1
|
Durant M, Mucelli X, Huang LS. Meiotic Cytokinesis in Saccharomyces cerevisiae: Spores That Just Need Closure. J Fungi (Basel) 2024; 10:132. [PMID: 38392804 PMCID: PMC10890087 DOI: 10.3390/jof10020132] [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: 01/12/2024] [Revised: 01/30/2024] [Accepted: 02/04/2024] [Indexed: 02/24/2024] Open
Abstract
In the budding yeast Saccharomyces cerevisiae, sporulation occurs during starvation of a diploid cell and results in the formation of four haploid spores forming within the mother cell ascus. Meiosis divides the genetic material that is encapsulated by the prospore membrane that grows to surround the haploid nuclei; this membrane will eventually become the plasma membrane of the haploid spore. Cellularization of the spores occurs when the prospore membrane closes to capture the haploid nucleus along with some cytoplasmic material from the mother cell, and thus, closure of the prospore membrane is the meiotic cytokinetic event. This cytokinetic event involves the removal of the leading-edge protein complex, a complex of proteins that localizes to the leading edge of the growing prospore membrane. The development and closure of the prospore membrane must be coordinated with other meiotic exit events such as spindle disassembly. Timing of the closure of the prospore membrane depends on the meiotic exit pathway, which utilizes Cdc15, a Hippo-like kinase, and Sps1, an STE20 family GCKIII kinase, acting in parallel to the E3 ligase Ama1-APC/C. This review describes the sporulation process and focuses on the development of the prospore membrane and the regulation of prospore membrane closure.
Collapse
Affiliation(s)
- Matthew Durant
- Department of Biology, University of Massachusetts Boston, Boston, MA 02125, USA
| | - Xheni Mucelli
- Department of Biology, University of Massachusetts Boston, Boston, MA 02125, USA
| | - Linda S Huang
- Department of Biology, University of Massachusetts Boston, Boston, MA 02125, USA
| |
Collapse
|
2
|
Genome-wide identification and functional analysis of circRNAs in Trichophyton mentagrophytes spores and hyphae. Microb Pathog 2023; 176:106003. [PMID: 36702368 DOI: 10.1016/j.micpath.2023.106003] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2022] [Revised: 01/19/2023] [Accepted: 01/20/2023] [Indexed: 01/24/2023]
|
3
|
Liu G, Yang Y, Yang G, Duan S, Yuan P, Zhang S, Li F, Gao XD, Nakanishi H. Triosephosphate Isomerase and Its Product Glyceraldehyde-3-Phosphate Are Involved in the Regulatory Mechanism That Suppresses Exit from the Quiescent State in Yeast Cells. Microbiol Spectr 2022; 10:e0089722. [PMID: 35924934 PMCID: PMC9430402 DOI: 10.1128/spectrum.00897-22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2022] [Accepted: 07/17/2022] [Indexed: 11/27/2022] Open
Abstract
Cells of the budding yeast Saccharomyces cerevisiae form spores or stationary cells upon nutrient starvation. These quiescent cells are known to resume mitotic growth in response to nutrient signals, but the mechanism remains elusive. Here, we report that quiescent yeast cells are equipped with a negative regulatory mechanism which suppresses the commencement of mitotic growth. The regulatory process involves a glycolytic enzyme, triosephosphate isomerase (Tpi1), and its product, glyceraldehyde-3-phosphate (GAP). GAP serves as an inhibitory signaling molecule; indeed, the return to growth of spores or stationary cells is suppressed by the addition of GAP even in nutrient-rich growth media, though mitotic cells are not affected. Reciprocally, dormancy is abolished by heat treatment because of the heat sensitivity of Tpi1. For example, spores commence germination merely upon heat treatment, which indicates that the negative regulatory mechanism is actively required for spores to prevent premature germination. Stationary cells of Candida glabrata are also manipulated by heat and GAP, suggesting that the regulatory process is conserved in the pathogenic yeast. IMPORTANCE Our results suggest that, in quiescent cells, nutrient signals do not merely provoke a positive regulatory process to commence mitotic growth. Exit from the quiescent state in yeast cells is regulated by balancing between the positive and negative signaling pathways. Identifying the negative regulatory pathway would provide new insight into the regulation of the transition from the quiescent to the mitotic state. Clinically, quiescent cells are problematic because they are resistant to environmental stresses and antibiotics. Given that the quiescent state is modulated by manipulation of the negative regulatory mechanism, understanding this process is important not only for its biological interest but also as a potential target for antifungal treatment.
Collapse
Affiliation(s)
- Guoyu Liu
- Key Laboratory of Carbohydrate Chemistry and Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi, China
- Beijing Key Laboratory of the Innovative Development of Functional Staple and Nutritional Intervention for Chronic Diseases, China National Research Institute of Food and Fermentation Industries Co., Ltd., Beijing, China
| | - Yan Yang
- Key Laboratory of Carbohydrate Chemistry and Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi, China
| | - Ganglong Yang
- Key Laboratory of Carbohydrate Chemistry and Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi, China
| | - Shenglin Duan
- Beijing Key Laboratory of the Innovative Development of Functional Staple and Nutritional Intervention for Chronic Diseases, China National Research Institute of Food and Fermentation Industries Co., Ltd., Beijing, China
| | - Peng Yuan
- Beijing Key Laboratory of the Innovative Development of Functional Staple and Nutritional Intervention for Chronic Diseases, China National Research Institute of Food and Fermentation Industries Co., Ltd., Beijing, China
| | - Shuang Zhang
- The State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi, China
| | - Feng Li
- Key Laboratory of Carbohydrate Chemistry and Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi, China
| | - Xiao-Dong Gao
- Key Laboratory of Carbohydrate Chemistry and Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi, China
| | - Hideki Nakanishi
- Key Laboratory of Carbohydrate Chemistry and Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi, China
| |
Collapse
|
4
|
Mating-Type Switching in Budding Yeasts, from Flip/Flop Inversion to Cassette Mechanisms. Microbiol Mol Biol Rev 2022; 86:e0000721. [PMID: 35195440 PMCID: PMC8941940 DOI: 10.1128/mmbr.00007-21] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Mating-type switching is a natural but unusual genetic control process that regulates cell identity in ascomycete yeasts. It involves physically replacing one small piece of genomic DNA by another, resulting in replacement of the master regulatory genes in the mating pathway and hence a switch of cell type and mating behavior. In this review, we concentrate on recent progress that has been made on understanding the origins and evolution of mating-type switching systems in budding yeasts (subphylum Saccharomycotina). Because of the unusual nature and the complexity of the mechanism in Saccharomyces cerevisiae, mating-type switching was assumed until recently to have originated only once or twice during yeast evolution. However, comparative genomics analysis now shows that switching mechanisms arose many times independently-at least 11 times in budding yeasts and once in fission yeasts-a dramatic example of convergent evolution. Most of these lineages switch mating types by a flip/flop mechanism that inverts a section of a chromosome and is simpler than the well-characterized 3-locus cassette mechanism (MAT/HML/HMR) used by S. cerevisiae. Mating-type switching (secondary homothallism) is one of the two possible mechanisms by which a yeast species can become self-fertile. The other mechanism (primary homothallism) has also emerged independently in multiple evolutionary lineages of budding yeasts, indicating that homothallism has been favored strongly by natural selection. Recent work shows that HO endonuclease, which makes the double-strand DNA break that initiates switching at the S. cerevisiae MAT locus, evolved from an unusual mobile genetic element that originally targeted a glycolytic gene, FBA1.
Collapse
|
5
|
Böwer F, Schnittger A. How to Switch from Mitosis to Meiosis: Regulation of Germline Entry in Plants. Annu Rev Genet 2021; 55:427-452. [PMID: 34530640 DOI: 10.1146/annurev-genet-112618-043553] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
One of the major cell fate transitions in eukaryotes is entry into meiosis. While in single-celled yeast this decision is triggered by nutrient starvation, in multicellular eukaryotes, such as plants, it is under developmental control. In contrast to animals, plants have only a short germline and instruct cells to become meiocytes in reproductive organs late in development. This situation argues for a fundamentally different mechanism of how plants recruit meiocytes, and consistently, none of the regulators known to control meiotic entry in yeast and animals are present in plants. In recent years, several factors involved in meiotic entry have been identified, especially in the model plant Arabidopsis, and pieces of a regulatory network of germline control in plants are emerging. However, the corresponding studies also show that the mechanisms of meiotic entry control are diversified in flowering plants, calling for further analyses in different plant species. Expected final online publication date for the Annual Review of Genetics, Volume 55 is November 2021. Please see http://www.annualreviews.org/page/journal/pubdates for revised estimates.
Collapse
Affiliation(s)
- Franziska Böwer
- Department of Developmental Biology, Institute for Plant Sciences and Microbiology, University of Hamburg, D-22609 Hamburg, Germany;
| | - Arp Schnittger
- Department of Developmental Biology, Institute for Plant Sciences and Microbiology, University of Hamburg, D-22609 Hamburg, Germany;
| |
Collapse
|
6
|
Post-Transcriptional Control of Mating-Type Gene Expression during Gametogenesis in Saccharomyces cerevisiae. Biomolecules 2021; 11:biom11081223. [PMID: 34439889 PMCID: PMC8394074 DOI: 10.3390/biom11081223] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2021] [Revised: 08/05/2021] [Accepted: 08/14/2021] [Indexed: 12/13/2022] Open
Abstract
Gametogenesis in diploid cells of the budding yeast Saccharomyces cerevisiae produces four haploid meiotic products called spores. Spores are dormant until nutrients trigger germination, when they bud asexually or mate to return to the diploid state. Each sporulating diploid produces a mix of spores of two haploid mating types, a and α. In asexually dividing haploids, the mating types result from distinct, mutually exclusive gene expression programs responsible for production of mating pheromones and the receptors to sense them, all of which are silent in diploids. It was assumed that spores only transcribe haploid- and mating-type-specific genes upon germination. We find that dormant spores of each mating type harbor transcripts representing all these genes, with the exception of Mata1, which we found to be enriched in a spores. Mata1 transcripts, from a rare yeast gene with two introns, were mostly unspliced. If the retained introns reflect tethering to the MATa locus, this could provide a mechanism for biased inheritance. Translation of pheromones and receptors were repressed at least until germination. We find antisense transcripts to many mating genes that may be responsible. These findings add to the growing number of examples of post-transcriptional regulation of gene expression during gametogenesis.
Collapse
|
7
|
Spiliotis ET, McMurray MA. Masters of asymmetry - lessons and perspectives from 50 years of septins. Mol Biol Cell 2021; 31:2289-2297. [PMID: 32991244 PMCID: PMC7851956 DOI: 10.1091/mbc.e19-11-0648] [Citation(s) in RCA: 24] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022] Open
Abstract
Septins are a unique family of GTPases, which were discovered 50 years ago as essential genes for the asymmetric cell shape and division of budding yeast. Septins assemble into filamentous nonpolar polymers, which associate with distinct membrane macrodomains and subpopulations of actin filaments and microtubules. While structurally a cytoskeleton-like element, septins function predominantly as spatial regulators of protein localization and interactions. Septin scaffolds and barriers have provided a long-standing paradigm for the generation and maintenance of asymmetry in cell membranes. Septins also promote asymmetry by regulating the spatial organization of the actin and microtubule cytoskeleton, and biasing the directionality of membrane traffic. In this 50th anniversary perspective, we highlight how septins have conserved and adapted their roles as effectors of membrane and cytoplasmic asymmetry across fungi and animals. We conclude by outlining principles of septin function as a module of symmetry breaking, which alongside the monomeric small GTPases provides a core mechanism for the biogenesis of molecular asymmetry and cell polarity.
Collapse
Affiliation(s)
| | - Michael A McMurray
- Department of Cell and Developmental Biology, University of Colorado Anschutz Medical Campus, Aurora, CO 80045
| |
Collapse
|
8
|
Alfatah M, Wong JH, Krishnan VG, Lee YC, Sin QF, Goh CJH, Kong KW, Lee WT, Lewis J, Hoon S, Arumugam P. TORC1 regulates the transcriptional response to glucose and developmental cycle via the Tap42-Sit4-Rrd1/2 pathway in Saccharomyces cerevisiae. BMC Biol 2021; 19:95. [PMID: 33957926 PMCID: PMC8103650 DOI: 10.1186/s12915-021-01030-3] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2019] [Accepted: 04/18/2021] [Indexed: 01/22/2023] Open
Abstract
BACKGROUND Target of Rapamycin Complex 1 (TORC1) is a highly conserved eukaryotic protein complex that couples the presence of growth factors and nutrients in the environment with cellular proliferation. TORC1 is primarily implicated in linking amino acid levels with cellular growth in yeast and mammals. Although glucose deprivation has been shown to cause TORC1 inactivation in yeast, the precise role of TORC1 in glucose signaling and the underlying mechanisms remain unclear. RESULTS We demonstrate that the presence of glucose in the growth medium is both necessary and sufficient for TORC1 activation. TORC1 activity increases upon addition of glucose to yeast cells growing in a non-fermentable carbon source. Conversely, shifting yeast cells from glucose to a non-fermentable carbon source reduces TORC1 activity. Analysis of transcriptomic data revealed that glucose and TORC1 co-regulate about 27% (1668/6004) of yeast genes. We demonstrate that TORC1 orchestrates the expression of glucose-responsive genes mainly via the Tap42-Sit4-Rrd1/2 pathway. To confirm TORC1's function in glucose signaling, we tested its role in spore germination, a glucose-dependent developmental state transition in yeast. TORC1 regulates the glucose-responsive genes during spore germination and inhibition of TORC1 blocks spore germination. CONCLUSIONS Our studies indicate that a regulatory loop that involves activation of TORC1 by glucose and regulation of glucose-responsive genes by TORC1, mediates nutritional control of growth and development in yeast.
Collapse
Affiliation(s)
- Mohammad Alfatah
- Bioinformatics Institute, 30 Biopolis Street, Singapore, 138671, Singapore
| | - Jin Huei Wong
- Bioinformatics Institute, 30 Biopolis Street, Singapore, 138671, Singapore
| | | | - Yong Cheow Lee
- Bioinformatics Institute, 30 Biopolis Street, Singapore, 138671, Singapore
| | - Quan Feng Sin
- Bioinformatics Institute, 30 Biopolis Street, Singapore, 138671, Singapore
| | | | - Kiat Whye Kong
- Molecular Engineering Lab, 61 Biopolis Drive, Singapore, 138673, Singapore
| | - Wei Ting Lee
- Bioinformatics Institute, 30 Biopolis Street, Singapore, 138671, Singapore
| | - Jacqueline Lewis
- Bioinformatics Institute, 30 Biopolis Street, Singapore, 138671, Singapore
| | - Shawn Hoon
- Molecular Engineering Lab, 61 Biopolis Drive, Singapore, 138673, Singapore
| | - Prakash Arumugam
- Bioinformatics Institute, 30 Biopolis Street, Singapore, 138671, Singapore. .,Singapore Institute for Food and Biotechnology Innovation, 31 Biopolis Way, #01-02 Nanos, Singapore, 138669, Singapore. .,School of Biological Sciences, Nanyang Technological University, 60 Nanyang Drive, Singapore, 637551, Singapore.
| |
Collapse
|
9
|
Heasley LR, Singer E, Cooperman BJ, McMurray MA. Saccharomyces spores are born prepolarized to outgrow away from spore-spore connections and penetrate the ascus wall. Yeast 2020; 38:90-101. [PMID: 33238051 PMCID: PMC7898352 DOI: 10.1002/yea.3540] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2020] [Revised: 11/17/2020] [Accepted: 11/19/2020] [Indexed: 01/19/2023] Open
Abstract
How nonspore haploid Saccharomyces cells choose sites of budding and polarize towards pheromone signals in order to mate has been a subject of intense study. Unlike nonspore haploids, sibling spores produced via meiosis and sporulation by a diploid cell are physically interconnected and encased in a sac derived from the old cell wall of the diploid, called the ascus. Nonspore haploids bud adjacent to previous sites of budding, relying on stable cortical landmarks laid down during prior divisions, but because spore membranes are made de novo, it was assumed that, as is known for fission yeast, Saccharomyces spores break symmetry and polarize at random locations. Here, we show that this assumption is incorrect: Saccharomyces cerevisiae spores are born prepolarized to outgrow, prior to budding or mating, away from interspore bridges. Consequently, when spores bud within an intact ascus, their buds locally penetrate the ascus wall, and when they mate, the resulting zygotes adopt a unique morphology reflective of repolarization towards pheromone. Long-lived cortical foci containing the septin Cdc10 mark polarity sites, but the canonical bud site selection programme is dispensable for spore polarity, thus the origin and molecular composition of these landmarks remain unknown. These findings demand further investigation of previously overlooked mechanisms of polarity establishment and local cell wall digestion and highlight how a key step in the Saccharomyces life cycle has been historically neglected.
Collapse
Affiliation(s)
- Lydia R Heasley
- Cell and Developmental Biology, University of Colorado Anschutz Medical Campus, Aurora, Colorado, USA.,Environmental Health and Radiological Sciences, Colorado State University, Fort Collins, Colorado, USA
| | - Emily Singer
- Cell and Developmental Biology, University of Colorado Anschutz Medical Campus, Aurora, Colorado, USA
| | - Benjamin J Cooperman
- Cell and Developmental Biology, University of Colorado Anschutz Medical Campus, Aurora, Colorado, USA
| | - Michael A McMurray
- Cell and Developmental Biology, University of Colorado Anschutz Medical Campus, Aurora, Colorado, USA
| |
Collapse
|
10
|
Plante S, Landry CR. Closely related budding yeast species respond to different ecological signals for spore activation. Yeast 2020; 38:81-89. [PMID: 33202071 DOI: 10.1002/yea.3538] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2020] [Revised: 09/27/2020] [Accepted: 11/10/2020] [Indexed: 01/20/2023] Open
Abstract
Spore activation is one of the most important developmental decisions in fungi as it initiates the transition from dormant and stress-resistant cells to vegetative cells. Because in many species mating follows spore activation and germination, signals that trigger this developmental transition can also contribute to species reproductive barriers. Here, we examine the biochemical signals triggering spore activation in a natural species complex of budding yeast, Saccharomyces paradoxus (lineages SpA, SpB, SpC and SpC*). We first demonstrate that we can quantitatively monitor spore activation in these closely related lineages. Second, we dissect the composition of culture media to identify components necessary and/or sufficient to activate spores in the four lineages. We show that, contrary to expectation, glucose is necessary but not sufficient to trigger spore activation. We also show that two of the North American lineages (SpC and SpC*) diverge from the other North American (SpB) and European (SpA) lineages in terms of germination signal as their spore activation requires inorganic phosphate. Our results show that the way budding yeast interpret environmental conditions during spore activation diverged among closely related and incipient species, which means that it may play a role in their ecological differentiation and reproductive isolation. TAKE AWAY: Sensing of multiple compounds allows spore activation in non-domesticated budding yeast. Spore activation cues differ among Saccharomyces paradoxus lineages. Dextrose and phosphate signal activation in SpC and SpC* spores.
Collapse
Affiliation(s)
- Samuel Plante
- Institut de Biologie Intégrative et des Systèmes (IBIS), Université Laval, Québec, Québec, Canada.,Regroupement Québécois de Recherche sur la Fonction, l'Ingénierie et les Applications des Protéines, (PROTEO), Université Laval, Québec, Québec, Canada.,Département de biologie, Université Laval, Québec, Québec, Canada.,Département de biochimie, microbiologie et bio-informatique, Université Laval, Québec, Québec, Canada.,Centre de recherche en données massives (CRDM), Université Laval, Québec, Québec, Canada
| | - Christian R Landry
- Institut de Biologie Intégrative et des Systèmes (IBIS), Université Laval, Québec, Québec, Canada.,Regroupement Québécois de Recherche sur la Fonction, l'Ingénierie et les Applications des Protéines, (PROTEO), Université Laval, Québec, Québec, Canada.,Département de biologie, Université Laval, Québec, Québec, Canada.,Département de biochimie, microbiologie et bio-informatique, Université Laval, Québec, Québec, Canada.,Centre de recherche en données massives (CRDM), Université Laval, Québec, Québec, Canada
| |
Collapse
|
11
|
Maire T, Allertz T, Betjes MA, Youk H. Dormancy-to-death transition in yeast spores occurs due to gradual loss of gene-expressing ability. Mol Syst Biol 2020; 16:e9245. [PMID: 33206464 PMCID: PMC7673291 DOI: 10.15252/msb.20199245] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2019] [Revised: 10/20/2020] [Accepted: 10/21/2020] [Indexed: 11/28/2022] Open
Abstract
Dormancy is colloquially considered as extending lifespan by being still. Starved yeasts form dormant spores that wake-up (germinate) when nutrients reappear but cannot germinate (die) after some time. What sets their lifespans and how they age are open questions because what processes occur-and by how much-within each dormant spore remains unclear. With single-cell-level measurements, we discovered how dormant yeast spores age and die: spores have a quantifiable gene-expressing ability during dormancy that decreases over days to months until it vanishes, causing death. Specifically, each spore has a different probability of germinating that decreases because its ability to-without nutrients-express genes decreases, as revealed by a synthetic circuit that forces GFP expression during dormancy. Decreasing amounts of molecules required for gene expression-including RNA polymerases-decreases gene-expressing ability which then decreases chances of germinating. Spores gradually lose these molecules because they are produced too slowly compared with their degradations, causing gene-expressing ability to eventually vanish and, thus, death. Our work provides a systems-level view of dormancy-to-death transition.
Collapse
Affiliation(s)
- Théo Maire
- Kavli Institute of NanoscienceDelftThe Netherlands
- Department of BionanoscienceDelft University of TechnologyDelftThe Netherlands
| | - Tim Allertz
- Kavli Institute of NanoscienceDelftThe Netherlands
- Department of BionanoscienceDelft University of TechnologyDelftThe Netherlands
| | - Max A Betjes
- Kavli Institute of NanoscienceDelftThe Netherlands
- Department of BionanoscienceDelft University of TechnologyDelftThe Netherlands
| | - Hyun Youk
- Kavli Institute of NanoscienceDelftThe Netherlands
- CIFARCIFAR Azrieli Global Scholars ProgramTorontoONCanada
- Program in Molecular MedicineUniversity of Massachusetts Medical SchoolWorcesterMAUSA
- Program in Systems BiologyUniversity of Massachusetts Medical SchoolWorcesterMAUSA
| |
Collapse
|
12
|
Sporulation in Ashbya gossypii. J Fungi (Basel) 2020; 6:jof6030157. [PMID: 32872517 PMCID: PMC7558398 DOI: 10.3390/jof6030157] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2020] [Revised: 08/26/2020] [Accepted: 08/28/2020] [Indexed: 12/28/2022] Open
Abstract
Ashbya gossypii is a filamentous ascomycete belonging to the yeast family of Saccharomycetaceae. At the end of its growth phase Ashbya generates abundant amounts of riboflavin and spores that form within sporangia derived from fragmented cellular compartments of hyphae. The length of spores differs within species of the genus. Needle-shaped Ashbya spores aggregate via terminal filaments. A. gossypii is a homothallic fungus which may possess a and α mating types. However, the solo-MATa type strain is self-fertile and sporulates abundantly apparently without the need of prior mating. The central components required for the regulation of sporulation, encoded by IME1, IME2, IME4, KAR4, are conserved with Saccharomyces cerevisiae. Nutrient depletion generates a strong positive signal for sporulation via the cAMP-PKA pathway and SOK2, which is also essential for sporulation. Strong inhibitors of sporulation besides mutations in the central regulatory genes are the addition of exogenous cAMP or the overexpression of the mating type gene MATα2. Sporulation has been dissected using gene-function analyses and global RNA-seq transcriptomics. This revealed a role of Msn2/4, another potential PKA-target, for spore wall formation and a key dual role of the protein A kinase Tpk2 at the onset of sporulation as well as for breaking the dormancy of spores to initiate germination. Recent work has provided an overview of ascus development, regulation of sporulation and spore maturation. This will be summarized in the current review with a focus on the central regulatory genes. Current research and open questions will also be discussed.
Collapse
|
13
|
Liu T, Huang Y, Chen XX, Long X, Yang YH, Zhu ML, Mo MH, Zhang KQ. Comparative Transcriptomics Reveals Features and Possible Mechanisms of Glucose-Mediated Soil Fungistasis Relief in Arthrobotrys oligospora. Front Microbiol 2020; 10:3143. [PMID: 32038576 PMCID: PMC6989558 DOI: 10.3389/fmicb.2019.03143] [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: 08/12/2019] [Accepted: 12/27/2019] [Indexed: 01/27/2023] Open
Abstract
Soil-borne pest diseases result in large annual agricultural losses globally. Fungal bio-control agents are an alternative means of controlling pest diseases; however, soil fungistasis limits the effect of fungal agents. Nutrients can relieve soil fungistasis, but the mechanisms behind this process remain poorly understood. In this study, we determined and quantified the transcriptomes of Arthrobotrys oligospora, a nematode-trapping fungus, derived from samples of fresh conidia, germinated conidia, soil fungistatic conidia, and glucose-relieved conidia. The transcriptomes of fungistatic and glucose-relieved conidia were significantly different from those of the other two conidia samples. KEGG pathway analyses showed that those genes upregulated in fungistatic and glucose-relieved conidia were mainly involved in translation and substance metabolism, and the downregulated genes were mainly involved in MAPK pathway, autophagy, mitophagy, and endocytosis. As being different from the transcriptome of fungistatic conidia, upregulated genes in the transcriptome of glucose-relieved conidia are also related to replication and repair, spliceosome, oxidative phosphorylation, autophagy, and degradation pathway (lysosome, proteasome, and RNA degradation). And the upregulated genes resulted from comparison of glucose-relieved conidia and fungistatic conidia were enriched in metabolic pathways, cycle, DNA replication, and repair. The differentially splicing events in the transcriptome of glucose-relieved conidia are far more than that of other two transcriptomes, and genes regulated by differentially splicing were analyzed through KEGG pathway analysis. Furthermore, autophagy genes were proved to play important role in resisting soil fungistasis and glucose-mediated soil fungistasis relief. These data indicate that, in addition to being a carbon and energy source for conidia germination, glucose may also help to relieve soil fungistasis by activating many cellular processes, including autophagy, DNA replication and repair, RNA alternative splicing, and degradation pathways.
Collapse
Affiliation(s)
- Tong Liu
- State Key Laboratory for Conservation and Utilization of Bio-Resources in Yunnan, Yunnan University, Kunming, China
| | - Ying Huang
- State Key Laboratory for Conservation and Utilization of Bio-Resources in Yunnan, Yunnan University, Kunming, China
| | - Xiang-Xiang Chen
- State Key Laboratory for Conservation and Utilization of Bio-Resources in Yunnan, Yunnan University, Kunming, China
| | - Xi Long
- State Key Laboratory for Conservation and Utilization of Bio-Resources in Yunnan, Yunnan University, Kunming, China
| | - Yun-He Yang
- State Key Laboratory for Conservation and Utilization of Bio-Resources in Yunnan, Yunnan University, Kunming, China
| | - Ming-Liang Zhu
- Yunnan of China National Tobacco Corporation, Kunming, China
| | - Ming-He Mo
- State Key Laboratory for Conservation and Utilization of Bio-Resources in Yunnan, Yunnan University, Kunming, China
- Biocontrol Engineering Research Center of Plant Disease and Pest, Yunnan University, Kunming, China
- Biocontrol Engineering Research Center of Crop Disease and Pest, Yunnan University, Kunming, China
| | - Ke-Qin Zhang
- State Key Laboratory for Conservation and Utilization of Bio-Resources in Yunnan, Yunnan University, Kunming, China
- Key Laboratory of Microbial Diversity in Southwest China, Ministry of Education, Yunnan Institute of Microbiology, Yunnan University, Kunming, China
| |
Collapse
|
14
|
Abstract
Spores are required for long-term survival of many organisms, including most fungi. For the majority of fatal human fungal pathogens, spore germination is the key process required to initiate vegetative growth and ultimately cause disease. Because germination is required for pathogenesis, the process could hold fungal-specific targets for new antifungal drug development. Compounds that inhibit germination could be developed into high efficacy, low-toxicity drugs for use in the prevention and/or treatment of fungal spore-mediated diseases. To identify drugs with the ability to inhibit pathogenic fungal spore germination, we developed a novel luciferase-based germination assay, using spores of the meningitis-causing yeast Cryptococcus. We screened the L1300 Selleck Library of FDA-approved drugs and identified 27 that inhibit germination. Of these, 22 inhibited both germination and yeast growth, and 21 have not been previously indicated for use in the treatment of fungal diseases. We quantitated the inhibition phenotypes of 10 specific germination/growth inhibitors in detail and tested one drug, the antiparasitic compound pentamidine, in our mouse intranasal model of cryptococcal infection. We discovered that pentamidine was effective at reducing lung fungal burdens when used in either prophylaxis (before infection) or treatment (after establishing an infection). Due to its efficacy in vivo and low intranasal toxicity, pentamidine is a lead candidate for repurposing for broader use as an antigerminant to prevent spore-mediated disease in immunocompromised patients. Not only does pentamidine provide an opportunity for prophylaxis against fungal spores, but it also provides proof of concept for targeting pathogenic spore germination for antifungal drug development.
Collapse
|
15
|
Chen L, Pan X, Zhang YH, Liu M, Huang T, Cai YD. Classification of Widely and Rarely Expressed Genes with Recurrent Neural Network. Comput Struct Biotechnol J 2018; 17:49-60. [PMID: 30595815 PMCID: PMC6307323 DOI: 10.1016/j.csbj.2018.12.002] [Citation(s) in RCA: 30] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2018] [Revised: 12/07/2018] [Accepted: 12/09/2018] [Indexed: 02/06/2023] Open
Abstract
A tissue-specific gene expression shapes the formation of tissues, while gene expression changes reflect the immune response of the human body to environmental stimulations or pressure, particularly in disease conditions, such as cancers. A few genes are commonly expressed across tissues or various cancers, while others are not. To investigate the functional differences between widely and rarely expressed genes, we defined the genes that were expressed in 32 normal tissues/cancers (i.e., called widely expressed genes; FPKM >1 in all samples) and those that were not detected (i.e., called rarely expressed genes; FPKM <1 in all samples) based on the large gene expression data set provided by Uhlen et al. Each gene was encoded using the gene ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment scores. Minimum redundancy maximum relevance (mRMR) was used to measure and rank these features on the mRMR feature list. Thereafter, we applied the incremental feature selection method with a supervised classifier recurrent neural network (RNN) to select the discriminate features for classifying widely expressed genes from rarely expressed genes and construct an optimum RNN classifier. The Youden's indexes generated by the optimum RNN classifier and evaluated using a 10-fold cross validation were 0.739 for normal tissues and 0.639 for cancers. Furthermore, the underlying mechanisms of the key discriminate GO and KEGG features were analyzed. Results can facilitate the identification of the expression landscape of genes and elucidation of how gene expression shapes tissues and the microenvironment of cancers. Some genes are widely expressed across tissues or various cancers. A number of genes are rarely expressed across tissues or various cancers. The functional differences between widely and rarely expressed genes were studied. Several GO terms and KEGG pathways were extracted and analyzed.
Collapse
Affiliation(s)
- Lei Chen
- School of Life Sciences, Shanghai University, Shanghai 200444, People's Republic of China.,College of Information Engineering, Shanghai Maritime University, Shanghai 201306, People's Republic of China.,Shanghai Key Laboratory of PMMP, East China Normal University, Shanghai 200241, People's Republic of China
| | - XiaoYong Pan
- Department of Medical Informatics, Erasmus MC, Rotterdam, the Netherlands
| | - Yu-Hang Zhang
- Institute of Health Sciences, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai 200031, People's Republic of China
| | - Min Liu
- College of Information Engineering, Shanghai Maritime University, Shanghai 201306, People's Republic of China
| | - Tao Huang
- Institute of Health Sciences, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai 200031, People's Republic of China
| | - Yu-Dong Cai
- School of Life Sciences, Shanghai University, Shanghai 200444, People's Republic of China
| |
Collapse
|
16
|
McClure AW, Jacobs KC, Zyla TR, Lew DJ. Mating in wild yeast: delayed interest in sex after spore germination. Mol Biol Cell 2018; 29:3119-3127. [PMID: 30355051 PMCID: PMC6340204 DOI: 10.1091/mbc.e18-08-0528] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022] Open
Abstract
Studies of laboratory strains of Saccharomyces cerevisiae have uncovered signaling pathways involved in mating, including information-processing strategies to optimize decisions to mate or to bud. However, lab strains are heterothallic (unable to self-mate), while wild yeast are homothallic. And while mating of lab strains is studied using cycling haploid cells, mating of wild yeast is thought to involve germinating spores. Thus, it was unclear whether lab strategies would be appropriate in the wild. Here, we have investigated the behavior of several yeast strains derived from wild isolates. Following germination, these strains displayed large differences in their propensity to mate or to enter the cell cycle. The variable interest in sex following germination was correlated with differences in pheromone production, which were due to both cis- and trans-acting factors. Our findings suggest that yeast spores germinating in the wild may often enter the cell cycle and form microcolonies before engaging in mating.
Collapse
Affiliation(s)
- Allison W McClure
- Department of Pharmacology and Cancer Biology, Duke University Medical Center, Durham, NC 27710
| | - Katherine C Jacobs
- Department of Pharmacology and Cancer Biology, Duke University Medical Center, Durham, NC 27710
| | - Trevin R Zyla
- Department of Pharmacology and Cancer Biology, Duke University Medical Center, Durham, NC 27710
| | - Daniel J Lew
- Department of Pharmacology and Cancer Biology, Duke University Medical Center, Durham, NC 27710
| |
Collapse
|
17
|
Plante S, Normant V, Ramos-Torres KM, Labbé S. Cell-surface copper transporters and superoxide dismutase 1 are essential for outgrowth during fungal spore germination. J Biol Chem 2017; 292:11896-11914. [PMID: 28572514 PMCID: PMC5512082 DOI: 10.1074/jbc.m117.794677] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2017] [Revised: 05/26/2017] [Indexed: 11/06/2022] Open
Abstract
During fungal spore germination, a resting spore returns to a conventional mode of cell division and resumes vegetative growth, but the requirements for spore germination are incompletely understood. Here, we show that copper is essential for spore germination in Schizosaccharomyces pombe Germinating spores develop a single germ tube that emerges from the outer spore wall in a process called outgrowth. Under low-copper conditions, the copper transporters Ctr4 and Ctr5 are maximally expressed at the onset of outgrowth. In the case of Ctr6, its expression is broader, taking place before and during outgrowth. Spores lacking Ctr4, Ctr5, and the copper sensor Cuf1 exhibit complete germination arrest at outgrowth. In contrast, ctr6 deletion only partially interferes with formation of outgrowing spores. At outgrowth, Ctr4-GFP and Ctr5-Cherry first co-localize at the spore contour, followed by re-location to a middle peripheral spore region. Subsequently, they move away from the spore body to occupy the periphery of the nascent cell. After breaking of spore dormancy, Ctr6 localizes to the vacuole membranes that are enriched in the spore body relative to the germ tube. Using a copper-binding tracker, results showed that labile copper is preferentially localized to the spore body. Further analysis showed that Ctr4 and Ctr6 are required for copper-dependent activation of the superoxide dismutase 1 (SOD1) during spore germination. This activation is critical because the loss of SOD1 activity blocked spore germination at outgrowth. Taken together, these results indicate that cell-surface copper transporters and SOD1 are required for completion of the spore germination program.
Collapse
MESH Headings
- Cation Transport Proteins/genetics
- Cation Transport Proteins/metabolism
- Copper/metabolism
- Enzyme Activation
- Gene Deletion
- Gene Expression Regulation, Fungal
- Green Fluorescent Proteins/genetics
- Green Fluorescent Proteins/metabolism
- Luminescent Proteins/genetics
- Luminescent Proteins/metabolism
- Microscopy, Fluorescence
- Microscopy, Interference
- Microscopy, Phase-Contrast
- Protein Isoforms/genetics
- Protein Isoforms/metabolism
- Protein Transport
- RNA, Fungal/metabolism
- RNA, Messenger/metabolism
- Recombinant Fusion Proteins/genetics
- Recombinant Fusion Proteins/metabolism
- SLC31 Proteins
- Schizosaccharomyces/cytology
- Schizosaccharomyces/growth & development
- Schizosaccharomyces/metabolism
- Schizosaccharomyces/physiology
- Schizosaccharomyces pombe Proteins/genetics
- Schizosaccharomyces pombe Proteins/metabolism
- Spores, Fungal/cytology
- Spores, Fungal/growth & development
- Spores, Fungal/metabolism
- Spores, Fungal/physiology
- Superoxide Dismutase-1/metabolism
- Transcription Factors/genetics
- Transcription Factors/metabolism
- Red Fluorescent Protein
Collapse
Affiliation(s)
- Samuel Plante
- Département de Biochimie, Faculté de Médecine et des Sciences de la Santé, Université de Sherbrooke, Sherbrooke, Quebec J1E 4K8, Canada
| | - Vincent Normant
- Département de Biochimie, Faculté de Médecine et des Sciences de la Santé, Université de Sherbrooke, Sherbrooke, Quebec J1E 4K8, Canada
| | - Karla M Ramos-Torres
- Department of Chemistry, University of California at Berkeley, Berkeley, California 94720
| | - Simon Labbé
- Département de Biochimie, Faculté de Médecine et des Sciences de la Santé, Université de Sherbrooke, Sherbrooke, Quebec J1E 4K8, Canada.
| |
Collapse
|
18
|
Sporulation: how to survive on planet Earth (and beyond). Curr Genet 2017; 63:831-838. [PMID: 28421279 DOI: 10.1007/s00294-017-0694-7] [Citation(s) in RCA: 38] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2017] [Revised: 04/06/2017] [Accepted: 04/08/2017] [Indexed: 02/07/2023]
Abstract
Sporulation is a strategy widely utilized by a wide variety of organisms to adapt to changes in their individual environmental niches and survive in time and/or space until they encounter conditions acceptable for vegetative growth. The spores produced by bacteria have been the subjects of extensive studies, and several systems such as Bacillus subtilis have provided ample opportunities to understand the molecular basis of spore biogenesis and germination. In contrast, the spores of other microbes, such as fungi, are relatively poorly understood. Studies of sporulation in model systems such as Saccharomyces cerevisiae and Aspergillus nidulans have established a basis for investigating eukaryotic spores, but very little is known at the molecular level about how spores function. This is especially true among the spores of human fungal pathogens such as the most common cause of fatal fungal disease, Cryptococcus neoformans. Recent proteomic studies are helping to determine the molecular mechanisms by which pathogenic fungal spores are formed, persist and germinate into actively growing agents of human disease.
Collapse
|
19
|
Barkal LJ, Walsh NM, Botts MR, Beebe DJ, Hull CM. Leveraging a high resolution microfluidic assay reveals insights into pathogenic fungal spore germination. Integr Biol (Camb) 2016; 8:603-15. [PMID: 27026574 PMCID: PMC4868663 DOI: 10.1039/c6ib00012f] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
Germination of spores into actively growing cells is a process essential for survival and pathogenesis of many microbes. Molecular mechanisms governing germination, however, are poorly understood in part because few tools exist for evaluating and interrogating the process. Here, we introduce an assay that leverages developments in microfluidic technology and image processing to quantitatively measure germination with unprecedented resolution, assessing both individual cells and the population as a whole. Using spores from Cryptococcus neoformans, a leading cause of fatal fungal disease in humans, we developed a platform to evaluate spores as they undergo morphological changes during differentiation into vegetatively growing yeast. The assay uses pipet-accessible microdevices that can be arrayed for efficient testing of diverse microenvironmental variables, including temperature and nutrients. We discovered that temperature influences germination rate, a carbon source alone is sufficient to induce germination, and the addition of a nitrogen source sustains it. Using this information, we optimized the assay for use with fungal growth inhibitors to pinpoint stages of germination inhibition. Unexpectedly, the clinical antifungal drugs amphotericin B and fluconazole did not significantly alter the process or timing of the transition from spore to yeast, indicating that vegetative growth and germination are distinct processes in C. neoformans. Finally, we used the high temporal resolution of the assay to determine the precise defect in a slow-germination mutant. Combining advances in microfluidics with a robust fungal molecular genetic system allowed us to identify and alter key temporal, morphological, and molecular events that occur during fungal germination.
Collapse
Affiliation(s)
- Layla J. Barkal
- Department of Biomedical Engineering, 1111 Highland Ave, University of Wisconsin-Madison, Madison, WI 53705, USA
| | - Naomi M. Walsh
- Department of Biomolecular Chemistry, 420 Henry Mall, University of Wisconsin-Madison, School of Medicine and Public Health, Madison, WI 53706, USA
| | - Michael R. Botts
- Department of Biomolecular Chemistry, 420 Henry Mall, University of Wisconsin-Madison, School of Medicine and Public Health, Madison, WI 53706, USA
| | - David J. Beebe
- Department of Biomedical Engineering, 1111 Highland Ave, University of Wisconsin-Madison, Madison, WI 53705, USA
| | - Christina M. Hull
- Department of Biomolecular Chemistry, 420 Henry Mall, University of Wisconsin-Madison, School of Medicine and Public Health, Madison, WI 53706, USA
- Department of Medical Microbiology and Immunology, 1550 Linden Drive, University of Wisconsin-Madison, School of Medicine and Public Health, Madison, WI 53706, USA
| |
Collapse
|
20
|
Stelkens RB, Miller EL, Greig D. Asynchronous spore germination in isogenic natural isolates ofSaccharomyces paradoxus. FEMS Yeast Res 2016; 16:fow012. [DOI: 10.1093/femsyr/fow012] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 02/10/2016] [Indexed: 12/18/2022] Open
|
21
|
Heasley LR, McMurray MA. Roles of septins in prospore membrane morphogenesis and spore wall assembly in Saccharomyces cerevisiae. Mol Biol Cell 2015; 27:442-50. [PMID: 26680739 PMCID: PMC4751596 DOI: 10.1091/mbc.e15-10-0721] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2015] [Accepted: 12/08/2015] [Indexed: 12/11/2022] Open
Abstract
In mitotically dividing cells, septin proteins form cytoskeletal filaments that function in cell morphogenesis and division. Gametogenesis in yeast couples meiosis with a fundamentally different form of cytokinesis involving de novo membrane synthesis. Budding yeast septins are critical for spore membrane extension and wall assembly. The highly conserved family of septin proteins has important functions in cytokinesis in mitotically proliferating cells. A different form of cytokinesis occurs during gametogenesis in Saccharomyces cerevisiae, in which four haploid meiotic products become encased by prospore membrane (PSMs) and specialized, stress-resistant spore walls. Septins are known to localize in a series of structures near the growing PSM, but previous studies noted only mild sporulation defects upon septin mutation. We report that directed PSM extension fails in many septin-mutant cells, and, for those that do succeed, walls are abnormal, leading to increased susceptibility to heating, freezing, and digestion by the Drosophila gut. Septin mutants mislocalize the leading-edge protein (LEP) complex required for normal PSM and wall biogenesis, and ectopic expression of the LEP protein Ssp1 perturbs mitotic septin localization and function, suggesting a functional interaction. Strikingly, extra copies of septin CDC10 rescue sporulation and LEP localization in cells lacking Sma1, a phospholipase D–associated protein dispensable for initiation of PSM assembly and PSM curvature but required for PSM extension. These findings point to key septin functions in directing efficient membrane and cell wall synthesis during budding yeast gametogenesis.
Collapse
Affiliation(s)
- Lydia R Heasley
- University of Colorado Denver Anschutz Medical Campus, Aurora, CO 80045
| | | |
Collapse
|
22
|
Deng GM, Yang QS, He WD, Li CY, Yang J, Zuo CW, Gao J, Sheng O, Lu SY, Zhang S, Yi GJ. Proteomic analysis of conidia germination in Fusarium oxysporum f. sp. cubense tropical race 4 reveals new targets in ergosterol biosynthesis pathway for controlling Fusarium wilt of banana. Appl Microbiol Biotechnol 2015; 99:7189-207. [DOI: 10.1007/s00253-015-6768-x] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2015] [Revised: 06/04/2015] [Accepted: 06/08/2015] [Indexed: 12/30/2022]
|
23
|
Danziger SA, Reiss DJ, Ratushny AV, Smith JJ, Plaisier CL, Aitchison JD, Baliga NS. Bicluster Sampled Coherence Metric (BSCM) provides an accurate environmental context for phenotype predictions. BMC SYSTEMS BIOLOGY 2015; 9 Suppl 2:S1. [PMID: 25881257 PMCID: PMC4407105 DOI: 10.1186/1752-0509-9-s2-s1] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
Background Biclustering is a popular method for identifying under which experimental conditions biological signatures are co-expressed. However, the general biclustering problem is NP-hard, offering room to focus algorithms on specific biological tasks. We hypothesize that conditional co-regulation of genes is a key factor in determining cell phenotype and that accurately segregating conditions in biclusters will improve such predictions. Thus, we developed a bicluster sampled coherence metric (BSCM) for determining which conditions and signals should be included in a bicluster. Results Our BSCM calculates condition and cluster size specific p-values, and we incorporated these into the popular integrated biclustering algorithm cMonkey. We demonstrate that incorporation of our new algorithm significantly improves bicluster co-regulation scores (p-value = 0.009) and GO annotation scores (p-value = 0.004). Additionally, we used a bicluster based signal to predict whether a given experimental condition will result in yeast peroxisome induction. Using the new algorithm, the classifier accuracy improves from 41.9% to 76.1% correct. Conclusions We demonstrate that the proposed BSCM helps determine which signals ought to be co-clustered, resulting in more accurately assigned bicluster membership. Furthermore, we show that BSCM can be extended to more accurately detect under which experimental conditions the genes are co-clustered. Features derived from this more accurate analysis of conditional regulation results in a dramatic improvement in the ability to predict a cellular phenotype in yeast. The latest cMonkey is available for download at https://github.com/baliga-lab/cmonkey2. The experimental data and source code featured in this paper is available http://AitchisonLab.com/BSCM. BSCM has been incorporated in the official cMonkey release.
Collapse
|
24
|
Liu Y, Stuparevic I, Xie B, Becker E, Law MJ, Primig M. The conserved histone deacetylase Rpd3 and the DNA binding regulator Ume6 repressBOI1's meiotic transcript isoform during vegetative growth inSaccharomyces cerevisiae. Mol Microbiol 2015; 96:861-74. [DOI: 10.1111/mmi.12976] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 02/17/2015] [Indexed: 12/26/2022]
Affiliation(s)
- Yuchen Liu
- Inserm U1085 IRSET; Inserm; 35042 Rennes France
| | | | | | - Emmanuelle Becker
- Inserm U1085 IRSET; Inserm; 35042 Rennes France
- Departement des sciences de la vie et de l'environnement; Université de Rennes 1; 35042 Rennes France
| | - Michael J. Law
- School of Osteopathic Medicine; Rowan University; Stratford NJ 08084 USA
| | | |
Collapse
|
25
|
Siozios S, Tosi L, Ferrarini A, Ferrari A, Tononi P, Bellin D, Maurhofer M, Gessler C, Delledonne M, Pertot I. Transcriptional Reprogramming of the Mycoparasitic Fungus Ampelomyces quisqualis During the Powdery Mildew Host-Induced Germination. PHYTOPATHOLOGY 2015; 105:199-209. [PMID: 25185010 DOI: 10.1094/phyto-01-14-0013-r] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/03/2023]
Abstract
Ampelomyces quisqualis is a mycoparasite of a diverse range of phytopathogenic fungi associated with the powdery mildew disease. Among them are several Erysiphaceae species with great economic impact on high-value crops such as grape. Due to its ability to parasitize and prevent the spread of powdery mildews, A. quisqualis has received considerable attention for its biocontrol potential. However, and in sharp contrast to the extensively studied biocontrol species belonging to the genus Trichoderma, little is known about the biology of A. quisqualis at the molecular and genetic levels. We present the first genome-wide transcription profiling in A. quisqualis during host-induced germination. A total of 1,536 putative genes showed significant changes in transcription during the germination of A. quisqualis. This finding denotes an extensive transcriptional reprogramming of A. quisqualis induced by the presence of the host. Several upregulated genes were predicted to encode for putative mycoparasitism-related proteins such as secreted proteases, virulence factors, and proteins related to toxin biosynthesis. Our data provide the most comprehensive sequence resource currently available for A. quisqualis in addition to offering valuable insights into the biology of A. quisqualis and its mycoparasitic lifestyle. Eventually, this may improve the biocontrol capacity of this mycoparasite.
Collapse
|
26
|
Treusch S, Albert FW, Bloom JS, Kotenko IE, Kruglyak L. Genetic mapping of MAPK-mediated complex traits Across S. cerevisiae. PLoS Genet 2015; 11:e1004913. [PMID: 25569670 PMCID: PMC4287466 DOI: 10.1371/journal.pgen.1004913] [Citation(s) in RCA: 32] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2014] [Accepted: 11/21/2014] [Indexed: 01/22/2023] Open
Abstract
Signaling pathways enable cells to sense and respond to their environment. Many cellular signaling strategies are conserved from fungi to humans, yet their activity and phenotypic consequences can vary extensively among individuals within a species. A systematic assessment of the impact of naturally occurring genetic variation on signaling pathways remains to be conducted. In S. cerevisiae, both response and resistance to stressors that activate signaling pathways differ between diverse isolates. Here, we present a quantitative trait locus (QTL) mapping approach that enables us to identify genetic variants underlying such phenotypic differences across the genetic and phenotypic diversity of S. cerevisiae. Using a Round-robin cross between twelve diverse strains, we identified QTL that influence phenotypes critically dependent on MAPK signaling cascades. Genetic variants under these QTL fall within MAPK signaling networks themselves as well as other interconnected signaling pathways. Finally, we demonstrate how the mapping results from multiple strain background can be leveraged to narrow the search space of causal genetic variants. Wild yeast strains differ in phenotypes that are controlled by highly conserved signaling pathways. Yet it remains unknown how naturally occurring genetic variants influence signaling pathways in yeast. We have developed an approach to facilitate the mapping of genetic variants that underlie these phenotypic differences in a set of wild strain. Our mapping approach requires minimal strain engineering and enables the rapid isolation of mapping populations from any strain background. In particular, we have mapped genetic variants in twelve highly diverse yeast strains. Further, we demonstrate how the mapping results from these twelve strains can be used jointly to narrow the number of genetic variants identified to a set of putative causal variants. We identify genetic variants in genes with various roles in cell signaling. Our results illustrate the interplay of different signaling pathways and which signaling genes are more likely to contain variants of large phenotypic impact.
Collapse
Affiliation(s)
- Sebastian Treusch
- Lewis Sigler Institute for Integrative Genomics, Princeton University, Princeton, New Jersey, United States of America
| | - Frank W. Albert
- Department of Human Genetics, University of California, Los Angeles, Los Angeles, California, United States of America
| | - Joshua S. Bloom
- Howard Hughes Medical Institute, Department of Human Genetics, University of California, Los Angeles, Los Angeles, California, United States of America
| | - Iulia E. Kotenko
- Lewis Sigler Institute for Integrative Genomics, Princeton University, Princeton, New Jersey, United States of America
| | - Leonid Kruglyak
- Howard Hughes Medical Institute, Department of Human Genetics, University of California, Los Angeles, Los Angeles, California, United States of America
- Howard Hughes Medical Institute, Department of Biological Chemistry, University of California, Los Angeles, Los Angeles, California, United States of America
- * E-mail:
| |
Collapse
|
27
|
Shi L, Li Z, Tachikawa H, Gao XD, Nakanishi H. Use of yeast spores for microencapsulation of enzymes. Appl Environ Microbiol 2014; 80:4502-10. [PMID: 24837390 PMCID: PMC4148785 DOI: 10.1128/aem.00153-14] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2014] [Accepted: 03/31/2014] [Indexed: 11/20/2022] Open
Abstract
Here, we report a novel method to produce microencapsulated enzymes using Saccharomyces cerevisiae spores. In sporulating cells, soluble secreted proteins are transported to the spore wall. Previous work has shown that the spore wall is capable of retaining soluble proteins because its outer layers work as a diffusion barrier. Accordingly, a red fluorescent protein (RFP) fusion of the α-galactosidase, Mel1, expressed in spores was observed in the spore wall even after spores were subjected to a high-salt wash in the presence of detergent. In vegetative cells, however, the cell wall cannot retain the RFP fusion. Although the spore wall prevents diffusion of proteins, it is likely that smaller molecules, such as sugars, pass through it. In fact, spores can contain much higher α-galactosidase activity to digest melibiose than vegetative cells. When present in the spore wall, the enzyme acquires resistance to environmental stresses including enzymatic digestion and high temperatures. The outer layers of the spore wall are required to retain enzymes but also decrease accessibility of the substrates. However, mutants with mild spore wall defects can retain and stabilize the enzyme while still permitting access to the substrate. In addition to Mel1, we also show that spores can retain the invertase. Interestingly the encapsulated invertase has significantly lower activity toward raffinose than toward sucrose.This suggests that substrate selectivity could be altered by the encapsulation.
Collapse
Affiliation(s)
- Libing Shi
- Key Laboratory of Carbohydrate Chemistry and Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi, China
| | - Zijie Li
- Key Laboratory of Carbohydrate Chemistry and Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi, China
| | - Hiroyuki Tachikawa
- Department of Applied Biological Chemistry, Graduate School of Agricultural and Life Sciences, University of Tokyo, Tokyo, Japan
| | - Xiao-Dong Gao
- Key Laboratory of Carbohydrate Chemistry and Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi, China
| | - Hideki Nakanishi
- Key Laboratory of Carbohydrate Chemistry and Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi, China
| |
Collapse
|
28
|
Valdés-Santiago L, Ruiz-Herrera J. Stress and polyamine metabolism in fungi. Front Chem 2014; 1:42. [PMID: 24790970 PMCID: PMC3982577 DOI: 10.3389/fchem.2013.00042] [Citation(s) in RCA: 58] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2013] [Accepted: 12/24/2013] [Indexed: 12/13/2022] Open
Abstract
Fungi, as well as the rest of living organisms must deal with environmental challenges such as stressful stimuli. Fungi are excellent models to study the general mechanisms of the response to stress, because of their simple, but conserved, signal-transduction and metabolic pathways that are often equivalent to those present in other eukaryotic systems. A factor that has been demonstrated to be involved in these responses is polyamine metabolism, essentially of the three most common polyamines: putrescine, spermidine and spermine. The gathered evidences on this subject suggest that polyamines are able to control cellular signal transduction, as well as to modulate protein-protein interactions. In the present review, we will address the recent advances on the study of fungal metabolism of polyamines, ranging from mutant characterization to potential mechanism of action during different kinds of stress in selected fungal models.
Collapse
Affiliation(s)
| | - José Ruiz-Herrera
- Departamento de Ingeniería Genética, Unidad Irapuato, Centro de Investigación y de Estudios Avanzados del Instituto Politécnico NacionalIrapuato, México
| |
Collapse
|
29
|
Modeling of fungal and bacterial spore germination under static and dynamic conditions. Appl Environ Microbiol 2013; 79:6765-75. [PMID: 23995922 DOI: 10.1128/aem.02521-13] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Isothermal germination curves, sigmoid and nonsigmoid, can be described by a variety of models reminiscent of growth models. Two of these, which are consistent with the percent of germinated spores being initially zero, were selected: one, Weibullian (or "stretched exponential"), for more or less symmetric curves, and the other, introduced by Dantigny's group, for asymmetric curves (P. Dantigny, S. P.-M. Nanguy, D. Judet-Correia, and M. Bensoussan, Int. J. Food Microbiol. 146:176-181, 2011). These static models were converted into differential rate models to simulate dynamic germination patterns, which passed a test for consistency. In principle, these and similar models, if validated experimentally, could be used to predict dynamic germination from isothermal data. The procedures to generate both isothermal and dynamic germination curves have been automated and posted as freeware on the Internet in the form of interactive Wolfram demonstrations. A fully stochastic model of individual and small groups of spores, developed in parallel, shows that when the germination probability is constant from the start, the germination curve is nonsigmoid. It becomes sigmoid if the probability monotonically rises from zero. If the probability rate function rises and then falls, the germination reaches an asymptotic level determined by the peak's location and height. As the number of individual spores rises, the germination curve of their assemblies becomes smoother. It also becomes more deterministic and can be described by the empirical phenomenological models.
Collapse
|
30
|
Geijer C, Pirkov I, Vongsangnak W, Ericsson A, Nielsen J, Krantz M, Hohmann S. Time course gene expression profiling of yeast spore germination reveals a network of transcription factors orchestrating the global response. BMC Genomics 2012; 13:554. [PMID: 23066959 PMCID: PMC3577491 DOI: 10.1186/1471-2164-13-554] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2012] [Accepted: 10/10/2012] [Indexed: 12/01/2022] Open
Abstract
Background Spore germination of the yeast Saccharomyces cerevisiae is a multi-step developmental path on which dormant spores re-enter the mitotic cell cycle and resume vegetative growth. Upon addition of a fermentable carbon source and nutrients, the outer layers of the protective spore wall are locally degraded, the tightly packed spore gains volume and an elongated shape, and eventually the germinating spore re-enters the cell cycle. The regulatory pathways driving this process are still largely unknown. Here we characterize the global gene expression profiles of germinating spores and identify potential transcriptional regulators of this process with the aim to increase our understanding of the mechanisms that control the transition from cellular dormancy to proliferation. Results Employing detailed gene expression time course data we have analysed the reprogramming of dormant spores during the transition to proliferation stimulated by a rich growth medium or pure glucose. Exit from dormancy results in rapid and global changes consisting of different sequential gene expression subprograms. The regulated genes reflect the transition towards glucose metabolism, the resumption of growth and the release of stress, similar to cells exiting a stationary growth phase. High resolution time course analysis during the onset of germination allowed us to identify a transient up-regulation of genes involved in protein folding and transport. We also identified a network of transcription factors that may be regulating the global response. While the expression outputs following stimulation by rich glucose medium or by glucose alone are qualitatively similar, the response to rich medium is stronger. Moreover, spores sense and react to amino acid starvation within the first 30 min after germination initiation, and this response can be linked to specific transcription factors. Conclusions Resumption of growth in germinating spores is characterized by a highly synchronized temporal organisation of up- and down-regulated genes which reflects the metabolic reshaping of the quickening spores.
Collapse
Affiliation(s)
- Cecilia Geijer
- Department of Chemistry and Molecular Biology, University of Gothenburg, Box 462, Gothenburg, S-40530, Sweden
| | | | | | | | | | | | | |
Collapse
|
31
|
Bryant JM, Govin J, Zhang L, Donahue G, Pugh BF, Berger SL. The linker histone plays a dual role during gametogenesis in Saccharomyces cerevisiae. Mol Cell Biol 2012; 32:2771-83. [PMID: 22586276 PMCID: PMC3416202 DOI: 10.1128/mcb.00282-12] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/29/2012] [Accepted: 05/07/2012] [Indexed: 11/20/2022] Open
Abstract
The differentiation of gametes involves dramatic changes to chromatin, affecting transcription, meiosis, and cell morphology. Sporulation in Saccharomyces cerevisiae shares many chromatin features with spermatogenesis, including a 10-fold compaction of the nucleus. To identify new proteins involved in spore nuclear organization, we purified chromatin from mature spores and discovered a significant enrichment of the linker histone (Hho1). The function of Hho1 has proven to be elusive during vegetative growth, but here we demonstrate its requirement for efficient sporulation and full compaction of the spore genome. Hho1 chromatin immunoprecipitation followed by sequencing (ChIP-seq) revealed increased genome-wide binding in mature spores and provides novel in vivo evidence of the linker histone binding to nucleosomal linker DNA. We also link Hho1 function to the transcription factor Ume6, the master repressor of early meiotic genes. Hho1 and Ume6 are depleted during meiosis, and analysis of published ChIP-chip data obtained during vegetative growth reveals a high binding correlation of both proteins at promoters of early meiotic genes. Moreover, Ume6 promotes binding of Hho1 to meiotic gene promoters. Thus, Hho1 may play a dual role during sporulation: Hho1 and Ume6 depletion facilitates the onset of meiosis via activation of Ume6-repressed early meiotic genes, whereas Hho1 enrichment in mature spores contributes to spore genome compaction.
Collapse
Affiliation(s)
- Jessica M. Bryant
- Department of Cell and Developmental Biology, University of Pennsylvania, Philadelphia, Pennsylvania, USA
- Biomedical Graduate Studies, The University of Pennsylvania Perelman School of Medicine, Philadelphia, Pennsylvania, USA
| | - Jérôme Govin
- Department of Cell and Developmental Biology, University of Pennsylvania, Philadelphia, Pennsylvania, USA
| | - Liye Zhang
- Center for Eukaryotic Gene Regulation, Department of Biochemistry and Molecular Biology, Pennsylvania State University, University Park, Pennsylvania, USA
- The Integrative Biosciences Graduate Program in Cell and Developmental Biology, Huck Institutes of the Life Sciences, Pennsylvania State University, University Park, Pennsylvania, USA
| | - Greg Donahue
- Department of Cell and Developmental Biology, University of Pennsylvania, Philadelphia, Pennsylvania, USA
| | - B. Franklin Pugh
- Center for Eukaryotic Gene Regulation, Department of Biochemistry and Molecular Biology, Pennsylvania State University, University Park, Pennsylvania, USA
| | - Shelley L. Berger
- Department of Cell and Developmental Biology, University of Pennsylvania, Philadelphia, Pennsylvania, USA
- Department of Genetics, University of Pennsylvania, Philadelphia, Pennsylvania, USA
- Department of Biology, University of Pennsylvania, Philadelphia, Pennsylvania, USA
| |
Collapse
|
32
|
A Screen for Germination Mutants in Saccharomyces cerevisiae. G3-GENES GENOMES GENETICS 2011; 1:143-9. [PMID: 22384326 PMCID: PMC3276131 DOI: 10.1534/g3.111.000323] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/16/2011] [Accepted: 05/13/2011] [Indexed: 11/29/2022]
Abstract
Spore germination in Saccharomyces cerevisiae is a process in which a quiescent cell begins to divide. During germination, the cell undergoes dramatic changes in cell wall and membrane composition, as well as in gene expression. To understand germination in greater detail, we screened the S. cerevisiae deletion set for germination mutants. Our results identified two genes, TRF4 and ERG6, that are required for normal germination on solid media. TRF4 is a member of the TRAMP complex that, together with the exosome, degrades RNA polymerase II transcripts. ERG6 encodes a key step in ergosterol biosynthesis. Taken together, these results demonstrate the complex nature of germination and two genes important in the process.
Collapse
|
33
|
Rolli E, Ragni E, de Medina-Redondo M, Arroyo J, de Aldana CRV, Popolo L. Expression, stability, and replacement of glucan-remodeling enzymes during developmental transitions in Saccharomyces cerevisiae. Mol Biol Cell 2011; 22:1585-98. [PMID: 21389112 PMCID: PMC3084680 DOI: 10.1091/mbc.e10-03-0268] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023] Open
Abstract
Sporulation is a developmental variation of the yeast life cycle whereby four spores are produced within a diploid cell, with proliferation resuming after germination. The GAS family of glycosylphosphatidylinositol-anchored glucan-remodeling enzymes exemplifies functional interplay between paralogous genes during the yeast life cycle. GAS1 and GAS5 are expressed in vegetative cells and repressed during sporulation while GAS2 and GAS4 exhibit a reciprocal pattern. GAS3 is weakly expressed in all the conditions and encodes an inactive protein. Although Gas1p functions in cell wall formation, we show that it persists during sporulation but is relocalized from the plasma membrane to the epiplasm in a process requiring End3p-mediated endocytosis and the Sps1 protein kinase of the p21-activated kinase family. Some Gas1p is also newly synthesized and localized to the spore membrane, but this fraction is dispensable for spore formation. By way of contrast, the Gas2-Gas4 proteins, which are essential for spore wall assembly, are rapidly degraded after spore formation. On germination, Gas1p is actively synthesized and concentrated in the growing part of the spore, which is essential for its elongation. Thus Gas1p is the primary glucan-remodeling enzyme required in vegetative growth and during reentry into the proliferative state. The dynamic interplay among Gas proteins is crucial to couple glucan remodeling with morphogenesis in developmental transitions.
Collapse
Affiliation(s)
- Eleonora Rolli
- Dipartimento di Scienze Biomolecolari e Biotecnologie, Università degli Studi di Milano, Milan, Italy
| | | | | | | | | | | |
Collapse
|
34
|
Strich R, Khakhina S, Mallory MJ. Ume6p is required for germination and early colony development of yeast ascospores. FEMS Yeast Res 2010; 11:104-13. [PMID: 21059190 DOI: 10.1111/j.1567-1364.2010.00696.x] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022] Open
Abstract
Ume6p is a nonessential transcription factor that represses meiotic gene expression during vegetative growth in budding yeast. To relieve this repression, Ume6p is destroyed as cells enter meiosis and is not resynthesized until spore wall assembly. The present study reveals that spores derived from a ume6 null homozygous diploid fail to germinate. In addition, mutant spores from a UME6/ume6 heterozygote exhibited reduced germination efficiency compared with their wild-type sister spores. Analysis of ume6 spore colonies that did germinate revealed that the majority of cells in microcolonies following the first few cell divisions were inviable. As the colony developed, the viability percentage increased and achieved wild-type levels within approximately six cell divisions, indicating that the requirement for Ume6p in cell viability is transient. This function is specific for germinating spores as Ume6p has no or only a modest impact on the return to the growth ability of cells arrested at other points in the cell cycle. These results define a new role for Ume6p in spore germination and the first few subsequent mitotic cell divisions.
Collapse
Affiliation(s)
- Randy Strich
- Department of Molecular Biology, University of Medicine and Dentistry of New Jersey, Newark, NJ 08055, USA.
| | | | | |
Collapse
|
35
|
Abstract
Bacteria can exist in metabolically inactive states that allow them to survive conditions that are not conducive for growth. Such dormant cells may sense when conditions have improved and re-initiate growth, lest they be outcompeted by their neighbours. Growing bacteria turn over and release large quantities of their cell walls into the environment. Drawing from recent work on the germination of Bacillus subtilis spores, we propose that many microorganisms exit dormancy in response to cell wall muropeptides.
Collapse
|
36
|
Govin J, Dorsey J, Gaucher J, Rousseaux S, Khochbin S, Berger SL. Systematic screen reveals new functional dynamics of histones H3 and H4 during gametogenesis. Genes Dev 2010; 24:1772-86. [PMID: 20713519 DOI: 10.1101/gad.1954910] [Citation(s) in RCA: 85] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
Abstract
Profound epigenetic differences exist between genomes derived from male and female gametes; however, the nature of these changes remains largely unknown. We undertook a systematic investigation of chromatin reorganization during gametogenesis, using the model eukaryote Saccharomyces cerevisiae to examine sporulation, which has strong similarities with higher eukaryotic spermatogenesis. We established a mutational screen of histones H3 and H4 to uncover substitutions that reduce sporulation efficiency. We discovered two patches of residues-one on H3 and a second on H4-that are crucial for sporulation but not critical for mitotic growth, and likely comprise interactive nucleosomal surfaces. Furthermore, we identified novel histone post-translational modifications that mark the chromatin reorganization process during sporulation. First, phosphorylation of H3T11 appears to be a key modification during meiosis, and requires the meiotic-specific kinase Mek1. Second, H4 undergoes amino tail acetylation at Lys 5, Lys 8, and Lys 12, and these are synergistically important for post-meiotic chromatin compaction, occurring subsequent to the post-meiotic transient peak in phosphorylation at H4S1, and crucial for recruitment of Bdf1, a bromodomain protein, to chromatin in mature spores. Strikingly, the presence and temporal succession of the new H3 and H4 modifications are detected during mouse spermatogenesis, indicating that they are conserved through evolution. Thus, our results show that investigation of gametogenesis in yeast provides novel insights into chromatin dynamics, which are potentially relevant to epigenetic modulation of the mammalian process.
Collapse
Affiliation(s)
- Jérôme Govin
- Department of Cell and Developmental Biology, University of Pennsylvania, Philadelphia, PA 19104, USA
| | | | | | | | | | | |
Collapse
|
37
|
Murphy HA, Zeyl CW. Yeast sex: surprisingly high rates of outcrossing between asci. PLoS One 2010; 5:e10461. [PMID: 20463964 PMCID: PMC2864747 DOI: 10.1371/journal.pone.0010461] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2010] [Accepted: 04/08/2010] [Indexed: 02/05/2023] Open
Abstract
Background Saccharomyces yeasts are an important model system in many areas of biological research. Very little is known about their ecology and evolution in the wild, but interest in this natural history is growing. Extensive work with lab strains in the last century uncovered the Saccharomyces life cycle. When nutrient limited, a diploid yeast cell will form four haploid spores encased in a protective outer layer called the ascus. Confinement within the ascus is thought to enforce mating between products of the same meiotic division, minimizing outcrossing in this stage of the life cycle. Methodology/Principal Findings Using a set of S. cerevisiae and S. paradoxus strains isolated from woodlands in North America, we set up trials in which pairs of asci were placed in contact with one another and allowed to germinate. We observed outcrossing in ∼40% of the trials, and multiple outcrossing events in trials with three asci in contact with each other. When entire populations of densely crowded asci germinated, ∼10–25% of the resulting colonies were outcrossed. There were differences between the species with S. cerevisiae having an increased tendency to outcross in mass mating conditions. Conclusions/Significance Our results highlight the potential for random mating between spores in natural strains, even in the presence of asci. If this type of mating does occur in nature and it is between close relatives, then a great deal of mating behavior may be undetectable from genome sequences.
Collapse
Affiliation(s)
- Helen A. Murphy
- Wake Forest University, Winston-Salem, North Carolina, United States of America
- * E-mail:
| | - Clifford W. Zeyl
- Wake Forest University, Winston-Salem, North Carolina, United States of America
| |
Collapse
|
38
|
Abstract
Multicellular organisms utilize cell-to-cell signals to build patterns of cell types within embryos, but the ability of fungi to form organized communities has been largely unexplored. Here we report that colonies of the yeast Saccharomyces cerevisiae formed sharply divided layers of sporulating and nonsporulating cells. Sporulation initiated in the colony's interior, and this region expanded upward as the colony matured. Two key activators of sporulation, IME1 and IME2, were initially transcribed in overlapping regions of the colony, and this overlap corresponded to the initial sporulation region. The development of colony sporulation patterns depended on cell-to-cell signals, as demonstrated by chimeric colonies, which contain a mixture of two strains. One such signal is alkaline pH, mediated through the Rim101p/PacC pathway. Meiotic-arrest mutants that increased alkali production stimulated expression of an early meiotic gene in neighboring cells, whereas a mutant that decreased alkali production (cit1Delta) decreased this expression. Addition of alkali to colonies accelerated the expansion of the interior region of sporulation, whereas inactivation of the Rim101p pathway inhibited this expansion. Thus, the Rim101 pathway mediates colony patterning by responding to cell-to-cell pH signals. Cell-to-cell signals coupled with nutrient gradients may allow efficient spore formation and spore dispersal in natural environments.
Collapse
|
39
|
Govin J, Berger SL. Genome reprogramming during sporulation. THE INTERNATIONAL JOURNAL OF DEVELOPMENTAL BIOLOGY 2009; 53:425-32. [PMID: 19412896 DOI: 10.1387/ijdb.082687jg] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Abstract
When environmental conditions compromise survival, single celled organisms, such as the budding yeast S. cerevisiae, induce and complete a differentiation program called sporulation. The first step consists of meiosis, which generates genetic diversity within the eventual haploid cells. The post-meiotic maturation stage reinforces protective barriers, such as the spore wall, against deleterious external conditions. In later stages of sporulation, the spore nucleus becomes highly compacted, likely sharing certain characteristics with the metazoan male gamete, the spermatozoon. The sporulation differentiation program involves many chromatin-related events, including execution of a precise transcription program involving more than one thousand genes. Here, we review how chromatin structure and genome reprogramming regulate the sporulation transcription program, and how post-meiotic events reorganize spore chromatin.
Collapse
Affiliation(s)
- Jerome Govin
- Gene Expression and Regulation Program, The Wistar Institute, Philadelphia, PA19104, USA
| | | |
Collapse
|
40
|
McMurray MA, Thorner J. Reuse, replace, recycle. Specificity in subunit inheritance and assembly of higher-order septin structures during mitotic and meiotic division in budding yeast. Cell Cycle 2009; 8:195-203. [PMID: 19164941 DOI: 10.4161/cc.8.2.7381] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022] Open
Abstract
Septins are guanine nucleotide-binding proteins that form hetero-oligomeric complexes, which assemble into filaments and higher-order structures at sites of cell division and morphogenesis in eukaryotes. Dynamic changes in the organization of septin-containing structures occur concomitantly with progression through the mitotic cell cycle and during cell differentiation. Septins also undergo stage-specific post-translational modifications, which have been implicated in regulating their dynamics, in some cases via purported effects on septin turnover. In our recent study, the fate of two of the five septins expressed in mitotic cells of budding yeast (Saccharomyces cerevisiae) was tracked using two complementary fluorescence-based methods for pulse-chase analysis. During mitotic growth, previously-made molecules of both septins (Cdc10 and Cdc12) persisted through multiple successive divisions and were incorporated equivalently with newly synthesized molecules into hetero-oligomers and higher-order structures. Similarly, in cells undergoing meiosis and the developmental program of sporulation, pre-existing copies of Cdc10 were incorporated into new structures. In marked contrast, Cdc12 was irreversibly excluded from septin complexes and replaced by another septin, Spr3. Here, we discuss the broader implications of these results and related findings with regard to how septin dynamics is coordinated with the mitotic cell cycle and in the yeast life cycle, and how these observations may relate to control of the dynamics of other complex multi-subunit assemblies.
Collapse
Affiliation(s)
- Michael A McMurray
- Division of Biochemistry and Molecular Biology, Department of Molecular and Cell Biology, University of California; Berkeley, California 94720-3202, USA
| | | |
Collapse
|
41
|
Current awareness on yeast. Yeast 2008. [DOI: 10.1002/yea.1563] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022] Open
|