1
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Cao C, Wang K, Wang Y, Liu TB, Rivera A, Xue C. Ubiquitin proteolysis of a CDK-related kinase regulates titan cell formation and virulence in the fungal pathogen Cryptococcus neoformans. Nat Commun 2022; 13:6397. [PMID: 36302775 PMCID: PMC9613880 DOI: 10.1038/s41467-022-34151-6] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [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: 10/17/2022] [Indexed: 12/25/2022] Open
Abstract
Fungal pathogens often undergo morphological switches, including cell size changes, to adapt to the host environment and cause disease. The pathogenic yeast Cryptococcus neoformans forms so-called 'titan cells' during infection. Titan cells are large, polyploid, display alterations in cell wall and capsule, and are more resistant to phagocytosis and various types of stress. Titan cell formation is regulated by the cAMP/PKA signal pathway, which is stimulated by the protein Gpa1. Here, we show that Gpa1 is activated through phosphorylation by a CDK-related kinase (Crk1), which is targeted for degradation by an E3 ubiquitin ligase (Fbp1). Strains overexpressing CRK1 or an allele lacking a PEST domain exhibit increased production of titan cells similarly to the fbp1∆ mutant. Conversely, CRK1 deletion results in reduced titan cell production, indicating that Crk1 stimulates titan cell formation. Crk1 phosphorylates Gpa1, which then localizes to the plasma membrane and activates the cAMP/PKA signal pathway to induce cell enlargement. Furthermore, titan cell-overproducing strains trigger increased Th1 and Th17 cytokine production in CD4+ T cells and show attenuated virulence in a mouse model of systemic cryptococcosis. Overall, our study provides insights into the regulation of titan cell formation and fungal virulence.
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Affiliation(s)
- Chengjun Cao
- Public Health Research Institute, New Jersey Medical School, Rutgers University, Newark, NJ, 07103, USA
| | - Keyi Wang
- Center for Immunity and Inflammation, New Jersey Medical School, Rutgers University, Newark, NJ, 07103, USA
| | - Yina Wang
- Public Health Research Institute, New Jersey Medical School, Rutgers University, Newark, NJ, 07103, USA
| | - Tong-Bao Liu
- Public Health Research Institute, New Jersey Medical School, Rutgers University, Newark, NJ, 07103, USA
- Medical Research Institute, Southwest University, Chongqing, 400715, China
| | - Amariliz Rivera
- Center for Immunity and Inflammation, New Jersey Medical School, Rutgers University, Newark, NJ, 07103, USA
| | - Chaoyang Xue
- Public Health Research Institute, New Jersey Medical School, Rutgers University, Newark, NJ, 07103, USA.
- Department of Microbiology, Biochemistry and Molecular Genetics, New Jersey Medical School, New Jersey Medical School, Rutgers University, Newark, NJ, 07103, USA.
- Rutgers Center for Lipid Research, Rutgers University, New Brunswick, NJ, 08901, USA.
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2
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Xiao J, Zhang Y, Yang K, Tang Y, Wei L, Liu E, Liang Z. Protein kinase Ime2 is associated with mycelial growth, conidiation, osmoregulation, and pathogenicity in Fusarium oxysporum. Arch Microbiol 2022; 204:455. [PMID: 35788908 PMCID: PMC9252944 DOI: 10.1007/s00203-022-02964-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2022] [Accepted: 05/10/2022] [Indexed: 11/30/2022]
Abstract
Fusarium oxysporum f.sp. niveum is one of the most serious diseases impairing watermelon yield and quality. Inducer of meiosis 2 (Ime2) is the founding member of a family of serine/threonine protein kinases and plays important roles in yeasts and other filamentous fungi. In this study, we analyzed the functions of FoIme2, the ortholog of Saccharomyces cerevisiae Ime2 in F. oxysporum f.sp. niveum. The FoIme2-deleted mutants exhibited obvious morphological abnormalities, including slower vegetative growth, more branches in the edge hyphae and a reduction in conidia production. Compared to the wild type, the mutants were hypersensitive to the osmotic stressor NaCl but were more insensitive to the membrane stressor SDS. The deletion of FoIme2 also caused a reduction in pathogenicity. Transcriptional analysis revealed that FoIme2 acts downstream of FoOpy2 which is an upstream sensor of the MAPK kinase cascade. These results indicate that FoIme2 is important in the development and pathogenicity of F. oxysporum, and provide new insight for the analysis of the pathogenic mechanism of F. oxysporum.
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Affiliation(s)
- Jiling Xiao
- College of Plant Protection, Hunan Agricultural University, Changsha, 410125, China.,Hunan Agricultural Biotechnology Research Institute, Changsha, 410125, China
| | - Yi Zhang
- Hunan Rice Research Institute, Changsha, 410125, China
| | - Ke Yang
- Hunan Agricultural Biotechnology Research Institute, Changsha, 410125, China
| | - Yanying Tang
- Hunan Plant Protection Institute, Changsha, 410125, China
| | - Lin Wei
- Hunan Plant Protection Institute, Changsha, 410125, China
| | - Erming Liu
- College of Plant Protection, Hunan Agricultural University, Changsha, 410125, China.
| | - Zhihuai Liang
- Hunan Agricultural Biotechnology Research Institute, Changsha, 410125, China.
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3
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Xie M, Bai N, Yang J, Jiang K, Zhou D, Zhao Y, Li D, Niu X, Zhang KQ, Yang J. Protein Kinase Ime2 Is Required for Mycelial Growth, Conidiation, Osmoregulation, and Pathogenicity in Nematode-Trapping Fungus Arthrobotrys oligospora. Front Microbiol 2020; 10:3065. [PMID: 31993040 PMCID: PMC6971104 DOI: 10.3389/fmicb.2019.03065] [Citation(s) in RCA: 23] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2019] [Accepted: 12/18/2019] [Indexed: 11/26/2022] Open
Abstract
Inducer of meiosis 2 (Ime2), a protein kinase that has been identified in diverse fungal species, functions in the regulation of various cellular processes, such as ascospore formation, pseudohyphal growth, and sexual reproduction. In this study, AoIme2, an ortholog of Saccharomyces cerevisiae Ime2, was characterized in the nematode-trapping fungus Arthrobotrys oligospora. Disruption of the gene Aoime2 caused defective growth, with slower mycelial growth in ΔAoime2 mutants than the wild type (WT) strain, and in the mutants, the number of hyphal septa in mycelia was higher and the number of cell nuclei in mycelia and conidia was considerably lower than in the WT strain. The conidial yields of the ΔAoime2 mutants were decreased by ∼33% relative to the WT strain, and the transcription of several sporulation-related genes, including abaA, fluG, rodA, aspB, velB, and vosA, was markedly downregulated during the conidiation stage. The ΔAoime2 mutants were highly sensitive to the osmotic stressors NaCl and sorbitol, and the cell wall of partial hyphae in the mutants was deformed. Further examination revealed that the cell wall of the traps produced by ΔAoime2 mutants became loose, and that the electron-dense bodies in trap cells were also few than in the WT strain. Moreover, Aoime2 disruption caused a reduction in trap formation and serine-protease production, and most hyphal traps produced by ΔAoime2 mutants did not form an intact hyphal loop; consequently, substantially fewer nematodes were captured by the mutants than by the WT strain. In summary, an Ime2-MAPK is identified here for the first time from a nematode-trapping fungus, and the kinase is shown to be involved in the regulation of mycelial growth and development, conidiation, osmolarity, and pathogenicity in A. oligospora.
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Affiliation(s)
- Meihua Xie
- State Key Laboratory for Conservation and Utilization of Bio-Resources in Yunnan, Yunnan University, Kunming, China.,School of Life Sciences, Yunnan University, Kunming, China.,Key Laboratory for Microbial Resources of the Ministry of Education, Yunnan University, Kunming, China.,Department of Chemistry and Life Science, Chuxiong Normal University, Chuxiong, China
| | - Na Bai
- State Key Laboratory for Conservation and Utilization of Bio-Resources in Yunnan, Yunnan University, Kunming, China.,School of Life Sciences, Yunnan University, Kunming, China.,Key Laboratory for Microbial Resources of the Ministry of Education, Yunnan University, Kunming, China
| | - Jiangliu Yang
- State Key Laboratory for Conservation and Utilization of Bio-Resources in Yunnan, Yunnan University, Kunming, China.,School of Life Sciences, Yunnan University, Kunming, China.,Key Laboratory for Microbial Resources of the Ministry of Education, Yunnan University, Kunming, China
| | - Kexin Jiang
- State Key Laboratory for Conservation and Utilization of Bio-Resources in Yunnan, Yunnan University, Kunming, China.,School of Life Sciences, Yunnan University, Kunming, China.,Key Laboratory for Microbial Resources of the Ministry of Education, Yunnan University, Kunming, China
| | - Duanxu Zhou
- State Key Laboratory for Conservation and Utilization of Bio-Resources in Yunnan, Yunnan University, Kunming, China.,School of Life Sciences, Yunnan University, Kunming, China.,Key Laboratory for Microbial Resources of the Ministry of Education, Yunnan University, Kunming, China
| | - Yining Zhao
- State Key Laboratory for Conservation and Utilization of Bio-Resources in Yunnan, Yunnan University, Kunming, China.,School of Life Sciences, Yunnan University, Kunming, China.,Key Laboratory for Microbial Resources of the Ministry of Education, Yunnan University, Kunming, China
| | - Dongni Li
- State Key Laboratory for Conservation and Utilization of Bio-Resources in Yunnan, Yunnan University, Kunming, China.,School of Life Sciences, Yunnan University, Kunming, China.,Key Laboratory for Microbial Resources of the Ministry of Education, Yunnan University, Kunming, China
| | - Xuemei Niu
- State Key Laboratory for Conservation and Utilization of Bio-Resources in Yunnan, Yunnan University, Kunming, China.,School of Life Sciences, Yunnan University, Kunming, China.,Key Laboratory for Microbial Resources of the Ministry of Education, Yunnan University, Kunming, China
| | - Ke-Qin Zhang
- State Key Laboratory for Conservation and Utilization of Bio-Resources in Yunnan, Yunnan University, Kunming, China.,School of Life Sciences, Yunnan University, Kunming, China.,Key Laboratory for Microbial Resources of the Ministry of Education, Yunnan University, Kunming, China
| | - Jinkui Yang
- State Key Laboratory for Conservation and Utilization of Bio-Resources in Yunnan, Yunnan University, Kunming, China.,School of Life Sciences, Yunnan University, Kunming, China.,Key Laboratory for Microbial Resources of the Ministry of Education, Yunnan University, Kunming, China
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4
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Usher J. The Mechanisms of Mating in Pathogenic Fungi-A Plastic Trait. Genes (Basel) 2019; 10:E831. [PMID: 31640207 PMCID: PMC6826560 DOI: 10.3390/genes10100831] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2019] [Revised: 09/30/2019] [Accepted: 10/17/2019] [Indexed: 01/20/2023] Open
Abstract
The impact of fungi on human and plant health is an ever-increasing issue. Recent studies have estimated that human fungal infections result in an excess of one million deaths per year and plant fungal infections resulting in the loss of crop yields worth approximately 200 million per annum. Sexual reproduction in these economically important fungi has evolved in response to the environmental stresses encountered by the pathogens as a method to target DNA damage. Meiosis is integral to this process, through increasing diversity through recombination. Mating and meiosis have been extensively studied in the model yeast Saccharomyces cerevisiae, highlighting that these mechanisms have diverged even between apparently closely related species. To further examine this, this review will inspect these mechanisms in emerging important fungal pathogens, such as Candida, Aspergillus, and Cryptococcus. It shows that both sexual and asexual reproduction in these fungi demonstrate a high degree of plasticity.
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Affiliation(s)
- Jane Usher
- Medical Research Council Centre for Medical Mycology, Department of Biosciences, University of Exeter, Geoffrey Pope Building, Exeter EX4 4QD, UK.
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5
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Bardetti P, Castanheira SM, Valerius O, Braus GH, Pérez-Martín J. Cytoplasmic retention and degradation of a mitotic inducer enable plant infection by a pathogenic fungus. eLife 2019; 8:e48943. [PMID: 31621584 PMCID: PMC6887120 DOI: 10.7554/elife.48943] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2019] [Accepted: 10/16/2019] [Indexed: 11/13/2022] Open
Abstract
In the fungus Ustilago maydis, sexual pheromones elicit mating resulting in an infective filament able to infect corn plants. Along this process a G2 cell cycle arrest is mandatory. Such as cell cycle arrest is initiated upon the pheromone recognition in each mating partner, and sustained once cell fusion occurred until the fungus enter the plant tissue. We describe that the initial cell cycle arrest resulted from inhibition of the nuclear transport of the mitotic inducer Cdc25 by targeting its importin, Kap123. Near cell fusion to take place, the increase on pheromone signaling promotes Cdc25 degradation, which seems to be important to ensure the maintenance of the G2 cell cycle arrest to lead the formation of the infective filament. This way, premating cell cycle arrest is linked to the subsequent steps required for establishment of the infection. Disabling this connection resulted in the inability of fungal cells to infect plants.
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Affiliation(s)
- Paola Bardetti
- Instituto de Biología Funcional y Genómica (CSIC)SalamancaSpain
| | | | - Oliver Valerius
- Department of Molecular Microbiology and Genetics, Institute for Microbiology and GeneticsGeorg-August-UniversityGöttingenGermany
| | - Gerhard H Braus
- Department of Molecular Microbiology and Genetics, Institute for Microbiology and GeneticsGeorg-August-UniversityGöttingenGermany
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6
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Xie M, Wang Y, Tang L, Yang L, Zhou D, Li Q, Niu X, Zhang KQ, Yang J. AoStuA, an APSES transcription factor, regulates the conidiation, trap formation, stress resistance and pathogenicity of the nematode-trapping fungus Arthrobotrys oligospora. Environ Microbiol 2019; 21:4648-4661. [PMID: 31433890 DOI: 10.1111/1462-2920.14785] [Citation(s) in RCA: 41] [Impact Index Per Article: 8.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2019] [Revised: 08/19/2019] [Accepted: 08/19/2019] [Indexed: 01/30/2023]
Abstract
The APSES protein family comprises a conserved class of fungus-specific transcriptional regulators. Some members have been identified in partial ascomycetes. In this study, the APSES protein StuA (AoStuA) of the nematode-trapping fungus Arthrobotrys oligospora was characterized. Compared with the wild-type (WT) strain, three ΔAoStuA mutants grew relatively slowly, displayed a 96% reduction in sporulation capacity and a delay in conidial germination. The reduced sporulation capacity correlated with transcriptional repression of several sporulation-related genes. The mutants were also more sensitive to chemical stressors than the WT strain. Importantly, the mutants were unable to produce mycelial traps for nematode predation. Moreover, peroxisomes and Woronin bodies were abundant in the WT cells but hardly found in the cells of those mutants. The lack of such organelles correlated with transcriptional repression of some genes involved in the biogenesis of peroxisomes and Woronin bodies. The transcript levels of several genes involved in the cAMP/PKA signalling pathway were also significantly reduced in the mutants versus the WT strain, implicating a regulatory role of AoStuA in the transcription of genes involved in the cAMP/PKA signalling pathway that regulates an array of cellular processes and events. In particular, AoStuA is indispensable for A. oligospora trap formation and virulence.
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Affiliation(s)
- Meihua Xie
- State Key Laboratory for Conservation and Utilization of Bio-Resources in Yunnan, Yunnan University, Kunming, 650091, P. R. China.,School of Life Sciences, Yunnan University, Kunming, 650091, P. R. China.,Department of Chemistry and Life Science, Chuxiong Normal University, Chuxiong, 675000, P. R. China
| | - Yunchuan Wang
- State Key Laboratory for Conservation and Utilization of Bio-Resources in Yunnan, Yunnan University, Kunming, 650091, P. R. China.,School of Life Sciences, Yunnan University, Kunming, 650091, P. R. China.,Key Laboratory for Microbial Resources of the Ministry of Education, Yunnan University, Kunming, 650091, P. R. China
| | - Liyan Tang
- State Key Laboratory for Conservation and Utilization of Bio-Resources in Yunnan, Yunnan University, Kunming, 650091, P. R. China.,School of Life Sciences, Yunnan University, Kunming, 650091, P. R. China.,Key Laboratory for Microbial Resources of the Ministry of Education, Yunnan University, Kunming, 650091, P. R. China
| | - Le Yang
- State Key Laboratory for Conservation and Utilization of Bio-Resources in Yunnan, Yunnan University, Kunming, 650091, P. R. China.,School of Life Sciences, Yunnan University, Kunming, 650091, P. R. China.,Key Laboratory for Microbial Resources of the Ministry of Education, Yunnan University, Kunming, 650091, P. R. China
| | - Duanxu Zhou
- State Key Laboratory for Conservation and Utilization of Bio-Resources in Yunnan, Yunnan University, Kunming, 650091, P. R. China.,School of Life Sciences, Yunnan University, Kunming, 650091, P. R. China.,Key Laboratory for Microbial Resources of the Ministry of Education, Yunnan University, Kunming, 650091, P. R. China
| | - Qing Li
- State Key Laboratory for Conservation and Utilization of Bio-Resources in Yunnan, Yunnan University, Kunming, 650091, P. R. China.,School of Life Sciences, Yunnan University, Kunming, 650091, P. R. China.,Key Laboratory for Microbial Resources of the Ministry of Education, Yunnan University, Kunming, 650091, P. R. China
| | - Xuemei Niu
- State Key Laboratory for Conservation and Utilization of Bio-Resources in Yunnan, Yunnan University, Kunming, 650091, P. R. China.,School of Life Sciences, Yunnan University, Kunming, 650091, P. R. China.,Key Laboratory for Microbial Resources of the Ministry of Education, Yunnan University, Kunming, 650091, P. R. China
| | - Ke-Qin Zhang
- State Key Laboratory for Conservation and Utilization of Bio-Resources in Yunnan, Yunnan University, Kunming, 650091, P. R. China.,School of Life Sciences, Yunnan University, Kunming, 650091, P. R. China.,Key Laboratory for Microbial Resources of the Ministry of Education, Yunnan University, Kunming, 650091, P. R. China
| | - Jinkui Yang
- State Key Laboratory for Conservation and Utilization of Bio-Resources in Yunnan, Yunnan University, Kunming, 650091, P. R. China.,School of Life Sciences, Yunnan University, Kunming, 650091, P. R. China.,Key Laboratory for Microbial Resources of the Ministry of Education, Yunnan University, Kunming, 650091, P. R. China
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7
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Jiang YY, Maier W, Baumeister R, Minevich G, Joachimiak E, Wloga D, Ruan Z, Kannan N, Bocarro S, Bahraini A, Vasudevan KK, Lechtreck K, Orias E, Gaertig J. LF4/MOK and a CDK-related kinase regulate the number and length of cilia in Tetrahymena. PLoS Genet 2019; 15:e1008099. [PMID: 31339880 PMCID: PMC6682161 DOI: 10.1371/journal.pgen.1008099] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2019] [Revised: 08/05/2019] [Accepted: 06/13/2019] [Indexed: 11/18/2022] Open
Abstract
The length of cilia is controlled by a poorly understood mechanism that involves members of the conserved RCK kinase group, and among them, the LF4/MOK kinases. The multiciliated protist model, Tetrahymena, carries two types of cilia (oral and locomotory) and the length of the locomotory cilia is dependent on their position with the cell. In Tetrahymena, loss of an LF4/MOK ortholog, LF4A, lengthened the locomotory cilia, but also reduced their number. Without LF4A, cilia assembled faster and showed signs of increased intraflagellar transport (IFT). Consistently, overproduced LF4A shortened cilia and downregulated IFT. GFP-tagged LF4A, expressed in the native locus and imaged by total internal reflection microscopy, was enriched at the basal bodies and distributed along the shafts of cilia. Within cilia, most LF4A-GFP particles were immobile and a few either diffused or moved by IFT. We suggest that the distribution of LF4/MOK along the cilium delivers a uniform dose of inhibition to IFT trains that travel from the base to the tip. In a longer cilium, the IFT machinery may experience a higher cumulative dose of inhibition by LF4/MOK. Thus, LF4/MOK activity could be a readout of cilium length that helps to balance the rate of IFT-driven assembly with the rate of disassembly at steady state. We used a forward genetic screen to identify a CDK-related kinase, CDKR1, whose loss-of-function suppressed the shortening of cilia caused by overexpression of LF4A, by reducing its kinase activity. Loss of CDKR1 alone lengthened both the locomotory and oral cilia. CDKR1 resembles other known ciliary CDK-related kinases: LF2 of Chlamydomonas, mammalian CCRK and DYF-18 of C. elegans, in lacking the cyclin-binding motif and acting upstream of RCKs. The new genetic tools we developed here for Tetrahymena have potential for further dissection of the principles of cilia length regulation in multiciliated cells.
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Affiliation(s)
- Yu-Yang Jiang
- Department of Cellular Biology, University of Georgia, Athens, Georgia, United States of America
| | - Wolfgang Maier
- Bio 3/Bioinformatics and Molecular Genetics, Faculty of Biology and ZBMZ, Faculty of Medicine, Albert-Ludwigs-University of Freiburg, Freiburg, Germany
| | - Ralf Baumeister
- Bio 3/Bioinformatics and Molecular Genetics, Faculty of Biology and ZBMZ, Faculty of Medicine, Albert-Ludwigs-University of Freiburg, Freiburg, Germany
| | - Gregory Minevich
- Department of Biochemistry and Molecular Biophysics, Columbia University Medical Center, New York, New York, United States of America
| | - Ewa Joachimiak
- Laboratory of Cytoskeleton and Cilia Biology, Nencki Institute of Experimental Biology of Polish Academy of Sciences, Warsaw, Poland
| | - Dorota Wloga
- Laboratory of Cytoskeleton and Cilia Biology, Nencki Institute of Experimental Biology of Polish Academy of Sciences, Warsaw, Poland
| | - Zheng Ruan
- Institute of Bioinformatics, University of Georgia, Athens, Georgia, United States of America
| | - Natarajan Kannan
- Institute of Bioinformatics, University of Georgia, Athens, Georgia, United States of America
- Department of Biochemistry and Molecular Biology, University of Georgia, Athens, Georgia, United States of America
| | - Stephen Bocarro
- Department of Cellular Biology, University of Georgia, Athens, Georgia, United States of America
| | - Anoosh Bahraini
- Department of Cellular Biology, University of Georgia, Athens, Georgia, United States of America
| | - Krishna Kumar Vasudevan
- Department of Cellular Biology, University of Georgia, Athens, Georgia, United States of America
| | - Karl Lechtreck
- Department of Cellular Biology, University of Georgia, Athens, Georgia, United States of America
| | - Eduardo Orias
- Department of Molecular, Cellular and Developmental Biology, University of California Santa Barbara, Santa Barbara, California, United States of America
| | - Jacek Gaertig
- Department of Cellular Biology, University of Georgia, Athens, Georgia, United States of America
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8
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Sawyer EM, Joshi PR, Jorgensen V, Yunus J, Berchowitz LE, Ünal E. Developmental regulation of an organelle tether coordinates mitochondrial remodeling in meiosis. J Cell Biol 2018; 218:559-579. [PMID: 30538140 PMCID: PMC6363441 DOI: 10.1083/jcb.201807097] [Citation(s) in RCA: 30] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2018] [Revised: 10/26/2018] [Accepted: 11/21/2018] [Indexed: 12/25/2022] Open
Abstract
Cellular differentiation involves remodeling cellular architecture to transform one cell type to another. By investigating mitochondrial dynamics during meiotic differentiation in budding yeast, we sought to understand how organelle morphogenesis is developmentally controlled in a system where regulators of differentiation and organelle architecture are known, but the interface between them remains unexplored. We analyzed the regulation of mitochondrial detachment from the cell cortex, a known meiotic alteration to mitochondrial morphology. We found that mitochondrial detachment is enabled by the programmed destruction of the mitochondria-endoplasmic reticulum-cortex anchor (MECA), an organelle tether that bridges mitochondria and the plasma membrane. MECA regulation is governed by a meiotic transcription factor, Ndt80, which promotes the activation of a conserved kinase, Ime2. We further present evidence for Ime2-dependent phosphorylation and degradation of MECA in a temporally controlled manner. Our study defines a key mechanism that coordinates mitochondrial morphogenesis with the landmark events of meiosis and demonstrates that cells can developmentally regulate tethering to induce organelle remodeling.
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Affiliation(s)
- Eric M Sawyer
- Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, CA
| | - Pallavi R Joshi
- Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, CA
| | - Victoria Jorgensen
- Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, CA
| | - Julius Yunus
- Department of Genetics and Development, Columbia University Medical Center, New York, NY
| | - Luke E Berchowitz
- Department of Genetics and Development, Columbia University Medical Center, New York, NY
| | - Elçin Ünal
- Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, CA
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9
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Abstract
Cell differentiation in yeast species is controlled by a reversible, programmed DNA-rearrangement process called mating-type switching. Switching is achieved by two functionally similar but structurally distinct processes in the budding yeast Saccharomyces cerevisiae and the fission yeast Schizosaccharomyces pombe. In both species, haploid cells possess one active and two silent copies of the mating-type locus (a three-cassette structure), the active locus is cleaved, and synthesis-dependent strand annealing is used to replace it with a copy of a silent locus encoding the opposite mating-type information. Each species has its own set of components responsible for regulating these processes. In this review, we summarize knowledge about the function and evolution of mating-type switching components in these species, including mechanisms of heterochromatin formation, MAT locus cleavage, donor bias, lineage tracking, and environmental regulation of switching. We compare switching in these well-studied species to others such as Kluyveromyces lactis and the methylotrophic yeasts Ogataea polymorpha and Komagataella phaffii. We focus on some key questions: Which cells switch mating type? What molecular apparatus is required for switching? Where did it come from? And what is the evolutionary purpose of switching?
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10
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Becker E, Com E, Lavigne R, Guilleux MH, Evrard B, Pineau C, Primig M. The protein expression landscape of mitosis and meiosis in diploid budding yeast. J Proteomics 2017; 156:5-19. [DOI: 10.1016/j.jprot.2016.12.016] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2016] [Revised: 12/14/2016] [Accepted: 12/26/2016] [Indexed: 12/12/2022]
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11
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Honigberg SM. Similar environments but diverse fates: Responses of budding yeast to nutrient deprivation. MICROBIAL CELL 2016; 3:302-328. [PMID: 27917388 PMCID: PMC5134742 DOI: 10.15698/mic2016.08.516] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Diploid budding yeast (Saccharomyces cerevisiae) can adopt one
of several alternative differentiation fates in response to nutrient limitation,
and each of these fates provides distinct biological functions. When different
strain backgrounds are taken into account, these various fates occur in response
to similar environmental cues, are regulated by the same signal transduction
pathways, and share many of the same master regulators. I propose that the
relationships between fate choice, environmental cues and signaling pathways are
not Boolean, but involve graded levels of signals, pathway activation and
master-regulator activity. In the absence of large differences between
environmental cues, small differences in the concentration of cues may be
reinforced by cell-to-cell signals. These signals are particularly essential for
fate determination within communities, such as colonies and biofilms, where fate
choice varies dramatically from one region of the community to another. The lack
of Boolean relationships between cues, signaling pathways, master regulators and
cell fates may allow yeast communities to respond appropriately to the wide
range of environments they encounter in nature.
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Affiliation(s)
- Saul M Honigberg
- Division of Cell Biology and Biophysics, University of Missouri-Kansas City, 5007 Rockhill Rd, Kansas City MO 64110, USA
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12
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Hegedus DD, Gerbrandt K, Coutu C. The eukaryotic protein kinase superfamily of the necrotrophic fungal plant pathogen, Sclerotinia sclerotiorum. MOLECULAR PLANT PATHOLOGY 2016; 17:634-647. [PMID: 26395470 PMCID: PMC6638376 DOI: 10.1111/mpp.12321] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/01/2023]
Abstract
Protein kinases have been implicated in the regulation of many processes that guide pathogen development throughout the course of infection. A survey of the Sclerotinia sclerotiorum genome for genes encoding proteins containing the highly conserved eukaryotic protein kinase (ePK) domain, the largest protein kinase superfamily, revealed 92 S. sclerotiorum ePKs. This review examines the composition of the S. sclerotiorum ePKs based on conserved motifs within the ePK domain family, and relates this to orthologues found in other filamentous fungi and yeasts. The ePKs are also discussed in terms of their proposed role(s) in aspects of host pathogenesis, including the coordination of mycelial growth/development and deployment of pathogenicity determinants in response to environmental stimuli, nutrients and stress.
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Affiliation(s)
- Dwayne D Hegedus
- Agriculture and Agri-Food Canada, Saskatoon, SK, Canada, S7N 0X2
- Department of Food and Bioproduct Sciences, University of Saskatchewan, Saskatoon, SK, Canada, S7N 5A9
| | - Kelsey Gerbrandt
- Agriculture and Agri-Food Canada, Saskatoon, SK, Canada, S7N 0X2
| | - Cathy Coutu
- Agriculture and Agri-Food Canada, Saskatoon, SK, Canada, S7N 0X2
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13
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Extreme Diversity in the Regulation of Ndt80-Like Transcription Factors in Fungi. G3-GENES GENOMES GENETICS 2015; 5:2783-92. [PMID: 26497142 PMCID: PMC4683649 DOI: 10.1534/g3.115.021378] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
The Saccharomyces cerevisiaeNdt80 protein is the founding member of a class of p53-like transcription factors that is known as the NDT80/PhoG-like DNA-binding family. The number of NDT80-like genes in different fungi is highly variable and their roles, which have been examined in only a few species, include regulation of meiosis, sexual development, biofilm formation, drug resistance, virulence, the response to nutrient stress and programmed cell death. The protein kinase Ime2 regulates the single NDT80 gene present in S. cerevisiae. In this study we used a genetic approach to investigate whether the Aspergillus nidulansIme2 homolog, ImeB, and/or protein kinases MpkC, PhoA and PhoB regulate the two NDT80-like genes (xprG and ndtA) in A. nidulans. Disruption of imeB, but not mpkC, phoA or phoB, led to increased extracellular protease activity and a defect in mycotoxin production similar to the xprG1 gain-of-function mutation. Quantitative RT-PCR showed that ImeB is a negative regulator of xprG expression and XprG is a negative regulator of xprG and ndtA expression. Thus, in contrast to Ime2, which is a positive regulator of NDT80 in S. cerevisiae, ImeB is a negative regulator as in Neurospora crassa. However, the ability of Ndt80 to autoregulate NDT80 is conserved in A. nidulans though the autoregulatory effect is negative rather than positive. Unlike N. crassa, a null mutation in imeB does not circumvent the requirement for XprG or NdtA. These results show that the regulatory activities of Ime2 and Ndt80-like proteins display an extraordinarily level of evolutionary flexibility.
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14
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Chen F, Chen XZ, Su XY, Qin LN, Huang ZB, Tao Y, Dong ZY. An Ime2-like mitogen-activated protein kinase is involved in cellulase expression in the filamentous fungus Trichoderma reesei. Biotechnol Lett 2015; 37:2055-62. [DOI: 10.1007/s10529-015-1888-z] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2015] [Accepted: 06/10/2015] [Indexed: 11/28/2022]
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15
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A protein kinase screen of Neurospora crassa mutant strains reveals that the SNF1 protein kinase promotes glycogen synthase phosphorylation. Biochem J 2014; 464:323-34. [PMID: 25253091 DOI: 10.1042/bj20140942] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Abstract
Glycogen functions as a carbohydrate reserve in a variety of organisms and its metabolism is highly regulated. The activities of glycogen synthase and glycogen phosphorylase, the rate-limiting enzymes of the synthesis and degradation processes, respectively, are regulated by allosteric modulation and reversible phosphorylation. To identify the protein kinases affecting glycogen metabolism in Neurospora crassa, we performed a screen of 84 serine/threonine kinase knockout strains. We identified multiple kinases that have already been described as controlling glycogen metabolism in different organisms, such as NcSNF1, NcPHO85, NcGSK3, NcPKA, PSK2 homologue and NcATG1. In addition, many hypothetical kinases have been implicated in the control of glycogen metabolism. Two kinases, NcIME-2 and NcNIMA, already functionally characterized but with no functions related to glycogen metabolism regulation, were also identified. Among the kinases identified, it is important to mention the role of NcSNF1. We showed in the present study that this kinase was implicated in glycogen synthase phosphorylation, as demonstrated by the higher levels of glycogen accumulated during growth, along with a higher glycogen synthase (GSN) ±glucose 6-phosphate activity ratio and a lesser set of phosphorylated GSN isoforms in strain Ncsnf1KO, when compared with the wild-type strain. The results led us to conclude that, in N. crassa, this kinase promotes phosphorylation of glycogen synthase either directly or indirectly, which is the opposite of what is described for Saccharomyces cerevisiae. The kinases also play a role in gene expression regulation, in that gdn, the gene encoding the debranching enzyme, was down-regulated by the proteins identified in the screen. Some kinases affected growth and development, suggesting a connection linking glycogen metabolism with cell growth and development.
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16
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Howard CJ, Hanson-Smith V, Kennedy KJ, Miller CJ, Lou HJ, Johnson AD, Turk BE, Holt LJ. Ancestral resurrection reveals evolutionary mechanisms of kinase plasticity. eLife 2014; 3:e04126. [PMID: 25310241 PMCID: PMC4228266 DOI: 10.7554/elife.04126] [Citation(s) in RCA: 51] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2014] [Accepted: 10/09/2014] [Indexed: 01/02/2023] Open
Abstract
Protein kinases have evolved diverse specificities to enable cellular information processing. To gain insight into the mechanisms underlying kinase diversification, we studied the CMGC protein kinases using ancestral reconstruction. Within this group, the cyclin dependent kinases (CDKs) and mitogen activated protein kinases (MAPKs) require proline at the +1 position of their substrates, while Ime2 prefers arginine. The resurrected common ancestor of CDKs, MAPKs, and Ime2 could phosphorylate substrates with +1 proline or arginine, with preference for proline. This specificity changed to a strong preference for +1 arginine in the lineage leading to Ime2 via an intermediate with equal specificity for proline and arginine. Mutant analysis revealed that a variable residue within the kinase catalytic cleft, DFGx, modulates +1 specificity. Expansion of Ime2 kinase specificity by mutation of this residue did not cause dominant deleterious effects in vivo. Tolerance of cells to new specificities likely enabled the evolutionary divergence of kinases.
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Affiliation(s)
- Conor J Howard
- Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, United States
| | - Victor Hanson-Smith
- Department of Microbiology and Immunology, University of California, San Francisco, San Francisco, United States
| | - Kristopher J Kennedy
- Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, United States
| | - Chad J Miller
- Department of Pharmacology, Yale University School of Medicine, New Haven, United States
| | - Hua Jane Lou
- Department of Pharmacology, Yale University School of Medicine, New Haven, United States
| | - Alexander D Johnson
- Department of Microbiology and Immunology, University of California, San Francisco, San Francisco, United States
| | - Benjamin E Turk
- Department of Pharmacology, Yale University School of Medicine, New Haven, United States
| | - Liam J Holt
- Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, United States
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17
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Sherwood RK, Scaduto CM, Torres SE, Bennett RJ. Convergent evolution of a fused sexual cycle promotes the haploid lifestyle. Nature 2014; 506:387-390. [PMID: 24390351 PMCID: PMC4051440 DOI: 10.1038/nature12891] [Citation(s) in RCA: 37] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2013] [Accepted: 11/18/2013] [Indexed: 12/29/2022]
Affiliation(s)
- Racquel Kim Sherwood
- Department of Microbiology and Immunology, Brown University, 171 Meeting St, Providence, RI, 02912
| | - Christine M Scaduto
- Department of Microbiology and Immunology, Brown University, 171 Meeting St, Providence, RI, 02912
| | - Sandra E Torres
- Department of Microbiology and Immunology, Brown University, 171 Meeting St, Providence, RI, 02912
| | - Richard J Bennett
- Department of Microbiology and Immunology, Brown University, 171 Meeting St, Providence, RI, 02912
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18
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Marston AL. Chromosome segregation in budding yeast: sister chromatid cohesion and related mechanisms. Genetics 2014; 196:31-63. [PMID: 24395824 PMCID: PMC3872193 DOI: 10.1534/genetics.112.145144] [Citation(s) in RCA: 69] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2013] [Accepted: 09/18/2013] [Indexed: 12/28/2022] Open
Abstract
Studies on budding yeast have exposed the highly conserved mechanisms by which duplicated chromosomes are evenly distributed to daughter cells at the metaphase-anaphase transition. The establishment of proteinaceous bridges between sister chromatids, a function provided by a ring-shaped complex known as cohesin, is central to accurate segregation. It is the destruction of this cohesin that triggers the segregation of chromosomes following their proper attachment to microtubules. Since it is irreversible, this process must be tightly controlled and driven to completion. Furthermore, during meiosis, modifications must be put in place to allow the segregation of maternal and paternal chromosomes in the first division for gamete formation. Here, I review the pioneering work from budding yeast that has led to a molecular understanding of the establishment and destruction of cohesion.
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Affiliation(s)
- Adele L Marston
- The Wellcome Trust Centre for Cell Biology, School of Biological Sciences, University of Edinburgh, Edinburgh EH9 3JR, United Kingdom
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19
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Carreras-Villaseñor N, Esquivel-Naranjo EU, Villalobos-Escobedo JM, Abreu-Goodger C, Herrera-Estrella A. The RNAi machinery regulates growth and development in the filamentous fungusTrichoderma atroviride. Mol Microbiol 2013; 89:96-112. [DOI: 10.1111/mmi.12261] [Citation(s) in RCA: 46] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 05/10/2013] [Indexed: 12/18/2022]
Affiliation(s)
- Nohemi Carreras-Villaseñor
- Laboratorio Nacional de Genómica para la Biodiversidad; Cinvestav Sede Irapuato; Km 9.6 Libramiento Norte Carretera Irapuato-León; 36821; Irapuato; Gto.; Mexico
| | - Edgardo U. Esquivel-Naranjo
- Laboratorio Nacional de Genómica para la Biodiversidad; Cinvestav Sede Irapuato; Km 9.6 Libramiento Norte Carretera Irapuato-León; 36821; Irapuato; Gto.; Mexico
| | - J. Manuel Villalobos-Escobedo
- Laboratorio Nacional de Genómica para la Biodiversidad; Cinvestav Sede Irapuato; Km 9.6 Libramiento Norte Carretera Irapuato-León; 36821; Irapuato; Gto.; Mexico
| | - Cei Abreu-Goodger
- Laboratorio Nacional de Genómica para la Biodiversidad; Cinvestav Sede Irapuato; Km 9.6 Libramiento Norte Carretera Irapuato-León; 36821; Irapuato; Gto.; Mexico
| | - Alfredo Herrera-Estrella
- Laboratorio Nacional de Genómica para la Biodiversidad; Cinvestav Sede Irapuato; Km 9.6 Libramiento Norte Carretera Irapuato-León; 36821; Irapuato; Gto.; Mexico
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20
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Activation of the Smk1 mitogen-activated protein kinase by developmentally regulated autophosphorylation. Mol Cell Biol 2012. [PMID: 23207907 DOI: 10.1128/mcb.00973-12] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022] Open
Abstract
Smk1 is a meiosis-specific mitogen-activated protein kinase (MAPK) in Saccharomyces cerevisiae that controls spore morphogenesis. Similar to other MAPKs, it is controlled by dual phosphorylation of its T-X-Y activation motif. However, Smk1 is not phosphorylated by a prototypical MAPK kinase. Here, we show that the T residue in Smk1's activation motif is phosphorylated by the cyclin-dependent kinase (CDK)-activating kinase, Cak1. The Y residue is autophosphorylated in an independent intramolecular reaction that requires the meiosis-specific protein Ssp2. Although both SMK1 and SSP2 are expressed as middle-meiosis-specific genes, Smk1 protein starts to accumulate before Ssp2. Thus, Smk1 exists in a low-activity (pT) form early in sporulation and a high-activity (pT/pY) form later in the program. Ssp2 must be present when Smk1 is being produced to activate the autophosphorylation reaction, suggesting that Ssp2 acts through a transitional intermediate form of Smk1. These findings provide a mechanistic explanation for how Smk1 activity thresholds are generated. They demonstrate that intramolecular autophosphorylation of MAPKs can be regulated and suggest new mechanisms for coupling MAPK outputs to developmental programs.
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21
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Diversification of a protein kinase cascade: IME-2 is involved in nonself recognition and programmed cell death in Neurospora crassa. Genetics 2012; 192:467-82. [PMID: 22813893 PMCID: PMC3454877 DOI: 10.1534/genetics.112.142612] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/04/2022] Open
Abstract
Kinase cascades and the modification of proteins by phosphorylation are major mechanisms for cell signaling and communication, and evolution of these signaling pathways can contribute to new developmental or environmental response pathways. The Saccharomyces cerevisiae kinase Ime2 has been well characterized for its role in meiosis. However, recent studies have revealed alternative functions for Ime2 in both S. cerevisiae and other fungi. In the filamentous fungus Neurospora crassa, the IME2 homolog (ime-2) is not required for meiosis. Here we determine that ime-2 interacts genetically with a transcription factor vib-1 during nonself recognition and programmed cell death (PCD). Mutations in vib-1 (Δvib-1) suppress PCD due to nonself recognition events; however, a Δvib-1 Δime-2 mutant restored wild-type levels of cell death. A role for ime-2 in the post-translational processing and localization of a mitochondrial matrix protein was identified, which may implicate mitochondria in N. crassa nonself recognition and PCD. Further, Δvib-1 strains do not produce extracellular proteases, but protease secretion reverted to near wild-type levels in a Δvib-1 Δime-2 strain. Mass spectrometry analysis revealed that the VIB-1 protein is phosphorylated at several sites, including a site that matches the IME-2 consensus. The genetic and biochemical data for ime-2 and vib-1 indicate that IME-2 is a negative regulator of VIB-1 and suggest parallel negative regulation by IME-2 of a cell death pathway in N. crassa that functions in concert with the VIB-1 cell death pathway. Thus, IME2 kinase function has evolved following the divergence of S. cerevisiae and N. crassa and provides insight into the evolution of kinases and their regulatory targets.
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22
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Sartorel E, Pérez-Martín J. The distinct interaction between cell cycle regulation and the widely conserved morphogenesis-related (MOR) pathway in the fungus Ustilago maydis determines morphology. J Cell Sci 2012; 125:4597-608. [PMID: 22767510 DOI: 10.1242/jcs.107862] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022] Open
Abstract
The morphogenesis-related NDR kinase (MOR) pathway regulates morphogenesis in fungi. In spite of the high conservation of its components, impairing their functions results in highly divergent cellular responses depending on the fungal species. The reasons for such differences are unclear. Here we propose that the species-specific connections between cell cycle regulation and the MOR pathway could be partly responsible for these divergences. We based our conclusion on the characterization of the MOR pathway in the fungus Ustilago maydis. Each gene that encodes proteins of this pathway in U. maydis was deleted. All mutants exhibited a constitutive hyperpolarized growth, contrasting with the loss of polarity observed in other fungi. Using a conditional allele of the central NDR kinase Ukc1, we found that impairing MOR function resulted in a prolonged G2 phase. This cell cycle delay appears to be the consequence of an increase in Cdk1 inhibitory phosphorylation. Strikingly, prevention of the inhibitory Cdk1 phosphorylation abolished the hyperpolarized growth associated with MOR pathway depletion. We found that the prolonged G2 phase resulted in higher levels of expression of crk1, a conserved kinase that promotes polar growth in U. maydis. Deletion of crk1 also abolished the dramatic activation of polar growth in cells lacking the MOR pathway. Taken together, our results suggest that Cdk1 inhibitory phosphorylation may act as an integrator of signaling cascades regulating fungal morphogenesis and that the distinct morphological response observed in U. maydis upon impairment of the MOR pathway could be due to a cell cycle deregulation.
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Affiliation(s)
- Elodie Sartorel
- Instituto de Biología Funcional y Genómica (CSIC), 37007 Salamanca, Spain
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23
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Winter E. The Sum1/Ndt80 transcriptional switch and commitment to meiosis in Saccharomyces cerevisiae. Microbiol Mol Biol Rev 2012; 76:1-15. [PMID: 22390969 PMCID: PMC3294429 DOI: 10.1128/mmbr.05010-11] [Citation(s) in RCA: 68] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Abstract
Cells encounter numerous signals during the development of an organism that induce division, differentiation, and apoptosis. These signals need to be present for defined intervals in order to induce stable changes in the cellular phenotype. The point after which an inducing signal is no longer needed for completion of a differentiation program can be termed the "commitment point." Meiotic development in the yeast Saccharomyces cerevisiae (sporulation) provides a model system to study commitment. Similar to differentiation programs in multicellular organisms, the sporulation program in yeast is regulated by a transcriptional cascade that produces early, middle, and late sets of sporulation-specific transcripts. Although critical meiosis-specific events occur as early genes are expressed, commitment does not take place until middle genes are induced. Middle promoters are activated by the Ndt80 transcription factor, which is produced and activated shortly before most middle genes are expressed. In this article, I discuss the connection between Ndt80 and meiotic commitment. A transcriptional regulatory pathway makes NDT80 transcription contingent on the prior expression of early genes. Once Ndt80 is produced, the recombination (pachytene) checkpoint prevents activation of the Ndt80 protein. Upon activation, Ndt80 triggers a positive autoregulatory loop that leads to the induction of genes that promote exit from prophase, the meiotic divisions, and spore formation. The pathway is controlled by multiple feed-forward loops that give switch-like properties to the commitment transition. The conservation of regulatory components of the meiotic commitment pathway and the recently reported ability of Ndt80 to increase replicative life span are discussed.
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Affiliation(s)
- Edward Winter
- Department of Biochemistry and Molecular Biology, Thomas Jefferson University, Philadelphia, Pennsylvania, USA.
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Lai ACW, Nguyen Ba AN, Moses AM. Predicting kinase substrates using conservation of local motif density. ACTA ACUST UNITED AC 2012; 28:962-9. [PMID: 22302575 DOI: 10.1093/bioinformatics/bts060] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
Abstract
MOTIVATION Protein kinases represent critical links in cell signaling. A central problem in computational biology is to systematically identify their substrates. RESULTS This study introduces a new method to predict kinase substrates by extracting evolutionary information from multiple sequence alignments in a manner that is tolerant to degenerate motif positioning. Given a known consensus, the new method (ConDens) compares the observed density of matches to a null model of evolution and does not require labeled training data. We confirmed that ConDens has improved performance compared with several existing methods in the field. Further, we show that it is generalizable and can predict interesting substrates for several important eukaryotic kinases where training data is not available. AVAILABILITY AND IMPLEMENTATION ConDens can be found at http://www.moseslab.csb.utoronto.ca/andyl/. CONTACT alan.moses@utoronto.ca SUPPLEMENTARY INFORMATION Supplementary data are available at Bioinformatics online.
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Affiliation(s)
- Andy C W Lai
- Department of Cell and Systems Biology, University of Toronto, Toronto, Canada M5S 3G5
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Global analysis of serine-threonine protein kinase genes in Neurospora crassa. EUKARYOTIC CELL 2011; 10:1553-64. [PMID: 21965514 DOI: 10.1128/ec.05140-11] [Citation(s) in RCA: 69] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Abstract
Serine/threonine (S/T) protein kinases are crucial components of diverse signaling pathways in eukaryotes, including the model filamentous fungus Neurospora crassa. In order to assess the importance of S/T kinases to Neurospora biology, we embarked on a global analysis of 86 S/T kinase genes in Neurospora. We were able to isolate viable mutants for 77 of the 86 kinase genes. Of these, 57% exhibited at least one growth or developmental phenotype, with a relatively large fraction (40%) possessing a defect in more than one trait. S/T kinase knockouts were subjected to chemical screening using a panel of eight chemical treatments, with 25 mutants exhibiting sensitivity or resistance to at least one chemical. This brought the total percentage of S/T mutants with phenotypes in our study to 71%. Mutants lacking apg-1, an S/T kinase required for autophagy in other organisms, possessed the greatest number of phenotypes, with defects in asexual and sexual growth and development and in altered sensitivity to five chemical treatments. We showed that NCU02245/stk-19 is required for chemotropic interactions between female and male cells during mating. Finally, we demonstrated allelism between the S/T kinase gene NCU00406 and velvet (vel), encoding a p21-activated protein kinase (PAK) gene important for asexual and sexual growth and development in Neurospora.
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