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Shi H, Meng S, Qiu J, Wang C, Shu Y, Luo C, Kou Y. MoWhi2 regulates appressorium formation and pathogenicity via the MoTor signalling pathway in Magnaporthe oryzae. MOLECULAR PLANT PATHOLOGY 2021; 22:969-983. [PMID: 34036714 PMCID: PMC8295519 DOI: 10.1111/mpp.13074] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/23/2020] [Revised: 01/13/2021] [Accepted: 04/21/2021] [Indexed: 05/17/2023]
Abstract
Magnaporthe oryzae causes rice blast disease, which seriously threatens the safety of food production. Understanding the mechanism of appressorium formation, which is one of the key steps for successful infection by M. oryzae, is helpful to formulate effective control strategies of rice blast. In this study, we identified MoWhi2, the homolog of Saccharomyces cerevisiae Whi2 (Whisky2), as an important regulator that controls appressorium formation in M. oryzae. When MoWHI2 was disrupted, multiple appressoria were formed by one conidium and pathogenicity was significantly reduced. A putative phosphatase, MoPsr1, was identified to interact with MoWhi2 using a yeast two-hybridization screening assay. The knockout mutant ΔMopsr1 displayed similar phenotypes to the ΔMowhi2 strain. Both the ΔMowhi2 and ΔMopsr1 mutants could form appressoria on a hydrophilic surface with cAMP levels increasing in comparison with the wild type (WT). The conidia of ΔMowhi2 and ΔMopsr1 formed a single appressorium per conidium, similar to WT, when the target of rapamycin (TOR) inhibitor rapamycin was present. In addition, compared with WT, the expression levels of MoTOR and the MoTor signalling activation marker gene MoRS3 were increased, suggesting that inappropriate activation of the MoTor signalling pathway is one of the important reasons for the defects in appressorium formation in the ΔMowhi2 and ΔMopsr1 strains. Our results provide insights into MoWhi2 and MoPsr1-mediated appressorium development and pathogenicity by regulating cAMP levels and the activation of MoTor signalling in M. oryzae.
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Affiliation(s)
- Huanbin Shi
- State Key Laboratory of Rice BiologyChina National Rice Research InstituteHangzhouChina
| | - Shuai Meng
- State Key Laboratory of Rice BiologyChina National Rice Research InstituteHangzhouChina
- Hubei Key Lab of Plant Pathology, and College of Plant Science and TechnologyHuazhong Agricultural UniversityWuhanChina
| | - Jiehua Qiu
- State Key Laboratory of Rice BiologyChina National Rice Research InstituteHangzhouChina
| | - Congcong Wang
- State Key Laboratory of Rice BiologyChina National Rice Research InstituteHangzhouChina
| | - Yazhou Shu
- State Key Laboratory of Rice BiologyChina National Rice Research InstituteHangzhouChina
| | - Chaoxi Luo
- Hubei Key Lab of Plant Pathology, and College of Plant Science and TechnologyHuazhong Agricultural UniversityWuhanChina
| | - Yanjun Kou
- State Key Laboratory of Rice BiologyChina National Rice Research InstituteHangzhouChina
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2
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The Whi2p-Psr1p/Psr2p complex regulates interference competition and expansion of cells with competitive advantage in yeast colonies. Proc Natl Acad Sci U S A 2020; 117:15123-15131. [PMID: 32541056 DOI: 10.1073/pnas.1922076117] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022] Open
Abstract
Yeast form complex highly organized colonies in which cells undergo spatiotemporal phenotypic differentiation in response to local gradients of nutrients, metabolites, and specific signaling molecules. Colony fitness depends on cell interactions, cooperation, and the division of labor between differentiated cell subpopulations. Here, we describe the regulation and dynamics of the expansion of papillae that arise during colony aging, which consist of cells that overcome colony regulatory rules and disrupt the synchronized colony structure. We show that papillae specifically expand within the U cell subpopulation in differentiated colonies. Papillae emerge more frequently in some strains than in others. Genomic analyses further revealed that the Whi2p-Psr1p/Psr2p complex (WPPC) plays a key role in papillae expansion. We show that cells lacking a functional WPPC have a sizable interaction-specific fitness advantage attributable to production of and resistance to a diffusible compound that inhibits growth of other cells. Competitive superiority and high relative fitness of whi2 and psr1psr2 strains are particularly pronounced in dense spatially structured colonies and are independent of TORC1 and Msn2p/Msn4p regulators previously associated with the WPPC function. The WPPC function, described here, might be a regulatory mechanism that balances cell competition and cooperation in dense yeast populations and, thus, contributes to cell synchronization, pattern formation, and the expansion of cells with a competitive fitness advantage.
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3
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Unique genetic basis of the distinct antibiotic potency of high acetic acid production in the probiotic yeast Saccharomyces cerevisiae var. boulardii. Genome Res 2020; 29:1478-1494. [PMID: 31467028 PMCID: PMC6724677 DOI: 10.1101/gr.243147.118] [Citation(s) in RCA: 39] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2018] [Accepted: 06/20/2019] [Indexed: 12/14/2022]
Abstract
The yeast Saccharomyces boulardii has been used worldwide as a popular, commercial probiotic, but the basis of its probiotic action remains obscure. It is considered conspecific with budding yeast Saccharomyces cerevisiae, which is generally used in classical food applications. They have an almost identical genome sequence, making the genetic basis of probiotic potency in S. boulardii puzzling. We now show that S. boulardii produces at 37°C unusually high levels of acetic acid, which is strongly inhibitory to bacterial growth in agar-well diffusion assays and could be vital for its unique application as a probiotic among yeasts. Using pooled-segregant whole-genome sequence analysis with S. boulardii and S. cerevisiae parent strains, we succeeded in mapping the underlying QTLs and identified mutant alleles of SDH1 and WHI2 as the causative alleles. Both genes contain a SNP unique to S. boulardii (sdh1F317Y and whi2S287*) and are fully responsible for its high acetic acid production. S. boulardii strains show different levels of acetic acid production, depending on the copy number of the whi2S287* allele. Our results offer the first molecular explanation as to why S. boulardii could exert probiotic action as opposed to S. cerevisiae. They reveal for the first time the molecular-genetic basis of a probiotic action-related trait in S. boulardii and show that antibacterial potency of a probiotic microorganism can be due to strain-specific mutations within the same species. We suggest that acquisition of antibacterial activity through medium acidification offered a selective advantage to S. boulardii in its ecological niche and for its application as a probiotic.
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Gonçalves AP, Chow KM, Cea-Sánchez S, Glass NL. WHI-2 Regulates Intercellular Communication via a MAP Kinase Signaling Complex. Front Microbiol 2020; 10:3162. [PMID: 32038591 PMCID: PMC6987382 DOI: 10.3389/fmicb.2019.03162] [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: 11/15/2019] [Accepted: 12/31/2019] [Indexed: 01/15/2023] Open
Abstract
The formation of the fungal mycelial network is facilitated by somatic cell fusion of germinating asexual spores (or germlings). Neurospora crassa germlings in close proximity display chemotropic growth that is dependent upon an intracellular network of mitogen-activated protein kinase (MAPK) signaling cascades. Approximately 80 genes involved in intercellular communication and fusion have been identified, including three mutants with similar morphological phenotypes: Δwhi-2, Δcsp-6, and Δamph-1. Here we show that WHI-2 localizes to the cell periphery and regulates endocytosis, mitochondrial organization, sporulation, and cell fusion. WHI-2 was required to transduce signals through a conserved MAPK pathway (NRC-1/MEK-2/MAK-2) and target transcription factors (PP-1/ADV-1). The amph-1 locus encodes a Bin/Amphiphysin/Rvs domain-containing protein and mis-expression of whi-2 compensated for the cell fusion and endocytosis deficiencies of a Δamph-1 mutant. The csp-6 locus encodes a haloacid dehalogenase phosphatase whose activity was essential for cell fusion. Although fusion-deficient with themselves, cells that lacked whi-2, csp-6, or amph-1 showed a low frequency of chemotropic interactions with wild type cells. We hypothesize that WHI-2 could be important for signal perception during chemotropic interactions via a role in endocytosis.
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Affiliation(s)
- A Pedro Gonçalves
- Department of Plant and Microbial Biology, University of California, Berkeley, Berkeley, CA, United States
| | - Karen M Chow
- Department of Plant and Microbial Biology, University of California, Berkeley, Berkeley, CA, United States
| | - Sara Cea-Sánchez
- Departamento de Genética, Universidad de Sevilla, Sevilla, Spain
| | - N Louise Glass
- Department of Plant and Microbial Biology, University of California, Berkeley, Berkeley, CA, United States.,Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, CA, United States
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5
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Teng X, Hardwick JM. Whi2: a new player in amino acid sensing. Curr Genet 2019; 65:701-709. [PMID: 30701278 DOI: 10.1007/s00294-018-00929-9] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2018] [Revised: 12/30/2018] [Accepted: 12/31/2018] [Indexed: 12/26/2022]
Abstract
A critical function of human, yeast, and bacterial cells is the ability to sense and respond to available nutrients such as glucose and amino acids. Cells must also detect declining nutrient levels to adequately prepare for starvation conditions by inhibiting cell growth and activating autophagy. The evolutionarily conserved protein complex TORC1 regulates these cellular responses to nutrients, and in particular to amino acid availability. Recently, we found that yeast Whi2 (Saccharomyces cerevisiae) and a human counterpart, KCTD11, that shares a conserved BTB structural domain, are required to suppress TORC1 activity under low amino acid conditions. Using yeast, the mechanisms were more readily dissected. Unexpectedly, Whi2 suppresses TORC1 activity independently of the well-known SEACIT-GTR pathway, analogous to the GATOR1-RAG pathway in mammals. Instead, Whi2 requires the plasma membrane-associated phosphatases Psr1 and Psr2, which were known to bind Whi2, although their role was unknown. Yeast WHI2 was previously reported to be involved in regulating several fundamental cellular processes including cell cycle arrest, general stress responses, the Ras-cAMP-PKA pathway, autophagy, and mitophagy, and to be frequently mutated in the yeast knockout collections and in genome evolution studies. Most of these observations are likely explained by the ability of Whi2 to inhibit TORC1. Thus, understanding the function of yeast Whi2 will provide deeper insights into the disease-related KCTD family proteins and the pathogenesis of plant and human fungal infections.
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Affiliation(s)
- Xinchen Teng
- Jiangsu Key Laboratory of Neuropsychiatric Diseases and College of Pharmaceutical Sciences, Soochow University, Suzhou, 215123, Jiangsu, China. .,W. Harry Feinstone Department of Molecular Microbiology and Immunology, Johns Hopkins University Bloomberg School of Public Health, Baltimore, MD, 21205, USA.
| | - J Marie Hardwick
- W. Harry Feinstone Department of Molecular Microbiology and Immunology, Johns Hopkins University Bloomberg School of Public Health, Baltimore, MD, 21205, USA.
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6
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Teng X, Yau E, Sing C, Hardwick JM. Whi2 signals low leucine availability to halt yeast growth and cell death. FEMS Yeast Res 2018; 18:5083179. [PMID: 30165592 PMCID: PMC6149368 DOI: 10.1093/femsyr/foy095] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2018] [Accepted: 08/26/2018] [Indexed: 12/16/2022] Open
Abstract
Cells are exquisitely tuned to environmental ques. Amino acid availability is rapidly sensed, allowing cells to adjust molecular processes and implement short or long-term metabolic shifts accordingly. How levels of most individual amino acids may be sensed and subsequently signaled to inform cells of their nutrient status is largely unknown. We made the unexpected observation that small changes in the levels of specific amino acids can have a profound effect on yeast cell growth, leading to the identification of yeast Whi2 as a negative regulator of cell growth in low amino acids. Although Whi2 was originally thought to be fungi-specific, Whi2 appears to share a conserved structural domain found in a family of 25 largely uncharacterized human genes encoding the KCTD (potassium channel tetramerization domain) protein family. Insights gained from yeast Whi2 are likely to be revealing about human KCTDs, many of which have been implicated or demonstrated to cause disease when mutated. Here we report new evidence that Whi2 responds to specific amino acids in the medium, particularly low leucine levels. We also discuss the known pathways of amino acid signaling and potential points of regulation by Whi2 in nutrient signaling in yeast and mammals.
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Affiliation(s)
- Xinchen Teng
- Department of Molecular Microbiology and Immunology, Johns Hopkins University Bloomberg School of Public Health, Baltimore, MD 21205-2103, USA
- Jiangsu Key Laboratory of Neuropsychiatric Diseases and College of Pharmaceutical Sciences, Soochow University, 215123 Suzhou, Jiangsu Province, People's Republic of China
- Department of Pharmacology and Molecular Sciences, Johns Hopkins University School of Medicine, Baltimore, MD 21205-2103, USA
| | - Eric Yau
- Department of Molecular Microbiology and Immunology, Johns Hopkins University Bloomberg School of Public Health, Baltimore, MD 21205-2103, USA
| | - Cierra Sing
- Department of Molecular Microbiology and Immunology, Johns Hopkins University Bloomberg School of Public Health, Baltimore, MD 21205-2103, USA
| | - J Marie Hardwick
- Department of Molecular Microbiology and Immunology, Johns Hopkins University Bloomberg School of Public Health, Baltimore, MD 21205-2103, USA
- Department of Pharmacology and Molecular Sciences, Johns Hopkins University School of Medicine, Baltimore, MD 21205-2103, USA
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7
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Metz KA, Teng X, Coppens I, Lamb HM, Wagner BE, Rosenfeld JA, Chen X, Zhang Y, Kim HJ, Meadow ME, Wang TS, Haberlandt ED, Anderson GW, Leshinsky-Silver E, Bi W, Markello TC, Pratt M, Makhseed N, Garnica A, Danylchuk NR, Burrow TA, Jayakar P, McKnight D, Agadi S, Gbedawo H, Stanley C, Alber M, Prehl I, Peariso K, Ong MT, Mordekar SR, Parker MJ, Crooks D, Agrawal PB, Berry GT, Loddenkemper T, Yang Y, Maegawa GHB, Aouacheria A, Markle JG, Wohlschlegel JA, Hartman AL, Hardwick JM. KCTD7 deficiency defines a distinct neurodegenerative disorder with a conserved autophagy-lysosome defect. Ann Neurol 2018; 84:766-780. [PMID: 30295347 DOI: 10.1002/ana.25351] [Citation(s) in RCA: 37] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2018] [Revised: 08/27/2018] [Accepted: 09/23/2018] [Indexed: 12/11/2022]
Abstract
OBJECTIVE Several small case series identified KCTD7 mutations in patients with a rare autosomal recessive disorder designated progressive myoclonic epilepsy (EPM3) and neuronal ceroid lipofuscinosis (CLN14). Despite the name KCTD (potassium channel tetramerization domain), KCTD protein family members lack predicted channel domains. We sought to translate insight gained from yeast studies to uncover disease mechanisms associated with deficiencies in KCTD7 of unknown function. METHODS Novel KCTD7 variants in new and published patients were assessed for disease causality using genetic analyses, cell-based functional assays of patient fibroblasts and knockout yeast, and electron microscopy of patient samples. RESULTS Patients with KCTD7 mutations can exhibit movement disorders or developmental regression before seizure onset, and are distinguished from similar disorders by an earlier age of onset. Although most published KCTD7 patient variants were excluded from a genome sequence database of normal human variations, most newly identified patient variants are present in this database, potentially challenging disease causality. However, genetic analysis and impaired biochemical interactions with cullin 3 support a causal role for patient KCTD7 variants, suggesting deleterious alleles of KCTD7 and other rare disease variants may be underestimated. Both patient-derived fibroblasts and yeast lacking Whi2 with sequence similarity to KCTD7 have impaired autophagy consistent with brain pathology. INTERPRETATION Biallelic KCTD7 mutations define a neurodegenerative disorder with lipofuscin and lipid droplet accumulation but without defining features of neuronal ceroid lipofuscinosis or lysosomal storage disorders. KCTD7 deficiency appears to cause an underlying autophagy-lysosome defect conserved in yeast, thereby assigning a biological role for KCTD7. Ann Neurol 2018;84:774-788.
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Affiliation(s)
- Kyle A Metz
- Department of Molecular Microbiology and Immunology, Johns Hopkins University Bloomberg School of Public Health, Baltimore, MD
| | - Xinchen Teng
- Department of Molecular Microbiology and Immunology, Johns Hopkins University Bloomberg School of Public Health, Baltimore, MD.,Jiangsu Key Laboratory of Neuropsychiatric Diseases and College of Pharmaceutical Sciences, Soochow University, Suzhou, Jiangsu Province, People's Republic of China
| | - Isabelle Coppens
- Department of Molecular Microbiology and Immunology, Johns Hopkins University Bloomberg School of Public Health, Baltimore, MD
| | - Heather M Lamb
- Department of Molecular Microbiology and Immunology, Johns Hopkins University Bloomberg School of Public Health, Baltimore, MD
| | - Bart E Wagner
- Histopathology Department, Royal Hallamshire Hospital, Sheffield, United Kingdom
| | - Jill A Rosenfeld
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX
| | - Xianghui Chen
- Jiangsu Key Laboratory of Neuropsychiatric Diseases and College of Pharmaceutical Sciences, Soochow University, Suzhou, Jiangsu Province, People's Republic of China
| | - Yu Zhang
- Jiangsu Key Laboratory of Neuropsychiatric Diseases and College of Pharmaceutical Sciences, Soochow University, Suzhou, Jiangsu Province, People's Republic of China
| | - Hee Jong Kim
- Department of Biological Chemistry, David Geffen School of Medicine at UCLA, Los Angeles, CA
| | - Michael E Meadow
- Department of Biological Chemistry, David Geffen School of Medicine at UCLA, Los Angeles, CA
| | - Tim Sen Wang
- Department of Molecular Microbiology and Immunology, Johns Hopkins University Bloomberg School of Public Health, Baltimore, MD.,Department of Pharmacology and Molecular Sciences, Johns Hopkins University School of Medicine, Baltimore, MD
| | - Edda D Haberlandt
- Clinical Department of Pediatrics I, Innsbruck Medical University, Innsbruck, Austria.,Department of Child and Youth Health, Hospital of Dornbirn, Dornbirn, Austria
| | - Glenn W Anderson
- Histopathology Department, Great Ormond Street Hospital for Children, London, United Kingdom
| | | | - Weimin Bi
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX
| | - Thomas C Markello
- NIH Undiagnosed Diseases Program, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD
| | - Marsha Pratt
- Department of Pediatrics, University of Oklahoma College of Medicine, Oklahoma City, OK
| | - Nawal Makhseed
- Department of Pediatrics, Jahra Hospital, Ministry of Health, Al Jahra, Kuwait
| | - Adolfo Garnica
- Department of Pediatrics, University of Arkansas for Medical Sciences and Arkansas Children's Hospital, Little Rock, AR
| | - Noelle R Danylchuk
- Department of Pediatrics, University of Arkansas for Medical Sciences and Arkansas Children's Hospital, Little Rock, AR
| | - Thomas A Burrow
- Department of Pediatrics, University of Arkansas for Medical Sciences and Arkansas Children's Hospital, Little Rock, AR
| | - Parul Jayakar
- Division of Genetics and Metabolism, Nicklaus Children's Hospital, Miami, FL
| | | | - Satish Agadi
- Department of Neurology, Texas Children's Hospital, Houston, TX
| | | | | | - Michael Alber
- Pediatric Neurology and Developmental Medicine, University of Tübingen, Tübingen, Germany
| | | | - Katrina Peariso
- Division of Neurology, Cincinnati Children's Hospital Medical Center, Cincinnati, OH
| | - Min Tsui Ong
- Department of Paediatric Neurology, Sheffield Children's National Health Service Foundation Trust, Sheffield, United Kingdom
| | - Santosh R Mordekar
- Department of Paediatric Neurology, Sheffield Children's National Health Service Foundation Trust, Sheffield, United Kingdom
| | - Michael J Parker
- Sheffield Clinical Genetics Service, Sheffield Children's National Health Service Foundation Trust, Sheffield, United Kingdom
| | - Daniel Crooks
- Department of Neuropathology, Walton Centre National Health Service Foundation Trust, Liverpool, United Kingdom
| | - Pankaj B Agrawal
- Division of Genetics and Genomics, Manton Center for Orphan Disease Research, Boston Children's Hospital, Harvard Medical School, Boston, MA
| | - Gerard T Berry
- Division of Genetics and Genomics, Manton Center for Orphan Disease Research, Boston Children's Hospital, Harvard Medical School, Boston, MA
| | | | - Yaping Yang
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX
| | - Gustavo H B Maegawa
- Department of Pediatrics/Genetics and Metabolism, University of Florida, Gainesville, FL
| | - Abdel Aouacheria
- Montpellier Institute of Evolution Sciences, University of Montpellier, CNRS, EPHE, IRD, Montpellier, France
| | - Janet G Markle
- Department of Molecular Microbiology and Immunology, Johns Hopkins University Bloomberg School of Public Health, Baltimore, MD
| | - James A Wohlschlegel
- Department of Biological Chemistry, David Geffen School of Medicine at UCLA, Los Angeles, CA
| | - Adam L Hartman
- Department of Neurology, Johns Hopkins University School of Medicine, Baltimore, MD
| | - J Marie Hardwick
- Department of Molecular Microbiology and Immunology, Johns Hopkins University Bloomberg School of Public Health, Baltimore, MD.,Department of Pharmacology and Molecular Sciences, Johns Hopkins University School of Medicine, Baltimore, MD.,Department of Neurology, Johns Hopkins University School of Medicine, Baltimore, MD
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8
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Chen X, Wang G, Zhang Y, Dayhoff-Brannigan M, Diny NL, Zhao M, He G, Sing CN, Metz KA, Stolp ZD, Aouacheria A, Cheng WC, Hardwick JM, Teng X. Whi2 is a conserved negative regulator of TORC1 in response to low amino acids. PLoS Genet 2018; 14:e1007592. [PMID: 30142151 PMCID: PMC6126876 DOI: 10.1371/journal.pgen.1007592] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2017] [Revised: 09/06/2018] [Accepted: 07/26/2018] [Indexed: 01/29/2023] Open
Abstract
Yeast WHI2 was originally identified in a genetic screen for regulators of cell cycle arrest and later suggested to function in general stress responses. However, the function of Whi2 is unknown. Whi2 has predicted structure and sequence similarity to human KCTD family proteins, which have been implicated in several cancers and are causally associated with neurological disorders but are largely uncharacterized. The identification of conserved functions between these yeast and human proteins may provide insight into disease mechanisms. We report that yeast WHI2 is a new negative regulator of TORC1 required to suppress TORC1 activity and cell growth specifically in response to low amino acids. In contrast to current opinion, WHI2 is dispensable for TORC1 inhibition in low glucose. The only widely conserved mechanism that actively suppresses both yeast and mammalian TORC1 specifically in response to low amino acids is the conserved SEACIT/GATOR1 complex that inactivates the TORC1-activating RAG-like GTPases. Unexpectedly, Whi2 acts independently and simultaneously with these established GATOR1-like Npr2-Npr3-Iml1 and RAG-like Gtr1-Gtr2 complexes, and also acts independently of the PKA pathway. Instead, Whi2 inhibits TORC1 activity through its binding partners, protein phosphatases Psr1 and Psr2, which were previously thought to only regulate amino acid levels downstream of TORC1. Furthermore, the ability to suppress TORC1 is conserved in the SKP1/BTB/POZ domain-containing, Whi2-like human protein KCTD11 but not other KCTD family members tested. Yeast and human cells respond to declining levels of available nutrients to prepare ahead for leaner times. The detailed mechanisms of nutrient sensing are not well understood, but defects in these processes have key roles in diseases such as cancer. The evolutionarily conserved protein complex TORC1 is the control hub for responding to both high and low nutrients, particularly amino acids. We identified yeast Whi2 and the human tumor suppressor KCTD11 as novel suppressors of TORC1 activity in low amino acid conditions, and we investigated the detailed mechanisms for Whi2. Unexpectedly, Whi2 works differently from the usual mechanism where TORC1 is controlled by the SEACIT-Gtr complex (mammalian GATOR1-RAG complex). Furthermore, both the Whi2 and the SEACIT-Gtr pathways work independently and together in parallel to suppress TORC1. For this function, Whi2 requires its binding partners, the yeast protein phosphatases Psr1 and Psr2, which were previously thought to function downstream of TORC1 in amino acid signaling. These studies have important implications for human KCTD11 to help advance the understanding of its pathological role.
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Affiliation(s)
- Xianghui Chen
- Jiangsu Key Laboratory of Neuropsychiatric Diseases and College of Pharmaceutical Sciences, Soochow University, Suzhou, Jiangsu, China
| | - Guiqin Wang
- Jiangsu Key Laboratory of Neuropsychiatric Diseases and College of Pharmaceutical Sciences, Soochow University, Suzhou, Jiangsu, China
| | - Yu Zhang
- Jiangsu Key Laboratory of Neuropsychiatric Diseases and College of Pharmaceutical Sciences, Soochow University, Suzhou, Jiangsu, China
| | - Margaret Dayhoff-Brannigan
- W. Harry Feinstone Department of Molecular Microbiology and Immunology, Johns Hopkins University Bloomberg School of Public Health, Baltimore, MD, United States of America
| | - Nicola L. Diny
- W. Harry Feinstone Department of Molecular Microbiology and Immunology, Johns Hopkins University Bloomberg School of Public Health, Baltimore, MD, United States of America
| | - Mingjun Zhao
- Jiangsu Key Laboratory of Neuropsychiatric Diseases and College of Pharmaceutical Sciences, Soochow University, Suzhou, Jiangsu, China
| | - Ge He
- Jiangsu Key Laboratory of Neuropsychiatric Diseases and College of Pharmaceutical Sciences, Soochow University, Suzhou, Jiangsu, China
| | - Cierra N. Sing
- W. Harry Feinstone Department of Molecular Microbiology and Immunology, Johns Hopkins University Bloomberg School of Public Health, Baltimore, MD, United States of America
| | - Kyle A. Metz
- W. Harry Feinstone Department of Molecular Microbiology and Immunology, Johns Hopkins University Bloomberg School of Public Health, Baltimore, MD, United States of America
| | - Zachary D. Stolp
- W. Harry Feinstone Department of Molecular Microbiology and Immunology, Johns Hopkins University Bloomberg School of Public Health, Baltimore, MD, United States of America
| | - Abdel Aouacheria
- ISEM, Institut des Sciences de l’Evolution de Montpellier, Université de Montpellier, CNRS, EPHE, IRD, Montpellier, France
| | - Wen-Chih Cheng
- W. Harry Feinstone Department of Molecular Microbiology and Immunology, Johns Hopkins University Bloomberg School of Public Health, Baltimore, MD, United States of America
| | - J. Marie Hardwick
- W. Harry Feinstone Department of Molecular Microbiology and Immunology, Johns Hopkins University Bloomberg School of Public Health, Baltimore, MD, United States of America
- Department of Pharmacology and Molecular Sciences, Johns Hopkins University School of Medicine, Baltimore, MD, United States of America
- * E-mail: (JMH); (XT)
| | - Xinchen Teng
- Jiangsu Key Laboratory of Neuropsychiatric Diseases and College of Pharmaceutical Sciences, Soochow University, Suzhou, Jiangsu, China
- W. Harry Feinstone Department of Molecular Microbiology and Immunology, Johns Hopkins University Bloomberg School of Public Health, Baltimore, MD, United States of America
- Department of Pharmacology and Molecular Sciences, Johns Hopkins University School of Medicine, Baltimore, MD, United States of America
- * E-mail: (JMH); (XT)
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9
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Lis P, Jurkiewicz P, Cal-Bąkowska M, Ko YH, Pedersen PL, Goffeau A, Ułaszewski S. Screening the yeast genome for energetic metabolism pathways involved in a phenotypic response to the anti-cancer agent 3-bromopyruvate. Oncotarget 2016; 7:10153-73. [PMID: 26862728 PMCID: PMC4891110 DOI: 10.18632/oncotarget.7174] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2015] [Accepted: 01/23/2016] [Indexed: 01/19/2023] Open
Abstract
In this study the detailed characteristic of the anti-cancer agent 3-bromopyruvate (3-BP) activity in the yeast Saccharomyces cerevisiae model is described, with the emphasis on its influence on energetic metabolism of the cell. It shows that 3-BP toxicity in yeast is strain-dependent and influenced by the glucose-repression system. Its toxic effect is mainly due to the rapid depletion of intracellular ATP. Moreover, lack of the Whi2p phosphatase results in strongly increased sensitivity of yeast cells to 3-BP, possibly due to the non-functional system of mitophagy of damaged mitochondria through the Ras-cAMP-PKA pathway. Single deletions of genes encoding glycolytic enzymes, the TCA cycle enzymes and mitochondrial carriers result in multiple effects after 3-BP treatment. However, it can be concluded that activity of the pentose phosphate pathway is necessary to prevent the toxicity of 3-BP, probably due to the fact that large amounts of NADPH are produced by this pathway, ensuring the reducing force needed for glutathione reduction, crucial to cope with the oxidative stress. Moreover, single deletions of genes encoding the TCA cycle enzymes and mitochondrial carriers generally cause sensitivity to 3-BP, while totally inactive mitochondrial respiration in the rho0 mutant resulted in increased resistance to 3-BP.
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Affiliation(s)
- Paweł Lis
- Department of Genetics, Institute of Genetics and Microbiology, University of Wrocław, Wrocław, Poland
| | - Paweł Jurkiewicz
- Department of Genetics, Institute of Genetics and Microbiology, University of Wrocław, Wrocław, Poland
| | - Magdalena Cal-Bąkowska
- Department of Genetics, Institute of Genetics and Microbiology, University of Wrocław, Wrocław, Poland
| | - Young H Ko
- KoDiscovery LLC, UM BioPark, Innovation Center, Baltimore, MD, USA
| | - Peter L Pedersen
- Departments of Biological Chemistry and Oncology, Sydney Kimmel Comprehensive Cancer Center and Center for Obesity Research and Metabolism, John Hopkins University School of Medicine, Baltimore, MD, USA
| | - Andre Goffeau
- Unité de Biochimie Physiologique, Institut des Sciences de la Vie, Université Catholique de Louvain-la-Neuve, Louvain-la-Neuve, Belgium
| | - Stanisław Ułaszewski
- Department of Genetics, Institute of Genetics and Microbiology, University of Wrocław, Wrocław, Poland
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10
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Timpano H, Chan Ho Tong L, Gautier V, Lalucque H, Silar P. The PaPsr1 and PaWhi2 genes are members of the regulatory network that connect stationary phase to mycelium differentiation and reproduction in Podospora anserina. Fungal Genet Biol 2016; 94:1-10. [PMID: 27353975 DOI: 10.1016/j.fgb.2016.06.006] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2016] [Revised: 06/21/2016] [Accepted: 06/24/2016] [Indexed: 11/20/2022]
Abstract
In filamentous fungi, entrance into stationary phase is complex as it is accompanied by several differentiation and developmental processes, including the synthesis of pigments, aerial hyphae, anastomoses and sporophores. The regulatory networks that control these processes are still incompletely known. The analysis of the "Impaired in the development of Crippled Growth (IDC)" mutants of the model filamentous ascomycete Podospora anserina has already yielded important information regarding the pathway regulating entrance into stationary phase. Here, the genes affected in two additional IDC mutants are identified as orthologues of the Saccharomyces cerevisiae WHI2 and PSR1 genes, known to regulate stationary phase in this yeast, arguing for a conserved role of these proteins throughout the evolution of ascomycetes.
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Affiliation(s)
- Hélène Timpano
- Univ Paris Diderot, Sorbonne Paris Cité, Laboratoire Interdisciplinaire des Energies de Demain, 75205 Paris CEDEX 13, France; Univ Paris Sud 11, Institut de Génétique et Microbiologie, 91405 Orsay cedex, France
| | - Laetitia Chan Ho Tong
- Univ Paris Diderot, Sorbonne Paris Cité, Laboratoire Interdisciplinaire des Energies de Demain, 75205 Paris CEDEX 13, France
| | - Valérie Gautier
- Univ Paris Diderot, Sorbonne Paris Cité, Laboratoire Interdisciplinaire des Energies de Demain, 75205 Paris CEDEX 13, France
| | - Hervé Lalucque
- Univ Paris Diderot, Sorbonne Paris Cité, Laboratoire Interdisciplinaire des Energies de Demain, 75205 Paris CEDEX 13, France
| | - Philippe Silar
- Univ Paris Diderot, Sorbonne Paris Cité, Laboratoire Interdisciplinaire des Energies de Demain, 75205 Paris CEDEX 13, France.
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11
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Harata K, Nishiuchi T, Kubo Y. Colletotrichum orbiculare WHI2, a Yeast Stress-Response Regulator Homolog, Controls the Biotrophic Stage of Hemibiotrophic Infection Through TOR Signaling. MOLECULAR PLANT-MICROBE INTERACTIONS : MPMI 2016; 29:468-483. [PMID: 27018615 DOI: 10.1094/mpmi-02-16-0030-r] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/05/2023]
Abstract
The hemibiotrophic fungus Colletotrichum orbiculare first establishes a biotrophic infection stage in cucumber (Cucumber sativus) epidermal cells and subsequently transitions to a necrotrophic stage. Here, we found that C. orbiculare established hemibiotrophic infection via C. orbiculare WHI2, a yeast stress regulator homolog, and TOR (target of rapamycin) signaling. Plant defense responses such as callose deposition, H2O2, and antimicrobial proteins were strongly induced by the C. orbiculare whi2Δ mutant, resulting in defective pathogenesis. Expression analysis of biotrophy-specific genes evaluated by the promoter VENUS fusion gene indicated weaker VENUS signal intensity in the whi2Δ mutant, thereby suggesting that C. orbiculare WHI2 plays a key role in regulating biotrophic infection of C. orbiculare. The involvement of CoWHI2 in biotrophic infection was further explored with a DNA microarray. In the Cowhi2Δ mutant, TOR-dependent ribosomal protein-related genes were strikingly upregulated compared with the wild type. Moreover, callose deposition in the host plant after inoculation with the Cowhi2Δ mutant treated with rapamycin, which inhibits TOR activity, was reduced, and the mutant remained biotrophic in contrast to the untreated mutant. Thus, regulation of TOR by Whi2 is apparently crucial to the biotrophic stage of hemibiotrophic infection in C. orbiculare.
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Affiliation(s)
- Ken Harata
- 1 Laboratory of Plant Pathology, Graduate School of Life and Environmental Sciences, Kyoto Prefectural University, Kyoto, Japan; and
| | - Takumi Nishiuchi
- 2 Division of Functional Genomics, Advanced Science Research Centre, Kanazawa University, Kanazawa, Japan
| | - Yasuyuki Kubo
- 1 Laboratory of Plant Pathology, Graduate School of Life and Environmental Sciences, Kyoto Prefectural University, Kyoto, Japan; and
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12
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Whi2 enhances methylmercury toxicity in yeast via inhibition of Akr1 palmitoyltransferase activity. Biochim Biophys Acta Gen Subj 2016; 1860:1326-33. [PMID: 27015763 DOI: 10.1016/j.bbagen.2016.03.026] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2015] [Revised: 02/20/2016] [Accepted: 03/20/2016] [Indexed: 11/23/2022]
Abstract
BACKGROUND We have previously reported that Whi2 enhances the toxicity of methylmercury in yeast. In the present study we examined the proteins known to interact with Whi2 to find those that influence the toxicity of methylmercury. METHODS Gene disruption and site-directed mutagenesis were employed to examine the relationship of mercury toxicity and palmitoylation. Protein palmitoylation was examined using the acyl-biotinyl exchange method. Protein-protein interactions were detected by immunoprecipitation and immunoblotting. RESULTS We found that deletion of Akr1, a palmitoyltransferase, rendered yeast cells highly sensitive to methylmercury, and Akr1 is necessary for the methylmercury resistance of Whi2-deleted yeast. Palmitoyltransferase activity of Akr1 has an important role in the alleviation of methylmercury toxicity. Whi2 deletion or methylmercury treatment enhanced the palmitoyltransferase activity of Akr1, and methylmercury treatment reduced the binding between Akr1 and Whi2. CONCLUSIONS Whi2 bonds to Akr1 (a protein that is able to alleviate methylmercury toxicity) and thus inhibits Akr1's palmitoyltransferase activity, which leads to enhanced methylmercury toxicity. In contrast, methylmercury might break the bond between Whi2 and Akr1, which enhances the palmitoyltransferase activity of Akr1 to alleviate methylmercury toxicity. GENERAL SIGNIFICANCE This study's findings propose that the Whi2/Akr1 system can be regarded as a defense mechanism that detects methylmercury incorporation of yeast cells and alleviates its toxicity.
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13
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Kang X, Jiang L, Chen X, Yuan H, Luo C, Ouyang Q. Pump-free multi-well-based microfluidic system for high-throughput analysis of size-control relative genes in budding yeast. Integr Biol (Camb) 2014; 6:685-93. [PMID: 24872017 DOI: 10.1039/c4ib00054d] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Time-lapse single cell imaging by microscopy can provide precise cell information such as the cell size, the cell cycle duration, protein localization and protein expression level. Usually, a microfluidic system is needed for these measurements in order to provide a constant culture environment and confine the cells so that they grow in a monolayer. However, complex connections are required between the channels inside the chip and the outside media, and a complex procedure is needed for loading of cells, thereby making this type of system unsuitable for application in high-throughput single cell scanning experiments. Here we provide a novel and easily operated pump-free multi-well-based microfluidic system which enables the high-throughput loading of many different budding yeast strains into monolayer growth conditions just by use of a multi-channel pipette. Wild type budding yeast (Saccharomyces cerevisiae) and 62 different budding yeast size control relative gene deletion strains were chosen for scanning. We obtained normalized statistical results for the mother cell doubling time, daughter cell doubling time, mother cell size and daughter cell size of different gene deletion strains relative to the corresponding parameters of the wild type cells. Meanwhile, we compared the typical cell morphology of different strains and analyzed the relationship between the cell genotype and phenotype. This method which can be easily used in a normal biology lab may help researchers who need to carry out the high-throughput scanning of cell morphology and growth.
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Affiliation(s)
- Xianjie Kang
- The State Key Laboratory for Artificial Microstructures and Mesoscopic Physics, School of Physics, Peking University, China.
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14
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Abstract
For centuries yeast species have been popular hosts for classical biotechnology processes, such as baking, brewing, and wine making, and more recently for recombinant proteins production, thanks to the advantages of unicellular organisms (i.e., ease of genetic manipulation and rapid growth) together with the ability to perform eukaryotic posttranslational modifications. Moreover, yeast cells have been used for few decades as a tool for identifying the genes and pathways involved in basic cellular processes such as the cell cycle, aging, and stress response. In the budding yeast S. cerevisiae the Ras/cAMP/PKA pathway is directly involved in the regulation of metabolism, cell growth, stress resistance, and proliferation in response to the availability of nutrients and in the adaptation to glucose, controlling cytosolic cAMP levels and consequently the cAMP-dependent protein kinase (PKA) activity. Moreover, Ras signalling has been identified in several pathogenic yeasts as a key controller for virulence, due to its involvement in yeast morphogenesis. Nowadays, yeasts are still useful for Ras-like proteins investigation, both as model organisms and as a test tube to study variants of heterologous Ras-like proteins.
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Affiliation(s)
- Renata Tisi
- Department of Biotechnology and Biosciences, University of Milano-Bicocca, Milan, Italy
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15
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Dungrawala H, Hua H, Wright J, Abraham L, Kasemsri T, McDowell A, Stilwell J, Schneider BL. Identification of new cell size control genes in S. cerevisiae. Cell Div 2012; 7:24. [PMID: 23234503 PMCID: PMC3541103 DOI: 10.1186/1747-1028-7-24] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2012] [Accepted: 12/04/2012] [Indexed: 12/13/2022] Open
Abstract
Cell size homeostasis is a conserved attribute in many eukaryotic species involving a tight regulation between the processes of growth and proliferation. In budding yeast S. cerevisiae, growth to a “critical cell size” must be achieved before a cell can progress past START and commit to cell division. Numerous studies have shown that progression past START is actively regulated by cell size control genes, many of which have implications in cell cycle control and cancer. Two initial screens identified genes that strongly modulate cell size in yeast. Since a second generation yeast gene knockout collection has been generated, we screened an additional 779 yeast knockouts containing 435 new ORFs (~7% of the yeast genome) to supplement previous cell size screens. Upon completion, 10 new strong size mutants were identified: nine in log-phase cells and one in saturation-phase cells, and 97% of the yeast genome has now been screened for cell size mutations. The majority of the logarithmic phase size mutants have functions associated with translation further implicating the central role of growth control in the cell division process. Genetic analyses suggest ECM9 is directly associated with the START transition. Further, the small (whi) mutants mrpl49Δ and cbs1Δ are dependent on CLN3 for cell size effects. In depth analyses of new size mutants may facilitate a better understanding of the processes that govern cell size homeostasis.
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Affiliation(s)
- Huzefa Dungrawala
- Department of Cell Biology and Biochemistry, Texas Tech University Health Sciences Center, 3601 4th St Rm, 5C119, Lubbock, TX, 79430, USA.
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16
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Van Rossom S, Op de Beeck K, Franssens V, Swinnen E, Schepers A, Ghillebert R, Caldara M, Van Camp G, Winderickx J. The splicing mutant of the human tumor suppressor protein DFNA5 induces programmed cell death when expressed in the yeast Saccharomyces cerevisiae. Front Oncol 2012; 2:77. [PMID: 22848872 PMCID: PMC3404532 DOI: 10.3389/fonc.2012.00077] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2012] [Accepted: 07/05/2012] [Indexed: 12/12/2022] Open
Abstract
DFNA5 was first identified as a gene responsible for autosomal dominant deafness. Different mutations were found, but they all resulted in exon 8 skipping during splicing and premature termination of the protein. Later, it became clear that the protein also has a tumor suppression function and that it can induce apoptosis. Epigenetic silencing of the DFNA5 gene is associated with different types of cancers, including gastric and colorectal cancers as well as breast tumors. We introduced the wild-type and mutant DFNA5 allele in the yeast Saccharomyces cerevisiae. The expression of the wild-type protein was well tolerated by the yeast cells, although the protein was subject of degradation and often deposited in distinct foci when cells entered the diauxic shift. In contrast, cells had problems to cope with mutant DFNA5 and despite an apparent compensatory reduction in expression levels, the mutant protein still triggered a marked growth defect, which in part can be ascribed to its interaction with mitochondria. Consistently, cells with mutant DFNA5 displayed significantly increased levels of ROS and signs of programmed cell death. The latter occurred independently of the yeast caspase, Mca1, but involved the mitochondrial fission protein, Fis1, the voltage-dependent anion channel protein, Por1 and the mitochondrial adenine nucleotide translocators, Aac1 and Aac3. Recent data proposed DFNA5 toxicity to be associated to a globular domain encoded by exon 2–6. We confirmed these data by showing that expression of solely this domain confers a strong growth phenotype. In addition, we identified a point mutant in this domain that completely abrogated its cytotoxicity in yeast as well as human Human Embryonic Kidney 293T cells (HEK293T). Combined, our data underscore that the yeast system offers a valuable tool to further dissect the apoptotic properties of DFNA5.
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Affiliation(s)
- Sofie Van Rossom
- Department of Biology, Functional Biology, KU Leuven Leuven-Heverlee, Belgium
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17
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Abstract
Autophagy is a fundamental cellular process promoting survival under various environmental stress conditions. Selective types of autophagy have gained much interest recently as they are involved in specific quality control mechanisms removing, for example, aggregated proteins or dysfunctional mitochondria. This is considered to counteract the development of a number of neurodegenerative disorders and aging. Here we review the role of mitophagy and mitochondrial dynamics in ensuring quality control of mitochondria. In particular, we provide possible explanations why mitophagy in yeast, in contrast with the situation in mammals, was found to be independent of mitochondrial fission. We further discuss recent findings linking these processes to nutrient sensing pathways and the general stress response in yeast. In particular, we propose a model for how the stress response protein Whi2 and the Ras/PKA (protein kinase A) signalling pathway are possibly linked and thereby regulate mitophagy.
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18
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Hwang GW, Ogiwara Y, Takahashi T, Naganuma A. Ubiquitin-conjugating enzyme Cdc34 mediates methylmercury resistance in Saccharomyces cerevisiae by increasing Whi2 degradation. J Toxicol Sci 2012. [DOI: 10.2131/jts.37.1283] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/02/2022]
Affiliation(s)
- Gi-Wook Hwang
- Laboratory of Molecular and Biochemical Toxicology, Graduate School of Pharmaceutical Sciences, Tohoku University
| | - Yousuke Ogiwara
- Laboratory of Molecular and Biochemical Toxicology, Graduate School of Pharmaceutical Sciences, Tohoku University
| | - Tsutomu Takahashi
- Laboratory of Molecular and Biochemical Toxicology, Graduate School of Pharmaceutical Sciences, Tohoku University
| | - Akira Naganuma
- Laboratory of Molecular and Biochemical Toxicology, Graduate School of Pharmaceutical Sciences, Tohoku University
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19
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Mendl N, Occhipinti A, Müller M, Wild P, Dikic I, Reichert AS. Mitophagy in yeast is independent of mitochondrial fission and requires the stress response gene WHI2. J Cell Sci 2011; 124:1339-50. [PMID: 21429936 DOI: 10.1242/jcs.076406] [Citation(s) in RCA: 134] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023] Open
Abstract
Dysfunctional mitochondria show a reduced capacity for fusion and, as mitochondrial fission is maintained, become spatially separated from the intact network. By that mechanism, dysfunctional mitochondria have been proposed to be targeted for selective degradation by mitophagy, thereby providing a quality control system for mitochondria. In yeast, conflicting results concerning the role of mitochondrial dynamics in mitophagy have been reported. Here, we investigate the effects on mitophagy of altering mitochondrial fission and fusion, using biochemical, as well as fluorescence-based, assays. Rapamycin-induced mitophagy was shown to depend upon the autophagy-related proteins Atg11, Atg20 and Atg24, confirming that a selective type of autophagy occurred. Both fragmentation of mitochondria and inhibition of oxidative phosphorylation were not sufficient to trigger mitophagy, and neither deletion of the fission factors Dnm1, Fis1, Mdv1 or Caf4 nor expression of dominant-negative variants of Dnm1 impaired mitophagy. The diminished mitophagy initially observed in a Δfis1 mutant was not due to the absence of Fis1 but rather due to a secondary mutation in WHI2, which encodes a factor reported to function in the general stress response and the Ras-protein kinase A (PKA) signaling pathway. We propose that, in yeast, mitochondrial fission is not a prerequisite for the selective degradation of mitochondria, and that mitophagy is linked to the general stress response and the Ras-PKA signaling pathway.
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Affiliation(s)
- Nadine Mendl
- Adolf-Butenandt-Institut für Physiologische Chemie, Ludwig-Maximilians-Universität München, Butenandtstr. 5, 81377 München, Germany
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20
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Leadsham JE, Miller K, Ayscough KR, Colombo S, Martegani E, Sudbery P, Gourlay CW. Whi2p links nutritional sensing to actin-dependent Ras-cAMP-PKA regulation and apoptosis in yeast. J Cell Sci 2009; 122:706-15. [PMID: 19208759 DOI: 10.1242/jcs.042424] [Citation(s) in RCA: 72] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023] Open
Abstract
Elucidating the mechanisms by which eukaryotic cells coordinate environmental signals with intracellular ;fate' decisions, such as apoptosis, remains one of the important challenges facing cell biologists. It has recently emerged that the dynamic nature of the actin cytoskeleton is an important factor in the linkage of sensation of extracellular stimuli to signalling mechanisms that regulate programmed cell death. In yeast, actin has been shown to play a role in the regulation of apoptosis as cells prepare themselves for quiescence in the face of nutritional exhaustion, by facilitating the shutdown of Ras-cAMP-PKA pathway activity. Here, we demonstrate that the loss of Whi2p function, a protein known to influence cell cycle exit under conditions of nutritional stress, leads to cell death in yeast that displays the hallmarks of actin-mediated apoptosis. We show that actin-mediated apoptosis occurs as a result of inappropriate Ras-cAMP-PKA activity in Deltawhi2 cells. Cells lacking Whi2p function exhibit an aberrant accumulation of activated Ras2 at the mitochondria in response to nutritional depletion. This study provides evidence that the shutdown of cAMP-PKA signalling activity in wild-type cells involves Whi2p-dependent targeting of Ras2p to the vacuole for proteolysis. We also demonstrate for the first time that Whi2p-dependent regulation of cAMP-PKA signalling plays a physiological role in the differentiation of yeast colonies by facilitating elaboration of distinct zones of cell death.
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Affiliation(s)
- Jane E Leadsham
- Department of Biosciences, University of Kent, Canterbury, Kent CT2 7NJ, UK
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21
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Fis1 deficiency selects for compensatory mutations responsible for cell death and growth control defects. Cell Death Differ 2008; 15:1838-46. [PMID: 18756280 DOI: 10.1038/cdd.2008.117] [Citation(s) in RCA: 55] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022] Open
Abstract
Genetic mutations affecting mitochondrial fission and fusion proteins cause human neurological disorders, but are assumed to be well tolerated in yeast. The conserved mitochondrial fission protein Dnm1/Drp1 is required for normal mitochondrial division, but also promotes cell death in mammals and yeast. Fis1, an outer mitochondrial membrane-anchored receptor for Dnm1/Drp1, also can promote cell death in mammals, but appears to have prosurvival activity in yeast. Here we report that deletion of the FIS1 gene in yeast consistently results in acquisition of a secondary mutation that confers sensitivity to cell death. In several independently derived FIS1 knockouts, tiling arrays and genomic sequencing identified the secondary mutation as a premature termination in the same stress-response gene, WHI2. The WHI2 mutation rescues the mitochondrial respiratory defect (petite formation) caused by FIS1 deficiency, but also causes a failure to suppress cell growth during amino-acid deprivation. Thus, loss of Fis1 drives the selection for specific compensatory mutations that confer defective growth control and cell death regulation, characteristic of human tumor cells. The important long-term survival function of Fis1 that is compensated by WHI2 mutation appears to be independent of fission factor Dnm1/Drp1 and its adaptor Mdv1, but may be mediated through a second adaptor Caf4, as WHI2 is also mutated in a CAF4 knockout.
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22
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Abstract
The ultimate stem cell, the oocyte, is frequently very large. For example, Drosophila and Xenopus oocytes are approximately 10(5) times larger than normal somatic cells. Importantly, once the large oocytes are fertilized, the resulting embryonic cells proliferate rapidly. Moreover, these divisions occur in the absence of cell growth and are not governed by normal cell cycle controls. Observations suggest that mitogens and cell growth signals modulate proliferation by upregulating G1-phase cyclins, which in turn promote cell division. Like embryonic cells, the proliferation of cancer cells is largely independent of mitogens and growth factors. This occurs, in part, because many proteins that are known to modulate G1-phase cyclin activity are frequently mutated in cancer cells. Interestingly, we have found that both the expression and the activity of G1-phase cyclins is modulated by growth rate and cell size in yeast. These and other data suggest that proliferative capacity correlates with cell size. Thus, a major goal of our laboratory is to use yeast to investigate the relationship between proliferation rate, G1-phase cyclins, growth rate, and cell size. The elucidation of this relationship will help clarify the role of cell size in promoting proliferation in both normal and cancer cells.
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Affiliation(s)
- Jian Zhang
- Department of Cell Biology and Biochemistry, Texas Tech University Health Sciences Center, Lubbock, Texas 79430, USA
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23
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Care A, Vousden KA, Binley KM, Radcliffe P, Trevethick J, Mannazzu I, Sudbery PE. A synthetic lethal screen identifies a role for the cortical actin patch/endocytosis complex in the response to nutrient deprivation in Saccharomyces cerevisiae. Genetics 2004; 166:707-19. [PMID: 15020461 PMCID: PMC1470737 DOI: 10.1534/genetics.166.2.707] [Citation(s) in RCA: 35] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Saccharomyces cerevisiae whi2Delta cells are unable to halt cell division in response to nutrient limitation and are sensitive to a wide variety of stresses. A synthetic lethal screen resulted in the isolation of siw mutants that had a phenotype similar to that of whi2Delta. Among these were mutations affecting SIW14, FEN2, SLT2, and THR4. Fluid-phase endocytosis is severely reduced or abolished in whi2Delta, siw14Delta, fen2Delta, and thr4Delta mutants. Furthermore, whi2Delta and siw14Delta mutants produce large actin clumps in stationary phase similar to those seen in prk1Delta ark1Delta mutants defective in protein kinases that regulate the actin cytoskeleton. Overexpression of SIW14 in a prk1Delta strain resulted in a loss of cortical actin patches and cables and was lethal. Overexpression of SIW14 also rescued the caffeine sensitivity of the slt2 mutant isolated in the screen, but this was not due to alteration of the phosphorylation state of Slt2. These observations suggest that endocytosis and the organization of the actin cytoskeleton are required for the proper response to nutrient limitation. This hypothesis is supported by the observation that rvs161Delta, sla1Delta, sla2Delta, vrp1Delta, ypt51Delta, ypt52Delta, and end3Delta mutations, which disrupt the organization of the actin cytoskeleton and/or reduce endocytosis, have a phenotype similar to that of whi2Delta mutants.
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Affiliation(s)
- Alison Care
- Department of Molecular Biology and Biotechnology, University of Sheffield, Sheffield S10 2TN, UK
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24
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Care A, Vousden KA, Binley KM, Radcliffe P, Trevethick J, Mannazzu I, Sudbery PE. A Synthetic Lethal Screen Identifies a Role for the Cortical Actin Patch/Endocytosis Complex in the Response to Nutrient Deprivation in Saccharomyces cerevisiae. Genetics 2004. [DOI: 10.1093/genetics/166.2.707] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
Abstract
Saccharomyces cerevisiae whi2Δ cells are unable to halt cell division in response to nutrient limitation and are sensitive to a wide variety of stresses. A synthetic lethal screen resulted in the isolation of siw mutants that had a phenotype similar to that of whi2Δ. Among these were mutations affecting SIW14, FEN2, SLT2, and THR4. Fluid-phase endocytosis is severely reduced or abolished in whi2Δ, siw14Δ, fen2Δ, and thr4Δ mutants. Furthermore, whi2Δ and siw14Δ mutants produce large actin clumps in stationary phase similar to those seen in prk1Δ ark1Δ mutants defective in protein kinases that regulate the actin cytoskeleton. Overexpression of SIW14 in a prk1Δ strain resulted in a loss of cortical actin patches and cables and was lethal. Overexpression of SIW14 also rescued the caffeine sensitivity of the slt2 mutant isolated in the screen, but this was not due to alteration of the phosphorylation state of Slt2. These observations suggest that endocytosis and the organization of the actin cytoskeleton are required for the proper response to nutrient limitation. This hypothesis is supported by the observation that rvs161Δ, sla1Δ, sla2Δ, vrp1Δ, ypt51Δ, ypt52Δ, and end3Δ mutations, which disrupt the organization of the actin cytoskeleton and/or reduce endocytosis, have a phenotype similar to that of whi2Δ mutants.
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Affiliation(s)
| | | | | | | | - Janet Trevethick
- Department of Molecular Biology and Biotechnology, University of Sheffield, Sheffield S10 2TN, United Kingdom
| | | | - Peter E Sudbery
- Department of Molecular Biology and Biotechnology, University of Sheffield, Sheffield S10 2TN, United Kingdom
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25
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Zhang J, Schneider C, Ottmers L, Rodriguez R, Day A, Markwardt J, Schneider BL. Genomic scale mutant hunt identifies cell size homeostasis genes in S. cerevisiae. Curr Biol 2002; 12:1992-2001. [PMID: 12477387 DOI: 10.1016/s0960-9822(02)01305-2] [Citation(s) in RCA: 111] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
Abstract
BACKGROUND In most eukaryotic cells, there is a relationship between cell size and proliferative capacity. For example, in order to commit to cell division, the yeast Saccharomyces cerevisiae must attain a "critical cell size." This mechanism coordinates growth with cell division to maintain cell size homeostasis. Because very few cell size control genes are known, the genetic pathways responsible for cell size homeostasis remain obscure. Furthermore, elucidation of the mechanism of cell size homeostasis has been recalcitrant to genetic analysis primarily due to the difficulty in cloning cell size control genes. RESULTS To identify new size control genes, the effect of 5958 single gene deletions (4792 homozygous and 1166 heterozygous gene deletions) on cell size in yeast grown to saturation was systematically determined. From these data, 49 genes were identified that dramatically altered cell size. Of these, 34 are involved in transcription, signal transduction, or cell cycle control; 88% of these genes have putative human homologs. Sixteen genes regulate cell size in a dosage-dependent manner, and the majority of mutants identified fail to correctly exit the cell cycle. Many of these genes are components of Ccr4-Not transcriptional complexes or function in the PKC-MAP kinase pathway. These genes may modulate cell size by altering the expression or activity of G1-phase cyclins. CONCLUSIONS These results illustrate how systematic genetic screens can be used to dissect intricate biological processes that are refractory to classic genetic approaches. This genomic-wide genetic screen yielded 46 new cell size mutants and systematically assessed the effect of 5958 single gene deletions on cell size as cells exited the cell cycle.
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Affiliation(s)
- Jian Zhang
- Department of Cell Biology and Biochemistry, Texas Tech University Health Sciences Center, Lubbock, TX 79430, USA
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26
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Kaida D, Yashiroda H, Toh-e A, Kikuchi Y. Yeast Whi2 and Psr1-phosphatase form a complex and regulate STRE-mediated gene expression. Genes Cells 2002; 7:543-52. [PMID: 12090248 DOI: 10.1046/j.1365-2443.2002.00538.x] [Citation(s) in RCA: 72] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
BACKGROUND In response to various stressful situations, including diauxic conditions, the Msn2 and Msn4 transcription factors induce STRE-mediated gene expression of many stress responsive genes in Saccharomyces cerevisiae. This is called the general stress response. The whi2 cells in the stationary phase are smaller than wild-type cells. RESULTS Here we demonstrate that STRE-mediated gene expression in whi2 cells is reduced to half of that in the wild-type cells under various stress conditions. It is also delayed for several hours when the mutant cells enter the stationary phase. Using the two-hybrid system, we isolated a WHI2-interacting gene, PSR1, which is one of the redundant genes encoding plasma membrane phosphatases. whi2 and psr1 psr2 mutants had similar phenotypes, including reduced STRE-mediated gene expression, higher sensitivity to sodium ions and heat shock, and hyper-phosphorylation of Msn2. The phosphatase activity of Psr1 was necessary for the full activation of STRE-mediated gene expression. Furthermore, both Psr1 and Msn2 were co-immunoprecipitated with Whi2. CONCLUSIONS Thus, Whi2 and its binding partner, Psr1-phosphatase, are required for a full activation of the general stress response, possibly through the dephosphorylation of Msn2. These results may explain why stationary phase whi2 cells are small.
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Affiliation(s)
- Daisuke Kaida
- Department of Biological Sciences, Graduate School of Science, The University of Tokyo, Japan
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Abstract
Using a complete set of budding-yeast mutants bearing deletions of all known open reading frames, a recent study has revealed multiple overlapping pathways that coordinately regulate cell-cycle progression with ribosome biogenesis and translation efficiency, providing new insights into the mechanisms governing cell-size homeostasis in eukaryotes..
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Affiliation(s)
- Jonathan B A Millar
- Division of Yeast Genetics, National Institute for Medical Research, The Ridgeway, Mill Hill, London NW7 1AA, UK, E-mail:
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Binley KM, Radcliffe PA, Trevethick J, Duffy KA, Sudbery PE. The yeast PRS3 gene is required for cell integrity, cell cycle arrest upon nutrient deprivation, ion homeostasis and the proper organization of the actin cytoskeleton. Yeast 1999; 15:1459-69. [PMID: 10514564 DOI: 10.1002/(sici)1097-0061(199910)15:14<1459::aid-yea472>3.0.co;2-a] [Citation(s) in RCA: 20] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023] Open
Abstract
PRS3 is one of a family of five genes encoding phosphoribosylpyrophosphate synthetase, an enzyme which catalyses the first step in a variety of biosynthetic pathways, including purine and pyrimidine biosynthesis. We report here that prs3Delta mutants have a number of phenotypes that suggest an unexpected role for PRS3 in linking nutrient availability to cell cycle progression, cell integrity and the actin cytoskeleton. Upon nutrient limitation, prs3Delta mutants fail to arrest in G(1)-cells remain budded and a significant fraction have a G(2) DNA content. Furthermore, in such conditions, prs3Delta mutants have a disorganized actin cytoskeleton: actin accumulates in one or two intensely staining clumps per cell. Prs3Delta mutants also show defects in ion homeostasis and cell integrity. They fail to grow on medium containing 1.0 M NaCl, 5 mM caffeine or when incubated at 37 degrees C. The caffeine and temperature sensitivity are rescued by supplementing the growth medium with 1.0 M sorbitol. These phenotypes resemble those of whi2Delta mutations and indeed, a prs3 allele was recovered in a colony-sectoring screen for mutations that are co-lethal with whi2Delta. However, further investigation showed that the prs3Delta whi2Delta double mutant was viable, with no obvious growth defect compared to either single mutant. In the same colony-sectoring assay, an mpk1 allele was also recovered. Multicopy PRS3 rescued the caffeine sensitivity of this mpk1 allele.
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Affiliation(s)
- K M Binley
- Department of Molecular Biology and Biotechnology, University of Sheffield, Western Bank, Sheffield S10 2TN, UK
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Mendenhall MD, Hodge AE. Regulation of Cdc28 cyclin-dependent protein kinase activity during the cell cycle of the yeast Saccharomyces cerevisiae. Microbiol Mol Biol Rev 1998; 62:1191-243. [PMID: 9841670 PMCID: PMC98944 DOI: 10.1128/mmbr.62.4.1191-1243.1998] [Citation(s) in RCA: 300] [Impact Index Per Article: 11.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
The cyclin-dependent protein kinase (CDK) encoded by CDC28 is the master regulator of cell division in the budding yeast Saccharomyces cerevisiae. By mechanisms that, for the most part, remain to be delineated, Cdc28 activity controls the timing of mitotic commitment, bud initiation, DNA replication, spindle formation, and chromosome separation. Environmental stimuli and progress through the cell cycle are monitored through checkpoint mechanisms that influence Cdc28 activity at key cell cycle stages. A vast body of information concerning how Cdc28 activity is timed and coordinated with various mitotic events has accrued. This article reviews that literature. Following an introduction to the properties of CDKs common to many eukaryotic species, the key influences on Cdc28 activity-cyclin-CKI binding and phosphorylation-dephosphorylation events-are examined. The processes controlling the abundance and activity of key Cdc28 regulators, especially transcriptional and proteolytic mechanisms, are then discussed in detail. Finally, the mechanisms by which environmental stimuli influence Cdc28 activity are summarized.
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Affiliation(s)
- M D Mendenhall
- L. P. Markey Cancer Center, University of Kentucky, Lexington, Kentucky 40536-0096, USA.
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