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Wang L, Li X, Shi J, Li LM. A four eigen-phase model of multi-omics unveils new insights into yeast metabolic cycle. NAR Genom Bioinform 2025; 7:lqaf022. [PMID: 40109351 PMCID: PMC11920873 DOI: 10.1093/nargab/lqaf022] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2024] [Revised: 01/17/2025] [Accepted: 02/24/2025] [Indexed: 03/22/2025] Open
Abstract
The yeast metabolic cycle (YMC), characterized by cyclic oscillations in transcripts and metabolites, is an ideal model for studying biological rhythms. Although multiple omics datasets on the YMC are available, a unified landscape for this process is missing. To address this gap, we integrated multi-omics datasets by singular value decompositions (SVDs), which stratify each dataset into two levels and define four eigen-phases: primary 1A/1B and secondary 2A/2B. The eigen-phases occur cyclically in the order 1B, 2A, 1A, and 2B, demonstrating an interplay of induction and repression: one eigen-phase induces the next one at a different level, while represses the other one at the same level. Distinct molecular characteristics were identified for each eigen-phase. Novel ones include the production and consumption of glycerol in eigen-phases 2A/2B, and the opposite regulation of ribosome biogenesis and aerobic respiration between 2A/2B. Moreover, we estimated the timing of multi-omics: histone modifications H3K9ac/H3K18ac precede mRNA transcription in ∼3 min, followed by metabolomic changes in ∼13 min. The transition to the next eigen-phase occurs roughly 38 min later. From epigenome H3K9ac/H3K18ac to metabolome, the eigen-entropy increases. This work provides a computational framework applicable to multi-omics data integration.
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Affiliation(s)
- Linting Wang
- State Key Laboratory of Mathematical Science, Academy of Mathematics and Systems Science, Chinese Academy of Sciences, Beijing, 100190, China
- School of Mathematical Sciences, University of the Chinese Academy of Sciences, Beijing, 101408, China
| | - Xiaojie Li
- State Key Laboratory of Mathematical Science, Academy of Mathematics and Systems Science, Chinese Academy of Sciences, Beijing, 100190, China
- School of Mathematical Sciences, University of the Chinese Academy of Sciences, Beijing, 101408, China
| | - Jianhui Shi
- State Key Laboratory of Mathematical Science, Academy of Mathematics and Systems Science, Chinese Academy of Sciences, Beijing, 100190, China
- School of Mathematical Sciences, University of the Chinese Academy of Sciences, Beijing, 101408, China
| | - Lei M Li
- State Key Laboratory of Mathematical Science, Academy of Mathematics and Systems Science, Chinese Academy of Sciences, Beijing, 100190, China
- School of Mathematical Sciences, University of the Chinese Academy of Sciences, Beijing, 101408, China
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2
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Kozubowski L, Berman J. The impact of phenotypic heterogeneity on fungal pathogenicity and drug resistance. FEMS Microbiol Rev 2025; 49:fuaf001. [PMID: 39809571 PMCID: PMC11756289 DOI: 10.1093/femsre/fuaf001] [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: 11/16/2023] [Revised: 11/26/2024] [Accepted: 01/13/2025] [Indexed: 01/16/2025] Open
Abstract
Phenotypic heterogeneity in genetically clonal populations facilitates cellular adaptation to adverse environmental conditions while enabling a return to the basal physiological state. It also plays a crucial role in pathogenicity and the acquisition of drug resistance in unicellular organisms and cancer cells, yet the exact contributing factors remain elusive. In this review, we outline the current state of understanding concerning the contribution of phenotypic heterogeneity to fungal pathogenesis and antifungal drug resistance.
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Affiliation(s)
- Lukasz Kozubowski
- Eukaryotic Pathogens Innovation Center, Department of Genetics and Biochemistry, Clemson University, Clemson, SC, 29634, USA
| | - Judith Berman
- Shmunis School of Biomedical and Cancer Research, The George S. Wise Faculty of Life Sciences, Tel Aviv University, Tel Aviv, 69978, Israel
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3
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Vidal PJ, Pérez AP, Yahya G, Aldea M. Transcriptomic balance and optimal growth are determined by cell size. Mol Cell 2024; 84:3288-3301.e3. [PMID: 39084218 DOI: 10.1016/j.molcel.2024.07.005] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2024] [Revised: 06/11/2024] [Accepted: 07/08/2024] [Indexed: 08/02/2024]
Abstract
Cell size and growth are intimately related across the evolutionary scale, but whether cell size is important to attain maximal growth or fitness is still an open question. We show that growth rate is a non-monotonic function of cell volume, with maximal values around the critical size of wild-type yeast cells. The transcriptome of yeast and mouse cells undergoes a relative inversion in response to cell size, which we associate theoretically and experimentally with the necessary genome-wide diversity in RNA polymerase II affinity for promoters. Although highly expressed genes impose strong negative effects on fitness when the DNA/mass ratio is reduced, transcriptomic alterations mimicking the relative inversion by cell size strongly restrain cell growth. In all, our data indicate that cells set the critical size to obtain a properly balanced transcriptome and, as a result, maximize growth and fitness during proliferation.
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Affiliation(s)
- Pedro J Vidal
- Molecular Biology Institute of Barcelona (IBMB), CSIC, 08028 Barcelona, Catalonia, Spain
| | - Alexis P Pérez
- Molecular Biology Institute of Barcelona (IBMB), CSIC, 08028 Barcelona, Catalonia, Spain; Department of Basic Sciences, Universitat Internacional de Catalunya, 08195 Sant Cugat del Vallès, Barcelona, Spain
| | - Galal Yahya
- Molecular Biology Institute of Barcelona (IBMB), CSIC, 08028 Barcelona, Catalonia, Spain; Department of Microbiology and Immunology, School of Pharmacy, Zagazig University, 44511 Zagazig, Egypt.
| | - Martí Aldea
- Molecular Biology Institute of Barcelona (IBMB), CSIC, 08028 Barcelona, Catalonia, Spain; Department of Basic Sciences, Universitat Internacional de Catalunya, 08195 Sant Cugat del Vallès, Barcelona, Spain.
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4
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Siebieszuk A, Sejbuk M, Witkowska AM. Studying the Human Microbiota: Advances in Understanding the Fundamentals, Origin, and Evolution of Biological Timekeeping. Int J Mol Sci 2023; 24:16169. [PMID: 38003359 PMCID: PMC10671191 DOI: 10.3390/ijms242216169] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2023] [Revised: 11/07/2023] [Accepted: 11/08/2023] [Indexed: 11/26/2023] Open
Abstract
The recently observed circadian oscillations of the intestinal microbiota underscore the profound nature of the human-microbiome relationship and its importance for health. Together with the discovery of circadian clocks in non-photosynthetic gut bacteria and circadian rhythms in anucleated cells, these findings have indicated the possibility that virtually all microorganisms may possess functional biological clocks. However, they have also raised many essential questions concerning the fundamentals of biological timekeeping, its evolution, and its origin. This narrative review provides a comprehensive overview of the recent literature in molecular chronobiology, aiming to bring together the latest evidence on the structure and mechanisms driving microbial biological clocks while pointing to potential applications of this knowledge in medicine. Moreover, it discusses the latest hypotheses regarding the evolution of timing mechanisms and describes the functions of peroxiredoxins in cells and their contribution to the cellular clockwork. The diversity of biological clocks among various human-associated microorganisms and the role of transcriptional and post-translational timekeeping mechanisms are also addressed. Finally, recent evidence on metabolic oscillators and host-microbiome communication is presented.
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Affiliation(s)
- Adam Siebieszuk
- Department of Physiology, Faculty of Medicine, Medical University of Bialystok, Mickiewicza 2C, 15-222 Białystok, Poland;
| | - Monika Sejbuk
- Department of Food Biotechnology, Faculty of Health Sciences, Medical University of Bialystok, Szpitalna 37, 15-295 Białystok, Poland;
| | - Anna Maria Witkowska
- Department of Food Biotechnology, Faculty of Health Sciences, Medical University of Bialystok, Szpitalna 37, 15-295 Białystok, Poland;
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5
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Piper-Brown E, Dresel F, Badr E, Gourlay CW. Elevated Levels of Mislocalised, Constitutive Ras Signalling Can Drive Quiescence by Uncoupling Cell-Cycle Regulation from Metabolic Homeostasis. Biomolecules 2023; 13:1619. [PMID: 38002301 PMCID: PMC10669370 DOI: 10.3390/biom13111619] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2023] [Revised: 10/28/2023] [Accepted: 10/30/2023] [Indexed: 11/26/2023] Open
Abstract
The small GTPase Ras plays an important role in connecting external and internal signalling cues to cell fate in eukaryotic cells. As such, the loss of RAS regulation, localisation, or expression level can drive changes in cell behaviour and fate. Post-translational modifications and expression levels are crucial to ensure Ras localisation, regulation, function, and cell fate, exemplified by RAS mutations and gene duplications that are common in many cancers. Here, we reveal that excessive production of yeast Ras2, in which the phosphorylation-regulated serine at position 225 is replaced with alanine or glutamate, leads to its mislocalisation and constitutive activation. Rather than inducing cell death, as has been widely reported to be a consequence of constitutive Ras2 signalling in yeast, the overexpression of RAS2S225A or RAS2S225E alleles leads to slow growth, a loss of respiration, reduced stress response, and a state of quiescence. These effects are mediated via cAMP/PKA signalling and transcriptional changes, suggesting that quiescence is promoted by an uncoupling of cell-cycle regulation from metabolic homeostasis. The quiescent cell fate induced by the overexpression of RAS2S225A or RAS2S225E could be rescued by the deletion of CUP9, a suppressor of the dipeptide transporter Ptr2, or the addition of peptone, implying that a loss of metabolic control, or a failure to pass a metabolic checkpoint, is central to this altered cell fate. Our data suggest that the combination of an increased RAS2 copy number and a dominant active mutation that leads to its mislocalisation can result in growth arrest and add weight to the possibility that approaches to retarget RAS signalling could be employed to develop new therapies.
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Affiliation(s)
| | | | | | - Campbell W. Gourlay
- Kent Fungal Group, School of Biosciences, University of Kent, Canterbury CT2 7NZ, UK
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Attfield PV. Crucial aspects of metabolism and cell biology relating to industrial production and processing of Saccharomyces biomass. Crit Rev Biotechnol 2023; 43:920-937. [PMID: 35731243 DOI: 10.1080/07388551.2022.2072268] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2021] [Revised: 02/27/2022] [Accepted: 04/21/2022] [Indexed: 12/16/2022]
Abstract
The multitude of applications to which Saccharomyces spp. are put makes these yeasts the most prolific of industrial microorganisms. This review considers biological aspects pertaining to the manufacture of industrial yeast biomass. It is proposed that the production of yeast biomass can be considered in two distinct but interdependent phases. Firstly, there is a cell replication phase that involves reproduction of cells by their transitions through multiple budding and metabolic cycles. Secondly, there needs to be a cell conditioning phase that enables the accrued biomass to withstand the physicochemical challenges associated with downstream processing and storage. The production of yeast biomass is not simply a case of providing sugar, nutrients, and other growth conditions to enable multiple budding cycles to occur. In the latter stages of culturing, it is important that all cells are induced to complete their current budding cycle and subsequently enter into a quiescent state engendering robustness. Both the cell replication and conditioning phases need to be optimized and considered in concert to ensure good biomass production economics, and optimum performance of industrial yeasts in food and fermentation applications. Key features of metabolism and cell biology affecting replication and conditioning of industrial Saccharomyces are presented. Alternatives for growth substrates are discussed, along with the challenges and prospects associated with defining the genetic bases of industrially important phenotypes, and the generation of new yeast strains."I must be cruel only to be kind: Thus bad begins, and worse remains behind." William Shakespeare: Hamlet, Act 3, Scene 4.
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Soultanas P, Janniere L. The metabolic control of DNA replication: mechanism and function. Open Biol 2023; 13:230220. [PMID: 37582405 PMCID: PMC10427196 DOI: 10.1098/rsob.230220] [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: 07/11/2023] [Accepted: 07/26/2023] [Indexed: 08/17/2023] Open
Abstract
Metabolism and DNA replication are the two most fundamental biological functions in life. The catabolic branch of metabolism breaks down nutrients to produce energy and precursors used by the anabolic branch of metabolism to synthesize macromolecules. DNA replication consumes energy and precursors for faithfully copying genomes, propagating the genetic material from generation to generation. We have exquisite understanding of the mechanisms that underpin and regulate these two biological functions. However, the molecular mechanism coordinating replication to metabolism and its biological function remains mostly unknown. Understanding how and why living organisms respond to fluctuating nutritional stimuli through cell-cycle dynamic changes and reproducibly and distinctly temporalize DNA synthesis in a wide-range of growth conditions is important, with wider implications across all domains of life. After summarizing the seminal studies that founded the concept of the metabolic control of replication, we review data linking metabolism to replication from bacteria to humans. Molecular insights underpinning these links are then presented to propose that the metabolic control of replication uses signalling systems gearing metabolome homeostasis to orchestrate replication temporalization. The remarkable replication phenotypes found in mutants of this control highlight its importance in replication regulation and potentially genetic stability and tumorigenesis.
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Affiliation(s)
- Panos Soultanas
- Biodiscovery Institute, School of Chemistry, University of Nottingham, University Park, Nottingham NG7 2RD, UK
| | - Laurent Janniere
- Génomique Métabolique, Genoscope, Institut François Jacob, CEA, CNRS, Université Evry, Université Paris-Saclay, 91057 Evry, France
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8
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Rödl S, den Brave F, Räschle M, Kizmaz B, Lenhard S, Groh C, Becker H, Zimmermann J, Morgan B, Richling E, Becker T, Herrmann JM. The metabolite-controlled ubiquitin conjugase Ubc8 promotes mitochondrial protein import. Life Sci Alliance 2022; 6:6/1/e202201526. [PMID: 36253107 PMCID: PMC9579816 DOI: 10.26508/lsa.202201526] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2022] [Revised: 09/30/2022] [Accepted: 09/30/2022] [Indexed: 11/26/2022] Open
Abstract
Mitochondria play a key role in cellular energy metabolism. Transitions between glycolytic and respiratory conditions induce considerable adaptations of the cellular proteome. These metabolism-dependent changes are particularly pronounced for the protein composition of mitochondria. Here, we show that the yeast cytosolic ubiquitin conjugase Ubc8 plays a crucial role in the remodeling process when cells transition from respiratory to fermentative conditions. Ubc8 is a conserved and well-studied component of the catabolite control system that is known to regulate the stability of gluconeogenic enzymes. Unexpectedly, we found that Ubc8 also promotes the assembly of the translocase of the outer membrane of mitochondria (TOM) and increases the levels of its cytosol-exposed receptor subunit Tom22. Ubc8 deficiency results in compromised protein import into mitochondria and reduced steady-state levels of mitochondrial proteins. Our observations show that Ubc8, which is controlled by the prevailing metabolic conditions, promotes the switch from glucose synthesis to glucose usage in the cytosol and induces the biogenesis of the mitochondrial TOM machinery to improve mitochondrial protein import during phases of metabolic transition.
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Affiliation(s)
- Saskia Rödl
- Cell Biology, University of Kaiserslautern, Kaiserslautern, Germany
| | - Fabian den Brave
- Institute of Biochemistry and Molecular Biology, Faculty of Medicine, University of Bonn, Bonn, Germany
| | - Markus Räschle
- Molecular Genetics, University of Kaiserslautern, Kaiserslautern, Germany
| | - Büsra Kizmaz
- Cell Biology, University of Kaiserslautern, Kaiserslautern, Germany
| | - Svenja Lenhard
- Cell Biology, University of Kaiserslautern, Kaiserslautern, Germany
| | - Carina Groh
- Cell Biology, University of Kaiserslautern, Kaiserslautern, Germany
| | - Hanna Becker
- Food Chemistry, University of Kaiserslautern, Kaiserslautern, Germany
| | - Jannik Zimmermann
- Biochemistry, Center for Human and Molecular Biology (ZHMB), Saarland University, Saarbrücken, Germany
| | - Bruce Morgan
- Biochemistry, Center for Human and Molecular Biology (ZHMB), Saarland University, Saarbrücken, Germany
| | - Elke Richling
- Food Chemistry, University of Kaiserslautern, Kaiserslautern, Germany
| | - Thomas Becker
- Institute of Biochemistry and Molecular Biology, Faculty of Medicine, University of Bonn, Bonn, Germany
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Lin WH, Jacobs-Wagner C. Connecting single-cell ATP dynamics to overflow metabolism, cell growth, and the cell cycle in Escherichia coli. Curr Biol 2022; 32:3911-3924.e4. [PMID: 35961315 DOI: 10.1016/j.cub.2022.07.035] [Citation(s) in RCA: 33] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2022] [Revised: 06/21/2022] [Accepted: 07/14/2022] [Indexed: 10/15/2022]
Abstract
Adenosine triphosphate (ATP) is an abundant and essential metabolite that cells consume and regenerate in large amounts to support growth. Although numerous studies have inferred the intracellular concentration of ATP in bacterial cultures, what happens in individual bacterial cells under stable growth conditions is less clear. Here, we use the QUEEN-2m biosensor to quantify ATP dynamics in single Escherichia coli cells in relation to their growth rate, metabolism, cell cycle, and cell lineage. We find that ATP dynamics are more complex than expected from population studies and are associated with growth-rate variability. Under stable nutrient-rich condition, cells can display large fluctuations in ATP level that are partially coordinated with the cell cycle. Abrogation of aerobic acetate fermentation (overflow metabolism) through genetic deletion considerably reduces both the amplitude of ATP level fluctuations and the cell-cycle trend. Similarly, growth in media in which acetate fermentation is lower or absent results in the reduction of ATP level fluctuation and cell-cycle trend. This suggests that overflow metabolism exhibits temporal dynamics, which contributes to fluctuating ATP levels during growth. Remarkably, at the single-cell level, growth rate negatively correlates with the amplitude of ATP fluctuation for each tested condition, linking ATP dynamics to growth-rate heterogeneity in clonal populations. Our work highlights the importance of single-cell analysis in studying metabolism and its implication to phenotypic diversity and cell growth.
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Affiliation(s)
- Wei-Hsiang Lin
- Department of Biology, Stanford University, Palo Alto, CA 94305, USA; Chemistry, Engineering, Medicine for Human Health Institute, Stanford University, Palo Alto, CA 94305, USA; Howard Hughes Medical Institute, Stanford University, Palo Alto, CA 94305, USA
| | - Christine Jacobs-Wagner
- Department of Biology, Stanford University, Palo Alto, CA 94305, USA; Chemistry, Engineering, Medicine for Human Health Institute, Stanford University, Palo Alto, CA 94305, USA; Howard Hughes Medical Institute, Stanford University, Palo Alto, CA 94305, USA.
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Computational method for untargeted determination of cycling yeast metabolites using comprehensive two-dimensional gas chromatography time-of-flight mass spectrometry. Talanta 2022; 244:123396. [DOI: 10.1016/j.talanta.2022.123396] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2022] [Revised: 03/14/2022] [Accepted: 03/16/2022] [Indexed: 11/23/2022]
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Genome-Wide Analysis of Yeast Metabolic Cycle through Metabolic Network Models Reveals Superiority of Integrated ATAC-seq Data over RNA-seq Data. mSystems 2022; 7:e0134721. [PMID: 35695574 PMCID: PMC9239220 DOI: 10.1128/msystems.01347-21] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Saccharomyces cerevisiae undergoes robust oscillations to regulate its physiology for adaptation and survival under nutrient-limited conditions. Environmental cues can induce rhythmic metabolic alterations in order to facilitate the coordination of dynamic metabolic behaviors. Of such metabolic processes, the yeast metabolic cycle enables adaptation of the cells to varying nutritional status through oscillations in gene expression and metabolite production levels. In this process, yeast metabolism is altered between diverse cellular states based on changing oxygen consumption levels: quiescent (reductive charging [RC]), growth (oxidative [OX]), and proliferation (reductive building [RB]) phases. We characterized metabolic alterations during the yeast metabolic cycle using a variety of approaches. Gene expression levels are widely used for condition-specific metabolic simulations, whereas the use of epigenetic information in metabolic modeling is still limited despite the clear relationship between epigenetics and metabolism. This prompted us to investigate the contribution of epigenomic information to metabolic predictions for progression of the yeast metabolic cycle. In this regard, we determined altered pathways through the prediction of regulated reactions and corresponding model genes relying on differential chromatin accessibility levels. The predicted metabolic alterations were confirmed via data analysis and literature. We subsequently utilized RNA sequencing (RNA-seq) and assay for transposase-accessible chromatin using sequencing (ATAC-seq) data sets in the contextualization of the yeast model. The use of ATAC-seq data considerably enhanced the predictive capability of the model. To the best of our knowledge, this is the first attempt to use genome-wide chromatin accessibility data in metabolic modeling. The preliminary results showed that epigenomic data sets can pave the way for more accurate metabolic simulations. IMPORTANCE Dynamic chromatin organization mediates the emergence of condition-specific phenotypes in eukaryotic organisms. Saccharomyces cerevisiae can alter its metabolic profile via regulation of genome accessibility and robust transcriptional oscillations under nutrient-limited conditions. Thus, both epigenetic information and transcriptomic information are crucial in the understanding of condition-specific metabolic behavior in this organism. Based on genome-wide alterations in chromatin accessibility and transcription, we investigated the yeast metabolic cycle, which is a remarkable example of coordinated and dynamic yeast behavior. In this regard, we assessed the use of ATAC-seq and RNA-seq data sets in condition-specific metabolic modeling. To our knowledge, this is the first attempt to use chromatin accessibility data in the reconstruction of context-specific metabolic models, despite the extensive use of transcriptomic data. As a result of comparative analyses, we propose that the incorporation of epigenetic information is a promising approach in the accurate prediction of metabolic dynamics.
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Horemans S, Pitoulias M, Holland A, Pateau E, Lechaplais C, Ekaterina D, Perret A, Soultanas P, Janniere L. Pyruvate kinase, a metabolic sensor powering glycolysis, drives the metabolic control of DNA replication. BMC Biol 2022; 20:87. [PMID: 35418203 PMCID: PMC9009071 DOI: 10.1186/s12915-022-01278-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2021] [Accepted: 03/11/2022] [Indexed: 12/04/2022] Open
Abstract
Background In all living organisms, DNA replication is exquisitely regulated in a wide range of growth conditions to achieve timely and accurate genome duplication prior to cell division. Failures in this regulation cause DNA damage with potentially disastrous consequences for cell viability and human health, including cancer. To cope with these threats, cells tightly control replication initiation using well-known mechanisms. They also couple DNA synthesis to nutrient richness and growth rate through a poorly understood process thought to involve central carbon metabolism. One such process may involve the cross-species conserved pyruvate kinase (PykA) which catalyzes the last reaction of glycolysis. Here we have investigated the role of PykA in regulating DNA replication in the model system Bacillus subtilis. Results On analysing mutants of the catalytic (Cat) and C-terminal (PEPut) domains of B. subtilis PykA we found replication phenotypes in conditions where PykA is dispensable for growth. These phenotypes are independent from the effect of mutations on PykA catalytic activity and are not associated with significant changes in the metabolome. PEPut operates as a nutrient-dependent inhibitor of initiation while Cat acts as a stimulator of replication fork speed. Disruption of either PEPut or Cat replication function dramatically impacted the cell cycle and replication timing even in cells fully proficient in known replication control functions. In vitro, PykA modulates activities of enzymes essential for replication initiation and elongation via functional interactions. Additional experiments showed that PEPut regulates PykA activity and that Cat and PEPut determinants important for PykA catalytic activity regulation are also important for PykA-driven replication functions. Conclusions We infer from our findings that PykA typifies a new family of cross-species replication control regulators that drive the metabolic control of replication through a mechanism involving regulatory determinants of PykA catalytic activity. As disruption of PykA replication functions causes dramatic replication defects, we suggest that dysfunctions in this new family of universal replication regulators may pave the path to genetic instability and carcinogenesis. Supplementary Information The online version contains supplementary material available at 10.1186/s12915-022-01278-3.
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Affiliation(s)
- Steff Horemans
- Génomique Métabolique, Genoscope, Institut François Jacob, CEA, CNRS, Université Evry, Université Paris-Saclay, 91057, Evry, France
| | - Matthaios Pitoulias
- Biodiscovery Institute, School of Chemistry, University of Nottingham, University Park, Nottingham, NG7 2RD, UK
| | - Alexandria Holland
- Biodiscovery Institute, School of Chemistry, University of Nottingham, University Park, Nottingham, NG7 2RD, UK
| | - Emilie Pateau
- Génomique Métabolique, Genoscope, Institut François Jacob, CEA, CNRS, Université Evry, Université Paris-Saclay, 91057, Evry, France
| | - Christophe Lechaplais
- Génomique Métabolique, Genoscope, Institut François Jacob, CEA, CNRS, Université Evry, Université Paris-Saclay, 91057, Evry, France
| | - Dariy Ekaterina
- Génomique Métabolique, Genoscope, Institut François Jacob, CEA, CNRS, Université Evry, Université Paris-Saclay, 91057, Evry, France
| | - Alain Perret
- Génomique Métabolique, Genoscope, Institut François Jacob, CEA, CNRS, Université Evry, Université Paris-Saclay, 91057, Evry, France
| | - Panos Soultanas
- Biodiscovery Institute, School of Chemistry, University of Nottingham, University Park, Nottingham, NG7 2RD, UK.
| | - Laurent Janniere
- Génomique Métabolique, Genoscope, Institut François Jacob, CEA, CNRS, Université Evry, Université Paris-Saclay, 91057, Evry, France.
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14
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Peroxiredoxins couple metabolism and cell division in an ultradian cycle. Nat Chem Biol 2021; 17:477-484. [PMID: 33574615 DOI: 10.1038/s41589-020-00728-9] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2019] [Accepted: 12/22/2020] [Indexed: 01/30/2023]
Abstract
Redox cycles have been reported in ultradian, circadian and cell cycle-synchronized systems. Redox cycles persist in the absence of transcription and cyclin-CDK activity, indicating that cells harbor multiple coupled oscillators. Nonetheless, the causal relationships and molecular mechanisms by which redox cycles are embedded within ultradian, circadian or cell division cycles remain largely elusive. Yeast harbor an ultradian oscillator, the yeast metabolic cycle (YMC), which comprises metabolic/redox cycles, transcriptional cycles and synchronized cell division. Here, we reveal the existence of robust cycling of H2O2 and peroxiredoxin oxidation during the YMC and show that peroxiredoxin inactivation disrupts metabolic cycling and abolishes coupling with cell division. We find that thiol-disulfide oxidants and reductants predictably modulate the switching between different YMC metabolic states, which in turn predictably perturbs cell cycle entry and exit. We propose that oscillatory H2O2-dependent protein thiol oxidation is a key regulator of metabolic cycling and its coordination with cell division.
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15
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O' Neill JS, Hoyle NP, Robertson JB, Edgar RS, Beale AD, Peak-Chew SY, Day J, Costa ASH, Frezza C, Causton HC. Eukaryotic cell biology is temporally coordinated to support the energetic demands of protein homeostasis. Nat Commun 2020; 11:4706. [PMID: 32943618 PMCID: PMC7499178 DOI: 10.1038/s41467-020-18330-x] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2020] [Accepted: 08/13/2020] [Indexed: 12/17/2022] Open
Abstract
Yeast physiology is temporally regulated, this becomes apparent under nutrient-limited conditions and results in respiratory oscillations (YROs). YROs share features with circadian rhythms and interact with, but are independent of, the cell division cycle. Here, we show that YROs minimise energy expenditure by restricting protein synthesis until sufficient resources are stored, while maintaining osmotic homeostasis and protein quality control. Although nutrient supply is constant, cells sequester and store metabolic resources via increased transport, autophagy and biomolecular condensation. Replete stores trigger increased H+ export which stimulates TORC1 and liberates proteasomes, ribosomes, chaperones and metabolic enzymes from non-membrane bound compartments. This facilitates translational bursting, liquidation of storage carbohydrates, increased ATP turnover, and the export of osmolytes. We propose that dynamic regulation of ion transport and metabolic plasticity are required to maintain osmotic and protein homeostasis during remodelling of eukaryotic proteomes, and that bioenergetic constraints selected for temporal organisation that promotes oscillatory behaviour.
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Affiliation(s)
- John S O' Neill
- MRC Laboratory of Molecular Biology, Cambridge, CB2 0QH, UK.
| | | | | | - Rachel S Edgar
- Molecular Virology, Department of Medicine, Imperial College, London, W2 1NY, UK
| | - Andrew D Beale
- MRC Laboratory of Molecular Biology, Cambridge, CB2 0QH, UK
| | | | - Jason Day
- Department of Earth Sciences, University of Cambridge, Cambridge, CB2 3EQ, UK
| | - Ana S H Costa
- MRC Cancer Unit, University of Cambridge, Cambridge, CB2 0XZ, UK.,Cold Spring Harbor Laboratory, Cold Spring Harbor, NY, 11724, USA
| | - Christian Frezza
- MRC Cancer Unit, University of Cambridge, Cambridge, CB2 0XZ, UK
| | - Helen C Causton
- Columbia University Medical Center, New York, NY, 10032, USA.
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16
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Varahan S, Sinha V, Walvekar A, Krishna S, Laxman S. Resource plasticity-driven carbon-nitrogen budgeting enables specialization and division of labor in a clonal community. eLife 2020; 9:e57609. [PMID: 32876564 PMCID: PMC7467726 DOI: 10.7554/elife.57609] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2020] [Accepted: 07/31/2020] [Indexed: 11/13/2022] Open
Abstract
Previously, we found that in glucose-limited Saccharomyces cerevisiae colonies, metabolic constraints drive cells into groups exhibiting gluconeogenic or glycolytic states. In that study, threshold amounts of trehalose - a limiting, produced carbon-resource, controls the emergence and self-organization of cells exhibiting the glycolytic state, serving as a carbon source that fuels glycolysis (Varahan et al., 2019). We now discover that the plasticity of use of a non-limiting resource, aspartate, controls both resource production and the emergence of heterogeneous cell states, based on differential metabolic budgeting. In gluconeogenic cells, aspartate is a carbon source for trehalose production, while in glycolytic cells using trehalose for carbon, aspartate is predominantly a nitrogen source for nucleotide synthesis. This metabolic plasticity of aspartate enables carbon-nitrogen budgeting, thereby driving the biochemical self-organization of distinct cell states. Through this organization, cells in each state exhibit true division of labor, providing growth/survival advantages for the whole community.
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Affiliation(s)
- Sriram Varahan
- InStem - Institute for Stem Cell Science and Regenerative MedicineBangaloreIndia
| | - Vaibhhav Sinha
- Simons Centre for the Study of Living Machines, National Center for Biological Sciences, Tata Institute for Fundamental ResearchBangaloreIndia
- Manipal Academy of Higher EducationManipalIndia
| | - Adhish Walvekar
- InStem - Institute for Stem Cell Science and Regenerative MedicineBangaloreIndia
| | - Sandeep Krishna
- Simons Centre for the Study of Living Machines, National Center for Biological Sciences, Tata Institute for Fundamental ResearchBangaloreIndia
| | - Sunil Laxman
- InStem - Institute for Stem Cell Science and Regenerative MedicineBangaloreIndia
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17
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Wright NR, Wulff T, Palmqvist EA, Jørgensen TR, Workman CT, Sonnenschein N, Rønnest NP, Herrgård MJ. Fluctuations in glucose availability prevent global proteome changes and physiological transition during prolonged chemostat cultivations of
Saccharomyces cerevisiae. Biotechnol Bioeng 2020; 117:2074-2088. [DOI: 10.1002/bit.27353] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2020] [Accepted: 04/09/2020] [Indexed: 11/06/2022]
Affiliation(s)
- Naia R. Wright
- Novo Nordisk A/S Bagsværd Denmark
- The Novo Nordisk Foundation Center for BiosustainabilityTechnical University of Denmark Lyngby Denmark
- Department of Biotechnology and BiomedicineTechnical University of Denmark Lyngby Denmark
| | - Tune Wulff
- The Novo Nordisk Foundation Center for BiosustainabilityTechnical University of Denmark Lyngby Denmark
| | | | - Thomas R. Jørgensen
- The Novo Nordisk Foundation Center for BiosustainabilityTechnical University of Denmark Lyngby Denmark
| | - Christopher T. Workman
- Department of Biotechnology and BiomedicineTechnical University of Denmark Lyngby Denmark
| | - Nikolaus Sonnenschein
- The Novo Nordisk Foundation Center for BiosustainabilityTechnical University of Denmark Lyngby Denmark
- Department of Biotechnology and BiomedicineTechnical University of Denmark Lyngby Denmark
| | | | - Markus J. Herrgård
- The Novo Nordisk Foundation Center for BiosustainabilityTechnical University of Denmark Lyngby Denmark
- BioInnovation Institute København N Denmark
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18
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Jackson CA, Castro DM, Saldi GA, Bonneau R, Gresham D. Gene regulatory network reconstruction using single-cell RNA sequencing of barcoded genotypes in diverse environments. eLife 2020; 9:e51254. [PMID: 31985403 PMCID: PMC7004572 DOI: 10.7554/elife.51254] [Citation(s) in RCA: 98] [Impact Index Per Article: 19.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2019] [Accepted: 01/10/2020] [Indexed: 11/13/2022] Open
Abstract
Understanding how gene expression programs are controlled requires identifying regulatory relationships between transcription factors and target genes. Gene regulatory networks are typically constructed from gene expression data acquired following genetic perturbation or environmental stimulus. Single-cell RNA sequencing (scRNAseq) captures the gene expression state of thousands of individual cells in a single experiment, offering advantages in combinatorial experimental design, large numbers of independent measurements, and accessing the interaction between the cell cycle and environmental responses that is hidden by population-level analysis of gene expression. To leverage these advantages, we developed a method for scRNAseq in budding yeast (Saccharomyces cerevisiae). We pooled diverse transcriptionally barcoded gene deletion mutants in 11 different environmental conditions and determined their expression state by sequencing 38,285 individual cells. We benchmarked a framework for learning gene regulatory networks from scRNAseq data that incorporates multitask learning and constructed a global gene regulatory network comprising 12,228 interactions.
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Affiliation(s)
- Christopher A Jackson
- Center For Genomics and Systems BiologyNew York UniversityNew YorkUnited States
- Department of BiologyNew York UniversityNew YorkUnited States
| | | | | | - Richard Bonneau
- Center For Genomics and Systems BiologyNew York UniversityNew YorkUnited States
- Department of BiologyNew York UniversityNew YorkUnited States
- Courant Institute of Mathematical Sciences, Computer Science DepartmentNew York UniversityNew YorkUnited States
- Center For Data ScienceNew York UniversityNew YorkUnited States
- Flatiron Institute, Center for Computational BiologySimons FoundationNew YorkUnited States
| | - David Gresham
- Center For Genomics and Systems BiologyNew York UniversityNew YorkUnited States
- Department of BiologyNew York UniversityNew YorkUnited States
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19
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Xu X, Huang M, Ouyang Y, Iha H, Xu Z. PSK1 coordinates glucose metabolism and utilization and regulates energy-metabolism oscillation in Saccharomyces cerevisiae. Yeast 2020; 37:261-268. [PMID: 31899805 DOI: 10.1002/yea.3458] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2019] [Revised: 12/05/2019] [Accepted: 12/20/2019] [Indexed: 12/12/2022] Open
Abstract
Energy-metabolism oscillations (EMO) are ultradian biological rhythms observed in in aerobic chemostat cultures of Saccharomyces cerevisiae. EMO regulates energy metabolism such as glucose, carbohydrate storage, O2 uptake, and CO2 production. PSK1 is a nutrient responsive protein kinase involved in regulation of glucose metabolism, sensory response to light, oxygen, and redox state. The aim of this investigation was to assess the function of PSK1 in regulation of EMO. The mRNA levels of PSK1 fluctuated in concert with EMO, and deletion of PSK1 resulted in unstable EMO with disappearance of the fluctuations and reduced amplitude, compared with the wild type. Furthermore, the mutant PSK1Δ showed downregulation of the synthesis and breakdown of glycogen with resultant decrease in glucose concentrations. The redox state represented by NADH also decreased in PSK1Δ compared with the wild type. These data suggest that PSK1 plays an important role in the regulation of energy metabolism and stabilizes ultradian biological rhythms. These results enhance our understanding of the mechanisms of biorhythms in the budding yeast.
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Affiliation(s)
- Xianyan Xu
- Departments of Anatomy, Pediatrics and Environmental Medicine, Quanzhou Medical College, Quanzhou, Fujian, China
| | - Meixian Huang
- Departments of Anatomy, Pediatrics and Environmental Medicine, Quanzhou Medical College, Quanzhou, Fujian, China
| | - Yuhui Ouyang
- Department of Otolaryngology Head and Neck Surgery and Department of Allergy, Beijing TongRen Hospital, Affiliated with the Capital University of Medical Science, Beijing, China
| | - Hidekatsu Iha
- Department of Microbiology, Faculty of Medicine, Oita University, Oita, Japan
| | - Zhaojun Xu
- Departments of Anatomy, Pediatrics and Environmental Medicine, Quanzhou Medical College, Quanzhou, Fujian, China.,Second Department of Biochemistry, Interdisciplinary Graduate School of Medicine and Engineering, University of Yamanashi, Yamanashi, Japan
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20
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Litsios A, Huberts DHEW, Terpstra HM, Guerra P, Schmidt A, Buczak K, Papagiannakis A, Rovetta M, Hekelaar J, Hubmann G, Exterkate M, Milias-Argeitis A, Heinemann M. Differential scaling between G1 protein production and cell size dynamics promotes commitment to the cell division cycle in budding yeast. Nat Cell Biol 2019; 21:1382-1392. [PMID: 31685990 DOI: 10.1038/s41556-019-0413-3] [Citation(s) in RCA: 48] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2018] [Accepted: 09/25/2019] [Indexed: 12/28/2022]
Abstract
In the unicellular eukaryote Saccharomyces cerevisiae, Cln3-cyclin-dependent kinase activity enables Start, the irreversible commitment to the cell division cycle. However, the concentration of Cln3 has been paradoxically considered to remain constant during G1, due to the presumed scaling of its production rate with cell size dynamics. Measuring metabolic and biosynthetic activity during cell cycle progression in single cells, we found that cells exhibit pulses in their protein production rate. Rather than scaling with cell size dynamics, these pulses follow the intrinsic metabolic dynamics, peaking around Start. Using a viral-based bicistronic construct and targeted proteomics to measure Cln3 at the single-cell and population levels, we show that the differential scaling between protein production and cell size leads to a temporal increase in Cln3 concentration, and passage through Start. This differential scaling causes Start in both daughter and mother cells across growth conditions. Thus, uncoupling between two fundamental physiological parameters drives cell cycle commitment.
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Affiliation(s)
- Athanasios Litsios
- Molecular Systems Biology, Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, Groningen, the Netherlands
| | - Daphne H E W Huberts
- Molecular Systems Biology, Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, Groningen, the Netherlands
- Cancer Research UK Cambridge Institute, University of Cambridge, Cambridge, UK
| | - Hanna M Terpstra
- Molecular Systems Biology, Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, Groningen, the Netherlands
| | - Paolo Guerra
- Molecular Systems Biology, Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, Groningen, the Netherlands
| | - Alexander Schmidt
- Proteomics Core Facility, Biozentrum, University of Basel, Basel, Switzerland
| | - Katarzyna Buczak
- Proteomics Core Facility, Biozentrum, University of Basel, Basel, Switzerland
| | - Alexandros Papagiannakis
- Molecular Systems Biology, Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, Groningen, the Netherlands
| | - Mattia Rovetta
- Molecular Systems Biology, Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, Groningen, the Netherlands
| | - Johan Hekelaar
- Molecular Systems Biology, Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, Groningen, the Netherlands
| | - Georg Hubmann
- Molecular Systems Biology, Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, Groningen, the Netherlands
- Department of Biology, Laboratory of Molecular Cell Biology, Institute of Botany and Microbiology, KU Leuven, Heverlee, Belgium
- Center for Microbiology, VIB, Heverlee, Belgium
| | - Marten Exterkate
- Molecular Systems Biology, Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, Groningen, the Netherlands
- Molecular Microbiology, Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, Groningen, the Netherlands
| | - Andreas Milias-Argeitis
- Molecular Systems Biology, Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, Groningen, the Netherlands.
| | - Matthias Heinemann
- Molecular Systems Biology, Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, Groningen, the Netherlands.
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21
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Gowans GJ, Bridgers JB, Zhang J, Dronamraju R, Burnetti A, King DA, Thiengmany AV, Shinsky SA, Bhanu NV, Garcia BA, Buchler NE, Strahl BD, Morrison AJ. Recognition of Histone Crotonylation by Taf14 Links Metabolic State to Gene Expression. Mol Cell 2019; 76:909-921.e3. [PMID: 31676231 DOI: 10.1016/j.molcel.2019.09.029] [Citation(s) in RCA: 93] [Impact Index Per Article: 15.5] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2018] [Revised: 09/07/2019] [Accepted: 09/23/2019] [Indexed: 10/25/2022]
Abstract
Metabolic signaling to chromatin often underlies how adaptive transcriptional responses are controlled. While intermediary metabolites serve as co-factors for histone-modifying enzymes during metabolic flux, how these modifications contribute to transcriptional responses is poorly understood. Here, we utilize the highly synchronized yeast metabolic cycle (YMC) and find that fatty acid β-oxidation genes are periodically expressed coincident with the β-oxidation byproduct histone crotonylation. Specifically, we found that H3K9 crotonylation peaks when H3K9 acetylation declines and energy resources become limited. During this metabolic state, pro-growth gene expression is dampened; however, mutation of the Taf14 YEATS domain, a H3K9 crotonylation reader, results in de-repression of these genes. Conversely, exogenous addition of crotonic acid results in increased histone crotonylation, constitutive repression of pro-growth genes, and disrupted YMC oscillations. Together, our findings expose an unexpected link between metabolic flux and transcription and demonstrate that histone crotonylation and Taf14 participate in the repression of energy-demanding gene expression.
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Affiliation(s)
- Graeme J Gowans
- Department of Biology, Stanford University, Stanford, CA 94305, USA
| | - Joseph B Bridgers
- Department of Biochemistry and Biophysics, University of North Carolina, Chapel Hill, NC 27599, USA
| | - Jibo Zhang
- Department of Biochemistry and Biophysics, University of North Carolina, Chapel Hill, NC 27599, USA
| | - Raghuvar Dronamraju
- Department of Biochemistry and Biophysics, University of North Carolina, Chapel Hill, NC 27599, USA
| | - Anthony Burnetti
- Department of Molecular Biomedical Sciences, North Carolina State University, Raleigh, NC 27607, USA
| | - Devin A King
- Department of Biology, Stanford University, Stanford, CA 94305, USA
| | | | - Stephen A Shinsky
- Department of Biochemistry and Biophysics, University of North Carolina, Chapel Hill, NC 27599, USA; Lineberger Comprehensive Cancer Center, University of North Carolina, Chapel Hill, NC 27599, USA
| | - Natarajan V Bhanu
- Epigenetics Institute, Department of Biochemistry and Biophysics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Benjamin A Garcia
- Epigenetics Institute, Department of Biochemistry and Biophysics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Nicolas E Buchler
- Department of Molecular Biomedical Sciences, North Carolina State University, Raleigh, NC 27607, USA
| | - Brian D Strahl
- Department of Biochemistry and Biophysics, University of North Carolina, Chapel Hill, NC 27599, USA; Lineberger Comprehensive Cancer Center, University of North Carolina, Chapel Hill, NC 27599, USA.
| | - Ashby J Morrison
- Department of Biology, Stanford University, Stanford, CA 94305, USA.
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22
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Özsezen S, Papagiannakis A, Chen H, Niebel B, Milias-Argeitis A, Heinemann M. Inference of the High-Level Interaction Topology between the Metabolic and Cell-Cycle Oscillators from Single-Cell Dynamics. Cell Syst 2019; 9:354-365.e6. [DOI: 10.1016/j.cels.2019.09.003] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2019] [Revised: 07/18/2019] [Accepted: 09/06/2019] [Indexed: 02/06/2023]
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23
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Gulli J, Cook E, Kroll E, Rosebrock A, Caudy A, Rosenzweig F. Diverse conditions support near-zero growth in yeast: Implications for the study of cell lifespan. MICROBIAL CELL 2019; 6:397-413. [PMID: 31528631 PMCID: PMC6717879 DOI: 10.15698/mic2019.09.690] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
Baker's yeast has a finite lifespan and ages in two ways: a mother cell can only divide so many times (its replicative lifespan), and a non-dividing cell can only live so long (its chronological lifespan). Wild and laboratory yeast strains exhibit natural variation for each type of lifespan, and the genetic basis for this variation has been generalized to other eukaryotes, including metazoans. To date, yeast chronological lifespan has chiefly been studied in relation to the rate and mode of functional decline among non-dividing cells in nutrient-depleted batch culture. However, this culture method does not accurately capture two major classes of long-lived metazoan cells: cells that are terminally differentiated and metabolically active for periods that approximate animal lifespan (e.g. cardiac myocytes), and cells that are pluripotent and metabolically quiescent (e.g. stem cells). Here, we consider alternative ways of cultivating Saccharomyces cerevisiae so that these different metabolic states can be explored in non-dividing cells: (i) yeast cultured as giant colonies on semi-solid agar, (ii) yeast cultured in retentostats and provided sufficient nutrients to meet minimal energy requirements, and (iii) yeast encapsulated in a semisolid matrix and fed ad libitum in bioreactors. We review the physiology of yeast cultured under each of these conditions, and explore their potential to provide unique insights into determinants of chronological lifespan in the cells of higher eukaryotes.
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Affiliation(s)
- Jordan Gulli
- School of Biological Sciences, Georgia Institute of Technology, Atlanta, GA 30332
| | - Emily Cook
- School of Biological Sciences, Georgia Institute of Technology, Atlanta, GA 30332
| | - Eugene Kroll
- School of Biological Sciences, Georgia Institute of Technology, Atlanta, GA 30332
| | - Adam Rosebrock
- Donnelly Centre for Cellular and Biological Research and Department of Molecular Genetics, University of Toronto, Toronto, Ontario, Canada.,Present address: Stony Brook School of Medicine, Stony Brook University, Stony Brook, NY 11794
| | - Amy Caudy
- Donnelly Centre for Cellular and Biological Research and Department of Molecular Genetics, University of Toronto, Toronto, Ontario, Canada
| | - Frank Rosenzweig
- School of Biological Sciences, Georgia Institute of Technology, Atlanta, GA 30332
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24
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INO80 Chromatin Remodeling Coordinates Metabolic Homeostasis with Cell Division. Cell Rep 2019; 22:611-623. [PMID: 29346761 PMCID: PMC5949282 DOI: 10.1016/j.celrep.2017.12.079] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2017] [Revised: 12/19/2017] [Accepted: 12/21/2017] [Indexed: 12/13/2022] Open
Abstract
Adaptive survival requires the coordination of nutrient availability with expenditure of cellular resources. For example, in nutrient-limited environments, 50% of all S. cerevisiae genes synchronize and exhibit periodic bursts of expression in coordination with respiration and cell division in the yeast metabolic cycle (YMC). Despite the importance of metabolic and proliferative synchrony, the majority of YMC regulators are currently unknown. Here, we demonstrate that the INO80 chromatin-remodeling complex is required to coordinate respiration and cell division with periodic gene expression. Specifically, INO80 mutants have severe defects in oxygen consumption and promiscuous cell division that is no longer coupled with metabolic status. In mutant cells, chromatin accessibility of periodic genes, including TORC1-responsive genes, is relatively static, concomitant with severely attenuated gene expression. Collectively, these results reveal that the INO80 complex mediates metabolic signaling to chromatin to restrict proliferation to metabolically optimal states.
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25
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Nouri H, Monnier AF, Fossum-Raunehaug S, Maciag-Dorszynska M, Cabin-Flaman A, Képès F, Wegrzyn G, Szalewska-Palasz A, Norris V, Skarstad K, Janniere L. Multiple links connect central carbon metabolism to DNA replication initiation and elongation in Bacillus subtilis. DNA Res 2019; 25:641-653. [PMID: 30256918 PMCID: PMC6289782 DOI: 10.1093/dnares/dsy031] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2018] [Accepted: 08/17/2018] [Indexed: 12/27/2022] Open
Abstract
DNA replication is coupled to growth by an unknown mechanism. Here, we investigated this coupling by analyzing growth and replication in 15 mutants of central carbon metabolism (CCM) cultivated in three rich media. In about one-fourth of the condition tested, defects in replication resulting from changes in initiation or elongation were detected. This uncovered 11 CCM genes important for replication and showed that some of these genes have an effect in one, two or three media. Additional results presented here and elsewhere (Jannière, L., Canceill, D., Suski, C., et al. (2007), PLoS One, 2, e447.) showed that, in the LB medium, the CCM genes important for DNA elongation (gapA and ackA) are genetically linked to the lagging strand polymerase DnaE while those important for initiation (pgk and pykA) are genetically linked to the replication enzymes DnaC (helicase), DnaG (primase) and DnaE. Our work thus shows that the coupling between growth and replication involves multiple, medium-dependent links between CCM and replication. They also suggest that changes in CCM may affect initiation by altering the functional recruitment of DnaC, DnaG and DnaE at the chromosomal origin, and may affect elongation by altering the activity of DnaE at the replication fork. The underlying mechanism is discussed.
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Affiliation(s)
- Hamid Nouri
- iSSB, Génopole, CNRS, UEVE, Université Paris-Saclay, Evry France.,MICALIS, INRA, Jouy en Josas, France
| | | | | | | | | | - François Képès
- iSSB, Génopole, CNRS, UEVE, Université Paris-Saclay, Evry France
| | - Grzegorz Wegrzyn
- Department of Molecular Biology, University of Gdansk, Gdansk, Poland
| | | | - Vic Norris
- Laboratoire MERCI, AMMIS, Faculté des Sciences, Mont-Saint-Aignan, France
| | - Kirsten Skarstad
- Department of Cell Biology, Oslo University Hospital, University of Oslo, Oslo, Norway
| | - Laurent Janniere
- iSSB, Génopole, CNRS, UEVE, Université Paris-Saclay, Evry France.,MICALIS, INRA, Jouy en Josas, France
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26
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Causton HC. Metabolic rhythms: A framework for coordinating cellular function. Eur J Neurosci 2018; 51:1-12. [PMID: 30548718 DOI: 10.1111/ejn.14296] [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: 07/01/2018] [Revised: 11/13/2018] [Accepted: 11/19/2018] [Indexed: 01/02/2023]
Abstract
Circadian clocks are widespread among eukaryotes and generally involve feedback loops coupled with metabolic processes and redox balance. The organising power of these oscillations has not only allowed organisms to anticipate day-night cycles, but also acts to temporally compartmentalise otherwise incompatible processes, enhance metabolic efficiency, make the system more robust to noise and propagate signals among cells. While daily rhythms and the function of the circadian transcription-translation loop have been the subject of extensive research over the past four decades, cycles of shorter period and respiratory oscillations, with which they are intertwined, have received less attention. Here, we describe features of yeast respiratory oscillations, which share many features with daily and 12 hr cellular oscillations in animal cells. This relatively simple system enables the analysis of dynamic rhythmic changes in metabolism, independent of cellular oscillations that are a product of the circadian transcription-translation feedback loop. Knowledge gained from studying ultradian oscillations in yeast will lead to a better understanding of the basic mechanistic principles and evolutionary origins of oscillatory behaviour among eukaryotes.
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Affiliation(s)
- Helen C Causton
- Department of Pathology and Cell Biology, Columbia University Medical Center, New York City, New York
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27
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Baumgartner BL, O'Laughlin R, Jin M, Tsimring LS, Hao N, Hasty J. Flavin-based metabolic cycles are integral features of growth and division in single yeast cells. Sci Rep 2018; 8:18045. [PMID: 30575765 PMCID: PMC6303410 DOI: 10.1038/s41598-018-35936-w] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2017] [Accepted: 11/02/2018] [Indexed: 11/08/2022] Open
Abstract
The yeast metabolic cycle (YMC) is a fascinating example of biological organization, in which cells constrain the function of specific genetic, protein and metabolic networks to precise temporal windows as they grow and divide. However, understanding the intracellular origins of the YMC remains a challenging goal, as measuring the oxygen oscillations traditionally associated with it requires the use of synchronized cultures growing in nutrient-limited chemostat environments. To address these limitations, we used custom-built microfluidic devices and time-lapse fluorescence microscopy to search for metabolic cycling in the form of endogenous flavin fluorescence in unsynchronized single yeast cells. We uncovered robust and pervasive metabolic cycles that were synchronized with the cell division cycle (CDC) and oscillated across four different nutrient conditions. We then studied the response of these metabolic cycles to chemical and genetic perturbations, showing that their phase synchronization with the CDC can be altered through treatment with rapamycin, and that metabolic cycles continue even in respiratory deficient strains. These results provide a foundation for future studies of the physiological importance of metabolic cycles in processes such as CDC control, metabolic regulation and cell aging.
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Affiliation(s)
- Bridget L Baumgartner
- Booz Allen Hamilton, 8283 Greensboro Drive, Hamilton Building, McLean, VA, 22102, USA
| | - Richard O'Laughlin
- University of California, San Diego, Department of Bioengineering, La Jolla, CA, 92093, USA
| | - Meng Jin
- BioCircuits Institute, University of California, San Diego, La Jolla, California, USA
| | - Lev S Tsimring
- BioCircuits Institute, University of California, San Diego, La Jolla, California, USA
| | - Nan Hao
- Molecular Biology Section, Division of Biological Science, University of California, San Diego, La Jolla, California, USA
| | - Jeff Hasty
- University of California, San Diego, Department of Bioengineering, La Jolla, CA, 92093, USA.
- BioCircuits Institute, University of California, San Diego, La Jolla, California, USA.
- Molecular Biology Section, Division of Biological Science, University of California, San Diego, La Jolla, California, USA.
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28
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Bárány B, Moses G, Young T. Instability of the steady state solution in cell cycle population structure models with feedback. J Math Biol 2018; 78:1365-1387. [PMID: 30523382 DOI: 10.1007/s00285-018-1312-0] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2015] [Revised: 11/19/2018] [Indexed: 12/19/2022]
Abstract
We show that when cell-cell feedback is added to a model of the cell cycle for a large population of cells, then instability of the steady state solution occurs in many cases. We show this in the context of a generic agent-based ODE model. If the feedback is positive, then instability of the steady state solution is proved for all parameter values except for a small set on the boundary of parameter space. For negative feedback we prove instability for half the parameter space. We also show by example that instability in the other half may be proved on a case by case basis.
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Affiliation(s)
- Balázs Bárány
- Mathematics Institute, Warwick University, Coventry, UK.,Department of Stochastics, Budapest University of Technology and Economics, Budapest, Hungary
| | | | - Todd Young
- Mathematics, Ohio University, Athens, OH, USA.
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29
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Lloyd D, Murray DB, Aon MA, Cortassa S, Roussel MR, Beckmann M, Poole RK. Temporal metabolic partitioning of the yeast and protist cellular networks: the cell is a global scale-invariant (fractal or self-similar) multioscillator. JOURNAL OF BIOMEDICAL OPTICS 2018; 24:1-17. [PMID: 30516036 PMCID: PMC6992908 DOI: 10.1117/1.jbo.24.5.051404] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 08/08/2018] [Accepted: 11/01/2018] [Indexed: 06/09/2023]
Abstract
Britton Chance, electronics expert when a teenager, became an enthusiastic student of biological oscillations, passing on this enthusiasm to many students and colleagues, including one of us (DL). This historical essay traces BC's influence through the accumulated work of DL to DL's many collaborators. The overall temporal organization of mass-energy, information, and signaling networks in yeast in self-synchronized continuous cultures represents, until now, the most characterized example of in vivo elucidation of time structure. Continuous online monitoring of dissolved gases by direct measurement (membrane-inlet mass spectrometry, together with NAD(P)H and flavin fluorescence) gives strain-specific dynamic information from timescales of minutes to hours as does two-photon imaging. The predominantly oscillatory behavior of network components becomes evident, with spontaneously synchronized cellular respiration cycles between discrete periods of increased oxygen consumption (oxidative phase) and decreased oxygen consumption (reductive phase). This temperature-compensated ultradian clock provides coordination, linking temporally partitioned functions by direct feedback loops between the energetic and redox state of the cell and its growing ultrastructure. Multioscillatory outputs in dissolved gases with 13 h, 40 min, and 4 min periods gave statistical self-similarity in power spectral and relative dispersional analyses: i.e., complex nonlinear (chaotic) behavior and a functional scale-free (fractal) network operating simultaneously over several timescales.
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Affiliation(s)
- David Lloyd
- Cardiff University, School of Biosciences, Cardiff, Wales, United Kingdom
| | - Douglas B. Murray
- Keio University, Institute for Advanced Biosciences, Tsuruoka, Japan
| | - Miguel A. Aon
- National Institutes of Health, National Institute on Aging, Laboratory of Cardiovascular Science, Baltimore, Maryland, United States
| | - Sonia Cortassa
- National Institutes of Health, National Institute on Aging, Laboratory of Cardiovascular Science, Baltimore, Maryland, United States
| | - Marc R. Roussel
- University of Lethbridge, Alberta RNA Research and Training Institute and Department of Chemistry and Biochemistry, Alberta, Canada
| | - Manfred Beckmann
- Institute of Biological, Environmental and Rural, Sciences, Aberystwyth, Wales, United Kingdom
| | - Robert K. Poole
- University of Sheffield, Department of Molecular Biology and Biotechnology, Firth Court, Western Bank, Sheffield, United Kingdom
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Siqueira JA, Hardoim P, Ferreira PCG, Nunes-Nesi A, Hemerly AS. Unraveling Interfaces between Energy Metabolism and Cell Cycle in Plants. TRENDS IN PLANT SCIENCE 2018; 23:731-747. [PMID: 29934041 DOI: 10.1016/j.tplants.2018.05.005] [Citation(s) in RCA: 38] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/22/2018] [Revised: 05/01/2018] [Accepted: 05/08/2018] [Indexed: 05/22/2023]
Abstract
Oscillation in energy levels is widely variable in dividing and differentiated cells. To synchronize cell proliferation and energy fluctuations, cell cycle-related proteins have been implicated in the regulation of mitochondrial energy-generating pathways in yeasts and animals. Plants have chloroplasts and mitochondria, coordinating the cell energy flow. Recent findings suggest an integrated regulation of these organelles and the nuclear cell cycle. Furthermore, reports indicate a set of interactions between the cell cycle and energy metabolism, coordinating the turnover of proteins in plants. Here, we discuss how cell cycle-related proteins directly interact with energy metabolism-related proteins to modulate energy homeostasis and cell cycle progression. We provide interfaces between cell cycle and energy metabolism-related proteins that could be explored to maximize plant yield.
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Affiliation(s)
- João Antonio Siqueira
- Instituto de Bioquímica Médica Leopoldo de Meis, Universidade Federal do Rio de Janeiro, Rio de Janeiro, RJ, 21491-902, Brazil; These authors share first authorship
| | - Pablo Hardoim
- Instituto de Bioquímica Médica Leopoldo de Meis, Universidade Federal do Rio de Janeiro, Rio de Janeiro, RJ, 21491-902, Brazil; These authors share first authorship
| | - Paulo C G Ferreira
- Instituto de Bioquímica Médica Leopoldo de Meis, Universidade Federal do Rio de Janeiro, Rio de Janeiro, RJ, 21491-902, Brazil
| | - Adriano Nunes-Nesi
- Departamento de Biologia Vegetal, Universidade Federal de Viçosa, 36570-900 Viçosa, MG, Brazil
| | - Adriana S Hemerly
- Instituto de Bioquímica Médica Leopoldo de Meis, Universidade Federal do Rio de Janeiro, Rio de Janeiro, RJ, 21491-902, Brazil.
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Krishna S, Laxman S. A minimal "push-pull" bistability model explains oscillations between quiescent and proliferative cell states. Mol Biol Cell 2018; 29:2243-2258. [PMID: 30044724 PMCID: PMC6249812 DOI: 10.1091/mbc.e18-01-0017] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023] Open
Abstract
A minimal model for oscillating between quiescent and growth/proliferation states, dependent on the availability of a central metabolic resource, is presented. From the yeast metabolic cycles, metabolic oscillations in oxygen consumption are represented as transitions between quiescent and growth states. We consider metabolic resource availability, growth rates, and switching rates (between states) to model a relaxation oscillator explaining transitions between these states. This frustrated bistability model reveals a required communication between the metabolic resource that determines oscillations and the quiescent and growth state cells. Cells in each state reflect memory, or hysteresis of their current state, and “push–pull” cells from the other state. Finally, a parsimonious argument is made for a specific central metabolite as the controller of switching between quiescence and growth states. We discuss how an oscillator built around the availability of such a metabolic resource is sufficient to generally regulate oscillations between growth and quiescence through committed transitions.
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Affiliation(s)
- Sandeep Krishna
- Simons Centre for the Study of Living Machines, National Centre for Biological Sciences, Tata Institute of Fundamental Research, Bangalore 560065, India
| | - Sunil Laxman
- Institute for Stem Cell Biology and Regenerative Medicine, Bangalore 560065, India
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32
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Gaucher J, Montellier E, Sassone-Corsi P. Molecular Cogs: Interplay between Circadian Clock and Cell Cycle. Trends Cell Biol 2018; 28:368-379. [DOI: 10.1016/j.tcb.2018.01.006] [Citation(s) in RCA: 84] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2017] [Revised: 01/21/2018] [Accepted: 01/22/2018] [Indexed: 12/29/2022]
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33
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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: 3.9] [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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Chawla K, Bürgel SC, Schmidt GW, Kaltenbach HM, Rudolf F, Frey O, Hierlemann A. Integrating impedance-based growth-rate monitoring into a microfluidic cell culture platform for live-cell microscopy. MICROSYSTEMS & NANOENGINEERING 2018; 4:8. [PMID: 31057898 PMCID: PMC6220194 DOI: 10.1038/s41378-018-0006-5] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/06/2017] [Revised: 01/12/2018] [Accepted: 02/03/2018] [Indexed: 05/11/2023]
Abstract
Growth rate is a widely studied parameter for various cell-based biological studies. Growth rates of cell populations can be monitored in chemostats and micro-chemostats, where nutrients are continuously replenished. Here, we present an integrated microfluidic platform that enables long-term culturing of non-adherent cells as well as parallel and mutually independent continuous monitoring of (i) growth rates of cells by means of impedance measurements and of (ii) specific other cellular events by means of high-resolution optical or fluorescence microscopy. Yeast colonies were grown in a monolayer under culturing pads, which enabled high-resolution microscopy, as all cells were in the same focal plane. Upon cell growth and division, cells leaving the culturing area passed over a pair of electrodes and were counted through impedance measurements. The impedance data could then be used to directly determine the growth rates of the cells in the culturing area. The integration of multiple culturing chambers with sensing electrodes enabled multiplexed long-term monitoring of growth rates of different yeast strains in parallel. As a demonstration, we modulated the growth rates of engineered yeast strains using calcium. The results indicated that impedance measurements provide a label-free readout method to continuously monitor the changes in the growth rates of the cells without compromising high-resolution optical imaging of single cells.
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Affiliation(s)
- Ketki Chawla
- ETH Zurich, Department of Biosystems Science and Engineering, Bio Engineering Laboratory, Basel, Switzerland
| | - Sebastian C. Bürgel
- ETH Zurich, Department of Biosystems Science and Engineering, Bio Engineering Laboratory, Basel, Switzerland
| | - Gregor W. Schmidt
- ETH Zurich, Department of Biosystems Science and Engineering, Bio Engineering Laboratory, Basel, Switzerland
| | - Hans-Michael Kaltenbach
- ETH Zurich, Department of Biosystems Science and Engineering, Computational Systems Biology Group, Basel, Switzerland
| | - Fabian Rudolf
- ETH Zurich, Department of Biosystems Science and Engineering, Computational Systems Biology Group, Basel, Switzerland
| | - Olivier Frey
- ETH Zurich, Department of Biosystems Science and Engineering, Bio Engineering Laboratory, Basel, Switzerland
| | - Andreas Hierlemann
- ETH Zurich, Department of Biosystems Science and Engineering, Bio Engineering Laboratory, Basel, Switzerland
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Gasch AP, Yu FB, Hose J, Escalante LE, Place M, Bacher R, Kanbar J, Ciobanu D, Sandor L, Grigoriev IV, Kendziorski C, Quake SR, McClean MN. Single-cell RNA sequencing reveals intrinsic and extrinsic regulatory heterogeneity in yeast responding to stress. PLoS Biol 2017; 15:e2004050. [PMID: 29240790 PMCID: PMC5746276 DOI: 10.1371/journal.pbio.2004050] [Citation(s) in RCA: 87] [Impact Index Per Article: 10.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2017] [Revised: 12/28/2017] [Accepted: 11/17/2017] [Indexed: 02/01/2023] Open
Abstract
From bacteria to humans, individual cells within isogenic populations can show significant variation in stress tolerance, but the nature of this heterogeneity is not clear. To investigate this, we used single-cell RNA sequencing to quantify transcript heterogeneity in single Saccharomyces cerevisiae cells treated with and without salt stress to explore population variation and identify cellular covariates that influence the stress-responsive transcriptome. Leveraging the extensive knowledge of yeast transcriptional regulation, we uncovered significant regulatory variation in individual yeast cells, both before and after stress. We also discovered that a subset of cells appears to decouple expression of ribosomal protein genes from the environmental stress response in a manner partly correlated with the cell cycle but unrelated to the yeast ultradian metabolic cycle. Live-cell imaging of cells expressing pairs of fluorescent regulators, including the transcription factor Msn2 with Dot6, Sfp1, or MAP kinase Hog1, revealed both coordinated and decoupled nucleocytoplasmic shuttling. Together with transcriptomic analysis, our results suggest that cells maintain a cellular filter against decoupled bursts of transcription factor activation but mount a stress response upon coordinated regulation, even in a subset of unstressed cells. Genetically identical cells growing in the same environment can vary in their cellular state and behavior. Such heterogeneity may explain why some cells in an isogenic population can survive sudden severe environmental stress whereas other cells succumb. Cell-to-cell variation in gene expression has been linked to variable stress survival, but how and why transcript levels vary across the transcriptome in single cells is only beginning to emerge. Here, we used single-cell RNA sequencing (scRNA-seq) to measure cell-to-cell heterogeneity in the transcriptome of budding yeast (Saccharomyces cerevisiae). We find surprising patterns of variation across known sets of transcription factor targets, indicating that cells vary in their transcriptome profile both before and after stress exposure. scRNA-seq analysis combined with live-cell imaging of transcription factor activation dynamics revealed some cells in which the stress response was coordinately activated and other cells in which the traditional response was decoupled, suggesting unrecognized regulatory nuances that expand our understanding of stress response and survival.
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Affiliation(s)
- 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
- * E-mail:
| | - Feiqiao Brian Yu
- Department of Bioengineering, Stanford University, Stanford, California, United States of America
| | - James Hose
- Laboratory of Genetics, University of Wisconsin–Madison, Madison, Wisconsin, United States of America
| | - Leah E. Escalante
- Laboratory of Genetics, University of Wisconsin–Madison, Madison, Wisconsin, United States of America
| | - Mike Place
- Great Lakes Bioenergy Research Center, University of Wisconsin–Madison, Madison, Wisconsin, United States of America
| | - Rhonda Bacher
- Department of Biostatistics and Medical Informatics, University of Wisconsin–Madison, Madison, Wisconsin, United States of America
| | - Jad Kanbar
- Department of Bioengineering, Stanford University, Stanford, California, United States of America
| | - Doina Ciobanu
- Department of Energy Joint Genome Institute, Walnut Creek, California, United States of America
| | - Laura Sandor
- Department of Energy Joint Genome Institute, Walnut Creek, California, United States of America
| | - Igor V. Grigoriev
- Department of Energy Joint Genome Institute, Walnut Creek, California, United States of America
| | - Christina Kendziorski
- Department of Biostatistics and Medical Informatics, University of Wisconsin–Madison, Madison, Wisconsin, United States of America
| | - Stephen R. Quake
- Department of Bioengineering, Stanford University, Stanford, California, United States of America
- Chan Zuckerberg Biohub, San Francisco, California, United States of America
| | - Megan N. McClean
- Department of Biomedical Engineering, University of Wisconsin–Madison, Madison, Wisconsin, United States of America
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36
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Ewald JC, Kuehne A, Zamboni N, Skotheim JM. The Yeast Cyclin-Dependent Kinase Routes Carbon Fluxes to Fuel Cell Cycle Progression. Mol Cell 2017; 62:532-45. [PMID: 27203178 DOI: 10.1016/j.molcel.2016.02.017] [Citation(s) in RCA: 81] [Impact Index Per Article: 10.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2015] [Revised: 10/26/2015] [Accepted: 02/11/2016] [Indexed: 01/12/2023]
Abstract
Cell division entails a sequence of processes whose specific demands for biosynthetic precursors and energy place dynamic requirements on metabolism. However, little is known about how metabolic fluxes are coordinated with the cell division cycle. Here, we examine budding yeast to show that more than half of all measured metabolites change significantly through the cell division cycle. Cell cycle-dependent changes in central carbon metabolism are controlled by the cyclin-dependent kinase (Cdk1), a major cell cycle regulator, and the metabolic regulator protein kinase A. At the G1/S transition, Cdk1 phosphorylates and activates the enzyme Nth1, which funnels the storage carbohydrate trehalose into central carbon metabolism. Trehalose utilization fuels anabolic processes required to reliably complete cell division. Thus, the cell cycle entrains carbon metabolism to fuel biosynthesis. Because the oscillation of Cdk activity is a conserved feature of the eukaryotic cell cycle, we anticipate its frequent use in dynamically regulating metabolism for efficient proliferation.
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Affiliation(s)
- Jennifer C Ewald
- Department of Biology, Stanford University, Stanford, CA 94305, USA
| | - Andreas Kuehne
- Institute of Molecular Systems Biology, ETH Zurich, 8093 Zurich, Switzerland; PhD Program Systems Biology, Life Science Zurich Graduate School, 8057 Zurich, Switzerland
| | - Nicola Zamboni
- Institute of Molecular Systems Biology, ETH Zurich, 8093 Zurich, Switzerland
| | - Jan M Skotheim
- Department of Biology, Stanford University, Stanford, CA 94305, USA.
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37
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Elements of biological oscillations in time and space. Nat Struct Mol Biol 2017; 23:1030-1034. [PMID: 27922613 DOI: 10.1038/nsmb.3320] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2016] [Accepted: 10/13/2016] [Indexed: 12/16/2022]
Abstract
Oscillations in time and space are ubiquitous in nature and play critical roles in dynamic cellular processes. Although the molecular mechanisms underlying the generation of the dynamics are diverse, several distinct regulatory elements have been recognized as being critical in producing and modulating oscillatory dynamics. These include negative and positive feedback, time delay, nonlinearity in regulation, and random fluctuations ('noise'). Here we discuss the specific roles of these five elements in promoting or attenuating oscillatory dynamics, by drawing on insights from quantitative analyses of natural or synthetic biological networks.
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38
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Mellor J. The molecular basis of metabolic cycles and their relationship to circadian rhythms. Nat Struct Mol Biol 2017; 23:1035-1044. [PMID: 27922609 DOI: 10.1038/nsmb.3311] [Citation(s) in RCA: 33] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2016] [Accepted: 09/23/2016] [Indexed: 12/12/2022]
Abstract
Metabolic cycles result from the partitioning of oxidative and reductive metabolism into rhythmic phases of gene expression and oscillating post-translational protein modifications. Relatively little is known about how these switches in gene expression are controlled, although recent studies have suggested that transcription itself may play a central role. This review explores the molecular basis of the metabolic and gene-expression oscillations in the yeast Saccharomyces cerevisiae, as well as how they relate to other biological time-keeping mechanisms, such as circadian rhythms.
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Affiliation(s)
- Jane Mellor
- Department of Biochemistry, University of Oxford, Oxford, UK
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39
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Papagiannakis A, Niebel B, Wit EC, Heinemann M. Autonomous Metabolic Oscillations Robustly Gate the Early and Late Cell Cycle. Mol Cell 2016; 65:285-295. [PMID: 27989441 DOI: 10.1016/j.molcel.2016.11.018] [Citation(s) in RCA: 97] [Impact Index Per Article: 10.8] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2016] [Revised: 09/26/2016] [Accepted: 11/09/2016] [Indexed: 10/20/2022]
Abstract
Eukaryotic cell division is known to be controlled by the cyclin/cyclin dependent kinase (CDK) machinery. However, eukaryotes have evolved prior to CDKs, and cells can divide in the absence of major cyclin/CDK components. We hypothesized that an autonomous metabolic oscillator provides dynamic triggers for cell-cycle initiation and progression. Using microfluidics, cell-cycle reporters, and single-cell metabolite measurements, we found that metabolism of budding yeast is a CDK-independent oscillator that oscillates across different growth conditions, both in synchrony with and also in the absence of the cell cycle. Using environmental perturbations and dynamic single-protein depletion experiments, we found that the metabolic oscillator and the cell cycle form a system of coupled oscillators, with the metabolic oscillator separately gating and maintaining synchrony with the early and late cell cycle. Establishing metabolism as a dynamic component within the cell-cycle network opens new avenues for cell-cycle research and therapeutic interventions for proliferative disorders.
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Affiliation(s)
- Alexandros Papagiannakis
- Molecular Systems Biology, Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, Nijenborgh 4, 9747 AG Groningen, the Netherlands
| | - Bastian Niebel
- Molecular Systems Biology, Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, Nijenborgh 4, 9747 AG Groningen, the Netherlands
| | - Ernst C Wit
- Probability and Statistics, Johann Bernoulli Institute of Mathematics and Computer Science, University of Groningen, Nijenborgh 9, 9747 AG Groningen, the Netherlands
| | - Matthias Heinemann
- Molecular Systems Biology, Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, Nijenborgh 4, 9747 AG Groningen, the Netherlands.
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