1
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Piccirillo S, Honigberg SM. Measuring effect of mutations & conditions on microbial respiratory rates. J Microbiol Methods 2024; 216:106864. [PMID: 38030085 PMCID: PMC10843655 DOI: 10.1016/j.mimet.2023.106864] [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: 08/11/2023] [Revised: 11/22/2023] [Accepted: 11/23/2023] [Indexed: 12/01/2023]
Abstract
Cellular respiration is central to a wide range of cellular processes. In microorganisms, the effect of a mutation or an environmental condition on the rate of respiration is usually determined by measuring oxygen consumption in the media. We describe this method and discuss caveats and controls for the method.
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Affiliation(s)
- Sarah Piccirillo
- Division of Biological and Biomedical Systems, 5007 Rockhill Rd, University of Missouri-Kansas City, Kansas City, MO 64110-1299, United States of America
| | - Saul M Honigberg
- Division of Biological and Biomedical Systems, 5007 Rockhill Rd, University of Missouri-Kansas City, Kansas City, MO 64110-1299, United States of America.
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2
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Opalek M, Tutaj H, Pirog A, Smug BJ, Rutkowska J, Wloch-Salamon D. A Systematic Review on Quiescent State Research Approaches in S. cerevisiae. Cells 2023; 12:1608. [PMID: 37371078 DOI: 10.3390/cells12121608] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2023] [Revised: 06/02/2023] [Accepted: 06/09/2023] [Indexed: 06/29/2023] Open
Abstract
Quiescence, the temporary and reversible arrest of cell growth, is a fundamental biological process. However, the lack of standardization in terms of reporting the experimental details of quiescent cells and populations can cause confusion and hinder knowledge transfer. We employ the systematic review methodology to comprehensively analyze the diversity of approaches used to study the quiescent state, focusing on all published research addressing the budding yeast Saccharomyces cerevisiae. We group research articles into those that consider all cells comprising the stationary-phase (SP) population as quiescent and those that recognize heterogeneity within the SP by distinguishing phenotypically distinct subpopulations. Furthermore, we investigate the chronological age of the quiescent populations under study and the methods used to induce the quiescent state, such as gradual starvation or abrupt environmental change. We also assess whether the strains used in research are prototrophic or auxotrophic. By combining the above features, we identify 48 possible experimental setups that can be used to study quiescence, which can be misleading when drawing general conclusions. We therefore summarize our review by proposing guidelines and recommendations pertaining to the information included in research articles. We believe that more rigorous reporting on the features of quiescent populations will facilitate knowledge transfer within and between disciplines, thereby stimulating valuable scientific discussion.
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Affiliation(s)
- Monika Opalek
- Institute of Environmental Sciences, Faculty of Biology, Jagiellonian University, 30-387 Krakow, Poland
| | - Hanna Tutaj
- Institute of Environmental Sciences, Faculty of Biology, Jagiellonian University, 30-387 Krakow, Poland
| | - Adrian Pirog
- Institute of Environmental Sciences, Faculty of Biology, Jagiellonian University, 30-387 Krakow, Poland
| | - Bogna J Smug
- Malopolska Centre of Biotechnology, Jagiellonian University, 30-387 Krakow, Poland
| | - Joanna Rutkowska
- Institute of Environmental Sciences, Faculty of Biology, Jagiellonian University, 30-387 Krakow, Poland
| | - Dominika Wloch-Salamon
- Institute of Environmental Sciences, Faculty of Biology, Jagiellonian University, 30-387 Krakow, Poland
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3
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Gene expression during the formation of resting spores induced by nitrogen starvation in the marine diatom Chaetoceros socialis. BMC Genomics 2023; 24:106. [PMID: 36899305 PMCID: PMC9999646 DOI: 10.1186/s12864-023-09175-x] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2022] [Accepted: 02/09/2023] [Indexed: 03/12/2023] Open
Abstract
BACKGROUND Dormancy is widespread in both multicellular and unicellular organisms. Among diatoms, unicellular microalgae at the base of all aquatic food webs, several species produce dormant cells (spores or resting cells) that can withstand long periods of adverse environmental conditions. RESULTS We present the first gene expression study during the process of spore formation induced by nitrogen depletion in the marine planktonic diatom Chaetoceros socialis. In this condition, genes related to photosynthesis and nitrate assimilation, including high-affinity nitrate transporters (NTRs), were downregulated. While the former result is a common reaction among diatoms under nitrogen stress, the latter seems to be exclusive of the spore-former C. socialis. The upregulation of catabolic pathways, such as tricarboxylic acid cycle, glyoxylate cycle and fatty acid beta-oxidation, suggests that this diatom could use lipids as a source of energy during the process of spore formation. Furthermore, the upregulation of a lipoxygenase and several aldehyde dehydrogenases (ALDHs) advocates the presence of oxylipin-mediated signaling, while the upregulation of genes involved in dormancy-related pathways conserved in other organisms (e.g. serine/threonine-protein kinases TOR and its inhibitor GATOR) provides interesting avenues for future explorations. CONCLUSIONS Our results demonstrate that the transition from an active growth phase to a resting one is characterized by marked metabolic changes and provides evidence for the presence of signaling pathways related to intercellular communication.
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4
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Evolution of yeast hybrids by aborted meiosis. Curr Opin Genet Dev 2022; 77:101980. [PMID: 36084497 DOI: 10.1016/j.gde.2022.101980] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2022] [Revised: 07/22/2022] [Accepted: 08/01/2022] [Indexed: 01/27/2023]
Abstract
Sterile hybrids are broadly considered evolutionary dead-ends because of their faulty sexual reproduction. While sterility in obligate sexual organisms is a clear constraint in perpetuating the species, some facultative sexual microbes such as yeasts can propagate asexually and maintain genome plasticity. Moreover, incomplete meiotic pathways in yeasts represent alternative routes to the standard meiosis that generates genetic combinations in the population and fuel adaptation. Here, we review how aborting meiosis promotes genome-wide allele shuffling in sterile Saccharomyces hybrids and describe approaches to identify evolved clones in a cell population. We further discuss possible implications of this process in generating phenotypic novelty and report cases of abortive meiosis across yeast species.
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5
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Leonov A, Feldman R, Piano A, Arlia-Ciommo A, Junio JAB, Orfanos E, Tafakori T, Lutchman V, Mohammad K, Elsaser S, Orfali S, Rajen H, Titorenko VI. Diverse geroprotectors differently affect a mechanism linking cellular aging to cellular quiescence in budding yeast. Oncotarget 2022; 13:918-943. [PMID: 35937500 PMCID: PMC9348708 DOI: 10.18632/oncotarget.28256] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2022] [Accepted: 07/01/2022] [Indexed: 11/25/2022] Open
Affiliation(s)
- Anna Leonov
- Department of Biology, Concordia University, Montreal, Quebec H4B 1R6, Canada
| | - Rachel Feldman
- Department of Biology, Concordia University, Montreal, Quebec H4B 1R6, Canada
| | - Amanda Piano
- Department of Biology, Concordia University, Montreal, Quebec H4B 1R6, Canada
| | | | | | - Emmanuel Orfanos
- Department of Biology, Concordia University, Montreal, Quebec H4B 1R6, Canada
| | - Tala Tafakori
- Department of Biology, Concordia University, Montreal, Quebec H4B 1R6, Canada
| | - Vicky Lutchman
- Department of Biology, Concordia University, Montreal, Quebec H4B 1R6, Canada
| | - Karamat Mohammad
- Department of Biology, Concordia University, Montreal, Quebec H4B 1R6, Canada
| | - Sarah Elsaser
- Department of Biology, Concordia University, Montreal, Quebec H4B 1R6, Canada
| | - Sandra Orfali
- Department of Biology, Concordia University, Montreal, Quebec H4B 1R6, Canada
| | - Harshvardhan Rajen
- Department of Biology, Concordia University, Montreal, Quebec H4B 1R6, Canada
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6
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Zhao G, Rusche LN. Sirtuins in Epigenetic Silencing and Control of Gene Expression in Model and Pathogenic Fungi. Annu Rev Microbiol 2022; 76:157-178. [PMID: 35609947 DOI: 10.1146/annurev-micro-041020-100926] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Fungi, including yeasts, molds, and mushrooms, proliferate on decaying matter and then adopt quiescent forms once nutrients are depleted. This review explores how fungi use sirtuin deacetylases to sense and respond appropriately to changing nutrients. Because sirtuins are NAD+-dependent deacetylases, their activity is sensitive to intracellular NAD+ availability. This allows them to transmit information about a cell's metabolic state on to the biological processes they influence. Fungal sirtuins are primarily known to deacetylate histones, repressing transcription and modulating genome stability. Their target genes include those involved in NAD+ homeostasis, metabolism, sporulation, secondary metabolite production, and virulence traits of pathogenic fungi. By targeting different genes over evolutionary time, sirtuins serve as rewiring points that allow organisms to evolve novel responses to low NAD+ stress by bringing relevant biological processes under the control of sirtuins. Expected final online publication date for the Annual Review of Microbiology, Volume 76 is September 2022. Please see http://www.annualreviews.org/page/journal/pubdates for revised estimates.
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Affiliation(s)
- Guolei Zhao
- Department of Biological Sciences, University at Buffalo, The State University of New York, Buffalo, New York, USA; ,
| | - Laura N Rusche
- Department of Biological Sciences, University at Buffalo, The State University of New York, Buffalo, New York, USA; ,
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7
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Piccirillo S, Morgan AP, Leon AY, Smith AL, Honigberg SM. Investigating cell autonomy in microorganisms. Curr Genet 2022; 68:305-318. [PMID: 35119506 PMCID: PMC9101301 DOI: 10.1007/s00294-022-01231-5] [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: 11/08/2021] [Revised: 01/04/2022] [Accepted: 01/18/2022] [Indexed: 11/28/2022]
Abstract
Cell-cell signaling in microorganisms is still poorly characterized. In this Methods paper, we describe a genetic procedure for detecting cell-nonautonomous genetic effects, and in particular cell-cell signaling, termed the chimeric colony assay (CCA). The CCA measures the effect of a gene on a biological response in a neighboring cell. This assay can measure cell autonomy for range of biological activities including transcript or protein accumulation, subcellular localization, and cell differentiation. To date, the CCA has been used exclusively to investigate colony patterning in the budding yeast Saccharomyces cerevisiae. To demonstrate the wider potential of the assay, we applied this assay to two other systems: the effect of Grr1 on glucose repression of GAL1 transcription in yeast and the effect of rpsL on stop-codon translational readthrough in Escherichia coli. We also describe variations of the standard CCA that address specific aspects of cell-cell signaling, and we delineate essential controls for this assay. Finally, we discuss complementary approaches to the CCA. Taken together, this Methods paper demonstrates how genetic assays can reveal and explore the roles of cell-cell signaling in microbial processes.
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Affiliation(s)
- Sarah Piccirillo
- Department of Genetics, Developmental and Evolutionary Biology, School of Biological and Chemical Sciences, University of Missouri-Kansas City, 5100 Rockhill Rd., Kansas City, MO 64110, USA
| | - Andrew P. Morgan
- Department of Genetics, Developmental and Evolutionary Biology, School of Biological and Chemical Sciences, University of Missouri-Kansas City, 5100 Rockhill Rd., Kansas City, MO 64110, USA
| | - Andy Y. Leon
- Department of Genetics, Developmental and Evolutionary Biology, School of Biological and Chemical Sciences, University of Missouri-Kansas City, 5100 Rockhill Rd., Kansas City, MO 64110, USA
| | - Annika L. Smith
- Department of Genetics, Developmental and Evolutionary Biology, School of Biological and Chemical Sciences, University of Missouri-Kansas City, 5100 Rockhill Rd., Kansas City, MO 64110, USA
| | - Saul M. Honigberg
- Department of Genetics, Developmental and Evolutionary Biology, School of Biological and Chemical Sciences, University of Missouri-Kansas City, 5100 Rockhill Rd., Kansas City, MO 64110, USA
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8
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Zhao X, Lian X, Liu Y, Zhou L, Wu B, Fu YV. A Peptide Derived from GAPDH Enhances Resistance to DNA Damage in Saccharomyces cerevisiae Cells. Appl Environ Microbiol 2022; 88:e0219421. [PMID: 34936834 PMCID: PMC8863060 DOI: 10.1128/aem.02194-21] [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: 11/11/2021] [Accepted: 12/16/2021] [Indexed: 11/20/2022] Open
Abstract
Social behaviors do not exist only in higher organisms but are also present in microbes that interact for the common good. Here, we report that budding yeast cells interact with their neighboring cells after exposure to DNA damage. Yeast cells irradiated with DNA-damaging UV light secrete signal peptides that can increase the survival of yeast cells exposed to DNA-damaging stress. The secreted peptide is derived from glyceraldehyde-3-phosphate dehydrogenase (GAPDH), and it induced cell death of a fraction of yeast cells in the group. The data suggest that the GAPDH-derived peptide serves in budding yeast's social interaction in response to DNA-damaging stress. IMPORTANCE Many studies have shown that microorganisms, including bacteria and yeast, display increased tolerance to stress after exposure to the same stressor. However, the mechanism remains unknown. In this study, we report a striking finding that Saccharomyces cerevisiae cells respond to DNA damage by secreting a peptide that facilitates resistance to DNA-damaging stress. Although it has been shown that GAPDH possesses many key functions in cells aside from its well-established role in glycolysis, this study demonstrated that GAPDH is also involved in the social behaviors response to DNA-damaging stress. The study opens the gate to an interesting research field about microbial social activity for adaptation to a harsh environment.
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Affiliation(s)
- Xi Zhao
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China
- Savaid Medical School, University of Chinese Academy of Sciences, Beijing, China
| | - Xianqiang Lian
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China
- Savaid Medical School, University of Chinese Academy of Sciences, Beijing, China
| | - Yan Liu
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China
- Savaid Medical School, University of Chinese Academy of Sciences, Beijing, China
| | - Liyan Zhou
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China
- Savaid Medical School, University of Chinese Academy of Sciences, Beijing, China
| | - Bian Wu
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China
| | - Yu V. Fu
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China
- Savaid Medical School, University of Chinese Academy of Sciences, Beijing, China
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9
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Annunziata R, Mele BH, Marotta P, Volpe M, Entrambasaguas L, Mager S, Stec K, d’Alcalà MR, Sanges R, Finazzi G, Iudicone D, Montresor M, Ferrante MI. Trade-off between sex and growth in diatoms: Molecular mechanisms and demographic implications. SCIENCE ADVANCES 2022; 8:eabj9466. [PMID: 35044817 PMCID: PMC8769554 DOI: 10.1126/sciadv.abj9466] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/04/2023]
Abstract
Diatoms are fast-growing and winning competitors in aquatic environments, possibly due to optimized growth performance. However, their life cycles are complex, heteromorphic, and not fully understood. Here, we report on the fine control of cell growth and physiology during the sexual phase of the marine diatom Pseudo-nitzschia multistriata. We found that mating, under nutrient replete conditions, induces a prolonged growth arrest in parental cells. Transcriptomic analyses revealed down-regulation of genes related to major metabolic functions from the early phases of mating. Single-cell photophysiology also pinpointed an inhibition of photosynthesis and storage lipids accumulated in the arrested population, especially in gametes and zygotes. Numerical simulations revealed that growth arrest affects the balance between parental cells and their siblings, possibly favoring the new generation. Thus, in addition to resources availability, life cycle traits contribute to shaping the species ecological niches and must be considered to describe and understand the structure of plankton communities.
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Affiliation(s)
- Rossella Annunziata
- Stazione Zoologica Anton Dohrn, Napoli, Italy
- Corresponding author. (R.A.); (M.I.F.)
| | | | | | | | | | | | | | | | - Remo Sanges
- International School for Advanced Studies (SISSA), Via Bonomea 265, Trieste 34136, Italy
| | - Giovanni Finazzi
- Université Grenoble Alpes (UGA), Centre National Recherche Scientifique (CNRS), Commissariat Energie Atomique, Energies Alternatives (CEA), Institut National Recherche Agriculture, Alimentation, Environnement (INRAE), Interdisciplinary Research Institute of Grenoble, IRIG-Laboratoire de Physiologie Cellulaire et Végétale, Grenoble, France
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10
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On the Ecological Significance of Phenotypic Heterogeneity in Microbial Populations Undergoing Starvation. Microbiol Spectr 2022; 10:e0045021. [PMID: 35019773 PMCID: PMC8754142 DOI: 10.1128/spectrum.00450-21] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
To persist in variable environments, populations of microorganisms have to survive periods of starvation and be able to restart cell division in nutrient-rich conditions. Typically, starvation signals initiate a transition to a quiescent state in a fraction of individual cells, while the rest of the cells remain nonquiescent. It is widely believed that, while quiescent (Q) cells help the population to survive long starvation, the nonquiescent (NQ) cells are a side effect of imperfect transition. We analyzed the regrowth of starved monocultures of Q and NQ cells compared to that of mixed, heterogeneous cultures from simple and complex starvation environments. Our experiments, as well as mathematical modeling, demonstrate that Q monocultures benefit from better survival during long starvation and from a shorter lag phase after resupply of rich medium. However, when the starvation period is very short, the NQ monocultures outperform Q and mixed cultures due to their short lag phase. In addition, only NQ monocultures benefit from complex starvation environments, where nutrient recycling is possible. Our study suggests that phenotypic heterogeneity in starved populations could be a form of bet hedging that is adaptive when environmental determinants, such as the length of the starvation period, the length of the regrowth phase, and the complexity of the starvation environment, vary over time. IMPORTANCE Nongenetic cell heterogeneity is present in glucose-starved yeast populations in the form of quiescent (Q) and nonquiescent (NQ) phenotypes. There is evidence that Q cells help the population survive long starvation. However, the role of the NQ cell type is not known, and it has been speculated that the NQ phenotype is just a side effect of the imperfect transition to the Q phenotype. Here, we show that, in contrast, there are ecological scenarios in which NQ cells perform better than monocultures of Q cells or naturally occurring mixed populations containing both Q and NQ cells. NQ cells benefit when the starvation period is very short and environmental conditions allow nutrient recycling during starvation. Our experimental and mathematical modeling results suggest a novel hypothesis: the presence of both Q and NQ phenotypes within starved yeast populations may reflect a form of bet hedging where different phenotypes provide fitness advantages depending on the environmental conditions.
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11
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Sun S, Gresham D. Cellular quiescence in budding yeast. Yeast 2021; 38:12-29. [PMID: 33350503 DOI: 10.1002/yea.3545] [Citation(s) in RCA: 31] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2020] [Revised: 12/11/2020] [Accepted: 12/14/2020] [Indexed: 12/20/2022] Open
Abstract
Cellular quiescence, the temporary and reversible exit from proliferative growth, is the predominant state of all cells. However, our understanding of the biological processes and molecular mechanisms that underlie cell quiescence remains incomplete. As with the mitotic cell cycle, budding and fission yeast are preeminent model systems for studying cellular quiescence owing to their rich experimental toolboxes and the evolutionary conservation across eukaryotes of pathways and processes that control quiescence. Here, we review current knowledge of cell quiescence in budding yeast and how it pertains to cellular quiescence in other organisms, including multicellular animals. Quiescence entails large-scale remodeling of virtually every cellular process, organelle, gene expression, and metabolic state that is executed dynamically as cells undergo the initiation, maintenance, and exit from quiescence. We review these major transitions, our current understanding of their molecular bases, and highlight unresolved questions. We summarize the primary methods employed for quiescence studies in yeast and discuss their relative merits. Understanding cell quiescence has important consequences for human disease as quiescent single-celled microbes are notoriously difficult to kill and quiescent human cells play important roles in diseases such as cancer. We argue that research on cellular quiescence will be accelerated through the adoption of common criteria, and methods, for defining cell quiescence. An integrated approach to studying cell quiescence, and a focus on the behavior of individual cells, will yield new insights into the pathways and processes that underlie cell quiescence leading to a more complete understanding of the life cycle of cells. TAKE AWAY: Quiescent cells are viable cells that have reversibly exited the cell cycle Quiescence is induced in response to a variety of nutrient starvation signals Quiescence is executed dynamically through three phases: initiation, maintenance, and exit Quiescence entails large-scale remodeling of gene expression, organelles, and metabolism Single-cell approaches are required to address heterogeneity among quiescent cells.
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Affiliation(s)
- Siyu Sun
- Center for Genomics and Systems Biology, New York University, New York, New York, 10003, USA.,Department of Biology, New York University, New York, New York, 10003, USA
| | - David Gresham
- Center for Genomics and Systems Biology, New York University, New York, New York, 10003, USA.,Department of Biology, New York University, New York, New York, 10003, USA
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12
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Nutrient Signaling, Stress Response, and Inter-organelle Communication Are Non-canonical Determinants of Cell Fate. Cell Rep 2020; 33:108446. [PMID: 33264609 PMCID: PMC9744185 DOI: 10.1016/j.celrep.2020.108446] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2020] [Revised: 10/06/2020] [Accepted: 11/06/2020] [Indexed: 12/14/2022] Open
Abstract
Isogenic cells manifest distinct cellular fates for a single stress; however, the nongenetic mechanisms driving such fates remain poorly understood. Here, we implement a robust multi-channel live-cell imaging approach to uncover noncanonical factors governing cell fate. We show that in response to acute glucose removal (AGR), budding yeast undergoes distinct fates, becoming either quiescent or senescent. Senescent cells fail to resume mitotic cycles following glucose replenishment but remain responsive to nutrient stimuli. Whereas quiescent cells manifest starvation-induced adaptation, senescent cells display perturbed endomembrane trafficking and defective nucleus-vacuole junction (NVJ) expansion. Surprisingly, senescence occurs even in the absence of lipid droplets. Importantly, we identify the nutrient-sensing kinase Rim15 as a key biomarker predicting cell fates before AGR stress. We propose that isogenic yeast challenged with acute nutrient shortage contains determinants influencing post-stress fate and demonstrate that specific nutrient signaling, stress response, trafficking, and inter-organelle biomarkers are early indicators for long-term fate outcomes.
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13
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De S, Rebnegger C, Moser J, Tatto N, Graf AB, Mattanovich D, Gasser B. Pseudohyphal differentiation in Komagataella phaffii: investigating the FLO gene family. FEMS Yeast Res 2020; 20:5884885. [PMID: 32766781 PMCID: PMC7419694 DOI: 10.1093/femsyr/foaa044] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2020] [Accepted: 08/05/2020] [Indexed: 12/12/2022] Open
Abstract
Many yeasts differentiate into multicellular phenotypes in adverse environmental conditions. Here, we investigate pseudohyphal growth in Komagataella phaffii and the involvement of the flocculin (FLO) gene family in its regulation. The K. phaffii FLO family consists of 13 members, and the conditions inducing pseudohyphal growth are different from Saccharomyces cerevisiae. So far, this phenotype was only observed when K. phaffii was cultivated at slow growth rates in glucose-limited chemostats, but not upon nitrogen starvation or the presence of fusel alcohols. Transcriptional analysis identified that FLO11, FLO400 and FLO5-1 are involved in the phenotype, all being controlled by the transcriptional regulator Flo8. The three genes exhibit a complex mechanism of expression and repression during transition from yeast to pseudohyphal form. Unlike in S. cerevisiae, deletion of FLO11 does not completely prevent the phenotype. In contrast, deletion of FLO400 or FLO5-1 prevents pseudohyphae formation, and hampers FLO11 expression. FAIRE-Seq data shows that the expression and repression of FLO400 and FLO5-1 are correlated to open or closed chromatin regions upstream of these genes, respectively. Our findings indicate that K. phaffii Flo400 and/or Flo5-1 act as upstream signals that lead to the induction of FLO11 upon glucose limitation in chemostats at slow growth and chromatin modulation is involved in the regulation of their expression.
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Affiliation(s)
- Sonakshi De
- Austrian Centre of Industrial Biotechnology, Muthgasse 11, 1190 Vienna, Austria.,Department of Biotechnology, BOKU University of Natural Resources and Life Sciences, Muthgasse 18, 1190 Vienna, Austria
| | - Corinna Rebnegger
- Department of Biotechnology, BOKU University of Natural Resources and Life Sciences, Muthgasse 18, 1190 Vienna, Austria.,CD-Laboratory for Growth-decoupled Protein Production in Yeast, BOKU University of Natural Resources and Life Sciences, Muthgasse 18, 1190 Vienna, Austria
| | - Josef Moser
- Austrian Centre of Industrial Biotechnology, Muthgasse 11, 1190 Vienna, Austria.,School of Bioengineering, University of Applied Sciences-FH Campus Wien, Muthgasse 11, 1190 Vienna, Austria
| | - Nadine Tatto
- Austrian Centre of Industrial Biotechnology, Muthgasse 11, 1190 Vienna, Austria.,Department of Biotechnology, BOKU University of Natural Resources and Life Sciences, Muthgasse 18, 1190 Vienna, Austria
| | - Alexandra B Graf
- Austrian Centre of Industrial Biotechnology, Muthgasse 11, 1190 Vienna, Austria.,School of Bioengineering, University of Applied Sciences-FH Campus Wien, Muthgasse 11, 1190 Vienna, Austria
| | - Diethard Mattanovich
- Austrian Centre of Industrial Biotechnology, Muthgasse 11, 1190 Vienna, Austria.,Department of Biotechnology, BOKU University of Natural Resources and Life Sciences, Muthgasse 18, 1190 Vienna, Austria
| | - Brigitte Gasser
- Austrian Centre of Industrial Biotechnology, Muthgasse 11, 1190 Vienna, Austria.,Department of Biotechnology, BOKU University of Natural Resources and Life Sciences, Muthgasse 18, 1190 Vienna, Austria.,CD-Laboratory for Growth-decoupled Protein Production in Yeast, BOKU University of Natural Resources and Life Sciences, Muthgasse 18, 1190 Vienna, Austria
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14
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Opalek M, Wloch-Salamon D. Aspects of Multicellularity in Saccharomyces cerevisiae Yeast: A Review of Evolutionary and Physiological Mechanisms. Genes (Basel) 2020; 11:genes11060690. [PMID: 32599749 PMCID: PMC7349301 DOI: 10.3390/genes11060690] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2020] [Revised: 06/22/2020] [Accepted: 06/22/2020] [Indexed: 12/11/2022] Open
Abstract
The evolutionary transition from single-celled to multicellular growth is a classic and intriguing problem in biology. Saccharomyces cerevisiae is a useful model to study questions regarding cell aggregation, heterogeneity and cooperation. In this review, we discuss scenarios of group formation and how this promotes facultative multicellularity in S. cerevisiae. We first describe proximate mechanisms leading to aggregation. These mechanisms include staying together and coming together, and can lead to group heterogeneity. Heterogeneity is promoted by nutrient limitation, structured environments and aging. We then characterize the evolutionary benefits and costs of facultative multicellularity in yeast. We summarize current knowledge and focus on the newest state-of-the-art discoveries that will fuel future research programmes aiming to understand facultative microbial multicellularity.
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15
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Piccirillo S, McCune AH, Dedert SR, Kempf CG, Jimenez B, Solst SR, Tiede-Lewis LM, Honigberg SM. How Boundaries Form: Linked Nonautonomous Feedback Loops Regulate Pattern Formation in Yeast Colonies. Genetics 2019; 213:1373-1386. [PMID: 31619446 PMCID: PMC6893387 DOI: 10.1534/genetics.119.302700] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2019] [Accepted: 10/15/2019] [Indexed: 12/28/2022] Open
Abstract
Under conditions in which budding yeast form colonies and then undergo meiosis/sporulation, the resulting colonies are organized such that a sharply defined layer of meiotic cells overlays a layer of unsporulated cells termed "feeder cells." This differentiation pattern requires activation of both the Rlm1/cell-wall integrity pathway and the Rim101/alkaline-response pathway. In the current study, we analyzed the connection between these two signaling pathways in regulating colony development by determining expression patterns and cell-autonomy relationships. We present evidence that two parallel cell-nonautonomous positive-feedback loops are active in colony patterning, an Rlm1-Slt2 loop active in feeder cells and an Rim101-Ime1 loop active in meiotic cells. The Rlm1-Slt2 loop is expressed first and subsequently activates the Rim101-Ime1 loop through a cell-nonautonomous mechanism. Once activated, each feedback loop activates the cell fate specific to its colony region. At the same time, cell-autonomous mechanisms inhibit ectopic fates within these regions. In addition, once the second loop is active, it represses the first loop through a cell-nonautonomous mechanism. Linked cell-nonautonomous positive-feedback loops, by amplifying small differences in microenvironments, may be a general mechanism for pattern formation in yeast and other organisms.
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Affiliation(s)
- Sarah Piccirillo
- Division of Cell Biology and Biophysics, School of Biological and Chemical Sciences, University of Missouri-Kansas City, Missouri 64110
| | - Abbigail H McCune
- Division of Cell Biology and Biophysics, School of Biological and Chemical Sciences, University of Missouri-Kansas City, Missouri 64110
| | - Samuel R Dedert
- Division of Cell Biology and Biophysics, School of Biological and Chemical Sciences, University of Missouri-Kansas City, Missouri 64110
| | - Cassandra G Kempf
- Division of Cell Biology and Biophysics, School of Biological and Chemical Sciences, University of Missouri-Kansas City, Missouri 64110
| | - Brian Jimenez
- Division of Cell Biology and Biophysics, School of Biological and Chemical Sciences, University of Missouri-Kansas City, Missouri 64110
| | - Shane R Solst
- Division of Cell Biology and Biophysics, School of Biological and Chemical Sciences, University of Missouri-Kansas City, Missouri 64110
| | - LeAnn M Tiede-Lewis
- UMKC Department of Oral and Craniofacial Sciences, University of Missouri-Kansas City, Missouri 64108
| | - Saul M Honigberg
- Division of Cell Biology and Biophysics, School of Biological and Chemical Sciences, University of Missouri-Kansas City, Missouri 64110
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16
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Affiliation(s)
- Chi V Dang
- Ludwig Institute for Cancer Research, New York, NY 10017, USA. .,The Wistar Institute, Philadelphia, PA 19104, USA
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17
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Tomova AA, Kujumdzieva AV, Petrova VY. Carbon source influences Saccharomyces cerevisiaeyeast cell survival strategies: quiescence or sporulation. BIOTECHNOL BIOTEC EQ 2019. [DOI: 10.1080/13102818.2019.1674188] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022] Open
Affiliation(s)
- Anna Atanasova Tomova
- Department “General and Industrial Microbiology”, Faculty of Biology, Sofia University “St. Kliment Ohridski”, Sofia, Bulgaria
| | - Anna Vengelova Kujumdzieva
- Department “General and Industrial Microbiology”, Faculty of Biology, Sofia University “St. Kliment Ohridski”, Sofia, Bulgaria
| | - Ventsislava Yankova Petrova
- Department “General and Industrial Microbiology”, Faculty of Biology, Sofia University “St. Kliment Ohridski”, Sofia, Bulgaria
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18
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Sipiczki M. Interspecies Hybridisation and Genome Chimerisation in Saccharomyces: Combining of Gene Pools of Species and Its Biotechnological Perspectives. Front Microbiol 2018; 9:3071. [PMID: 30619156 PMCID: PMC6297871 DOI: 10.3389/fmicb.2018.03071] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2018] [Accepted: 11/28/2018] [Indexed: 12/31/2022] Open
Abstract
Over the last one and a half decade, interspecies hybridisation has gained continuously increasing attention as a breeding technique suitable for transferring of genetic information between Saccharomyces species and mixing of their gene pools without genetic engineering. The hybrids frequently show positive transgressive phenotypes. Segregation of the hybrid genome results in mosaic (chimeric) strains that can outperform both the parents and the hybrids or exhibit novel positive phenotypic properties. Mitotic segregation can take place during the vegetative propagation of the sterile allodiploid hybrid cells. Meiotic segregation becomes possible after genome duplication (tetraploidisation) if it is followed by break-down of sterility. The allotetraploid cells are seemingly fertile because they form viable spores. But because of the autodiploidisation of the meiosis, sterile allodiploid spores are produced and thus the hybrid genome does not segregate (the second sterility barrier). However, malsegregation of MAT-carrying chromosomes in one of the subgenomes during allotetraploid meiosis (loss of MAT heterozygosity) results in fertile alloaneuploid spores. The breakdown of (the second) sterility barrier is followed by the loss of additional chromosomes in rapid succession and recombination between the subgenomes. The process (genome autoreduction in meiosis or GARMe) chimerises the genome and generates strains with chimeric (mosaic) genomes composed of various combinations of the genes of the parental strains. Since one of the subgenomes is preferentially reduced, the outcome is usually a strain having an (almost) complete genome from one parent and only a few genes or mosaics from the genome of the other parent. The fertility of the spores produced during GARMe provides possibilities also for introgressive backcrossing with one or the other parental strain, but genome chimerisation and gene transfer through series of backcrosses always with the same parent is likely to be less efficient than through meiotic or mitotic genome autoreduction. Hybridisation and the evolution of the hybrid genome (resizing and chimerisation) have been exploited in the improvement of industrial strains and applied to the breeding of new strains for specific purposes. Lists of successful projects are shown and certain major trends are discussed.
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Affiliation(s)
- Matthias Sipiczki
- Department of Genetics and Applied Microbiology, University of Debrecen, Debrecen, Hungary
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19
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Laporte D, Gouleme L, Jimenez L, Khemiri I, Sagot I. Mitochondria reorganization upon proliferation arrest predicts individual yeast cell fate. eLife 2018; 7:35685. [PMID: 30299253 PMCID: PMC6177259 DOI: 10.7554/elife.35685] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2018] [Accepted: 09/14/2018] [Indexed: 02/06/2023] Open
Abstract
Most cells spend the majority of their life in a non-proliferating state. When proliferation cessation is irreversible, cells are senescent. By contrast, if the arrest is only temporary, cells are defined as quiescent. These cellular states are hardly distinguishable without triggering proliferation resumption, hampering thus the study of quiescent cells properties. Here we show that quiescent and senescent yeast cells are recognizable based on their mitochondrial network morphology. Indeed, while quiescent yeast cells display numerous small vesicular mitochondria, senescent cells exhibit few globular mitochondria. This allowed us to reconsider at the individual-cell level, properties previously attributed to quiescent cells using population-based approaches. We demonstrate that cell’s propensity to enter quiescence is not influenced by replicative age, volume or density. Overall, our findings reveal that quiescent cells are not all identical but that their ability to survive is significantly improved when they exhibit the specific reorganization of several cellular machineries.
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Affiliation(s)
- Damien Laporte
- Centre National de la Recherche Scientifique, Université de Bordeaux - Institut de Biochimie et Génétique Cellulaires, Bordeaux, France
| | - Laëtitia Gouleme
- Centre National de la Recherche Scientifique, Université de Bordeaux - Institut de Biochimie et Génétique Cellulaires, Bordeaux, France
| | - Laure Jimenez
- Centre National de la Recherche Scientifique, Université de Bordeaux - Institut de Biochimie et Génétique Cellulaires, Bordeaux, France
| | - Ines Khemiri
- Centre National de la Recherche Scientifique, Université de Bordeaux - Institut de Biochimie et Génétique Cellulaires, Bordeaux, France
| | - Isabelle Sagot
- Centre National de la Recherche Scientifique, Université de Bordeaux - Institut de Biochimie et Génétique Cellulaires, Bordeaux, France
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20
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Marshall RS, Vierstra RD. Proteasome storage granules protect proteasomes from autophagic degradation upon carbon starvation. eLife 2018; 7:34532. [PMID: 29624167 PMCID: PMC5947986 DOI: 10.7554/elife.34532] [Citation(s) in RCA: 73] [Impact Index Per Article: 12.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2017] [Accepted: 04/05/2018] [Indexed: 12/14/2022] Open
Abstract
26S proteasome abundance is tightly regulated at multiple levels, including the elimination of excess or inactive particles by autophagy. In yeast, this proteaphagy occurs upon nitrogen starvation but not carbon starvation, which instead stimulates the rapid sequestration of proteasomes into cytoplasmic puncta termed proteasome storage granules (PSGs). Here, we show that PSGs help protect proteasomes from autophagic degradation. Both the core protease and regulatory particle sub-complexes are sequestered separately into PSGs via pathways dependent on the accessory proteins Blm10 and Spg5, respectively. Modulating PSG formation, either by perturbing cellular energy status or pH, or by genetically eliminating factors required for granule assembly, not only influences the rate of proteasome degradation, but also impacts cell viability upon recovery from carbon starvation. PSG formation and concomitant protection against proteaphagy also occurs in Arabidopsis, suggesting that PSGs represent an evolutionarily conserved cache of proteasomes that can be rapidly re-mobilized based on energy availability. Proteins perform many jobs within an organism, including providing structure and support, and protecting against infection. The levels of the many proteins in a cell need to be carefully controlled so that the correct amounts are present at the right place and time to perform these tasks. This control can be achieved by balancing the production of new proteins with the break down (or degradation) of proteins that are no longer required or become dysfunctional. Most cells have two pathways for degrading proteins. One pathway breaks down individual proteins specifically marked for elimination; this causes them to be recognized by a structure called the proteasome, which chops proteins into smaller pieces. Larger protein assemblies – including the proteasome itself – are to big for the proteasome and thus need to be degraded by another pathway called autophagy. This process engulfs and delivers parts of a cell to a membrane-bound compartment called the vacuole, which ‘digests’ and recycles these larger constituents. Proteasomes are degraded by autophagy when they are not working correctly and when nitrogen (a crucial nutrient) is in short supply. However, proteasomes are not degraded when cells lack carbon, even though this starvation is known to activate autophagy in the same way that an absence of nitrogen does. So how do proteasomes escape degradation when cells are starved for carbon? Marshall and Vierstra now show that upon carbon starvation, proteasomes rapidly exit the cell nucleus and cluster together in the main part of the cell (termed the cytosol). These clusters are known as proteasome storage granules (PSGs). In fungi and plants, mutations or conditions inside the cell that make it difficult for PSGs to assemble cause proteasomes to instead be broken down in the vacuole when carbon availability is low. Clustering into PSGs therefore protects proteasomes from autophagy. This clustering appears advantageous to cells; yeast cells that could form PSGs were better able to start growing again when their nutrient supply improved. Protein clustering (also known as aggregation) is an important strategy that cells use to survive stressful conditions. However, it can also be harmful when proteins aggregate inappropriately, such as occurs in Alzheimer’s disease. Researchers may be able to use PSG assembly as a convenient model to study the causes and consequences of protein aggregation; this knowledge could ultimately be applied to improve human health and crop productivity.
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Affiliation(s)
- Richard S Marshall
- Department of Biology, Washington University in St. Louis, St. Louis, United States
| | - Richard D Vierstra
- Department of Biology, Washington University in St. Louis, St. Louis, United States
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21
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Hanson SJ, Byrne KP, Wolfe KH. Flip/flop mating-type switching in the methylotrophic yeast Ogataea polymorpha is regulated by an Efg1-Rme1-Ste12 pathway. PLoS Genet 2017; 13:e1007092. [PMID: 29176810 PMCID: PMC5720833 DOI: 10.1371/journal.pgen.1007092] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2017] [Revised: 12/07/2017] [Accepted: 10/31/2017] [Indexed: 01/01/2023] Open
Abstract
In haploid cells of Ogataea (Hansenula) polymorpha an environmental signal, nitrogen starvation, induces a reversible change in the structure of a chromosome. This process, mating-type switching, inverts a 19-kb DNA region to place either MATa or MATα genes under centromeric repression of transcription, depending on the orientation of the region. Here, we investigated the genetic pathway that controls switching. We characterized the transcriptomes of haploid and diploid O. polymorpha by RNAseq in rich and nitrogen-deficient media, and found that there are no constitutively a-specific or α-specific genes other than the MAT genes themselves. We mapped a switching defect in a sibling species (O. parapolymorpha strain DL-1) by interspecies bulk segregant analysis to a frameshift in the transcription factor EFG1, which in Candida albicans regulates filamentous growth and white-opaque switching. Gene knockout, overexpression and ChIPseq experiments show that EFG1 regulates RME1, which in turn regulates STE12, to achieve mating-type switching. All three genes are necessary both for switching and for mating. Overexpression of RME1 or STE12 is sufficient to induce switching without a nitrogen depletion signal. The homologous recombination genes RAD51 and RAD17 are also necessary for switching. The pathway controlling switching in O. polymorpha shares no components with the regulation of HO in S. cerevisiae, which does not involve any environmental signal, but it shares some components with mating-type switching in Kluyveromyces lactis and with white-opaque phenotypic switching in C. albicans. The molecular mechanisms of self-fertility (homothallism) vary enormously among fungal species. We previously found that in the yeast Ogataea polymorpha, homothallism is achieved by a novel mating-type switching mechanism that exchanges the locations of MATa and MATα genes between expression and repression contexts. Switching in this species is induced by nitrogen depletion, unlike the analogous process in Saccharomyces cerevisiae. Here, we show that the upstream parts of the genetic pathway controlling the environmental induction of switching in O. polymorpha are the same as the environmental pathway that induces competence for mating in this species.
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Affiliation(s)
- Sara J. Hanson
- UCD Conway Institute, School of Medicine, University College Dublin, Dublin 4, Ireland
- Department of Molecular Biology, Colorado College, Colorado Springs, Colorado, United States of America
- * E-mail:
| | - Kevin P. Byrne
- UCD Conway Institute, School of Medicine, University College Dublin, Dublin 4, Ireland
| | - Kenneth H. Wolfe
- UCD Conway Institute, School of Medicine, University College Dublin, Dublin 4, Ireland
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22
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Leonov A, Feldman R, Piano A, Arlia-Ciommo A, Lutchman V, Ahmadi M, Elsaser S, Fakim H, Heshmati-Moghaddam M, Hussain A, Orfali S, Rajen H, Roofigari-Esfahani N, Rosanelli L, Titorenko VI. Caloric restriction extends yeast chronological lifespan via a mechanism linking cellular aging to cell cycle regulation, maintenance of a quiescent state, entry into a non-quiescent state and survival in the non-quiescent state. Oncotarget 2017; 8:69328-69350. [PMID: 29050207 PMCID: PMC5642482 DOI: 10.18632/oncotarget.20614] [Citation(s) in RCA: 41] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2017] [Accepted: 08/14/2017] [Indexed: 12/22/2022] Open
Abstract
A yeast culture grown in a nutrient-rich medium initially containing 2% glucose is not limited in calorie supply. When yeast cells cultured in this medium consume glucose, they undergo cell cycle arrest at a checkpoint in late G1 and differentiate into quiescent and non-quiescent cell populations. Studies of such differentiation have provided insights into mechanisms of yeast chronological aging under conditions of excessive calorie intake. Caloric restriction is an aging-delaying dietary intervention. Here, we assessed how caloric restriction influences the differentiation of chronologically aging yeast cultures into quiescent and non-quiescent cells, and how it affects their properties. We found that caloric restriction extends yeast chronological lifespan via a mechanism linking cellular aging to cell cycle regulation, maintenance of quiescence, entry into a non-quiescent state and survival in this state. Our findings suggest that caloric restriction delays yeast chronological aging by causing specific changes in the following: 1) a checkpoint in G1 for cell cycle arrest and entry into a quiescent state; 2) a growth phase in which high-density quiescent cells are committed to become low-density quiescent cells; 3) the differentiation of low-density quiescent cells into low-density non-quiescent cells; and 4) the conversion of high-density quiescent cells into high-density non-quiescent cells.
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Affiliation(s)
- Anna Leonov
- Department of Biology, Concordia University, Montreal, Quebec, Canada
| | - Rachel Feldman
- Department of Biology, Concordia University, Montreal, Quebec, Canada
| | - Amanda Piano
- Department of Biology, Concordia University, Montreal, Quebec, Canada
| | | | - Vicky Lutchman
- Department of Biology, Concordia University, Montreal, Quebec, Canada
| | - Masoumeh Ahmadi
- Department of Biology, Concordia University, Montreal, Quebec, Canada
| | - Sarah Elsaser
- Department of Biology, Concordia University, Montreal, Quebec, Canada
| | - Hana Fakim
- Department of Biology, Concordia University, Montreal, Quebec, Canada
| | | | - Asimah Hussain
- Department of Biology, Concordia University, Montreal, Quebec, Canada
| | - Sandra Orfali
- Department of Biology, Concordia University, Montreal, Quebec, Canada
| | | | | | - Leana Rosanelli
- Department of Biology, Concordia University, Montreal, Quebec, Canada
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23
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Abstract
Cell differentiation in yeast species is controlled by a reversible, programmed DNA-rearrangement process called mating-type switching. Switching is achieved by two functionally similar but structurally distinct processes in the budding yeast Saccharomyces cerevisiae and the fission yeast Schizosaccharomyces pombe. In both species, haploid cells possess one active and two silent copies of the mating-type locus (a three-cassette structure), the active locus is cleaved, and synthesis-dependent strand annealing is used to replace it with a copy of a silent locus encoding the opposite mating-type information. Each species has its own set of components responsible for regulating these processes. In this review, we summarize knowledge about the function and evolution of mating-type switching components in these species, including mechanisms of heterochromatin formation, MAT locus cleavage, donor bias, lineage tracking, and environmental regulation of switching. We compare switching in these well-studied species to others such as Kluyveromyces lactis and the methylotrophic yeasts Ogataea polymorpha and Komagataella phaffii. We focus on some key questions: Which cells switch mating type? What molecular apparatus is required for switching? Where did it come from? And what is the evolutionary purpose of switching?
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24
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Shrinking Daughters: Rlm1-Dependent G 1/S Checkpoint Maintains Saccharomyces cerevisiae Daughter Cell Size and Viability. Genetics 2017. [PMID: 28637712 DOI: 10.1534/genetics.117.204206] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023] Open
Abstract
The Rlm1 transcription factor is a target of the cell wall integrity pathway. We report that an rlm1Δ mutant grown on a nonfermentable carbon source at low osmolarity forms cell groups in which a mother cell is surrounded by smaller "satellite-daughter" cells. Mother cells in these groups progressed through repeated rounds of cell division with normal rates of bud growth and genetic stability; however, these cells underwent precocious START relative to wild-type mothers. Thus, once activated, Rlm1 delays the transition from G1 to S, a mechanism we term the cell wall/START (CW/START) checkpoint. The rlm1Δ satellite-cell phenotype is suppressed by deletion of either SLT2, which encodes the kinase that activates Rlm1, or SWI4, which is also activated by Slt2; suggesting that Slt2 can have opposing roles in regulating the START transition. Consistent with an Rlm1-dependent CW/START checkpoint, rlm1Δ satellite daughters were unable to grow or divide further even after transfer to rich medium, but UV irradiation in G1 could partially rescue rlm1Δ satellite daughters in the next division. Indeed, after cytokinesis, these satellite daughters shrank rapidly, displayed amorphous actin staining, and became more permeable. As a working hypothesis, we propose that duplication of an "actin-organizing center" in late G1 may be required both to progress through START and to reestablish the actin cytoskeleton in daughter cells.
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Adaptive Roles of SSY1 and SIR3 During Cycles of Growth and Starvation in Saccharomyces cerevisiae Populations Enriched for Quiescent or Nonquiescent Cells. G3-GENES GENOMES GENETICS 2017; 7:1899-1911. [PMID: 28450371 PMCID: PMC5473767 DOI: 10.1534/g3.117.041749] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
Over its evolutionary history, Saccharomyces cerevisiae has evolved to be well-adapted to fluctuating nutrient availability. In the presence of sufficient nutrients, yeast cells continue to proliferate, but upon starvation haploid yeast cells enter stationary phase and differentiate into nonquiescent (NQ) and quiescent (Q) cells. Q cells survive stress better than NQ cells and show greater viability when nutrient-rich conditions are restored. To investigate the genes that may be involved in the differentiation of Q and NQ cells, we serially propagated yeast populations that were enriched for either only Q or only NQ cell types over many repeated growth–starvation cycles. After 30 cycles (equivalent to 300 generations), each enriched population produced a higher proportion of the enriched cell type compared to the starting population, suggestive of adaptive change. We also observed differences in each population’s fitness suggesting possible tradeoffs: clones from NQ lines were better adapted to logarithmic growth, while clones from Q lines were better adapted to starvation. Whole-genome sequencing of clones from Q- and NQ-enriched lines revealed mutations in genes involved in the stress response and survival in limiting nutrients (ECM21, RSP5, MSN1, SIR4, and IRA2) in both Q and NQ lines, but also differences between the two lines: NQ line clones had recurrent independent mutations affecting the Ssy1p-Ptr3p-Ssy5p (SPS) amino acid sensing pathway, while Q line clones had recurrent, independent mutations in SIR3 and FAS1. Our results suggest that both sets of enriched-cell type lines responded to common, as well as distinct, selective pressures.
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