1
|
Cockrell AJ, Lange JJ, Wood C, Mattingly M, McCroskey SM, Bradford WD, Conkright-Fincham J, Weems L, Guo MS, Gerton JL. Regulators of rDNA array morphology in fission yeast. PLoS Genet 2024; 20:e1011331. [PMID: 38968290 DOI: 10.1371/journal.pgen.1011331] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2023] [Accepted: 06/04/2024] [Indexed: 07/07/2024] Open
Abstract
Nucleolar morphology is a well-established indicator of ribosome biogenesis activity that has served as the foundation of many screens investigating ribosome production. Missing from this field of study is a broad-scale investigation of the regulation of ribosomal DNA morphology, despite the essential role of rRNA gene transcription in modulating ribosome output. We hypothesized that the morphology of rDNA arrays reflects ribosome biogenesis activity. We established GapR-GFP, a prokaryotic DNA-binding protein that recognizes transcriptionally-induced overtwisted DNA, as a live visual fluorescent marker for quantitative analysis of rDNA organization in Schizosaccharomyces pombe. We found that the morphology-which we refer to as spatial organization-of the rDNA arrays is dynamic throughout the cell cycle, under glucose starvation, RNA pol I inhibition, and TOR activation. Screening the haploid S. pombe Bioneer deletion collection for spatial organization phenotypes revealed large ribosomal protein (RPL) gene deletions that alter rDNA organization. Further work revealed RPL gene deletion mutants with altered rDNA organization also demonstrate resistance to the TOR inhibitor Torin1. A genetic analysis of signaling pathways essential for this resistance phenotype implicated many factors including a conserved MAPK, Pmk1, previously linked to extracellular stress responses. We propose RPL gene deletion triggers altered rDNA morphology due to compensatory changes in ribosome biogenesis via multiple signaling pathways, and we further suggest compensatory responses may contribute to human diseases such as ribosomopathies. Altogether, GapR-GFP is a powerful tool for live visual reporting on rDNA morphology under myriad conditions.
Collapse
Affiliation(s)
- Alexandria J Cockrell
- Stowers Institute for Medical Research, Kansas City, Missouri, United States of America
- Department of Biochemistry and Molecular Biology, University of Kansas Medical Center, Kansas City, Kansas, United States of America
| | - Jeffrey J Lange
- Stowers Institute for Medical Research, Kansas City, Missouri, United States of America
| | - Christopher Wood
- Stowers Institute for Medical Research, Kansas City, Missouri, United States of America
| | - Mark Mattingly
- Stowers Institute for Medical Research, Kansas City, Missouri, United States of America
| | - Scott M McCroskey
- Stowers Institute for Medical Research, Kansas City, Missouri, United States of America
| | - William D Bradford
- Stowers Institute for Medical Research, Kansas City, Missouri, United States of America
| | - Juliana Conkright-Fincham
- Stowers Institute for Medical Research, Kansas City, Missouri, United States of America
- Promega Corporation, Madison, Wisconsin, United States of America
| | - Lauren Weems
- Stowers Institute for Medical Research, Kansas City, Missouri, United States of America
| | - Monica S Guo
- Department of Microbiology, University of Washington School of Medicine, Seattle, state of Washington, United States of America
| | - Jennifer L Gerton
- Stowers Institute for Medical Research, Kansas City, Missouri, United States of America
- Department of Biochemistry and Molecular Biology, University of Kansas Medical Center, Kansas City, Kansas, United States of America
| |
Collapse
|
2
|
Ibisoglu MS, Tan M, Yilmazer M, Yilmaz S, Uzuner SK, Topal-Sarikaya A, Palabiyik B. Effects of ScRgt1-Like DNA-binding transcription factor SpRgt1 (SPCC320.03) on Hexose transporters gene expression in Schizosaccharomyces pombe. Arch Microbiol 2024; 206:155. [PMID: 38480568 DOI: 10.1007/s00203-024-03901-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2023] [Revised: 02/16/2024] [Accepted: 02/17/2024] [Indexed: 03/17/2024]
Abstract
Glucose, which plays an essential role in carbon and energy metabolism in eukaryotes, is vital in directing various energy-consuming cellular processes. In S. cerevisiae, transcription factors involved in regulating hexose transporters and their mechanisms of action under different carbon sources were revealed in detail. However, there is limited information on these processes in S. pombe. In this study, the effect of SPCC320.03 (named SpRgt1), the ortholog of ScRgt1 whose molecular mechanism is known in detail in S. cerevisiae, on the transcriptional regulation of hexose transporters (ght1-8) dependent on different carbon sources was investigated. We measured the transcript levels of ght1-8 using the qPCR technique and performed relative evaluation in S. pombe strains (parental, rgt1 deleted mutant, rgt1 overexpressed, and vectoral rgt1 carrying mutant). We aimed to investigate the transcriptional changes caused by the protein product of the rgt1 (SPCC320.03) gene in terms of ght1-8 genes in strains that are grown in different carbon sources (2% glucose, 2% glycerol + 0.1% glucose, and 2% gluconate). Here, we show that SpRgt1 is involved in the regulation of the ght3, ght4, ght6, and ght7 genes but that the ght1, ght2, ght5, and ght8 gene expression vary depending on carbon sources, independently of SpRgt1.
Collapse
Affiliation(s)
- Merve Seda Ibisoglu
- Institute of Graduate Studies in Sciences, Department of Molecular Biology and Genetics, Istanbul University, Istanbul, Turkey
- Faculty of Science and Literature, Department of Molecular Biology and Genetics, Istanbul Yeni Yuzyil University, Istanbul, Turkey
| | - Medet Tan
- Institute of Graduate Studies in Sciences, Department of Molecular Biology and Genetics, Istanbul University, Istanbul, Turkey
| | - Merve Yilmazer
- Faculty of Science, Department of Molecular Biology and Genetics, Istanbul University, Istanbul, Turkey
| | - Sibel Yilmaz
- Faculty of Science and Literature, Department of Molecular Biology and Genetics, Istanbul Yeni Yuzyil University, Istanbul, Turkey
| | - Semian Karaer Uzuner
- Faculty of Science, Department of Molecular Biology and Genetics, Istanbul University, Istanbul, Turkey
| | - Ayşegül Topal-Sarikaya
- Faculty of Science and Literature, Department of Molecular Biology and Genetics, Istanbul Yeni Yuzyil University, Istanbul, Turkey
- Department of Medical Biology and Genetics, Istanbul Yeni Yuzyil University, Istanbul, Turkey
| | - Bedia Palabiyik
- Faculty of Science, Department of Molecular Biology and Genetics, Istanbul University, Istanbul, Turkey.
| |
Collapse
|
3
|
Cranz-Mileva S, Reilly E, Chalhoub N, Patel R, Atanassova T, Cao W, Ellison C, Zaratiegui M. Transposon Removal Reveals Their Adaptive Fitness Contribution. Genome Biol Evol 2024; 16:evae010. [PMID: 38245838 PMCID: PMC10836971 DOI: 10.1093/gbe/evae010] [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: 08/15/2023] [Revised: 01/04/2024] [Accepted: 01/12/2024] [Indexed: 01/22/2024] Open
Abstract
Transposable elements are molecular parasites that persist in their host genome by generating new copies to outpace natural selection. Transposable elements exert a large influence on host genome evolution, in some cases providing adaptive changes. Here we measure the fitness effect of the transposable element insertions in the fission yeast Schizosaccharomyces pombe type strain by removing all insertions of its only native transposable element family, the long terminal repeat retrotransposon Tf2. We show that Tf2 elements provide a positive fitness contribution to its host. Tf2 ablation results in changes to the regulation of a mitochondrial gene and, consistently, the fitness effect are sensitive to growth conditions. We propose that Tf2 influences host fitness in a directed manner by dynamically rewiring the transcriptional response to metabolic stress.
Collapse
Affiliation(s)
- Susanne Cranz-Mileva
- Department of Molecular Biology and Biochemistry, Rutgers, the State University of New Jersey, Piscataway, NJ, USA
| | - Eve Reilly
- Department of Molecular Biology and Biochemistry, Rutgers, the State University of New Jersey, Piscataway, NJ, USA
| | - Noor Chalhoub
- Department of Molecular Biology and Biochemistry, Rutgers, the State University of New Jersey, Piscataway, NJ, USA
| | - Rohan Patel
- Department of Molecular Biology and Biochemistry, Rutgers, the State University of New Jersey, Piscataway, NJ, USA
| | - Tania Atanassova
- Department of Molecular Biology and Biochemistry, Rutgers, the State University of New Jersey, Piscataway, NJ, USA
| | - Weihuan Cao
- Department of Genetics, Rutgers, the State University of New Jersey, Piscataway, NJ, USA
| | - Christopher Ellison
- Department of Genetics, Rutgers, the State University of New Jersey, Piscataway, NJ, USA
| | - Mikel Zaratiegui
- Department of Molecular Biology and Biochemistry, Rutgers, the State University of New Jersey, Piscataway, NJ, USA
| |
Collapse
|
4
|
Pérez-Díaz AJ, Vázquez-Marín B, Vicente-Soler J, Prieto-Ruiz F, Soto T, Franco A, Cansado J, Madrid M. cAMP-Protein kinase A and stress-activated MAP kinase signaling mediate transcriptional control of autophagy in fission yeast during glucose limitation or starvation. Autophagy 2023; 19:1311-1331. [PMID: 36107819 PMCID: PMC10012941 DOI: 10.1080/15548627.2022.2125204] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2022] [Revised: 09/08/2022] [Accepted: 09/09/2022] [Indexed: 11/02/2022] Open
Abstract
Macroautophagy/autophagy is an essential adaptive physiological response in eukaryotes induced during nutrient starvation, including glucose, the primary immediate carbon and energy source for most cells. Although the molecular mechanisms that induce autophagy during glucose starvation have been extensively explored in the budding yeast Saccharomyces cerevisiae, little is known about how this coping response is regulated in the evolutionary distant fission yeast Schizosaccharomyces pombe. Here, we show that S. pombe autophagy in response to glucose limitation relies on mitochondrial respiration and the electron transport chain (ETC), but, in contrast to S. cerevisiae, the AMP-activated protein kinase (AMPK) and DNA damage response pathway components do not modulate fission yeast autophagic flux under these conditions. In the presence of glucose, the cAMP-protein kinase A (PKA) signaling pathway constitutively represses S. pombe autophagy by downregulating the transcription factor Rst2, which promotes the expression of respiratory genes required for autophagy induction under limited glucose availability. Furthermore, the stress-activated protein kinase (SAPK) signaling pathway, and its central mitogen-activated protein kinase (MAPK) Sty1, positively modulate autophagy upon glucose limitation at the transcriptional level through its downstream effector Atf1 and by direct in vivo phosphorylation of Rst2 at S292. Thus, our data indicate that the signaling pathways that govern autophagy during glucose shortage or starvation have evolved differently in S. pombe and uncover the existence of sophisticated and multifaceted mechanisms that control this self-preservation and survival response.
Collapse
Affiliation(s)
- Armando Jesús Pérez-Díaz
- Yeast Physiology Group. Department of Genetics and Microbiology. Campus de Excelencia Internacional de Ámbito Regional (CEIR) Campus Mare Nostrum, Universidad de Murcia, Murcia, Spain
| | - Beatriz Vázquez-Marín
- Yeast Physiology Group. Department of Genetics and Microbiology. Campus de Excelencia Internacional de Ámbito Regional (CEIR) Campus Mare Nostrum, Universidad de Murcia, Murcia, Spain
| | - Jero Vicente-Soler
- Yeast Physiology Group. Department of Genetics and Microbiology. Campus de Excelencia Internacional de Ámbito Regional (CEIR) Campus Mare Nostrum, Universidad de Murcia, Murcia, Spain
| | - Francisco Prieto-Ruiz
- Yeast Physiology Group. Department of Genetics and Microbiology. Campus de Excelencia Internacional de Ámbito Regional (CEIR) Campus Mare Nostrum, Universidad de Murcia, Murcia, Spain
| | - Teresa Soto
- Yeast Physiology Group. Department of Genetics and Microbiology. Campus de Excelencia Internacional de Ámbito Regional (CEIR) Campus Mare Nostrum, Universidad de Murcia, Murcia, Spain
| | - Alejandro Franco
- Yeast Physiology Group. Department of Genetics and Microbiology. Campus de Excelencia Internacional de Ámbito Regional (CEIR) Campus Mare Nostrum, Universidad de Murcia, Murcia, Spain
| | - José Cansado
- Yeast Physiology Group. Department of Genetics and Microbiology. Campus de Excelencia Internacional de Ámbito Regional (CEIR) Campus Mare Nostrum, Universidad de Murcia, Murcia, Spain
| | - Marisa Madrid
- Yeast Physiology Group. Department of Genetics and Microbiology. Campus de Excelencia Internacional de Ámbito Regional (CEIR) Campus Mare Nostrum, Universidad de Murcia, Murcia, Spain
| |
Collapse
|
5
|
Maruyama T, Hayashi K, Matsui K, Maekawa Y, Shimasaki T, Ohtsuka H, Shigeaki S, Aiba H. Characterization of hexose transporter genes in the views of the chronological life span and glucose uptake in fission yeast. J GEN APPL MICROBIOL 2023; 68:270-277. [PMID: 35781263 DOI: 10.2323/jgam.2022.05.006] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
Abstract
Fission yeast, Schizosaccharomyces pombe, possesses eight hexose transporters, Ght1~8. In order to clarify the role of each hexose transporter on glucose uptake, a glucose uptake assay system was established and the actual glucose uptake activity of each hexose transporter-deletion mutant was measured. Under normal growth condition containing 2% glucose, ∆ght5 and ∆ght2 mutants showed large and small decrease in glucose uptake activity, respectively. On the other hand, the other deletion mutants did not show any decrease in glucose uptake activity indicating that, in the presence of Ght5 and Ght2, the other hexose transporters do not play a significant role in glucose uptake. To understand the relevance between glucose uptake and lifespan regulation, we measured the chronological lifespan of each hexose transporter deletion mutant, and found that only ∆ght5 mutant showed a significant lifespan extension. Based on these results we showed that Ght5 is mainly involved in the glucose uptake in Schizosaccharomyces pombe, and suggested that the ∆ght5 mutant has prolonged lifespan due to physiological changes similar to calorie restriction.
Collapse
Affiliation(s)
- Teppei Maruyama
- Laboratory of Molecular Microbiology, Department of Basic Medicinal Sciences, Graduate School of Pharmaceutical Sciences, Nagoya University
| | - Kanako Hayashi
- Laboratory of Molecular Microbiology, Department of Basic Medicinal Sciences, Graduate School of Pharmaceutical Sciences, Nagoya University
| | - Kotaro Matsui
- Laboratory of Molecular Microbiology, Department of Basic Medicinal Sciences, Graduate School of Pharmaceutical Sciences, Nagoya University
| | - Yasukichi Maekawa
- Laboratory of Molecular Microbiology, Department of Basic Medicinal Sciences, Graduate School of Pharmaceutical Sciences, Nagoya University
| | - Takafumi Shimasaki
- Laboratory of Molecular Microbiology, Department of Basic Medicinal Sciences, Graduate School of Pharmaceutical Sciences, Nagoya University
| | - Hokuto Ohtsuka
- Laboratory of Molecular Microbiology, Department of Basic Medicinal Sciences, Graduate School of Pharmaceutical Sciences, Nagoya University
| | | | - Hirofumi Aiba
- Laboratory of Molecular Microbiology, Department of Basic Medicinal Sciences, Graduate School of Pharmaceutical Sciences, Nagoya University
| |
Collapse
|
6
|
Rodriguez-Lopez M, Anver S, Cotobal C, Kamrad S, Malecki M, Correia-Melo C, Hoti M, Townsend S, Marguerat S, Pong SK, Wu MY, Montemayor L, Howell M, Ralser M, Bähler J. Functional profiling of long intergenic non-coding RNAs in fission yeast. eLife 2022; 11:e76000. [PMID: 34984977 PMCID: PMC8730722 DOI: 10.7554/elife.76000] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2021] [Accepted: 12/02/2021] [Indexed: 12/19/2022] Open
Abstract
Eukaryotic genomes express numerous long intergenic non-coding RNAs (lincRNAs) that do not overlap any coding genes. Some lincRNAs function in various aspects of gene regulation, but it is not clear in general to what extent lincRNAs contribute to the information flow from genotype to phenotype. To explore this question, we systematically analysed cellular roles of lincRNAs in Schizosaccharomyces pombe. Using seamless CRISPR/Cas9-based genome editing, we deleted 141 lincRNA genes to broadly phenotype these mutants, together with 238 diverse coding-gene mutants for functional context. We applied high-throughput colony-based assays to determine mutant growth and viability in benign conditions and in response to 145 different nutrient, drug, and stress conditions. These analyses uncovered phenotypes for 47.5% of the lincRNAs and 96% of the protein-coding genes. For 110 lincRNA mutants, we also performed high-throughput microscopy and flow cytometry assays, linking 37% of these lincRNAs with cell-size and/or cell-cycle control. With all assays combined, we detected phenotypes for 84 (59.6%) of all lincRNA deletion mutants tested. For complementary functional inference, we analysed colony growth of strains ectopically overexpressing 113 lincRNA genes under 47 different conditions. Of these overexpression strains, 102 (90.3%) showed altered growth under certain conditions. Clustering analyses provided further functional clues and relationships for some of the lincRNAs. These rich phenomics datasets associate lincRNA mutants with hundreds of phenotypes, indicating that most of the lincRNAs analysed exert cellular functions in specific environmental or physiological contexts. This study provides groundwork to further dissect the roles of these lincRNAs in the relevant conditions.
Collapse
Affiliation(s)
- Maria Rodriguez-Lopez
- University College London, Institute of Healthy Ageing and Department of Genetics, Evolution & EnvironmentLondonUnited Kingdom
| | - Shajahan Anver
- University College London, Institute of Healthy Ageing and Department of Genetics, Evolution & EnvironmentLondonUnited Kingdom
| | - Cristina Cotobal
- University College London, Institute of Healthy Ageing and Department of Genetics, Evolution & EnvironmentLondonUnited Kingdom
| | - Stephan Kamrad
- University College London, Institute of Healthy Ageing and Department of Genetics, Evolution & EnvironmentLondonUnited Kingdom
- The Francis Crick Institute, Molecular Biology of Metabolism LaboratoryLondonUnited Kingdom
- Charité Universitätsmedizin Berlin, Institute of BiochemistryBerlinGermany
| | - Michal Malecki
- University College London, Institute of Healthy Ageing and Department of Genetics, Evolution & EnvironmentLondonUnited Kingdom
| | - Clara Correia-Melo
- The Francis Crick Institute, Molecular Biology of Metabolism LaboratoryLondonUnited Kingdom
| | - Mimoza Hoti
- University College London, Institute of Healthy Ageing and Department of Genetics, Evolution & EnvironmentLondonUnited Kingdom
| | - StJohn Townsend
- University College London, Institute of Healthy Ageing and Department of Genetics, Evolution & EnvironmentLondonUnited Kingdom
- The Francis Crick Institute, Molecular Biology of Metabolism LaboratoryLondonUnited Kingdom
| | - Samuel Marguerat
- University College London, Institute of Healthy Ageing and Department of Genetics, Evolution & EnvironmentLondonUnited Kingdom
| | - Sheng Kai Pong
- University College London, Institute of Healthy Ageing and Department of Genetics, Evolution & EnvironmentLondonUnited Kingdom
| | - Mary Y Wu
- The Francis Crick Institute, High Throughput ScreeningLondonUnited Kingdom
| | - Luis Montemayor
- University College London, Institute of Healthy Ageing and Department of Genetics, Evolution & EnvironmentLondonUnited Kingdom
| | - Michael Howell
- The Francis Crick Institute, High Throughput ScreeningLondonUnited Kingdom
| | - Markus Ralser
- The Francis Crick Institute, Molecular Biology of Metabolism LaboratoryLondonUnited Kingdom
- Charité Universitätsmedizin Berlin, Institute of BiochemistryBerlinGermany
| | - Jürg Bähler
- University College London, Institute of Healthy Ageing and Department of Genetics, Evolution & EnvironmentLondonUnited Kingdom
| |
Collapse
|
7
|
Malina C, Yu R, Björkeroth J, Kerkhoven EJ, Nielsen J. Adaptations in metabolism and protein translation give rise to the Crabtree effect in yeast. Proc Natl Acad Sci U S A 2021; 118:e2112836118. [PMID: 34903663 PMCID: PMC8713813 DOI: 10.1073/pnas.2112836118] [Citation(s) in RCA: 24] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 11/09/2021] [Indexed: 11/24/2022] Open
Abstract
Aerobic fermentation, also referred to as the Crabtree effect in yeast, is a well-studied phenomenon that allows many eukaryal cells to attain higher growth rates at high glucose availability. Not all yeasts exhibit the Crabtree effect, and it is not known why Crabtree-negative yeasts can grow at rates comparable to Crabtree-positive yeasts. Here, we quantitatively compared two Crabtree-positive yeasts, Saccharomyces cerevisiae and Schizosaccharomyces pombe, and two Crabtree-negative yeasts, Kluyveromyces marxianus and Scheffersomyces stipitis, cultivated under glucose excess conditions. Combining physiological and proteome quantification with genome-scale metabolic modeling, we found that the two groups differ in energy metabolism and translation efficiency. In Crabtree-positive yeasts, the central carbon metabolism flux and proteome allocation favor a glucose utilization strategy minimizing proteome cost as proteins translation parameters, including ribosomal content and/or efficiency, are lower. Crabtree-negative yeasts, however, use a strategy of maximizing ATP yield, accompanied by higher protein translation parameters. Our analyses provide insight into the underlying reasons for the Crabtree effect, demonstrating a coupling to adaptations in both metabolism and protein translation.
Collapse
Affiliation(s)
- Carl Malina
- Department of Biology and Biological Engineering, Chalmers University of Technology, SE-412 96, Gothenburg, Sweden
- Wallenberg Center for Protein Research, Chalmers University of Technology, SE-412 96, Gothenburg, Sweden
| | - Rosemary Yu
- Department of Biology and Biological Engineering, Chalmers University of Technology, SE-412 96, Gothenburg, Sweden
- Novo Nordisk Foundation Center for Biosustainability, Chalmers University of Technology, SE-412 96, Gothenburg, Sweden
| | - Johan Björkeroth
- Department of Biology and Biological Engineering, Chalmers University of Technology, SE-412 96, Gothenburg, Sweden
| | - Eduard J Kerkhoven
- Department of Biology and Biological Engineering, Chalmers University of Technology, SE-412 96, Gothenburg, Sweden
- Novo Nordisk Foundation Center for Biosustainability, Chalmers University of Technology, SE-412 96, Gothenburg, Sweden
| | - Jens Nielsen
- Department of Biology and Biological Engineering, Chalmers University of Technology, SE-412 96, Gothenburg, Sweden;
- Wallenberg Center for Protein Research, Chalmers University of Technology, SE-412 96, Gothenburg, Sweden
- Novo Nordisk Foundation Center for Biosustainability, Chalmers University of Technology, SE-412 96, Gothenburg, Sweden
- Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, DK-2800 Kgs Lyngby, Denmark
- BioInnovation Institute, DK-2200, Copenhagen N, Denmark
| |
Collapse
|
8
|
Mohamed RA, Ren K, Mou YN, Ying SH, Feng MG. Genome-Wide Insight into Profound Effect of Carbon Catabolite Repressor (Cre1) on the Insect-Pathogenic Lifecycle of Beauveriabassiana. J Fungi (Basel) 2021; 7:jof7110895. [PMID: 34829184 PMCID: PMC8622151 DOI: 10.3390/jof7110895] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2021] [Revised: 10/19/2021] [Accepted: 10/20/2021] [Indexed: 11/16/2022] Open
Abstract
Carbon catabolite repression (CCR) is critical for the preferential utilization of glucose derived from environmental carbon sources and regulated by carbon catabolite repressor A (Cre1/CreA) in filamentous fungi. However, a role of Cre1-mediated CCR in insect-pathogenic fungal utilization of host nutrients during normal cuticle infection (NCI) and hemocoel colonization remains explored insufficiently. Here, we report an indispensability of Cre1 for Beauveriabassiana's utilization of nutrients in insect integument and hemocoel. Deletion of cre1 resulted in severe defects in radial growth on various media, hypersensitivity to oxidative stress, abolished pathogenicity via NCI or intrahemocoel injection (cuticle-bypassing infection) but no change in conidial hydrophobicity and adherence to insect cuticle. Markedly reduced biomass accumulation in the Δcre1 cultures was directly causative of severe defect in aerial conidiation and reduced secretion of various cuticle-degrading enzymes. The majority (1117) of 1881 dysregulated genes identified from the Δcre1 versus wild-type cultures were significantly downregulated, leading to substantial repression of many enriched function terms and pathways, particularly those involved in carbon and nitrogen metabolisms, cuticle degradation, antioxidant response, cellular transport and homeostasis, and direct/indirect gene mediation. These findings offer a novel insight into profound effect of Cre1 on the insect-pathogenic lifestyle of B. bassiana.
Collapse
|
9
|
Tarhan Ç, Çakır Ö. Transcriptome sequencing and screening of genes related to glucose availability in Schizosaccharomyces pombe by RNA-seq analysis. Genet Mol Biol 2021; 44:e20200245. [PMID: 34460892 PMCID: PMC8404550 DOI: 10.1590/1678-4685-gmb-2020-0245] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2020] [Accepted: 06/01/2021] [Indexed: 11/21/2022] Open
Abstract
While calorie restriction is the most used experimental intervention to increase lifespan in numerous model organisms, increasing evidence suggests that excess glucose leads to decreased lifespan in various organisms. To fully understand the molecular basis of the pro-aging effect of glucose, it is still important to discover genetic interactions, gene expression patterns, and molecular responses depending on glucose availability. Here, we compared the gene expression profiles in Schizosaccharomyces pombe mid-log-phase cells grown in three different Synthetic Dextrose media with 3%, 5%, and 8% glucose, using the RNA sequencing method. Expression patterns of genes that function in carbohydrate metabolism were downregulated as expected, and these genes were downregulated in line with the increase in glucose content. Significant and consistent changes in the expression were observed such as genes that encoding retrotransposable elements, heat shock proteins, glutathione S-transferase, cell agglutination protein, and conserved fungal proteins. We group some genes that function together in the transcription process and mitotic regulation, which have recently been associated with glucose availability. Our results shed light on the relationship between excess glucose, diverse cellular processes, and aging.
Collapse
Affiliation(s)
- Çağatay Tarhan
- Istanbul University, Faculty of Science, Department of Molecular Biology and Genetics, Istanbul, Turkey
| | - Özgür Çakır
- Istanbul University, Faculty of Science, Department of Molecular Biology and Genetics, Istanbul, Turkey
| |
Collapse
|
10
|
Carbon Catabolite Repression Governs Diverse Physiological Processes and Development in Aspergillus nidulans. mBio 2021; 13:e0373421. [PMID: 35164551 PMCID: PMC8844935 DOI: 10.1128/mbio.03734-21] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023] Open
Abstract
Carbon catabolite repression (CCR) is a common phenomenon of microorganisms that enable efficient utilization of carbon nutrients, critical for the fitness of microorganisms in the wild and for pathogenic species to cause infection. In most filamentous fungal species, the conserved transcription factor CreA/Cre1 mediates CCR. Previous studies demonstrated a primary function for CreA/Cre1 in carbon metabolism; however, the phenotype of creA/cre1 mutants indicated broader roles. The global function and regulatory mechanism of this wide-domain transcription factor has remained elusive. Here, we applied two powerful genomics methods (transcriptome sequencing and chromatin immunoprecipitation sequencing) to delineate the direct and indirect roles of Aspergillus nidulans CreA across diverse physiological processes, including secondary metabolism, iron homeostasis, oxidative stress response, development, N-glycan biosynthesis, unfolded protein response, and nutrient and ion transport. The results indicate intricate connections between the regulation of carbon metabolism and diverse cellular functions. Moreover, our work also provides key mechanistic insights into CreA regulation and identifies CreA as a master regulator controlling many transcription factors of different regulatory networks. The discoveries for this highly conserved transcriptional regulator in a model fungus have important implications for CCR in related pathogenic and industrial species. IMPORTANCE The ability to scavenge and use a wide range of nutrients for growth is crucial for microorganisms' survival in the wild. Carbon catabolite repression (CCR) is a transcriptional regulatory phenomenon of both bacteria and fungi to coordinate the expression of genes required for preferential utilization of carbon sources. Since carbon metabolism is essential for growth, CCR is central to the fitness of microorganisms. In filamentous fungi, CCR is mediated by the conserved transcription factor CreA/Cre1, whose function in carbon metabolism has been well established. However, the global roles and regulatory mechanism of CreA/Cre1 are poorly defined. This study uncovers the direct and indirect functions of CreA in the model organism Aspergillus nidulans over diverse physiological processes and development and provides mechanistic insights into how CreA controls different regulatory networks. The work also reveals an interesting functional divergence between filamentous fungal and yeast CreA/Cre1 orthologues.
Collapse
|
11
|
Jiang G, Liu Q, Kato T, Miao H, Gao X, Liu K, Chen S, Sakamoto N, Kuno T, Fang Y. Role of mitochondrial complex III/IV in the activation of transcription factor Rst2 in Schizosaccharomyces pombe. Mol Microbiol 2021; 115:1323-1338. [PMID: 33400299 DOI: 10.1111/mmi.14678] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2020] [Revised: 12/31/2020] [Accepted: 12/31/2020] [Indexed: 11/30/2022]
Abstract
Mitochondria play essential roles in eukaryotic cells for glucose metabolism to produce ATP. In Schizosaccharomyces pombe, transcription factor Rst2 can be activated upon glucose deprivation. However, the link between Rst2 and mitochondrial function remains elusive. Here, we monitored Rst2 transcriptional activity in living cells using a Renilla luciferase reporter system, and found that inhibition of mitochondrial complex III/IV caused cells to produce reactive oxygen species (ROS) and nitric oxide (NO), which in turn activated Rst2. Furthermore, Rst2-GFP was observed to translocate from cytoplasm to nucleus upon mitochondrial complex III/IV inhibitors treatment, and deletion of genes associated with complex III/IV resulted in delayed process of Rst2-GFP nuclear exportation under glucose-rich condition. In particular, we found that Rst2 was phosphorylated following the treatment of complex III/IV inhibitors or SNAP. Altogether, our findings suggest that mitochondrial complex III/IV participates in the activation of Rst2 through ROS and NO generation in Schizosaccharomyces pombe.
Collapse
Affiliation(s)
- Guanglie Jiang
- Department of Microbial and Biochemical Pharmacy, School of Pharmacy, China Medical University, Shenyang, China
| | - Qiannan Liu
- Department of Microbial and Biochemical Pharmacy, School of Pharmacy, China Medical University, Shenyang, China
| | - Toshiaki Kato
- Division of Food and Drug Evaluation Science, Kobe University Graduate School of Medicine, Kobe, Japan
| | - Hao Miao
- Department of Microbial and Biochemical Pharmacy, School of Pharmacy, China Medical University, Shenyang, China
| | - Xiang Gao
- Department of Microbial and Biochemical Pharmacy, School of Pharmacy, China Medical University, Shenyang, China
| | - Kun Liu
- Department of Microbial and Biochemical Pharmacy, School of Pharmacy, China Medical University, Shenyang, China
| | - Si Chen
- Department of Microbial and Biochemical Pharmacy, School of Pharmacy, China Medical University, Shenyang, China
| | - Norihiro Sakamoto
- Division of Food and Drug Evaluation Science, Kobe University Graduate School of Medicine, Kobe, Japan
| | - Takayoshi Kuno
- Department of Microbial and Biochemical Pharmacy, School of Pharmacy, China Medical University, Shenyang, China.,Division of Food and Drug Evaluation Science, Kobe University Graduate School of Medicine, Kobe, Japan
| | - Yue Fang
- Department of Microbial and Biochemical Pharmacy, School of Pharmacy, China Medical University, Shenyang, China
| |
Collapse
|
12
|
Garg A. A lncRNA-regulated gene expression system with rapid induction kinetics in the fission yeast Schizosaccharomyces pombe. RNA (NEW YORK, N.Y.) 2020; 26:1743-1752. [PMID: 32788323 PMCID: PMC7566572 DOI: 10.1261/rna.076000.120] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/20/2020] [Accepted: 08/07/2020] [Indexed: 06/11/2023]
Abstract
The fission yeast Schizosaccharomyces pombe is an excellent model organism for the study of eukaryotic cellular physiology. The organism is genetically tractable and several tools to study the functions of individual genes are available. One such tool is regulatable gene expression and overproduction of proteins. Limitations of currently available overexpression systems include delay in expression after induction, narrow dynamic range, and system-wide changes due to induction conditions. Here I describe a new long noncoding RNA (lncRNA)-regulated, thiamine-inducible expression system that integrates lncRNA-based transcriptional interference at the fission yeast tgp1 promoter with the fast repression kinetics of the thiamine-repressible nmt1 promoter. This hybrid system has rapid induction kinetics, broad dynamic range, and tunable expression via thiamine concentration. The lncRNA-regulated thiamine-inducible system will be advantageous for the study of individual genes and for potential applications in the production of heterologous proteins in fission yeast.
Collapse
Affiliation(s)
- Angad Garg
- Molecular Biology Program, Sloan-Kettering Institute, New York, New York 10065, USA
| |
Collapse
|
13
|
Li C, Chen X, Wen L, Cheng Y, An X, Li T, Zang H, Zhao X, Li D, Hou N. An enhancement strategy for the biodegradation of high-concentration aliphatic nitriles: Utilizing the glucose-mediated carbon catabolite repression mechanism. ENVIRONMENTAL POLLUTION (BARKING, ESSEX : 1987) 2020; 265:114302. [PMID: 32480233 DOI: 10.1016/j.envpol.2020.114302] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/21/2019] [Revised: 01/23/2020] [Accepted: 02/29/2020] [Indexed: 06/11/2023]
Abstract
Wastewater containing high concentrations of nitriles, if discharged without an appropriate nonhazardous disposal strategy, will cause serious environmental pollution. During secondary sewage biological treatment, most existing bacteria cannot endure high-concentration nitriles due to poor tolerance and low degradation ability. The Rhodococcus rhodochrous strain BX2 screened by our laboratory shows high resistance to nitriles and can efficiently degrade these compounds. Compared with sole high-concentration nitriles present in the biodegradation process, the addition of glucose at a suitable concentration can effectively increase the biomass of BX2, promote the expression of nitrile-degrading enzyme genes, improve the activities of these enzymes and enhance the pollutant removal efficiency via carbon catabolite repression (CCR) mechanisms. Whole-genome sequencing revealed that the four key regulators of CCR identified in gram-negative and gram-positive bacteria are concomitant in BX2. This study provides an economically feasible strategy for the microbial remediation of high-concentration nitriles and other organic pollutants.
Collapse
Affiliation(s)
- Chunyan Li
- College of Resources and Environment, Northeast Agricultural University, Harbin, 150030, Heilongjiang, PR China
| | - Xi Chen
- College of Resources and Environment, Northeast Agricultural University, Harbin, 150030, Heilongjiang, PR China
| | - Luming Wen
- College of Resources and Environment, Northeast Agricultural University, Harbin, 150030, Heilongjiang, PR China
| | - Yi Cheng
- College of Science, China Agricultural University, Beijing, 100083, PR China
| | - Xuejiao An
- College of Bioscience and Bioengineering, Jiangxi Agricultural University, Jiangxi, 330045, PR China
| | - Tianzhu Li
- College of Resources and Environment, Northeast Agricultural University, Harbin, 150030, Heilongjiang, PR China
| | - Hailian Zang
- College of Resources and Environment, Northeast Agricultural University, Harbin, 150030, Heilongjiang, PR China
| | - Xinyue Zhao
- College of Resources and Environment, Northeast Agricultural University, Harbin, 150030, Heilongjiang, PR China
| | - Dapeng Li
- College of Resources and Environment, Northeast Agricultural University, Harbin, 150030, Heilongjiang, PR China
| | - Ning Hou
- College of Resources and Environment, Northeast Agricultural University, Harbin, 150030, Heilongjiang, PR China.
| |
Collapse
|
14
|
Adaptation to Industrial Stressors Through Genomic and Transcriptional Plasticity in a Bioethanol Producing Fission Yeast Isolate. G3-GENES GENOMES GENETICS 2020; 10:1375-1391. [PMID: 32086247 PMCID: PMC7144085 DOI: 10.1534/g3.119.400986] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
Schizosaccharomyces pombe is a model unicellular eukaryote with ties to the basic research, oenology and industrial biotechnology sectors. While most investigations into S. pombe cell biology utilize Leupold’s 972h- laboratory strain background, recent studies have described a wealth of genetic and phenotypic diversity within wild populations of S. pombe including stress resistance phenotypes which may be of interest to industry. Here we describe the genomic and transcriptomic characterization of Wilmar-P, an S. pombe isolate used for bioethanol production from sugarcane molasses at industrial scale. Novel sequences present in Wilmar-P but not in the laboratory S. pombe genome included multiple coding sequences with near-perfect nucleotide identity to Schizosaccharomyces octosporus sequences. Wilmar-P also contained a ∼100kb duplication in the right arm of chromosome III, a region harboring ght5+, the predominant hexose transporter encoding gene. Transcriptomic analysis of Wilmar-P grown in molasses revealed strong downregulation of core environmental stress response genes and upregulation of hexose transporters and drug efflux pumps compared to laboratory S. pombe. Finally, examination of the regulatory network of Scr1, which is involved in the regulation of several genes differentially expressed on molasses, revealed expanded binding of this transcription factor in Wilmar-P compared to laboratory S. pombe in the molasses condition. Together our results point to both genomic plasticity and transcriptomic adaptation as mechanisms driving phenotypic adaptation of Wilmar-P to the molasses environment and therefore adds to our understanding of genetic diversity within industrial fission yeast strains and the capacity of this strain for commercial scale bioethanol production.
Collapse
|
15
|
Fraile R, Sánchez-Mir L, Hidalgo E. A new adaptation strategy to glucose starvation: modulation of the gluconate shunt and pentose phosphate pathway by the transcriptional repressor Rsv1. FEBS J 2019; 287:874-877. [PMID: 31777167 DOI: 10.1111/febs.15131] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2019] [Accepted: 11/08/2019] [Indexed: 11/27/2022]
Abstract
Survival upon glucose starvation requires a delicate balance between different metabolic pathways. A recent work by the Roe laboratory provides a mechanistic link between glucose deprivation and the regulation of the pentose phosphate pathway, with the transcriptional repressor Rsv1 playing a key role in the process. Rsv1 regulates the flow of glucose into its possible metabolic fates and promotes long-term survival under low glucose.
Collapse
Affiliation(s)
- Rodrigo Fraile
- Oxidative Stress and Cell Cycle Group, Universitat Pompeu Fabra, Barcelona, Spain
| | - Laura Sánchez-Mir
- Oxidative Stress and Cell Cycle Group, Universitat Pompeu Fabra, Barcelona, Spain
| | - Elena Hidalgo
- Oxidative Stress and Cell Cycle Group, Universitat Pompeu Fabra, Barcelona, Spain
| |
Collapse
|
16
|
Carmona M, de Cubas L, Bautista E, Moral-Blanch M, Medraño-Fernández I, Sitia R, Boronat S, Ayté J, Hidalgo E. Monitoring cytosolic H 2O 2 fluctuations arising from altered plasma membrane gradients or from mitochondrial activity. Nat Commun 2019; 10:4526. [PMID: 31586057 PMCID: PMC6778086 DOI: 10.1038/s41467-019-12475-0] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2019] [Accepted: 09/13/2019] [Indexed: 12/21/2022] Open
Abstract
Genetically encoded probes monitoring H2O2 fluctuations in living organisms are key to decipher redox signaling events. Here we use a new probe, roGFP2-Tpx1.C169S, to monitor pre-toxic fluctuations of peroxides in fission yeast, where the concentrations linked to signaling or to toxicity have been established. This probe is able to detect nanomolar fluctuations of intracellular H2O2 caused by extracellular peroxides; expression of human aquaporin 8 channels H2O2 entry into fission yeast decreasing membrane gradients. The probe also detects H2O2 bursts from mitochondria after addition of electron transport chain inhibitors, the extent of probe oxidation being proportional to the mitochondrial activity. The oxidation of this probe is an indicator of steady-state levels of H2O2 in different genetic backgrounds. Metabolic reprogramming during growth in low-glucose media causes probe reduction due to the activation of antioxidant cascades. We demonstrate how peroxiredoxin-based probes can be used to monitor physiological H2O2 fluctuations. Reliable methods of measuring intracellular H2O2 fluctuations are necessary to advance redox biology. Here the authors design a H2O2 sensor based on the fission yeast peroxiredoxin Tpx1 to sense nanomolar fluctuations of intracellular H2O2 in response to genetic and environmental perturbations.
Collapse
Affiliation(s)
- Mercè Carmona
- Oxidative Stress and Cell Cycle Group, Universitat Pompeu Fabra, C/Dr. Aiguader 88, 08003, Barcelona, Spain
| | - Laura de Cubas
- Oxidative Stress and Cell Cycle Group, Universitat Pompeu Fabra, C/Dr. Aiguader 88, 08003, Barcelona, Spain
| | - Eric Bautista
- Oxidative Stress and Cell Cycle Group, Universitat Pompeu Fabra, C/Dr. Aiguader 88, 08003, Barcelona, Spain
| | - Marta Moral-Blanch
- Oxidative Stress and Cell Cycle Group, Universitat Pompeu Fabra, C/Dr. Aiguader 88, 08003, Barcelona, Spain
| | - Iria Medraño-Fernández
- Protein Transport and Secretion Unit, Division of Genetics and Cell Biology, Istituto di Ricovero e Cura a Carattere Scientifico (IRCCS) Ospedale San Raffaele, Università Vita-Salute San Raffaele, 20132, Milan, Italy
| | - Roberto Sitia
- Protein Transport and Secretion Unit, Division of Genetics and Cell Biology, Istituto di Ricovero e Cura a Carattere Scientifico (IRCCS) Ospedale San Raffaele, Università Vita-Salute San Raffaele, 20132, Milan, Italy
| | - Susanna Boronat
- Oxidative Stress and Cell Cycle Group, Universitat Pompeu Fabra, C/Dr. Aiguader 88, 08003, Barcelona, Spain
| | - José Ayté
- Oxidative Stress and Cell Cycle Group, Universitat Pompeu Fabra, C/Dr. Aiguader 88, 08003, Barcelona, Spain
| | - Elena Hidalgo
- Oxidative Stress and Cell Cycle Group, Universitat Pompeu Fabra, C/Dr. Aiguader 88, 08003, Barcelona, Spain.
| |
Collapse
|