis (GSEA) using Kyoto Encyclopedia of Genes and Genomes (KEGG) signaling pathways and gene ontology biologic process. Quantitative reverse transcription polymerase chain reaction was performed in thyroid cancer samples using our validation cohort. RESULTS In contrast to low expression of LXRα, LXRβ was highly expressed in thyroid cancer compared to the other types of human cancers. High LXRβ expression was correlated with the expression of LXRβ transcriptional targets genes, such as apolipoprotein C1 (APOC1), APOC2, apolipoprotein E (APOE), ATP binding cassette subfamily G member 8 (ABCG8), sterol regulatory elementbinding protein 1c (SREBP1c), and SPOT14. Furthermore, High LXRβ expression group indicated poor clinicopathological characteristics and aggressive molecular biological features independently from the drive mutation status. Mechanistically, high LXRβ expression was coordinately related to ribosome-related gene sets. CONCLUSION The mechanistic link between LXRβ and ribosomal activity will be addressed to develop new diagnostic and therapeutic targets in thyroid cancers.
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Affiliation(s)
- Seonhyang Jeong
- Department of Internal Medicine, Yonsei University College of Medicine, Seoul, Korea
| | - In-Kyu Kim
- Department of Surgery, Open NBI Convergence Technology Research Laboratory, Severance Hospital, Yonsei Cancer Center, Yonsei University College of Medicine, Seoul, Korea
| | - Hyunji Kim
- Department of Surgery, Open NBI Convergence Technology Research Laboratory, Severance Hospital, Yonsei Cancer Center, Yonsei University College of Medicine, Seoul, Korea
| | - Moon Jung Choi
- Department of Surgery, Open NBI Convergence Technology Research Laboratory, Severance Hospital, Yonsei Cancer Center, Yonsei University College of Medicine, Seoul, Korea
| | - Jandee Lee
- Department of Surgery, Open NBI Convergence Technology Research Laboratory, Severance Hospital, Yonsei Cancer Center, Yonsei University College of Medicine, Seoul, Korea
| | - Young Suk Jo
- Department of Internal Medicine, Yonsei University College of Medicine, Seoul, Korea
- Brain Korea 21 PLUS Project for Medical Science, Yonsei University, Seoul, Korea
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191
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Begam N, Da Vela S, Matsarskaia O, Braun MK, Mariani A, Zhang F, Schreiber F. Packing and dynamics of a protein solution approaching the jammed state. SOFT MATTER 2020; 16:7751-7759. [PMID: 32744265 DOI: 10.1039/d0sm00962h] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/11/2023]
Abstract
The packing of proteins and their collective behavior in crowded media is crucial for the understanding of biological processes. Here we study the structural and dynamical evolution of solutions of the globular protein bovine serum albumin with increasing concentration via drying using small angle X-ray scattering and dynamic light scattering. We probe an evolving correlation peak on the scattering profile, corresponding to the inter-protein distance, ξ, which decreases following a power law of the protein volume fraction, φ. The rate of decrease in ξ becomes faster above a protein concentration of ∼200 mg ml-1 (φ = 0.15). The power law exponent changes from 0.33, which is typical of colloidal or protein solutions, to 0.41. During the entire drying process, we observe the development and the growth of two-step relaxation dynamics with increasing φ as revealed by dynamic light scattering. We find three different regimes of the dependence of ξ as a function of φ. In the dilute regime (φ < 0.22), protein molecules are far apart from each other compared to their size. In this case, the dynamics mainly corresponds to Brownian motion. At an intermediate concentration (0.22 < φ < 0.47), inter-protein distances become comparable to the size of protein molecules, leading to a preferential orientation of the ellipsoidal protein molecules along with a possible deformation. In this regime, the dynamics shows two distinct relaxation times. At a very high concentration (φ > 0.47), the system reaches a jammed state. Subsequently, the secondary relaxation time in this state becomes extremely slow. In this state, the protein molecules have approximately one hydration layer. This study contributes to the understanding of protein molecular packing in crowded environments and the phenomenon of density-driven jamming for soft matter systems.
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Affiliation(s)
- Nafisa Begam
- Institut für Angewandte Physik, Universtitat Tübingen, 70276, Tübingen, Germany.
| | - Stefano Da Vela
- Institut für Angewandte Physik, Universtitat Tübingen, 70276, Tübingen, Germany.
| | - Olga Matsarskaia
- Institut für Angewandte Physik, Universtitat Tübingen, 70276, Tübingen, Germany.
| | - Michal K Braun
- Institut für Angewandte Physik, Universtitat Tübingen, 70276, Tübingen, Germany.
| | - Alessandro Mariani
- ESRF-The European Synchrotron, 71 Avenue des Martyrs, 38000, Grenoble, France
| | - Fajun Zhang
- Institut für Angewandte Physik, Universtitat Tübingen, 70276, Tübingen, Germany.
| | - Frank Schreiber
- Institut für Angewandte Physik, Universtitat Tübingen, 70276, Tübingen, Germany.
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192
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Chaki S, Chakrabarti R. Escape of a passive particle from an activity-induced energy landscape: emergence of slow and fast effective diffusion. SOFT MATTER 2020; 16:7103-7115. [PMID: 32657294 DOI: 10.1039/d0sm00711k] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/11/2023]
Abstract
Spontaneous persistent motions driven by active processes play a central role in maintaining living cells far from equilibrium. In the majority of research studies, the steady state dynamics of an active system has been described in terms of an effective temperature. By contrast, we have examined a prototype model for diffusion in an activity-induced rugged energy landscape to describe the slow dynamics of a tagged particle in a dense active environment. The expression for the mean escape time from the activity-induced rugged energy landscape holds only in the limit of low activity and the mean escape time from the rugged energy landscape increases with activity. The precise form of the active correlation will determine whether the mean escape time will depend on the persistence time or not. The activity-induced rugged energy landscape approach also allows an estimate of the non-equilibrium effective diffusivity characterizing the slow diffusive motion of the tagged particle due to activity. On the other hand, in a dilute environment, high activity augments the diffusion of the tagged particle. The enhanced diffusion can be attributed to an effective temperature higher than the ambient temperature and this is used to calculate the Kramers' mean escape time, which decreases with activity. Our results have direct relevance to recent experiments on tagged particle diffusion in condensed phases.
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Affiliation(s)
- Subhasish Chaki
- Department of Chemistry, Indian Institute of Technology Bombay, Mumbai, Powai 400076, India.
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193
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The In Situ Structure of Parkinson's Disease-Linked LRRK2. Cell 2020; 182:1508-1518.e16. [PMID: 32783917 DOI: 10.1016/j.cell.2020.08.004] [Citation(s) in RCA: 115] [Impact Index Per Article: 28.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2019] [Revised: 05/28/2020] [Accepted: 07/31/2020] [Indexed: 12/31/2022]
Abstract
Mutations in leucine-rich repeat kinase 2 (LRRK2) are the most frequent cause of familial Parkinson's disease. LRRK2 is a multi-domain protein containing a kinase and GTPase. Using correlative light and electron microscopy, in situ cryo-electron tomography, and subtomogram analysis, we reveal a 14-Å structure of LRRK2 bearing a pathogenic mutation that oligomerizes as a right-handed double helix around microtubules, which are left-handed. Using integrative modeling, we determine the architecture of LRRK2, showing that the GTPase and kinase are in close proximity, with the GTPase closer to the microtubule surface, whereas the kinase is exposed to the cytoplasm. We identify two oligomerization interfaces mediated by non-catalytic domains. Mutation of one of these abolishes LRRK2 microtubule-association. Our work demonstrates the power of cryo-electron tomography to generate models of previously unsolved structures in their cellular environment.
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194
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Wu CCC, Peterson A, Zinshteyn B, Regot S, Green R. Ribosome Collisions Trigger General Stress Responses to Regulate Cell Fate. Cell 2020; 182:404-416.e14. [PMID: 32610081 PMCID: PMC7384957 DOI: 10.1016/j.cell.2020.06.006] [Citation(s) in RCA: 221] [Impact Index Per Article: 55.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2020] [Revised: 05/18/2020] [Accepted: 06/02/2020] [Indexed: 01/01/2023]
Abstract
Problems arising during translation of mRNAs lead to ribosome stalling and collisions that trigger a series of quality control events. However, the global cellular response to ribosome collisions has not been explored. Here, we uncover a function for ribosome collisions in signal transduction. Using translation elongation inhibitors and general cellular stress conditions, including amino acid starvation and UV irradiation, we show that ribosome collisions activate the stress-activated protein kinase (SAPK) and GCN2-mediated stress response pathways. We show that the MAPKKK ZAK functions as the sentinel for ribosome collisions and is required for immediate early activation of both SAPK (p38/JNK) and GCN2 signaling pathways. Selective ribosome profiling and biochemistry demonstrate that although ZAK generally associates with elongating ribosomes on polysomal mRNAs, it specifically auto-phosphorylates on the minimal unit of colliding ribosomes, the disome. Together, these results provide molecular insights into how perturbation of translational homeostasis regulates cell fate.
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Affiliation(s)
- Colin Chih-Chien Wu
- Department of Molecular Biology and Genetics, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA; Howard Hughes Medical Institute, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
| | - Amy Peterson
- Department of Molecular Biology and Genetics, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
| | - Boris Zinshteyn
- Department of Molecular Biology and Genetics, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA; Howard Hughes Medical Institute, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
| | - Sergi Regot
- Department of Molecular Biology and Genetics, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
| | - Rachel Green
- Department of Molecular Biology and Genetics, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA; Howard Hughes Medical Institute, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA.
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195
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Brunkard JO. Exaptive Evolution of Target of Rapamycin Signaling in Multicellular Eukaryotes. Dev Cell 2020; 54:142-155. [PMID: 32649861 PMCID: PMC7346820 DOI: 10.1016/j.devcel.2020.06.022] [Citation(s) in RCA: 44] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2020] [Revised: 06/12/2020] [Accepted: 06/18/2020] [Indexed: 12/16/2022]
Abstract
Target of rapamycin (TOR) is a protein kinase that coordinates metabolism with nutrient and energy availability in eukaryotes. TOR and its primary interactors, RAPTOR and LST8, have been remarkably evolutionarily static since they arose in the unicellular last common ancestor of plants, fungi, and animals, but the upstream regulatory mechanisms and downstream effectors of TOR signaling have evolved considerable diversity in these separate lineages. Here, I focus on the roles of exaptation and adaptation in the evolution of novel signaling axes in the TOR network in multicellular eukaryotes, concentrating especially on amino acid sensing, cell-cell signaling, and cell differentiation.
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Affiliation(s)
- Jacob O. Brunkard
- Department of Plant and Microbial Biology, University of California at Berkeley, Berkeley, CA 94720, USA,Plant Gene Expression Center, U.S. Department of Agriculture Agricultural Research Service, Albany, CA 94710, USA,Laboratory of Genetics, University of Wisconsin-Madison, Madison, WI 53706, USA,Corresponding author
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196
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Regulation of stem cell function and neuronal differentiation by HERV-K via mTOR pathway. Proc Natl Acad Sci U S A 2020; 117:17842-17853. [PMID: 32669437 DOI: 10.1073/pnas.2002427117] [Citation(s) in RCA: 31] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023] Open
Abstract
Stem cells are capable of unlimited proliferation but can be induced to form brain cells. Factors that specifically regulate human development are poorly understood. We found that human stem cells expressed high levels of the envelope protein of an endogenized human-specific retrovirus (HERV-K, HML-2) from loci in chromosomes 12 and 19. The envelope protein was expressed on the cell membrane of the stem cells and was critical in maintaining the stemness via interactions with CD98HC, leading to triggering of human-specific signaling pathways involving mammalian target of rapamycin (mTOR) and lysophosphatidylcholine acyltransferase (LPCAT1)-mediated epigenetic changes. Down-regulation or epigenetic silencing of HML-2 env resulted in dissociation of the stem cell colonies and enhanced differentiation along neuronal pathways. Thus HML-2 regulation is critical for human embryonic and neurodevelopment, while it's dysregulation may play a role in tumorigenesis and neurodegeneration.
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197
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The environmental stress response causes ribosome loss in aneuploid yeast cells. Proc Natl Acad Sci U S A 2020; 117:17031-17040. [PMID: 32632008 DOI: 10.1073/pnas.2005648117] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022] Open
Abstract
Aneuploidy, a condition characterized by whole chromosome gains and losses, is often associated with significant cellular stress and decreased fitness. However, how cells respond to the aneuploid state has remained controversial. In aneuploid budding yeast, two opposing gene-expression patterns have been reported: the "environmental stress response" (ESR) and the "common aneuploidy gene-expression" (CAGE) signature, in which many ESR genes are oppositely regulated. Here, we investigate this controversy. We show that the CAGE signature is not an aneuploidy-specific gene-expression signature but the result of normalizing the gene-expression profile of actively proliferating aneuploid cells to that of euploid cells grown into stationary phase. Because growth into stationary phase is among the strongest inducers of the ESR, the ESR in aneuploid cells was masked when stationary phase euploid cells were used for normalization in transcriptomic studies. When exponentially growing euploid cells are used in gene-expression comparisons with aneuploid cells, the CAGE signature is no longer evident in aneuploid cells. Instead, aneuploid cells exhibit the ESR. We further show that the ESR causes selective ribosome loss in aneuploid cells, providing an explanation for the decreased cellular density of aneuploid cells. We conclude that aneuploid budding yeast cells mount the ESR, rather than the CAGE signature, in response to aneuploidy-induced cellular stresses, resulting in selective ribosome loss. We propose that the ESR serves two purposes in aneuploid cells: protecting cells from aneuploidy-induced cellular stresses and preventing excessive cellular enlargement during slowed cell cycles by down-regulating translation capacity.
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198
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Wang H, Gu L, Tan R, Ma X, Zhou X, Liu Y. Macromolecule crowding effects on the phase separation of semi-flexible polymer in spherical confined space. J Biol Phys 2020; 46:223-231. [PMID: 32613446 DOI: 10.1007/s10867-020-09550-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2020] [Accepted: 05/13/2020] [Indexed: 11/27/2022] Open
Abstract
Current works focus on detecting macromolecule crowding effects on the phase separation of the mixture between semi-flexible polymer and crowders (hydrophilic polymers) in confined space by Monte Carlo simulations. With the increasing addition of crowders into the spherical confined space, the semi-flexible polymer was first compressed into a condensed state from the initial coil state, and then the condensed conformation expanded and deposited on the inner surface of the spherical confined space with an extended state. The phase diagram in the phase space of the volume fraction of crowders and the scaled radius of spherical confined space by crowder diameter, and the direct conformation transition of semi-flexible polymer have validated the phase transition process successfully. In addition, the deposition of extended conformation on the inner surface of the spherical confined space was qualified by the vertex density, its curve shifted along the radial direction with the increasing volume fraction of crowder. During the phase separation process, the critical volume fraction φ∗ relates to the crowder diameter approximately linearly and the relation between the critical volume fraction and the crowder diameter strongly depends on the size of the spherical confined space.
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Affiliation(s)
- Hongchang Wang
- School of Physics and Electronic Science, Guizhou Normal University, Guiyang, 550025, China
| | - Lingyun Gu
- School of Physics and Astronomy, Sun Yat-Sen University, Zhuhai, 519082, China
| | - Rongri Tan
- College of Communication and Electronics, Jiangxi Science and Technology Normal University, Nanchang, 330013, China
| | - Xiaotian Ma
- School of Physics and Electronic Science, Guizhou Normal University, Guiyang, 550025, China
| | - Xun Zhou
- School of Physics and Electronic Science, Guizhou Normal University, Guiyang, 550025, China.
| | - Yanhui Liu
- College of Physics, Guizhou University, Guiyang, 550025, China.
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199
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Toward Organism-scale Structural Biology: S-layer Reined in by Bacterial LPS. Trends Biochem Sci 2020; 45:549-551. [DOI: 10.1016/j.tibs.2020.03.006] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2020] [Revised: 03/03/2020] [Accepted: 03/12/2020] [Indexed: 12/29/2022]
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200
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McLaughlin GA, Langdon EM, Crutchley JM, Holt LJ, Forest MG, Newby JM, Gladfelter AS. Spatial heterogeneity of the cytosol revealed by machine learning-based 3D particle tracking. Mol Biol Cell 2020; 31:1498-1511. [PMID: 32401664 PMCID: PMC7359570 DOI: 10.1091/mbc.e20-03-0210] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2020] [Revised: 05/04/2020] [Accepted: 05/05/2020] [Indexed: 11/11/2022] Open
Abstract
The spatial structure and physical properties of the cytosol are not well understood. Measurements of the material state of the cytosol are challenging due to its spatial and temporal heterogeneity. Recent development of genetically encoded multimeric nanoparticles (GEMs) has opened up study of the cytosol at the length scales of multiprotein complexes (20-60 nm). We developed an image analysis pipeline for 3D imaging of GEMs in the context of large, multinucleate fungi where there is evidence of functional compartmentalization of the cytosol for both the nuclear division cycle and branching. We applied a neural network to track particles in 3D and then created quantitative visualizations of spatially varying diffusivity. Using this pipeline to analyze spatial diffusivity patterns, we found that there is substantial variability in the properties of the cytosol. We detected zones where GEMs display especially low diffusivity at hyphal tips and near some nuclei, showing that the physical state of the cytosol varies spatially within a single cell. Additionally, we observed significant cell-to-cell variability in the average diffusivity of GEMs. Thus, the physical properties of the cytosol vary substantially in time and space and can be a source of heterogeneity within individual cells and across populations.
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Affiliation(s)
- Grace A. McLaughlin
- Department of Biology, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599
| | - Erin M. Langdon
- Department of Biology, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599
| | - John M. Crutchley
- Department of Biology, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599
| | - Liam J. Holt
- Institute for Systems Genetics, New York University Langone Health, New York, NY 10016
| | - M. Gregory Forest
- UNC/NCSU Joint Department of Biomedical Engineering, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599
- Department of Mathematics, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599
- Department of Applied Physical Sciences, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599
| | - Jay M. Newby
- Department of Mathematical and Statistical Sciences, University of Alberta, Edmonton, AB T6G 2G1, Canada
| | - Amy S. Gladfelter
- Department of Biology, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599
- Marine Biological Laboratory, Woods Hole, MA 02543
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