1
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Chambers KL, Watson MG, Myerscough MR. A Lipid-Structured Model of Atherosclerosis with Macrophage Proliferation. Bull Math Biol 2024; 86:104. [PMID: 38980556 PMCID: PMC11233351 DOI: 10.1007/s11538-024-01333-w] [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: 12/11/2023] [Accepted: 06/21/2024] [Indexed: 07/10/2024]
Abstract
Atherosclerotic plaques are fatty deposits that form in the walls of major arteries and are one of the major causes of heart attacks and strokes. Macrophages are the main immune cells in plaques and macrophage dynamics influence whether plaques grow or regress. Macrophage proliferation is a key process in atherosclerosis, particularly in the development of mid-stage plaques, but very few mathematical models include proliferation. In this paper we reframe the lipid-structured model of Ford et al. (J Theor Biol 479:48-63, 2019. https://doi.org/10.1016/j.jtbi.2019.07.003 ) to account for macrophage proliferation. Proliferation is modelled as a non-local decrease in the lipid structural variable. Steady state analysis indicates that proliferation assists in reducing eventual necrotic core lipid content and spreads the lipid load of the macrophage population amongst the cells. The contribution of plaque macrophages from proliferation relative to recruitment from the bloodstream is also examined. The model suggests that a more proliferative plaque differs from an equivalent (defined as having the same lipid content and cell numbers) recruitment-dominant plaque in the way lipid is distributed amongst the macrophages. The macrophage lipid distribution of an equivalent proliferation-dominant plaque is less skewed and exhibits a local maximum near the endogenous lipid content.
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Affiliation(s)
- Keith L Chambers
- School of Mathematics and Statistics, The University of Sydney, Sydney, NSW, 2006, Australia
- Mathematical Institute, The University of Oxford, Oxford, Oxfordshire, OX2 6GG, UK
| | - Michael G Watson
- School of Mathematics and Statistics, The University of Sydney, Sydney, NSW, 2006, Australia
- School of Mathematics and Statistics, The University of New South Wales, Sydney, NSW, 2052, Australia
| | - Mary R Myerscough
- School of Mathematics and Statistics, The University of Sydney, Sydney, NSW, 2006, Australia.
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2
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Blank HM, Alonso A, Fabritius AS, Valk E, Loog M, Winey M, Polymenis M. Translational control of MPS1 links protein synthesis with the initiation of cell division and spindle pole body duplication in Saccharomyces cerevisiae. Genetics 2024; 227:iyae069. [PMID: 38713088 DOI: 10.1093/genetics/iyae069] [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: 02/21/2024] [Revised: 04/10/2024] [Accepted: 04/23/2024] [Indexed: 05/08/2024] Open
Abstract
Protein synthesis underpins cell growth and controls when cells commit to a new round of cell division at a point in late G1 of the cell cycle called Start. Passage through Start also coincides with the duplication of the microtubule-organizing centers, the yeast spindle pole bodies, which will form the 2 poles of the mitotic spindle that segregates the chromosomes in mitosis. The conserved Mps1p kinase governs the duplication of the spindle pole body (SPB) in Saccharomyces cerevisiae. Here, we show that the MPS1 transcript has a short upstream open reading frame (uORF) that represses the synthesis of Mps1p. Mutating the MPS1 uORF makes the cells smaller, accelerates the appearance of Mps1p in late G1, and promotes completion of Start. Monitoring the SPB in the cell cycle using structured illumination microscopy revealed that mutating the MPS1 uORF enabled cells to duplicate their SPB earlier at a smaller cell size. The accelerated Start of MPS1 uORF mutants depends on the G1 cyclin Cln3p and the transcriptional repressor Whi5p but not on the Cln1,2p G1 cyclins. These results identify growth inputs in mechanisms that control duplication of the microtubule-organizing center and implicate these processes in the coupling of cell growth with division.
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Affiliation(s)
- Heidi M Blank
- Department of Biochemistry and Biophysics, Texas A&M University, 2128 TAMU, College Station, TX 77843, USA
| | - Annabel Alonso
- Department of Molecular and Cellular Biology, University of California, Davis, Davis, CA 95616, USA
| | - Amy S Fabritius
- Department of Molecular and Cellular Biology, University of California, Davis, Davis, CA 95616, USA
| | - Ervin Valk
- Institute of Technology, University of Tartu, Tartu 50411, Estonia
| | - Mart Loog
- Institute of Technology, University of Tartu, Tartu 50411, Estonia
| | - Mark Winey
- Department of Molecular and Cellular Biology, University of California, Davis, Davis, CA 95616, USA
| | - Michael Polymenis
- Department of Biochemistry and Biophysics, Texas A&M University, 2128 TAMU, College Station, TX 77843, USA
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3
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Wu W, Lam AR, Suarez K, Smith GN, Duquette SM, Yu J, Mankus D, Bisher M, Lytton-Jean A, Manalis SR, Miettinen TP. Constant surface area-to-volume ratio during cell growth as a design principle in mammalian cells. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.07.02.601447. [PMID: 39005340 PMCID: PMC11244959 DOI: 10.1101/2024.07.02.601447] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/16/2024]
Abstract
All cells are subject to geometric constraints, such as surface area-to-volume (SA/V) ratio, that impact cell functions and force biological adaptations. Like the SA/V ratio of a sphere, it is generally assumed that the SA/V ratio of cells decreases as cell size increases. Here, we investigate this in near-spherical mammalian cells using single-cell measurements of cell mass and surface proteins, as well as imaging of plasma membrane morphology. We find that the SA/V ratio remains surprisingly constant as cells grow larger. This observation is largely independent of the cell cycle and the amount of cell growth. Consequently, cell growth results in increased plasma membrane folding, which simplifies cellular design by ensuring sufficient membrane area for cell division, nutrient uptake and deformation at all cell sizes.
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Affiliation(s)
- Weida Wu
- Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Alice R. Lam
- Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Kayla Suarez
- Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Grace N. Smith
- Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Sarah M. Duquette
- Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Jiaquan Yu
- Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - David Mankus
- Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Margaret Bisher
- Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Abigail Lytton-Jean
- Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Scott R. Manalis
- Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
- Department of Mechanical Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Teemu P. Miettinen
- Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
- Lead contact
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4
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Köberlin MS, Fan Y, Liu C, Chung M, Pinto AFM, Jackson PK, Saghatelian A, Meyer T. A fast-acting lipid checkpoint in G1 prevents mitotic defects. Nat Commun 2024; 15:2441. [PMID: 38499565 PMCID: PMC10948896 DOI: 10.1038/s41467-024-46696-9] [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: 07/24/2023] [Accepted: 03/06/2024] [Indexed: 03/20/2024] Open
Abstract
Lipid synthesis increases during the cell cycle to ensure sufficient membrane mass, but how insufficient synthesis restricts cell-cycle entry is not understood. Here, we identify a lipid checkpoint in G1 phase of the mammalian cell cycle by using live single-cell imaging, lipidome, and transcriptome analysis of a non-transformed cell. We show that synthesis of fatty acids in G1 not only increases lipid mass but extensively shifts the lipid composition to unsaturated phospholipids and neutral lipids. Strikingly, acute lowering of lipid synthesis rapidly activates the PERK/ATF4 endoplasmic reticulum (ER) stress pathway that blocks cell-cycle entry by increasing p21 levels, decreasing Cyclin D levels, and suppressing Retinoblastoma protein phosphorylation. Together, our study identifies a rapid anticipatory ER lipid checkpoint in G1 that prevents cells from starting the cell cycle as long as lipid synthesis is low, thereby preventing mitotic defects, which are triggered by low lipid synthesis much later in mitosis.
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Affiliation(s)
- Marielle S Köberlin
- Department of Chemical and Systems Biology, Stanford University School of Medicine, Stanford, CA, 94305, USA.
- Baxter Laboratory, Department of Microbiology & Immunology, Stanford University School of Medicine, Stanford, CA, 94305, USA.
| | - Yilin Fan
- Department of Chemical and Systems Biology, Stanford University School of Medicine, Stanford, CA, 94305, USA
- Department of Pathology and Center for Cancer Research, Massachusetts General Hospital and Harvard Medical School, Boston, MA, 02114, USA
| | - Chad Liu
- Department of Chemical and Systems Biology, Stanford University School of Medicine, Stanford, CA, 94305, USA
- Chan Zuckerberg Biohub, San Francisco, CA, 94111, USA
| | - Mingyu Chung
- Department of Chemical and Systems Biology, Stanford University School of Medicine, Stanford, CA, 94305, USA
- Department of Neurology and Neurological Sciences, Stanford University School of Medicine, Stanford, CA, 94305, USA
| | - Antonio F M Pinto
- Clayton Foundation Laboratories for Peptide Biology and Mass Spectrometry Core, Salk Institute for Biological Studies, La Jolla, CA, 92037, USA
| | - Peter K Jackson
- Baxter Laboratory, Department of Microbiology & Immunology, Stanford University School of Medicine, Stanford, CA, 94305, USA
- Department of Pathology, Stanford University School of Medicine, Stanford, CA, 94305, USA
| | - Alan Saghatelian
- Clayton Foundation Laboratories for Peptide Biology and Mass Spectrometry Core, Salk Institute for Biological Studies, La Jolla, CA, 92037, USA
| | - Tobias Meyer
- Department of Chemical and Systems Biology, Stanford University School of Medicine, Stanford, CA, 94305, USA.
- Department of Cell and Developmental Biology, Weill Cornell Medicine, New York, NY, 10065, USA.
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5
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Diehl FF, Sapp KM, Vander Heiden MG. The bidirectional relationship between metabolism and cell cycle control. Trends Cell Biol 2024; 34:136-149. [PMID: 37385879 DOI: 10.1016/j.tcb.2023.05.012] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2023] [Revised: 05/30/2023] [Accepted: 05/31/2023] [Indexed: 07/01/2023]
Abstract
The relationship between metabolism and cell cycle progression is complex and bidirectional. Cells must rewire metabolism to meet changing biosynthetic demands across cell cycle phases. In turn, metabolism can influence cell cycle progression through direct regulation of cell cycle proteins, through nutrient-sensing signaling pathways, and through its impact on cell growth, which is linked to cell division. Furthermore, metabolism is a key player in mediating quiescence-proliferation transitions in physiologically important cell types, such as stem cells. How metabolism impacts cell cycle progression, exit, and re-entry, as well as how these processes impact metabolism, is not fully understood. Recent advances uncovering mechanistic links between cell cycle regulators and metabolic processes demonstrate a complex relationship between metabolism and cell cycle control, with many questions remaining.
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Affiliation(s)
- Frances F Diehl
- Department of Molecular Biology and Genetics, Howard Hughes Medical Institute, Johns Hopkins University School of Medicine, Baltimore, MD, USA; Koch Institute for Integrative Cancer Research and the Department of Biology, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Kiera M Sapp
- Koch Institute for Integrative Cancer Research and the Department of Biology, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Matthew G Vander Heiden
- Koch Institute for Integrative Cancer Research and the Department of Biology, Massachusetts Institute of Technology, Cambridge, MA, USA; Dana-Farber Cancer Institute, Boston, MA, USA.
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6
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Blank HM, Griffith WP, Polymenis M. Targeting APEX2 to the mRNA encoding fatty acid synthase β in yeast identifies interacting proteins that control its abundance in the cell cycle. Mol Biol Cell 2023; 34:br20. [PMID: 37792491 PMCID: PMC10848943 DOI: 10.1091/mbc.e23-05-0166] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2023] [Revised: 09/25/2023] [Accepted: 09/29/2023] [Indexed: 10/06/2023] Open
Abstract
Profiling the repertoire of proteins associated with a given mRNA during the cell cycle is unstudied. Furthermore, it is easier to ask and answer what mRNAs a specific protein might bind to than the other way around. Here, we implemented an RNA-centric proximity labeling technology at different points in the cell cycle in highly synchronous yeast cultures. To understand how the abundance of FAS1, encoding fatty acid synthase, peaks late in the cell cycle, we identified proteins that interact with the FAS1 transcript in a cell cycle-dependent manner. We used dCas13d-APEX2 fusions to target FAS1 and label nearby proteins, which were then identified by mass spectrometry. The glycolytic enzyme Tdh3p, a known RNA-binding protein, interacted with the FAS1 mRNA, and it was necessary for the periodic abundance of Fas1p in the cell cycle. These results point to unexpected connections between major metabolic pathways. They also underscore the role of mRNA-protein interactions for gene expression during cell division.
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Affiliation(s)
- Heidi M. Blank
- Department of Biochemistry and Biophysics, Texas A&M University, College Station, TX 77843
| | - Wendell P. Griffith
- Department of Chemistry, The University of Texas at San Antonio, San Antonio, TX 78249
| | - Michael Polymenis
- Department of Biochemistry and Biophysics, Texas A&M University, College Station, TX 77843
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7
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Blank HM, Reuse C, Schmidt‐Hohagen K, Hammer SE, Hiller K, Polymenis M. Branched-chain amino acid synthesis is coupled to TOR activation early in the cell cycle in yeast. EMBO Rep 2023; 24:e57372. [PMID: 37497662 PMCID: PMC10481666 DOI: 10.15252/embr.202357372] [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: 04/21/2023] [Revised: 07/05/2023] [Accepted: 07/07/2023] [Indexed: 07/28/2023] Open
Abstract
How cells coordinate their metabolism with division determines the rate of cell proliferation. Dynamic patterns of metabolite synthesis during the cell cycle are unexplored. We report the first isotope tracing analysis in synchronous, growing budding yeast cells. Synthesis of leucine, a branched-chain amino acid (BCAA), increases through the G1 phase of the cell cycle, peaking later during DNA replication. Cells lacking Bat1, a mitochondrial aminotransferase that synthesizes BCAAs, grow slower, are smaller, and are delayed in the G1 phase, phenocopying cells in which the growth-promoting kinase complex TORC1 is moderately inhibited. Loss of Bat1 lowers the levels of BCAAs and reduces TORC1 activity. Exogenous provision of valine and, to a lesser extent, leucine to cells lacking Bat1 promotes cell division. Valine addition also increases TORC1 activity. In wild-type cells, TORC1 activity is dynamic in the cell cycle, starting low in early G1 but increasing later in the cell cycle. These results suggest a link between BCAA synthesis from glucose to TORC1 activation in the G1 phase of the cell cycle.
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Affiliation(s)
- Heidi M Blank
- Department of Biochemistry and BiophysicsTexas A&M UniversityCollege StationTXUSA
| | - Carsten Reuse
- Department of Bioinformatics and Biochemistry, BRICSTechnische Universität BraunschweigBraunschweigGermany
| | - Kerstin Schmidt‐Hohagen
- Department of Bioinformatics and Biochemistry, BRICSTechnische Universität BraunschweigBraunschweigGermany
| | - Staci E Hammer
- Department of Biochemistry and BiophysicsTexas A&M UniversityCollege StationTXUSA
| | - Karsten Hiller
- Department of Bioinformatics and Biochemistry, BRICSTechnische Universität BraunschweigBraunschweigGermany
| | - Michael Polymenis
- Department of Biochemistry and BiophysicsTexas A&M UniversityCollege StationTXUSA
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8
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Wagner ER, Nightingale NM, Jen A, Overmyer KA, McGee M, Coon JJ, Gasch AP. PKA regulatory subunit Bcy1 couples growth, lipid metabolism, and fermentation during anaerobic xylose growth in Saccharomyces cerevisiae. PLoS Genet 2023; 19:e1010593. [PMID: 37410771 DOI: 10.1371/journal.pgen.1010593] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2022] [Accepted: 06/22/2023] [Indexed: 07/08/2023] Open
Abstract
Organisms have evolved elaborate physiological pathways that regulate growth, proliferation, metabolism, and stress response. These pathways must be properly coordinated to elicit the appropriate response to an ever-changing environment. While individual pathways have been well studied in a variety of model systems, there remains much to uncover about how pathways are integrated to produce systemic changes in a cell, especially in dynamic conditions. We previously showed that deletion of Protein Kinase A (PKA) regulatory subunit BCY1 can decouple growth and metabolism in Saccharomyces cerevisiae engineered for anaerobic xylose fermentation, allowing for robust fermentation in the absence of division. This provides an opportunity to understand how PKA signaling normally coordinates these processes. Here, we integrated transcriptomic, lipidomic, and phospho-proteomic responses upon a glucose to xylose shift across a series of strains with different genetic mutations promoting either coupled or decoupled xylose-dependent growth and metabolism. Together, results suggested that defects in lipid homeostasis limit growth in the bcy1Δ strain despite robust metabolism. To further understand this mechanism, we performed adaptive laboratory evolutions to re-evolve coupled growth and metabolism in the bcy1Δ parental strain. The evolved strain harbored mutations in PKA subunit TPK1 and lipid regulator OPI1, among other genes, and evolved changes in lipid profiles and gene expression. Deletion of the evolved opi1 gene partially reverted the strain's phenotype to the bcy1Δ parent, with reduced growth and robust xylose fermentation. We suggest several models for how cells coordinate growth, metabolism, and other responses in budding yeast and how restructuring these processes enables anaerobic xylose utilization.
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Affiliation(s)
- Ellen R Wagner
- Laboratory of Genetics, University of Wisconsin-Madison, Madison, Wisconsin, United States of America
- Great Lakes Bioenergy Research Center, University of Wisconsin-Madison, Madison, Wisconsin, United States of America
- Center for Genomic Science Innovation, University of Wisconsin-Madison, Madison, Wisconsin, United States of America
| | - Nicole M Nightingale
- Great Lakes Bioenergy Research Center, University of Wisconsin-Madison, Madison, Wisconsin, United States of America
- Department of Biomolecular Chemistry, University of Wisconsin-Madison, Madison, Wisconsin, United States of America
| | - Annie Jen
- Great Lakes Bioenergy Research Center, University of Wisconsin-Madison, Madison, Wisconsin, United States of America
- Department of Biomolecular Chemistry, University of Wisconsin-Madison, Madison, Wisconsin, United States of America
| | - Katherine A Overmyer
- Department of Biomolecular Chemistry, University of Wisconsin-Madison, Madison, Wisconsin, United States of America
- Morgridge Institute for Research, Madison, Wisconsin, United States of America
- National Center for Quantitative Biology of Complex Systems, Madison, Wisconsin, United States of America
| | - Mick McGee
- Great Lakes Bioenergy Research Center, University of Wisconsin-Madison, Madison, Wisconsin, United States of America
| | - Joshua J Coon
- Great Lakes Bioenergy Research Center, University of Wisconsin-Madison, Madison, Wisconsin, United States of America
- Center for Genomic Science Innovation, University of Wisconsin-Madison, Madison, Wisconsin, United States of America
- Department of Biomolecular Chemistry, University of Wisconsin-Madison, Madison, Wisconsin, United States of America
- Morgridge Institute for Research, Madison, Wisconsin, United States of America
- National Center for Quantitative Biology of Complex Systems, Madison, Wisconsin, United States of America
- Department of Chemistry, University of Wisconsin-Madison, Madison, Wisconsin, United States of America
| | - Audrey P Gasch
- Laboratory of Genetics, University of Wisconsin-Madison, Madison, Wisconsin, United States of America
- Great Lakes Bioenergy Research Center, University of Wisconsin-Madison, Madison, Wisconsin, United States of America
- Center for Genomic Science Innovation, University of Wisconsin-Madison, Madison, Wisconsin, United States of America
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9
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Zhang Y, van der Zee L, Barberis M. Two-way communication between cell cycle and metabolism in budding yeast: what do we know? Front Microbiol 2023; 14:1187304. [PMID: 37396387 PMCID: PMC10309209 DOI: 10.3389/fmicb.2023.1187304] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2023] [Accepted: 05/30/2023] [Indexed: 07/04/2023] Open
Abstract
Coordination of cell cycle and metabolism exists in all cells. The building of a new cell is a process that requires metabolic commitment to the provision of both Gibbs energy and building blocks for proteins, nucleic acids, and membranes. On the other hand, the cell cycle machinery will assess and regulate its metabolic environment before it makes decisions on when to enter the next cell cycle phase. Furthermore, more and more evidence demonstrate that the metabolism can be regulated by cell cycle progression, as different biosynthesis pathways are preferentially active in different cell cycle phases. Here, we review the available literature providing a critical overview on how cell cycle and metabolism may be coupled with one other, bidirectionally, in the budding yeast Saccharomyces cerevisiae.
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Affiliation(s)
- Yanfei Zhang
- Molecular Systems Biology, School of Biosciences, Faculty of Health and Medical Sciences, University of Surrey, Guildford, Surrey, United Kingdom
- Synthetic Systems Biology and Nuclear Organization, Swammerdam Institute for Life Sciences, University of Amsterdam, Amsterdam, Netherlands
| | - Lucas van der Zee
- Synthetic Systems Biology and Nuclear Organization, Swammerdam Institute for Life Sciences, University of Amsterdam, Amsterdam, Netherlands
| | - Matteo Barberis
- Molecular Systems Biology, School of Biosciences, Faculty of Health and Medical Sciences, University of Surrey, Guildford, Surrey, United Kingdom
- Synthetic Systems Biology and Nuclear Organization, Swammerdam Institute for Life Sciences, University of Amsterdam, Amsterdam, Netherlands
- Centre for Mathematical and Computational Biology, CMCB, University of Surrey, Guildford, Surrey, United Kingdom
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10
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Hammer SE, Polymenis M. One-carbon metabolic enzymes are regulated during cell division and make distinct contributions to the metabolome and cell cycle progression in Saccharomyces cerevisiae. G3 (BETHESDA, MD.) 2023; 13:6983127. [PMID: 36627750 PMCID: PMC9997564 DOI: 10.1093/g3journal/jkad005] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/27/2022] [Revised: 12/21/2022] [Accepted: 12/23/2022] [Indexed: 01/12/2023]
Abstract
Enzymes of one-carbon (1C) metabolism play pivotal roles in proliferating cells. They are involved in the metabolism of amino acids, nucleotides, and lipids and the supply of all cellular methylations. However, there is limited information about how these enzymes are regulated during cell division and how cell cycle kinetics are affected in several loss-of-function mutants of 1C metabolism. Here, we report that the levels of the S. cerevisiae enzymes Ade17p and Cho2p, involved in the de novo synthesis of purines and phosphatidylcholine (PC), respectively, are cell cycle-regulated. Cells lacking Ade17p, Cho2p, or Shm2p (an enzyme that supplies 1C units from serine) have distinct alterations in size homeostasis and cell cycle kinetics. Loss of Ade17p leads to a specific delay at START, when cells commit to a new round of cell division, while loss of Shm2p has broader effects, reducing growth rate. Furthermore, the inability to synthesize PC de novo in cho2Δ cells delays START and reduces the coherence of nuclear elongation late in the cell cycle. Loss of Cho2p also leads to profound metabolite changes. Besides the expected changes in the lipidome, cho2Δ cells have reduced levels of amino acids, resembling cells shifted to poorer media. These results reveal the different ways that 1C metabolism allocates resources to affect cell proliferation at multiple cell cycle transitions.
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Affiliation(s)
- Staci E Hammer
- Department of Biochemistry and Biophysics, Texas A&M University, College Station, TX 77843, USA
| | - Michael Polymenis
- Department of Biochemistry and Biophysics, Texas A&M University, College Station, TX 77843, USA
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11
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Takhaveev V, Özsezen S, Smith EN, Zylstra A, Chaillet ML, Chen H, Papagiannakis A, Milias-Argeitis A, Heinemann M. Temporal segregation of biosynthetic processes is responsible for metabolic oscillations during the budding yeast cell cycle. Nat Metab 2023; 5:294-313. [PMID: 36849832 PMCID: PMC9970877 DOI: 10.1038/s42255-023-00741-x] [Citation(s) in RCA: 10] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/26/2021] [Accepted: 01/10/2023] [Indexed: 03/01/2023]
Abstract
Many cell biological and biochemical mechanisms controlling the fundamental process of eukaryotic cell division have been identified; however, the temporal dynamics of biosynthetic processes during the cell division cycle are still elusive. Here, we show that key biosynthetic processes are temporally segregated along the cell cycle. Using budding yeast as a model and single-cell methods to dynamically measure metabolic activity, we observe two peaks in protein synthesis, in the G1 and S/G2/M phase, whereas lipid and polysaccharide synthesis peaks only once, during the S/G2/M phase. Integrating the inferred biosynthetic rates into a thermodynamic-stoichiometric metabolic model, we find that this temporal segregation in biosynthetic processes causes flux changes in primary metabolism, with an acceleration of glucose-uptake flux in G1 and phase-shifted oscillations of oxygen and carbon dioxide exchanges. Through experimental validation of the model predictions, we demonstrate that primary metabolism oscillates with cell-cycle periodicity to satisfy the changing demands of biosynthetic processes exhibiting unexpected dynamics during the cell cycle.
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Affiliation(s)
- Vakil Takhaveev
- Molecular Systems Biology, Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, Groningen, The Netherlands
- Department of Health Sciences and Technology, ETH Zurich, Zurich, Switzerland
| | - Serdar Özsezen
- Molecular Systems Biology, Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, Groningen, The Netherlands
- Department of Microbiology and Systems Biology, The Netherlands Organization for Applied Scientific Research (TNO), Leiden, The Netherlands
| | - Edward N Smith
- Molecular Systems Biology, Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, Groningen, The Netherlands
| | - Andre Zylstra
- Molecular Systems Biology, Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, Groningen, The Netherlands
| | - Marten L Chaillet
- Molecular Systems Biology, Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, Groningen, The Netherlands
- Structural Biochemistry, Bijvoet Center for Biomolecular Research, Utrecht University, Utrecht, The Netherlands
| | - Haoqi Chen
- Molecular Systems Biology, Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, Groningen, The Netherlands
| | - Alexandros Papagiannakis
- Molecular Systems Biology, Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, Groningen, The Netherlands
- Department of Biology and Sarafan Chemistry, Engineering, and Medicine for Human Health Institute, Stanford University, Stanford, CA, USA
| | - Andreas Milias-Argeitis
- Molecular Systems Biology, Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, Groningen, The Netherlands
| | - Matthias Heinemann
- Molecular Systems Biology, Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, Groningen, The Netherlands.
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12
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Zhang L, Cervantes MD, Pan S, Lindsley J, Dabney A, Kapler GM. Transcriptome analysis of the binucleate ciliate Tetrahymena thermophila with asynchronous nuclear cell cycles. Mol Biol Cell 2023; 34:rs1. [PMID: 36475712 PMCID: PMC9930529 DOI: 10.1091/mbc.e22-08-0326] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
Tetrahymena thermophila harbors two functionally and physically distinct nuclei within a shared cytoplasm. During vegetative growth, the "cell cycles" of the diploid micronucleus and polyploid macronucleus are offset. Micronuclear S phase initiates just before cytokinesis and is completed in daughter cells before onset of macronuclear DNA replication. Mitotic micronuclear division occurs mid-cell cycle, while macronuclear amitosis is coupled to cell division. Here we report the first RNA-seq cell cycle analysis of a binucleated ciliated protozoan. RNA was isolated across 1.5 vegetative cell cycles, starting with a macronuclear G1 population synchronized by centrifugal elutriation. Using MetaCycle, 3244 of the 26,000+ predicted genes were shown to be cell cycle regulated. Proteins present in both nuclei exhibit a single mRNA peak that always precedes their macronuclear function. Nucleus-limited genes, including nucleoporins and importins, are expressed before their respective nucleus-specific role. Cyclin D and A/B gene family members exhibit different expression patterns that suggest nucleus-restricted roles. Periodically expressed genes cluster into seven cyclic patterns. Four clusters have known PANTHER gene ontology terms associated with G1/S and G2/M phase. We propose that these clusters encode known and novel factors that coordinate micro- and macronuclear-specific events such as mitosis, amitosis, DNA replication, and cell division.
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Affiliation(s)
- L. Zhang
- Department of Cell Biology and Genetics, Texas A&M University Health Science Center, College Station, TX 77840,Department of Statistics, Texas A&M University, College Station, TX 77843
| | - M. D. Cervantes
- Department of Cell Biology and Genetics, Texas A&M University Health Science Center, College Station, TX 77840
| | - S. Pan
- Department of Cell Biology and Genetics, Texas A&M University Health Science Center, College Station, TX 77840,Department of Statistics, Texas A&M University, College Station, TX 77843
| | - J. Lindsley
- Department of Cell Biology and Genetics, Texas A&M University Health Science Center, College Station, TX 77840
| | - A. Dabney
- Department of Statistics, Texas A&M University, College Station, TX 77843,*Address correspondence to: Geoffrey Kapler (); A. Dabney ()
| | - G. M. Kapler
- Department of Cell Biology and Genetics, Texas A&M University Health Science Center, College Station, TX 77840,*Address correspondence to: Geoffrey Kapler (); A. Dabney ()
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13
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Matos-Perdomo E, Santana-Sosa S, Ayra-Plasencia J, Medina-Suárez S, Machín F. The vacuole shapes the nucleus and the ribosomal DNA loop during mitotic delays. Life Sci Alliance 2022; 5:5/10/e202101161. [PMID: 35961781 PMCID: PMC9375157 DOI: 10.26508/lsa.202101161] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2021] [Revised: 07/20/2022] [Accepted: 07/20/2022] [Indexed: 11/24/2022] Open
Abstract
Chromosome structuring and condensation is one of the main features of mitosis. Here, Matos-Perdomo et al show how the nuclear envelope reshapes around the vacuole to give rise to the outstanding ribosomal DNA loop in budding yeast. The ribosomal DNA (rDNA) array of Saccharomyces cerevisiae has served as a model to address chromosome organization. In cells arrested before anaphase (mid-M), the rDNA acquires a highly structured chromosomal organization referred to as the rDNA loop, whose length can double the cell diameter. Previous works established that complexes such as condensin and cohesin are essential to attain this structure. Here, we report that the rDNA loop adopts distinct presentations that arise as spatial adaptations to changes in the nuclear morphology triggered during mid-M arrests. Interestingly, the formation of the rDNA loop results in the appearance of a space under the loop (SUL) which is devoid of nuclear components yet colocalizes with the vacuole. We show that the rDNA-associated nuclear envelope (NE) often reshapes into a ladle to accommodate the vacuole in the SUL, with the nucleus becoming bilobed and doughnut-shaped. Finally, we demonstrate that the formation of the rDNA loop and the SUL require TORC1, membrane synthesis and functional vacuoles, yet is independent of nucleus–vacuole junctions and rDNA-NE tethering.
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Affiliation(s)
- Emiliano Matos-Perdomo
- Unidad de Investigación, Hospital Universitario Nuestra Señora de Candelaria, Santa Cruz de Tenerife, Spain.,Escuela de Doctorado y Estudios de Postgrado, Universidad de La Laguna, Santa Cruz de Tenerife, Spain
| | - Silvia Santana-Sosa
- Unidad de Investigación, Hospital Universitario Nuestra Señora de Candelaria, Santa Cruz de Tenerife, Spain.,Escuela de Doctorado y Estudios de Postgrado, Universidad de La Laguna, Santa Cruz de Tenerife, Spain
| | - Jessel Ayra-Plasencia
- Unidad de Investigación, Hospital Universitario Nuestra Señora de Candelaria, Santa Cruz de Tenerife, Spain.,Escuela de Doctorado y Estudios de Postgrado, Universidad de La Laguna, Santa Cruz de Tenerife, Spain
| | - Sara Medina-Suárez
- Unidad de Investigación, Hospital Universitario Nuestra Señora de Candelaria, Santa Cruz de Tenerife, Spain.,Escuela de Doctorado y Estudios de Postgrado, Universidad de La Laguna, Santa Cruz de Tenerife, Spain
| | - Félix Machín
- Unidad de Investigación, Hospital Universitario Nuestra Señora de Candelaria, Santa Cruz de Tenerife, Spain .,Instituto de Tecnologías Biomédicas, Universidad de La Laguna, Santa Cruz de Tenerife, Spain.,Facultad de Ciencias de la Salud, Universidad Fernando Pessoa Canarias, Santa María de Guía, Spain
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14
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Pham T, Walden E, Huard S, Pezacki J, Fullerton MD, Baetz K. Fine tuning Acetyl-CoA Carboxylase 1 activity through localization: Functional genomics reveal a role for the lysine acetyltransferase NuA4 and sphingolipid metabolism in regulating Acc1 activity and localization. Genetics 2022; 221:6591204. [PMID: 35608294 PMCID: PMC9339284 DOI: 10.1093/genetics/iyac086] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2022] [Accepted: 05/10/2022] [Indexed: 11/29/2022] Open
Abstract
Acetyl-CoA Carboxylase 1 catalyzes the conversion of acetyl-CoA to malonyl-CoA, the committed step of de novo fatty acid synthesis. As a master regulator of lipid synthesis, acetyl-CoA carboxylase 1 has been proposed to be a therapeutic target for numerous metabolic diseases. We have shown that acetyl-CoA carboxylase 1 activity is reduced in the absence of the lysine acetyltransferase NuA4 in Saccharomyces cerevisiae. This change in acetyl-CoA carboxylase 1 activity is correlated with a change in localization. In wild-type cells, acetyl-CoA carboxylase 1 is localized throughout the cytoplasm in small punctate and rod-like structures. However, in NuA4 mutants, acetyl-CoA carboxylase 1 localization becomes diffuse. To uncover mechanisms regulating acetyl-CoA carboxylase 1 localization, we performed a microscopy screen to identify other deletion mutants that impact acetyl-CoA carboxylase 1 localization and then measured acetyl-CoA carboxylase 1 activity in these mutants through chemical genetics and biochemical assays. Three phenotypes were identified. Mutants with hyper-active acetyl-CoA carboxylase 1 form 1 or 2 rod-like structures centrally within the cytoplasm, mutants with mid-low acetyl-CoA carboxylase 1 activity displayed diffuse acetyl-CoA carboxylase 1, while the mutants with the lowest acetyl-CoA carboxylase 1 activity (hypomorphs) formed thick rod-like acetyl-CoA carboxylase 1 structures at the periphery of the cell. All the acetyl-CoA carboxylase 1 hypomorphic mutants were implicated in sphingolipid metabolism or very long-chain fatty acid elongation and in common, their deletion causes an accumulation of palmitoyl-CoA. Through exogenous lipid treatments, enzyme inhibitors, and genetics, we determined that increasing palmitoyl-CoA levels inhibits acetyl-CoA carboxylase 1 activity and remodels acetyl-CoA carboxylase 1 localization. Together this study suggests yeast cells have developed a dynamic feed-back mechanism in which downstream products of acetyl-CoA carboxylase 1 can fine-tune the rate of fatty acid synthesis.
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Affiliation(s)
- Trang Pham
- Ottawa Institute of Systems Biology, University of Ottawa, Ottawa, K1H 8M5 Canada.,Department of Biochemistry, Microbiology and Immunology, Faculty of Medicine, University of Ottawa, Ottawa, K1H 8M5 Canada
| | - Elizabeth Walden
- Ottawa Institute of Systems Biology, University of Ottawa, Ottawa, K1H 8M5 Canada.,Department of Biochemistry, Microbiology and Immunology, Faculty of Medicine, University of Ottawa, Ottawa, K1H 8M5 Canada
| | - Sylvain Huard
- Ottawa Institute of Systems Biology, University of Ottawa, Ottawa, K1H 8M5 Canada.,Department of Biochemistry, Microbiology and Immunology, Faculty of Medicine, University of Ottawa, Ottawa, K1H 8M5 Canada
| | - John Pezacki
- Ottawa Institute of Systems Biology, University of Ottawa, Ottawa, K1H 8M5 Canada.,Department of Chemistry and Biomolecular Sciences, Faculty of Science, University of Ottawa, Ottawa K1N6N5 Canada
| | - Morgan D Fullerton
- Department of Biochemistry, Microbiology and Immunology, Faculty of Medicine, University of Ottawa, Ottawa, K1H 8M5 Canada
| | - Kristin Baetz
- Ottawa Institute of Systems Biology, University of Ottawa, Ottawa, K1H 8M5 Canada.,Department of Biochemistry, Microbiology and Immunology, Faculty of Medicine, University of Ottawa, Ottawa, K1H 8M5 Canada.,Department of Biological Sciences, Faculty of Science, University of Calgary, Calgary T2N 1N4, Canada
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15
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Maitra N, Hammer S, Kjerfve C, Bankaitis VA, Polymenis M. Translational control of lipogenesis links protein synthesis and phosphoinositide signaling with nuclear division in Saccharomyces cerevisiae. Genetics 2022; 220:iyab171. [PMID: 34849864 PMCID: PMC8733439 DOI: 10.1093/genetics/iyab171] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2021] [Accepted: 09/23/2021] [Indexed: 12/21/2022] Open
Abstract
Continuously dividing cells coordinate their growth and division. How fast cells grow in mass determines how fast they will multiply. Yet, there are few, if any, examples of a metabolic pathway that actively drives a cell cycle event instead of just being required for it. Here, we show that translational upregulation of lipogenic enzymes in Saccharomyces cerevisiae increased the abundance of lipids and promoted nuclear elongation and division. Derepressing translation of acetyl-CoA carboxylase and fatty acid synthase also suppressed cell cycle-related phenotypes, including delayed nuclear division, associated with Sec14p phosphatidylinositol transfer protein deficiencies, and the irregular nuclear morphologies of mutants defective in phosphatidylinositol 4-OH kinase activities. Our results show that increased lipogenesis drives a critical cell cycle landmark and report a phosphoinositide signaling axis in control of nuclear division. The broad conservation of these lipid metabolic and signaling pathways raises the possibility these activities similarly govern nuclear division in other eukaryotes.
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Affiliation(s)
- Nairita Maitra
- Department of Biochemistry and Biophysics, Texas A&M University, College Station, TX 77843, USA
| | - Staci Hammer
- Department of Biochemistry and Biophysics, Texas A&M University, College Station, TX 77843, USA
| | - Clara Kjerfve
- Department of Biochemistry and Biophysics, Texas A&M University, College Station, TX 77843, USA
| | - Vytas A Bankaitis
- Department of Biochemistry and Biophysics, Texas A&M University, College Station, TX 77843, USA
- Department of Molecular & Cellular Medicine, Texas A&M Health Sciences Center, College Station, TX 77843, USA
- Department of Chemistry, Texas A&M University, College Station, TX 77843, USA
| | - Michael Polymenis
- Department of Biochemistry and Biophysics, Texas A&M University, College Station, TX 77843, USA
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16
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Lemière J, Real-Calderon P, Holt LJ, Fai TG, Chang F. Control of nuclear size by osmotic forces in Schizosaccharomyces pombe. eLife 2022; 11:76075. [PMID: 35856499 PMCID: PMC9410708 DOI: 10.7554/elife.76075] [Citation(s) in RCA: 17] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2021] [Accepted: 07/19/2022] [Indexed: 11/13/2022] Open
Abstract
The size of the nucleus scales robustly with cell size so that the nuclear-to-cell volume ratio (N/C ratio) is maintained during cell growth in many cell types. The mechanism responsible for this scaling remains mysterious. Previous studies have established that the N/C ratio is not determined by DNA amount but is instead influenced by factors such as nuclear envelope mechanics and nuclear transport. Here, we developed a quantitative model for nuclear size control based upon colloid osmotic pressure and tested key predictions in the fission yeast Schizosaccharomyces pombe. This model posits that the N/C ratio is determined by the numbers of macromolecules in the nucleoplasm and cytoplasm. Osmotic shift experiments showed that the fission yeast nucleus behaves as an ideal osmometer whose volume is primarily dictated by osmotic forces. Inhibition of nuclear export caused accumulation of macromolecules in the nucleoplasm, leading to nuclear swelling. We further demonstrated that the N/C ratio is maintained by a homeostasis mechanism based upon synthesis of macromolecules during growth. These studies demonstrate the functions of colloid osmotic pressure in intracellular organization and size control.
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Affiliation(s)
- Joël Lemière
- Department of Cell and Tissue Biology, University of California, San FranciscoSan FranciscoUnited States
| | - Paula Real-Calderon
- Department of Cell and Tissue Biology, University of California, San FranciscoSan FranciscoUnited States,Centro Andaluz de Biología del DesarrolloSevillaSpain
| | - Liam J Holt
- Institute for Systems Genetics, New York University Langone HealthNew YorkUnited States
| | - Thomas G Fai
- Department of Mathematics and Volen Center for Complex Systems, Brandeis UniversityWalthamUnited States
| | - Fred Chang
- Department of Cell and Tissue Biology, University of California, San FranciscoSan FranciscoUnited States
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17
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DeJarnette C, Meyer CJ, Jenner AR, Butts A, Peters T, Cheramie MN, Phelps GA, Vita NA, Loudon-Hossler VC, Lee RE, Palmer GE. Identification of Inhibitors of Fungal Fatty Acid Biosynthesis. ACS Infect Dis 2021; 7:3210-3223. [PMID: 34786940 DOI: 10.1021/acsinfecdis.1c00404] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Fungal fatty acid (FA) synthase and desaturase enzymes are essential for the growth and virulence of human fungal pathogens. These enzymes are structurally distinct from their mammalian counterparts, making them attractive targets for antifungal development. However, there has been little progress in identifying chemotypes that target fungal FA biosynthesis. To accomplish this, we applied a whole-cell-based method known as Target Abundance-based FItness Screening using Candida albicans. Strains with varying levels of FA synthase or desaturase expression were grown in competition to screen a custom small-molecule library. Hit compounds were defined as preferentially inhibiting the growth of the low target-expressing strains. Dose-response experiments confirmed that 16 hits (11 with an acyl hydrazide core) differentially inhibited the growth of strains with an altered desaturase expression, indicating a specific chemical-target interaction. Exogenous unsaturated FAs restored C. albicans growth in the presence of inhibitory concentrations of the most potent acyl hydrazides, further supporting the primary mechanism being inhibition of FA desaturase. A systematic analysis of the structure-activity relationship confirmed the acyl hydrazide core as essential for inhibitory activity. This collection demonstrated broad-spectrum activity against Candida auris and mucormycetes and retained the activity against azole-resistant candida isolates. Finally, a preliminary analysis of toxicity to mammalian cells identified potential lead compounds with desirable selectivities. Collectively, these results establish a scaffold that targets fungal FA biosynthesis with a potential for development into novel therapeutics.
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Affiliation(s)
- Christian DeJarnette
- Department of Pharmaceutical Sciences, St. Jude Children’s Research Hospital, Memphis, Tennessee 38163, United States
| | - Chris J. Meyer
- Department of Chemical Biology and Therapeutics, St. Jude Children’s Research Hospital, Memphis, Tennessee 38105, United States
| | - Alexander R. Jenner
- Department of Chemical Biology and Therapeutics, St. Jude Children’s Research Hospital, Memphis, Tennessee 38105, United States
| | - Arielle Butts
- Department of Clinical Pharmacy and Translational Science, College of Pharmacy, University of Tennessee Health Sciences Center, Memphis, Tennessee 38163, United States
| | - Tracy Peters
- Department of Clinical Pharmacy and Translational Science, College of Pharmacy, University of Tennessee Health Sciences Center, Memphis, Tennessee 38163, United States
| | - Martin N. Cheramie
- Department of Chemical Biology and Therapeutics, St. Jude Children’s Research Hospital, Memphis, Tennessee 38105, United States
| | - Gregory A. Phelps
- Department of Chemical Biology and Therapeutics, St. Jude Children’s Research Hospital, Memphis, Tennessee 38105, United States
- Graduate School of Biomedical Sciences, St. Jude Children’s Research Hospital, Memphis Tennessee 38103, United States
| | - Nicole A. Vita
- Department of Pharmaceutical Sciences, St. Jude Children’s Research Hospital, Memphis, Tennessee 38163, United States
| | - Victoria C. Loudon-Hossler
- Department of Chemical Biology and Therapeutics, St. Jude Children’s Research Hospital, Memphis, Tennessee 38105, United States
| | - Richard E. Lee
- Department of Chemical Biology and Therapeutics, St. Jude Children’s Research Hospital, Memphis, Tennessee 38105, United States
| | - Glen E. Palmer
- Department of Clinical Pharmacy and Translational Science, College of Pharmacy, University of Tennessee Health Sciences Center, Memphis, Tennessee 38163, United States
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18
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Extensive Translational Regulation through the Proliferative Transition of Trypanosoma cruzi Revealed by Multi-Omics. mSphere 2021; 6:e0036621. [PMID: 34468164 PMCID: PMC8550152 DOI: 10.1128/msphere.00366-21] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022] Open
Abstract
Trypanosoma cruzi is the etiological agent for Chagas disease, a neglected parasitic disease in Latin America. Gene transcription control governs the eukaryotic cell replication but is absent in trypanosomatids; thus, it must be replaced by posttranscriptional regulatory events. We investigated the entrance into the T. cruzi replicative cycle using ribosome profiling and proteomics on G1/S epimastigote cultures synchronized with hydroxyurea. We identified 1,784 translationally regulated genes (change > 2, false-discovery rate [FDR] < 0.05) and 653 differentially expressed proteins (change > 1.5, FDR < 0.05), respectively. A major translational remodeling accompanied by an extensive proteome change is found, while the transcriptome remains largely unperturbed at the replicative entrance of the cell cycle. The differentially expressed genes comprise specific cell cycle processes, confirming previous findings while revealing candidate cell cycle regulators that undergo previously unnoticed translational regulation. Clusters of genes showing a coordinated regulation at translation and protein abundance share related biological functions such as cytoskeleton organization and mitochondrial metabolism; thus, they may represent posttranscriptional regulons. The translatome and proteome of the coregulated clusters change in both coupled and uncoupled directions, suggesting that complex cross talk between the two processes is required to achieve adequate protein levels of different regulons. This is the first simultaneous assessment of the transcriptome, translatome, and proteome of trypanosomatids, which represent a paradigm for the absence of transcriptional control. The findings suggest that gene expression chronology along the T. cruzi cell cycle is controlled mainly by translatome and proteome changes coordinated using different mechanisms for specific gene groups. IMPORTANCE Trypanosoma cruzi is an ancient eukaryotic unicellular parasite causing Chagas disease, a potentially life-threatening illness that affects 6 to 7 million people, mostly in Latin America. The antiparasitic treatments for the disease have incomplete efficacy and adverse reactions; thus, improved drugs are needed. We study the mechanisms governing the replication of the parasite, aiming to find differences with the human host, valuable for the development of parasite-specific antiproliferative drugs. Transcriptional regulation is essential for replication in most eukaryotes, but in trypanosomatids, it must be replaced by subsequent gene regulation steps since they lack transcription initiation control. We identified the genome-wide remodeling of mRNA translation and protein abundance during the entrance to the replicative phase of the cell cycle. We found that translation is strongly regulated, causing variation in protein levels of specific cell cycle processes, representing the first simultaneous study of the translatome and proteome in trypanosomatids.
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19
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Vítová M, Lanta V, Čížková M, Jakubec M, Rise F, Halskau Ø, Bišová K, Furse S. The biosynthesis of phospholipids is linked to the cell cycle in a model eukaryote. Biochim Biophys Acta Mol Cell Biol Lipids 2021; 1866:158965. [PMID: 33992808 PMCID: PMC8202326 DOI: 10.1016/j.bbalip.2021.158965] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2021] [Revised: 04/28/2021] [Accepted: 04/30/2021] [Indexed: 12/15/2022]
Abstract
The structural challenges faced by eukaryotic cells through the cell cycle are key for understanding cell viability and proliferation. We tested the hypothesis that the biosynthesis of structural lipids is linked to the cell cycle. If true, this would suggest that the cell's structure is important for progress through and perhaps even control of the cell cycle. Lipidomics (31P NMR and MS), proteomics (Western immunoblotting) and transcriptomics (RT-qPCR) techniques were used to profile the lipid fraction and characterise aspects of its metabolism at seven stages of the cell cycle of the model eukaryote, Desmodesmus quadricauda. We found considerable, transient increases in the abundance of phosphatidylethanolamine during the G1 phase (+35%, ethanolamine phosphate cytidylyltransferase increased 2·5×) and phosphatidylglycerol (+100%, phosphatidylglycerol synthase increased 22×) over the G1/pre-replication phase boundary. The relative abundance of phosphatidylcholine fell by ~35% during the G1. N-Methyl transferases for the conversion of phosphatidylethanolamine into phosphatidylcholine were not found in the de novo transcriptome profile, though a choline phosphate transferase was found, suggesting that the Kennedy pathway is the principal route for the synthesis of PC. The fatty acid profiles of the four most abundant lipids suggested that these lipids were not generally converted between one another. This study shows for the first time that there are considerable changes in the biosynthesis of the three most abundant phospholipid classes in the normal cell cycle of D. quadricauda, by margins large enough to elicit changes to the physical properties of membranes.
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Affiliation(s)
- Milada Vítová
- Laboratory of Cell Cycles of Algae (Laboratoř buněčných cyklů řas), Centre Algatech, Institute of Microbiology of the Czech Academy of Sciences, Novohradská 237, 379 01 Třeboň, Czech Republic
| | - Vojtěch Lanta
- Laboratory of Cell Cycles of Algae (Laboratoř buněčných cyklů řas), Centre Algatech, Institute of Microbiology of the Czech Academy of Sciences, Novohradská 237, 379 01 Třeboň, Czech Republic; Department of Functional Ecology, Institute of Botany of the Czech Academy of Sciences, Dukelská 135, 379 81 Třeboň, Czech Republic
| | - Mária Čížková
- Laboratory of Cell Cycles of Algae (Laboratoř buněčných cyklů řas), Centre Algatech, Institute of Microbiology of the Czech Academy of Sciences, Novohradská 237, 379 01 Třeboň, Czech Republic
| | - Martin Jakubec
- Department of Molecular Biology, University of Bergen, Thormøhlens gate 55, NO-5008 Bergen, Norway
| | - Frode Rise
- Department of Chemistry, Universitetet i Oslo, P. O. Box 1033, Blindern, NO-0315 Oslo, Norway
| | - Øyvind Halskau
- Department of Molecular Biology, University of Bergen, Thormøhlens gate 55, NO-5008 Bergen, Norway
| | - Kateřina Bišová
- Laboratory of Cell Cycles of Algae (Laboratoř buněčných cyklů řas), Centre Algatech, Institute of Microbiology of the Czech Academy of Sciences, Novohradská 237, 379 01 Třeboň, Czech Republic
| | - Samuel Furse
- Department of Molecular Biology, University of Bergen, Thormøhlens gate 55, NO-5008 Bergen, Norway; Core Metabolomics and Lipidomics Laboratory, Wellcome Trust-MRL Institute of Metabolic Science, University of Cambridge, Level 4, Pathology Building, Addenbrooke's Hospital, Cambridge CB2 0QQ, United Kingdom; Biological chemistry group, Jodrell laboratory, Royal Botanic Gardens Kew, United Kingdom.
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20
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Wang C, Meng X, Zhou Y, Yu J, Li Q, Liao Z, Gu Y, Han J, Linghu S, Jiao Z, Wang T, Zhang CY, Chen X. Long Noncoding RNA CTD-2245E15.3 Promotes Anabolic Enzymes ACC1 and PC to Support Non-Small Cell Lung Cancer Growth. Cancer Res 2021; 81:3509-3524. [PMID: 33941610 DOI: 10.1158/0008-5472.can-19-3806] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2019] [Revised: 09/09/2020] [Accepted: 04/29/2021] [Indexed: 11/16/2022]
Abstract
Long noncoding RNAs (lncRNA) have been shown to play critical regulatory roles in the onset and progression of human cancers. However, the functions of a large proportion of lncRNAs are still unexplored. Here we describe a novel lncRNA, CTD-2245E15.3, that promotes lung tumorigenesis by regulating the anabolic enzymes acetyl-CoA carboxylase 1 (ACC1, encoded by the ACACA gene) and pyruvate carboxylase (PC). Differentially expressed lncRNAs between non-small cell lung cancer (NSCLC) and paired adjacent nontumor tissues were identified by a microarray and validated using quantitative real-time polymerase chain reaction. CTD-2245E15.3 was significantly upregulated in NSCLC and was mainly located in the cytoplasm. Knockdown of CTD-2245E15.3 by specific antisense oligonucleotides suppressed cell growth in vitro and in vivo, largely due to cell-cycle arrest and induction of apoptosis. Overexpression of CTD-2245E15.3 in an orthotopic model of lung cancer led to a significant increase in total tumor burden. CTD-2245E15.3 exerted its oncogenic function by binding ACC1 and PC, which are key anabolic factors for biomolecule synthesis in rapidly proliferating tumor cells. Knockdown of CTD-2245E15.3 increased phosphorylation of ACC1 at an inhibitory site for enzymatic activity and promoted PC degradation via ubiquitination. Supplements of palmitate or oxaloacetate, products of ACC1 and PC, alleviated the suppression of cell growth caused by loss of CTD-2245E15.3. These findings reveal the important role of CTD-2245E15.3 as an oncogenic lncRNA in the anabolic process for tumor growth. SIGNIFICANCE: These findings demonstrate a novel lncRNA CTD-2245E15.3 that binds and positively regulates anabolic enzymes ACC1 and PC to promote tumor growth. GRAPHICAL ABSTRACT: http://cancerres.aacrjournals.org/content/canres/81/13/3509/F1.large.jpg.
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Affiliation(s)
- Chen Wang
- State Key Laboratory of Pharmaceutical Biotechnology, Jiangsu Engineering Research Center for MicroRNA Biology and Biotechnology, NJU Advanced Institute for Life Sciences, School of Life Sciences, Nanjing University, Nanjing, Jiangsu, China.
| | - Xiangfeng Meng
- State Key Laboratory of Pharmaceutical Biotechnology, Jiangsu Engineering Research Center for MicroRNA Biology and Biotechnology, NJU Advanced Institute for Life Sciences, School of Life Sciences, Nanjing University, Nanjing, Jiangsu, China
| | - Yu Zhou
- State Key Laboratory of Pharmaceutical Biotechnology, Jiangsu Engineering Research Center for MicroRNA Biology and Biotechnology, NJU Advanced Institute for Life Sciences, School of Life Sciences, Nanjing University, Nanjing, Jiangsu, China
| | - Jing Yu
- State Key Laboratory of Pharmaceutical Biotechnology, Jiangsu Engineering Research Center for MicroRNA Biology and Biotechnology, NJU Advanced Institute for Life Sciences, School of Life Sciences, Nanjing University, Nanjing, Jiangsu, China
| | - Qing Li
- State Key Laboratory of Pharmaceutical Biotechnology, Jiangsu Engineering Research Center for MicroRNA Biology and Biotechnology, NJU Advanced Institute for Life Sciences, School of Life Sciences, Nanjing University, Nanjing, Jiangsu, China
| | - Zhicong Liao
- Department of Cardiothoracic Surgery, Nanjing Drum Tower Hospital, Nanjing University Medical School, Nanjing Medical University, Nanjing, China
| | - Yuanyuan Gu
- State Key Laboratory of Pharmaceutical Biotechnology, Jiangsu Engineering Research Center for MicroRNA Biology and Biotechnology, NJU Advanced Institute for Life Sciences, School of Life Sciences, Nanjing University, Nanjing, Jiangsu, China
| | - Jiayi Han
- Tianjin Medical University Cancer Institute and Hospital, Tianjin, China
| | - Shuo Linghu
- State Key Laboratory of Pharmaceutical Biotechnology, Jiangsu Engineering Research Center for MicroRNA Biology and Biotechnology, NJU Advanced Institute for Life Sciences, School of Life Sciences, Nanjing University, Nanjing, Jiangsu, China
| | - Zichen Jiao
- Department of Cardiothoracic Surgery, Nanjing Drum Tower Hospital, Nanjing University Medical School, Nanjing Medical University, Nanjing, China
| | - Tao Wang
- Department of Cardiothoracic Surgery, Nanjing Drum Tower Hospital, Nanjing University Medical School, Nanjing Medical University, Nanjing, China
| | - Chen-Yu Zhang
- State Key Laboratory of Pharmaceutical Biotechnology, Jiangsu Engineering Research Center for MicroRNA Biology and Biotechnology, NJU Advanced Institute for Life Sciences, School of Life Sciences, Nanjing University, Nanjing, Jiangsu, China.
| | - Xi Chen
- State Key Laboratory of Pharmaceutical Biotechnology, Jiangsu Engineering Research Center for MicroRNA Biology and Biotechnology, NJU Advanced Institute for Life Sciences, School of Life Sciences, Nanjing University, Nanjing, Jiangsu, China.
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21
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Hsu PJ, Tan MC, Shen HL, Chen YH, Wang YY, Hwang SG, Chiang MH, Le QV, Kuo WS, Chou YC, Lin SY, Jauh GY, Cheng WH. The nucleolar protein SAHY1 is involved in pre-rRNA processing and normal plant growth. PLANT PHYSIOLOGY 2021; 185:1039-1058. [PMID: 33793900 PMCID: PMC8133687 DOI: 10.1093/plphys/kiaa085] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/07/2020] [Accepted: 12/01/2020] [Indexed: 05/29/2023]
Abstract
Although the nucleolus is involved in ribosome biogenesis, the functions of numerous nucleolus-localized proteins remain unclear. In this study, we genetically isolated Arabidopsis thaliana salt hypersensitive mutant 1 (sahy1), which exhibits slow growth, short roots, pointed leaves, and sterility. SAHY1 encodes an uncharacterized protein that is predominantly expressed in root tips, early developing seeds, and mature pollen grains and is mainly restricted to the nucleolus. Dysfunction of SAHY1 primarily causes the accumulation of 32S, 18S-A3, and 27SB pre-rRNA intermediates. Coimmunoprecipitation experiments further revealed the interaction of SAHY1 with ribosome proteins and ribosome biogenesis factors. Moreover, sahy1 mutants are less sensitive to protein translation inhibitors and show altered expression of structural constituents of ribosomal genes and ribosome subunit profiles, reflecting the involvement of SAHY1 in ribosome composition and ribosome biogenesis. Analyses of ploidy, S-phase cell cycle progression, and auxin transport and signaling indicated the impairment of mitotic activity, translation of auxin transport carrier proteins, and expression of the auxin-responsive marker DR5::GFP in the root tips or embryos of sahy1 plants. Collectively, these data demonstrate that SAHY1, a nucleolar protein involved in ribosome biogenesis, plays critical roles in normal plant growth in association with auxin transport and signaling.
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Affiliation(s)
- Pei-jung Hsu
- Institute of Plant and Microbial Biology, Academia Sinica, Taipei, Taiwan
| | - Mei-Chen Tan
- Institute of Plant and Microbial Biology, Academia Sinica, Taipei, Taiwan
| | - Hwei-Ling Shen
- Institute of Plant and Microbial Biology, Academia Sinica, Taipei, Taiwan
| | - Ya-Huei Chen
- Institute of Plant and Microbial Biology, Academia Sinica, Taipei, Taiwan
- Graduate Institute of Life Sciences, National Defense Medical Center, Taipei, Taiwan
| | - Ya-Ying Wang
- Institute of Plant and Microbial Biology, Academia Sinica, Taipei, Taiwan
| | - San-Gwang Hwang
- Institute of Plant and Microbial Biology, Academia Sinica, Taipei, Taiwan
| | - Ming-Hau Chiang
- Institute of Plant and Microbial Biology, Academia Sinica, Taipei, Taiwan
| | - Quang-Vuong Le
- Institute of Plant and Microbial Biology, Academia Sinica, Taipei, Taiwan
| | - Wen-Shuo Kuo
- Institute of Plant and Microbial Biology, Academia Sinica, Taipei, Taiwan
| | - Ying-Chan Chou
- Institute of Plant and Microbial Biology, Academia Sinica, Taipei, Taiwan
- Department of Biological Science and Technology, National Pingtung University of Science and Technology, Neipu, Pingtung County,Taiwan
| | - Shih-Yun Lin
- Institute of Plant and Microbial Biology, Academia Sinica, Taipei, Taiwan
| | - Guang-Yuh Jauh
- Institute of Plant and Microbial Biology, Academia Sinica, Taipei, Taiwan
| | - Wan-Hsing Cheng
- Institute of Plant and Microbial Biology, Academia Sinica, Taipei, Taiwan
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22
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Yan C, Li X, Zhang G, Zhu Y, Bi J, Hao H, Hou H. Quorum Sensing-Mediated and Growth Phase-Dependent Regulation of Metabolic Pathways in Hafnia alvei H4. Front Microbiol 2021; 12:567942. [PMID: 33737914 PMCID: PMC7960787 DOI: 10.3389/fmicb.2021.567942] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2020] [Accepted: 01/26/2021] [Indexed: 11/13/2022] Open
Abstract
Quorum sensing (QS) is a widespread regulatory mechanism in bacteria used to coordinate target gene expression with cell density. Thus far, little is known about the regulatory relationship between QS and cell density in terms of metabolic pathways in Hafnia alvei H4. In this study, transcriptomics analysis was performed under two conditions to address this question. The comparative transcriptome of H. alvei H4 wild-type at high cell density (OD600 = 1.7) relative to low cell density (OD600 = 0.3) was considered as growth phase-dependent manner (GPDM), and the transcriptome profile of luxI/R deletion mutant (ΔluxIR) compared to the wild-type was considered as QS-mediated regulation. In all, we identified 206 differentially expressed genes (DEGs) mainly presented in chemotaxis, TCA cycle, two-component system, ABC transporters and pyruvate metabolism, co-regulated by the both density-dependent regulation, and the results were validated by qPCR and swimming phenotypic assays. Aside from the co-regulated DEGs, we also found that 59 DEGs, mediated by density-independent QS, function in pentose phosphate and histidine metabolism and that 2084 cell-density-dependent DEGs involved in glycolysis/gluconeogenesis and phenylalanine metabolism were influenced only by GPDM from significantly enriched analysis of transcriptome data. The findings provided new information about the interplay between two density-dependent metabolic regulation, which could assist with the formulation of control strategies for this opportunistic pathogen, especially at high cell density.
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Affiliation(s)
- Congyang Yan
- School of Food Science and Technology, Dalian Polytechnic University, Dalian, China.,Liaoning Key Lab for Aquatic Processing Quality and Safety, Dalian, China
| | - Xue Li
- School of Food Science and Technology, Dalian Polytechnic University, Dalian, China.,Liaoning Key Lab for Aquatic Processing Quality and Safety, Dalian, China
| | - Gongliang Zhang
- School of Food Science and Technology, Dalian Polytechnic University, Dalian, China.,Liaoning Key Lab for Aquatic Processing Quality and Safety, Dalian, China
| | - Yaolei Zhu
- School of Food Science and Technology, Dalian Polytechnic University, Dalian, China.,Liaoning Key Lab for Aquatic Processing Quality and Safety, Dalian, China
| | - Jingran Bi
- School of Food Science and Technology, Dalian Polytechnic University, Dalian, China.,Liaoning Key Lab for Aquatic Processing Quality and Safety, Dalian, China
| | - Hongshun Hao
- Liaoning Key Lab for Aquatic Processing Quality and Safety, Dalian, China
| | - Hongman Hou
- School of Food Science and Technology, Dalian Polytechnic University, Dalian, China.,Liaoning Key Lab for Aquatic Processing Quality and Safety, Dalian, China
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23
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Vasdekis AE, Singh A. Microbial metabolic noise. WIREs Mech Dis 2020; 13:e1512. [PMID: 33225608 DOI: 10.1002/wsbm.1512] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2019] [Revised: 09/23/2020] [Accepted: 10/26/2020] [Indexed: 11/06/2022]
Abstract
From the time a cell was first placed under the microscope, it became apparent that identifying two clonal cells that "look" identical is extremely challenging. Since then, cell-to-cell differences in shape, size, and protein content have been carefully examined, informing us of the ultimate limits that hinder two cells from occupying an identical phenotypic state. Here, we present recent experimental and computational evidence that similar limits emerge also in cellular metabolism. These limits pertain to stochastic metabolic dynamics and, thus, cell-to-cell metabolic variability, including the resulting adapting benefits. We review these phenomena with a focus on microbial metabolism and conclude with a brief outlook on the potential relationship between metabolic noise and adaptive evolution. This article is categorized under: Metabolic Diseases > Computational Models Metabolic Diseases > Biomedical Engineering.
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Affiliation(s)
| | - Abhyudai Singh
- Department of Electrical and Computer Engineering, University of Delaware, Newark, Delaware, USA
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24
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Maitra N, He C, Blank HM, Tsuchiya M, Schilling B, Kaeberlein M, Aramayo R, Kennedy BK, Polymenis M. Translational control of one-carbon metabolism underpins ribosomal protein phenotypes in cell division and longevity. eLife 2020; 9:53127. [PMID: 32432546 PMCID: PMC7263821 DOI: 10.7554/elife.53127] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2019] [Accepted: 05/20/2020] [Indexed: 12/12/2022] Open
Abstract
A long-standing problem is how cells that lack one of the highly similar ribosomal proteins (RPs) often display distinct phenotypes. Yeast and other organisms live longer when they lack specific ribosomal proteins, especially of the large 60S subunit of the ribosome. However, longevity is neither associated with the generation time of RP deletion mutants nor with bulk inhibition of protein synthesis. Here, we queried actively dividing RP mutants through the cell cycle. Our data link transcriptional, translational, and metabolic changes to phenotypes associated with the loss of paralogous RPs. We uncovered translational control of transcripts encoding enzymes of methionine and serine metabolism, which are part of one-carbon (1C) pathways. Cells lacking Rpl22Ap, which are long-lived, have lower levels of metabolites associated with 1C metabolism. Loss of 1C enzymes increased the longevity of wild type cells. 1C pathways exist in all organisms and targeting the relevant enzymes could represent longevity interventions.
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Affiliation(s)
- Nairita Maitra
- Department of Biochemistry and Biophysics, Texas A&M University, College Station, United States
| | - Chong He
- Buck Institute for Research on Aging, Novato, United States
| | - Heidi M Blank
- Department of Biochemistry and Biophysics, Texas A&M University, College Station, United States
| | - Mitsuhiro Tsuchiya
- Department of Pathology, University of Washington, Seattle, United States
| | | | - Matt Kaeberlein
- Department of Pathology, University of Washington, Seattle, United States
| | - Rodolfo Aramayo
- Department of Biology, Texas A&M University, College Station, United States
| | - Brian K Kennedy
- Buck Institute for Research on Aging, Novato, United States.,Departments of Biochemistry and Physiology, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore.,Centre for Healthy Ageing, National University of Singapore, National University Health System, Singapore, Singapore
| | - Michael Polymenis
- Department of Biochemistry and Biophysics, Texas A&M University, College Station, United States
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25
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Blank HM, Papoulas O, Maitra N, Garge R, Kennedy BK, Schilling B, Marcotte EM, Polymenis M. Abundances of transcripts, proteins, and metabolites in the cell cycle of budding yeast reveal coordinate control of lipid metabolism. Mol Biol Cell 2020; 31:1069-1084. [PMID: 32129706 PMCID: PMC7346729 DOI: 10.1091/mbc.e19-12-0708] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023] Open
Abstract
Establishing the pattern of abundance of molecules of interest during cell division has been a long-standing goal of cell cycle studies. Here, for the first time in any system, we present experiment-matched datasets of the levels of RNAs, proteins, metabolites, and lipids from unarrested, growing, and synchronously dividing yeast cells. Overall, transcript and protein levels were correlated, but specific processes that appeared to change at the RNA level (e.g., ribosome biogenesis) did not do so at the protein level, and vice versa. We also found no significant changes in codon usage or the ribosome content during the cell cycle. We describe an unexpected mitotic peak in the abundance of ergosterol and thiamine biosynthesis enzymes. Although the levels of several metabolites changed in the cell cycle, by far the most significant changes were in the lipid repertoire, with phospholipids and triglycerides peaking strongly late in the cell cycle. Our findings provide an integrated view of the abundance of biomolecules in the eukaryotic cell cycle and point to a coordinate mitotic control of lipid metabolism.
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Affiliation(s)
- Heidi M Blank
- Department of Biochemistry and Biophysics, Texas A&M University, College Station, TX 77843
| | - Ophelia Papoulas
- Center for Systems and Synthetic Biology, University of Texas at Austin, Austin, TX 78712.,Department of Molecular Biosciences, University of Texas at Austin, Austin, TX 78712
| | - Nairita Maitra
- Department of Biochemistry and Biophysics, Texas A&M University, College Station, TX 77843
| | - Riddhiman Garge
- Center for Systems and Synthetic Biology, University of Texas at Austin, Austin, TX 78712.,Department of Molecular Biosciences, University of Texas at Austin, Austin, TX 78712
| | - Brian K Kennedy
- Departments of Biochemistry and Physiology, Yong Loo Lin School of Medicine, National University of Singapore, Singapore 117596.,Centre for Healthy Ageing, National University of Singapore, National University Health System, Singapore 117609.,Buck Institute for Research on Aging, Novato, CA 94945
| | | | - Edward M Marcotte
- Center for Systems and Synthetic Biology, University of Texas at Austin, Austin, TX 78712.,Department of Molecular Biosciences, University of Texas at Austin, Austin, TX 78712
| | - Michael Polymenis
- Department of Biochemistry and Biophysics, Texas A&M University, College Station, TX 77843
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26
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Cell trapping microfluidic chip made of Cyclo olefin polymer enabling two concurrent cell biology experiments with long term durability. Biomed Microdevices 2020; 22:20. [DOI: 10.1007/s10544-020-0474-x] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
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27
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Panchy NL, Lloyd JP, Shiu SH. Improved recovery of cell-cycle gene expression in Saccharomyces cerevisiae from regulatory interactions in multiple omics data. BMC Genomics 2020; 21:159. [PMID: 32054475 PMCID: PMC7020519 DOI: 10.1186/s12864-020-6554-8] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2019] [Accepted: 02/04/2020] [Indexed: 12/11/2022] Open
Abstract
BACKGROUND Gene expression is regulated by DNA-binding transcription factors (TFs). Together with their target genes, these factors and their interactions collectively form a gene regulatory network (GRN), which is responsible for producing patterns of transcription, including cyclical processes such as genome replication and cell division. However, identifying how this network regulates the timing of these patterns, including important interactions and regulatory motifs, remains a challenging task. RESULTS We employed four in vivo and in vitro regulatory data sets to investigate the regulatory basis of expression timing and phase-specific patterns cell-cycle expression in Saccharomyces cerevisiae. Specifically, we considered interactions based on direct binding between TF and target gene, indirect effects of TF deletion on gene expression, and computational inference. We found that the source of regulatory information significantly impacts the accuracy and completeness of recovering known cell-cycle expressed genes. The best approach involved combining TF-target and TF-TF interactions features from multiple datasets in a single model. In addition, TFs important to multiple phases of cell-cycle expression also have the greatest impact on individual phases. Important TFs regulating a cell-cycle phase also tend to form modules in the GRN, including two sub-modules composed entirely of unannotated cell-cycle regulators (STE12-TEC1 and RAP1-HAP1-MSN4). CONCLUSION Our findings illustrate the importance of integrating both multiple omics data and regulatory motifs in order to understand the significance regulatory interactions involved in timing gene expression. This integrated approached allowed us to recover both known cell-cycles interactions and the overall pattern of phase-specific expression across the cell-cycle better than any single data set. Likewise, by looking at regulatory motifs in the form of TF-TF interactions, we identified sets of TFs whose co-regulation of target genes was important for cell-cycle expression, even when regulation by individual TFs was not. Overall, this demonstrates the power of integrating multiple data sets and models of interaction in order to understand the regulatory basis of established biological processes and their associated gene regulatory networks.
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Affiliation(s)
- Nicholas L Panchy
- Genetics Graduate Program, Michigan State University, East Lansing, MI, 48824, USA.,Present address: National Institute for Mathematical and Biological Synthesis, University of Tennessee, 1122 Volunteer Blvd., Suite 106, Knoxville, TN, 37996-3410, USA
| | - John P Lloyd
- Department of Human Genetics and Internal Medicine, University of Michigan, Ann Arbor, MI, 48109, USA
| | - Shin-Han Shiu
- Genetics Graduate Program, Michigan State University, East Lansing, MI, 48824, USA. .,Department of Computational Mathematics, Science and Engineering, Michigan State University, East Lansing, MI, 48824, USA. .,Michigan State University, Plant Biology Laboratories, 612 Wilson Road, Room 166, East Lansing, MI, 48824-1312, USA.
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28
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Relevance and Regulation of Cell Density. Trends Cell Biol 2020; 30:213-225. [PMID: 31980346 DOI: 10.1016/j.tcb.2019.12.006] [Citation(s) in RCA: 55] [Impact Index Per Article: 13.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2019] [Revised: 12/17/2019] [Accepted: 12/17/2019] [Indexed: 01/05/2023]
Abstract
Cell density shows very little variation within a given cell type. For example, in humans variability in cell density among cells of a given cell type is 100 times smaller than variation in cell mass. This tight control indicates that maintenance of a cell type-specific cell density is important for cell function. Indeed, pathological conditions such as cellular senescence are accompanied by changes in cell density. Despite the apparent importance of cell-type-specific density, we know little about how cell density affects cell function, how it is controlled, and how it sometimes changes as part of a developmental process or in response to changes in the environment. The recent development of new technologies to accurately measure the cell density of single cells in suspension and in tissues is likely to provide answers to these important questions.
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29
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Madeira JB, Matos GS, Messias LS, Bozaquel-Morais BL, Masuda CA, Montero-Lomeli M. Induction of triacylglycerol synthesis in yeast by cell cycle arrest. FEMS Yeast Res 2019; 19:5462652. [PMID: 30985885 DOI: 10.1093/femsyr/foz030] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2018] [Accepted: 04/13/2019] [Indexed: 12/13/2022] Open
Abstract
In this study, we found that cell cycle arrest induced by alpha-factor mating pheromone (G1), hydroxyurea (S) or nocodazole (G2/M) was associated to increased lipid droplet (LD) content. To identify novel cell cycle genes involved in LD homeostasis, we screened a deletion library for strains with altered LD levels. Among the mutants related to mitotic cell cycle, we found 24 hits that displayed a significantly higher LD content. Ontology mapping showed that neither a biological process nor a specific cell cycle phase was enriched among the hits. We decided to further study the role of SWI4 on LD homeostasis as it is involved in G1/S transition, a stage where lipolysis is active. The high LD content of swi4Δ mutant was not due to inhibition of lipolysis, but due to an increase in triacylglycerol (TAG) synthesis. In addition, deletion of the AMP kinase gene SNF1 or inhibition of TORC1 activity, both known regulators of LD homeostasis, further increased the LD content of a swi4Δ mutant. These findings highlight a role of the cell cycle regulator SWI4 in the coordination of lipid metabolism which is independent of the TORC1 and SNF1/AMPK pathways.
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Affiliation(s)
- Juliana B Madeira
- Instituto de Bioquimica Médica Leoplodo de Meis, Universidade Federal do Rio de Janeiro, Av. Carlos Chagas Filho 373, cep 21941-902, Rio de Janeiro, Rio de Janeiro Brazil
| | - Gabriel S Matos
- Instituto de Bioquimica Médica Leoplodo de Meis, Universidade Federal do Rio de Janeiro, Av. Carlos Chagas Filho 373, cep 21941-902, Rio de Janeiro, Rio de Janeiro Brazil
| | - Laryssa S Messias
- Instituto de Bioquimica Médica Leoplodo de Meis, Universidade Federal do Rio de Janeiro, Av. Carlos Chagas Filho 373, cep 21941-902, Rio de Janeiro, Rio de Janeiro Brazil
| | - Bruno L Bozaquel-Morais
- Instituto de Bioquimica Médica Leoplodo de Meis, Universidade Federal do Rio de Janeiro, Av. Carlos Chagas Filho 373, cep 21941-902, Rio de Janeiro, Rio de Janeiro Brazil
| | - Claudio A Masuda
- Instituto de Bioquimica Médica Leoplodo de Meis, Universidade Federal do Rio de Janeiro, Av. Carlos Chagas Filho 373, cep 21941-902, Rio de Janeiro, Rio de Janeiro Brazil
| | - Monica Montero-Lomeli
- Instituto de Bioquimica Médica Leoplodo de Meis, Universidade Federal do Rio de Janeiro, Av. Carlos Chagas Filho 373, cep 21941-902, Rio de Janeiro, Rio de Janeiro Brazil
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30
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Boye E, Grallert B. eIF2α phosphorylation and the regulation of translation. Curr Genet 2019; 66:293-297. [PMID: 31485739 DOI: 10.1007/s00294-019-01026-1] [Citation(s) in RCA: 28] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2019] [Revised: 08/13/2019] [Accepted: 08/16/2019] [Indexed: 12/27/2022]
Abstract
We discuss novel insight into the role and consequences of the phosphorylation of the translation initiation factor eIF2α in the context of stress responses and cell-cycle regulation. eIF2α is centrally located to regulate translation and its phosphorylation in response to different environmental challenges is one of the best characterized stress-response pathways. In addition to its role in stress management, eIF2α phosphorylation is also linked to cell-cycle progression and memory consolidation in the nervous system. The best known consequences of eIF2α phosphorylation are downregulation of global translation and stimulation of translation of some mRNAs. However, recent evidence shows that (i) eIF2α phosphorylation is not always required for the downregulation of global translation after exposure to stress and (ii) eIF2α phosphorylation does not necessarily lead to the downregulation of global translation. These results suggest that the textbook view of eIF2α phosphorylation needs to be revised and that there must be additional regulatory mechanisms at play.
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Affiliation(s)
- Erik Boye
- Department of Radiation Biology, Institute for Cancer Research, Oslo University Hospital, Oslo, Norway
| | - Beáta Grallert
- Department of Radiation Biology, Institute for Cancer Research, Oslo University Hospital, Oslo, Norway.
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31
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Prioretti L, Carriere F, Field B, Avilan L, Montané MH, Menand B, Gontero B. Targeting TOR signaling for enhanced lipid productivity in algae. Biochimie 2019; 169:12-17. [PMID: 31265860 DOI: 10.1016/j.biochi.2019.06.016] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2019] [Accepted: 06/26/2019] [Indexed: 01/21/2023]
Abstract
Microalgae can produce large quantities of triacylglycerols (TAGs) and other neutral lipids that are suitable for making biofuels and as feedstocks for green chemistry. However, TAGs accumulate under stress conditions that also stop growth, leading to a trade-off between biomass production and TAG yield. Recently, in the model marine diatom Phaeodactylum tricornutum it was shown that inhibition of the target of rapamycin (TOR) kinase boosts lipid productivity by promoting TAG production without stopping growth. We believe that basic knowledge in this emerging field is required to develop innovative strategies to improve neutral lipid accumulation in oleaginous microalgae. In this minireview, we discuss current research on the TOR signaling pathway with a focus on its control on lipid homeostasis. We first provide an overview of the well characterized roles of TOR in mammalian lipogenesis, adipogenesis and lipolysis. We then present evidence of a role for TOR in controlling TAG accumulation in microalgae, and draw parallels between the situation in animals, plants and microalgae to propose a model of TOR signaling for TAG accumulation in microalgae.
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Affiliation(s)
- Laura Prioretti
- Aix Marseille Univ, CNRS, BIP UMR 7281, 31 Chemin Joseph Aiguier, 13402, Marseille, Cedex 09, France
| | - Frédéric Carriere
- Aix Marseille Univ, CNRS, BIP UMR 7281, 31 Chemin Joseph Aiguier, 13402, Marseille, Cedex 09, France
| | - Ben Field
- Aix Marseille Univ, CEA, CNRS, UMR 7265 BIAM, 163 Avenue de Luminy, 13288, Marseille, France
| | - Luisana Avilan
- Aix Marseille Univ, CNRS, BIP UMR 7281, 31 Chemin Joseph Aiguier, 13402, Marseille, Cedex 09, France
| | - Marie-Hélène Montané
- Aix Marseille Univ, CEA, CNRS, UMR 7265 BIAM, 163 Avenue de Luminy, 13288, Marseille, France
| | - Benoît Menand
- Aix Marseille Univ, CEA, CNRS, UMR 7265 BIAM, 163 Avenue de Luminy, 13288, Marseille, France.
| | - Brigitte Gontero
- Aix Marseille Univ, CNRS, BIP UMR 7281, 31 Chemin Joseph Aiguier, 13402, Marseille, Cedex 09, France.
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32
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Anda S, Grallert B. Cell-Cycle-Dependent Regulation of Translation: New Interpretations of Old Observations in Light of New Approaches. Bioessays 2019; 41:e1900022. [PMID: 31210378 DOI: 10.1002/bies.201900022] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2019] [Revised: 04/29/2019] [Indexed: 12/22/2022]
Abstract
It is a long-standing view that global translation varies during the cell cycle and is much lower in mitosis than in other cell-cycle phases. However, the central papers in the literature are not in agreement about the extent of downregulation in mitosis, ranging from a dramatic decrease to only a marginal reduction. Herein, it is argued that the discrepancy derives from technical challenges. Cell-cycle-dependent variations are most conveniently studied in synchronized cells, but the synchronization methods by themselves often evoke stress responses that, in turn, affect translation rates. Further, it is argued that previously reported cell-cycle-dependent changes in the global translation rate to a large extent reflect responses to the synchronization methods. Recent findings strongly suggest that the global translation rate is not regulated in a cell-cycle-dependent manner. Novel techniques allowing a genome-wide analysis of translational profiles suggest that the extent and importance of selective translational regulation associated with cell-cycle transitions have been underestimated. Therefore, the main question is which messenger RNAs (mRNAs) are translated, rather than whether the global translation rate is decreased.
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Affiliation(s)
- Silje Anda
- Department of Radiation Biology, Institute for Cancer Research, Oslo University Hospital, 0379, Oslo, Norway
| | - Beáta Grallert
- Department of Radiation Biology, Institute for Cancer Research, Oslo University Hospital, 0379, Oslo, Norway
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33
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Rodriguez CM, Chun SY, Mills RE, Todd PK. Translation of upstream open reading frames in a model of neuronal differentiation. BMC Genomics 2019; 20:391. [PMID: 31109297 PMCID: PMC6528255 DOI: 10.1186/s12864-019-5775-1] [Citation(s) in RCA: 26] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2019] [Accepted: 05/07/2019] [Indexed: 12/17/2022] Open
Abstract
Background Upstream open reading frames (uORFs) initiate translation within mRNA 5′ leaders, and have the potential to alter main coding sequence (CDS) translation on transcripts in which they reside. Ribosome profiling (RP) studies suggest that translating ribosomes are pervasive within 5′ leaders across model systems. However, the significance of this observation remains unclear. To explore a role for uORF usage in a model of neuronal differentiation, we performed RP on undifferentiated and differentiated human neuroblastoma cells. Results Using a spectral coherence algorithm (SPECtre), we identify 4954 consistently translated uORFs across 31% of all neuroblastoma transcripts. These uORFs predominantly utilize non-AUG initiation codons and exhibit translational efficiencies (TE) comparable to annotated coding regions. On a population basis, the global impact of both AUG and non-AUG initiated uORFs on basal CDS translation were small, even when analysis is limited to conserved and consistently translated uORFs. However, uORFs did alter the translation of a subset of genes, including the Diamond-Blackfan Anemia associated ribosomal gene RPS24. With retinoic acid induced differentiation, we observed an overall positive correlation in translational shifts between uORF/CDS pairs. However, CDSs downstream of uORFs show smaller shifts in TE with differentiation relative to CDSs without a predicted uORF, suggesting that uORF translation buffers cell state dependent fluctuations in CDS translation. Conclusion This work provides insights into the dynamic relationships and potential regulatory functions of uORF/CDS pairs in a model of neuronal differentiation. Electronic supplementary material The online version of this article (10.1186/s12864-019-5775-1) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Caitlin M Rodriguez
- Department of Neurology, University of Michigan, Ann Arbor, MI, USA.,Neuroscience Graduate Program, University of Michigan, Ann Arbor, MI, USA
| | - Sang Y Chun
- Department of Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, MI, 48109, USA
| | - Ryan E Mills
- Department of Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, MI, 48109, USA. .,Department of Human Genetics, University of Michigan, Ann Arbor, MI, 48109, USA.
| | - Peter K Todd
- Department of Neurology, University of Michigan, Ann Arbor, MI, USA. .,VA Ann Arbor Healthcare System, Ann Arbor, MI, USA.
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34
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Pervasive, Coordinated Protein-Level Changes Driven by Transcript Isoform Switching during Meiosis. Cell 2019; 172:910-923.e16. [PMID: 29474919 DOI: 10.1016/j.cell.2018.01.035] [Citation(s) in RCA: 95] [Impact Index Per Article: 19.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2017] [Revised: 12/04/2017] [Accepted: 01/26/2018] [Indexed: 12/22/2022]
Abstract
To better understand the gene regulatory mechanisms that program developmental processes, we carried out simultaneous genome-wide measurements of mRNA, translation, and protein through meiotic differentiation in budding yeast. Surprisingly, we observed that the levels of several hundred mRNAs are anti-correlated with their corresponding protein products. We show that rather than arising from canonical forms of gene regulatory control, the regulation of at least 380 such cases, or over 8% of all measured genes, involves temporally regulated switching between production of a canonical, translatable transcript and a 5' extended isoform that is not efficiently translated into protein. By this pervasive mechanism for the modulation of protein levels through a natural developmental program, a single transcription factor can coordinately activate and repress protein synthesis for distinct sets of genes. The distinction is not based on whether or not an mRNA is induced but rather on the type of transcript produced.
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35
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Takeuchi T, Benning C. Nitrogen-dependent coordination of cell cycle, quiescence and TAG accumulation in Chlamydomonas. BIOTECHNOLOGY FOR BIOFUELS 2019; 12:292. [PMID: 31890020 PMCID: PMC6927116 DOI: 10.1186/s13068-019-1635-0] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/15/2019] [Accepted: 12/12/2019] [Indexed: 05/07/2023]
Abstract
Microalgae hold great promises as sustainable cellular factories for the production of alternative fuels, feeds, and biopharmaceuticals for human health. While the biorefinery approach for fuels along with the coproduction of high-value compounds with industrial, therapeutic, or nutraceutical applications have the potential to make algal biofuels more economically viable, a number of challenges continue to hamper algal production systems at all levels. One such hurdle includes the metabolic trade-off often observed between the increased yields of desired products, such as triacylglycerols (TAG), and the growth of an organism. Initial genetic engineering strategies to improve lipid productivity in microalgae, which focused on overproducing the enzymes involved in fatty acid and TAG biosynthesis or inactivating competing carbon (C) metabolism, have seen some successes albeit at the cost of often greatly reduced biomass. Emergent approaches that aim at modifying the dynamics of entire metabolic pathways by engineering of pertinent transcription factors or signaling networks appear to have successfully achieved a balance between growth and neutral lipid accumulation. However, the biological knowledge of key signaling networks and molecular components linking these two processes is still incomplete in photosynthetic eukaryotes, making it difficult to optimize metabolic engineering strategies for microalgae. Here, we focus on nitrogen (N) starvation of the model green microalga, Chlamydomonas reinhardtii, to present the current understanding of the nutrient-dependent switch between proliferation and quiescence, and the drastic reprogramming of metabolism that results in the storage of C compounds following N starvation. We discuss the potential components mediating the transcriptional repression of cell cycle genes and the establishment of quiescence in Chlamydomonas, and highlight the importance of signaling pathways such as those governed by the target of rapamycin (TOR) and sucrose nonfermenting-related (SnRK) kinases in the coordination of metabolic status with cellular growth. A better understanding of how the cell division cycle is regulated in response to nutrient scarcity and of the signaling pathways linking cellular growth to energy and lipid homeostasis, is essential to improve the prospects of biofuels and biomass production in microalgae.
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Affiliation(s)
- Tomomi Takeuchi
- Department of Biochemistry and Molecular Biology, Michigan State University, East Lansing, MI 48824 USA
- Department of Energy-Plant Research Laboratory, Michigan State University, East Lansing, MI 48824 USA
| | - Christoph Benning
- Department of Biochemistry and Molecular Biology, Michigan State University, East Lansing, MI 48824 USA
- Department of Energy-Plant Research Laboratory, Michigan State University, East Lansing, MI 48824 USA
- Department of Plant Biology, Michigan State University, East Lansing, MI 48824 USA
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36
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Blank HM, Callahan M, Pistikopoulos IPE, Polymenis AO, Polymenis M. Scaling of G1 Duration with Population Doubling Time by a Cyclin in Saccharomyces cerevisiae. Genetics 2018; 210:895-906. [PMID: 30150288 PMCID: PMC6218239 DOI: 10.1534/genetics.118.301507] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2018] [Accepted: 08/24/2018] [Indexed: 01/09/2023] Open
Abstract
The longer cells stay in particular phases of the cell cycle, the longer it will take these cell populations to increase. However, the above qualitative description has very little predictive value, unless it can be codified mathematically. A quantitative relation that defines the population doubling time (Td) as a function of the time eukaryotic cells spend in specific cell cycle phases would be instrumental for estimating rates of cell proliferation and for evaluating introduced perturbations. Here, we show that in human cells, the length of the G1 phase (TG1) regressed on Td with a slope of ≈0.75, while in the yeast Saccharomyces cerevisiae, the slope was slightly smaller, at ≈0.60. On the other hand, cell size was not strongly associated with Td or TG1 in cell cultures that were proliferating at different rates. Furthermore, we show that levels of the yeast G1 cyclin Cln3p were positively associated with rates of cell proliferation over a broad range, at least in part through translational control mediated by a short upstream ORF (uORF) in the CLN3 transcript. Cln3p was also necessary for the proper scaling between TG1 and Td In contrast, yeast lacking the Whi5p transcriptional repressor maintained the scaling between TG1 and Td These data reveal fundamental scaling relationships between the duration of eukaryotic cell cycle phases and rates of cell proliferation, point to the necessary role of Cln3p in these relationships in yeast, and provide a mechanistic basis linking Cln3p levels to proliferation rates and the scaling of G1 with doubling time.
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Affiliation(s)
- Heidi M Blank
- Department of Biochemistry and Biophysics, Texas A&M University, College Station, Texas 77843
| | - Michelle Callahan
- Department of Biochemistry and Biophysics, Texas A&M University, College Station, Texas 77843
| | | | - Aggeliki O Polymenis
- Department of Biochemistry and Biophysics, Texas A&M University, College Station, Texas 77843
| | - Michael Polymenis
- Department of Biochemistry and Biophysics, Texas A&M University, College Station, Texas 77843
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37
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Walters AD, Amoateng K, Wang R, Chen JH, McDermott G, Larabell CA, Gadal O, Cohen-Fix O. Nuclear envelope expansion in budding yeast is independent of cell growth and does not determine nuclear volume. Mol Biol Cell 2018; 30:131-145. [PMID: 30379612 PMCID: PMC6337908 DOI: 10.1091/mbc.e18-04-0204] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022] Open
Abstract
Most cells exhibit a constant ratio between nuclear and cell volume. The mechanism dictating this constant ratio and the nuclear component(s) that scale with cell size are not known. To address this, we examined the consequences to the size and shape of the budding yeast nucleus when cell expansion is inhibited by down-regulating components of the secretory pathway. We find that under conditions where cell size increase is restrained, the nucleus becomes bilobed, with the bulk of the DNA in one lobe and the nucleolus in the other. The formation of bilobed nuclei is dependent on fatty acid and phospholipid synthesis, suggesting that it is associated with nuclear membrane expansion. Bilobed nuclei appeared predominantly after spindle pole body separation, suggesting that nuclear envelope expansion follows cell-cycle cues rather than cell size. Importantly, cells with bilobed nuclei had the same nuclear:cell volume ratio as cells with round nuclei. Therefore, the bilobed nucleus could be a consequence of continued NE expansion as cells traverse the cell cycle without an accompanying increase in nuclear volume due to the inhibition of cell growth. Our data suggest that nuclear volume is not determined by nuclear envelope availability but by one or more nucleoplasmic factors.
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Affiliation(s)
- Alison D Walters
- Laboratory of Molecular and Cellular Biology, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, MD 20892
| | - Kwabena Amoateng
- Laboratory of Molecular and Cellular Biology, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, MD 20892
| | - Renjie Wang
- Laboratoire de Biologie Moléculaire Eucaryote, Centre de Biologie Intégrative, Université de Toulouse, CNRS, UPS, 31000 Toulouse, France
| | - Jian-Hua Chen
- Department of Anatomy, University of California, San Francisco, San Francisco, CA 94158.,Molecular Biophysics and Integrated Bioimaging, Lawrence Berkeley National Laboratory, Berkeley, CA 94720
| | - Gerry McDermott
- Department of Anatomy, University of California, San Francisco, San Francisco, CA 94158.,Molecular Biophysics and Integrated Bioimaging, Lawrence Berkeley National Laboratory, Berkeley, CA 94720
| | - Carolyn A Larabell
- Department of Anatomy, University of California, San Francisco, San Francisco, CA 94158.,Molecular Biophysics and Integrated Bioimaging, Lawrence Berkeley National Laboratory, Berkeley, CA 94720
| | - Olivier Gadal
- Laboratoire de Biologie Moléculaire Eucaryote, Centre de Biologie Intégrative, Université de Toulouse, CNRS, UPS, 31000 Toulouse, France
| | - Orna Cohen-Fix
- Laboratory of Molecular and Cellular Biology, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, MD 20892
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38
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Metabolic heterogeneity in clonal microbial populations. Curr Opin Microbiol 2018; 45:30-38. [DOI: 10.1016/j.mib.2018.02.004] [Citation(s) in RCA: 65] [Impact Index Per Article: 10.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2018] [Revised: 02/07/2018] [Accepted: 02/08/2018] [Indexed: 11/22/2022]
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39
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Crawford RA, Pavitt GD. Translational regulation in response to stress in Saccharomyces cerevisiae. Yeast 2018; 36:5-21. [PMID: 30019452 PMCID: PMC6492140 DOI: 10.1002/yea.3349] [Citation(s) in RCA: 51] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2018] [Revised: 06/08/2018] [Accepted: 06/25/2018] [Indexed: 12/19/2022] Open
Abstract
The budding yeast Saccharomyces cerevisiae must dynamically alter the composition of its proteome in order to respond to diverse stresses. The reprogramming of gene expression during stress typically involves initial global repression of protein synthesis, accompanied by the activation of stress‐responsive mRNAs through both translational and transcriptional responses. The ability of specific mRNAs to counter the global translational repression is therefore crucial to the overall response to stress. Here we summarize the major repressive mechanisms and discuss mechanisms of translational activation in response to different stresses in S. cerevisiae. Taken together, a wide range of studies indicate that multiple elements act in concert to bring about appropriate translational responses. These include regulatory elements within mRNAs, altered mRNA interactions with RNA‐binding proteins and the specialization of ribosomes that each contribute towards regulating protein expression to suit the changing environmental conditions.
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Affiliation(s)
- Robert A Crawford
- Division of Molecular and Cellular Function, School of Biological Sciences, Faculty of Biology, Medicine and Health, Manchester Academic Health Science Centre, The University of Manchester, Michael Smith Building, Dover Street, Manchester, M13 9PT, UK
| | - Graham D Pavitt
- Division of Molecular and Cellular Function, School of Biological Sciences, Faculty of Biology, Medicine and Health, Manchester Academic Health Science Centre, The University of Manchester, Michael Smith Building, Dover Street, Manchester, M13 9PT, UK
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40
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Zach R, Tvarůžková J, Schätz M, Ťupa O, Grallert B, Převorovský M. Mitotic defects in fission yeast lipid metabolism 'cut' mutants are suppressed by ammonium chloride. FEMS Yeast Res 2018; 18:5040229. [PMID: 29931271 PMCID: PMC6037054 DOI: 10.1093/femsyr/foy064] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2018] [Accepted: 06/15/2018] [Indexed: 01/01/2023] Open
Abstract
Fission yeast 'cut' mutants show defects in temporal coordination of nuclear division with cytokinesis, resulting in aberrant mitosis and lethality. Among other causes, the 'cut' phenotype can be triggered by genetic or chemical perturbation of lipid metabolism, supposedly resulting in shortage of membrane phospholipids and insufficient nuclear envelope expansion during anaphase. Interestingly, penetrance of the 'cut' phenotype in mutants of the transcription factor cbf11 and acetyl-coenzyme A carboxylase cut6, both related to lipid metabolism, is highly dependent on growth media, although the specific nutrient(s) affecting 'cut' occurrence is not known. In this study, we set out to identify the growth media component(s) responsible for 'cut' phenotype suppression in Δcbf11 and cut6-621 cells. We show that mitotic defects occur rapidly in Δcbf11 cells upon shift from the minimal EMM medium ('cut' suppressing) to the complex YES medium ('cut' promoting). By growing cells in YES medium supplemented with individual EMM components, we identified ammonium chloride, an efficiently utilized nitrogen source, as a specific and potent suppressor of the 'cut' phenotype in both Δcbf11 and cut6-621. Furthermore, we found that ammonium chloride boosts lipid droplet formation in wild-type cells. Our findings suggest a possible involvement of nutrient-responsive signaling in 'cut' suppression.
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Affiliation(s)
- Róbert Zach
- Department of Cell Biology, Faculty of Science, Charles University, Prague, Czech Republic
| | - Jarmila Tvarůžková
- Department of Cell Biology, Faculty of Science, Charles University, Prague, Czech Republic
| | - Martin Schätz
- Department of Cell Biology, Faculty of Science, Charles University, Prague, Czech Republic
- Department of Computing and Control Engineering, University of Chemistry and Technology, Prague, Czech Republic
| | - Ondřej Ťupa
- Department of Cell Biology, Faculty of Science, Charles University, Prague, Czech Republic
- Department of Computing and Control Engineering, University of Chemistry and Technology, Prague, Czech Republic
| | - Beáta Grallert
- Department of Radiation Biology, Institute for Cancer Research, Oslo University Hospital, Oslo, Norway
| | - Martin Převorovský
- Department of Cell Biology, Faculty of Science, Charles University, Prague, Czech Republic
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41
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Abstract
Cells depend on hugely diverse lipidomes for many functions. The actions and structural integrity of the plasma membrane and most organelles also critically depend on membranes and their lipid components. Despite the biological importance of lipids, our understanding of lipid engagement, especially the roles of lipid hydrophobic alkyl side chains, in key cellular processes is still developing. Emerging research has begun to dissect the importance of lipids in intricate events such as cell division. This review discusses how these structurally diverse biomolecules are spatially and temporally regulated during cell division, with a focus on cytokinesis. We analyze how lipids facilitate changes in cellular morphology during division and how they participate in key signaling events. We identify which cytokinesis proteins are associated with membranes, suggesting lipid interactions. More broadly, we highlight key unaddressed questions in lipid cell biology and techniques, including mass spectrometry, advanced imaging, and chemical biology, which will help us gain insights into the functional roles of lipids.
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Affiliation(s)
- Elisabeth M Storck
- Randall Centre for Cell and Molecular Biophysics, School of Basic and Medical Biosciences, King's College London, London SE1 1UL, United Kingdom;
| | - Cagakan Özbalci
- Randall Centre for Cell and Molecular Biophysics, School of Basic and Medical Biosciences, King's College London, London SE1 1UL, United Kingdom;
| | - Ulrike S Eggert
- Randall Centre for Cell and Molecular Biophysics, School of Basic and Medical Biosciences, King's College London, London SE1 1UL, United Kingdom; .,Department of Chemistry, King's College London, London SE1 1DB, United Kingdom
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42
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Ferreira R, Teixeira PG, Gossing M, David F, Siewers V, Nielsen J. Metabolic engineering of Saccharomyces cerevisiae for overproduction of triacylglycerols. Metab Eng Commun 2018; 6:22-27. [PMID: 29896445 PMCID: PMC5994799 DOI: 10.1016/j.meteno.2018.01.002] [Citation(s) in RCA: 45] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2017] [Revised: 01/05/2018] [Accepted: 01/23/2018] [Indexed: 11/08/2022] Open
Abstract
Triacylglycerols (TAGs) are valuable versatile compounds that can be used as metabolites for nutrition and health, as well as feedstocks for biofuel production. Although Saccharomyces cerevisiae is the favored microbial cell factory for industrial production of biochemicals, it does not produce large amounts of lipids and TAGs comprise only ~1% of its cell dry weight. Here, we engineered S. cerevisiae to reorient its metabolism for overproduction of TAGs, by regulating lipid droplet associated-proteins involved in TAG synthesis and hydrolysis. We implemented a push-and-pull strategy by overexpressing genes encoding a deregulated acetyl-CoA carboxylase, ACC1S659A/S1157A(ACC1**), as well as the last two steps of TAG formation: phosphatidic phosphatase (PAH1) and diacylglycerol acyltransferase (DGA1), ultimately leading to 129 mg∙gCDW−1 of TAGs. Disruption of TAG lipase genes TGL3, TGL4, TGL5 and sterol acyltransferase gene ARE1 increased the TAG content to 218 mg∙gCDW−1. Further disruption of the beta-oxidation by deletion of POX1, as well as glycerol-3-phosphate utilization through deletion of GUT2, did not affect TAGs levels. Finally, disruption of the peroxisomal fatty acyl-CoA transporter PXA1 led to accumulation of 254 mg∙gCDW−1. The TAG levels achieved here are the highest titer reported in S. cerevisiae, reaching 27.4% of the maximum theoretical yield in minimal medium with 2% glucose. This work shows the potential of using an industrially established and robust yeast species for high level lipid production. Saccharomyces cerevisiae was engineered towards triacylglycerol (TAG) accumulation. Overexpression of TAG biosynthesis genes, and deletion of degradation pathways were targeted. Final strain reached 254 mg/gCDW TAG on 2% glucose media, achieving 27.4% of the maximum theoretical yield.
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Affiliation(s)
- Raphael Ferreira
- Department of Biology and Biological Engineering, Chalmers University of Technology, SE412 96 Gothenburg, Sweden.,Novo Nordisk Foundation Center for Biosustainability, Chalmers University of Technology, SE412 96 Gothenburg, Sweden
| | - Paulo Gonçalves Teixeira
- Department of Biology and Biological Engineering, Chalmers University of Technology, SE412 96 Gothenburg, Sweden.,Novo Nordisk Foundation Center for Biosustainability, Chalmers University of Technology, SE412 96 Gothenburg, Sweden
| | - Michael Gossing
- Department of Biology and Biological Engineering, Chalmers University of Technology, SE412 96 Gothenburg, Sweden.,Novo Nordisk Foundation Center for Biosustainability, Chalmers University of Technology, SE412 96 Gothenburg, Sweden
| | - Florian David
- Department of Biology and Biological Engineering, Chalmers University of Technology, SE412 96 Gothenburg, Sweden.,Novo Nordisk Foundation Center for Biosustainability, Chalmers University of Technology, SE412 96 Gothenburg, Sweden
| | - Verena Siewers
- Department of Biology and Biological Engineering, Chalmers University of Technology, SE412 96 Gothenburg, Sweden.,Novo Nordisk Foundation Center for Biosustainability, Chalmers University of Technology, SE412 96 Gothenburg, Sweden
| | - Jens Nielsen
- Department of Biology and Biological Engineering, Chalmers University of Technology, SE412 96 Gothenburg, Sweden.,Novo Nordisk Foundation Center for Biosustainability, Chalmers University of Technology, SE412 96 Gothenburg, Sweden.,Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, DK2800 Kgs Lyngby, Denmark
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43
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Ewald JC. How yeast coordinates metabolism, growth and division. Curr Opin Microbiol 2018; 45:1-7. [PMID: 29334655 DOI: 10.1016/j.mib.2017.12.012] [Citation(s) in RCA: 27] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2017] [Revised: 12/12/2017] [Accepted: 12/27/2017] [Indexed: 11/18/2022]
Abstract
All cells, especially single cell organisms, need to adapt their metabolism, growth and division coordinately to the available nutrients. This coordination is mediated by extensive cross-talk between nutrient signaling, metabolism, growth, and the cell division cycle, which is only gradually being uncovered: Nutrient signaling not only controls entry into the cell cycle at the G1/S transition, but all phases of the cell cycle. Metabolites are even sensed directly by cell cycle regulators to prevent cell cycle progression in absence of sufficient metabolic fluxes. In turn, cell cycle regulators such as the cyclin-dependent kinase directly control metabolic fluxes during cell cycle progression. In this review, I highlight some recent advances in our understanding of how metabolism and the cell division cycle are coordinated in the model organism Saccharomyces cerevisiae.
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Affiliation(s)
- Jennifer C Ewald
- Eberhard Karls Universität Tübingen, Interfaculty Institute of Cell Biology, Auf der Morgenstelle 15, 72076 Tübingen, Germany.
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44
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Ribosome profiling the cell cycle: lessons and challenges. Curr Genet 2017; 63:959-964. [PMID: 28451847 DOI: 10.1007/s00294-017-0698-3] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2017] [Revised: 04/14/2017] [Accepted: 04/20/2017] [Indexed: 12/31/2022]
Abstract
Understanding the causes and consequences of dynamic changes in the abundance and activity of cellular components during cell division is what most cell cycle studies are about. Here we focus on control of gene expression in the cell cycle at the level of translation. The advent of deep sequencing methodologies led to technologies that quantify the levels of all mRNAs that are bound by ribosomes and engaged in translation in the cell (Ingolia et al. Science 324:218-223, 2009). This approach has been applied recently to synchronous cell populations to find transcripts under translational control at different cell cycle phases (Blank et al. EMBO J 36:487-502, 2017; Stumpf et al. Mol Cell 52:574-582, 2013; Tanenbaum et al. Elife 4:e07957, 2015). These studies revealed new biology, but they also have limitations, pointing to challenges that need to be addressed in the future.
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45
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Blank HM, Maitra N, Polymenis M. Lipid biosynthesis: When the cell cycle meets protein synthesis? Cell Cycle 2017; 16:905-906. [PMID: 28418768 DOI: 10.1080/15384101.2017.1312851] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022] Open
Affiliation(s)
- Heidi M Blank
- a Department of Biochemistry and Biophysics , Texas A&M University , College Station , TX , USA
| | - Nairita Maitra
- a Department of Biochemistry and Biophysics , Texas A&M University , College Station , TX , USA
| | - Michael Polymenis
- a Department of Biochemistry and Biophysics , Texas A&M University , College Station , TX , USA
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46
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Blank HM, Perez R, He C, Maitra N, Metz R, Hill J, Lin Y, Johnson CD, Bankaitis VA, Kennedy BK, Aramayo R, Polymenis M. Translational control of lipogenic enzymes in the cell cycle of synchronous, growing yeast cells. EMBO J 2017; 36:487-502. [PMID: 28057705 PMCID: PMC5694946 DOI: 10.15252/embj.201695050] [Citation(s) in RCA: 43] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2016] [Revised: 11/09/2016] [Accepted: 11/18/2016] [Indexed: 02/04/2023] Open
Abstract
Translational control during cell division determines when cells start a new cell cycle, how fast they complete it, the number of successive divisions, and how cells coordinate proliferation with available nutrients. The translational efficiencies of mRNAs in cells progressing synchronously through the mitotic cell cycle, while preserving the coupling of cell division with cell growth, remain uninvestigated. We now report comprehensive ribosome profiling of a yeast cell size series from the time of cell birth, to identify mRNAs under periodic translational control. The data reveal coordinate translational activation of mRNAs encoding lipogenic enzymes late in the cell cycle including Acc1p, the rate-limiting enzyme acetyl-CoA carboxylase. An upstream open reading frame (uORF) confers the translational control of ACC1 and adjusts Acc1p protein levels in different nutrients. The ACC1 uORF is relevant for cell division because its ablation delays cell cycle progression, reduces cell size, and suppresses the replicative longevity of cells lacking the Sch9p protein kinase regulator of ribosome biogenesis. These findings establish an unexpected relationship between lipogenesis and protein synthesis in mitotic cell divisions.
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Affiliation(s)
- Heidi M Blank
- Department of Biochemistry and Biophysics, Texas A&M University, College Station, TX, USA
| | - Ricardo Perez
- Department of Biology, Texas A&M University, College Station, TX, USA
| | - Chong He
- The Buck Institute for Research on Aging, Novato, CA, USA
| | - Nairita Maitra
- Department of Biochemistry and Biophysics, Texas A&M University, College Station, TX, USA
| | - Richard Metz
- Genomics and Bioinformatics Services, Texas A&M Agrilife Research, College Station, TX, USA
| | - Joshua Hill
- Genomics and Bioinformatics Services, Texas A&M Agrilife Research, College Station, TX, USA
| | - Yuhong Lin
- Department of Biochemistry and Biophysics, Texas A&M University, College Station, TX, USA
| | - Charles D Johnson
- Genomics and Bioinformatics Services, Texas A&M Agrilife Research, College Station, TX, USA
| | - Vytas A Bankaitis
- Department of Biochemistry and Biophysics, Texas A&M University, College Station, TX, USA
- Department of Molecular & Cellular Medicine, Texas A&M Health Sciences Center, College Station, TX, USA
- Department of Chemistry, Texas A&M University, College Station, TX, USA
| | | | - Rodolfo Aramayo
- Department of Biology, Texas A&M University, College Station, TX, USA
| | - Michael Polymenis
- Department of Biochemistry and Biophysics, Texas A&M University, College Station, TX, USA
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