1
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Rong Y, Darnell AM, Sapp KM, Vander Heiden MG, Spencer SL. Cells use multiple mechanisms for cell-cycle arrest upon withdrawal of individual amino acids. Cell Rep 2023; 42:113539. [PMID: 38070134 DOI: 10.1016/j.celrep.2023.113539] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2023] [Revised: 09/29/2023] [Accepted: 11/17/2023] [Indexed: 12/30/2023] Open
Abstract
Amino acids are required for cell growth and proliferation, but it remains unclear when and how amino acid availability impinges on the proliferation-quiescence decision. Here, we used time-lapse microscopy and single-cell tracking of cyclin-dependent kinase 2 (CDK2) activity to assess the response of individual cells to withdrawal of single amino acids and found strikingly different cell-cycle effects depending on the amino acid. For example, upon leucine withdrawal, MCF10A cells complete two cell cycles and then enter a CDK2-low quiescence, whereas lysine withdrawal causes immediate cell-cycle stalling. Methionine withdrawal triggers a restriction point phenotype similar to serum starvation or Mek inhibition: upon methionine withdrawal, cells complete their current cell cycle and enter a CDK2-low quiescence after mitosis. Modulation of restriction point regulators p21/p27 or cyclin D1 enables short-term rescue of proliferation under methionine and leucine withdrawal, and to a lesser extent lysine withdrawal, revealing a checkpoint connecting nutrient signaling to cell-cycle entry.
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Affiliation(s)
- Yao Rong
- Department of Molecular, Cellular, and Developmental Biology and BioFrontiers Institute, University of Colorado Boulder, Boulder, CO 80303, USA
| | - Alicia M Darnell
- Koch Institute for Integrative Cancer Research, Cambridge, MA, USA; Department of Biology, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Kiera M Sapp
- Koch Institute for Integrative Cancer Research, Cambridge, MA, USA; Department of Biology, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Matthew G Vander Heiden
- Koch Institute for Integrative Cancer Research, Cambridge, MA, USA; Department of Biology, Massachusetts Institute of Technology, Cambridge, MA 02139, USA; Dana-Farber Cancer Institute, Boston, MA 02215, USA; Broad Institute, Cambridge, MA 02139, USA
| | - Sabrina L Spencer
- Department of Biochemistry and BioFrontiers Institute, University of Colorado Boulder, Boulder, CO 80303, USA.
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2
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Sparta B, Kosaisawe N, Pargett M, Patankar M, DeCuzzi N, Albeck JG. Continuous sensing of nutrients and growth factors by the mTORC1-TFEB axis. eLife 2023; 12:e74903. [PMID: 37698461 PMCID: PMC10547473 DOI: 10.7554/elife.74903] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2021] [Accepted: 09/11/2023] [Indexed: 09/13/2023] Open
Abstract
mTORC1 senses nutrients and growth factors and phosphorylates downstream targets, including the transcription factor TFEB, to coordinate metabolic supply and demand. These functions position mTORC1 as a central controller of cellular homeostasis, but the behavior of this system in individual cells has not been well characterized. Here, we provide measurements necessary to refine quantitative models for mTORC1 as a metabolic controller. We developed a series of fluorescent protein-TFEB fusions and a multiplexed immunofluorescence approach to investigate how combinations of stimuli jointly regulate mTORC1 signaling at the single-cell level. Live imaging of individual MCF10A cells confirmed that mTORC1-TFEB signaling responds continuously to individual, sequential, or simultaneous treatment with amino acids and the growth factor insulin. Under physiologically relevant concentrations of amino acids, we observe correlated fluctuations in TFEB, AMPK, and AKT signaling that indicate continuous activity adjustments to nutrient availability. Using partial least squares regression modeling, we show that these continuous gradations are connected to protein synthesis rate via a distributed network of mTORC1 effectors, providing quantitative support for the qualitative model of mTORC1 as a homeostatic controller and clarifying its functional behavior within individual cells.
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Affiliation(s)
- Breanne Sparta
- Department of Molecular and Cellular Biology, University of California, DavisDavisUnited States
| | - Nont Kosaisawe
- Department of Molecular and Cellular Biology, University of California, DavisDavisUnited States
| | - Michael Pargett
- Department of Molecular and Cellular Biology, University of California, DavisDavisUnited States
| | - Madhura Patankar
- Department of Molecular and Cellular Biology, University of California, DavisDavisUnited States
| | - Nicholaus DeCuzzi
- Department of Molecular and Cellular Biology, University of California, DavisDavisUnited States
| | - John G Albeck
- Department of Molecular and Cellular Biology, University of California, DavisDavisUnited States
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3
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Cacioppo R, Akman HB, Tuncer T, Erson-Bensan AE, Lindon C. Differential translation of mRNA isoforms underlies oncogenic activation of cell cycle kinase Aurora A. eLife 2023; 12:RP87253. [PMID: 37384380 DOI: 10.7554/elife.87253] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/01/2023] Open
Abstract
Aurora Kinase A (AURKA) is an oncogenic kinase with major roles in mitosis, but also exerts cell cycle- and kinase-independent functions linked to cancer. Therefore, control of its expression, as well as its activity, is crucial. A short and a long 3'UTR isoform exist for AURKA mRNA, resulting from alternative polyadenylation (APA). We initially observed that in triple-negative breast cancer, where AURKA is typically overexpressed, the short isoform is predominant and this correlates with faster relapse times of patients. The short isoform is characterized by higher translational efficiency since translation and decay rate of the long isoform are targeted by hsa-let-7a tumor-suppressor miRNA. Additionally, hsa-let-7a regulates the cell cycle periodicity of translation of the long isoform, whereas the short isoform is translated highly and constantly throughout interphase. Finally, disrupted production of the long isoform led to an increase in proliferation and migration rates of cells. In summary, we uncovered a new mechanism dependent on the cooperation between APA and miRNA targeting likely to be a route of oncogenic activation of human AURKA.
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Affiliation(s)
- Roberta Cacioppo
- Department of Pharmacology, University of Cambridge, Cambridge, United Kingdom
| | - Hesna Begum Akman
- Department of Pharmacology, University of Cambridge, Cambridge, United Kingdom
- Department of Biological Sciences, Orta Dogu Teknik Universitesi, Ankara, Turkey
| | - Taner Tuncer
- Department of Biology, Ondokuz Mayis Universitesi, Samsun, Turkey
| | | | - Catherine Lindon
- Department of Pharmacology, University of Cambridge, Cambridge, United Kingdom
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4
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Diehl FF, Miettinen TP, Elbashir R, Nabel CS, Darnell AM, Do BT, Manalis SR, Lewis CA, Vander Heiden MG. Nucleotide imbalance decouples cell growth from cell proliferation. Nat Cell Biol 2022; 24:1252-1264. [PMID: 35927450 PMCID: PMC9359916 DOI: 10.1038/s41556-022-00965-1] [Citation(s) in RCA: 29] [Impact Index Per Article: 14.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2021] [Accepted: 06/21/2022] [Indexed: 12/26/2022]
Abstract
Nucleotide metabolism supports RNA synthesis and DNA replication to enable cell growth and division. Nucleotide depletion can inhibit cell growth and proliferation, but how cells sense and respond to changes in the relative levels of individual nucleotides is unclear. Moreover, the nucleotide requirement for biomass production changes over the course of the cell cycle, and how cells coordinate differential nucleotide demands with cell cycle progression is not well understood. Here we find that excess levels of individual nucleotides can inhibit proliferation by disrupting the relative levels of nucleotide bases needed for DNA replication and impeding DNA replication. The resulting purine and pyrimidine imbalances are not sensed by canonical growth regulatory pathways like mTORC1, Akt and AMPK signalling cascades, causing excessive cell growth despite inhibited proliferation. Instead, cells rely on replication stress signalling to survive during, and recover from, nucleotide imbalance during S phase. We find that ATR-dependent replication stress signalling is activated during unperturbed S phases and promotes nucleotide availability to support DNA replication. Together, these data reveal that imbalanced nucleotide levels are not detected until S phase, rendering cells reliant on replication stress signalling to cope with this metabolic problem and disrupting the coordination of cell growth and division.
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Affiliation(s)
- Frances F Diehl
- Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA, USA
- Department of Biology, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Teemu P Miettinen
- Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA, USA
- Medical Research Council Laboratory for Molecular Cell Biology, University College London, London, UK
| | - Ryan Elbashir
- Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA, USA
- Department of Biology, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Christopher S Nabel
- Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA, USA
- Massachusetts General Hospital Cancer Center, Boston, MA, USA
| | - Alicia M Darnell
- Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA, USA
- Department of Biology, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Brian T Do
- Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA, USA
- Department of Biology, Massachusetts Institute of Technology, Cambridge, MA, USA
- Harvard-MIT Health Sciences and Technology, Cambridge, MA, USA
| | - Scott R Manalis
- Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA, USA
- Departments of Biological Engineering and Mechanical Engineering, Massachusetts Institute of Technology, Cambridge, MA, USA
| | | | - Matthew G Vander Heiden
- Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA, USA.
- Department of Biology, Massachusetts Institute of Technology, Cambridge, MA, USA.
- Dana-Farber Cancer Institute, Boston, MA, USA.
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5
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Phan TP, Boatwright CA, Drown CG, Skinner MW, Strong MA, Jordan PW, Holland AJ. Upstream open reading frames control PLK4 translation and centriole duplication in primordial germ cells. Genes Dev 2022; 36:718-736. [PMID: 35772791 PMCID: PMC9296005 DOI: 10.1101/gad.349604.122] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2022] [Accepted: 06/09/2022] [Indexed: 11/24/2022]
Abstract
Centrosomes are microtubule-organizing centers comprised of a pair of centrioles and the surrounding pericentriolar material. Abnormalities in centriole number are associated with cell division errors and can contribute to diseases such as cancer. Centriole duplication is limited to once per cell cycle and is controlled by the dosage-sensitive Polo-like kinase 4 (PLK4). Here, we show that PLK4 abundance is translationally controlled through conserved upstream open reading frames (uORFs) in the 5' UTR of the mRNA. Plk4 uORFs suppress Plk4 translation and prevent excess protein synthesis. Mice with homozygous knockout of Plk4 uORFs (Plk4 Δu/Δu ) are viable but display dramatically reduced fertility because of a significant depletion of primordial germ cells (PGCs). The remaining PGCs in Plk4 Δu/Δu mice contain extra centrioles and display evidence of increased mitotic errors. PGCs undergo hypertranscription and have substantially more Plk4 mRNA than somatic cells. Reducing Plk4 mRNA levels in mice lacking Plk4 uORFs restored PGC numbers and fully rescued fertility. Together, our data uncover a specific requirement for uORF-dependent control of PLK4 translation in counterbalancing the increased Plk4 transcription in PGCs. Thus, uORF-mediated translational suppression of PLK4 has a critical role in preventing centriole amplification and preserving the genomic integrity of future gametes.
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Affiliation(s)
- Thao P Phan
- Department of Molecular Biology and Genetics, Johns Hopkins University School of Medicine, Baltimore, Maryland 21205, USA
| | - Christina A Boatwright
- Department of Molecular Biology and Genetics, Johns Hopkins University School of Medicine, Baltimore, Maryland 21205, USA
| | - Chelsea G Drown
- Department of Molecular Biology and Genetics, Johns Hopkins University School of Medicine, Baltimore, Maryland 21205, USA
| | - Marnie W Skinner
- Department of Biochemistry and Molecular Biology, Bloomberg School of Public Health, Johns Hopkins University, Baltimore, Maryland 21205, USA
- Department of Biochemistry and Molecular Biology, Uniformed Services University of the Health Sciences, Bethesda, Maryland 20814, USA
| | - Margaret A Strong
- Department of Molecular Biology and Genetics, Johns Hopkins University School of Medicine, Baltimore, Maryland 21205, USA
| | - Philip W Jordan
- Department of Biochemistry and Molecular Biology, Bloomberg School of Public Health, Johns Hopkins University, Baltimore, Maryland 21205, USA
- Department of Biochemistry and Molecular Biology, Uniformed Services University of the Health Sciences, Bethesda, Maryland 20814, USA
| | - Andrew J Holland
- Department of Molecular Biology and Genetics, Johns Hopkins University School of Medicine, Baltimore, Maryland 21205, USA
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6
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Translational control of E2f1 regulates the Drosophila cell cycle. Proc Natl Acad Sci U S A 2022; 119:2113704119. [PMID: 35074910 PMCID: PMC8795540 DOI: 10.1073/pnas.2113704119] [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] [Accepted: 12/10/2021] [Indexed: 12/21/2022] Open
Abstract
E2F transcription factors are master regulators of the eukaryotic cell cycle. In Drosophila, the sole activating E2F, E2F1, is both required for and sufficient to promote G1→S progression. E2F1 activity is regulated both by binding to RB Family repressors and by posttranscriptional control of E2F1 protein levels by the EGFR and TOR signaling pathways. Here, we investigate cis-regulatory elements in the E2f1 messenger RNA (mRNA) that enable E2f1 translation to respond to these signals and promote mitotic proliferation of wing imaginal disc and intestinal stem cells. We show that small upstream open reading frames (uORFs) in the 5' untranslated region (UTR) of the E2f1 mRNA limit its translation, impacting rates of cell proliferation. E2f1 transgenes lacking these 5'UTR uORFs caused TOR-independent expression and excess cell proliferation, suggesting that TOR activity can bypass uORF-mediated translational repression. EGFR signaling also enhanced translation but through a mechanism less dependent on 5'UTR uORFs. Further, we mapped a region in the E2f1 mRNA that contains a translational enhancer, which may also be targeted by TOR signaling. This study reveals translational control mechanisms through which growth signaling regulates cell cycle progression.
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7
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Kfoury YS, Ji F, Mazzola M, Sykes DB, Scherer AK, Anselmo A, Akiyama Y, Mercier F, Severe N, Kokkaliaris KD, Zhao T, Brouse T, Saez B, Seidl J, Papazian A, Ivanov P, Mansour MK, Sadreyev RI, Scadden DT. tiRNA signaling via stress-regulated vesicle transfer in the hematopoietic niche. Cell Stem Cell 2021; 28:2090-2103.e9. [PMID: 34551362 PMCID: PMC8642285 DOI: 10.1016/j.stem.2021.08.014] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2020] [Revised: 06/23/2021] [Accepted: 08/17/2021] [Indexed: 12/11/2022]
Abstract
Extracellular vesicles (EVs) transfer complex biologic material between cells. However, the role of this process in vivo is poorly defined. Here, we demonstrate that osteoblastic cells in the bone marrow (BM) niche elaborate extracellular vesicles that are taken up by hematopoietic progenitor cells in vivo. Genotoxic or infectious stress rapidly increased stromal-derived extracellular vesicle transfer to granulocyte-monocyte progenitors. The extracellular vesicles contained processed tRNAs (tiRNAs) known to modulate protein translation. 5'-ti-Pro-CGG-1 was preferentially abundant in osteoblast-derived extracellular vesicles and, when transferred to granulocyte-monocyte progenitors, increased protein translation, cell proliferation, and myeloid differentiation. Upregulating EV transfer improved hematopoietic recovery from genotoxic injury and survival from fungal sepsis. Therefore, EV-mediated tiRNA transfer provides a stress-modulated signaling axis in the BM niche distinct from conventional cytokine-driven stress responses.
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Affiliation(s)
- Youmna S Kfoury
- Center for Regenerative Medicine, Massachusetts General Hospital, 185 Cambridge Street, Boston, MA 02114, USA; Harvard Stem Cell Institute, 7 Divinity Avenue, Cambridge, MA 02138, USA; Department of Stem Cell and Regenerative Biology, Harvard University, Cambridge, MA 02138, USA.
| | - Fei Ji
- Department of Molecular Biology, Massachusetts General Hospital, 185 Cambridge Street, Boston, MA 02114, USA; Department of Genetics, Harvard Medical School, Boston, MA 02115, USA
| | - Michael Mazzola
- Center for Regenerative Medicine, Massachusetts General Hospital, 185 Cambridge Street, Boston, MA 02114, USA; Harvard Stem Cell Institute, 7 Divinity Avenue, Cambridge, MA 02138, USA; Department of Stem Cell and Regenerative Biology, Harvard University, Cambridge, MA 02138, USA
| | - David B Sykes
- Center for Regenerative Medicine, Massachusetts General Hospital, 185 Cambridge Street, Boston, MA 02114, USA; Harvard Stem Cell Institute, 7 Divinity Avenue, Cambridge, MA 02138, USA; Department of Stem Cell and Regenerative Biology, Harvard University, Cambridge, MA 02138, USA
| | - Allison K Scherer
- Division of Infectious Diseases, Massachusetts General Hospital, Boston, MA 02114, USA
| | - Anthony Anselmo
- Department of Molecular Biology, Massachusetts General Hospital, 185 Cambridge Street, Boston, MA 02114, USA; Department of Genetics, Harvard Medical School, Boston, MA 02115, USA
| | - Yasutoshi Akiyama
- Division of Rheumatology, Immunology and Allergy, Brigham and Women's Hospital, Boston, MA 02115, USA; Department of Medicine, Harvard Medical School, Boston, MA 02115, USA
| | - Francois Mercier
- Center for Regenerative Medicine, Massachusetts General Hospital, 185 Cambridge Street, Boston, MA 02114, USA; Harvard Stem Cell Institute, 7 Divinity Avenue, Cambridge, MA 02138, USA; Department of Stem Cell and Regenerative Biology, Harvard University, Cambridge, MA 02138, USA
| | - Nicolas Severe
- Center for Regenerative Medicine, Massachusetts General Hospital, 185 Cambridge Street, Boston, MA 02114, USA; Harvard Stem Cell Institute, 7 Divinity Avenue, Cambridge, MA 02138, USA; Department of Stem Cell and Regenerative Biology, Harvard University, Cambridge, MA 02138, USA
| | - Konstantinos D Kokkaliaris
- Center for Regenerative Medicine, Massachusetts General Hospital, 185 Cambridge Street, Boston, MA 02114, USA; Harvard Stem Cell Institute, 7 Divinity Avenue, Cambridge, MA 02138, USA; Department of Stem Cell and Regenerative Biology, Harvard University, Cambridge, MA 02138, USA
| | - Ting Zhao
- Center for Regenerative Medicine, Massachusetts General Hospital, 185 Cambridge Street, Boston, MA 02114, USA; Harvard Stem Cell Institute, 7 Divinity Avenue, Cambridge, MA 02138, USA; Department of Stem Cell and Regenerative Biology, Harvard University, Cambridge, MA 02138, USA
| | - Thomas Brouse
- Center for Regenerative Medicine, Massachusetts General Hospital, 185 Cambridge Street, Boston, MA 02114, USA; Harvard Stem Cell Institute, 7 Divinity Avenue, Cambridge, MA 02138, USA; Department of Stem Cell and Regenerative Biology, Harvard University, Cambridge, MA 02138, USA
| | - Borja Saez
- Center for Regenerative Medicine, Massachusetts General Hospital, 185 Cambridge Street, Boston, MA 02114, USA; Harvard Stem Cell Institute, 7 Divinity Avenue, Cambridge, MA 02138, USA; Department of Stem Cell and Regenerative Biology, Harvard University, Cambridge, MA 02138, USA
| | - Jefferson Seidl
- Center for Regenerative Medicine, Massachusetts General Hospital, 185 Cambridge Street, Boston, MA 02114, USA; Harvard Stem Cell Institute, 7 Divinity Avenue, Cambridge, MA 02138, USA; Department of Stem Cell and Regenerative Biology, Harvard University, Cambridge, MA 02138, USA
| | - Ani Papazian
- Center for Regenerative Medicine, Massachusetts General Hospital, 185 Cambridge Street, Boston, MA 02114, USA; Harvard Stem Cell Institute, 7 Divinity Avenue, Cambridge, MA 02138, USA; Department of Stem Cell and Regenerative Biology, Harvard University, Cambridge, MA 02138, USA
| | - Pavel Ivanov
- Division of Rheumatology, Immunology and Allergy, Brigham and Women's Hospital, Boston, MA 02115, USA; Department of Medicine, Harvard Medical School, Boston, MA 02115, USA; Harvard Initiative for RNA Medicine, Boston, MA 02115, USA
| | - Michael K Mansour
- Harvard Stem Cell Institute, 7 Divinity Avenue, Cambridge, MA 02138, USA; Division of Infectious Diseases, Massachusetts General Hospital, Boston, MA 02114, USA; Department of Medicine, Harvard Medical School, Boston, MA 02115, USA
| | - Ruslan I Sadreyev
- Department of Molecular Biology, Massachusetts General Hospital, 185 Cambridge Street, Boston, MA 02114, USA; Department of Pathology, Massachusetts General Hospital and Harvard Medical School, Boston, MA 02114, USA
| | - David T Scadden
- Center for Regenerative Medicine, Massachusetts General Hospital, 185 Cambridge Street, Boston, MA 02114, USA; Harvard Stem Cell Institute, 7 Divinity Avenue, Cambridge, MA 02138, USA; Department of Stem Cell and Regenerative Biology, Harvard University, Cambridge, MA 02138, USA.
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8
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Translational regulation in pathogenic and beneficial plant-microbe interactions. Biochem J 2021; 478:2775-2788. [PMID: 34297042 DOI: 10.1042/bcj20210066] [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: 05/12/2021] [Revised: 07/01/2021] [Accepted: 07/02/2021] [Indexed: 11/17/2022]
Abstract
Plants are surrounded by a vast diversity of microorganisms. Limiting pathogenic microorganisms is crucial for plant survival. On the other hand, the interaction of plants with beneficial microorganisms promotes their growth or allows them to overcome nutrient deficiencies. Balancing the number and nature of these interactions is crucial for plant growth and development, and thus, for crop productivity in agriculture. Plants use sophisticated mechanisms to recognize pathogenic and beneficial microorganisms and genetic programs related to immunity or symbiosis. Although most research has focused on characterizing changes in the transcriptome during plant-microbe interactions, the application of techniques such as Translating Ribosome Affinity Purification (TRAP) and Ribosome profiling allowed examining the dynamic association of RNAs to the translational machinery, highlighting the importance of the translational level of control of gene expression in both pathogenic and beneficial interactions. These studies revealed that the transcriptional and the translational responses are not always correlated, and that translational control operates at cell-specific level. In addition, translational control is governed by cis-elements present in the 5'mRNA leader of regulated mRNAs, e.g. upstream open reading frames (uORFs) and sequence-specific motifs. In this review, we summarize and discuss the recent advances made in the field of translational control during pathogenic and beneficial plant-microbe interactions.
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9
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Kosaisawe N, Sparta B, Pargett M, Teragawa CK, Albeck JG. Transient phases of OXPHOS inhibitor resistance reveal underlying metabolic heterogeneity in single cells. Cell Metab 2021; 33:649-665.e8. [PMID: 33561427 PMCID: PMC8005262 DOI: 10.1016/j.cmet.2021.01.014] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/09/2019] [Revised: 10/13/2020] [Accepted: 01/13/2021] [Indexed: 12/16/2022]
Abstract
Cell-to-cell heterogeneity in metabolism plays an unknown role in physiology and pharmacology. To functionally characterize cellular variability in metabolism, we treated cells with inhibitors of oxidative phosphorylation (OXPHOS) and monitored their responses with live-cell reporters for ATP, ADP/ATP, or activity of the energy-sensing kinase AMPK. Across multiple OXPHOS inhibitors and cell types, we identified a subpopulation of cells resistant to activation of AMPK and reduction of ADP/ATP ratio. This resistant state persists transiently for at least several hours and can be inherited during cell divisions. OXPHOS inhibition suppresses the mTORC1 and ERK growth signaling pathways in sensitive cells, but not in resistant cells. Resistance is linked to a multi-factorial combination of increased glucose uptake, reduced protein biosynthesis, and G0/G1 cell-cycle status. Our results reveal dynamic fluctuations in cellular energetic balance and provide a basis for measuring and predicting the distribution of cellular responses to OXPHOS inhibition.
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Affiliation(s)
- Nont Kosaisawe
- Department of Molecular and Cellular Biology, University of California, Davis, Davis, CA 95616, USA
| | - Breanne Sparta
- Department of Molecular and Cellular Biology, University of California, Davis, Davis, CA 95616, USA
| | - Michael Pargett
- Department of Molecular and Cellular Biology, University of California, Davis, Davis, CA 95616, USA
| | - Carolyn K Teragawa
- Department of Molecular and Cellular Biology, University of California, Davis, Davis, CA 95616, USA
| | - John G Albeck
- Department of Molecular and Cellular Biology, University of California, Davis, Davis, CA 95616, USA.
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10
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Lau AN, Li Z, Danai LV, Westermark AM, Darnell AM, Ferreira R, Gocheva V, Sivanand S, Lien EC, Sapp KM, Mayers JR, Biffi G, Chin CR, Davidson SM, Tuveson DA, Jacks T, Matheson NJ, Yilmaz O, Vander Heiden MG. Dissecting cell-type-specific metabolism in pancreatic ductal adenocarcinoma. eLife 2020; 9:56782. [PMID: 32648540 PMCID: PMC7406355 DOI: 10.7554/elife.56782] [Citation(s) in RCA: 51] [Impact Index Per Article: 12.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2020] [Accepted: 07/09/2020] [Indexed: 02/07/2023] Open
Abstract
Tumors are composed of many different cell types including cancer cells, fibroblasts, and immune cells. Dissecting functional metabolic differences between cell types within a mixed population can be challenging due to the rapid turnover of metabolites relative to the time needed to isolate cells. To overcome this challenge, we traced isotope-labeled nutrients into macromolecules that turn over more slowly than metabolites. This approach was used to assess differences between cancer cell and fibroblast metabolism in murine pancreatic cancer organoid-fibroblast co-cultures and tumors. Pancreatic cancer cells exhibited increased pyruvate carboxylation relative to fibroblasts, and this flux depended on both pyruvate carboxylase and malic enzyme 1 activity. Consequently, expression of both enzymes in cancer cells was necessary for organoid and tumor growth, demonstrating that dissecting the metabolism of specific cell populations within heterogeneous systems can identify dependencies that may not be evident from studying isolated cells in culture or bulk tissue. Tumors contain a mixture of many different types of cells, including cancer cells and non-cancer cells. The interactions between these two groups of cells affect how the cancer cells use nutrients, which, in turn, affects how fast these cells grow and divide. Furthermore, different cell types may use nutrients in diverse ways to make other molecules – known as metabolites – that the cell needs to survive. Fibroblasts are a subset of non-cancer cells that are typically found in tumors and can help them form. Separating fibroblasts from cancer cells in a tumor takes a lot longer than the chemical reactions in each cell of the tumor that produce and use up nutrients, also known as the cell’s metabolism. Therefore, measuring the levels of glucose (the sugar that is the main energy source for cells) and other metabolites in each tumor cell after separating them does not necessarily provide accurate information about the tumor cell’s metabolism. This makes it difficult to study how cancer cells and fibroblasts use nutrients differently. Lau et al. have developed a strategy to study the metabolism of cancer cells and fibroblasts in tumors. Mice with tumors in their pancreas were provided glucose that had been labelled using biochemical techniques. As expected, when the cell processed the glucose, the label was transferred into metabolites that got used up very quickly. But the label also became incorporated into larger, more stable molecules, such as proteins. Unlike the small metabolites, these larger molecules do not change in the time it takes to separate the cancer cells from the fibroblasts. Lau et al. sorted cells from whole pancreatic tumors and analyzed large, stable molecules that can incorporate the label from glucose in cancer cells and fibroblasts. The experiments showed that, in cancer cells, these molecules were more likely to have labeling patterns that are characteristic of two specific enzymes called pyruvate carboxylase and malic enzyme 1. This suggests that these enzymes are more active in cancer cells. Lau et al. also found that pancreatic cancer cells needed these two enzymes to metabolize glucose and to grow into large tumors. Pancreatic cancer is one of the most lethal cancers and current therapies offer limited benefit to many patients. Therefore, it is important to develop new drugs to treat this disease. Understanding how cancer cells and non-cancer cells in pancreatic tumors use nutrients differently is important for developing drugs that only target cancer cells.
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Affiliation(s)
- Allison N Lau
- Koch Institute for Integrative Cancer Research and the Department of Biology at Massachusetts Institute of Technology, Cambridge, United States
| | - Zhaoqi Li
- Koch Institute for Integrative Cancer Research and the Department of Biology at Massachusetts Institute of Technology, Cambridge, United States
| | - Laura V Danai
- Koch Institute for Integrative Cancer Research and the Department of Biology at Massachusetts Institute of Technology, Cambridge, United States.,Department of Biochemistry and Molecular Biology, University of Massachusetts, Amherst, Amherst, United States
| | - Anna M Westermark
- Koch Institute for Integrative Cancer Research and the Department of Biology at Massachusetts Institute of Technology, Cambridge, United States
| | - Alicia M Darnell
- Koch Institute for Integrative Cancer Research and the Department of Biology at Massachusetts Institute of Technology, Cambridge, United States
| | - Raphael Ferreira
- Koch Institute for Integrative Cancer Research and the Department of Biology at Massachusetts Institute of Technology, Cambridge, United States.,Department of Biology and Biological Engineering, Chalmers University of Technology, Gothenburg, Sweden
| | - Vasilena Gocheva
- Koch Institute for Integrative Cancer Research and the Department of Biology at Massachusetts Institute of Technology, Cambridge, United States
| | - Sharanya Sivanand
- Koch Institute for Integrative Cancer Research and the Department of Biology at Massachusetts Institute of Technology, Cambridge, United States
| | - Evan C Lien
- Koch Institute for Integrative Cancer Research and the Department of Biology at Massachusetts Institute of Technology, Cambridge, United States
| | - Kiera M Sapp
- Koch Institute for Integrative Cancer Research and the Department of Biology at Massachusetts Institute of Technology, Cambridge, United States
| | - Jared R Mayers
- Koch Institute for Integrative Cancer Research and the Department of Biology at Massachusetts Institute of Technology, Cambridge, United States
| | - Giulia Biffi
- Cold Spring Harbor Laboratory, Cold Spring Harbor, New York, United States.,Lustgarten Foundation Pancreatic Cancer Research Laboratory, Cold Spring Harbor, New York, United States.,Cancer Research United Kingdom Cambridge Institute, University of Cambridge, Cambridge, United Kingdom
| | - Christopher R Chin
- Koch Institute for Integrative Cancer Research and the Department of Biology at Massachusetts Institute of Technology, Cambridge, United States
| | - Shawn M Davidson
- Koch Institute for Integrative Cancer Research and the Department of Biology at Massachusetts Institute of Technology, Cambridge, United States.,Lewis-Sigler Institute for Integrative Genomics, Princeton University, Princeton, United States.,Department of Molecular Biology, Princeton University, Princeton, United States
| | - David A Tuveson
- Cold Spring Harbor Laboratory, Cold Spring Harbor, New York, United States.,Lustgarten Foundation Pancreatic Cancer Research Laboratory, Cold Spring Harbor, New York, United States
| | - Tyler Jacks
- Koch Institute for Integrative Cancer Research and the Department of Biology at Massachusetts Institute of Technology, Cambridge, United States
| | - Nicholas J Matheson
- Koch Institute for Integrative Cancer Research and the Department of Biology at Massachusetts Institute of Technology, Cambridge, United States.,Department of Medicine, University of Cambridge, Cambridge, United Kingdom.,Cambridge Institute for Therapeutic Immunology and Infectious Disease, University of Cambridge, Cambridge, United Kingdom
| | - Omer Yilmaz
- Koch Institute for Integrative Cancer Research and the Department of Biology at Massachusetts Institute of Technology, Cambridge, United States.,Department of Pathology, Massachusetts General Hospital, Boston, United States
| | - Matthew G Vander Heiden
- Koch Institute for Integrative Cancer Research and the Department of Biology at Massachusetts Institute of Technology, Cambridge, United States.,Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, United States
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11
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Koltun B, Ironi S, Gershoni-Emek N, Barrera I, Hleihil M, Nanguneri S, Sasmal R, Agasti SS, Nair D, Rosenblum K. Measuring mRNA translation in neuronal processes and somata by tRNA-FRET. Nucleic Acids Res 2020; 48:e32. [PMID: 31974573 PMCID: PMC7102941 DOI: 10.1093/nar/gkaa042] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2019] [Revised: 12/04/2019] [Accepted: 01/15/2020] [Indexed: 01/12/2023] Open
Abstract
In neurons, the specific spatial and temporal localization of protein synthesis is of great importance for function and survival. Here, we visualized tRNA and protein synthesis events in fixed and live mouse primary cortical culture using fluorescently-labeled tRNAs. We were able to characterize the distribution and transport of tRNAs in different neuronal sub-compartments and to study their association with the ribosome. We found that tRNA mobility in neural processes is lower than in somata and corresponds to patterns of slow transport mechanisms, and that larger tRNA puncta co-localize with translational machinery components and are likely the functional fraction. Furthermore, chemical induction of long-term potentiation (LTP) in culture revealed up-regulation of mRNA translation with a similar effect in dendrites and somata, which appeared to be GluR-dependent 6 h post-activation. Importantly, measurement of protein synthesis in neurons with high resolutions offers new insights into neuronal function in health and disease states.
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Affiliation(s)
- Bella Koltun
- Sagol Department of Neurobiology, University of Haifa, Haifa, Israel
| | - Sivan Ironi
- Sagol Department of Neurobiology, University of Haifa, Haifa, Israel
| | | | - Iliana Barrera
- Sagol Department of Neurobiology, University of Haifa, Haifa, Israel
| | - Mohammad Hleihil
- Sagol Department of Neurobiology, University of Haifa, Haifa, Israel
| | | | - Ranjan Sasmal
- New Chemistry Unit and Chemistry & Physics of Materials Unit, Jawaharlal Nehru Centre for Advanced Scientific Research (JNCASR), Bangalore, Karnataka, India
| | - Sarit S Agasti
- New Chemistry Unit and Chemistry & Physics of Materials Unit, Jawaharlal Nehru Centre for Advanced Scientific Research (JNCASR), Bangalore, Karnataka, India
| | - Deepak Nair
- Centre for Neuroscience, Indian Institute of Science, Bangalore, India
| | - Kobi Rosenblum
- Sagol Department of Neurobiology, University of Haifa, Haifa, Israel.,Center for Gene Manipulation in the Brain, University of Haifa, Haifa, Israel
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12
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Quantification of mRNA translation in live cells using single-molecule imaging. Nat Protoc 2020; 15:1371-1398. [PMID: 32076351 DOI: 10.1038/s41596-019-0284-x] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2019] [Accepted: 12/13/2019] [Indexed: 11/09/2022]
Abstract
mRNA translation is a key step in gene expression. Proper regulation of translation efficiency ensures correct protein expression levels in the cell, which is essential to cell function. Different methods used to study translational control in the cell rely on population-based assays that do not provide information about translational heterogeneity between cells or between mRNAs of the same gene within a cell, and generally provide only a snapshot of translation. To study translational heterogeneity and measure translation dynamics, we have developed microscopy-based methods that enable visualization of translation of single mRNAs in live cells. These methods consist of a set of genetic tools, an imaging-based approach and sophisticated computational tools. Using the translation imaging method, one can investigate many new aspects of translation in single living cells, such as translation start-site selection, 3'-UTR (untranslated region) translation and translation-coupled mRNA decay. Here, we describe in detail how to perform such experiments, including reporter design, cell line generation, image acquisition and analysis. This protocol also provides a detailed description of the image analysis pipeline and computational modeling that will enable non-experts to correctly interpret fluorescence measurements. The protocol takes 2-4 d to complete (after cell lines expressing all required transgenes have been generated).
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13
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Lee S, Micalizzi D, Truesdell SS, Bukhari SIA, Boukhali M, Lombardi-Story J, Kato Y, Choo MK, Dey-Guha I, Ji F, Nicholson BT, Myers DT, Lee D, Mazzola MA, Raheja R, Langenbucher A, Haradhvala NJ, Lawrence MS, Gandhi R, Tiedje C, Diaz-Muñoz MD, Sweetser DA, Sadreyev R, Sykes D, Haas W, Haber DA, Maheswaran S, Vasudevan S. A post-transcriptional program of chemoresistance by AU-rich elements and TTP in quiescent leukemic cells. Genome Biol 2020; 21:33. [PMID: 32039742 PMCID: PMC7011231 DOI: 10.1186/s13059-020-1936-4] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2019] [Accepted: 01/15/2020] [Indexed: 02/07/2023] Open
Abstract
BACKGROUND Quiescence (G0) is a transient, cell cycle-arrested state. By entering G0, cancer cells survive unfavorable conditions such as chemotherapy and cause relapse. While G0 cells have been studied at the transcriptome level, how post-transcriptional regulation contributes to their chemoresistance remains unknown. RESULTS We induce chemoresistant and G0 leukemic cells by serum starvation or chemotherapy treatment. To study post-transcriptional regulation in G0 leukemic cells, we systematically analyzed their transcriptome, translatome, and proteome. We find that our resistant G0 cells recapitulate gene expression profiles of in vivo chemoresistant leukemic and G0 models. In G0 cells, canonical translation initiation is inhibited; yet we find that inflammatory genes are highly translated, indicating alternative post-transcriptional regulation. Importantly, AU-rich elements (AREs) are significantly enriched in the upregulated G0 translatome and transcriptome. Mechanistically, we find the stress-responsive p38 MAPK-MK2 signaling pathway stabilizes ARE mRNAs by phosphorylation and inactivation of mRNA decay factor, Tristetraprolin (TTP) in G0. This permits expression of ARE mRNAs that promote chemoresistance. Conversely, inhibition of TTP phosphorylation by p38 MAPK inhibitors and non-phosphorylatable TTP mutant decreases ARE-bearing TNFα and DUSP1 mRNAs and sensitizes leukemic cells to chemotherapy. Furthermore, co-inhibiting p38 MAPK and TNFα prior to or along with chemotherapy substantially reduces chemoresistance in primary leukemic cells ex vivo and in vivo. CONCLUSIONS These studies uncover post-transcriptional regulation underlying chemoresistance in leukemia. Our data reveal the p38 MAPK-MK2-TTP axis as a key regulator of expression of ARE-bearing mRNAs that promote chemoresistance. By disrupting this pathway, we develop an effective combination therapy against chemosurvival.
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Affiliation(s)
- Sooncheol Lee
- Massachusetts General Hospital Cancer Center, Harvard Medical School, 185 Cambridge St, CPZN4202, Boston, MA, 02114, USA.,Department of Medicine, Massachusetts General Hospital and Harvard Medical School, Boston, 02114, Massachusetts, USA.,Center for Regenerative Medicine, Massachusetts General Hospital, Harvard Medical School, Boston, MA, 02114, USA.,Harvard Stem Cell Institute, Harvard University, Cambridge, MA, 02138, USA
| | - Douglas Micalizzi
- Massachusetts General Hospital Cancer Center, Harvard Medical School, 185 Cambridge St, CPZN4202, Boston, MA, 02114, USA.,Department of Medicine, Massachusetts General Hospital and Harvard Medical School, Boston, 02114, Massachusetts, USA
| | - Samuel S Truesdell
- Massachusetts General Hospital Cancer Center, Harvard Medical School, 185 Cambridge St, CPZN4202, Boston, MA, 02114, USA.,Center for Regenerative Medicine, Massachusetts General Hospital, Harvard Medical School, Boston, MA, 02114, USA.,Harvard Stem Cell Institute, Harvard University, Cambridge, MA, 02138, USA
| | - Syed I A Bukhari
- Massachusetts General Hospital Cancer Center, Harvard Medical School, 185 Cambridge St, CPZN4202, Boston, MA, 02114, USA.,Department of Medicine, Massachusetts General Hospital and Harvard Medical School, Boston, 02114, Massachusetts, USA.,Center for Regenerative Medicine, Massachusetts General Hospital, Harvard Medical School, Boston, MA, 02114, USA.,Harvard Stem Cell Institute, Harvard University, Cambridge, MA, 02138, USA
| | - Myriam Boukhali
- Massachusetts General Hospital Cancer Center, Harvard Medical School, 185 Cambridge St, CPZN4202, Boston, MA, 02114, USA.,Department of Medicine, Massachusetts General Hospital and Harvard Medical School, Boston, 02114, Massachusetts, USA
| | - Jennifer Lombardi-Story
- Massachusetts General Hospital Cancer Center, Harvard Medical School, 185 Cambridge St, CPZN4202, Boston, MA, 02114, USA.,Department of Medicine, Massachusetts General Hospital and Harvard Medical School, Boston, 02114, Massachusetts, USA
| | - Yasutaka Kato
- Laboratory of Oncology, Hokuto Hospital, Obihiro, Japan
| | - Min-Kyung Choo
- Cutaneous Biology Research Center, Massachusetts General Hospital and Harvard Medical School, Charlestown, MA, 02129, USA
| | - Ipsita Dey-Guha
- Massachusetts General Hospital Cancer Center, Harvard Medical School, 185 Cambridge St, CPZN4202, Boston, MA, 02114, USA.,Department of Medicine, Massachusetts General Hospital and Harvard Medical School, Boston, 02114, Massachusetts, USA
| | - Fei Ji
- Department of Molecular Biology, Massachusetts General Hospital, Harvard Medical School, Boston, MA, 02114, USA
| | - Benjamin T Nicholson
- Massachusetts General Hospital Cancer Center, Harvard Medical School, 185 Cambridge St, CPZN4202, Boston, MA, 02114, USA
| | - David T Myers
- Massachusetts General Hospital Cancer Center, Harvard Medical School, 185 Cambridge St, CPZN4202, Boston, MA, 02114, USA
| | - Dongjun Lee
- Department of Convergence Medical Science, Pusan National University School of Medicine, Yangsan, 50612, 1257-1258, South Korea
| | - Maria A Mazzola
- Center for Neurological Diseases, Brigham & Women's Hospital, Harvard Medical School, Boston, MA, 02115, USA
| | - Radhika Raheja
- Center for Neurological Diseases, Brigham & Women's Hospital, Harvard Medical School, Boston, MA, 02115, USA
| | - Adam Langenbucher
- Massachusetts General Hospital Cancer Center, Harvard Medical School, 185 Cambridge St, CPZN4202, Boston, MA, 02114, USA.,Department of Pathology, Massachusetts General Hospital, Harvard Medical School, Charlestown, MA, 02129, USA
| | - Nicholas J Haradhvala
- Massachusetts General Hospital Cancer Center, Harvard Medical School, 185 Cambridge St, CPZN4202, Boston, MA, 02114, USA.,Department of Pathology, Massachusetts General Hospital, Harvard Medical School, Charlestown, MA, 02129, USA.,Broad Institute of Harvard & MIT, Cambridge, MA, 02142, USA
| | - Michael S Lawrence
- Massachusetts General Hospital Cancer Center, Harvard Medical School, 185 Cambridge St, CPZN4202, Boston, MA, 02114, USA.,Department of Pathology, Massachusetts General Hospital, Harvard Medical School, Charlestown, MA, 02129, USA.,Broad Institute of Harvard & MIT, Cambridge, MA, 02142, USA
| | - Roopali Gandhi
- Center for Neurological Diseases, Brigham & Women's Hospital, Harvard Medical School, Boston, MA, 02115, USA
| | - Christopher Tiedje
- Department of Cellular and Molecular Medicine, Center for Healthy Aging, University of Copenhagen, Blegdamsvej 3B, 2200, Copenhagen, Denmark
| | - Manuel D Diaz-Muñoz
- Centre de Physiopathologie Toulouse-Purpan, INSERM UMR1043/CNRS U5282, Toulouse, France
| | - David A Sweetser
- Massachusetts General Hospital Cancer Center, Harvard Medical School, 185 Cambridge St, CPZN4202, Boston, MA, 02114, USA.,Department of Pediatrics, Divisions of Pediatric Hematology/Oncology and Medical Genetics, Massachusetts General Hospital, Harvard Medical School, Boston, MA, 02114, USA
| | - Ruslan Sadreyev
- Department of Molecular Biology, Massachusetts General Hospital, Harvard Medical School, Boston, MA, 02114, USA.,Department of Pathology, Massachusetts General Hospital, Harvard Medical School, Charlestown, MA, 02129, USA
| | - David Sykes
- Department of Medicine, Massachusetts General Hospital and Harvard Medical School, Boston, 02114, Massachusetts, USA.,Center for Regenerative Medicine, Massachusetts General Hospital, Harvard Medical School, Boston, MA, 02114, USA.,Harvard Stem Cell Institute, Harvard University, Cambridge, MA, 02138, USA
| | - Wilhelm Haas
- Massachusetts General Hospital Cancer Center, Harvard Medical School, 185 Cambridge St, CPZN4202, Boston, MA, 02114, USA.,Department of Medicine, Massachusetts General Hospital and Harvard Medical School, Boston, 02114, Massachusetts, USA
| | - Daniel A Haber
- Massachusetts General Hospital Cancer Center, Harvard Medical School, 185 Cambridge St, CPZN4202, Boston, MA, 02114, USA.,Department of Medicine, Massachusetts General Hospital and Harvard Medical School, Boston, 02114, Massachusetts, USA.,Howard Hughes Medical Institute, Chevy Chase, MD, 20815, USA
| | - Shyamala Maheswaran
- Massachusetts General Hospital Cancer Center, Harvard Medical School, 185 Cambridge St, CPZN4202, Boston, MA, 02114, USA.,Department of Surgery, Massachusetts General Hospital and Harvard Medical School, Charlestown, MA, 02129, USA
| | - Shobha Vasudevan
- Massachusetts General Hospital Cancer Center, Harvard Medical School, 185 Cambridge St, CPZN4202, Boston, MA, 02114, USA. .,Department of Medicine, Massachusetts General Hospital and Harvard Medical School, Boston, 02114, Massachusetts, USA. .,Center for Regenerative Medicine, Massachusetts General Hospital, Harvard Medical School, Boston, MA, 02114, USA. .,Harvard Stem Cell Institute, Harvard University, Cambridge, MA, 02138, USA.
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14
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Wang WD, Shang Y, Li Y, Chen SZ. Honokiol inhibits breast cancer cell metastasis by blocking EMT through modulation of Snail/Slug protein translation. Acta Pharmacol Sin 2019; 40:1219-1227. [PMID: 31235819 DOI: 10.1038/s41401-019-0240-x] [Citation(s) in RCA: 37] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2019] [Accepted: 04/25/2019] [Indexed: 02/06/2023] Open
Abstract
Honokiol (HNK), an active compound isolated from traditional Chinese medicine Magnolia officinalis, has shown potent anticancer activities. In the present study, we investigated the effects of HNK on breast cancer metastasis in vitro and in vivo, as well as the underlying molecular mechanisms. We showed that HNK (10-70 μmol/L) dose-dependently inhibited the viability of human mammary epithelial tumor cell lines MCF7, MDA-MB-231, and mouse mammary tumor cell line 4T1. In the transwell and scratch migration assays, HNK (10, 20, 30 μmol/L) dose-dependently suppressed the invasion and migration of the breast cancer cells. We demonstrated that HNK (10-50 μmol/L) dose-dependently upregulated the epithelial marker E-cadherin and downregulated the mesenchymal markers such as Snail, Slug, and vimentin at the protein level in breast cancer cells. Using a puromycin incorporation assay, we showed that HNK decreased the Snail translation efficiency in the breast cancer cells. In a mouse model of tumor metastasis, administration of HNK (50 mg/kg every day, intraperitoneal (i.p.), 6 times per week for 30 days) significantly decreased the number of metastatic 4T1 cell-derived nodules and ameliorated the histological alterations in the lungs. In addition, HNK-treated mice showed decreased Snail expression and increased E-cadherin expression in metastatic nodules. In conclusion, HNK inhibits EMT in the breast cancer cells by downregulating Snail and Slug protein expression at the mRNA translation level. HNK has potential as an integrative medicine for combating breast cancer by targeting EMT.
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15
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Lyon K, Aguilera LU, Morisaki T, Munsky B, Stasevich TJ. Live-Cell Single RNA Imaging Reveals Bursts of Translational Frameshifting. Mol Cell 2019; 75:172-183.e9. [PMID: 31178355 DOI: 10.1016/j.molcel.2019.05.002] [Citation(s) in RCA: 34] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2018] [Revised: 03/14/2019] [Accepted: 04/30/2019] [Indexed: 11/25/2022]
Abstract
Ribosomal frameshifting during the translation of RNA is implicated in human disease and viral infection. While previous work has uncovered many details about single RNA frameshifting kinetics in vitro, little is known about how single RNA frameshift in living systems. To confront this problem, we have developed technology to quantify live-cell single RNA translation dynamics in frameshifted open reading frames. Applying this technology to RNA encoding the HIV-1 frameshift sequence reveals a small subset (∼8%) of the translating pool robustly frameshift. Frameshifting RNA are translated at similar rates as non-frameshifting RNA (∼3 aa/s) and can continuously frameshift for more than four rounds of translation. Fits to a bursty model of frameshifting constrain frameshifting kinetic rates and demonstrate how ribosomal traffic jams contribute to the persistence of the frameshifting state. These data provide insight into retroviral frameshifting and could lead to alternative strategies to perturb the process in living cells.
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Affiliation(s)
- Kenneth Lyon
- Department of Biochemistry and Molecular Biology, Institute of Genome Architecture and Function, Colorado State University, Fort Collins, CO 80523, USA
| | - Luis U Aguilera
- Department of Chemical and Biological Engineering and School of Biomedical Engineering, Colorado State University, Fort Collins, CO 80523, USA
| | - Tatsuya Morisaki
- Department of Biochemistry and Molecular Biology, Institute of Genome Architecture and Function, Colorado State University, Fort Collins, CO 80523, USA
| | - Brian Munsky
- Department of Chemical and Biological Engineering and School of Biomedical Engineering, Colorado State University, Fort Collins, CO 80523, USA.
| | - Timothy J Stasevich
- Department of Biochemistry and Molecular Biology, Institute of Genome Architecture and Function, Colorado State University, Fort Collins, CO 80523, USA; World Research Hub Initiative, Institute of Innovative Research, Tokyo Institute of Technology, Yokohama, Kanagawa 226-8503, Japan.
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16
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Grandi P, Bantscheff M. Advanced proteomics approaches to unravel protein homeostasis. DRUG DISCOVERY TODAY. TECHNOLOGIES 2019; 31:99-108. [PMID: 31200865 DOI: 10.1016/j.ddtec.2019.02.001] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/07/2018] [Revised: 02/03/2019] [Accepted: 02/05/2019] [Indexed: 05/22/2023]
Abstract
Quantitative proteomics methods are instrumental in measuring the interplay between protein synthesis and protein degradation in cells and tissues in different conditions and substantially contribute to the understanding of control mechanisms for protein homeostasis. Proteomics and chemoproteomics approaches enable the characterization of small molecule modifiers of protein degradation for therapeutic applications. Here, we review recent developments and applications of mass spectrometry-based (chemo-)proteomics methods for the study of cellular homeostasis.
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Affiliation(s)
- Paola Grandi
- Cellzome GmbH, GlaxoSmithKline, Meyerhofstrasse 1, 69117 Heidelberg, Germany.
| | - Marcus Bantscheff
- Cellzome GmbH, GlaxoSmithKline, Meyerhofstrasse 1, 69117 Heidelberg, Germany.
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17
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Alber AB, Suter DM. Dynamics of protein synthesis and degradation through the cell cycle. Cell Cycle 2019; 18:784-794. [PMID: 30907235 PMCID: PMC6527273 DOI: 10.1080/15384101.2019.1598725] [Citation(s) in RCA: 28] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2018] [Revised: 02/18/2019] [Accepted: 03/12/2019] [Indexed: 01/05/2023] Open
Abstract
Protein expression levels depend on the balance between their synthesis and degradation rates. Even quiescent (G0) cells display a continuous turnover of proteins, despite protein levels remaining largely constant over time. In cycling cells, global protein levels need to be precisely doubled at each cell division in order to maintain cellular homeostasis, but we still lack a quantitative understanding of how this is achieved. Recent studies have shed light on cell cycle-dependent changes in protein synthesis and degradation rates. Here we discuss current population-based and single cell approaches used to assess protein synthesis and degradation, and review the insights they have provided into the dynamics of protein turnover in different cell cycle phases.
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Affiliation(s)
- Andrea Brigitta Alber
- Institute of Bioengineering, Ecole Polytechnique Fédérale de Lausanne, Lausanne, Switzerland
| | - David Michael Suter
- Institute of Bioengineering, Ecole Polytechnique Fédérale de Lausanne, Lausanne, Switzerland
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18
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Pargett M, Albeck JG. Live-Cell Imaging and Analysis with Multiple Genetically Encoded Reporters. ACTA ACUST UNITED AC 2019; 78:4.36.1-4.36.19. [PMID: 30040182 DOI: 10.1002/cpcb.38] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/23/2023]
Abstract
Genetically encoded live-cell reporters measure signaling pathway activity at the cellular level with high temporal resolution, often revealing a high degree of cell-to-cell heterogeneity. By using multiple spectrally distinct reporters within the same cell, signal transmission from one node to another within a signaling pathway can be analyzed to quantify factors such as signaling efficiency and delay. With other reporter configurations, correlation between different signaling pathways can be quantified. Such analyses can be used to establish the mechanisms and consequences of cell-to-cell heterogeneity and can inform new models of the functional properties of signaling pathways. In this unit, we describe an approach for designing and executing live-cell multiplexed reporter experiments. We also describe approaches for analyzing the resulting time-course data to quantify correlations and trends between the measured parameters at the single-cell level. © 2018 by John Wiley & Sons, Inc.
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Affiliation(s)
- Michael Pargett
- Department of Molecular and Cellular Biology, University of California, Davis, Davis, California
| | - John G Albeck
- Department of Molecular and Cellular Biology, University of California, Davis, Davis, California
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19
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Darnell AM, Subramaniam AR, O'Shea EK. Translational Control through Differential Ribosome Pausing during Amino Acid Limitation in Mammalian Cells. Mol Cell 2019; 71:229-243.e11. [PMID: 30029003 DOI: 10.1016/j.molcel.2018.06.041] [Citation(s) in RCA: 90] [Impact Index Per Article: 18.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2017] [Revised: 05/07/2018] [Accepted: 06/26/2018] [Indexed: 12/22/2022]
Abstract
Limitation for amino acids is thought to regulate translation in mammalian cells primarily by signaling through the kinases mTORC1 and GCN2. We find that a selective loss of arginine tRNA charging during limitation for arginine regulates translation through ribosome pausing at two of six arginine codons. Surprisingly, limitation for leucine, an essential and abundant amino acid in protein, results in little or no ribosome pausing. Chemical and genetic perturbation of mTORC1 and GCN2 signaling revealed that their robust response to leucine limitation prevents ribosome pausing, while an insufficient response to arginine limitation leads to loss of tRNA charging and ribosome pausing. Ribosome pausing decreases protein production and triggers premature ribosome termination without reducing mRNA levels. Together, our results suggest that amino acids that are not optimally sensed by the mTORC1 and GCN2 pathways still regulate translation through an evolutionarily conserved mechanism based on codon-specific ribosome pausing.
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Affiliation(s)
- Alicia M Darnell
- Department of Molecular and Cellular Biology, Harvard University, Cambridge, MA 02138, USA
| | - Arvind R Subramaniam
- Basic Sciences Division and Computational Biology Program of Public Health Sciences Division, Fred Hutchinson Cancer Research Center, Seattle, WA 98109, USA.
| | - Erin K O'Shea
- Department of Molecular and Cellular Biology, Harvard University, Cambridge, MA 02138, USA; Howard Hughes Medical Institute, Harvard University, Cambridge, MA 02138, USA; Department of Chemistry and Chemical Biology and Faculty of Arts and Sciences Center for Systems Biology, Harvard University, Cambridge, MA 02138, USA.
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20
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Translation of Human β-Actin mRNA is Regulated by mTOR Pathway. Genes (Basel) 2019; 10:genes10020096. [PMID: 30700035 PMCID: PMC6410274 DOI: 10.3390/genes10020096] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2018] [Revised: 01/22/2019] [Accepted: 01/24/2019] [Indexed: 01/09/2023] Open
Abstract
The mammalian target of rapamycin (mTOR) kinase is a well-known master regulator of growth-dependent gene expression in higher eukaryotes. Translation regulation is an important function of the mTORC1 pathway that controls the synthesis of many ribosomal proteins and translation factors. Housekeeping genes such as β-actin (ACTB) are widely used as negative control genes in studies of growth-dependent translation. Here we demonstrate that translation of both endogenous and reporter ACTB mRNA is inhibited in the presence of mTOR kinase inhibitor (Torin1) and under amino acid starvation. Notably, 5’UTR and promoter of ACTB are sufficient for the mTOR-dependent translational response, and the degree of mTOR-sensitivity of ACTB mRNA translation is cell type-dependent.
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21
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Morisaki T, Stasevich TJ. Quantifying Single mRNA Translation Kinetics in Living Cells. Cold Spring Harb Perspect Biol 2018; 10:a032078. [PMID: 30385605 PMCID: PMC6211384 DOI: 10.1101/cshperspect.a032078] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Abstract
One of the last hurdles to quantifying the full central dogma of molecular biology in living cells with single-molecule resolution has been the imaging of single messenger RNA (mRNA) translation. Here we describe how recent advances in protein tagging and imaging technologies are being used to precisely visualize and quantify the synthesis of nascent polypeptide chains from single mRNA in living cells. We focus on recent applications of repeat-epitope tags and describe how they enable quantification of single mRNA ribosomal densities, translation initiation and elongation rates, and translation site mobility and higher-order structure. Together with complementary live-cell assays to monitor translation using fast-maturing fluorophores and mRNA-binding protein knockoff, single-molecule studies are beginning to uncover striking and unexpected heterogeneity in gene expression at the level of translation.
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Affiliation(s)
- Tatsuya Morisaki
- Institute of Genome Architecture and Function and Department of Biochemistry & Molecular Biology, Colorado State University, Fort Collins, Colorado 80523
| | - Timothy J Stasevich
- Institute of Genome Architecture and Function and Department of Biochemistry & Molecular Biology, Colorado State University, Fort Collins, Colorado 80523
- Cell Biology Unit, Institute of Innovative Research, Tokyo Institute of Technology, Midori-ku, Yokohama, Kanagawa, 226-8503, Japan
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22
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Tréfier A, Musnier A, Landomiel F, Bourquard T, Boulo T, Ayoub MA, León K, Bruneau G, Chevalier M, Durand G, Blache MC, Inoue A, Fontaine J, Gauthier C, Tesseraud S, Reiter E, Poupon A, Crépieux P. G protein-dependent signaling triggers a β-arrestin-scaffolded p70S6K/ rpS6 module that controls 5'TOP mRNA translation. FASEB J 2018; 32:1154-1169. [PMID: 29084767 DOI: 10.1096/fj.201700763r] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
Many interaction partners of β-arrestins intervene in the control of mRNA translation. However, how β-arrestins regulate this cellular process has been poorly explored. In this study, we show that β-arrestins constitutively assemble a p70S6K/ribosomal protein S6 (rpS6) complex in HEK293 cells and in primary Sertoli cells of the testis. We demonstrate that this interaction is direct, and experimentally validate the interaction interface between β-arrestin 1 and p70S6K predicted by our docking algorithm. Like most GPCRs, the biological function of follicle-stimulating hormone receptor (FSHR) is transduced by G proteins and β-arrestins. Upon follicle-stimulating hormone (FSH) stimulation, activation of G protein-dependent signaling enhances p70S6K activity within the β-arrestin/p70S6K/rpS6 preassembled complex, which is not recruited to the FSHR. In agreement, FSH-induced rpS6 phosphorylation within the β-arrestin scaffold was decreased in cells depleted of Gαs. Integration of the cooperative action of β-arrestin and G proteins led to the translation of 5' oligopyrimidine track mRNA with high efficacy within minutes of FSH input. Hence, this work highlights new relationships between G proteins and β-arrestins when acting cooperatively on a common signaling pathway, contrasting with their previously shown parallel action on the ERK MAP kinase pathway. In addition, this study provides insights into how GPCR can exert trophic effects in the cell.-Tréfier, A., Musnier, A., Landomiel, F., Bourquard, T., Boulo, T., Ayoub, M. A., León, K., Bruneau, G., Chevalier, M., Durand, G., Blache, M.-C., Inoue, A., Fontaine, J., Gauthier, C., Tesseraud, S., Reiter, E., Poupon, A., Crépieux, P. G protein-dependent signaling triggers a β-arrestin-scaffolded p70S6K/ rpS6 module that controls 5'TOP mRNA translation.
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Affiliation(s)
- Aurélie Tréfier
- Biology and Bioinformatics of Signaling Systems (BIOS) Group, Unité Mixtes de Recherche 85, Unité Physiologie de la Reproduction et des Comportements, Institut National de la Recherche Agronomique (INRA), Nouzilly, France.,Centre National de la Recherche Scientifique (CNRS), Unité Mixte de Recherche 7247, Nouzilly, France.,Université François Rabelais, Tours, France.,Institut Français du Cheval et de l'Équitation (IFCE), Nouzilly, France
| | - Astrid Musnier
- Biology and Bioinformatics of Signaling Systems (BIOS) Group, Unité Mixtes de Recherche 85, Unité Physiologie de la Reproduction et des Comportements, Institut National de la Recherche Agronomique (INRA), Nouzilly, France.,Centre National de la Recherche Scientifique (CNRS), Unité Mixte de Recherche 7247, Nouzilly, France.,Université François Rabelais, Tours, France.,Institut Français du Cheval et de l'Équitation (IFCE), Nouzilly, France
| | - Flavie Landomiel
- Biology and Bioinformatics of Signaling Systems (BIOS) Group, Unité Mixtes de Recherche 85, Unité Physiologie de la Reproduction et des Comportements, Institut National de la Recherche Agronomique (INRA), Nouzilly, France.,Centre National de la Recherche Scientifique (CNRS), Unité Mixte de Recherche 7247, Nouzilly, France.,Université François Rabelais, Tours, France.,Institut Français du Cheval et de l'Équitation (IFCE), Nouzilly, France
| | - Thomas Bourquard
- Biology and Bioinformatics of Signaling Systems (BIOS) Group, Unité Mixtes de Recherche 85, Unité Physiologie de la Reproduction et des Comportements, Institut National de la Recherche Agronomique (INRA), Nouzilly, France.,Centre National de la Recherche Scientifique (CNRS), Unité Mixte de Recherche 7247, Nouzilly, France.,Université François Rabelais, Tours, France.,Institut Français du Cheval et de l'Équitation (IFCE), Nouzilly, France
| | - Thomas Boulo
- Biology and Bioinformatics of Signaling Systems (BIOS) Group, Unité Mixtes de Recherche 85, Unité Physiologie de la Reproduction et des Comportements, Institut National de la Recherche Agronomique (INRA), Nouzilly, France.,Centre National de la Recherche Scientifique (CNRS), Unité Mixte de Recherche 7247, Nouzilly, France.,Université François Rabelais, Tours, France.,Institut Français du Cheval et de l'Équitation (IFCE), Nouzilly, France
| | - Mohammed Akli Ayoub
- Biology and Bioinformatics of Signaling Systems (BIOS) Group, Unité Mixtes de Recherche 85, Unité Physiologie de la Reproduction et des Comportements, Institut National de la Recherche Agronomique (INRA), Nouzilly, France.,Centre National de la Recherche Scientifique (CNRS), Unité Mixte de Recherche 7247, Nouzilly, France.,Université François Rabelais, Tours, France.,Institut Français du Cheval et de l'Équitation (IFCE), Nouzilly, France.,Biology Department, College of Science, United Arab Emirates University, Al Ain, United Arab Emirates
| | - Kelly León
- Biology and Bioinformatics of Signaling Systems (BIOS) Group, Unité Mixtes de Recherche 85, Unité Physiologie de la Reproduction et des Comportements, Institut National de la Recherche Agronomique (INRA), Nouzilly, France.,Centre National de la Recherche Scientifique (CNRS), Unité Mixte de Recherche 7247, Nouzilly, France.,Université François Rabelais, Tours, France.,Institut Français du Cheval et de l'Équitation (IFCE), Nouzilly, France
| | - Gilles Bruneau
- Biology and Bioinformatics of Signaling Systems (BIOS) Group, Unité Mixtes de Recherche 85, Unité Physiologie de la Reproduction et des Comportements, Institut National de la Recherche Agronomique (INRA), Nouzilly, France.,Centre National de la Recherche Scientifique (CNRS), Unité Mixte de Recherche 7247, Nouzilly, France.,Université François Rabelais, Tours, France.,Institut Français du Cheval et de l'Équitation (IFCE), Nouzilly, France
| | - Manon Chevalier
- Biology and Bioinformatics of Signaling Systems (BIOS) Group, Unité Mixtes de Recherche 85, Unité Physiologie de la Reproduction et des Comportements, Institut National de la Recherche Agronomique (INRA), Nouzilly, France.,Centre National de la Recherche Scientifique (CNRS), Unité Mixte de Recherche 7247, Nouzilly, France.,Université François Rabelais, Tours, France.,Institut Français du Cheval et de l'Équitation (IFCE), Nouzilly, France
| | - Guillaume Durand
- Biology and Bioinformatics of Signaling Systems (BIOS) Group, Unité Mixtes de Recherche 85, Unité Physiologie de la Reproduction et des Comportements, Institut National de la Recherche Agronomique (INRA), Nouzilly, France.,Centre National de la Recherche Scientifique (CNRS), Unité Mixte de Recherche 7247, Nouzilly, France.,Université François Rabelais, Tours, France.,Institut Français du Cheval et de l'Équitation (IFCE), Nouzilly, France
| | - Marie-Claire Blache
- Plateau d'Imagerie Cellulaire (PIC), Unité Mixte de Recherche 85, Unité Physiologie de la Reproduction et des Comportements, Institut National de la Recherche Agronomique (INRA), Nouzilly, France.,Centre National de la Recherche Scientifique (CNRS), Unité Mixte de Recherche 7247, Nouzilly, France.,Université François Rabelais, Tours, France.,Institut Français du Cheval et de l'Équitation (IFCE), Nouzilly, France
| | - Asuka Inoue
- Graduate School of Pharmaceutical Sciences, Tohoku University, Sendai, Japan; and
| | - Joël Fontaine
- Biology and Bioinformatics of Signaling Systems (BIOS) Group, Unité Mixtes de Recherche 85, Unité Physiologie de la Reproduction et des Comportements, Institut National de la Recherche Agronomique (INRA), Nouzilly, France.,Centre National de la Recherche Scientifique (CNRS), Unité Mixte de Recherche 7247, Nouzilly, France.,Université François Rabelais, Tours, France.,Institut Français du Cheval et de l'Équitation (IFCE), Nouzilly, France
| | - Christophe Gauthier
- Biology and Bioinformatics of Signaling Systems (BIOS) Group, Unité Mixtes de Recherche 85, Unité Physiologie de la Reproduction et des Comportements, Institut National de la Recherche Agronomique (INRA), Nouzilly, France.,Centre National de la Recherche Scientifique (CNRS), Unité Mixte de Recherche 7247, Nouzilly, France.,Université François Rabelais, Tours, France.,Institut Français du Cheval et de l'Équitation (IFCE), Nouzilly, France
| | - Sophie Tesseraud
- Metabolism of Birds, Quality and Adaptation (MOQA) Group, Unité de Recherches 83, Unité de Recherches Avicoles, Institut National de la Recherche Agronomique (INRA), Nouzilly, France
| | - Eric Reiter
- Biology and Bioinformatics of Signaling Systems (BIOS) Group, Unité Mixtes de Recherche 85, Unité Physiologie de la Reproduction et des Comportements, Institut National de la Recherche Agronomique (INRA), Nouzilly, France.,Centre National de la Recherche Scientifique (CNRS), Unité Mixte de Recherche 7247, Nouzilly, France.,Université François Rabelais, Tours, France.,Institut Français du Cheval et de l'Équitation (IFCE), Nouzilly, France
| | - Anne Poupon
- Biology and Bioinformatics of Signaling Systems (BIOS) Group, Unité Mixtes de Recherche 85, Unité Physiologie de la Reproduction et des Comportements, Institut National de la Recherche Agronomique (INRA), Nouzilly, France.,Centre National de la Recherche Scientifique (CNRS), Unité Mixte de Recherche 7247, Nouzilly, France.,Université François Rabelais, Tours, France.,Institut Français du Cheval et de l'Équitation (IFCE), Nouzilly, France
| | - Pascale Crépieux
- Biology and Bioinformatics of Signaling Systems (BIOS) Group, Unité Mixtes de Recherche 85, Unité Physiologie de la Reproduction et des Comportements, Institut National de la Recherche Agronomique (INRA), Nouzilly, France.,Centre National de la Recherche Scientifique (CNRS), Unité Mixte de Recherche 7247, Nouzilly, France.,Université François Rabelais, Tours, France.,Institut Français du Cheval et de l'Équitation (IFCE), Nouzilly, France
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23
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Tycko J, Van MV, Elowitz MB, Bintu L. Advancing towards a global mammalian gene regulation model through single-cell analysis and synthetic biology. CURRENT OPINION IN BIOMEDICAL ENGINEERING 2017. [DOI: 10.1016/j.cobme.2017.10.011] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
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24
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Wadsworth GM, Parikh RY, Choy JS, Kim HD. mRNA detection in budding yeast with single fluorophores. Nucleic Acids Res 2017; 45:e141. [PMID: 28666354 PMCID: PMC5587780 DOI: 10.1093/nar/gkx568] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2017] [Accepted: 06/21/2017] [Indexed: 12/29/2022] Open
Abstract
Quantitative measurement of mRNA levels in single cells is necessary to understand phenotypic variability within an otherwise isogenic population of cells. Single-molecule mRNA Fluorescence In Situ Hybridization (FISH) has been established as the standard method for this purpose, but current protocols require a long region of mRNA to be targeted by multiple DNA probes. Here, we introduce a new single-probe FISH protocol termed sFISH for budding yeast, Saccharomyces cerevisiae using a single DNA probe labeled with a single fluorophore. In sFISH, we markedly improved probe specificity and signal-to-background ratio by using methanol fixation and inclined laser illumination. We show that sFISH reports mRNA changes that correspond to protein levels and gene copy number. Using this new FISH protocol, we can detect >50% of the total target mRNA. We also demonstrate the versatility of sFISH using FRET detection and mRNA isoform profiling as examples. Our FISH protocol with single-fluorophore sensitivity significantly reduces cost and time compared to the conventional FISH protocols and opens up new opportunities to investigate small changes in RNA at the single cell level.
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Affiliation(s)
- Gable M Wadsworth
- School of Physics, Georgia Institute of Technology, 837 State Street, Atlanta, GA 30332-0430, USA
| | - Rasesh Y Parikh
- School of Physics, Georgia Institute of Technology, 837 State Street, Atlanta, GA 30332-0430, USA
| | - John S Choy
- Department of Biology, The Catholic University of America, 620 Michigan Avenue NE, Washington, DC 20064, USA
| | - Harold D Kim
- School of Physics, Georgia Institute of Technology, 837 State Street, Atlanta, GA 30332-0430, USA
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25
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Goodman CA, Coenen AM, Frey JW, You JS, Barker RG, Frankish BP, Murphy RM, Hornberger TA. Insights into the role and regulation of TCTP in skeletal muscle. Oncotarget 2017; 8:18754-18772. [PMID: 27813490 PMCID: PMC5386645 DOI: 10.18632/oncotarget.13009] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2016] [Accepted: 09/28/2016] [Indexed: 01/07/2023] Open
Abstract
The translationally controlled tumor protein (TCTP) is upregulated in a range of cancer cell types, in part, by the activation of the mechanistic target of rapamycin (mTOR). Recently, TCTP has also been proposed to act as an indirect activator of mTOR. While it is known that mTOR plays a major role in the regulation of skeletal muscle mass, very little is known about the role and regulation of TCTP in this post-mitotic tissue. This study shows that muscle TCTP and mTOR signaling are upregulated in a range of mouse models (mdx mouse, mechanical load-induced hypertrophy, and denervation- and immobilization-induced atrophy). Furthermore, the increase in TCTP observed in the hypertrophic and atrophic conditions occurred, in part, via a rapamycin-sensitive mTOR-dependent mechanism. However, the overexpression of TCTP was not sufficient to activate mTOR signaling (or increase protein synthesis) and is thus unlikely to take part in a recently proposed positive feedback loop with mTOR. Nonetheless, TCTP overexpression was sufficient to induce muscle fiber hypertrophy. Finally, TCTP overexpression inhibited the promoter activity of the muscle-specific ubiquitin proteasome E3-ligase, MuRF1, suggesting that TCTP may play a role in inhibiting protein degradation. These findings provide novel data on the role and regulation of TCTP in skeletal muscle in vivo.
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Affiliation(s)
- Craig A Goodman
- Department of Comparative Biosciences, School of Veterinary Medicine, University of Wisconsin-Madison, Madison, Wisconsin, 53706, USA.,Centre for Chronic Disease Prevention and Management, College of Health and Biomedicine, Victoria University, Melbourne, Victoria, 8001, Australia.,Institute for Sport, Exercise and Active Living (ISEAL), Victoria University, Melbourne, Victoria, 8001, Australia
| | - Allison M Coenen
- Department of Comparative Biosciences, School of Veterinary Medicine, University of Wisconsin-Madison, Madison, Wisconsin, 53706, USA
| | - John W Frey
- Department of Comparative Biosciences, School of Veterinary Medicine, University of Wisconsin-Madison, Madison, Wisconsin, 53706, USA
| | - Jae-Sung You
- Department of Comparative Biosciences, School of Veterinary Medicine, University of Wisconsin-Madison, Madison, Wisconsin, 53706, USA
| | - Robert G Barker
- Department of Biochemistry and Genetics, La Trobe Institute for Molecular Science, La Trobe University, Melbourne, Victoria, 3086, Australia
| | - Barnaby P Frankish
- Department of Biochemistry and Genetics, La Trobe Institute for Molecular Science, La Trobe University, Melbourne, Victoria, 3086, Australia
| | - Robyn M Murphy
- Department of Biochemistry and Genetics, La Trobe Institute for Molecular Science, La Trobe University, Melbourne, Victoria, 3086, Australia
| | - Troy A Hornberger
- Department of Comparative Biosciences, School of Veterinary Medicine, University of Wisconsin-Madison, Madison, Wisconsin, 53706, USA
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26
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The molecular basis of mTORC1-regulated translation. Biochem Soc Trans 2017; 45:213-221. [PMID: 28202675 DOI: 10.1042/bst20160072] [Citation(s) in RCA: 58] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2016] [Revised: 12/05/2016] [Accepted: 12/08/2016] [Indexed: 12/26/2022]
Abstract
The mammalian target of rapamycin (mTOR) signaling pathway is a master regulator of cell growth throughout eukaryotes. The pathway senses nutrient and other growth signals, and then orchestrates the complex systems of anabolic and catabolic metabolism that underpin the growth process. A central target of mTOR signaling is the translation machinery. mTOR uses a multitude of translation factors to drive the bulk production of protein that growth requires, but also to direct a post-transcriptional program of growth-specific gene expression. This review will discuss current understanding of how mTOR controls these mechanisms and their functions in growth control.
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27
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Goodarzi H, Nguyen HCB, Zhang S, Dill BD, Molina H, Tavazoie SF. Modulated Expression of Specific tRNAs Drives Gene Expression and Cancer Progression. Cell 2016; 165:1416-1427. [PMID: 27259150 DOI: 10.1016/j.cell.2016.05.046] [Citation(s) in RCA: 295] [Impact Index Per Article: 36.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2016] [Revised: 04/04/2016] [Accepted: 05/13/2016] [Indexed: 01/01/2023]
Abstract
Transfer RNAs (tRNAs) are primarily viewed as static contributors to gene expression. By developing a high-throughput tRNA profiling method, we find that specific tRNAs are upregulated in human breast cancer cells as they gain metastatic activity. Through loss-of-function, gain-of-function, and clinical-association studies, we implicate tRNAGluUUC and tRNAArgCCG as promoters of breast cancer metastasis. Upregulation of these tRNAs enhances stability and ribosome occupancy of transcripts enriched for their cognate codons. Specifically, tRNAGluUUC promotes metastatic progression by directly enhancing EXOSC2 expression and enhancing GRIPAP1-constituting an "inducible" pathway driven by a tRNA. The cellular proteomic shift toward a pro-metastatic state mirrors global tRNA shifts, allowing for cell-state and cell-type transgene expression optimization through codon content quantification. TRNA modulation represents a mechanism by which cells achieve altered expression of specific transcripts and proteins. TRNAs are thus dynamic regulators of gene expression and the tRNA codon landscape can causally and specifically impact disease progression.
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Affiliation(s)
- Hani Goodarzi
- Laboratory of Systems Cancer Biology, The Rockefeller University, 1230 York Avenue, New York, NY 10065, USA.
| | - Hoang C B Nguyen
- Laboratory of Systems Cancer Biology, The Rockefeller University, 1230 York Avenue, New York, NY 10065, USA
| | - Steven Zhang
- Laboratory of Systems Cancer Biology, The Rockefeller University, 1230 York Avenue, New York, NY 10065, USA
| | - Brian D Dill
- Proteome Resource Center, The Rockefeller University, 1230 York Avenue, New York, NY 10065, USA
| | - Henrik Molina
- Proteome Resource Center, The Rockefeller University, 1230 York Avenue, New York, NY 10065, USA
| | - Sohail F Tavazoie
- Laboratory of Systems Cancer Biology, The Rockefeller University, 1230 York Avenue, New York, NY 10065, USA.
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28
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Yan X, Hoek TA, Vale RD, Tanenbaum ME. Dynamics of Translation of Single mRNA Molecules In Vivo. Cell 2016; 165:976-89. [PMID: 27153498 PMCID: PMC4889334 DOI: 10.1016/j.cell.2016.04.034] [Citation(s) in RCA: 291] [Impact Index Per Article: 36.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2016] [Revised: 04/04/2016] [Accepted: 04/11/2016] [Indexed: 11/16/2022]
Abstract
Regulation of mRNA translation, the process by which ribosomes decode mRNAs into polypeptides, is used to tune cellular protein levels. Currently, methods for observing the complete process of translation from single mRNAs in vivo are unavailable. Here, we report the long-term (>1 hr) imaging of single mRNAs undergoing hundreds of rounds of translation in live cells, enabling quantitative measurements of ribosome initiation, elongation, and stalling. This approach reveals a surprising heterogeneity in the translation of individual mRNAs within the same cell, including rapid and reversible transitions between a translating and non-translating state. Applying this method to the cell-cycle gene Emi1, we find strong overall repression of translation initiation by specific 5' UTR sequences, but individual mRNA molecules in the same cell can exhibit dramatically different translational efficiencies. The ability to observe translation of single mRNA molecules in live cells provides a powerful tool to study translation regulation.
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Affiliation(s)
- Xiaowei Yan
- Department of Cellular and Molecular Pharmacology, Howard Hughes Medical Institute, University of California, San Francisco, San Francisco, CA 94158-2517, USA
| | - Tim A Hoek
- Hubrecht Institute, The Royal Netherlands Academy of Arts and Sciences (KNAW) and University Medical Center Utrecht, Utrecht 3584CT, the Netherlands
| | - Ronald D Vale
- Department of Cellular and Molecular Pharmacology, Howard Hughes Medical Institute, University of California, San Francisco, San Francisco, CA 94158-2517, USA
| | - Marvin E Tanenbaum
- Hubrecht Institute, The Royal Netherlands Academy of Arts and Sciences (KNAW) and University Medical Center Utrecht, Utrecht 3584CT, the Netherlands.
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29
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Floor SN, Doudna JA. Tunable protein synthesis by transcript isoforms in human cells. eLife 2016; 5:e10921. [PMID: 26735365 DOI: 10.7554/elife.10921.001] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2015] [Accepted: 01/05/2016] [Indexed: 05/25/2023] Open
Abstract
Eukaryotic genes generate multiple RNA transcript isoforms though alternative transcription, splicing, and polyadenylation. However, the relationship between human transcript diversity and protein production is complex as each isoform can be translated differently. We fractionated a polysome profile and reconstructed transcript isoforms from each fraction, which we term Transcript Isoforms in Polysomes sequencing (TrIP-seq). Analysis of these data revealed regulatory features that control ribosome occupancy and translational output of each transcript isoform. We extracted a panel of 5' and 3' untranslated regions that control protein production from an unrelated gene in cells over a 100-fold range. Select 5' untranslated regions exert robust translational control between cell lines, while 3' untranslated regions can confer cell type-specific expression. These results expose the large dynamic range of transcript-isoform-specific translational control, identify isoform-specific sequences that control protein output in human cells, and demonstrate that transcript isoform diversity must be considered when relating RNA and protein levels.
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Affiliation(s)
- Stephen N Floor
- Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, United States
- Howard Hughes Medical Institute, University of California, Berkeley, Berkeley, United States
| | - Jennifer A Doudna
- Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, United States
- Howard Hughes Medical Institute, University of California, Berkeley, Berkeley, United States
- Innovative Genomics Initiative, University of California, Berkeley, Berkeley, United States
- Physical Biosciences Division, Lawrence Berkeley National Laboratory, Berkeley, United States
- Department of Chemistry, University of California, Berkeley, Berkeley, California, United States
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30
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Floor SN, Doudna JA. Tunable protein synthesis by transcript isoforms in human cells. eLife 2016; 5. [PMID: 26735365 PMCID: PMC4764583 DOI: 10.7554/elife.10921] [Citation(s) in RCA: 184] [Impact Index Per Article: 23.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2015] [Accepted: 01/05/2016] [Indexed: 12/27/2022] Open
Abstract
Eukaryotic genes generate multiple RNA transcript isoforms though alternative transcription, splicing, and polyadenylation. However, the relationship between human transcript diversity and protein production is complex as each isoform can be translated differently. We fractionated a polysome profile and reconstructed transcript isoforms from each fraction, which we term Transcript Isoforms in Polysomes sequencing (TrIP-seq). Analysis of these data revealed regulatory features that control ribosome occupancy and translational output of each transcript isoform. We extracted a panel of 5′ and 3′ untranslated regions that control protein production from an unrelated gene in cells over a 100-fold range. Select 5′ untranslated regions exert robust translational control between cell lines, while 3′ untranslated regions can confer cell type-specific expression. These results expose the large dynamic range of transcript-isoform-specific translational control, identify isoform-specific sequences that control protein output in human cells, and demonstrate that transcript isoform diversity must be considered when relating RNA and protein levels. DOI:http://dx.doi.org/10.7554/eLife.10921.001 To produce a protein, a gene’s DNA is first copied to make molecules of messenger RNA (mRNA). The mRNAs pass through a molecular machine known as the ribosome, which translates the genetic code to make a protein. Not all of an mRNA is translated to make a protein; the “untranslated” regions play crucial roles in regulating how much of the protein is produced. In animals, plants and other eukaryotes, many mRNAs are made up of small pieces that are “spliced” together. During this process, proteins are deposited on the mRNA to mark the splice junctions, which are then cleared when the mRNA is translated. Many different mRNAs can be produced from the same gene by splicing different combinations of RNA pieces. Each of these mRNA “isoforms” can, in principle, contain a unique set of features that control its translation. Hence each mRNA isoform can be translated differently so that different amounts of the corresponding protein product are produced. However, the relationship between the variety of isoforms and the control of translation is complex and not well understood. To address these questions, Floor and Doudna measured the translation of over 60,000 mRNA isoforms made from almost 14,000 human genes. The experiments show that untranslated regions at the end of the mRNA (known as the 3′ end) strongly influence translation, even if the protein coding regions remain the same. Furthermore, the data showed that mRNAs with more splice junctions are translated better, implying an mRNA has some sort of memory of how many junctions it had even after the protein markers have been cleared. Next, Floor and Doudna inserted regulatory sequences from differently translated isoforms into an unrelated “reporter” gene. This dramatically changed the amount of protein produced from the reporter gene, in a manner predicted by the earlier experiments. Untranslated regions at the beginning of the mRNAs (known as the 5′ end) controlled the amount of protein produced from the reporter consistently across different types of cells from the body. On the other hand, the 3′ regions can tune the level of protein production in particular types of cells. Floor and Doudna’s findings demonstrate that differences between mRNA isoforms of a gene can have a big effect on the level of protein production. Changes in the types of mRNA made from a gene are often associated with human diseases, and these findings suggest one reason why. Additionally, the ability to engineer translation of an mRNA using the data is likely to aid the development of mRNA-based therapies. DOI:http://dx.doi.org/10.7554/eLife.10921.002
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Affiliation(s)
- Stephen N Floor
- Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, United States.,Howard Hughes Medical Institute, University of California, Berkeley, Berkeley, United States
| | - Jennifer A Doudna
- Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, United States.,Howard Hughes Medical Institute, University of California, Berkeley, Berkeley, United States.,Innovative Genomics Initiative, University of California, Berkeley, Berkeley, United States.,Physical Biosciences Division, Lawrence Berkeley National Laboratory, Berkeley, United States.,Department of Chemistry, University of California, Berkeley, Berkeley, California, United States
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31
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The Transcription and Translation Landscapes during Human Cytomegalovirus Infection Reveal Novel Host-Pathogen Interactions. PLoS Pathog 2015; 11:e1005288. [PMID: 26599541 PMCID: PMC4658056 DOI: 10.1371/journal.ppat.1005288] [Citation(s) in RCA: 88] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2015] [Accepted: 10/29/2015] [Indexed: 01/06/2023] Open
Abstract
Viruses are by definition fully dependent on the cellular translation machinery, and develop diverse mechanisms to co-opt this machinery for their own benefit. Unlike many viruses, human cytomegalovirus (HCMV) does suppress the host translation machinery, and the extent to which translation machinery contributes to the overall pattern of viral replication and pathogenesis remains elusive. Here, we combine RNA sequencing and ribosomal profiling analyses to systematically address this question. By simultaneously examining the changes in transcription and translation along HCMV infection, we uncover extensive transcriptional control that dominates the response to infection, but also diverse and dynamic translational regulation for subsets of host genes. We were also able to show that, at late time points in infection, translation of viral mRNAs is higher than that of cellular mRNAs. Lastly, integration of our translation measurements with recent measurements of protein abundance enabled comprehensive identification of dozens of host proteins that are targeted for degradation during HCMV infection. Since targeted degradation indicates a strong biological importance, this approach should be applicable for discovering central host functions during viral infection. Our work provides a framework for studying the contribution of transcription, translation and degradation during infection with any virus. Viruses are fully dependent on the cellular translation machinery, and develop diverse mechanisms to co-opt it for their own benefit. However, fundamental questions such as: what is the effect that infection has on the spectrum of host mRNAs that are being translated, and whether, and to what extent, a virus possesses mechanisms to commandeer the translation machinery are still hard to address. Here we show that by simultaneously examining the changes in transcription and translation along Human cytomegalovirus (HCMV) infection, we can uncover extensive transcriptional regulation, but also diverse and dynamic translational control. We were also able to show that, at late time points in infection, translation of viral mRNAs is higher than that of cellular mRNAs. Lastly, we take advantage of our measurements of translation (protein synthesis rate) and integrate these with mass spectrometry measurements (protein abundance). This integration allowed us to unbiasedly reveal dozens of cellular proteins that are being degraded during HCMV infection. Since targeted degradation indicates a strong biological importance, this approach should be applicable for discovering central host functions during viral infection. Our work provides a framework for studying the contribution of transcription, translation and degradation during infection with any virus.
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Tanenbaum ME, Stern-Ginossar N, Weissman JS, Vale RD. Regulation of mRNA translation during mitosis. eLife 2015; 4. [PMID: 26305499 PMCID: PMC4548207 DOI: 10.7554/elife.07957] [Citation(s) in RCA: 112] [Impact Index Per Article: 12.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2015] [Accepted: 08/02/2015] [Indexed: 12/21/2022] Open
Abstract
Passage through mitosis is driven by precisely-timed changes in transcriptional regulation and protein degradation. However, the importance of translational regulation during mitosis remains poorly understood. Here, using ribosome profiling, we find both a global translational repression and identified ∼200 mRNAs that undergo specific translational regulation at mitotic entry. In contrast, few changes in mRNA abundance are observed, indicating that regulation of translation is the primary mechanism of modulating protein expression during mitosis. Interestingly, 91% of the mRNAs that undergo gene-specific regulation in mitosis are translationally repressed, rather than activated. One of the most pronounced translationally-repressed genes is Emi1, an inhibitor of the anaphase promoting complex (APC) which is degraded during mitosis. We show that full APC activation requires translational repression of Emi1 in addition to its degradation. These results identify gene-specific translational repression as a means of controlling the mitotic proteome, which may complement post-translational mechanisms for inactivating protein function. DOI:http://dx.doi.org/10.7554/eLife.07957.001 The human body contains billions of cells, most of which formed via a process called mitosis in which a single cell divides to produce two new daughter cells. Actively dividing cells pass through a series of events (or phases) that are collectively known as the cell cycle. These phases allow the cell to grow in size, copy its genetic material, and then make preparations for cell division before taking the final decision to divide. Many proteins are involved in regulating the cell cycle and each protein has a particular role in specific phases. The levels of these proteins in cells may change during the cycle, which is often crucial to allow the cell to progress to the next phase. For example, cells need a group of proteins called the anaphase-promoting complex (or APC for short) to destroy other specific proteins at the end of mitosis. Another way in which the amount of protein in a cell can be adjusted is by controlling how much new protein is made during a process known as translation. During this process, a molecule called a messenger RNA (mRNA)—which contains information copied from a particular gene—is used as a template to assemble a new protein. However, it is not clear whether regulation of translation is involved in control of the cell division. Tanenbaum et al. now address this question using a technique called ribosome profiling to measure the translation of individual mRNA molecules. The experiments analysed the changes in protein production before, during and after mitosis. The overall level of translation of all the mRNAs was about 35% lower during mitosis. However, some mRNAs in particular experienced a very large reduction in the level of translation (between three- and ten-fold less than the levels before mitosis). One example of an mRNA whose translation is turned off in mitosis is the mRNA that makes a protein called Emi1. It is known from previous work that Emi1 inhibits the activity of the APC. Therefore, Emi1 needs to be inactivated in mitosis so that the APC can become active and promote progression to the next phase of the cell cycle. It was previously shown that Emi1 is destroyed during mitosis to allow the APC to operate. Tanenbaum et al. found that translation of the Emi1 mRNA must also be suppressed during mitosis in order to keep Emi1 protein levels very low and allow the APC to become fully active. These findings uncover a new role for the control of protein production in regulating the cell cycle. The next challenge will be to find out whether suppression of translation is also used in other biological systems where proteins need to be rapidly inactivated. DOI:http://dx.doi.org/10.7554/eLife.07957.002
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Affiliation(s)
- Marvin E Tanenbaum
- Department of Cellular and Molecular Pharmacology, Howard Hughes Medical Institute, University of California, San Francisco, San Francisco, United States
| | - Noam Stern-Ginossar
- Department of Cellular and Molecular Pharmacology, Howard Hughes Medical Institute, University of California, San Francisco, San Francisco, United States
| | - Jonathan S Weissman
- Department of Cellular and Molecular Pharmacology, Howard Hughes Medical Institute, University of California, San Francisco, San Francisco, United States
| | - Ronald D Vale
- Department of Cellular and Molecular Pharmacology, Howard Hughes Medical Institute, University of California, San Francisco, San Francisco, United States
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Chowdhury T, Köhler JR. Ribosomal protein S6 phosphorylation is controlled by TOR and modulated by PKA in Candida albicans. Mol Microbiol 2015; 98:384-402. [PMID: 26173379 DOI: 10.1111/mmi.13130] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 07/10/2015] [Indexed: 12/25/2022]
Abstract
TOR and PKA signaling pathways control eukaryotic cell growth and proliferation. TOR activity in model fungi, such as Saccharomyces cerevisiae, responds principally to nutrients, e.g., nitrogen and phosphate sources, which are incorporated into the growing cell mass; PKA signaling responds to the availability of the cells' major energy source, glucose. In the fungal commensal and pathogen, Candida albicans, little is known of how these pathways interact. Here, the signal from phosphorylated ribosomal protein S6 (P-S6) was defined as a surrogate marker for TOR-dependent anabolic activity in C. albicans. Nutritional, pharmacologic and genetic modulation of TOR activity elicited corresponding changes in P-S6 levels. The P-S6 signal corresponded to translational activity of a GFP reporter protein. Contributions of four PKA pathway components to anabolic activation were then examined. In high glucose concentrations, only Tpk2 was required to upregulate P-S6 to physiologic levels, whereas all four tested components were required to downregulate P-S6 in low glucose. TOR was epistatic to PKA components with respect to P-S6. In many host niches inhabited by C. albicans, glucose is scarce, with protein being available as a nitrogen source. We speculate that PKA may modulate TOR-dependent cell growth to a rate sustainable by available energy sources, when monomers of anabolic processes, such as amino acids, are abundant.
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Affiliation(s)
- Tahmeena Chowdhury
- Division of Infectious Diseases, Boston Children's Hospital/Harvard Medical School, Boston, MA, 02115, USA
| | - Julia R Köhler
- Division of Infectious Diseases, Boston Children's Hospital/Harvard Medical School, Boston, MA, 02115, USA
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Buszczak M, Signer RAJ, Morrison SJ. Cellular differences in protein synthesis regulate tissue homeostasis. Cell 2015; 159:242-51. [PMID: 25303523 DOI: 10.1016/j.cell.2014.09.016] [Citation(s) in RCA: 147] [Impact Index Per Article: 16.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2014] [Indexed: 12/12/2022]
Abstract
Although sometimes considered a "house-keeping" function, multiple aspects of protein synthesis are regulated differently among somatic cells, including stem cells, and can be modulated in a cell-type-specific manner. These differences are required to establish and maintain differences in cell identity, cell function, tissue homeostasis, and tumor suppression.
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Affiliation(s)
- Michael Buszczak
- Department of Molecular Biology, Children's Research Institute, Department of Pediatrics, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
| | - Robert A J Signer
- Howard Hughes Medical Institute, Children's Research Institute, Department of Pediatrics, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
| | - Sean J Morrison
- Howard Hughes Medical Institute, Children's Research Institute, Department of Pediatrics, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA.
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Abstract
Single-cell analysis heralds a new era that allows “omics” analysis, notably genomics, transcriptomics, epigenomics and proteomics at the single-cell level. It enables the identification of the minor subpopulations that may play a critical role in a biological process of a population of cells, which conventionally are regarded as homogeneous. It provides an ultra-sensitive tool to clarify specific molecular mechanisms and pathways and reveal the nature of cell heterogeneity. It also facilitates the clinical investigation of patients when a very low quantity or a single cell is available for analysis, such as noninvasive prenatal diagnosis and cancer screening, and genetic evaluation for in vitro fertilization. Within a few short years, single-cell analysis, especially whole genomic sequencing and transcriptomic sequencing, is becoming robust and broadly accessible, although not yet a routine practice. Here, with single cell RNA-seq emphasized, an overview of the discipline, progresses, and prospects of single-cell analysis and its applications in biology and medicine are given with a series of logic and theoretical considerations.
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Affiliation(s)
- Xinghua Pan
- Department of Genetics, School of Medicine, Yale University, New Haven, CT, USA
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Li JJ, Bickel PJ, Biggin MD. System wide analyses have underestimated protein abundances and the importance of transcription in mammals. PeerJ 2014; 2:e270. [PMID: 24688849 PMCID: PMC3940484 DOI: 10.7717/peerj.270] [Citation(s) in RCA: 207] [Impact Index Per Article: 20.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2013] [Accepted: 01/22/2014] [Indexed: 12/17/2022] Open
Abstract
Large scale surveys in mammalian tissue culture cells suggest that the protein expressed at the median abundance is present at 8,000–16,000 molecules per cell and that differences in mRNA expression between genes explain only 10–40% of the differences in protein levels. We find, however, that these surveys have significantly underestimated protein abundances and the relative importance of transcription. Using individual measurements for 61 housekeeping proteins to rescale whole proteome data from Schwanhausser et al. (2011), we find that the median protein detected is expressed at 170,000 molecules per cell and that our corrected protein abundance estimates show a higher correlation with mRNA abundances than do the uncorrected protein data. In addition, we estimated the impact of further errors in mRNA and protein abundances using direct experimental measurements of these errors. The resulting analysis suggests that mRNA levels explain at least 56% of the differences in protein abundance for the 4,212 genes detected by Schwanhausser et al. (2011), though because one major source of error could not be estimated the true percent contribution should be higher. We also employed a second, independent strategy to determine the contribution of mRNA levels to protein expression. We show that the variance in translation rates directly measured by ribosome profiling is only 12% of that inferred by Schwanhausser et al. (2011), and that the measured and inferred translation rates correlate poorly (R2 = 0.13). Based on this, our second strategy suggests that mRNA levels explain ∼81% of the variance in protein levels. We also determined the percent contributions of transcription, RNA degradation, translation and protein degradation to the variance in protein abundances using both of our strategies. While the magnitudes of the two estimates vary, they both suggest that transcription plays a more important role than the earlier studies implied and translation a much smaller role. Finally, the above estimates only apply to those genes whose mRNA and protein expression was detected. Based on a detailed analysis by Hebenstreit et al. (2012), we estimate that approximately 40% of genes in a given cell within a population express no mRNA. Since there can be no translation in the absence of mRNA, we argue that differences in translation rates can play no role in determining the expression levels for the ∼40% of genes that are non-expressed.
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Affiliation(s)
- Jingyi Jessica Li
- Department of Statistics, University of California , Berkeley, CA , USA ; Departments of Statistics and Human Genetics, University of California , Los Angeles, CA , USA
| | - Peter J Bickel
- Department of Statistics, University of California , Berkeley, CA , USA
| | - Mark D Biggin
- Genomics Division, Lawrence Berkeley National Laboratory , Berkeley, CA , USA
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