1
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Sun Q, Li J, Dong H, Zhan J, Xiong X, Ding J, Li Y, He L, Wang J. UQCRFS1 serves as a prognostic biomarker and promotes the progression of ovarian cancer. Sci Rep 2023; 13:8335. [PMID: 37221238 DOI: 10.1038/s41598-023-35572-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2023] [Accepted: 05/20/2023] [Indexed: 05/25/2023] Open
Abstract
UQCRFS1 has been reported to be highly expressed in gastric and breast cancer, but the mechanism remains unclear. The prognosis and biological functions of UQCRFS1 in ovarian cancer (OC) have not been evaluated. The expression of UQCRFS1 in EOC was detected by GEPIA and HPA websites, and the prognosis value was investigated by Kaplan-Meier analysis. Then the correlation between the UQCRFS1 gene and tumor-related signature were analyzed by Spearman correlation analysis and rank sum test. Subsequently, the expression of the UQCRFS1 gene in four ovarian cancer cell lines was detected. A2780 and OVCAR8 with the highest expression of UQCRFS1 were selected in the following biological experiments. Cell proliferation was detected by CCK8 assay, cell cycle and apoptosis were determined by flow cytometry, reactive oxygen species (ROS) production was detected by DCFH-DA, DNA damage gene mRNA expression was analyzed by RT-PCR, and AKT/mTOR pathway protein expression were also examined by western blot after siRNA transfection. We found that UQCRFS1 was high-expression in EOC and associated with poor prognosis. Spearman correlation analysis revealed that the high expression of UQCRFS1 is associated with the cell cycle, apoptosis, oxidative phosphorylation, and DNA damage. Further studies found that knockdown of UQCRFS1 cells reduced cell proliferation, cell cycle arrest at the G1 phase, increased proportion of apoptosis, ROS production, and expression of DNA damage genes, inhibited ATK/mTOR pathway. The study suggested that UQCRFS1 may be a candidated target for diagnosis and treatments in OC.
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Affiliation(s)
- Qiran Sun
- Medical College, Nanchang University, Nanchang, Jiangxi, China
| | - Jiaqi Li
- Department of Obstetrics and Gynecology, The First Affiliated Hospital of Nanchang University, Nanchang, Jiangxi, China
| | - Hao Dong
- Medical College, Nanchang University, Nanchang, Jiangxi, China
| | - Jiao Zhan
- Medical College, Nanchang University, Nanchang, Jiangxi, China
| | - Xiaoming Xiong
- Department of Obstetrics and Gynecology, The First Affiliated Hospital of Nanchang University, Nanchang, Jiangxi, China
| | - Jiashan Ding
- Department of Obstetrics and Gynecology, The First Affiliated Hospital of Nanchang University, Nanchang, Jiangxi, China
| | - Yuan Li
- Department of Obstetrics and Gynecology, First People's Hospital of Foshan, Foshan, Guangdong, China
| | - Linsheng He
- Department of Obstetrics and Gynecology, The First Affiliated Hospital of Nanchang University, Nanchang, Jiangxi, China.
| | - Jing Wang
- Department of Nursing, The First Affiliated Hospital of Nanchang University, Nanchang, Jiangxi, China.
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2
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Daalman WKG, Sweep E, Laan L. A tractable physical model for the yeast polarity predicts epistasis and fitness. Philos Trans R Soc Lond B Biol Sci 2023; 378:20220044. [PMID: 37004720 PMCID: PMC10067261 DOI: 10.1098/rstb.2022.0044] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/04/2023] Open
Abstract
Accurate phenotype prediction based on genetic information has numerous societal applications, such as crop design or cellular factories. Epistasis, when biological components interact, complicates modelling phenotypes from genotypes. Here we show an approach to mitigate this complication for polarity establishment in budding yeast, where mechanistic information is abundant. We coarse-grain molecular interactions into a so-called mesotype, which we combine with gene expression noise into a physical cell cycle model. First, we show with computer simulations that the mesotype allows validation of the most current biochemical polarity models by quantitatively matching doubling times. Second, the mesotype elucidates epistasis emergence as exemplified by evaluating the predicted mutational effect of key polarity protein Bem1p when combined with known interactors or under different growth conditions. This example also illustrates how unlikely evolutionary trajectories can become more accessible. The tractability of our biophysically justifiable approach inspires a road-map towards bottom-up modelling complementary to statistical inferences. This article is part of the theme issue ‘Interdisciplinary approaches to predicting evolutionary biology’.
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Affiliation(s)
| | - Els Sweep
- Department of Bionanoscience, TU Delft, 2629 HZ Delft, The Netherlands
| | - Liedewij Laan
- Department of Bionanoscience, TU Delft, 2629 HZ Delft, The Netherlands
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3
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Hernández JA, Chifflet S, Justet C, Torriglia A. A mathematical model of wound healing in bovine corneal endothelium. J Theor Biol 2023; 559:111374. [PMID: 36460056 DOI: 10.1016/j.jtbi.2022.111374] [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: 01/08/2022] [Revised: 11/24/2022] [Accepted: 11/25/2022] [Indexed: 11/30/2022]
Abstract
We developed a mathematical model to describe healing processes in bovine corneal endothelial (BCE) cells in culture, triggered by mechanical wounds with parallel edges. Previous findings from our laboratory show that, in these cases, BCE monolayers exhibit an approximately constant healing velocity. Also, that caspase-dependent apoptosis occurs, with the fraction of apoptotic cells increasing with the distance traveled by the healing edge. In addition, in this study we report the novel findings that, for wound scratch assays performed preserving the basal extracellular matrix: i) the healing cells increase their en face surface area in a characteristic fashion, and ii) the average length of the segments of the cell columns actively participating in the healing process increases linearly with time. These latter observations preclude the utilization of standard traveling wave formalisms to model wound healing in BCE cells. Instead, we developed and studied a simple phenomenological model based on a plausible formula for the spreading dynamics of the individual healing cells, that incorporates original evidence about the process in BCE cells. The model can be simulated to: i) obtain an approximately constant healing velocity; ii) reproduce the profile of the healing cell areas, and iii) obtain approximately linear time dependences of the mean cell area and average length of the front active segments per column. In view of its accuracy to account for the experimental observations, the model can also be acceptably employed to quantify the appearance of apoptotic cells during BCE wound healing. The strategy utilized here could offer a novel formal framework to represent modifications undergone by some epithelial cell lines during wound healing.
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Affiliation(s)
- Julio A Hernández
- Sección Biofísica y Biología de Sistemas, Facultad de Ciencias, Universidad de la República, Iguá s/n esq. Mataojo, 11400 Montevideo, Uruguay.
| | - Silvia Chifflet
- Departamento de Bioquímica, Facultad de Medicina, Universidad de la República, Gral. Flores 2125, 11800 Montevideo, Uruguay
| | - Cristian Justet
- Departamento de Bioquímica, Facultad de Medicina, Universidad de la República, Gral. Flores 2125, 11800 Montevideo, Uruguay
| | - Alicia Torriglia
- Centre de Recherche des Cordeliers, Sorbonne Université, Inserm, Université de Paris, F-75006 Paris, France
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4
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Takhaveev V, Özsezen S, Smith EN, Zylstra A, Chaillet ML, Chen H, Papagiannakis A, Milias-Argeitis A, Heinemann M. Temporal segregation of biosynthetic processes is responsible for metabolic oscillations during the budding yeast cell cycle. Nat Metab 2023; 5:294-313. [PMID: 36849832 PMCID: PMC9970877 DOI: 10.1038/s42255-023-00741-x] [Citation(s) in RCA: 10] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/26/2021] [Accepted: 01/10/2023] [Indexed: 03/01/2023]
Abstract
Many cell biological and biochemical mechanisms controlling the fundamental process of eukaryotic cell division have been identified; however, the temporal dynamics of biosynthetic processes during the cell division cycle are still elusive. Here, we show that key biosynthetic processes are temporally segregated along the cell cycle. Using budding yeast as a model and single-cell methods to dynamically measure metabolic activity, we observe two peaks in protein synthesis, in the G1 and S/G2/M phase, whereas lipid and polysaccharide synthesis peaks only once, during the S/G2/M phase. Integrating the inferred biosynthetic rates into a thermodynamic-stoichiometric metabolic model, we find that this temporal segregation in biosynthetic processes causes flux changes in primary metabolism, with an acceleration of glucose-uptake flux in G1 and phase-shifted oscillations of oxygen and carbon dioxide exchanges. Through experimental validation of the model predictions, we demonstrate that primary metabolism oscillates with cell-cycle periodicity to satisfy the changing demands of biosynthetic processes exhibiting unexpected dynamics during the cell cycle.
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Affiliation(s)
- Vakil Takhaveev
- Molecular Systems Biology, Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, Groningen, The Netherlands
- Department of Health Sciences and Technology, ETH Zurich, Zurich, Switzerland
| | - Serdar Özsezen
- Molecular Systems Biology, Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, Groningen, The Netherlands
- Department of Microbiology and Systems Biology, The Netherlands Organization for Applied Scientific Research (TNO), Leiden, The Netherlands
| | - Edward N Smith
- Molecular Systems Biology, Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, Groningen, The Netherlands
| | - Andre Zylstra
- Molecular Systems Biology, Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, Groningen, The Netherlands
| | - Marten L Chaillet
- Molecular Systems Biology, Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, Groningen, The Netherlands
- Structural Biochemistry, Bijvoet Center for Biomolecular Research, Utrecht University, Utrecht, The Netherlands
| | - Haoqi Chen
- Molecular Systems Biology, Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, Groningen, The Netherlands
| | - Alexandros Papagiannakis
- Molecular Systems Biology, Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, Groningen, The Netherlands
- Department of Biology and Sarafan Chemistry, Engineering, and Medicine for Human Health Institute, Stanford University, Stanford, CA, USA
| | - Andreas Milias-Argeitis
- Molecular Systems Biology, Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, Groningen, The Netherlands
| | - Matthias Heinemann
- Molecular Systems Biology, Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, Groningen, The Netherlands.
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5
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Terhorst A, Sandikci A, Whittaker CA, Szórádi T, Holt LJ, Neurohr GE, Amon A. The environmental stress response regulates ribosome content in cell cycle-arrested S. cerevisiae. Front Cell Dev Biol 2023; 11:1118766. [PMID: 37123399 PMCID: PMC10130656 DOI: 10.3389/fcell.2023.1118766] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2022] [Accepted: 03/21/2023] [Indexed: 05/02/2023] Open
Abstract
Prolonged cell cycle arrests occur naturally in differentiated cells and in response to various stresses such as nutrient deprivation or treatment with chemotherapeutic agents. Whether and how cells survive prolonged cell cycle arrests is not clear. Here, we used S. cerevisiae to compare physiological cell cycle arrests and genetically induced arrests in G1-, meta- and anaphase. Prolonged cell cycle arrest led to growth attenuation in all studied conditions, coincided with activation of the Environmental Stress Response (ESR) and with a reduced ribosome content as determined by whole ribosome purification and TMT mass spectrometry. Suppression of the ESR through hyperactivation of the Ras/PKA pathway reduced cell viability during prolonged arrests, demonstrating a cytoprotective role of the ESR. Attenuation of cell growth and activation of stress induced signaling pathways also occur in arrested human cell lines, raising the possibility that the response to prolonged cell cycle arrest is conserved.
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Affiliation(s)
- Allegra Terhorst
- David H. Koch Institute for Integrative Cancer Research, Howard Hughes Medical Institute, Massachusetts Institute of Technology, Cambridge, MA, United States
| | - Arzu Sandikci
- David H. Koch Institute for Integrative Cancer Research, Howard Hughes Medical Institute, Massachusetts Institute of Technology, Cambridge, MA, United States
| | - Charles A. Whittaker
- David H. Koch Institute for Integrative Cancer Research, Howard Hughes Medical Institute, Massachusetts Institute of Technology, Cambridge, MA, United States
| | - Tamás Szórádi
- Institute for Systems Genetics, New York University Langone Health, New York City, NY, United States
| | - Liam J. Holt
- Institute for Systems Genetics, New York University Langone Health, New York City, NY, United States
| | - Gabriel E. Neurohr
- David H. Koch Institute for Integrative Cancer Research, Howard Hughes Medical Institute, Massachusetts Institute of Technology, Cambridge, MA, United States
- Institute of Biochemistry, ETH Zurich, Zurich, Switzerland
- *Correspondence: Gabriel E. Neurohr,
| | - Angelika Amon
- David H. Koch Institute for Integrative Cancer Research, Howard Hughes Medical Institute, Massachusetts Institute of Technology, Cambridge, MA, United States
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6
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FGF9 promotes cell proliferation and tumorigenesis in TM3 mouse Leydig progenitor cells. Am J Cancer Res 2022; 12:5613-5630. [PMID: 36628285 PMCID: PMC9827084] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2022] [Accepted: 12/06/2022] [Indexed: 01/12/2023] Open
Abstract
Fibroblast growth factor 9 (FGF9) modulates cell proliferation, differentiation and motility for development and tissue repair in normal cells. Growing evidence shows that abnormal activation of FGF9 signaling is associated with tumor malignancy. We have previously reported that FGF9 increases MA-10 mouse Leydig tumor cell proliferation, in vitro, and tumor growth, in vivo. Also, FGF9 promotes the tumor growth and liver metastasis of mouse Lewis lung cancer cells, in vivo. However, the effects of FGF9 in the early stage of tumorigenesis remains elusive. In this study, TM3 mouse Leydig progenitor cells, that are not tumorigenic in immunocompromised mice, were used as a model cell line to investigate the role of FGF9 in tumorigenesis. The results demonstrated that FGF9 significantly induced cell proliferation and activated the MAPK, PI3K and PLCγ signaling pathways in TM3 cells. The percentage of the cell number in G1 phase was reduced and that in S and G2/M phases was increased after FGF9 stimulation in TM3 cells. Cyclin D1, cyclin A1, CDK2, CDK1, and p21 expressions and the phosphorylation level of Rb were all induced in FGF9-treated TM3 cells. In addition, FGF9 increased the expression of FGF receptor 1-4 in TM3 cells, suggesting the positive feedback loop between FGF9 and FGFRs. Furthermore, in the allograft mouse model, FGF9 promoted the tumorigenesis of TM3 cells characterized by higher expression of tumor markers, such as tumor necrosis factor alpha (TNFα) and α-fetoprotein (AFP), in the subcutaneously inoculated TM3 cell tissue. Conclusively, FGF9 induced cell cycle to increase cell proliferation of TM3 cells through FAK, MAPK, PI3K/Akt and PLCγ signaling pathways, in vitro, and promoted the tumorigenesis of TM3 cell allograft tissue, in vivo, which is a potential marker for tumor as well as a target for cancer therapeutic strategies.
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7
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Kellogg DR, Levin PA. Nutrient availability as an arbiter of cell size. Trends Cell Biol 2022; 32:908-919. [PMID: 35851491 PMCID: PMC9588502 DOI: 10.1016/j.tcb.2022.06.008] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2022] [Revised: 06/07/2022] [Accepted: 06/16/2022] [Indexed: 01/21/2023]
Abstract
Pioneering work carried out over 60 years ago discovered that bacterial cell size is proportional to the growth rate set by nutrient availability. This relationship is traditionally referred to as the 'growth law'. Subsequent studies revealed the growth law to hold across all orders of life, a remarkable degree of conservation. However, recent work suggests the relationship between growth rate, nutrients, and cell size is far more complicated and less deterministic than originally thought. Focusing on bacteria and yeast, here we review efforts to understand the molecular mechanisms underlying the relationship between growth rate and cell size.
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Affiliation(s)
- Douglas R Kellogg
- Department of Molecular, Cell, and Developmental Biology, University of California, Santa Cruz, Santa Cruz, CA 95064, USA.
| | - Petra Anne Levin
- Department of Biology, Washington University in St. Louis, St Louis, MO 63130, USA; Center for Science & Engineering of Living Systems (CSELS), McKelvey School of Engineering, Washington University in St Louis, St Louis, MO 63130, USA.
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8
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Chien CC, Jiang J, Gong B, Li T, Gaitas A. AFM Microfluidic Cantilevers as Weight Sensors for Live Single Cell Mass Measurements. MEASUREMENT SCIENCE & TECHNOLOGY 2022; 33:095009. [PMID: 35832465 PMCID: PMC9273105 DOI: 10.1088/1361-6501/ac7280] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/15/2023]
Abstract
Reliably measuring small mass changes at the single-cell level is challenging. In this manuscript, we report the use of microfluidic cantilevers in liquid with sub-nanogram scale weight sensing capability for the measurement of cellular mass changes of living single cells. With this instrumentation, we were able to perform fast mass measurements within 3 minutes. We show results of mass measurements of polystyrene and metal beads of various sizes (smallest weight measured at 280 ± 95 pg) and live single-cell mass measurements in a physiologically relevant environment. We also performed finite element analysis to simulate and optimize the structural design and materials of cantilevers. Our simulation results indicate that using polymer materials, such as SU8 and polyimide, could improve the minimal detectable mass by 3-fold compared to conventional silicon cantilevers. The simulations also suggest that smaller dimensions of length, width, and thickness would improve the mass detection capability of microfluidic cantilevers.
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Affiliation(s)
- Chen-Chi Chien
- The Estelle and Daniel Maggin Department of Neurology, Icahn School of Medicine at Mount Sinai, New York, New York 10029, USA
| | - Jiaxin Jiang
- Department of Electrical Engineering and Computer Science, University of Cincinnati, Cincinnati, OH 45221, USA
| | - Bin Gong
- Department of Pathology, University of Texas Medical Branch, Galveston, Texas 77555, USA. Sealy Center for Vector Borne and Zoonotic Diseases, University of Texas Medical Branch, Galveston, Texas 77555, USA
- Center of Biodefense and Emerging Infectious Diseases, University of Texas Medical Branch, Galveston, Texas 77555, USA
- Institute for Human Infectious and Immunity, University of Texas Medical Branch, Galveston, Texas 77555, USA
| | - Tao Li
- Department of Electrical Engineering and Computer Science, University of Cincinnati, Cincinnati, OH 45221, USA
| | - Angelo Gaitas
- The Estelle and Daniel Maggin Department of Neurology, Icahn School of Medicine at Mount Sinai, New York, New York 10029, USA
- BioMedical Engineering & Imaging Institute, Leon and Norma Hess Center for Science and Medicine, New York, New York 10029, USA
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9
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Torvi JR, Wong J, Serwas D, Moayed A, Drubin DG, Barnes G. Reconstitution of kinetochore motility and microtubule dynamics reveals a role for a kinesin-8 in establishing end-on attachments. eLife 2022; 11:e78450. [PMID: 35791811 PMCID: PMC9259035 DOI: 10.7554/elife.78450] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2022] [Accepted: 06/21/2022] [Indexed: 11/30/2022] Open
Abstract
During mitosis, individual microtubules make attachments to chromosomes via a specialized protein complex called the kinetochore to faithfully segregate the chromosomes to daughter cells. Translocation of kinetochores on the lateral surface of the microtubule has been proposed to contribute to high fidelity chromosome capture and alignment at the mitotic midzone, but has been difficult to observe in vivo because of spatial and temporal constraints. To overcome these barriers, we used total internal reflection fluorescence (TIRF) microscopy to track the interactions between microtubules, kinetochore proteins, and other microtubule-associated proteins in lysates from metaphase-arrested Saccharomyces cerevisiae. TIRF microscopy and cryo-correlative light microscopy and electron tomography indicated that we successfully reconstituted interactions between intact kinetochores and microtubules. These kinetochores translocate on the lateral microtubule surface toward the microtubule plus end and transition to end-on attachment, whereupon microtubule depolymerization commences. The directional kinetochore movement is dependent on the highly processive kinesin-8, Kip3. We propose that Kip3 facilitates stable kinetochore attachment to microtubule plus ends through its abilities to move the kinetochore laterally on the surface of the microtubule and to regulate microtubule plus end dynamics.
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Affiliation(s)
- Julia R Torvi
- Department of Molecular and Cell Biology, University of California, BerkeleyBerkeleyUnited States
- Biophysics Graduate Group, University of California, BerkeleyBerkeleyUnited States
| | - Jonathan Wong
- Department of Molecular and Cell Biology, University of California, BerkeleyBerkeleyUnited States
| | - Daniel Serwas
- Department of Molecular and Cell Biology, University of California, BerkeleyBerkeleyUnited States
| | - Amir Moayed
- Department of Molecular and Cell Biology, University of California, BerkeleyBerkeleyUnited States
| | - David G Drubin
- Department of Molecular and Cell Biology, University of California, BerkeleyBerkeleyUnited States
- Biophysics Graduate Group, University of California, BerkeleyBerkeleyUnited States
| | - Georjana Barnes
- Department of Molecular and Cell Biology, University of California, BerkeleyBerkeleyUnited States
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10
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Production of Carotenoids and Phospholipids by Thraustochytrium sp. in Batch and Repeated-Batch Culture. Mar Drugs 2022; 20:md20070416. [PMID: 35877709 PMCID: PMC9325111 DOI: 10.3390/md20070416] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2022] [Revised: 06/07/2022] [Accepted: 06/21/2022] [Indexed: 02/06/2023] Open
Abstract
The carotenogenic thraustochytrid Thraustochytrium sp. RT2316-16 was grown in batch and repeated-batch cultures using different feeds containing glucose, or glycerol, and yeast extract, for the production of lipids, phospholipids and carotenoids. RT2316-16 produced canthaxanthin, astaxanthin and β-carotene. The effects of biotin, ascorbic acid, light and temperature were evaluated in some of the experiments. In 2-day-old batch cultures, the combined mass percentage of eicosapentaenoic acid and docosahexaenoic acid in total lipids was between 16.5% (glycerol-based medium in the dark; biomass concentration = 4.2 ± 1.1 g L−1) and 42.6% (glucose-based medium under light; biomass concentration = 3.3 ± 0.1 g L−1), decreasing to 3.8% and 6.1%, respectively, after day 4. In repeated-batch cultures, the total lipids in the biomass increased after glucose or glycerol was fed alone, whereas the total carotenoids (168 ± 7 μg g−1 dry weight (DW)) and phospholipids in the biomass increased after feeding with yeast extract. The biomass with the highest content of phospholipids (28.7 ± 4.3 mg g−1 DW) was obtained using a feed medium formulated with glycerol, yeast extract and ascorbic acid. Glycerol was the best carbon source for the production of a biomass enriched with total lipids (467 ± 45 mg g−1 DW). The composition of carotenoids depended strongly on the composition of the feed. Repeated-batch cultures fed with yeast extract contained canthaxanthin as the main carotenoid, whereas in the cultures fed only with glucose, the biomass contained mainly β-carotene.
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11
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High-resolution mass measurements of single budding yeast reveal linear growth segments. Nat Commun 2022; 13:3483. [PMID: 35732645 PMCID: PMC9217925 DOI: 10.1038/s41467-022-30781-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2019] [Accepted: 05/18/2022] [Indexed: 11/08/2022] Open
Abstract
The regulation of cell growth has fundamental physiological, biotechnological and medical implications. However, methods that can continuously monitor individual cells at sufficient mass and time resolution hardly exist. Particularly, detecting the mass of individual microbial cells, which are much smaller than mammalian cells, remains challenging. Here, we modify a previously described cell balance ('picobalance') to monitor the proliferation of single cells of the budding yeast, Saccharomyces cerevisiae, under culture conditions in real time. Combined with optical microscopy to monitor the yeast morphology and cell cycle phase, the picobalance approaches a total mass resolution of 0.45 pg. Our results show that single budding yeast cells (S/G2/M phase) increase total mass in multiple linear segments sequentially, switching their growth rates. The growth rates weakly correlate with the cell mass of the growth segments, and the duration of each growth segment correlates negatively with cell mass. We envision that our technology will be useful for direct, accurate monitoring of the growth of single cells throughout their cycle.
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12
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Microfluidic-Enabled Multi-Cell-Densities-Patterning and Culture Device for Characterization of Yeast Strains’ Growth Rates under Mating Pheromone. CHEMOSENSORS 2022. [DOI: 10.3390/chemosensors10040141] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]
Abstract
Yeast studies usually focus on exploring diversity in terms of a specific trait (such as growth rate, antibiotic resistance, or fertility) among extensive strains. Microfluidic chips improve these biological studies in a manner of high throughput and high efficiency. For a population study of yeast, it is of great significance to set a proper initial cell density for every strain under specific circumstances. Herein, we introduced a novel design of chip, which enables users to load cells in a gradient order (six alternatives) of initial cell density within one channel. We discussed several guidelines to choose the appropriate chamber to ensure successful data recording. With this chip, we successfully studied the growth rate of yeast strains under a mating response, which is crucial for yeasts to control growth behaviors for prosperous mating. We investigated the growth rate of eight different yeast strains under three different mating pheromone levels (0.3 μM, 1 μM, and 10 μM). Strains with, even, a six-fold in growth rate can be recorded, with the available data produced simultaneously. This work has provided an efficient and time-saving microfluidic platform, which enables loading cells in a pattern of multi-cell densities for a yeast population experiment, especially for a high-throughput study. Besides, a quantitatively analyzed growth rate of different yeast strains shall reveal inspiring perspectives for studies concerning yeast population behavior with a stimulated mating pheromone.
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13
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Population balance modelling captures host cell protein dynamics in CHO cell cultures. PLoS One 2022; 17:e0265886. [PMID: 35320326 PMCID: PMC8959726 DOI: 10.1371/journal.pone.0265886] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2021] [Accepted: 03/09/2022] [Indexed: 11/19/2022] Open
Abstract
Monoclonal antibodies (mAbs) have been extensively studied for their wide therapeutic and research applications. Increases in mAb titre has been achieved mainly by cell culture media/feed improvement and cell line engineering to increase cell density and specific mAb productivity. However, this improvement has shifted the bottleneck to downstream purification steps. The higher accumulation of the main cell-derived impurities, host cell proteins (HCPs), in the supernatant can negatively affect product integrity and immunogenicity in addition to increasing the cost of capture and polishing steps. Mathematical modelling of bioprocess dynamics is a valuable tool to improve industrial production at fast rate and low cost. Herein, a single stage volume-based population balance model (PBM) has been built to capture Chinese hamster ovary (CHO) cell behaviour in fed-batch bioreactors. Using cell volume as the internal variable, the model captures the dynamics of mAb and HCP accumulation extracellularly under physiological and mild hypothermic culture conditions. Model-based analysis and orthogonal measurements of lactate dehydrogenase activity and double-stranded DNA concentration in the supernatant show that a significant proportion of HCPs found in the extracellular matrix is secreted by viable cells. The PBM then served as a platform for generating operating strategies that optimise antibody titre and increase cost-efficiency while minimising impurity levels.
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14
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Guerra P, Vuillemenot LA, Rae B, Ladyhina V, Milias-Argeitis A. Systematic In Vivo Characterization of Fluorescent Protein Maturation in Budding Yeast. ACS Synth Biol 2022; 11:1129-1141. [PMID: 35180343 PMCID: PMC8938947 DOI: 10.1021/acssynbio.1c00387] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
![]()
Fluorescent protein
(FP) maturation can limit the accuracy with
which dynamic intracellular processes are captured and reduce the in vivo brightness of a given FP in fast-dividing cells.
The knowledge of maturation timescales can therefore help users determine
the appropriate FP for each application. However, in vivo maturation rates can greatly deviate from in vitro estimates that are mostly available. In this work, we present the
first systematic study of in vivo maturation for
12 FPs in budding yeast. To overcome the technical limitations of
translation inhibitors commonly used to study FP maturation, we implemented
a new approach based on the optogenetic stimulations of FP expression
in cells grown under constant nutrient conditions. Combining the rapid
and orthogonal induction of FP transcription with a mathematical model
of expression and maturation allowed us to accurately estimate maturation
rates from microscopy data in a minimally invasive manner. Besides
providing a useful resource for the budding yeast community, we present
a new joint experimental and computational approach for characterizing
FP maturation, which is applicable to a wide range of organisms.
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Affiliation(s)
- Paolo Guerra
- Molecular Systems Biology, Groningen Biomolecular Sciences & Biotechnology Institute, University of Groningen, 9747 AG Groningen, Netherlands
| | - Luc-Alban Vuillemenot
- Molecular Systems Biology, Groningen Biomolecular Sciences & Biotechnology Institute, University of Groningen, 9747 AG Groningen, Netherlands
| | - Brady Rae
- Molecular Systems Biology, Groningen Biomolecular Sciences & Biotechnology Institute, University of Groningen, 9747 AG Groningen, Netherlands
| | - Valeriia Ladyhina
- Molecular Systems Biology, Groningen Biomolecular Sciences & Biotechnology Institute, University of Groningen, 9747 AG Groningen, Netherlands
| | - Andreas Milias-Argeitis
- Molecular Systems Biology, Groningen Biomolecular Sciences & Biotechnology Institute, University of Groningen, 9747 AG Groningen, Netherlands
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15
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Bordhan P, Razavi Bazaz S, Jin D, Ebrahimi Warkiani M. Advances and enabling technologies for phase-specific cell cycle synchronisation. LAB ON A CHIP 2022; 22:445-462. [PMID: 35076046 DOI: 10.1039/d1lc00724f] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/14/2023]
Abstract
Cell cycle synchronisation is the process of isolating cell populations at specific phases of the cell cycle from heterogeneous, asynchronous cell cultures. The process has important implications in targeted gene-editing and drug efficacy of cells and in studying cell cycle events and regulatory mechanisms involved in the cell cycle progression of multiple cell species. Ideally, cell cycle synchrony techniques should be applicable for all cell types, maintain synchrony across multiple cell cycle events, maintain cell viability and be robust against metabolic and physiological perturbations. In this review, we categorize cell cycle synchronisation approaches and discuss their operational principles and performance efficiencies. We highlight the advances and technological development trends from conventional methods to the more recent microfluidics-based systems. Furthermore, we discuss the opportunities and challenges for implementing high throughput cell synchronisation and provide future perspectives on synchronisation platforms, specifically hybrid cell synchrony modalities, to allow the highest level of phase-specific synchrony possible with minimal alterations in diverse types of cell cultures.
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Affiliation(s)
- Pritam Bordhan
- School of Biomedical Engineering, University of Technology Sydney, Sydney, New South Wales 2007, Australia.
- Institute for Biomedical Materials & Devices, Faculty of Science, University of Technology Sydney, New South Wales 2007, Australia
| | - Sajad Razavi Bazaz
- School of Biomedical Engineering, University of Technology Sydney, Sydney, New South Wales 2007, Australia.
- Institute for Biomedical Materials & Devices, Faculty of Science, University of Technology Sydney, New South Wales 2007, Australia
| | - Dayong Jin
- Institute for Biomedical Materials & Devices, Faculty of Science, University of Technology Sydney, New South Wales 2007, Australia
| | - Majid Ebrahimi Warkiani
- School of Biomedical Engineering, University of Technology Sydney, Sydney, New South Wales 2007, Australia.
- Institute for Biomedical Materials & Devices, Faculty of Science, University of Technology Sydney, New South Wales 2007, Australia
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16
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Wang Q, Zhang L, Qu J, Wu X, Sun X, Ji D, Li Y. DUSP6 inhibits the proliferation of hair follicle stem cells (HFSCs) in vitro. Anim Biotechnol 2022. [PMID: 37524308 DOI: 10.1080/10495398.2021.2016433] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/01/2022]
Abstract
RNA-seq has shown that the DUSP6 and MAPK signaling pathways are associated with the production of high-quality brush hair (type III hair) in Yangtze River Delta white goats. However, there are few reports on the regulatory effects of DUSP6 expression on hair follicle stem cells (HFSCs) and cellular processes, as well as the underlying mechanism. Here, we investigated the effect of DUSP6 level in HFSCs and the molecular mechanism underlying the functional regulation of HFSCs by DUSP6. Overexpression of DUSP6 significantly suppressed the proliferation of HFSCs by inducing cell cycle arrest in the G1 phase and by promoting apoptosis. Transcriptome analysis revealed a total of 217 differentially expressed genes between DUSP6-overexpressing and control HFSCs, of which 33 (15.2%) were upregulated in DUSP6-overexpressing cells. The two pathways with the most significant enrichment of differentially expressed genes were the TNF signaling pathway and cytokine-cytokine receptor interaction pathway, and the significantly enriched terms in the GO enrichment analysis involved cell attachment and cytokines. These results indicate that DUSP6 can function as an inhibitory factor in HFSCs through the induction of cell cycle arrest in the G1 phase and can promote apoptosis by mediating crosstalk among several pathways and cytokines.HighlightsWe constructed DUSP6 overexpression vectors to detect mRNA and protein expression levels related to high-quality brush hair in MAPK signaling pathway.We found that high expression level of DUSP6 can inhibit the proliferation of hair follicle stem cells (HFSCs) and promote cell apoptosis of HFSCs.DUSP6 may be involved in the growth regulation of HFSCs like Other studies in cancer, tumors by regulating the expression of cytokines, changing the transmission of signals between cells, activating or suppressing immune-related pathways.
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Affiliation(s)
- Qiang Wang
- Key Laboratory for Animal Genetics & Molecular Breeding of Jiangsu Province, College of Animal Science and Technology, Yangzhou University, Yangzhou, China
| | - Liuming Zhang
- Key Laboratory for Animal Genetics & Molecular Breeding of Jiangsu Province, College of Animal Science and Technology, Yangzhou University, Yangzhou, China
| | - Jingwen Qu
- Key Laboratory for Animal Genetics & Molecular Breeding of Jiangsu Province, College of Animal Science and Technology, Yangzhou University, Yangzhou, China
| | - Xi Wu
- Key Laboratory for Animal Genetics & Molecular Breeding of Jiangsu Province, College of Animal Science and Technology, Yangzhou University, Yangzhou, China
| | - XiaoMei Sun
- Key Laboratory for Animal Genetics & Molecular Breeding of Jiangsu Province, College of Animal Science and Technology, Yangzhou University, Yangzhou, China
| | - Dejun Ji
- Key Laboratory for Animal Genetics & Molecular Breeding of Jiangsu Province, College of Animal Science and Technology, Yangzhou University, Yangzhou, China
| | - Yongjun Li
- Key Laboratory for Animal Genetics & Molecular Breeding of Jiangsu Province, College of Animal Science and Technology, Yangzhou University, Yangzhou, China
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17
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Wang N, Yang Q, Wang J, Shi R, Li M, Gao J, Xu W, Yang Y, Chen Y, Chen S. Integration of Transcriptome and Methylome Highlights the Roles of Cell Cycle and Hippo Signaling Pathway in Flatfish Sexual Size Dimorphism. Front Cell Dev Biol 2021; 9:743722. [PMID: 34926443 PMCID: PMC8675331 DOI: 10.3389/fcell.2021.743722] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2021] [Accepted: 10/29/2021] [Indexed: 01/14/2023] Open
Abstract
Sexual size dimorphism (SSD) is the difference in segments or body size between sexes prevalent in various species. Understanding the genetic architecture of SSD has remained a significant challenge owing to the complexity of growth mechanisms and the sexual influences among species. The Chinese tongue sole (Cynoglossus semilaevis), which exhibits a female-biased SSD and sex reversal from female to pseudomale, is an ideal model for exploring SSD mechanism at the molecular level. The present study aimed to integrate transcriptome and methylome analysis to unravel the genetic and epigenetic changes in female, male, and pseudomale C. semilaevis. The somatotropic and reproductive tissues (brain, liver, gonad, and muscle) transcriptomes were characterized by RNA-seq technology. Transcriptomic analysis unravelled numerous differentially expressed genes (DEGs) involved in cell growth and death-related pathways. The gonad and muscle methylomes were further employed for screening differentially methylated genes (DMGs). Relatively higher DNA methylation levels were observed in the male and pseudomale individuals. In detail, hypermethylation of the chromosome W was pronounced in the pseudomale group than in the female group. Furthermore, weighted gene co-expression network analysis showed that turquoise and brown modules positively and negatively correlated with the female-biased SSD, respectively. A combined analysis of the module genes and DMGs revealed the female-biased mRNA transcripts and hypomethylated levels in the upstream and downstream regions across the cell cycle-related genes. Moreover, the male and pseudomale-biased gene expression in the hippo signaling pathway were positively correlated with their hypermethylation levels in the gene body. These findings implied that the activation of the cell cycle and the inhibition of the hippo signaling pathway were implicated in C. semilaevis female-biased SSD. In addition, the dynamic expression pattern of the epigenetic regulatory factors, including dnmt1, dnmt3a, dnmt3b, and uhrf1, among the different sexes correspond with their distinct DNA methylation levels. Herein, we provide valuable clues for understanding female-biased SSD in C. semilaevis.
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Affiliation(s)
- Na Wang
- Key Laboratory for Sustainable Development of Marine Fisheries, Ministry of Agriculture and Rural Affairs, Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Qingdao, China.,Laboratory for Marine Fisheries Science and Food Production Processes, Qingdao National Laboratory for Marine Science and Technology, Qingdao, China.,Shandong Key Laboratory of Marine Fisheries Biotechnology and Genetic Breeding, Qingdao, China
| | - Qian Yang
- Key Laboratory for Sustainable Development of Marine Fisheries, Ministry of Agriculture and Rural Affairs, Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Qingdao, China.,College of Fisheries and Life Science, Shanghai Ocean University, Shanghai, China
| | - Jialin Wang
- Key Laboratory for Sustainable Development of Marine Fisheries, Ministry of Agriculture and Rural Affairs, Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Qingdao, China.,College of Fisheries and Life Science, Shanghai Ocean University, Shanghai, China
| | - Rui Shi
- Key Laboratory for Sustainable Development of Marine Fisheries, Ministry of Agriculture and Rural Affairs, Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Qingdao, China.,College of Fisheries and Life Science, Shanghai Ocean University, Shanghai, China
| | - Ming Li
- Key Laboratory for Sustainable Development of Marine Fisheries, Ministry of Agriculture and Rural Affairs, Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Qingdao, China.,Laboratory for Marine Fisheries Science and Food Production Processes, Qingdao National Laboratory for Marine Science and Technology, Qingdao, China
| | - Jin Gao
- College of Fisheries and Life Science, Shanghai Ocean University, Shanghai, China
| | - Wenteng Xu
- Key Laboratory for Sustainable Development of Marine Fisheries, Ministry of Agriculture and Rural Affairs, Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Qingdao, China.,Laboratory for Marine Fisheries Science and Food Production Processes, Qingdao National Laboratory for Marine Science and Technology, Qingdao, China.,Shandong Key Laboratory of Marine Fisheries Biotechnology and Genetic Breeding, Qingdao, China
| | - Yingming Yang
- Key Laboratory for Sustainable Development of Marine Fisheries, Ministry of Agriculture and Rural Affairs, Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Qingdao, China.,Laboratory for Marine Fisheries Science and Food Production Processes, Qingdao National Laboratory for Marine Science and Technology, Qingdao, China.,Shandong Key Laboratory of Marine Fisheries Biotechnology and Genetic Breeding, Qingdao, China
| | - Yadong Chen
- Key Laboratory for Sustainable Development of Marine Fisheries, Ministry of Agriculture and Rural Affairs, Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Qingdao, China.,Laboratory for Marine Fisheries Science and Food Production Processes, Qingdao National Laboratory for Marine Science and Technology, Qingdao, China.,Shandong Key Laboratory of Marine Fisheries Biotechnology and Genetic Breeding, Qingdao, China
| | - Songlin Chen
- Key Laboratory for Sustainable Development of Marine Fisheries, Ministry of Agriculture and Rural Affairs, Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Qingdao, China.,Laboratory for Marine Fisheries Science and Food Production Processes, Qingdao National Laboratory for Marine Science and Technology, Qingdao, China.,Shandong Key Laboratory of Marine Fisheries Biotechnology and Genetic Breeding, Qingdao, China
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18
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Wang YC, Ku WC, Liu CY, Cheng YC, Chien CC, Chang KW, Huang CJ. Supplementation of Probiotic Butyricicoccus pullicaecorum Mediates Anticancer Effect on Bladder Urothelial Cells by Regulating Butyrate-Responsive Molecular Signatures. Diagnostics (Basel) 2021; 11:diagnostics11122270. [PMID: 34943506 PMCID: PMC8700285 DOI: 10.3390/diagnostics11122270] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2021] [Revised: 11/30/2021] [Accepted: 12/02/2021] [Indexed: 11/30/2022] Open
Abstract
In bladder cancer, urothelial carcinoma is the most common histologic subtype, accounting for more than 90% of cases. Pathogenic effects due to the dysbiosis of gut microbiota are localized not only in the colon, but also in regulating bladder cancer distally. Butyrate, a short-chain fatty acid produced by gut microbial metabolism, is mainly studied in colon diseases. Therefore, the resolution of the anti-cancer effects of butyrate-producing microbes on bladder urothelial cells and knowledge of the butyrate-responsive molecules must have clinical significance. Here, we demonstrate a correlation between urothelial cancer of the bladder and Butyricicoccus pullicaecorum. This butyrate-producing microbe or their metabolite, butyrate, mediated anti-cancer effects on bladder urothelial cells by regulating cell cycle, cell growth, apoptosis, and gene expression. For example, a tumor suppressor against urothelial cancer of the bladder, bladder cancer-associated protein, was induced in butyrate-treated HT1376 cells, a human urinary bladder cancer cell line. In conclusion, urothelial cancer of the bladder is a significant health problem. To improve the health of bladder urothelial cells, supplementation of B. pullicaecorum may be necessary and can further regulate butyrate-responsive molecular signatures.
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Affiliation(s)
- Yen-Chieh Wang
- Department of Urology, Cathay General Hospital, Taipei 106438, Taiwan;
- School of Medicine, College of Medicine, Fu Jen Catholic University, New Taipei 242062, Taiwan; (W.-C.K.); (C.-Y.L.); (Y.-C.C.); (C.-C.C.)
| | - Wei-Chi Ku
- School of Medicine, College of Medicine, Fu Jen Catholic University, New Taipei 242062, Taiwan; (W.-C.K.); (C.-Y.L.); (Y.-C.C.); (C.-C.C.)
| | - Chih-Yi Liu
- School of Medicine, College of Medicine, Fu Jen Catholic University, New Taipei 242062, Taiwan; (W.-C.K.); (C.-Y.L.); (Y.-C.C.); (C.-C.C.)
- Department of Pathology, Sijhih Cathay General Hospital, New Taipei 221037, Taiwan
| | - Yu-Che Cheng
- School of Medicine, College of Medicine, Fu Jen Catholic University, New Taipei 242062, Taiwan; (W.-C.K.); (C.-Y.L.); (Y.-C.C.); (C.-C.C.)
- Department of Medical Research, Cathay General Hospital, Taipei 106438, Taiwan
- Department of Biomedical Sciences and Engineering, National Central University, Taoyuan 320317, Taiwan
| | - Chih-Cheng Chien
- School of Medicine, College of Medicine, Fu Jen Catholic University, New Taipei 242062, Taiwan; (W.-C.K.); (C.-Y.L.); (Y.-C.C.); (C.-C.C.)
- Department of Anesthesiology, Cathay General Hospital, Taipei 106438, Taiwan
| | - Kang-Wei Chang
- Taipei Neuroscience Institute, Taipei Medical University, Taipei 110301, Taiwan;
- Laboratory Animal Center, Taipei Medical University, Taipei 110301, Taiwan
| | - Chi-Jung Huang
- Department of Medical Research, Cathay General Hospital, Taipei 106438, Taiwan
- Department of Biochemistry, National Defense Medical Center, Taipei 114201, Taiwan
- Correspondence:
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19
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Sharmin MM, Hayashi S, Miyaji M, Ishizaki H, Matsuyama H, Haga S, Yonekura S. IGF-1 induces IRE1-XBP1-dependent endoplasmic reticulum biogenesis in bovine mammary epithelial cells. J Dairy Sci 2021; 104:12094-12104. [PMID: 34364639 DOI: 10.3168/jds.2021-20268] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2021] [Accepted: 06/18/2021] [Indexed: 11/19/2022]
Abstract
Insulin-like growth factor-1 (IGF-1) plays a key role in proliferation and galactopoiesis in mammary epithelial cells (MEC), but its definitive functions on endoplasmic reticulum (ER) during protein synthesis remain unknown. The present study aimed to elucidate the effects of IGF-1 on ER biogenesis in MEC in vitro and examined the expression of ER biogenesis-associated genes in the mammary gland during early lactation. We treated mammary alveolar cells-large T antigen cells (immortalized bovine MEC line established via stable transfection with simian virus-40 large T-antigen) with IGF-1 and examined ER biogenesis using the fluorescence intensity of an ER tracker and quantitative real-time PCR. We found IGF-1 significantly increased ER tracker staining and upregulated mRNA levels of ER biogenesis-related genes, such as CHKA (choline kinase α), PCYT1A (choline-phosphate cytidylyltransferase A), and SURF4 (surfeit locus protein 4). We focused on unfolded protein response to explore molecular mechanisms by which IGF-1 induces ER biogenesis. We found IGF-1 significantly increased mRNA levels of the XBP1 splicing form (XBP1s). Based on western blot analysis, IGF-1 induced the expression of (inositol-requiring kinase 1 α) protein, upstream of XBP1s, and phosphorylated-IRE1α. The inhibition of IRE1 endoribonuclease activity with 4-methylumbelliferone 8-carbaldehyde (4μ8C) significantly suppressed the increase in ER tracker fluorescence and ER biogenesis-related gene expression induced by IGF-1. Also, IGF-1-induced XBP1s and ER biogenesis-associated gene expression was inhibited by rapamycin, an inhibitor of mTORC1 (mammalian target of rapamycin complex 1), indicating that IRE1-XBP1 activation by IGF-1 is mediated by mTORC1. Moreover, to clarify the expression of XBP1s and ER biogenesis-associated genes expression under normal physiological conditions, mammary gland tissue from biopsies of dairy cows during late gestation and lactation were analyzed. In vivo data highlighted the significant increases in the mRNA levels of XBP1s and ER biogenesis-related genes in mammary gland tissue immediately after calving through 6 wk of lactation. The mRNA levels of IGF1R (IGF-1 receptor) in mammary glands increased during 6 wk of lactation. Therefore, the present study indicated for the first time that IGF-1 induces ER biogenesis by activating the IRE1-XBP1 axis under the regulation of mTORC1 in bovine MEC line.
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Affiliation(s)
- Mst Mamuna Sharmin
- Graduate School of Medicine, Science and Technology, Shinshu University, 8304 Minamiminowa, Kamiina, Nagano 399-4598, Japan
| | - Satoko Hayashi
- Graduate School of Medicine, Science and Technology, Shinshu University, 8304 Minamiminowa, Kamiina, Nagano 399-4598, Japan
| | - Makoto Miyaji
- Feed Production and Utilization Group, Division of Dairy Production Research, Hokkaido Agricultural Research Center, NARO, 1 Hitsujigaoka, Toyohira, Sapporo, Hokkaido 062-8555, Japan
| | - Hiroshi Ishizaki
- Grazing Animal Unit, Division of Grassland Farming, Institute of Livestock and Grassland Science, NARO, 768 Senbonmatsu, Nasushiobara, Tochigi 329-2793, Japan
| | - Hiroki Matsuyama
- Faculty of Agriculture, Yamagata University, Tsuruoka, Yamagata 997-8555, Japan
| | - Satoshi Haga
- Grazing Animal Unit, Division of Grassland Farming, Institute of Livestock and Grassland Science, NARO, 768 Senbonmatsu, Nasushiobara, Tochigi 329-2793, Japan
| | - Shinichi Yonekura
- Graduate School of Medicine, Science and Technology, Shinshu University, 8304 Minamiminowa, Kamiina, Nagano 399-4598, Japan; Department of Biomolecular Innovation, Institute for Biomedical Sciences, Shinshu University, 8304 Minamiminowa, Kamiina, Nagano 399-4598, Japan.
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20
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Kusuhara A, Babayev E, Zhou LT, Singh VP, Gerton JL, Duncan FE. Immature Follicular Origins and Disrupted Oocyte Growth Pathways Contribute to Decreased Gamete Quality During Reproductive Juvenescence in Mice. Front Cell Dev Biol 2021; 9:693742. [PMID: 34222262 PMCID: PMC8244820 DOI: 10.3389/fcell.2021.693742] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2021] [Accepted: 05/24/2021] [Indexed: 12/26/2022] Open
Abstract
Egg quality dictates fertility outcomes, and although there is a well-documented decline with advanced reproductive age, how it changes during puberty is less understood. Such knowledge is critical, since advances in Assisted Reproductive Technologies are enabling pre- and peri-pubertal patients to preserve fertility in the medical setting. Therefore, we investigated egg quality parameters in a mouse model of the pubertal transition or juvenescence (postnatal day; PND 11-40). Animal weight, vaginal opening, serum inhibin B levels, oocyte yield, oocyte diameter, and zona pellucida thickness increased with age. After PND 15, there was an age-associated ability of oocytes to resume meiosis and reach metaphase of meiosis II (MII) following in vitro maturation (IVM). However, eggs from the younger cohort (PND 16-20) had significantly more chromosome configuration abnormalities relative to the older cohorts and many were at telophase I instead of MII, indicative of a cell cycle delay. Oocytes from the youngest mouse cohorts originated from the smallest antral follicles with the fewest cumulus layers per oocyte, suggesting a more developmentally immature state. RNA Seq analysis of oocytes from mice at distinct ages revealed that the genes involved in cellular growth signaling pathways (PI3K, mTOR, and Hippo) were consistently repressed with meiotic competence, whereas genes involved in cellular communication were upregulated in oocytes with age. Taken together, these data demonstrate that gametes harvested during the pubertal transition have low meiotic maturation potential and derive from immature follicular origins.
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Affiliation(s)
- Atsuko Kusuhara
- Department of Obstetrics and Gynecology, Feinberg School of Medicine, Northwestern University, Chicago, IL, United States
| | - Elnur Babayev
- Department of Obstetrics and Gynecology, Feinberg School of Medicine, Northwestern University, Chicago, IL, United States
| | - Luhan T. Zhou
- Department of Obstetrics and Gynecology, Feinberg School of Medicine, Northwestern University, Chicago, IL, United States
| | - Vijay P. Singh
- Stowers Institute for Medical Research, Kansas City, MO, United States
| | | | - Francesca E. Duncan
- Department of Obstetrics and Gynecology, Feinberg School of Medicine, Northwestern University, Chicago, IL, United States
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21
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Fang R, Wang X, Xia Q, Zhao M, Zhang H, Wang X, Ye S, Cheng K, Liang Y, Cheng Y, Gu Y, Rao Q. Nuclear translocation of ASPL-TFE3 fusion protein creates favorable metabolism by mediating autophagy in translocation renal cell carcinoma. Oncogene 2021; 40:3303-3317. [PMID: 33846569 DOI: 10.1038/s41388-021-01776-8] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2020] [Revised: 03/10/2021] [Accepted: 03/29/2021] [Indexed: 02/01/2023]
Abstract
The ASPL-TFE3 fusion gene, resulting from t(X;17)(p11.2;q25.3), is one of the most commonly identified fusion genes in Xp11 translocation renal cell carcinoma (tRCC). However, its roles and underlying mechanism in RCC development are not yet clear. Here, we identified ASPL-TFE3 fusion as the most common tRCC subtype in a Chinese population (29/126, 23.03%). This fusion protein translocated into the nucleus and promoted RCC cell proliferation both in vitro and in vivo. Mechanistically, the fusion protein transcriptionally activated the lysosome-autophagy pathway by binding to the promoters of lysosome-related genes. Autophagy, activated by ASPL-TFE3, enabled RCC cells to escape energy stress by promoting the utilization of proteins and lipids. Moreover, we found that the ASPL-TFE3 fusion escaped regulation by the classic mTOR-TFE3 signal and instead activated phospho-mTOR and its downstream targets. Finally, targeting both autophagy and the mTOR axis resulted in a greater antiproliferative effect than single pathway inhibition. In summary, these results confirmed the ASPL-TFE3 fusion as a master regulator of metabolic adaptation mediated by autophagy in tRCC. The simultaneous manipulation of autophagy and the mTOR axis may represent a novel treatment strategy for ASPL-TFE3 fusion RCC.
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Affiliation(s)
- Ru Fang
- Department of Pathology, Jinling Hospital, Nanjing University School of Medicine, Nanjing, Jiangsu, China
| | - Xiaotong Wang
- Department of Pathology, Jinling Hospital, Nanjing University School of Medicine, Nanjing, Jiangsu, China
| | - Qiuyuan Xia
- Department of Pathology, Jinling Hospital, Nanjing University School of Medicine, Nanjing, Jiangsu, China
| | - Ming Zhao
- Department of Pathology, Zhejiang Provincial People's Hospital, People's Hospital of Hangzhou Medical College, Hangzhou, Zhejiang, China
| | - Hao Zhang
- Department of Nephrology, Nanjing First Hospital, Nanjing Medical University, Nanjing, Jiangsu, China
| | - Xuan Wang
- Department of Pathology, Jinling Hospital, Nanjing University School of Medicine, Nanjing, Jiangsu, China
| | - Shengbing Ye
- Department of Pathology, Jinling Hospital, Nanjing University School of Medicine, Nanjing, Jiangsu, China
| | - Kai Cheng
- Department of Pathology, Jinling Hospital, Nanjing University School of Medicine, Nanjing, Jiangsu, China
| | - Yan Liang
- Department of Pathology, Jinling Hospital, Nanjing University School of Medicine, Nanjing, Jiangsu, China
| | - Yang Cheng
- Health Management Center, Geriatric Hospital of Nanjing Medical University, Nanjing, Jiangsu, China.
| | - Yayun Gu
- State Key Laboratory of Reproductive Medicine, Center for Global Health, School of Public Health, Nanjing Medical University, Nanjing, Jiangsu, China.
| | - Qiu Rao
- Department of Pathology, Jinling Hospital, Nanjing University School of Medicine, Nanjing, Jiangsu, China.
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22
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The linkage of cell cycle and DNA replication with growth difference in female Chinese tongue sole (Cynoglossus semilaevis): Analysis from transcriptomic study and WGCNA. COMPARATIVE BIOCHEMISTRY AND PHYSIOLOGY D-GENOMICS & PROTEOMICS 2021; 39:100833. [PMID: 33848768 DOI: 10.1016/j.cbd.2021.100833] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/20/2021] [Revised: 03/19/2021] [Accepted: 04/02/2021] [Indexed: 11/21/2022]
Abstract
In addition to the typical sexual size dimorphism, considerable size differences within the female population of the Chinese tongue sole (Cynoglossus semilaevis) have become a further bottleneck of the improvement of sole aquaculture. To identify the internal mechanism, transcriptomic analysis and weighted gene co-expression network analysis (WGCNA) were employed simultaneously. Transcriptomic analyses of brain, pituitary gland, liver, gonad, and muscle tissues from two female groups with size differences identified 109, 698, 1325, 2299, and 2141 differentially expressed genes (DEGs), respectively. The results of these enrichment analyses suggest that the up-regulation of neuroactive ligand-receptor interaction, cell cycle, DNA replication, and MAPK signaling pathway in the group with larger females may be involved in the regulation of the observed growth differences. WGCNA of DEGs showed that cell cycle and DNA replication might be crucial pathways for accelerating cell growth in the groups with larger females. Finally, a series of hub genes including 6-phosphofructokinase type C (pfkp), ribosome biogenesis protein (wdr12), bleomycin hydrolase (blmh), and semaphorin-3A (sema3a) were recognized by the illustrated network map of modules. The linkage of cell cycle, DNA replication, and hub genes in the growth regulation of C. semilaevis provides further information for a better understanding of growth differences in fish.
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23
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Hochwagen A, Berchowitz LE. Remembering Angelika Amon (1967–2020). J Cell Sci 2020. [DOI: 10.1242/jcs.257444] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Affiliation(s)
| | - Luke E. Berchowitz
- Department of Genetics and Development, Columbia University Irving Medical Center, New York, NY 10032, USA
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24
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Gu Y, Oliferenko S. The principles of cellular geometry scaling. Curr Opin Cell Biol 2020; 68:20-27. [PMID: 32950004 DOI: 10.1016/j.ceb.2020.08.013] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2020] [Revised: 08/14/2020] [Accepted: 08/17/2020] [Indexed: 01/11/2023]
Abstract
Cellular dimensions profoundly influence cellular physiology. For unicellular organisms, this has direct bearing on their ecology and evolution. The morphology of a cell is governed by scaling rules. As it grows, the ratio of its surface area to volume is expected to decrease. Similarly, if environmental conditions force proliferating cells to settle on different size optima, cells of the same type may exhibit size-dependent variation in cellular processes. In fungi, algae and plants where cells are surrounded by a rigid wall, division at smaller size often produces immediate changes in geometry, decreasing cell fitness. Here, we discuss how cells interpret their size, buffer against changes in shape and, if necessary, scale their polarity to maintain optimal shape at different cell volumes.
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Affiliation(s)
- Ying Gu
- The Francis Crick Institute, 1 Midland Road, London, NW1 1AT, UK; Randall Centre for Cell and Molecular Biophysics, School of Basic and Medical Biosciences, King's College London, London, SE1 1UL, UK
| | - Snezhana Oliferenko
- The Francis Crick Institute, 1 Midland Road, London, NW1 1AT, UK; Randall Centre for Cell and Molecular Biophysics, School of Basic and Medical Biosciences, King's College London, London, SE1 1UL, UK.
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Mass measurements during lymphocytic leukemia cell polyploidization decouple cell cycle- and cell size-dependent growth. Proc Natl Acad Sci U S A 2020; 117:15659-15665. [PMID: 32581119 PMCID: PMC7355023 DOI: 10.1073/pnas.1922197117] [Citation(s) in RCA: 34] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023] Open
Abstract
Cell size is believed to influence cell growth through limited transport efficiency in larger cells. However, this has not been experimentally investigated due to a lack of noninvasive, high-precision growth quantification methods suitable for measuring large cells. Here, we have engineered large versions of microfluidic mass sensors called suspended microchannel resonators in order to study the growth of single mammalian cells that range 100-fold in mass. Our measurements, which decouple growth effects caused by cell cycle and cell size, revealed that absolute cell size does not impose strict transport or other limitations that would inhibit growth and that cell cycle has a large influence on growth. Cell size is believed to influence cell growth and metabolism. Consistently, several studies have revealed that large cells have lower mass accumulation rates per unit mass (i.e., growth efficiency) than intermediate-sized cells in the same population. Size-dependent growth is commonly attributed to transport limitations, such as increased diffusion timescales and decreased surface-to-volume ratio. However, separating cell size- and cell cycle-dependent growth is challenging. To address this, we monitored growth efficiency of pseudodiploid mouse lymphocytic leukemia cells during normal proliferation and polyploidization. This was enabled by the development of large-channel suspended microchannel resonators that allow us to monitor buoyant mass of single cells ranging from 40 pg (small pseudodiploid cell) to over 4,000 pg, with a resolution ranging from ∼1% to ∼0.05%. We find that cell growth efficiency increases, plateaus, and then decreases as cell cycle proceeds. This growth behavior repeats with every endomitotic cycle as cells grow into polyploidy. Overall, growth efficiency changes 33% throughout the cell cycle. In contrast, increasing cell mass by over 100-fold during polyploidization did not change growth efficiency, indicating exponential growth. Consistently, growth efficiency remained constant when cell cycle was arrested in G2. Thus, cell cycle is a primary determinant of growth efficiency. As growth remains exponential over large size scales, our work finds no evidence for transport limitations that would decrease growth efficiency.
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Cell-size regulation in budding yeast does not depend on linear accumulation of Whi5. Proc Natl Acad Sci U S A 2020; 117:14243-14250. [PMID: 32518113 DOI: 10.1073/pnas.2001255117] [Citation(s) in RCA: 23] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023] Open
Abstract
Cells must couple cell-cycle progress to their growth rate to restrict the spread of cell sizes present throughout a population. Linear, rather than exponential, accumulation of Whi5, was proposed to provide this coordination by causing a higher Whi5 concentration in cells born at a smaller size. We tested this model using the inducible GAL1 promoter to make the Whi5 concentration independent of cell size. At an expression level that equalizes the mean cell size with that of wild-type cells, the size distributions of cells with galactose-induced Whi5 expression and wild-type cells are indistinguishable. Fluorescence microscopy confirms that the endogenous and GAL1 promoters produce different relationships between Whi5 concentration and cell volume without diminishing size control in the G1 phase. We also expressed Cln3 from the GAL1 promoter, finding that the spread in cell sizes for an asynchronous population is unaffected by this perturbation. Our findings indicate that size control in budding yeast does not fundamentally originate from the linear accumulation of Whi5, contradicting a previous claim and demonstrating the need for further models of cell-cycle regulation to explain how cell size controls passage through Start.
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27
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Growth-Dependent Activation of Protein Kinases Suggests a Mechanism for Measuring Cell Growth. Genetics 2020; 215:729-746. [PMID: 32461268 DOI: 10.1534/genetics.120.303200] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2020] [Accepted: 05/17/2020] [Indexed: 11/18/2022] Open
Abstract
In all cells, progression through the cell cycle occurs only when sufficient growth has occurred. Thus, cells must translate growth into a proportional signal that can be used to measure and transmit information about growth. Previous genetic studies in budding yeast suggested that related kinases called Gin4 and Hsl1 could function in mechanisms that measure bud growth; however, interpretation of the data was complicated by the use of gene deletions that cause complex terminal phenotypes. Here, we used the first conditional alleles of Gin4 and Hsl1 to more precisely define their functions. We show that excessive bud growth during a prolonged mitotic delay is an immediate consequence of inactivating Gin4 and Hsl1 Thus, acute loss of Gin4 and Hsl1 causes cells to behave as though they cannot detect that bud growth has occurred. We further show that Gin4 and Hsl1 undergo gradual hyperphosphorylation during bud growth that is dependent upon growth and correlated with the extent of growth. Moreover, gradual hyperphosphorylation of Gin4 during bud growth requires binding to anionic phospholipids that are delivered to the growing bud. While alternative models are possible, the data suggest that signaling lipids delivered to the growing bud generate a growth-dependent signal that could be used to measure bud growth.
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28
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Ali A, Al-Tobasei R, Lourenco D, Leeds T, Kenney B, Salem M. Genome-wide identification of loci associated with growth in rainbow trout. BMC Genomics 2020; 21:209. [PMID: 32138655 PMCID: PMC7059289 DOI: 10.1186/s12864-020-6617-x] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2019] [Accepted: 02/24/2020] [Indexed: 12/22/2022] Open
Abstract
Background Growth is a major economic production trait in aquaculture. Improvements in growth performance will reduce time and cost for fish to reach market size. However, genes underlying growth have not been fully explored in rainbow trout. Results A previously developed 50 K gene-transcribed SNP chip, containing ~ 21 K SNPs showing allelic imbalances potentially associated with important aquaculture production traits including body weight, muscle yield, was used for genotyping a total of 789 fish with available phenotypic data for bodyweight gain. Genotyped fish were obtained from two consecutive generations produced in the NCCCWA growth-selection breeding program. Weighted single-step GBLUP (WssGBLUP) was used to perform a genome-wide association (GWA) analysis to identify quantitative trait loci (QTL) associated with bodyweight gain. Using genomic sliding windows of 50 adjacent SNPs, 247 SNPs associated with bodyweight gain were identified. SNP-harboring genes were involved in cell growth, cell proliferation, cell cycle, lipid metabolism, proteolytic activities, chromatin modification, and developmental processes. Chromosome 14 harbored the highest number of SNPs (n = 50). An SNP window explaining the highest additive genetic variance for bodyweight gain (~ 6.4%) included a nonsynonymous SNP in a gene encoding inositol polyphosphate 5-phosphatase OCRL-1. Additionally, based on a single-marker GWA analysis, 33 SNPs were identified in association with bodyweight gain. The highest SNP explaining variation in bodyweight gain was identified in a gene coding for thrombospondin-1 (THBS1) (R2 = 0.09). Conclusion The majority of SNP-harboring genes, including OCRL-1 and THBS1, were involved in developmental processes. Our results suggest that development-related genes are important determinants for growth and could be prioritized and used for genomic selection in breeding programs.
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Affiliation(s)
- Ali Ali
- Department of Animal and Avian Sciences, University of Maryland, College Park, MD, 20742, USA
| | - Rafet Al-Tobasei
- Computational Science Program, Middle Tennessee State University, Murfreesboro, TN, 37132, USA
| | - Daniela Lourenco
- Department of Animal and Dairy Science, University of Georgia, Athens, GA, 30602, USA
| | - Tim Leeds
- United States Department of Agriculture Kearneysville, National Center for Cool and Cold Water Aquaculture, Agricultural Research Service, Kearneysville, WV, USA
| | - Brett Kenney
- Division of Animal and Nutritional Sciences, West Virginia University, Morgantown, WV, 26506, USA
| | - Mohamed Salem
- Department of Animal and Avian Sciences, University of Maryland, College Park, MD, 20742, USA.
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29
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Litsios A, Huberts DHEW, Terpstra HM, Guerra P, Schmidt A, Buczak K, Papagiannakis A, Rovetta M, Hekelaar J, Hubmann G, Exterkate M, Milias-Argeitis A, Heinemann M. Differential scaling between G1 protein production and cell size dynamics promotes commitment to the cell division cycle in budding yeast. Nat Cell Biol 2019; 21:1382-1392. [PMID: 31685990 DOI: 10.1038/s41556-019-0413-3] [Citation(s) in RCA: 40] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2018] [Accepted: 09/25/2019] [Indexed: 12/28/2022]
Abstract
In the unicellular eukaryote Saccharomyces cerevisiae, Cln3-cyclin-dependent kinase activity enables Start, the irreversible commitment to the cell division cycle. However, the concentration of Cln3 has been paradoxically considered to remain constant during G1, due to the presumed scaling of its production rate with cell size dynamics. Measuring metabolic and biosynthetic activity during cell cycle progression in single cells, we found that cells exhibit pulses in their protein production rate. Rather than scaling with cell size dynamics, these pulses follow the intrinsic metabolic dynamics, peaking around Start. Using a viral-based bicistronic construct and targeted proteomics to measure Cln3 at the single-cell and population levels, we show that the differential scaling between protein production and cell size leads to a temporal increase in Cln3 concentration, and passage through Start. This differential scaling causes Start in both daughter and mother cells across growth conditions. Thus, uncoupling between two fundamental physiological parameters drives cell cycle commitment.
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Affiliation(s)
- Athanasios Litsios
- Molecular Systems Biology, Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, Groningen, the Netherlands
| | - Daphne H E W Huberts
- Molecular Systems Biology, Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, Groningen, the Netherlands
- Cancer Research UK Cambridge Institute, University of Cambridge, Cambridge, UK
| | - Hanna M Terpstra
- Molecular Systems Biology, Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, Groningen, the Netherlands
| | - Paolo Guerra
- Molecular Systems Biology, Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, Groningen, the Netherlands
| | - Alexander Schmidt
- Proteomics Core Facility, Biozentrum, University of Basel, Basel, Switzerland
| | - Katarzyna Buczak
- Proteomics Core Facility, Biozentrum, University of Basel, Basel, Switzerland
| | - Alexandros Papagiannakis
- Molecular Systems Biology, Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, Groningen, the Netherlands
| | - Mattia Rovetta
- Molecular Systems Biology, Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, Groningen, the Netherlands
| | - Johan Hekelaar
- Molecular Systems Biology, Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, Groningen, the Netherlands
| | - Georg Hubmann
- Molecular Systems Biology, Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, Groningen, the Netherlands
- Department of Biology, Laboratory of Molecular Cell Biology, Institute of Botany and Microbiology, KU Leuven, Heverlee, Belgium
- Center for Microbiology, VIB, Heverlee, Belgium
| | - Marten Exterkate
- Molecular Systems Biology, Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, Groningen, the Netherlands
- Molecular Microbiology, Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, Groningen, the Netherlands
| | - Andreas Milias-Argeitis
- Molecular Systems Biology, Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, Groningen, the Netherlands.
| | - Matthias Heinemann
- Molecular Systems Biology, Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, Groningen, the Netherlands.
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30
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Leitao RM, Jasani A, Talavara RA, Pham A, Okobi QJ, Kellogg DR. A Conserved PP2A Regulatory Subunit Enforces Proportional Relationships Between Cell Size and Growth Rate. Genetics 2019; 213:517-528. [PMID: 31488515 PMCID: PMC6781898 DOI: 10.1534/genetics.119.301012] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2019] [Accepted: 08/10/2019] [Indexed: 11/18/2022] Open
Abstract
Cell size is proportional to growth rate. Thus, cells growing rapidly in rich nutrients can be nearly twice the size of cells growing slowly in poor nutrients. This proportional relationship appears to hold across all orders of life, yet the underlying mechanisms are unknown. In budding yeast, most growth occurs during mitosis, and the proportional relationship between cell size and growth rate is therefore enforced primarily by modulating growth in mitosis. When growth is slow, the duration of mitosis is increased to allow more time for growth, yet the amount of growth required to complete mitosis is reduced, which leads to the birth of small daughter cells. Previous studies have found that Rts1, a member of the conserved B56 family of protein phosphatase 2A regulatory subunits, works in a TORC2 signaling network that influences cell size and growth rate. However, it was unclear whether Rts1 influences cell growth and size in mitosis. Here, we show that Rts1 is required for the proportional relationship between cell size and growth rate during mitosis. Moreover, nutrients and Rts1 influence the duration and extent of growth in mitosis via Wee1 and Pds1/securin, two conserved regulators of mitotic progression. Together, the data are consistent with a model in which global signals that set growth rate also set the critical amount of growth required for cell cycle progression, which would provide a simple mechanistic explanation for the proportional relationship between cell size and growth rate.
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Affiliation(s)
- Ricardo M Leitao
- Department of Molecular, Cell and Developmental Biology, University of California, Santa Cruz, California 95064
| | - Akshi Jasani
- Department of Molecular, Cell and Developmental Biology, University of California, Santa Cruz, California 95064
| | - Rafael A Talavara
- Department of Molecular, Cell and Developmental Biology, University of California, Santa Cruz, California 95064
| | - Annie Pham
- Department of Molecular, Cell and Developmental Biology, University of California, Santa Cruz, California 95064
| | - Quincy J Okobi
- Department of Molecular, Cell and Developmental Biology, University of California, Santa Cruz, California 95064
| | - Douglas R Kellogg
- Department of Molecular, Cell and Developmental Biology, University of California, Santa Cruz, California 95064
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31
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O'Rourke MB, Town SEL, Dalla PV, Bicknell F, Koh Belic N, Violi JP, Steele JR, Padula MP. What is Normalization? The Strategies Employed in Top-Down and Bottom-Up Proteome Analysis Workflows. Proteomes 2019; 7:proteomes7030029. [PMID: 31443461 PMCID: PMC6789750 DOI: 10.3390/proteomes7030029] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2019] [Revised: 08/19/2019] [Accepted: 08/20/2019] [Indexed: 12/20/2022] Open
Abstract
The accurate quantification of changes in the abundance of proteins is one of the main applications of proteomics. The maintenance of accuracy can be affected by bias and error that can occur at many points in the experimental process, and normalization strategies are crucial to attempt to overcome this bias and return the sample to its regular biological condition, or normal state. Much work has been published on performing normalization on data post-acquisition with many algorithms and statistical processes available. However, there are many other sources of bias that can occur during experimental design and sample handling that are currently unaddressed. This article aims to cast light on the potential sources of bias and where normalization could be applied to return the sample to its normal state. Throughout we suggest solutions where possible but, in some cases, solutions are not available. Thus, we see this article as a starting point for discussion of the definition of and the issues surrounding the concept of normalization as it applies to the proteomic analysis of biological samples. Specifically, we discuss a wide range of different normalization techniques that can occur at each stage of the sample preparation and analysis process.
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Affiliation(s)
- Matthew B O'Rourke
- Bowel Cancer & Biomarker Lab, Northern Clinical School, Faculty of Medicine and Health, The University of Sydney Lvl 8, Kolling Institute. Royal North Shore Hospital, St. Leonards, NSW 2065, Australia
| | - Stephanie E L Town
- School of Life Sciences and Proteomics Core Facility, Faculty of Science, The University of Technology Sydney, Ultimo 2007, Australia
| | - Penelope V Dalla
- School of Life Sciences and Proteomics Core Facility, Faculty of Science, The University of Technology Sydney, Ultimo 2007, Australia
- Respiratory Cellular and Molecular Biology, Woolcock Institute of Medical Research, The University of Sydney, Glebe 2037, Australia
| | - Fiona Bicknell
- School of Life Sciences and Proteomics Core Facility, Faculty of Science, The University of Technology Sydney, Ultimo 2007, Australia
| | - Naomi Koh Belic
- School of Life Sciences and Proteomics Core Facility, Faculty of Science, The University of Technology Sydney, Ultimo 2007, Australia
| | - Jake P Violi
- School of Life Sciences and Proteomics Core Facility, Faculty of Science, The University of Technology Sydney, Ultimo 2007, Australia
| | - Joel R Steele
- School of Life Sciences and Proteomics Core Facility, Faculty of Science, The University of Technology Sydney, Ultimo 2007, Australia
| | - Matthew P Padula
- School of Life Sciences and Proteomics Core Facility, Faculty of Science, The University of Technology Sydney, Ultimo 2007, Australia.
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Abstract
BACKGROUND Cell size is a key characteristic that significantly affects many aspects of cellular physiology. There are specific control mechanisms during cell cycle that maintain the cell size within a range from generation to generation. Such control mechanisms introduce substantial variabilities to important properties of the cell cycle such as growth and division. To quantitatively study the effect of such variability in progression through cell cycle, detailed stochastic models are required. RESULTS In this paper, a new hybrid stochastic model is proposed to study the effect of molecular noise and size control mechanism on the variabilities in cell cycle of the budding yeast Saccharomyces cerevisiae. The proposed model provides an accurate, yet computationally efficient approach for simulation of an intricate system by integrating the deterministic and stochastic simulation schemes. The developed hybrid stochastic model can successfully capture several key features of the cell cycle observed in experimental data. In particular, the proposed model: 1) confirms that the majority of noise in size control stems from low copy numbers of transcripts in the G1 phase, 2) identifies the size and time regulation modules in the size control mechanism, and 3) conforms with phenotypes of early G1 mutants in exquisite detail. CONCLUSIONS Hybrid stochastic modeling approach can be used to provide quantitative descriptions for stochastic properties of the cell cycle within a computationally efficient framework.
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Affiliation(s)
| | - John J Tyson
- Department of Biological Sciences, Virginia Tech, Blacksburg, VA, USA
| | - Yang Cao
- Department of Computer Science, Virginia Tech, Blacksburg, VA, USA.
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33
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Duan Y, Guo Q, Zhang T, Meng Y, Sun D, Luo G, Liu Y. Cyclin-dependent kinase-mediated phosphorylation of the exocyst subunit Exo84 in late G 1 phase suppresses exocytic secretion and cell growth in yeast. J Biol Chem 2019; 294:11323-11332. [PMID: 31171719 DOI: 10.1074/jbc.ra119.008591] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2019] [Revised: 05/10/2019] [Indexed: 12/22/2022] Open
Abstract
In eukaryotic cells, the growth rate is strictly regulated for proper progression of the cell cycle. In the budding yeast Saccharomyces cerevisiae, it was previously shown that cell growth dramatically slows down when the cells start budding at the G1/S transition. However, the molecular mechanism for this G1/S-associated growth arrest is unclear. In this study, using exocytic secretion, cyclin-dependent kinase (CDK) assay, immunoprecipitation, and microscopy, we demonstrate that the exocyst subunit Exo84, which is known to be phosphorylated in mitosis, can also be phosphorylated directly by Cdk1 in the late G1 phase. Of note, we found that the Cdk1-mediated Exo84 phosphorylation impairs exocytic secretion in the late G1 phase. Using conditional cdc mutants and phosphodeficient and phosphomimetic exo84 mutants, we further observed that Cdk1-phosphoryated Exo84 inhibits the exocyst complex assembly, exocytic secretion, and cell growth, which may be important for proper execution of the G1/S-phase transition before commitment to a complete cell cycle. Our results suggest that the direct Cdk1-mediated regulation of the exocyst complex critically contributes to the coordination of cell growth and cell cycle progression.
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Affiliation(s)
- Yuran Duan
- Department of Biochemistry and Molecular Biology, China Medical University, Shenyang 110122, China
| | - Qingguo Guo
- Department of Biochemistry and Molecular Biology, China Medical University, Shenyang 110122, China
| | - Tianrui Zhang
- Department of Biochemistry and Molecular Biology, China Medical University, Shenyang 110122, China
| | - Yuan Meng
- Department of Biochemistry and Molecular Biology, China Medical University, Shenyang 110122, China
| | - Dong Sun
- Institute of Translational Medicine, China Medical University, Shenyang 110122, China
| | - Guangzuo Luo
- Institute of Translational Medicine, China Medical University, Shenyang 110122, China
| | - Ying Liu
- Department of Biochemistry and Molecular Biology, China Medical University, Shenyang 110122, China
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34
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Zhang T, Sun D, Luo G, Liu Y. Spatial and Translational Regulation of Exocyst Subunits by Cell Cycle in Budding Yeast. Med Sci Monit 2019; 25:4059-4067. [PMID: 31150370 PMCID: PMC6559343 DOI: 10.12659/msm.914194] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022] Open
Abstract
BACKGROUND Previous studies have shown that exocyst complex is located at polarized growth sites at different cell cycle stages in budding yeast. But how cell cycle and the cyclin-dependent kinase, Cdk1, regulate the distribution of exocyst complex on the plasma membrane and the protein level of each exocyst subunit is not clear. MATERIAL AND METHODS Using budding yeast as a research material, regulation of cell cycle and Cdk1 on exocyst localization on the plasma membrane and on level of each exocyst subunit were examined by methods of cell biology and molecular biology. RESULTS Exocyst complex is located at growth sites on the plasma membrane in both budding and non-budding stages. Cdk1 activity is required for polarized distribution of exocyst complex in late G1, S and M phases, but not in cytokinesis stage. Cdk1 is not required for the assembly and localization of exocyst complex on plasma membrane. The protein level of Sec3 but not other exocyst subunits is regulated by the cell cycle. CONCLUSIONS Cdk1 activity is required for exocyst polarization before cytokinesis during the cell cycle progression, but not for its assembly and localization on the plasma membrane. Dynamic localization and protein level of the complex subunits are regulated by the cell cycle.
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Affiliation(s)
- Tianrui Zhang
- Department of Biochemistry and Molecular Biology, China Medical University, Shenyang, Liaoning, China (mainland)
| | - Dong Sun
- Institute of Translational Research, China Medical University, Shenyang, Liaoning, China (mainland)
| | - Guangzuo Luo
- Institute of Translational Research, China Medical University, Shenyang, Liaoning, China (mainland)
| | - Ying Liu
- Department of Biochemistry and Molecular Biology, China Medical University, Shenyang, Liaoning, China (mainland)
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35
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Diaz Arias CA, Molino JVD, de Araújo Viana Marques D, Queiroz Maranhão A, Abdalla Saes Parra D, Pessoa Junior A, Converti A. Influence of carbon source on cell size and production of anti LDL (-) single-chain variable fragment by a recombinant Pichia pastoris strain. Mol Biol Rep 2019; 46:3257-3264. [PMID: 31073913 DOI: 10.1007/s11033-019-04785-9] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2019] [Accepted: 03/22/2019] [Indexed: 10/26/2022]
Abstract
The aim of this work was to study the effect of the carbon source (glycerol, sucrose, glucose or a sucrose/glucose mixture) on the production of the anti LDL (-) single-chain variable fragment (scFv) by the recombinant Pichia pastoris SMD 1168 strain as well as on the cell size. The use of glucose as a carbon source in the growth phase led to a remarkable increase in cell size compared with glycerol, while the smallest cells were obtained with sucrose likely due to the occurrence of an energetic stress. The scFv concentration seemed to be related to cell number rather than to cell concentration, which in its turn showed no significant dependence on the carbon source. Yeast cells grown on sucrose had a mean diameter (0.736 ± 0.097 μm) about 35% shorter than those grown on glucose and allowed for the highest final concentration of the scFv antibody fragment (93.7 ± 0.2 mg/L). These results demonstrate that sucrose is the best carbon source for the expression of such an antibody fragment by the recombinant P. pastoris strain, which may be very useful for the diagnostic analysis of the so-called "bad cholesterol".
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Affiliation(s)
- Cesar Andres Diaz Arias
- Department of Biochemical and Pharmaceutical Technology, University of São Paulo, Prof. Lineu Prestes 580, Bloco 16, São Paulo, SP, 05508-000, Brazil
| | - João Vitor Dutra Molino
- Department of Biochemical and Pharmaceutical Technology, University of São Paulo, Prof. Lineu Prestes 580, Bloco 16, São Paulo, SP, 05508-000, Brazil
| | | | - Andrea Queiroz Maranhão
- Department of Cell Biology, Brasilia University, Campus Universitario Darcy RibeiroBloco K, 2 pavimento, Asa Norte, Brasília, DF, 70910-900, Brazil
| | - Dulcineia Abdalla Saes Parra
- Department of Clinical and Toxicological Analyses, University of São Paulo, Prof. Lineu Prestes, 580, Bloco 18, São Paulo, SP, 05508-000, Brazil
| | - Adalberto Pessoa Junior
- Department of Biochemical and Pharmaceutical Technology, University of São Paulo, Prof. Lineu Prestes 580, Bloco 16, São Paulo, SP, 05508-000, Brazil
| | - Attilio Converti
- Department of Civil, Chemical and Environmental Engineering, Pole of Chemical Engineering, University of Genoa, Via Opera Pia 15, 16145, Genoa, Italy.
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36
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Corno A, Chiroli E, Gross F, Vernieri C, Matafora V, Maffini S, Cosentino Lagomarsino M, Bachi A, Ciliberto A. Cellular response upon proliferation in the presence of an active mitotic checkpoint. Life Sci Alliance 2019; 2:2/3/e201900380. [PMID: 31068378 PMCID: PMC6507650 DOI: 10.26508/lsa.201900380] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2019] [Revised: 04/26/2019] [Accepted: 04/29/2019] [Indexed: 11/24/2022] Open
Abstract
Cells that replicate with an active mitotic checkpoint remain capable to mount multiple times an efficient arrest, are bigger than unperturbed cells, rely more heavily on Cdh1, and have an altered protein expression profile. Eukaryotic cells treated with microtubule-targeting agents activate the spindle assembly checkpoint to arrest in mitosis and prevent chromosome mis-segregation. A fraction of mitotically arrested cells overcomes the block and proliferates even under persistent checkpoint-activating conditions. Here, we asked what allows proliferation in such unfavourable conditions. We report that yeast cells are delayed in mitosis at each division, implying that their spindle assembly checkpoint remains responsive. The arrest causes their cell cycle to be elongated and results in a size increase. Growth saturates at mitosis and correlates with the repression of various factors involved in translation. Contrary to unperturbed cells, growth of cells with an active checkpoint requires Cdh1. This peculiar cell cycle correlates with global changes in protein expression whose signatures partly overlap with the environmental stress response. Hence, cells dividing with an active checkpoint develop recognisable specific traits that allow them to successfully complete cell division notwithstanding a constant mitotic checkpoint arrest. These properties distinguish them from unperturbed cells. Our observation may have implications for the identification of new therapeutic windows and targets in tumors.
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Affiliation(s)
- Andrea Corno
- Istituto Firc di Oncologia Molecolare, Milan, Italy
| | | | | | - Claudio Vernieri
- Istituto Firc di Oncologia Molecolare, Milan, Italy.,Medical Oncology Department, Fondazione IRCCS Istituto Nazionale Tumori, Milan, Italy
| | | | - Stefano Maffini
- Department of Mechanistic Cell Biology, Max Planck Institute of Molecular Physiology, Dortmund, Germany
| | | | - Angela Bachi
- Istituto Firc di Oncologia Molecolare, Milan, Italy
| | - Andrea Ciliberto
- Istituto Firc di Oncologia Molecolare, Milan, Italy .,Istituto di Genetica Molecolare, Consiglio Nazionale delle Ricerche, Pavia, Italy
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37
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Takaine M, Ueno M, Kitamura K, Imamura H, Yoshida S. Reliable imaging of ATP in living budding and fission yeast. J Cell Sci 2019; 132:jcs.230649. [PMID: 30858198 DOI: 10.1242/jcs.230649] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2019] [Accepted: 03/04/2019] [Indexed: 01/12/2023] Open
Abstract
Adenosine triphosphate (ATP) is a main metabolite essential for all living organisms. However, our understanding of ATP dynamics within a single living cell is very limited. Here, we optimized the ATP-biosensor QUEEN and monitored the dynamics of ATP with good spatial and temporal resolution in living yeasts. We found stable maintenance of ATP concentration in wild-type yeasts, regardless of carbon sources or cell cycle stages, suggesting that mechanism exists to maintain ATP at a specific concentration. We further found that ATP concentration is not necessarily an indicator of metabolic activity, as there is no clear correlation between ATP level and growth rates. During fission yeast meiosis, we found a reduction in ATP levels, suggesting that ATP homeostasis is controlled by differentiation. The use of QUEEN in yeasts offers an easy and reliable assay for ATP dynamicity and will answer several unaddressed questions about cellular metabolism in eukaryotes.
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Affiliation(s)
- Masak Takaine
- Gunma University Initiative for Advanced Research (GIAR), Gunma University, Maebashi 371-8512, Japan .,Institute for Molecular and Cellular Regulation (IMCR), Gunma University, Maebashi 371-8512, Japan
| | - Masaru Ueno
- Department of Molecular Biotechnology, Graduate School of Advanced Sciences of Matter, Hiroshima University, Japan.,Research Center for the Mathematics on Chromatin Live Dynamics, Hiroshima University, Japan
| | - Kenji Kitamura
- Center for Gene Science, Hiroshima University, 1-4-2 Kagamiyama, Higashi-Hiroshima 739-8527, Japan
| | - Hiromi Imamura
- Department of Functional Biology, Graduate School of Biostudies, Kyoto University, Kyoto 606-8501, Japan
| | - Satoshi Yoshida
- Gunma University Initiative for Advanced Research (GIAR), Gunma University, Maebashi 371-8512, Japan .,Institute for Molecular and Cellular Regulation (IMCR), Gunma University, Maebashi 371-8512, Japan.,School of International Liberal Studies, Waseda University, Tokyo, 169-8050, Japan.,Japan Science and Technology Agency, PREST
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38
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Neurohr GE, Terry RL, Lengefeld J, Bonney M, Brittingham GP, Moretto F, Miettinen TP, Vaites LP, Soares LM, Paulo JA, Harper JW, Buratowski S, Manalis S, van Werven FJ, Holt LJ, Amon A. Excessive Cell Growth Causes Cytoplasm Dilution And Contributes to Senescence. Cell 2019; 176:1083-1097.e18. [PMID: 30739799 PMCID: PMC6386581 DOI: 10.1016/j.cell.2019.01.018] [Citation(s) in RCA: 252] [Impact Index Per Article: 50.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2018] [Revised: 11/15/2018] [Accepted: 01/09/2019] [Indexed: 11/23/2022]
Abstract
Cell size varies greatly between cell types, yet within a specific cell type and growth condition, cell size is narrowly distributed. Why maintenance of a cell-type specific cell size is important remains poorly understood. Here we show that growing budding yeast and primary mammalian cells beyond a certain size impairs gene induction, cell-cycle progression, and cell signaling. These defects are due to the inability of large cells to scale nucleic acid and protein biosynthesis in accordance with cell volume increase, which effectively leads to cytoplasm dilution. We further show that loss of scaling beyond a certain critical size is due to DNA becoming limiting. Based on the observation that senescent cells are large and exhibit many of the phenotypes of large cells, we propose that the range of DNA:cytoplasm ratio that supports optimal cell function is limited and that ratios outside these bounds contribute to aging.
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Affiliation(s)
- Gabriel E Neurohr
- David H. Koch Institute for Integrative Cancer Research, Howard Hughes Medical Institute, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Rachel L Terry
- David H. Koch Institute for Integrative Cancer Research, Howard Hughes Medical Institute, Massachusetts Institute of Technology, Cambridge, MA 02139, USA; Department of Biology, Massachusetts Institute of Technology, Cambridge, MA 02139, USA; Department of Systems Biology, Harvard Medical School, Boston, Massachusetts 02115, USA
| | - Jette Lengefeld
- David H. Koch Institute for Integrative Cancer Research, Howard Hughes Medical Institute, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Megan Bonney
- David H. Koch Institute for Integrative Cancer Research, Howard Hughes Medical Institute, Massachusetts Institute of Technology, Cambridge, MA 02139, USA; Department of Biology, Massachusetts Institute of Technology, Cambridge, MA 02139, USA; Novartis Institute for Biomedical Research, Oncology Department, Cambridge, MA 02139
| | - Gregory P Brittingham
- Institute for Systems Genetics, New York University Langone Health, New York, NY 10016, USA
| | - Fabien Moretto
- Cell Fate and Gene Regulation Laboratory, The Francis Crick Institute, 1 Midland Road, NW1 1AT London, UK
| | - Teemu P Miettinen
- David H. Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA 02139, USA; MRC Laboratory for Molecular Cell Biology, University College London, Gower Street, London, WC1E 6BT, UK
| | | | - Luis M Soares
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA 02115, USA
| | - Joao A Paulo
- Department of Cell Biology, Harvard Medical School, Boston, MA 02115, USA
| | - J Wade Harper
- Department of Cell Biology, Harvard Medical School, Boston, MA 02115, USA
| | - Stephen Buratowski
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA 02115, USA
| | - Scott Manalis
- David H. Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA 02139, USA; Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139, USA; Department of Mechanical Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Folkert J van Werven
- Cell Fate and Gene Regulation Laboratory, The Francis Crick Institute, 1 Midland Road, NW1 1AT London, UK
| | - Liam J Holt
- Institute for Systems Genetics, New York University Langone Health, New York, NY 10016, USA
| | - Angelika Amon
- David H. Koch Institute for Integrative Cancer Research, Howard Hughes Medical Institute, Massachusetts Institute of Technology, Cambridge, MA 02139, USA; Department of Biology, Massachusetts Institute of Technology, Cambridge, MA 02139, USA.
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39
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Jung DW, Ro HJ, Kim J, Kim SI, Yi GR, Lee G, Jun S. Biophysical restriction of growth area using a monodispersed gold sphere nanobarrier prolongs the mitotic phase in HeLa cells. RSC Adv 2019; 9:37497-37506. [PMID: 35542263 PMCID: PMC9075507 DOI: 10.1039/c9ra08410j] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2019] [Accepted: 11/08/2019] [Indexed: 11/21/2022] Open
Abstract
Homogeneous 83 nm gold nanospheres with a human fibronectin-coated substrate surrounding the cells induce biophysical cues which result in a delay in the mitotic phase of the cell cycle.
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Affiliation(s)
- Dae-Woong Jung
- Korea Basic Science Institute
- Daejeon
- Republic of Korea
- Department of Chemical Engineering
- Sungkyunkwan University
| | - Hyun-Joo Ro
- Korea Basic Science Institute
- Daejeon
- Republic of Korea
- Convergent Research Center for Emerging Virus Infection
- Korea Research Institute of Chemical Technology
| | - Junmin Kim
- Korea Basic Science Institute
- Daejeon
- Republic of Korea
- Department of Chemical Engineering
- Sungkyunkwan University
| | - Seung Il Kim
- Korea Basic Science Institute
- Daejeon
- Republic of Korea
- Convergent Research Center for Emerging Virus Infection
- Korea Research Institute of Chemical Technology
| | - Gi-Ra Yi
- Department of Chemical Engineering
- Sungkyunkwan University
- Suwon
- Republic of Korea
| | - Gaehang Lee
- Korea Basic Science Institute
- Daejeon
- Republic of Korea
| | - Sangmi Jun
- Korea Basic Science Institute
- Daejeon
- Republic of Korea
- Convergent Research Center for Emerging Virus Infection
- Korea Research Institute of Chemical Technology
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40
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Allard CAH, Decker F, Weiner OD, Toettcher JE, Graziano BR. A size-invariant bud-duration timer enables robustness in yeast cell size control. PLoS One 2018; 13:e0209301. [PMID: 30576342 PMCID: PMC6303054 DOI: 10.1371/journal.pone.0209301] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2018] [Accepted: 11/28/2018] [Indexed: 12/20/2022] Open
Abstract
Cell populations across nearly all forms of life generally maintain a characteristic cell type-dependent size, but how size control is achieved has been a long-standing question. The G1/S boundary of the cell cycle serves as a major point of size control, and mechanisms operating here restrict passage of cells to Start if they are too small. In contrast, it is less clear how size is regulated post-Start, during S/G2/M. To gain further insight into post-Start size control, we prepared budding yeast that can be reversibly blocked from bud initiation. While blocked, cells continue to grow isotropically, increasing their volume by more than an order of magnitude over unperturbed cells. Upon release from their block, giant mothers reenter the cell cycle and their progeny rapidly return to the original unperturbed size. We found this behavior to be consistent with a size-invariant 'timer' specifying the duration of S/G2/M. These results indicate that yeast use at least two distinct mechanisms at different cell cycle phases to ensure size homeostasis.
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Affiliation(s)
- Corey A. H. Allard
- Marine Biological Laboratory, Woods Hole, MA, United States of America
- Dept. of Biochemistry and Cell Biology, The Geisel School of Medicine at Dartmouth, Hanover, NH, United States of America
| | - Franziska Decker
- Marine Biological Laboratory, Woods Hole, MA, United States of America
- Max Planck Institute for the Physics of Complex Systems, Max Planck Institute of Molecular Cell Biology and Genetics, Center for Systems Biology Dresden, Dresden, Germany
| | - Orion D. Weiner
- Marine Biological Laboratory, Woods Hole, MA, United States of America
- Cardiovascular Research Institute and Dept. of Biochemistry and Biophysics, UC San Francisco, San Francisco, United States of America
| | - Jared E. Toettcher
- Marine Biological Laboratory, Woods Hole, MA, United States of America
- Department of Molecular Biology, Princeton University, Princeton, NJ, United States of America
| | - Brian R. Graziano
- Marine Biological Laboratory, Woods Hole, MA, United States of America
- Cardiovascular Research Institute and Dept. of Biochemistry and Biophysics, UC San Francisco, San Francisco, United States of America
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41
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Kelliher CM, Foster MW, Motta FC, Deckard A, Soderblom EJ, Moseley MA, Haase SB. Layers of regulation of cell-cycle gene expression in the budding yeast Saccharomyces cerevisiae. Mol Biol Cell 2018; 29:2644-2655. [PMID: 30207828 PMCID: PMC6249835 DOI: 10.1091/mbc.e18-04-0255] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2018] [Revised: 08/30/2018] [Accepted: 09/04/2018] [Indexed: 11/11/2022] Open
Abstract
In the budding yeast Saccharomyces cerevisiae, transcription factors (TFs) regulate the periodic expression of many genes during the cell cycle, including gene products required for progression through cell-cycle events. Experimental evidence coupled with quantitative models suggests that a network of interconnected TFs is capable of regulating periodic genes over the cell cycle. Importantly, these dynamical models were built on transcriptomics data and assumed that TF protein levels and activity are directly correlated with mRNA abundance. To ask whether TF transcripts match protein expression levels as cells progress through the cell cycle, we applied a multiplexed targeted mass spectrometry approach (parallel reaction monitoring) to synchronized populations of cells. We found that protein expression of many TFs and cell-cycle regulators closely followed their respective mRNA transcript dynamics in cycling wild-type cells. Discordant mRNA/protein expression dynamics was also observed for a subset of cell-cycle TFs and for proteins targeted for degradation by E3 ubiquitin ligase complexes such as SCF (Skp1/Cul1/F-box) and APC/C (anaphase-promoting complex/cyclosome). We further profiled mutant cells lacking B-type cyclin/CDK activity ( clb1-6) where oscillations in ubiquitin ligase activity, cyclin/CDKs, and cell-cycle progression are halted. We found that a number of proteins were no longer periodically degraded in clb1-6 mutants compared with wild type, highlighting the importance of posttranscriptional regulation. Finally, the TF complexes responsible for activating G1/S transcription (SBF and MBF) were more constitutively expressed at the protein level than at periodic mRNA expression levels in both wild-type and mutant cells. This comprehensive investigation of cell-cycle regulators reveals that multiple layers of regulation (transcription, protein stability, and proteasome targeting) affect protein expression dynamics during the cell cycle.
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Affiliation(s)
| | - Matthew W. Foster
- Duke Center for Genomic and Computational Biology, Proteomics and Metabolomics Shared Resource, Durham, NC 27701
| | | | | | - Erik J. Soderblom
- Duke Center for Genomic and Computational Biology, Proteomics and Metabolomics Shared Resource, Durham, NC 27701
| | - M. Arthur Moseley
- Duke Center for Genomic and Computational Biology, Proteomics and Metabolomics Shared Resource, Durham, NC 27701
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42
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Hasan T, Kumari K, Devi SC, Handa J, Rehman T, Ansari NA, Singh LR. Osmolytes in vaccine production, flocculation and storage: a critical review. Hum Vaccin Immunother 2018; 15:514-525. [PMID: 30273503 DOI: 10.1080/21645515.2018.1526585] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022] Open
Abstract
Small molecule osmolytes, responsible for protecting stresses have long been known to rescue proteins and enzymes from loss of function. In addition to protecting macromolecules integrity, many osmolytes also act as potential antioxidant and also help to prevent protein aggregation, amyloid formation or misfolding, and therefore are considered promising molecules for neurodegenerative and many other genetic diseases. Osmolytes are also known to be involved in the regulation of several key immunological processes. In the present review we discuss in detail the effect of these compounds on important aspects of vaccines i.e., increasing the efficiency, production and purification steps. The present review therefore will help researchers to make a better strategy in vaccine production to formulation by incorporating specific and appropriate osmolytes in the processes.
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Affiliation(s)
- Tauheed Hasan
- a Dr. B.R. Ambedkar Center for Biomedical Research , University of Delhi , Delhi , India
| | - Kritika Kumari
- a Dr. B.R. Ambedkar Center for Biomedical Research , University of Delhi , Delhi , India
| | | | - Jaya Handa
- a Dr. B.R. Ambedkar Center for Biomedical Research , University of Delhi , Delhi , India
| | - Tabish Rehman
- a Dr. B.R. Ambedkar Center for Biomedical Research , University of Delhi , Delhi , India
| | - Nasim Akhtar Ansari
- a Dr. B.R. Ambedkar Center for Biomedical Research , University of Delhi , Delhi , India
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43
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Björklund M. Cell size homeostasis: Metabolic control of growth and cell division. BIOCHIMICA ET BIOPHYSICA ACTA-MOLECULAR CELL RESEARCH 2018; 1866:409-417. [PMID: 30315834 DOI: 10.1016/j.bbamcr.2018.10.002] [Citation(s) in RCA: 39] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/09/2018] [Revised: 09/25/2018] [Accepted: 10/03/2018] [Indexed: 12/14/2022]
Abstract
Joint regulation of growth rate and cell division rate determines cell size. Here we discuss how animal cells achieve cell size homeostasis potentially involving multiple signaling pathways converging at metabolic regulation of growth rate and cell cycle progression. While several models have been developed to explain cell size control, comparison of the two predominant models shows that size homeostasis is dependent on the ability to adjust cellular growth rate based on cell size. Consequently, maintenance of size homeostasis requires that larger cells can grow slower than small cells in relative terms. We review recent experimental evidence showing that such size adjustment occurs primarily at or immediately before the G1/S transition of the cell cycle. We further propose that bidirectional feedback between growth rate and size results in cell size sensing and discuss potential mechanisms how this may be accomplished.
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Affiliation(s)
- Mikael Björklund
- Zhejiang University-University of Edinburgh (ZJU-UoE) Institute, Zhejiang University School of Medicine, International Campus, 718 East Haizhou Rd., Haining, Zhejiang 314400, PR China.
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44
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Bergman ZJ, Wong J, Drubin DG, Barnes G. Microtubule dynamics regulation reconstituted in budding yeast lysates. J Cell Sci 2018; 132:jcs.219386. [PMID: 30185524 DOI: 10.1242/jcs.219386] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2018] [Accepted: 08/23/2018] [Indexed: 01/14/2023] Open
Abstract
Microtubules (MTs) are important for cellular structure, transport of cargoes and segregation of chromosomes and organelles during mitosis. The stochastic growth and shrinkage of MTs, known as dynamic instability, is necessary for these functions. Previous studies to determine how individual MT-associated proteins (MAPs) affect MT dynamics have been performed either through in vivo studies, which provide limited opportunity for observation of individual MTs or manipulation of conditions, or in vitro studies, which focus either on purified proteins, and therefore lack cellular complexity, or on cell extracts made from genetically intractable organisms. In order to investigate the ensemble activities of all MAPs on MT dynamics using lysates made from a genetically tractable organism, we developed a cell-free assay for budding yeast lysates using total internal reflection fluorescence (TIRF) microscopy. Lysates were prepared from yeast strains expressing GFP-tubulin. MT polymerization from pre-assembled MT seeds adhered to a coverslip was observed in real time. Through use of cell division cycle (cdc) and MT depolymerase mutants, we found that MT polymerization and dynamic instability are dependent on the cell cycle state and the activities of specific MAPs.
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Affiliation(s)
- Zane J Bergman
- Department of Molecular and Cell Biology, University of California, Berkeley, CA 94720, USA
| | - Jonathan Wong
- Department of Molecular and Cell Biology, University of California, Berkeley, CA 94720, USA
| | - David G Drubin
- Department of Molecular and Cell Biology, University of California, Berkeley, CA 94720, USA
| | - Georjana Barnes
- Department of Molecular and Cell Biology, University of California, Berkeley, CA 94720, USA
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45
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Modulation of TORC2 Signaling by a Conserved Lkb1 Signaling Axis in Budding Yeast. Genetics 2018; 210:155-170. [PMID: 29986907 DOI: 10.1534/genetics.118.301296] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2018] [Accepted: 06/29/2018] [Indexed: 01/03/2023] Open
Abstract
Nutrient availability, growth rate, and cell size are closely linked. For example, in budding yeast, the rate of cell growth is proportional to nutrient availability, cell size is proportional to growth rate, and growth rate is proportional to cell size. Thus, cells grow slowly in poor nutrients and are nearly half the size of cells growing in rich nutrients. Moreover, large cells grow faster than small cells. A signaling network that surrounds TOR kinase complex 2 (TORC2) plays an important role in enforcing these proportional relationships. Cells that lack components of the TORC2 network fail to modulate their growth rate or size in response to changes in nutrient availability. Here, we show that budding yeast homologs of the Lkb1 tumor suppressor kinase are required for normal modulation of TORC2 signaling in response to changes in carbon source. Lkb1 kinases activate Snf1/AMPK to initiate transcription of genes required for utilization of poor carbon sources. However, Lkb1 influences TORC2 signaling via a novel pathway that is independent of Snf1/AMPK. Of the three Lkb1 homologs in budding yeast, Elm1 plays the most important role in modulating TORC2. Elm1 activates a pair of related kinases called Gin4 and Hsl1. Previous work found that loss of Gin4 and Hsl1 causes cells to undergo unrestrained growth during a prolonged mitotic arrest, which suggests that they play a role in linking cell cycle progression to cell growth. We found that Gin4 and Hsl1 also control the TORC2 network. In addition, Gin4 and Hsl1 are themselves influenced by signals from the TORC2 network, consistent with previous work showing that the TORC2 network constitutes a feedback loop. Together, the data suggest a model in which the TORC2 network sets growth rate in response to carbon source, while also relaying signals via Gin4 and Hsl1 that set the critical amount of growth required for cell cycle progression. This kind of close linkage between control of cell growth and size would suggest a simple mechanistic explanation for the proportional relationship between cell size and growth rate.
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46
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Lai H, Chiou JG, Zhurikhina A, Zyla TR, Tsygankov D, Lew DJ. Temporal regulation of morphogenetic events in Saccharomyces cerevisiae. Mol Biol Cell 2018; 29:2069-2083. [PMID: 29927361 PMCID: PMC6232962 DOI: 10.1091/mbc.e18-03-0188] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023] Open
Abstract
Tip growth in fungi involves highly polarized secretion and modification of the cell wall at the growing tip. The genetic requirements for initiating polarized growth are perhaps best understood for the model budding yeast Saccharomyces cerevisiae. Once the cell is committed to enter the cell cycle by activation of G1 cyclin/cyclin-dependent kinase (CDK) complexes, the polarity regulator Cdc42 becomes concentrated at the presumptive bud site, actin cables are oriented toward that site, and septin filaments assemble into a ring around the polarity site. Several minutes later, the bud emerges. Here, we investigated the mechanisms that regulate the timing of these events at the single-cell level. Septin recruitment was delayed relative to polarity establishment, and our findings suggest that a CDK-dependent septin “priming” facilitates septin recruitment by Cdc42. Bud emergence was delayed relative to the initiation of polarized secretion, and our findings suggest that the delay reflects the time needed to weaken the cell wall sufficiently for the cell to bud. Rho1 activation by Rom2 occurred at around the time of bud emergence, perhaps in response to local cell-wall weakening. This report reveals regulatory mechanisms underlying the morphogenetic events in the budding yeast.
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Affiliation(s)
- Helen Lai
- Department of Pharmacology and Cancer Biology, Duke University, Durham, NC 27710.,Department of Molecular Genetics and Microbiology, Duke University, Durham, NC 27710
| | - Jian-Geng Chiou
- Department of Pharmacology and Cancer Biology, Duke University, Durham, NC 27710
| | - Anastasia Zhurikhina
- Wallace H. Coulter Department of Biomedical Engineering, Georgia Institute of Technology and Emory University School of Medicine, Atlanta, GA 30332
| | - Trevin R Zyla
- Department of Pharmacology and Cancer Biology, Duke University, Durham, NC 27710
| | - Denis Tsygankov
- Wallace H. Coulter Department of Biomedical Engineering, Georgia Institute of Technology and Emory University School of Medicine, Atlanta, GA 30332
| | - Daniel J Lew
- Department of Pharmacology and Cancer Biology, Duke University, Durham, NC 27710.,Department of Molecular Genetics and Microbiology, Duke University, Durham, NC 27710
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47
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Ginzberg MB, Chang N, D'Souza H, Patel N, Kafri R, Kirschner MW. Cell size sensing in animal cells coordinates anabolic growth rates and cell cycle progression to maintain cell size uniformity. eLife 2018; 7:26957. [PMID: 29889021 PMCID: PMC6031432 DOI: 10.7554/elife.26957] [Citation(s) in RCA: 71] [Impact Index Per Article: 11.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2017] [Accepted: 06/07/2018] [Indexed: 12/30/2022] Open
Abstract
Cell size uniformity in healthy tissues suggests that control mechanisms might coordinate cell growth and division. We derived a method to assay whether cellular growth rates depend on cell size, by monitoring how variance in size changes as cells grow. Our data revealed that, twice during the cell cycle, growth rates are selectively increased in small cells and reduced in large cells, ensuring cell size uniformity. This regulation was also observed directly by monitoring nuclear growth in live cells. We also detected cell-size-dependent adjustments of G1 length, which further reduce variability. Combining our assays with chemical/genetic perturbations confirmed that cells employ two strategies, adjusting both cell cycle length and growth rate, to maintain the appropriate size. Additionally, although Rb signaling is not required for these regulatory behaviors, perturbing Cdk4 activity still influences cell size, suggesting that the Cdk4 pathway may play a role in designating the cell’s target size. Animal cells come in many different sizes. In humans, for example, egg cells are thousands of times larger than sperm cells. Yet cells of any given type are often strikingly similar in size. The cells that line the surface of organs including the skin and kidneys are especially uniform; in fact a loss of size uniformity in certain tumors is a sign of malignancy. What kind of regulation could enable separate cells within a tissue to have the same size? One possibility is that each type of cell is programmed with a specific target size, and that a cell can sense if it strays from its target and take steps to compensate. Animal cells sensing their own size was first reported in the 1960s, and now Ginzberg et al. confirm that human cells grown in the laboratory do indeed monitor their size and correct deviations from their target. It turns out that two separate and independent processes help to keep all the cells in the population roughly uniform in size. Firstly, proliferating human cells that are smaller than their target size spend longer growing before they divide. Secondly, at two time points between cell divisions, large cells adjust their growth rate such that they grow slower than small cells. To show these processes in action, Ginzberg et al. introduced mutations or chemicals that perturbed the length of time between cell divisions or the rate of a cell’s growth. As expected, most of these perturbations had only a modest influence on cell size, due to the cell’s compensatory strategies. Cells that had less time to grow compensated by more quickly making new protein molecules, meaning that they still had enough material to build two new cells by the time they had to divide. In contrast, if a cell’s division was artificially delayed, it reduced its growth rate to stop it from becoming too large. Similarly, cells grown in conditions that slow the production of proteins extended the time between their cell divisions to give them enough time to accumulate the material required for two new cells. In a recent related study, Liu, Ginzberg et al. identified some of the molecules that a human cell uses to sense its own size. Together these two studies now pave the road to answering a fundamental question in cell biology: what is the elusive cell size sensor? Understanding how cells sense their size will open a window onto how quantitative information is programmed, sensed and communicated within living cells. These findings will shed also new light onto how cells specialize into cell types of different sizes, and what happens when cells lose the ability to sense or regulate their size in diseases like cancers.
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Affiliation(s)
- Miriam Bracha Ginzberg
- Department of Systems Biology, Harvard Medical School, Boston, United States.,Cell Biology Program, The Hospital for Sick Children, Toronto, Canada
| | - Nancy Chang
- Cell Biology Program, The Hospital for Sick Children, Toronto, Canada
| | - Heather D'Souza
- Cell Biology Program, The Hospital for Sick Children, Toronto, Canada
| | - Nish Patel
- Cell Biology Program, The Hospital for Sick Children, Toronto, Canada
| | - Ran Kafri
- Cell Biology Program, The Hospital for Sick Children, Toronto, Canada
| | - Marc W Kirschner
- Department of Systems Biology, Harvard Medical School, Boston, United States
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48
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Perez DE, Henle AM, Amsterdam A, Hagen HR, Lees JA. Uveal melanoma driver mutations in GNAQ/11 yield numerous changes in melanocyte biology. Pigment Cell Melanoma Res 2018; 31:604-613. [PMID: 29570931 DOI: 10.1111/pcmr.12700] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2017] [Accepted: 02/09/2018] [Indexed: 11/27/2022]
Abstract
Uveal melanoma (UM) is the most common primary intraocular cancer and has a high incidence of metastasis, which lacks any effective treatment. Here, we present zebrafish models of UM, which are driven by melanocyte-specific expression of activating GNAQ or GNA11 alleles, GNAQ/11Q209L , the predominant initiating mutations for human UM. When combined with mutant tp53, GNAQ/11Q209L transgenics develop various melanocytic tumors, including UM, with near complete penetrance. These tumors display nuclear YAP localization and thus phenocopy human UM. We show that GNAQ/11Q209L expression induces profound melanocyte defects independent of tp53 mutation, which are apparent within 3 days of development. First, increases in melanocyte number, melanin content, and subcellular melanin distribution result in hyperpigmentation. Additionally, altered melanocyte migration, survival properties, and evasion of normal boundary cues lead to aberrant melanocyte localization and stripe patterning. Collectively, these data show that GNAQ/11Q209L is sufficient to induce numerous protumorigenic changes within melanocytes.
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Affiliation(s)
- Dahlia E Perez
- Department of Biology and The David H. Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Andrea M Henle
- Department of Biology and The David H. Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA, USA.,Biology Department, Carthage College, Kenosha, WI, USA
| | - Adam Amsterdam
- Department of Biology and The David H. Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Hannah R Hagen
- Department of Biology and The David H. Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Jacqueline A Lees
- Department of Biology and The David H. Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA, USA
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Ding J, Aronow BJ, Kaminski N, Kitzmiller J, Whitsett JA, Bar-Joseph Z. Reconstructing differentiation networks and their regulation from time series single-cell expression data. Genome Res 2018; 28:gr.225979.117. [PMID: 29317474 PMCID: PMC5848617 DOI: 10.1101/gr.225979.117] [Citation(s) in RCA: 27] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2017] [Accepted: 12/21/2017] [Indexed: 12/26/2022]
Abstract
Generating detailed and accurate organogenesis models using single-cell RNA-seq data remains a major challenge. Current methods have relied primarily on the assumption that descendant cells are similar to their parents in terms of gene expression levels. These assumptions do not always hold for in vivo studies, which often include infrequently sampled, unsynchronized, and diverse cell populations. Thus, additional information may be needed to determine the correct ordering and branching of progenitor cells and the set of transcription factors (TFs) that are active during advancing stages of organogenesis. To enable such modeling, we have developed a method that learns a probabilistic model that integrates expression similarity with regulatory information to reconstruct the dynamic developmental cell trajectories. When applied to mouse lung developmental data, the method accurately distinguished different cell types and lineages. Existing and new experimental data validated the ability of the method to identify key regulators of cell fate.
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Affiliation(s)
- Jun Ding
- Computational Biology Department, School of Computer Science, Carnegie Mellon University, Pittsburgh, Pennsylvania 15213, USA
| | - Bruce J Aronow
- Division of Biomedical Informatics, Cincinnati Children's Hospital Medical Center, Cincinnati, Ohio 45229, USA
| | - Naftali Kaminski
- Section of Pulmonary, Critical Care and Sleep Medicine, Yale School of Medicine, New Haven, Connecticut 06520, USA
| | - Joseph Kitzmiller
- Section of Neonatology, Perinatal and Pulmonary Biology, Perinatal Institute, Cincinnati Children's Hospital Medical Center, Cincinnati, Ohio 45229, USA
| | - Jeffrey A Whitsett
- Section of Neonatology, Perinatal and Pulmonary Biology, Perinatal Institute, Cincinnati Children's Hospital Medical Center, Cincinnati, Ohio 45229, USA
| | - Ziv Bar-Joseph
- Computational Biology Department, School of Computer Science, Carnegie Mellon University, Pittsburgh, Pennsylvania 15213, USA
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50
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The phenomenology of cell size control. Curr Opin Cell Biol 2017; 49:53-58. [DOI: 10.1016/j.ceb.2017.11.011] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2017] [Revised: 11/05/2017] [Accepted: 11/26/2017] [Indexed: 01/27/2023]
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