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Olivares-Yañez C, Alessandri MP, Salas L, Larrondo LF. Methylxanthines Modulate Circadian Period Length Independently of the Action of Phosphodiesterase. Microbiol Spectr 2023; 11:e0372722. [PMID: 37272789 PMCID: PMC10434132 DOI: 10.1128/spectrum.03727-22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2022] [Accepted: 05/22/2023] [Indexed: 06/06/2023] Open
Abstract
In Neurospora crassa, caffeine and other methylxanthines are known to inhibit phosphodiesterase (PDE) activity, leading to augmented cAMP levels. In this organism, it has also been shown that the addition of these drugs significantly lengthens the circadian period, as seen by conidiation rhythms. Utilizing in vivo bioluminescence reporters, pharmacological inhibitors, and cAMP analogs, we revisited the effect of methylxanthines and the role of cAMP signaling in the Neurospora clockworks. We observed that caffeine, like all tested methylxanthines, led to significant period lengthening, visualized with both core-clock transcriptional and translational reporters. Remarkably, this phenotype is still observed when phosphodiesterase (PDE) activity is genetically or chemically (via 3-isobutyl-1-methylxanthine) abrogated. Likewise, methylxanthines still exert a period effect in several cAMP signaling pathway mutants, including adenylate cyclase (cr-1) and protein kinase A (PKA) (Δpkac-1) mutants, suggesting that these drugs lead to circadian phenotypes through mechanisms different from the canonical PDE-cAMP-PKA signaling axis. Thus, this study highlights the strong impact of methylxanthines on circadian period in Neurospora, albeit the exact mechanisms somehow remain elusive. IMPORTANCE Evidence from diverse organisms show that caffeine causes changes in the circadian clock, causing period lengthening. The fungus Neurospora crassa is no exception; here, several methylxanthines such as caffeine, theophylline, and aminophylline cause period lengthening in a concentration-dependent manner. Although methylxanthines are expected to inhibit phosphodiesterase activity, we were able to show by genetic and pharmacological means that these drugs exert their effects through a different mechanism. Moreover, our results indicate that increases in cAMP levels and changes in PKA activity do not impact the circadian period and therefore are not part of underlying effects of methylxanthine. These results set the stage for future analyses dissecting the molecular mechanisms by which these drugs dramatically modify the circadian period.
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Affiliation(s)
- Consuelo Olivares-Yañez
- ANID-Millennium Science Initiative Program, Millennium Institute for Integrative Biology (iBio), Santiago, Chile
- Centro de Biotecnología Vegetal, Facultad de Ciencias de la Vida, Universidad Andrés Bello, Santiago, Chile
| | - María P. Alessandri
- ANID-Millennium Science Initiative Program, Millennium Institute for Integrative Biology (iBio), Santiago, Chile
- Departamento de Genética Molecular y Microbiología, Facultad de Ciencias Biológicas, Pontificia Universidad Católica de Chile, Santiago, Chile
| | - Loreto Salas
- ANID-Millennium Science Initiative Program, Millennium Institute for Integrative Biology (iBio), Santiago, Chile
- Departamento de Genética Molecular y Microbiología, Facultad de Ciencias Biológicas, Pontificia Universidad Católica de Chile, Santiago, Chile
| | - Luis F. Larrondo
- ANID-Millennium Science Initiative Program, Millennium Institute for Integrative Biology (iBio), Santiago, Chile
- Departamento de Genética Molecular y Microbiología, Facultad de Ciencias Biológicas, Pontificia Universidad Católica de Chile, Santiago, Chile
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2
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Zinn-Brooks L, Roper ML. Circadian rhythm shows potential for mRNA efficiency and self-organized division of labor in multinucleate cells. PLoS Comput Biol 2021; 17:e1008828. [PMID: 34339411 PMCID: PMC8360590 DOI: 10.1371/journal.pcbi.1008828] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2021] [Revised: 08/12/2021] [Accepted: 07/12/2021] [Indexed: 11/23/2022] Open
Abstract
Multinucleate cells occur in every biosphere and across the kingdoms of life, including in the human body as muscle cells and bone-forming cells. Data from filamentous fungi suggest that, even when bathed in a common cytoplasm, nuclei are capable of autonomous behaviors, including division. How does this potential for autonomy affect the organization of cellular processes between nuclei? Here we analyze a simplified model of circadian rhythm, a form of cellular oscillator, in a mathematical model of the filamentous fungus Neurospora crassa. Our results highlight a potential role played by mRNA-protein phase separation to keep mRNAs close to the nuclei from which they originate, while allowing proteins to diffuse freely between nuclei. Our modeling shows that syncytism allows for extreme mRNA efficiency-we demonstrate assembly of a robust oscillator with a transcription rate a thousand-fold less than in comparable uninucleate cells. We also show self-organized division of the labor of mRNA production, with one nucleus in a two-nucleus syncytium producing at least twice as many mRNAs as the other in 30% of cycles. This division can occur spontaneously, but division of labor can also be controlled by regulating the amount of cytoplasmic volume available to each nucleus. Taken together, our results show the intriguing richness and potential for emergent organization among nuclei in multinucleate cells. They also highlight the role of previously studied mechanisms of cellular organization, including nuclear space control and localization of mRNAs through RNA-protein phase separation, in regulating nuclear coordination.
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Affiliation(s)
- Leif Zinn-Brooks
- Department of Mathematics, Harvey Mudd College, Claremont, California, United States of America
| | - Marcus L. Roper
- Department of Mathematics, UCLA, Los Angeles, California, United States of America
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3
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Huberman LB, Wu VW, Kowbel DJ, Lee J, Daum C, Grigoriev IV, O'Malley RC, Glass NL. DNA affinity purification sequencing and transcriptional profiling reveal new aspects of nitrogen regulation in a filamentous fungus. Proc Natl Acad Sci U S A 2021; 118:e2009501118. [PMID: 33753477 PMCID: PMC8020665 DOI: 10.1073/pnas.2009501118] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Sensing available nutrients and efficiently utilizing them is a challenge common to all organisms. The model filamentous fungus Neurospora crassa is capable of utilizing a variety of inorganic and organic nitrogen sources. Nitrogen utilization in N. crassa is regulated by a network of pathway-specific transcription factors that activate genes necessary to utilize specific nitrogen sources in combination with nitrogen catabolite repression regulatory proteins. We identified an uncharacterized pathway-specific transcription factor, amn-1, that is required for utilization of the nonpreferred nitrogen sources proline, branched-chain amino acids, and aromatic amino acids. AMN-1 also plays a role in regulating genes involved in responding to the simple sugar mannose, suggesting an integration of nitrogen and carbon metabolism. The utilization of nonpreferred nitrogen sources, which require metabolic processing before being used as a nitrogen source, is also regulated by the nitrogen catabolite regulator NIT-2. Using RNA sequencing combined with DNA affinity purification sequencing, we performed a survey of the role of NIT-2 and the pathway-specific transcription factors NIT-4 and AMN-1 in directly regulating genes involved in nitrogen utilization. Although previous studies suggested promoter binding by both a pathway-specific transcription factor and NIT-2 may be necessary for activation of nitrogen-responsive genes, our data show that pathway-specific transcription factors regulate genes involved in the catabolism of specific nitrogen sources, while NIT-2 regulates genes involved in utilization of all nonpreferred nitrogen sources, such as nitrogen transporters. Together, these transcription factors form a nutrient sensing network that allows N. crassa cells to regulate nitrogen utilization.
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Affiliation(s)
- Lori B Huberman
- Plant and Microbial Biology Department, University of California, Berkeley, CA 94720;
- Energy Biosciences Institute, University of California, Berkeley, CA 94720
| | - Vincent W Wu
- Plant and Microbial Biology Department, University of California, Berkeley, CA 94720
- Energy Biosciences Institute, University of California, Berkeley, CA 94720
| | - David J Kowbel
- Plant and Microbial Biology Department, University of California, Berkeley, CA 94720
| | - Juna Lee
- US Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA 94720
| | - Chris Daum
- US Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA 94720
| | - Igor V Grigoriev
- Plant and Microbial Biology Department, University of California, Berkeley, CA 94720
- US Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA 94720
- Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720
| | - Ronan C O'Malley
- US Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA 94720
- Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720
| | - N Louise Glass
- Plant and Microbial Biology Department, University of California, Berkeley, CA 94720;
- Energy Biosciences Institute, University of California, Berkeley, CA 94720
- Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720
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4
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Grum-Grzhimaylo AA, Bastiaans E, van den Heuvel J, Berenguer Millanes C, Debets AJM, Aanen DK. Somatic deficiency causes reproductive parasitism in a fungus. Nat Commun 2021; 12:783. [PMID: 33542245 PMCID: PMC7862218 DOI: 10.1038/s41467-021-21050-5] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2020] [Accepted: 01/05/2021] [Indexed: 12/05/2022] Open
Abstract
Some multicellular organisms can fuse because mergers potentially provide mutual benefits. However, experimental evolution in the fungus Neurospora crassa has demonstrated that free fusion of mycelia favours cheater lineages, but the mechanism and evolutionary dynamics of this exploitation are unknown. Here we show, paradoxically, that all convergently evolved cheater lineages have similar fusion deficiencies. These mutants are unable to initiate fusion but retain access to wild-type mycelia that fuse with them. This asymmetry reduces cheater-mutant contributions to somatic substrate-bound hyphal networks, but increases representation of their nuclei in the aerial reproductive hyphae. Cheaters only benefit when relatively rare and likely impose genetic load reminiscent of germline senescence. We show that the consequences of somatic fusion can be unequally distributed among fusion partners, with the passive non-fusing partner profiting more. We discuss how our findings may relate to the extensive variation in fusion frequency of fungi found in nature.
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Affiliation(s)
- Alexey A Grum-Grzhimaylo
- Laboratory of Genetics, Wageningen University, Wageningen, The Netherlands
- Microbial Ecology Department, NIOO-KNAW, Wageningen, The Netherlands
| | - Eric Bastiaans
- Laboratory of Genetics, Wageningen University, Wageningen, The Netherlands
| | | | | | - Alfons J M Debets
- Laboratory of Genetics, Wageningen University, Wageningen, The Netherlands
| | - Duur K Aanen
- Laboratory of Genetics, Wageningen University, Wageningen, The Netherlands.
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5
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Upadhyay A, Marzoll D, Diernfellner A, Brunner M, Herzel H. Multiple random phosphorylations in clock proteins provide long delays and switches. Sci Rep 2020; 10:22224. [PMID: 33335302 PMCID: PMC7746754 DOI: 10.1038/s41598-020-79277-z] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2020] [Accepted: 11/25/2020] [Indexed: 12/27/2022] Open
Abstract
Theory predicts that self-sustained oscillations require robust delays and nonlinearities (ultrasensitivity). Delayed negative feedback loops with switch-like inhibition of transcription constitute the core of eukaryotic circadian clocks. The kinetics of core clock proteins such as PER2 in mammals and FRQ in Neurospora crassa is governed by multiple phosphorylations. We investigate how multiple, slow and random phosphorylations control delay and molecular switches. We model phosphorylations of intrinsically disordered clock proteins (IDPs) using conceptual models of sequential and distributive phosphorylations. Our models help to understand the underlying mechanisms leading to delays and ultrasensitivity. The model shows temporal and steady state switches for the free kinase and the phosphoprotein. We show that random phosphorylations and sequestration mechanisms allow high Hill coefficients required for self-sustained oscillations.
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Affiliation(s)
- Abhishek Upadhyay
- Institute for Theoretical Biology, Charité, Universitätsmedizin Berlin, Humboldt University of Berlin, Philippstr. 13, 10115, Berlin, Germany.
| | - Daniela Marzoll
- Biochemistry Center, University of Heidelberg, Im Neuenheimer Feld 328, 69120, Heidelberg, Germany
| | - Axel Diernfellner
- Biochemistry Center, University of Heidelberg, Im Neuenheimer Feld 328, 69120, Heidelberg, Germany
| | - Michael Brunner
- Biochemistry Center, University of Heidelberg, Im Neuenheimer Feld 328, 69120, Heidelberg, Germany
| | - Hanspeter Herzel
- Institute for Theoretical Biology, Charité, Universitätsmedizin Berlin, Humboldt University of Berlin, Philippstr. 13, 10115, Berlin, Germany.
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6
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Itoh Y, Naschberger A, Mortezaei N, Herrmann JM, Amunts A. Analysis of translating mitoribosome reveals functional characteristics of translation in mitochondria of fungi. Nat Commun 2020; 11:5187. [PMID: 33056988 PMCID: PMC7560712 DOI: 10.1038/s41467-020-18830-w] [Citation(s) in RCA: 27] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2020] [Accepted: 09/11/2020] [Indexed: 11/16/2022] Open
Abstract
Mitoribosomes are specialized protein synthesis machineries in mitochondria. However, how mRNA binds to its dedicated channel, and tRNA moves as the mitoribosomal subunit rotate with respect to each other is not understood. We report models of the translating fungal mitoribosome with mRNA, tRNA and nascent polypeptide, as well as an assembly intermediate. Nicotinamide adenine dinucleotide (NAD) is found in the central protuberance of the large subunit, and the ATPase inhibitory factor 1 (IF1) in the small subunit. The models of the active mitoribosome explain how mRNA binds through a dedicated protein platform on the small subunit, tRNA is translocated with the help of the protein mL108, bridging it with L1 stalk on the large subunit, and nascent polypeptide paths through a newly shaped exit tunnel involving a series of structural rearrangements. An assembly intermediate is modeled with the maturation factor Atp25, providing insight into the biogenesis of the mitoribosomal large subunit and translation regulation.
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Affiliation(s)
- Yuzuru Itoh
- Science for Life Laboratory, Department of Biochemistry and Biophysics, Stockholm University, 17165, Solna, Sweden
- Department of Medical Biochemistry and Biophysics, Karolinska Institutet, 17165, Solna, Sweden
| | - Andreas Naschberger
- Science for Life Laboratory, Department of Biochemistry and Biophysics, Stockholm University, 17165, Solna, Sweden
| | - Narges Mortezaei
- Science for Life Laboratory, Department of Biochemistry and Biophysics, Stockholm University, 17165, Solna, Sweden
| | - Johannes M Herrmann
- Cell Biology, University of Kaiserslautern, Erwin-Schrödinger-Straße 13, 67663, Kaiserslautern, Germany
| | - Alexey Amunts
- Science for Life Laboratory, Department of Biochemistry and Biophysics, Stockholm University, 17165, Solna, Sweden.
- Department of Medical Biochemistry and Biophysics, Karolinska Institutet, 17165, Solna, Sweden.
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7
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Abstract
Sessile organisms constantly face environmental fluctuations and especially drought is a common stressor. One adaptive mechanism is "stress priming," the ability to cope with a severe stress ("triggering") by retaining information from a previous mild stress event ("priming"). While plants have been extensively investigated for drought-induced stress priming, no information is available for saprotrophic filamentous fungi, which are highly important for nutrient cycles. Here, we investigated the potential for drought-induced stress priming of one strain each of two ubiquitous species, Neurospora crassa and Penicillium chrysogenum. A batch experiment with 4 treatments was conducted on a sandy soil: exposure to priming and/or triggering as well as non-stressed controls. A priming stress was caused by desiccation to pF 4. The samples were then rewetted and after 1-, 7-, or 14-days of recovery triggered (pF 6). After triggering, fungal biomass, respiration, and β-glucosidase activity were quantified. P. chrysogenum showed positive stress priming effects. After 1 day of recovery, biomass as well as β-glucosidase activity and respiration were 0.5 to 5 times higher during triggering. Effects on biomass and activity decreased with prolonged recovery but lasted for 7 days and minor effects were still detectable after 14 days. Without triggering, stress priming had a temporary negative impact on biomass but this reversed after 14 days. For N. crassa, no stress priming effect was observed on the tested variables. The potential for drought-induced stress priming seems to be species specific with potentially high impact on composition and activity of fungal communities considering the expected increase of drought events.
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Affiliation(s)
- Alexander Guhr
- Department of Soil Ecology, BayCEER, University of Bayreuth, Dr.-Hans-Frisch-Straße 1-3, 95448, Bayreuth, Germany.
| | - Sophia Kircher
- Department of Soil Ecology, BayCEER, University of Bayreuth, Dr.-Hans-Frisch-Straße 1-3, 95448, Bayreuth, Germany
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8
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Bayram ÖS, Dettmann A, Karahoda B, Moloney NM, Ormsby T, McGowan J, Cea-Sánchez S, Miralles-Durán A, Brancini GTP, Luque EM, Fitzpatrick DA, Cánovas D, Corrochano LM, Doyle S, Selker EU, Seiler S, Bayram Ö. Control of Development, Secondary Metabolism and Light-Dependent Carotenoid Biosynthesis by the Velvet Complex of Neurospora crassa. Genetics 2019; 212:691-710. [PMID: 31068340 PMCID: PMC6614901 DOI: 10.1534/genetics.119.302277] [Citation(s) in RCA: 27] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2019] [Accepted: 05/04/2019] [Indexed: 01/24/2023] Open
Abstract
Neurospora crassa is an established reference organism to investigate carotene biosynthesis and light regulation. However, there is little evidence of its capacity to produce secondary metabolites. Here, we report the role of the fungal-specific regulatory velvet complexes in development and secondary metabolism (SM) in N. crassa Three velvet proteins VE-1, VE-2, VOS-1, and a putative methyltransferase LAE-1 show light-independent nucleocytoplasmic localization. Two distinct velvet complexes, a heterotrimeric VE-1/VE-2/LAE-1 and a heterodimeric VE-2/VOS-1 are found in vivo The heterotrimer-complex, which positively regulates sexual development and represses asexual sporulation, suppresses siderophore coprogen production under iron starvation conditions. The VE-1/VE-2 heterodimer controls carotene production. VE-1 regulates the expression of >15% of the whole genome, comprising mainly regulatory and developmental features. We also studied intergenera functions of the velvet complex through complementation of Aspergillus nidulans veA, velB, laeA, vosA mutants with their N. crassa orthologs ve-1, ve-2, lae-1, and vos-1, respectively. Expression of VE-1 and VE-2 in A. nidulans successfully substitutes the developmental and SM functions of VeA and VelB by forming two functional chimeric velvet complexes in vivo, VelB/VE-1/LaeA and VE-2/VeA/LaeA, respectively. Reciprocally, expression of veA restores the phenotypes of the N. crassa ve-1 mutant. All N. crassa velvet proteins heterologously expressed in A. nidulans are localized to the nuclear fraction independent of light. These data highlight the conservation of the complex formation in N. crassa and A. nidulans However, they also underline the intergenera similarities and differences of velvet roles according to different life styles, niches and ontogenetic processes.
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Affiliation(s)
| | - Anne Dettmann
- Institute for Biology II, Molecular Plant Physiology, Albert-Ludwigs-University 79104 Freiburg, Germany
| | - Betim Karahoda
- Department of Biology, Maynooth University, Co. Kildare, W23 F2H6, Ireland
| | - Nicola M Moloney
- Department of Biology, Maynooth University, Co. Kildare, W23 F2H6, Ireland
| | - Tereza Ormsby
- Institute of Molecular Biology, University of Oregon, Eugene, 97403 Oregon
| | - Jamie McGowan
- Department of Biology, Maynooth University, Co. Kildare, W23 F2H6, Ireland
| | - Sara Cea-Sánchez
- Departmento de Genética, Facultad de Biologia, Universidad de Sevilla, 41012 Sevilla, Spain
| | | | - Guilherme T P Brancini
- Departmento de Genética, Facultad de Biologia, Universidad de Sevilla, 41012 Sevilla, Spain
| | - Eva M Luque
- Departmento de Genética, Facultad de Biologia, Universidad de Sevilla, 41012 Sevilla, Spain
| | | | - David Cánovas
- Departmento de Genética, Facultad de Biologia, Universidad de Sevilla, 41012 Sevilla, Spain
| | - Luis M Corrochano
- Departmento de Genética, Facultad de Biologia, Universidad de Sevilla, 41012 Sevilla, Spain
| | - Sean Doyle
- Department of Biology, Maynooth University, Co. Kildare, W23 F2H6, Ireland
| | - Eric U Selker
- Institute of Molecular Biology, University of Oregon, Eugene, 97403 Oregon
| | - Stephan Seiler
- Institute for Biology II, Molecular Plant Physiology, Albert-Ludwigs-University 79104 Freiburg, Germany
| | - Özgür Bayram
- Department of Biology, Maynooth University, Co. Kildare, W23 F2H6, Ireland
- Human Health Research Institute, Maynooth University, Co. Kildare, W23 F2H6, Ireland
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9
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Anderson JL, Nieuwenhuis BPS, Johannesson H. Asexual reproduction and growth rate: independent and plastic life history traits in Neurospora crassa. ISME J 2019; 13:780-788. [PMID: 30413765 PMCID: PMC6462030 DOI: 10.1038/s41396-018-0294-7] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/25/2018] [Revised: 09/07/2018] [Accepted: 09/19/2018] [Indexed: 11/24/2022]
Abstract
Trade-offs among traits influencing fitness are predicted by life history theory because resources allocated to one function are unavailable to another. Here we examine the relationship between two such traits, asexual reproduction and growth rate, in the filamentous fungus Neurospora crassa, where shared genetic and physiological factors and a source-sink energetic relationship between growth and reproduction may constrain the evolution of these traits. To test growth-reproduction relationships in this species, we independently selected on mycelial growth rate or asexual spore production in a heterogeneous lab-derived population and evaluated the response of the non-selected traits. Combined with phenotypes for the 20 wild strains used to produce the heterogeneous population and the genome-wide genotypes of 468 strains, these data show that growth and reproduction are highly plastic in N. crassa and do not trade off either among wild strains or after laboratory selection in two environments. Rather, we find no predictable growth-reproduction relationship in the environments tested, indicating an effective absence of genetic constraint between these traits. Our results suggest that growth rate and asexual reproduction may not respond predictably to environmental change and suggest that reliance on a single trait as a proxy for fitness in fungal studies may be inadvisable.
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Affiliation(s)
- Jennifer L Anderson
- Department of Organismal Biology, Uppsala University, Norbyvägen 18D, SE-752 36, Uppsala, Sweden.
- Department of Ecology and Genetics, Uppsala University, Norbyvägen 18D, SE-752 36, Uppsala, Sweden.
| | - Bart P S Nieuwenhuis
- Department of Ecology and Genetics, Uppsala University, Norbyvägen 18D, SE-752 36, Uppsala, Sweden
- Division of Evolutionary Biology, Faculty of Biology, Ludwig-Maximilians-Universität München, Grosshaderner Strasse 2, Planegg-Martinsried, 82152, München, Germany
| | - Hanna Johannesson
- Department of Organismal Biology, Uppsala University, Norbyvägen 18D, SE-752 36, Uppsala, Sweden
- Department of Ecology and Genetics, Uppsala University, Norbyvägen 18D, SE-752 36, Uppsala, Sweden
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10
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Cao X, Liu X, Li H, Fan Y, Duan J, Liu Y, He Q. Transcription factor CBF-1 is critical for circadian gene expression by modulating WHITE COLLAR complex recruitment to the frq locus. PLoS Genet 2018; 14:e1007570. [PMID: 30208021 PMCID: PMC6152987 DOI: 10.1371/journal.pgen.1007570] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2017] [Revised: 09/24/2018] [Accepted: 07/16/2018] [Indexed: 01/24/2023] Open
Abstract
Transcription of the Neurospora crassa circadian clock gene frequency (frq) is an essential process in the negative feedback loop that controls circadian rhythms. WHITE COLLAR 1 (WC-1) and WHITE COLLAR 2 (WC-2) forms the WC complex (WCC) that is the main activator of frq transcription by binding to its promoter. Here, we show that Centromere Binding Factor 1 (CBF-1) is a critical component of the N. crassa circadian clock by regulating frq transcription. Deletion of cbf-1 resulted in long period and low amplitude rhythms, whereas overexpression of CBF-1 abolished the circadian rhythms. Loss of CBF-1 resulted in WC-independent FRQ expression and suppression of WCC activity. As WCC, CBF-1 also binds to the C-box at the frq promoter. Overexpression of CBF-1 impaired WCC binding to the C-box to suppress frq transcription. Together, our results suggest that the proper level of CBF-1 is critical for circadian clock function by suppressing WC-independent FRQ expression and by regulating WCC binding to the frq promoter. Circadian clocks, which measure time on a scale of approximately 24 hours, are generated by a cell-autonomous circadian oscillator comprised of autoregulatory feedback loops. In the Neurospora crassa circadian oscillator, WHITE COLLAR complex (WCC) actives transcription of the frequency (frq) gene. FRQ inhibits the activity of WCC to close the negative feedback loop. Here, we showed that the transcription factor CBF-1 functions as a repressor to modulate WCC recruitment to the C-box of frq promoter. Our data showed that deletion or overexpression of CBF-1 dampened circadian rhythm due to impaired WCC binding at the frq promoter. As CBF-1 is conserved in eukaryotes, our data provide novel insights into the negative feedback mechanism that controls the biological clocks in other organisms.
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Affiliation(s)
- Xuemei Cao
- State Key Laboratory of Agrobiotechnology and MOA Key Laboratory of Soil Microbiology, College of Biological Sciences, China Agricultural University, Beijing, China
| | - Xiao Liu
- State Key Laboratory of Agrobiotechnology and MOA Key Laboratory of Soil Microbiology, College of Biological Sciences, China Agricultural University, Beijing, China
- Department of Physiology, University of Texas Southwestern Medical Center, Dallas, Texas, United States of America
| | - Hongda Li
- State Key Laboratory of Agrobiotechnology and MOA Key Laboratory of Soil Microbiology, College of Biological Sciences, China Agricultural University, Beijing, China
| | - Yumeng Fan
- State Key Laboratory of Agrobiotechnology and MOA Key Laboratory of Soil Microbiology, College of Biological Sciences, China Agricultural University, Beijing, China
| | - Jiabin Duan
- State Key Laboratory of Agrobiotechnology and MOA Key Laboratory of Soil Microbiology, College of Biological Sciences, China Agricultural University, Beijing, China
| | - Yi Liu
- Department of Physiology, University of Texas Southwestern Medical Center, Dallas, Texas, United States of America
| | - Qun He
- State Key Laboratory of Agrobiotechnology and MOA Key Laboratory of Soil Microbiology, College of Biological Sciences, China Agricultural University, Beijing, China
- * E-mail:
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11
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Morales Y, Olsen KJ, Bulcher JM, Johnson SJ. Structure of frequency-interacting RNA helicase from Neurospora crassa reveals high flexibility in a domain critical for circadian rhythm and RNA surveillance. PLoS One 2018; 13:e0196642. [PMID: 29718972 PMCID: PMC5931499 DOI: 10.1371/journal.pone.0196642] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2017] [Accepted: 04/17/2018] [Indexed: 11/18/2022] Open
Abstract
The FRH (frequency-interacting RNA helicase) protein is the Neurospora crassa homolog of yeast Mtr4, an essential RNA helicase that plays a central role in RNA metabolism as an activator of the nuclear RNA exosome. FRH is also a required component of the circadian clock, mediating protein interactions that result in the rhythmic repression of gene expression. Here we show that FRH unwinds RNA substrates in vitro with a kinetic profile similar to Mtr4, indicating that while FRH has acquired additional functionality, its core helicase function remains intact. In contrast with the earlier FRH structures, a new crystal form of FRH results in an ATP binding site that is undisturbed by crystal contacts and adopts a conformation consistent with nucleotide binding and hydrolysis. Strikingly, this new FRH structure adopts an arch domain conformation that is dramatically altered from previous structures. Comparison of the existing FRH structures reveals conserved hinge points that appear to facilitate arch motion. Regions in the arch have been previously shown to mediate a variety of protein-protein interactions critical for RNA surveillance and circadian clock functions. The conformational changes highlighted in the FRH structures provide a platform for investigating the relationship between arch dynamics and Mtr4/FRH function.
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Affiliation(s)
- Yalemi Morales
- Department of Chemistry and Biochemistry, Utah State University, Logan, Utah, United States of America
| | - Keith J. Olsen
- Department of Chemistry and Biochemistry, Utah State University, Logan, Utah, United States of America
| | - Jacqueline M. Bulcher
- Department of Chemistry and Biochemistry, Utah State University, Logan, Utah, United States of America
| | - Sean J. Johnson
- Department of Chemistry and Biochemistry, Utah State University, Logan, Utah, United States of America
- * E-mail:
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12
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Qi S, He L, Zhang Q, Dong Q, Wang Y, Yang Q, Tian C, He Q, Wang Y. Cross-pathway control gene CPC1/GCN4 coordinates with histone acetyltransferase GCN5 to regulate catalase-3 expression under oxidative stress in Neurospora crassa. Free Radic Biol Med 2018; 117:218-227. [PMID: 29421311 DOI: 10.1016/j.freeradbiomed.2018.02.003] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/25/2017] [Revised: 01/04/2018] [Accepted: 02/02/2018] [Indexed: 12/16/2022]
Abstract
Catalase is an important enzyme found in nearly all aerobic organisms and plays an essential role in protecting cells from oxidative damage by catalyzing the degradation of hydrogen peroxide into water and oxygen. In filamentous fungus Neurospora crassa, the expression levels of catalases are rigorously regulated by morphogenetic transition during growth and development in cells. Our study revealed that catalase-3 transcription is positively regulated by histone acetyltransferase GCN5 and the cross-pathway control gene cpc-1, as the cat-3 expression level is significantly decreased in gcn5KO and cpc-1 (j-5) mutants. Moreover, gcn5KO and cpc-1 (j-5) mutants could not respond to H2O2 treatment due to the inadequate cat-3 transcription, while wild-type strains showed high expression levels of catalase upon H2O2 treatment. The global H3 acetylation and the acetylation of H3 at cat-3 locus dramatically decreased in gcn5KO under normal or oxidative stress conditions. Meanwhile, the expression of CAT-3 is reduced in gcn5E146Q, the catalytically dead mutant, suggesting that the catalytic activity of GCN5 functions in regulation of cat-3 transcription. In addition, GCN5 cannot acetylate histone H3 efficiently at cat-3 locus in cpc-1 (j-5) mutant strains under normal or oxidative stress conditions. Furthermore, ChIP assays data revealed that the CPC1/GCN4 can directly target the cat-3 promoter region, which may recruit GCN5 to modify the histone acetylation of this region. These results disclosed a distinctive function of CPC1/GCN4 in the regulatory pathway of cat-3 transcription, which is mediated by GCN5-dependent acetylation.
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Affiliation(s)
- Shaohua Qi
- State Key Laboratory of Agro-biotechnology and MOA Key Laboratory of Soil Microbiology, College of Biological Sciences, China Agricultural University, Beijing 100193, China
| | - Lingaonan He
- State Key Laboratory of Agro-biotechnology and MOA Key Laboratory of Soil Microbiology, College of Biological Sciences, China Agricultural University, Beijing 100193, China
| | - Qin Zhang
- State Key Laboratory of Agro-biotechnology and MOA Key Laboratory of Soil Microbiology, College of Biological Sciences, China Agricultural University, Beijing 100193, China
| | - Qing Dong
- State Key Laboratory of Agro-biotechnology and MOA Key Laboratory of Soil Microbiology, College of Biological Sciences, China Agricultural University, Beijing 100193, China
| | - Yajun Wang
- State Key Laboratory of Agro-biotechnology and MOA Key Laboratory of Soil Microbiology, College of Biological Sciences, China Agricultural University, Beijing 100193, China
| | - Qiuying Yang
- State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing 100193, China
| | - Chaoguang Tian
- Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin 300308, China
| | - Qun He
- State Key Laboratory of Agro-biotechnology and MOA Key Laboratory of Soil Microbiology, College of Biological Sciences, China Agricultural University, Beijing 100193, China
| | - Ying Wang
- State Key Laboratory of Agro-biotechnology and MOA Key Laboratory of Soil Microbiology, College of Biological Sciences, China Agricultural University, Beijing 100193, China.
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13
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Dekhang R, Wu C, Smith KM, Lamb TM, Peterson M, Bredeweg EL, Ibarra O, Emerson JM, Karunarathna N, Lyubetskaya A, Azizi E, Hurley JM, Dunlap JC, Galagan JE, Freitag M, Sachs MS, Bell-Pedersen D. The Neurospora Transcription Factor ADV-1 Transduces Light Signals and Temporal Information to Control Rhythmic Expression of Genes Involved in Cell Fusion. G3 (Bethesda) 2017; 7:129-142. [PMID: 27856696 PMCID: PMC5217103 DOI: 10.1534/g3.116.034298] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/05/2016] [Accepted: 11/01/2016] [Indexed: 12/20/2022]
Abstract
Light and the circadian clock have a profound effect on the biology of organisms through the regulation of large sets of genes. Toward understanding how light and the circadian clock regulate gene expression, we used genome-wide approaches to identify the direct and indirect targets of the light-responsive and clock-controlled transcription factor ADV-1 in Neurospora crassa A large proportion of ADV-1 targets were found to be light- and/or clock-controlled, and enriched for genes involved in development, metabolism, cell growth, and cell fusion. We show that ADV-1 is necessary for transducing light and/or temporal information to its immediate downstream targets, including controlling rhythms in genes critical to somatic cell fusion. However, while ADV-1 targets are altered in predictable ways in Δadv-1 cells in response to light, this is not always the case for rhythmic target gene expression. These data suggest that a complex regulatory network downstream of ADV-1 functions to generate distinct temporal dynamics of target gene expression relative to the central clock mechanism.
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Affiliation(s)
- Rigzin Dekhang
- Department of Biology, Texas A&M University, College Station, Texas 77843
| | - Cheng Wu
- Department of Biology, Texas A&M University, College Station, Texas 77843
| | - Kristina M Smith
- Department of Biochemistry and Biophysics, Oregon State University, Corvallis, Oregon 97331
| | - Teresa M Lamb
- Department of Biology, Texas A&M University, College Station, Texas 77843
| | | | - Erin L Bredeweg
- Department of Biochemistry and Biophysics, Oregon State University, Corvallis, Oregon 97331
| | - Oneida Ibarra
- Department of Biology, Texas A&M University, College Station, Texas 77843
| | - Jillian M Emerson
- Department of Genetics, Geisel School of Medicine at Dartmouth, Hanover, New Hampshire 03755
| | | | | | - Elham Azizi
- Bioinformatics Program, Boston University, Massachusetts 02215
| | - Jennifer M Hurley
- Department of Biological Sciences, Rensselaer Polytechnic Institute, Troy, New York 12180
| | - Jay C Dunlap
- Department of Genetics, Geisel School of Medicine at Dartmouth, Hanover, New Hampshire 03755
| | - James E Galagan
- Bioinformatics Program, Boston University, Massachusetts 02215
- National Emerging Infectious Diseases Laboratories, Boston University, Massachusetts 02118
- Department of Microbiology, Boston University, Massachusetts 02215
- Department of Biomedical Engineering, Boston University, Massachusetts 02215
| | - Michael Freitag
- Department of Biochemistry and Biophysics, Oregon State University, Corvallis, Oregon 97331
| | - Matthew S Sachs
- Department of Biology, Texas A&M University, College Station, Texas 77843
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14
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Abstract
The filamentous fungus Neurospora crassa has frequently served as a model organism for the study of circadian rhythms through its ability to form conidial spores on a daily basis. This phenomenon leaves a spatial pattern of conidiation bands along a solid surface of agar after several days of growth. Using time-lapse video, the authors have quantified the rate of conidiation. They have found that conidia do not form at a specified lag time after the growth front is laid down, but rather the band region tends to simultaneously develop over a short time frame. This produces a sharp peak when the conidiation rate is plotted against time. In addition, the authors used time-lapse video to assay growth rate with greater accuracy than previously reported. It is usually assumed that Neurospora’s rate of growth is constant, and this assumption of linear growth has been used extensively to determine period and phase of the conidiation circadian rhythm. The authors have confirmed an earlier report of nonlinear growth rate and have shown that the growth rate varies by a factor of about 2 with each circadian cycle. They have demonstrated that the errors in calculating times of conidiation peaks are maximally 1 to 2 h if linearity is assumed. The conidiation rate and growth rate rhythms are not apparent under conditions (using mutants or high or low temperatures) where the spatial banding rhythm is not observed. In light/dark entraining conditions, the conidiation rate and growth rate rhythms maintain the same phase relationship in different T-cycles. These data are consistent with the hypothesis that the growth rate rhythm is a consequence of the conidiation rate rhythm.
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Affiliation(s)
- Van D Gooch
- Division of Science and Mathematics, University of Minnesota-Morris, Morris, Minnesota, USA
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15
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de Paula RM, Lewis ZA, Greene AV, Seo KS, Morgan LW, Vitalini MW, Bennett L, Gomer RH, Bell-Pedersen D. Two Circadian Timing Circuits in Neurospora crassa Cells Share Components and Regulate Distinct Rhythmic Processes. J Biol Rhythms 2016; 21:159-68. [PMID: 16731655 DOI: 10.1177/0748730406288338] [Citation(s) in RCA: 47] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
In Neurospora crassa, FRQ, WC-1, and WC-2 proteins comprise the core circadian FRQ-based oscillator that is directly responsive to light and drives daily rhythms in spore development and gene expression. However, physiological and biochemical studies have demonstrated the existence of additional oscillators in the cell that function in the absence of FRQ (collectively termed FRQ-less oscillators [FLOs]). Whether or not these represent temperature-compensated, entrainable circadian oscillators is not known. The authors previously identified an evening-peaking gene, W06H2 (now called clock-controlled gene 16 [ ccg-16]), which is expressed with a robust daily rhythm in cells that lack FRQ protein, suggesting that ccg-16 is regulated by a FLO. In this study, the authors provide evidence that the FLO driving ccg-16 rhythmicity is a circadian oscillator. They find that ccg-16 rhythms are generated by a temperature-responsive, temperature-compensated circadian FLO that, similar to the FRQ-based oscillator, requires functional WC-1 and WC-2 proteins for activity. They also find that FRQ is not essential for rhythmic WC-1 protein levels, raising the possibility that this WCFLO is involved in the generation of WC-1 rhythms. The results are consistent with the presence of 2 circadian oscillators within Neurospora cells, which the authors speculate may interact with each other through the shared WC proteins.
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Affiliation(s)
- Renato M de Paula
- Department of Biology, Center for Research on Biological Clocks, Texas A&M University, College Station, TX 77843, USA
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16
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Abstract
The eukaryotic filamentous fungus Neurospora crassa has proven to be a durable and dependable model system for the analysis of the cellular and molecular bases of circadian rhythms. Pioneering genetic analyses identified clock genes, and beginning with the cloning of frequency ( frq), work over the past 2 decades has revealed the molecular basis of a core circadian clock feedback loop that has illuminated our understanding of circadian oscillators in microbes, plants, and animals. In this transcription/translation-based feedback loop, a heterodimer of the White Collar-1 (WC-1) and WC-2 proteins acts both as the circadian photoreceptor and, in the dark, as a transcription factor that promotes the expression of the frq gene. FRQ dimerizes and feeds back to block the activity of its activators (making a negative feedback loop), as well as feeding forward to promote the synthesis of its activator, WC-1. Phosphorylation of FRQ by several kinases leads to its ubiquitination and turnover, releasing the WC-1/WC-2 dimer to reactivate frq expression and restart the circadian cycle. Light resetting of the clock can be understood through the rapid light induction of frq expression and temperature resetting through the influence of elevated temperaturesin driving higher levels of FRQ. Several FRQ- and WC-independent, noncircadian FRQ-less oscillators (FLOs) have been described, each of which appears to regulate aspects of Neurospora growth or development. Overall, the FRQ/white collar complex feedback loop appears to coordinate the circadian system through its activity to regulate downstream-target clock-controlled genes, either directly or via regulation of driven FLOs.
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Affiliation(s)
- Jay C Dunlap
- Department of Genetics, Dartmouth Medical School, Hannover, NH 03755-3844, USA.
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17
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Jolma IW, Falkeid G, Bamerni M, Ruoff P. Lithium Leads to an Increased FRQ Protein Stability and to a Partial Loss of Temperature Compensation in the Neurospora Circadian Clock. J Biol Rhythms 2016; 21:327-34. [PMID: 16998153 DOI: 10.1177/0748730406292453] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
In many organisms, the presence of lithium leads to an increase of the circadian period length. In Neurospora crassa, it was earlier found that lithium results in a decrease of overall growth and increased circadian periods. In this article, the authors show that lithium leads to a reduction of FRQ degradation with elevated FRQ levels and to a partial loss of temperature compensation. At a concentration of 13 mM lithium, FRQ degradation is reduced by about 60% while, surprisingly, the activity of the 20S proteasome remains unaffected. Experiments and model calculations have shown that the stability of FRQ is dependent on its phosphorylation state and that increased FRQ protein stabilities lead to increased circadian periods, consistent with the observed increase of the period when lithium is present. Because in Neurospora the proteasome activity is unaffected by lithium concentrations that lead to significant FRQ stabilization, it appears that lithium acts as an inhibitor of kinases that affect phosphorylation of FRQ and other proteins. A competition between Li+and Mg2+ions for Mg2+-binding sites may be a mechanism to how certain kinases are inhibited by Li+. A possible kinase in this respect is GSK-3, which in other organisms is known to be inhibited by lithium. The partial loss of temperature compensation in the presence of lithium can be understood as an increase in the overall activation energy of FRQ degradation. This increase in activation energy may be related to a reduction in FRQ phosphorylation so that more kinase activity, that is, higher temperature and longer times, is required to achieve the necessary amount of FRQ phosphorylation leading to turnover. Using a modified Goodwin oscillator as a semiquantitative model for the Neurospora clock, the effects of lithium can be described by adding lithium inhibitory terms of FRQ degradation to the model.
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Affiliation(s)
- Ingunn W Jolma
- Department of Mathematics and Natural Science, University of Stavanger, Stavanger, Norway
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18
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Abstract
Plants and animals use day or night length for seasonal control of reproduction and other biological functions. Overwhelming evidence suggests that this photoperiodic mechanism relies on a functional circadian system. Recent progress has defined how flowering time in plants is regulated by photoperiodic control of output pathways, but the underlying mechanisms of photoperiodism remain to be described. The authors investigate photoperiodism in a genetic model system for circadian rhythms research, Neurospora crassa. They find that both propagation and reproduction respond systematically to photoperiod. Furthermore, a nonreproductive light-regulated function is also enhanced under certain photoperiodic conditions. All of these photoperiodic responses require a functional circadian clock, in that they are absent in a clock mutant. Night break experiments show that measuring night length is one of the mechanisms used for photoperiod assessment. This represents the first formal report of photoperiodism in the fungi.
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Affiliation(s)
- Ying Tan
- Institute for Medical Psychology, University of Munich, Munich, Germany
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19
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Turrà D, Di Pietro A. Chemotropic sensing in fungus-plant interactions. Curr Opin Plant Biol 2015; 26:135-40. [PMID: 26247120 DOI: 10.1016/j.pbi.2015.07.004] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/01/2015] [Revised: 07/13/2015] [Accepted: 07/14/2015] [Indexed: 05/14/2023]
Abstract
Growth of fungal hyphae is guided by a variety of chemical gradients, including nutrients, mating pheromones or host compounds. Over 100 years after chemotropism was first reported in fungus-plant interactions, our knowledge on the host signals, fungal receptors and cellular pathways is still rudimentary. Genetic analysis in the model organisms Saccharomyces cerevisiae and Neurospora crassa has provided valuable insights into the chemotropic machinery of the fungal hypha. Moreover, recent studies in the root-infecting pathogen Fusarium oxysporum reveal an unanticipated complexity in chemotropic sensing of nutrient sources, peptide pheromones and host plant signals.
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Affiliation(s)
- David Turrà
- Departamento de Genética, Campus de Excelencia Internacional Agroalimentario ceiA3, Universidad de Córdoba, 14071 Córdoba, Spain
| | - Antonio Di Pietro
- Departamento de Genética, Campus de Excelencia Internacional Agroalimentario ceiA3, Universidad de Córdoba, 14071 Córdoba, Spain.
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20
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Filippovich S, Bachurina G, Shcherbakov D. [Quantitative Assessment of the Combined Effect of the Nitrogen Status, Light and Dehydration of Mycelium on Conidiation in Neurospora crassa]. ACTA ACUST UNITED AC 2015. [PMID: 26204777 DOI: 10.7868/s055510991503006x] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
Abstract
We performed a quantitative assessment of the conidia yield in Neurospora crassa in response to treatment with different conidiation effectors. Depending on nitrogen source and intactness of nitrite reductase (NiR) and nitrate reductase (NR), light and dehydration affected the number of viable conidia produced by the ascomycete. In most variants of the nitrogen status, the combined action of light and dehydration synergistically increased the conidia yield. Conidiation in wild-type cells cultivated on the medium with NH4Cl as a sole nitrogen source did not respond to light, whereas illumination of the same culture grown on NH4NO3- or NaNO3-containing medium stimulated the process of spore formation. In response to light exposure, conidia formation occurred in the same way in the nit-2 (no NR and NiR) and nit-6 (no NiR) mutants cultivated in the presence of NH4Cl, but differed greatly when grown on the medium with NH4NO3. The results obtained indicate the possibility that NR and NiR participate in the photoconidiation regulation (wild-type strain on the medium with secondary nitrogen source); however, they cannot be necessary because light-dependent stimulation of spore formation was observed in nit-2 and nit-6 mutants.
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21
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Lehr NA, Wang Z, Li N, Hewitt DA, López-Giráldez F, Trail F, Townsend JP. Gene expression differences among three Neurospora species reveal genes required for sexual reproduction in Neurospora crassa. PLoS One 2014; 9:e110398. [PMID: 25329823 PMCID: PMC4203796 DOI: 10.1371/journal.pone.0110398] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2014] [Accepted: 09/16/2014] [Indexed: 12/23/2022] Open
Abstract
Many fungi form complex three-dimensional fruiting bodies, within which the meiotic machinery for sexual spore production has been considered to be largely conserved over evolutionary time. Indeed, much of what we know about meiosis in plant and animal taxa has been deeply informed by studies of meiosis in Saccharomyces and Neurospora. Nevertheless, the genetic basis of fruiting body development and its regulation in relation to meiosis in fungi is barely known, even within the best studied multicellular fungal model Neurospora crassa. We characterized morphological development and genome-wide transcriptomics in the closely related species Neurospora crassa, Neurospora tetrasperma, and Neurospora discreta, across eight stages of sexual development. Despite diverse life histories within the genus, all three species produce vase-shaped perithecia. Transcriptome sequencing provided gene expression levels of orthologous genes among all three species. Expression of key meiosis genes and sporulation genes corresponded to known phenotypic and developmental differences among these Neurospora species during sexual development. We assembled a list of genes putatively relevant to the recent evolution of fruiting body development by sorting genes whose relative expression across developmental stages increased more in N. crassa relative to the other species. Then, in N. crassa, we characterized the phenotypes of fruiting bodies arising from crosses of homozygous knockout strains of the top genes. Eight N. crassa genes were found to be critical for the successful formation of perithecia. The absence of these genes in these crosses resulted in either no perithecium formation or in arrested development at an early stage. Our results provide insight into the genetic basis of Neurospora sexual reproduction, which is also of great importance with regard to other multicellular ascomycetes, including perithecium-forming pathogens, such as Claviceps purpurea, Ophiostoma ulmi, and Glomerella graminicola.
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Affiliation(s)
- Nina A. Lehr
- Department of Ecology and Evolutionary Biology, Yale University, New Haven, Connecticut, United States of America
| | - Zheng Wang
- Department of Ecology and Evolutionary Biology, Yale University, New Haven, Connecticut, United States of America
- Department of Biostatistics, Yale University, New Haven, Connecticut, United States of America
| | - Ning Li
- Department of Ecology and Evolutionary Biology, Yale University, New Haven, Connecticut, United States of America
| | - David A. Hewitt
- Department of Botany, Academy of Natural Sciences, Philadelphia, Pennsylvania, United States of America
- Wagner Free Institute of Science, Philadelphia, Pennsylvania, United States of America
| | - Francesc López-Giráldez
- Department of Ecology and Evolutionary Biology, Yale University, New Haven, Connecticut, United States of America
| | - Frances Trail
- Department of Plant Biology, Michigan State University, East Lansing, Michigan, United States of America
- Department of Plant, Soil and Microbial Sciences, Michigan State University, East Lansing, Michigan, United States of America
| | - Jeffrey P. Townsend
- Department of Ecology and Evolutionary Biology, Yale University, New Haven, Connecticut, United States of America
- Department of Biostatistics, Yale University, New Haven, Connecticut, United States of America
- Program in Computational Biology and Bioinformatics, Yale University, New Haven, Connecticut, United States of America
- Program in Microbiology, Yale University, New Haven, Connecticut, United States of America
- * E-mail:
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22
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Fu C, Ao J, Dettmann A, Seiler S, Free SJ. Characterization of the Neurospora crassa cell fusion proteins, HAM-6, HAM-7, HAM-8, HAM-9, HAM-10, AMPH-1 and WHI-2. PLoS One 2014; 9:e107773. [PMID: 25279949 PMCID: PMC4184795 DOI: 10.1371/journal.pone.0107773] [Citation(s) in RCA: 38] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2014] [Accepted: 08/14/2014] [Indexed: 11/19/2022] Open
Abstract
Intercellular communication of vegetative cells and their subsequent cell fusion is vital for different aspects of growth, fitness, and differentiation of filamentous fungi. Cell fusion between germinating spores is important for early colony establishment, while hyphal fusion in the mature colony facilitates the movement of resources and organelles throughout an established colony. Approximately 50 proteins have been shown to be important for somatic cell-cell communication and fusion in the model filamentous fungus Neurospora crassa. Genetic, biochemical, and microscopic techniques were used to characterize the functions of seven previously poorly characterized cell fusion proteins. HAM-6, HAM-7 and HAM-8 share functional characteristics and are proposed to function in the same signaling network. Our data suggest that these proteins may form a sensor complex at the cell wall/plasma membrane for the MAK-1 cell wall integrity mitogen-activated protein kinase (MAPK) pathway. We also demonstrate that HAM-9, HAM-10, AMPH-1 and WHI-2 have more general functions and are required for normal growth and development. The activation status of the MAK-1 and MAK-2 MAPK pathways are altered in mutants lacking these proteins. We propose that these proteins may function to coordinate the activities of the two MAPK modules with other signaling pathways during cell fusion.
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Affiliation(s)
- Ci Fu
- Department of Biological Sciences, SUNY University at Buffalo, Buffalo, New York, United States of America
| | - Jie Ao
- Department of Biological Sciences, SUNY University at Buffalo, Buffalo, New York, United States of America
| | - Anne Dettmann
- Institute for Biology II, Albert-Ludwigs University Freiburg, Freiburg, Germany
| | - Stephan Seiler
- Institute for Biology II, Albert-Ludwigs University Freiburg, Freiburg, Germany
- Freiburg Institute for Advanced Studies (FRIAS), Albert-Ludwigs University Freiburg, Freiburg, Germany
| | - Stephen J. Free
- Department of Biological Sciences, SUNY University at Buffalo, Buffalo, New York, United States of America
- * E-mail:
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23
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Abstract
Mutualistic symbioses shape the evolution of species and ecosystems and catalyze the emergence of biological complexity, yet how such symbioses first form is unclear. We show that an obligate mutualism between the yeast Saccharomyces cerevisiae and the alga Chlamydomonas reinhardtii--two model eukaryotes with very different life histories--can arise spontaneously in an environment requiring reciprocal carbon and nitrogen exchange. This capacity for mutualism is phylogenetically broad, extending to other Chlamydomonas and fungal species. Furthermore, we witnessed the spontaneous association of Chlamydomonas algal cells physically interacting with filamentous fungi. These observations demonstrate that under specific conditions, environmental change induces free-living species to become obligate mutualists and establishes a set of experimentally tractable, phylogenetically related, synthetic systems for studying the evolution of symbiosis.
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Affiliation(s)
- Erik F Y Hom
- Department of Molecular and Cellular Biology, Harvard University, Cambridge, MA 02138, USA. Faculty of Arts and Sciences Center for Systems Biology, Harvard University, Cambridge, MA 02138, USA.
| | - Andrew W Murray
- Department of Molecular and Cellular Biology, Harvard University, Cambridge, MA 02138, USA. Faculty of Arts and Sciences Center for Systems Biology, Harvard University, Cambridge, MA 02138, USA.
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24
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Abstract
Neurospora crassa has a long history as an excellent model for genetic, cellular, and biochemical research. Although this fungus is known as a saprotroph, it normally appears on burned vegetations or trees after forest fires. However, due to a lack of experimental evidence, the nature of its association with living plants remains enigmatic. Here we report that Scots pine (Pinus sylvestris) is a host plant for N. crassa. The endophytic lifestyle of N. crassa was found in its interaction with Scots pine. Moreover, the fungus can switch to a pathogenic state when its balanced interaction with the host is disrupted. Our data reveal previously unknown lifestyles of N. crassa, which are likely controlled by both environmental and host factors. Switching among the endophytic, pathogenic, and saprotrophic lifestyles confers upon fungi phenotypic plasticity in adapting to changing environments and drives the evolution of fungi and associated plants.
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Affiliation(s)
- Hsiao-Che Kuo
- Department of Forest Sciences, University of Helsinki, Helsinki, Finland
| | - Sun Hui
- Department of Forest Sciences, University of Helsinki, Helsinki, Finland
| | - Jaeyoung Choi
- Department of Agricultural Biotechnology, Center for Fungal Pathogenesis, and Center for Fungal Genetic Resources, Seoul National University, Seoul 151-921, Korea
| | | | - Jari P. T. Valkonen
- Department of Agricultural Sciences, University of Helsinki, Helsinki, Finland
| | - Yong-Hwan Lee
- Department of Forest Sciences, University of Helsinki, Helsinki, Finland
- Department of Agricultural Sciences, University of Helsinki, Helsinki, Finland
- Department of Agricultural Biotechnology, Center for Fungal Pathogenesis, and Center for Fungal Genetic Resources, Seoul National University, Seoul 151-921, Korea
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25
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Abstract
Proper cell division is essential for growth and development of uni- and multicellular organisms. The fungal septation initiation network (SIN) functions as kinase cascade that connects cell cycle progression with the initiation of cytokinesis. Miss-regulation of the homologous Hippo pathway in animals results in excessive cell proliferation and formation of tumors, underscoring the conservation of both pathways. How SIN proteins interact and transmit signals through the cascade is only beginning to be understood. Moreover, our understanding of septum formation and its regulation in filamentous fungi, which represent the vast majority of the fungal kingdom, is highly fragmentary. We determined that a tripartite kinase cascade, consisting of CDC-7, SID-1 and DBF-2, together with their regulatory subunits CDC-14 and MOB-1, is important for septum formation in the model mold Neurospora crassa. DBF-2 activity and septum formation requires auto-phosphorylation at Ser499 within the activation segment and phosphorylation of Thr671 in the hydrophobic motif by SID-1. Moreover, SID-1-stimulated DBF-2 activity is further enhanced by CDC-7, supporting a stepwise activation mechanism of the tripartite SIN kinase cascade in fungi. However, in contrast to the situation described for unicellular yeasts, the localization of the entire SIN cascade to spindle pole bodies is constitutive and cell cycle independent. Moreover, all SIN proteins except CDC-7 form cortical rings prior to septum initiation and localize to constricting septa. Thus, SIN localization and activity regulation significantly differs in unicellular versus syncytial ascomycete fungi.
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Affiliation(s)
- Yvonne Heilig
- Institute for Biology II – Molecular Plant Physiology, Albert-Ludwigs University Freiburg, Freiburg, Germany
| | - Kerstin Schmitt
- Institute for Microbiology and Genetics, University of Goettingen, Goettingen, Germany
| | - Stephan Seiler
- Institute for Biology II – Molecular Plant Physiology, Albert-Ludwigs University Freiburg, Freiburg, Germany
- Freiburg Institute for Advanced Studies (FRIAS), Albert-Ludwigs University Freiburg, Freiburg, Germany
- * E-mail:
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26
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Palma-Guerrero J, Hall CR, Kowbel D, Welch J, Taylor JW, Brem RB, Glass NL. Genome wide association identifies novel loci involved in fungal communication. PLoS Genet 2013; 9:e1003669. [PMID: 23935534 PMCID: PMC3731230 DOI: 10.1371/journal.pgen.1003669] [Citation(s) in RCA: 74] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2013] [Accepted: 06/10/2013] [Indexed: 01/25/2023] Open
Abstract
Understanding how genomes encode complex cellular and organismal behaviors has become the outstanding challenge of modern genetics. Unlike classical screening methods, analysis of genetic variation that occurs naturally in wild populations can enable rapid, genome-scale mapping of genotype to phenotype with a medium-throughput experimental design. Here we describe the results of the first genome-wide association study (GWAS) used to identify novel loci underlying trait variation in a microbial eukaryote, harnessing wild isolates of the filamentous fungus Neurospora crassa. We genotyped each of a population of wild Louisiana strains at 1 million genetic loci genome-wide, and we used these genotypes to map genetic determinants of microbial communication. In N. crassa, germinated asexual spores (germlings) sense the presence of other germlings, grow toward them in a coordinated fashion, and fuse. We evaluated germlings of each strain for their ability to chemically sense, chemotropically seek, and undergo cell fusion, and we subjected these trait measurements to GWAS. This analysis identified one gene, NCU04379 (cse-1, encoding a homolog of a neuronal calcium sensor), at which inheritance was strongly associated with the efficiency of germling communication. Deletion of cse-1 significantly impaired germling communication and fusion, and two genes encoding predicted interaction partners of CSE1 were also required for the communication trait. Additionally, mining our association results for signaling and secretion genes with a potential role in germling communication, we validated six more previously unknown molecular players, including a secreted protease and two other genes whose deletion conferred a novel phenotype of increased communication and multi-germling fusion. Our results establish protein secretion as a linchpin of germling communication in N. crassa and shed light on the regulation of communication molecules in this fungus. Our study demonstrates the power of population-genetic analyses for the rapid identification of genes contributing to complex traits in microbial species. Many phenotypes of interest are controlled by multiple loci, and in biological systems identifying determinants of such complex traits is challenging. Here, we genotyped 112 wild isolates of Neurospora crassa and used this resource to identify genes that mediate a fundamental but poorly-understood attribute of this filamentous fungus: the ability of germinating spores to sense each other at a distance, extend projections toward one another, and fuse. Inheritance at a secretion gene, cse-1, was associated strongly with germling communication across wild strains; this association was validated in experiments showing reduced communication in a cse-1 deletion strain. By testing interacting partners of CSE1, and by assessing additional secretion and signaling factors whose inheritance associated more modestly with germling communication in wild strains, we identified eight other novel determinants of this phenotype. Our population of genotyped wild isolates provides a flexible and powerful community resource for the rapid identification of any varying, complex phenotype in N. crassa. The success of our approach, which used a phenotyping scheme far more tractable than would be required in a screen of the entire N. crassa gene deletion collection, serves as a proof of concept for association studies of wild populations for any organism.
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Affiliation(s)
- Javier Palma-Guerrero
- Department of Plant and Microbial Biology, University of California, Berkeley, California, United States of America
| | - Charles R. Hall
- Department of Plant and Microbial Biology, University of California, Berkeley, California, United States of America
| | - David Kowbel
- Department of Plant and Microbial Biology, University of California, Berkeley, California, United States of America
| | - Juliet Welch
- Department of Plant and Microbial Biology, University of California, Berkeley, California, United States of America
| | - John W. Taylor
- Department of Plant and Microbial Biology, University of California, Berkeley, California, United States of America
| | - Rachel B. Brem
- Department of Molecular and Cell Biology, University of California, Berkeley, California, United States of America
- * E-mail: (RBB); (NLG)
| | - N. Louise Glass
- Department of Plant and Microbial Biology, University of California, Berkeley, California, United States of America
- * E-mail: (RBB); (NLG)
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27
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Berepiki A, Read ND. Septins are important for cell polarity, septation and asexual spore formation in Neurospora crassa and show different patterns of localisation at germ tube tips. PLoS One 2013; 8:e63843. [PMID: 23691103 PMCID: PMC3653863 DOI: 10.1371/journal.pone.0063843] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2012] [Accepted: 04/10/2013] [Indexed: 12/24/2022] Open
Abstract
Septins are GTP-binding cytoskeletal proteins that contribute to cell polarity, vesicle trafficking, cytokinesis and cell morphogenesis. Here we have characterised the six septins encoded by the genome of the model filamentous fungus Neurospora crassa. Analysis of septin null mutants demonstrated that septins limit the sites of emergence of germ tubes and are important for septation and conidiation in N. crassa. Septins constituted a range of different higher-order structures in N. crassa – rings, loops, fibres, bands, and caps – which can co-exist within the same cell. They showed different patterns of localisation at germ tube tips, with GFP-CDC-10 and CDC-11-GFP forming a subapical collar with lower signal intensity at the tip apex, CDC-3-GFP and CDC-12-GFP organized as a cap at the tip apex and GFP-ASP-1 forming an extended subapical collar. Purification of the septin complex and mass spectrometry of isolated proteins revealed that the septin complex consists predominantly of CDC-3, CDC-10, CDC-11 and CDC-12. Immunoprecipitation of the putative septin ASP-1 revealed that this protein interacts with the core septin complex.
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Affiliation(s)
| | - Nick D. Read
- Fungal Cell Biology Group, Institute of Cell Biology, University of Edinburgh, Edinburgh, United Kingdom
- * E-mail:
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28
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Gyöngyösi N, Nagy D, Makara K, Ella K, Káldi K. Reactive oxygen species can modulate circadian phase and period in Neurospora crassa. Free Radic Biol Med 2013; 58:134-43. [PMID: 23277144 DOI: 10.1016/j.freeradbiomed.2012.12.016] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/22/2012] [Revised: 11/14/2012] [Accepted: 12/17/2012] [Indexed: 11/24/2022]
Abstract
Reactive oxygen species (ROS) may serve as signals coupling metabolism to other cell functions. In addition to being by-products of normal metabolism, they are generated at elevated levels under environmental stress situations. We analyzed how reactive oxygen species affect the circadian clock in the model organism Neurospora crassa. In light/dark cycles, an increase in the levels of reactive oxygen species advanced the phase of both the conidiation rhythm and the expression of the clock gene frequency. Our results indicate a dominant role of the superoxide anion in the control of the phase. Elevation of superoxide production resulted in the activation of protein phosphatase 2A, a regulator of the positive element of the circadian clock. Our data indicate that even under nonstress conditions, reactive oxygen species affect circadian timekeeping. Reduction of their basal levels results in a delay of the phase in light/dark cycles and a longer period under constant conditions. We show that under entrained conditions the phase depends on the temperature and reactive oxygen species contribute to this effect. Our results suggest that the superoxide anion is an important factor controlling the circadian oscillator and is able to reset the clock most probably by activating protein phosphatase 2A, thereby modulating the activity of the White Collar complex.
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Affiliation(s)
- Norbert Gyöngyösi
- Department of Physiology, Semmelweis University, H-1092 Budapest, Hungary
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29
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Simonin A, Palma-Guerrero J, Fricker M, Glass NL. Physiological significance of network organization in fungi. Eukaryot Cell 2012; 11:1345-52. [PMID: 22962278 PMCID: PMC3486018 DOI: 10.1128/ec.00213-12] [Citation(s) in RCA: 72] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/30/2012] [Accepted: 09/01/2012] [Indexed: 01/16/2023]
Abstract
The evolution of multicellularity has occurred in diverse lineages and in multiple ways among eukaryotic species. For plants and fungi, multicellular forms are derived from ancestors that failed to separate following cell division, thus retaining cytoplasmic continuity between the daughter cells. In networked organisms, such as filamentous fungi, cytoplasmic continuity facilitates the long-distance transport of resources without the elaboration of a separate vascular system. Nutrient translocation in fungi is essential for nutrient cycling in ecosystems, mycorrhizal symbioses, virulence, and substrate utilization. It has been proposed that an interconnected mycelial network influences resource translocation, but the theory has not been empirically tested. Here we show, by using mutants that disrupt network formation in Neurospora crassa (Δso mutant, no fusion; ΔPrm-1 mutant, ∼50% fusion), that the translocation of labeled nutrients is adversely affected in homogeneous environments and is even more severely impacted in heterogeneous environments. We also show that the ability to share resources and genetic exchange between colonies (via hyphal fusion) is very limited in mature colonies, in contrast to in young colonies and germlings that readily share nutrients and genetic resources. The differences in genetic/resource sharing between young and mature colonies were associated with variations in colony architecture (hyphal differentiation/diameters, branching patterns, and angles). Thus, the ability to share resources and genetic material between colonies is developmentally regulated and is a function of the age of a colony. This study highlights the necessity of hyphal fusion for efficient nutrient translocation within an N. crassa colony but also shows that established N. crassa colonies do not share resources in a significant manner.
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Affiliation(s)
- Anna Simonin
- Plant and Microbial Biology Department, The University of California, Berkeley, California, USA
| | - Javier Palma-Guerrero
- Plant and Microbial Biology Department, The University of California, Berkeley, California, USA
| | - Mark Fricker
- Department of Plant Sciences, University of Oxford, Oxford, United Kingdom
| | - N. Louise Glass
- Plant and Microbial Biology Department, The University of California, Berkeley, California, USA
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30
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Eaton CJ, Cabrera IE, Servin JA, Wright SJ, Cox MP, Borkovich KA. The guanine nucleotide exchange factor RIC8 regulates conidial germination through Gα proteins in Neurospora crassa. PLoS One 2012; 7:e48026. [PMID: 23118921 PMCID: PMC3485287 DOI: 10.1371/journal.pone.0048026] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2012] [Accepted: 09/25/2012] [Indexed: 11/20/2022] Open
Abstract
Heterotrimeric G protein signaling is essential for normal hyphal growth in the filamentous fungus Neurospora crassa. We have previously demonstrated that the non-receptor guanine nucleotide exchange factor RIC8 acts upstream of the Gα proteins GNA-1 and GNA-3 to regulate hyphal extension. Here we demonstrate that regulation of hyphal extension results at least in part, from an important role in control of asexual spore (conidia) germination. Loss of GNA-3 leads to a drastic reduction in conidial germination, which is exacerbated in the absence of GNA-1. Mutation of RIC8 leads to a reduction in germination similar to that in the Δgna-1, Δgna-3 double mutant, suggesting that RIC8 regulates conidial germination through both GNA-1 and GNA-3. Support for a more significant role for GNA-3 is indicated by the observation that expression of a GTPase-deficient, constitutively active gna-3 allele in the Δric8 mutant leads to a significant increase in conidial germination. Localization of the three Gα proteins during conidial germination was probed through analysis of cells expressing fluorescently tagged proteins. Functional TagRFP fusions of each of the three Gα subunits were constructed through insertion of TagRFP in a conserved loop region of the Gα subunits. The results demonstrated that GNA-1 localizes to the plasma membrane and vacuoles, and also to septa throughout conidial germination. GNA-2 and GNA-3 localize to both the plasma membrane and vacuoles during early germination, but are then found in intracellular vacuoles later during hyphal outgrowth.
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Affiliation(s)
- Carla J. Eaton
- Department of Plant Pathology and Microbiology and Institute for Integrative Genome Biology, University of California Riverside, Riverside, California, United States of America
| | - Ilva E. Cabrera
- Department of Plant Pathology and Microbiology and Institute for Integrative Genome Biology, University of California Riverside, Riverside, California, United States of America
| | - Jacqueline A. Servin
- Department of Plant Pathology and Microbiology and Institute for Integrative Genome Biology, University of California Riverside, Riverside, California, United States of America
| | - Sara J. Wright
- Department of Plant Pathology and Microbiology and Institute for Integrative Genome Biology, University of California Riverside, Riverside, California, United States of America
| | - Murray P. Cox
- Institute of Molecular BioSciences, Massey University, The Bio-Protection Research Centre and The Allan Wilson Centre for Molecular Ecology and Evolution, Palmerston North, New Zealand
| | - Katherine A. Borkovich
- Department of Plant Pathology and Microbiology and Institute for Integrative Genome Biology, University of California Riverside, Riverside, California, United States of America
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31
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Hamam A, Lew RR. Electrical phenotypes of calcium transport mutant strains of a filamentous fungus, Neurospora crassa. Eukaryot Cell 2012; 11:694-702. [PMID: 22408225 PMCID: PMC3346425 DOI: 10.1128/ec.05329-11] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/30/2011] [Accepted: 02/28/2012] [Indexed: 12/27/2022]
Abstract
We characterized the electrical phenotypes of mutants with mutations in genes encoding calcium transporters-a mechanosensitive channel homolog (MscS), a Ca(2+)/H(+) exchange protein (cax), and Ca(2+)-ATPases (nca-1, nca-2, nca-3)-as well as those of double mutants (the nca-2 cax, nca-2 nca-3, and nca-3 cax mutants). The electrical characterization used dual impalements to obtain cable-corrected current-voltage measurements. Only two types of mutants (the MscS mutant; the nca-2 mutant and nca-2-containing double mutants) exhibited lower resting potentials. For the nca-2 mutant, on the basis of unchanged conductance and cyanide-induced depolarization of the potential, the cause is attenuated H(+)-ATPase activity. The growth of the nca-2 mutant-containing strains was inhibited by elevated extracellular Ca(2+) levels, indicative of lesions in Ca(2+) homeostasis. However, the net Ca(2+) effluxes of the nca-2 mutant, measured noninvasively with a self-referencing Ca(2+)-selective microelectrode, were similar to those of the wild type. All of the mutants exhibited osmosensitivity similar to that of the wild type (the turgor of the nca-2 mutant was also similar to that of the wild type), suggesting that Ca(2+) signaling does not play a role in osmoregulation. The hyphal tip morphology and tip-localized mitochondria of the nca-2 mutant were similar to those of the wild type, even when the external [Ca(2+)] was elevated. Thus, although Ca(2+) homeostasis is perturbed in the nca-2 mutant (B. J. Bowman et al., Eukaryot. Cell 10:654-661, 2011), the phenotype does not extend to tip growth or to osmoregulation but is revealed by lower H(+)-ATPase activity.
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Affiliation(s)
- Ahmed Hamam
- Biology Department, York University, Toronto, Ontario, Canada
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32
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Abstract
In Neurospora crassa, the interactions between products of the frequency (frq), frequency-interacting RNA helicase (frh), white collar-1 (wc-1), and white collar-2 (wc-2) genes establish a molecular circadian clockwork, called the FRQ-WC-Oscillator (FWO), which is required for the generation of molecular and overt circadian rhythmicity. In strains carrying nonfunctional frq alleles, circadian rhythms in asexual spore development (conidiation) are abolished in constant conditions, yet conidiation remains rhythmic in temperature cycles. Certain characteristics of these temperature-synchronized rhythms have been attributed to the activity of a FRQ-less oscillator (FLO). The molecular components of this FLO are as yet unknown. To test whether the FLO depends on other circadian clock components, we created a strain that carries deletions in the frq, wc-1, wc-2, and vivid (vvd) genes. Conidiation in this ΔFWO strain was still synchronized to cyclic temperature programs, but temperature-induced rhythmicity was distinct from that seen in single frq knockout strains. These results and other evidence presented indicate that components of the FWO are part of the temperature-induced FLO.
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Affiliation(s)
- Suzanne Hunt
- Faculty of Life Sciences, University of Manchester, Manchester M13 9PT, United Kingdom
| | - Mark Elvin
- Faculty of Life Sciences, University of Manchester, Manchester M13 9PT, United Kingdom
| | - Christian Heintzen
- Faculty of Life Sciences, University of Manchester, Manchester M13 9PT, United Kingdom
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33
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Tseng YY, Hunt SM, Heintzen C, Crosthwaite SK, Schwartz JM. Comprehensive modelling of the Neurospora circadian clock and its temperature compensation. PLoS Comput Biol 2012; 8:e1002437. [PMID: 22496627 PMCID: PMC3320131 DOI: 10.1371/journal.pcbi.1002437] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2011] [Accepted: 02/06/2012] [Indexed: 11/19/2022] Open
Abstract
Circadian clocks provide an internal measure of external time allowing organisms to anticipate and exploit predictable daily changes in the environment. Rhythms driven by circadian clocks have a temperature compensated periodicity of approximately 24 hours that persists in constant conditions and can be reset by environmental time cues. Computational modelling has aided our understanding of the molecular mechanisms of circadian clocks, nevertheless it remains a major challenge to integrate the large number of clock components and their interactions into a single, comprehensive model that is able to account for the full breadth of clock phenotypes. Here we present a comprehensive dynamic model of the Neurospora crassa circadian clock that incorporates its key components and their transcriptional and post-transcriptional regulation. The model accounts for a wide range of clock characteristics including: a periodicity of 21.6 hours, persistent oscillation in constant conditions, arrhythmicity in constant light, resetting by brief light pulses, and entrainment to full photoperiods. Crucial components influencing the period and amplitude of oscillations were identified by control analysis. Furthermore, simulations enabled us to propose a mechanism for temperature compensation, which is achieved by simultaneously increasing the translation of frq RNA and decreasing the nuclear import of FRQ protein. Circadian clocks are internal timekeepers that integrate signals from the environment and orchestrate cellular events to occur at the most favourable time of day. Circadian clocks in animals, plants, fungi and bacteria have similar characteristic properties and molecular architecture. They have a periodicity of approximately 24 hours, persist in constant conditions and can be reset by environmental time cues such as light and temperature. Another essential property, whose molecular basis is poorly understood, is that the period is temperature compensated i.e. it remains the same over a range of temperatures. Computational modelling has become a valuable tool to predict and understand the underlying mechanisms of such complex molecular systems, but existing clock models are often restricted in the scope of molecular reactions they cover and in the breadth of conditions they are able to reproduce. We therefore built a comprehensive model of the circadian clock of the fungus Neurospora crassa, which encompasses existing knowledge of the biochemistry of the Neurospora clock. We validated this model against a wide range of experimental phenotypes and then used the model to investigate possible molecular explanations of temperature compensation. Our simulations suggest that temperature compensation of period is achieved by changing the abundance and cellular localisation of a key clock protein.
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Affiliation(s)
- Yu-Yao Tseng
- Faculty of Life Sciences, University of Manchester, Manchester, United Kingdom
- Manchester Interdisciplinary Biocentre, Faculty of Life Sciences, University of Manchester, Manchester, United Kingdom
| | - Suzanne M. Hunt
- Faculty of Life Sciences, University of Manchester, Manchester, United Kingdom
| | - Christian Heintzen
- Faculty of Life Sciences, University of Manchester, Manchester, United Kingdom
| | - Susan K. Crosthwaite
- Faculty of Life Sciences, University of Manchester, Manchester, United Kingdom
- * E-mail: (SKC); (JMS)
| | - Jean-Marc Schwartz
- Manchester Interdisciplinary Biocentre, Faculty of Life Sciences, University of Manchester, Manchester, United Kingdom
- * E-mail: (SKC); (JMS)
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Lichius A, Yáñez-Gutiérrez ME, Read ND, Castro-Longoria E. Comparative live-cell imaging analyses of SPA-2, BUD-6 and BNI-1 in Neurospora crassa reveal novel features of the filamentous fungal polarisome. PLoS One 2012; 7:e30372. [PMID: 22291944 PMCID: PMC3265482 DOI: 10.1371/journal.pone.0030372] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2011] [Accepted: 12/14/2011] [Indexed: 12/15/2022] Open
Abstract
A key multiprotein complex involved in regulating the actin cytoskeleton and secretory machinery required for polarized growth in fungi, is the polarisome. Recognized core constituents in budding yeast are the proteins Spa2, Pea2, Aip3/Bud6, and the key effector Bni1. Multicellular fungi display a more complex polarized morphogenesis than yeasts, suggesting that the filamentous fungal polarisome might fulfill additional functions. In this study, we compared the subcellular organization and dynamics of the putative polarisome components BUD-6 and BNI-1 with those of the bona fide polarisome marker SPA-2 at various developmental stages of Neurospora crassa. All three proteins exhibited a yeast-like polarisome configuration during polarized germ tube growth, cell fusion, septal pore plugging and tip repolarization. However, the localization patterns of all three proteins showed spatiotemporally distinct characteristics during the establishment of new polar axes, septum formation and cytokinesis, and maintained hyphal tip growth. Most notably, in vegetative hyphal tips BUD-6 accumulated as a subapical cloud excluded from the Spitzenkörper (Spk), whereas BNI-1 and SPA-2 partially colocalized with the Spk and the tip apex. Novel roles during septal plugging and cytokinesis, connected to the reinitiation of tip growth upon physical injury and conidial maturation, were identified for BUD-6 and BNI-1, respectively. Phenotypic analyses of gene deletion mutants revealed additional functions for BUD-6 and BNI-1 in cell fusion regulation, and the maintenance of Spk integrity. Considered together, our findings reveal novel polarisome-independent functions of BUD-6 and BNI-1 in Neurospora, but also suggest that all three proteins cooperate at plugged septal pores, and their complex arrangement within the apical dome of mature hypha might represent a novel aspect of filamentous fungal polarisome architecture.
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Affiliation(s)
- Alexander Lichius
- Department of Microbiology, Center for Scientific Research and Higher Education of Ensenada (CICESE), Ensenada, Baja California, Mexico
- Fungal Cell Biology Group, Institute of Cell Biology, Rutherford Building, The University of Edinburgh, Edinburgh, United Kingdom
| | - Mario E. Yáñez-Gutiérrez
- Department of Microbiology, Center for Scientific Research and Higher Education of Ensenada (CICESE), Ensenada, Baja California, Mexico
| | - Nick D. Read
- Fungal Cell Biology Group, Institute of Cell Biology, Rutherford Building, The University of Edinburgh, Edinburgh, United Kingdom
| | - Ernestina Castro-Longoria
- Department of Microbiology, Center for Scientific Research and Higher Education of Ensenada (CICESE), Ensenada, Baja California, Mexico
- * E-mail:
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35
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Yoshida Y, Iigusa H, Wang N, Hasunuma K. Cross-talk between the cellular redox state and the circadian system in Neurospora. PLoS One 2011; 6:e28227. [PMID: 22164247 PMCID: PMC3229512 DOI: 10.1371/journal.pone.0028227] [Citation(s) in RCA: 43] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2011] [Accepted: 11/03/2011] [Indexed: 01/03/2023] Open
Abstract
The circadian system is composed of a number of feedback loops, and multiple feedback loops in the form of oscillators help to maintain stable rhythms. The filamentous fungus Neurospora crassa exhibits a circadian rhythm during asexual spore formation (conidiation banding) and has a major feedback loop that includes the FREQUENCY (FRQ)/WHITE COLLAR (WC) -1 and -2 oscillator (FWO). A mutation in superoxide dismutase (sod)-1, an antioxidant gene, causes a robust and stable circadian rhythm compared with that of wild-type (Wt). However, the mechanisms underlying the functions of reactive oxygen species (ROS) remain unknown. Here, we show that cellular ROS concentrations change in a circadian manner (ROS oscillation), and the amplitudes of ROS oscillation increase with each cycle and then become steady (ROS homeostasis). The ROS oscillation and homeostasis are produced by the ROS-destroying catalases (CATs) and ROS-generating NADPH oxidase (NOX). cat-1 is also induced by illumination, and it reduces ROS levels. Although ROS oscillation persists in the absence of frq, wc-1 or wc-2, its homeostasis is altered. Furthermore, genetic and biochemical evidence reveals that ROS concentration regulates the transcriptional function of WCC and a higher ROS concentration enhances conidiation banding. These findings suggest that the circadian system engages in cross-talk with the cellular redox state via ROS-regulatory factors.
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Affiliation(s)
- Yusuke Yoshida
- Kihara Institute for Biological Research, Graduate School of Integrated Science, Yokohama City University, Totsuka-ku, Yokohama, Japan.
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36
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Li S, Motavaze K, Kafes E, Suntharalingam S, Lakin-Thomas P. A new mutation affecting FRQ-less rhythms in the circadian system of Neurospora crassa. PLoS Genet 2011; 7:e1002151. [PMID: 21731506 PMCID: PMC3121751 DOI: 10.1371/journal.pgen.1002151] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2010] [Accepted: 05/09/2011] [Indexed: 11/23/2022] Open
Abstract
We are using the fungus Neurospora crassa as a model organism to study the circadian system of eukaryotes. Although the FRQ/WCC feedback loop is said to be central to the circadian system in Neurospora, rhythms can still be seen under many conditions in FRQ-less (frq knockout) strains. To try to identify components of the FRQ-less oscillator (FLO), we carried out a mutagenesis screen in a FRQ-less strain and selected colonies with altered conidiation (spore-formation) rhythms. A mutation we named UV90 affects rhythmicity in both FRQ-less and FRQ-sufficient strains. The UV90 mutation affects FRQ-less rhythms in two conditions: the free-running long-period rhythm in choline-depleted chol-1 strains becomes arrhythmic, and the heat-entrained rhythm in the frq10 knockout is severely altered. In a FRQ-sufficient background, the UV90 mutation causes damping of the free-running conidiation rhythm, reduction of the amplitude of the FRQ protein rhythm, and increased phase-resetting responses to both light and heat pulses, consistent with a decreased amplitude of the circadian oscillator. The UV90 mutation also has small but significant effects on the period of the conidiation rhythm and on growth rate. The wild-type UV90 gene product appears to be required for a functional FLO and for sustained, high-amplitude rhythms in FRQ-sufficient conditions. The UV90 gene product may therefore be a good candidate for a component of the FRQ-less oscillator. These results support a model of the Neurospora circadian system in which the FRQ/WCC feedback loop mutually interacts with a single FLO in an integrated circadian system. All eukaryotes (including humans), and some bacteria, have evolved internal biological clocks that control activity and physiology in a daily (circadian) cycle. The molecular oscillators that drive these circadian rhythms are said to depend on rhythmic expression and feedback regulation of a small set of “clock genes.” However, there is increasing evidence that there is more to the story than these well-studied feedback loops. In the fungus Neurospora crassa, rhythms can still be seen in mutants that are missing one of the clock genes, frq. There is currently a controversy as to whether there are many different frq-less oscillators and whether they interact with the frq clock. To identify the molecular mechanism that drives these frq-less rhythms, we started with a frq-less strain and mutagenized it to look for genes that affect the frq-less rhythms. We found a new mutation that not only disrupted two frq-less rhythms but also affected the rhythm when the frq gene is present. Our results suggest there is only one frq-less oscillator, and it interacts with the frq clock. Our new mutation may identify a gene that is critical to both oscillators. We suggest that a similar clock architecture may be common to all organisms.
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Affiliation(s)
- Sanshu Li
- Department of Biology, York University, Toronto, Canada
| | - Kamyar Motavaze
- Department of Biology, York University, Toronto, Canada
- Department of Microbiology, Tehran North Branch, Islamic Azad University, Tehran, Iran
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37
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Abstract
Light not only is indispensable as an energy source for life on earth but also serves as an essential environmental cue conveying the information of daily and seasonal time to organisms across different kingdoms. Although the molecular mechanisms underlying light responses are actively explored in various light-sensitive organisms, these studies are either hindered by the complexity of the systems or an incomplete familiarity with the light signaling components involved in the scheme. Therefore, study of a simple and well-characterized model system is desirable to expand our knowledge of basic properties underlying the regulation of biological light responses. This review will briefly introduce the basic light sensing machinery in Neurospora crassa, a filamentous fungus, and then focus on the most recent advances in employing Neurospora as a model to study light signaling cascades, photoadaptation, and circadian clock-modulated effects in eukaryotic cells. Also, we will summarize the functions of a number of putative photoreceptors in Neurospora, and discuss the implications of the study of Neurospora to the field of fungal photobiology and some challenges for future studies.
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Affiliation(s)
- Chen-Hui Chen
- Department of Genetics, Dartmouth Medical School, Hanover, NH 03755
| | - Jay C. Dunlap
- Department of Genetics, Dartmouth Medical School, Hanover, NH 03755
| | - Jennifer J. Loros
- Department of Biochemistry, Dartmouth Medical School, Hanover, NH 03755
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38
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Abstract
Neurospora crassa has been systematically investigated for circadian entrainment behavior. Many aspects of synchronization can be investigated in this simple, cellular system, ranging from systematic entrainment and drivenness to masking. Clock gene expression during entrainment and entrainment without clock genes suggest that the known transcription/translation feedback loop is not alone responsible for entrainment in Neurospora.
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Affiliation(s)
- Martha Merrow
- Biologisch Centrum, University of Groningen, Haren, The Netherlands.
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39
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Abstract
Light and temperature are major environmental cues that influence circadian clocks. The molecular effects of these zeitgebers on the circadian clock of Neurospora crassa have been studied intensively during the last decade. While signal transduction of light into the circadian clock is quite well characterized, we have only recently begun to understand the molecular mechanisms that underlie temperature sensing. Here we summarize briefly the current knowledge about the effects of temperature on the circadian clock of Neurospora crassa.
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Affiliation(s)
- Michael Brunner
- University of Heidelberg (BZH), Biochemistry Center, Heidelberg, Germany
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40
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Abstract
Posttranslational modification of circadian clock proteins by phosphorylation is an essential regulatory process in the control of eukaryotic circadian clocks. In the Neurospora circadian clock, the key clock protein FREQUENCY (FRQ) is progressively phosphorylated. The phosphorylation of FRQ is regulated by both kinases and phosphatases, and the phosphorylation is important for regulating FRQ stability and its function in the circadian negative feedback loop. The degradation of FRQ is mediated by the ubiquitin/proteasome pathway. This article discusses posttranslational regulations of the Neurospora clock and describes the methods used in the studies of FRQ phosphorylation, FRQ kinases and phosphatases, and FRQ degradation.
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Affiliation(s)
- Yi Liu
- Department of Physiology, University of Texas Southwestern Medical Center, Dallas, Texas 75390, USA
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41
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Lew RR, Abbas Z, Anderca MI, Free SJ. Phenotype of a mechanosensitive channel mutant, mid-1, in a filamentous fungus, Neurospora crassa. Eukaryot Cell 2008; 7:647-55. [PMID: 18296620 PMCID: PMC2292622 DOI: 10.1128/ec.00411-07] [Citation(s) in RCA: 39] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/08/2007] [Accepted: 02/12/2008] [Indexed: 12/21/2022]
Abstract
In the yeast Saccharomyces cerevisiae, the MID1 (mating-induced death) gene encodes a stretch-activated channel which is required for successful mating; the mutant phenotype is rescued by elevated extracellular calcium. Homologs of the MID1 gene are found in fungi that are morphologically complex compared to yeast, both Basidiomycetes and Ascomycetes. We explored the phenotype of a mid-1 knockout mutant in the filamentous ascomycete Neurospora crassa. The mutant exhibits lower growth vigor than the wild type (which is not rescued by replete calcium) and mates successfully. Thus, the role of the MID-1 protein differs from that of the homologous gene product in yeast. Hyphal cytology, growth on diverse carbon sources, turgor regulation, and circadian rhythms of the mid-1 mutant are all similar to those of the wild type. However, basal turgor is lower than wild type, as is the activity of the plasma membrane H(+)-ATPase (measured by cyanide [CN(-)]-induced depolarization of the energy-dependent component of the membrane potential). In addition, the mutant is unable to grow at low extracellular Ca(2+) levels or when cytoplasmic Ca(2+) is elevated with the Ca(2+) ionophore A23187. We conclude that the MID-1 protein plays a role in regulation of ion transport via Ca(2+) homeostasis and signaling. In the absence of normal ion transport activity, the mutant exhibits poorer growth.
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Affiliation(s)
- Roger R Lew
- Department of Biology, York University, 4700 Keele Street, Toronto, Ontario M3J 1P3, Canada.
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42
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Gessler NN, Rudchenko MN, Belozerskaia TA. [Stress factor-induced changes in the activity of antioxidant protective mechanisms in the wild type strain of Neurospora crassa and in its photoreceptor complex mutants]. Mikrobiologiia 2008; 77:163-170. [PMID: 18522316] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 05/26/2023]
Abstract
The effect of stress factors (changes in oxygen content, temperature, and illumination) on superoxide dismutase (SOD) and catalase activity, as well as on the content of thiol and disulfide groups in low-molecular-weight compounds and proteins of Neurospora crassa mycelium was studied in the wild type strain and white collar-1 (wc-1) and white collar-2 (wc-2) mutants. Environmental stress factors induced the activation of both SOD and catalase, as well as an increase in the thiol level in the wild type strain of Neurospora crassa. In the wc-1 and wc-2 mutants, an increase in catalase activity and in the total thiol level was revealed; however, activation of superoxide dismutase was not observed. A decrease in the formation of disulfide bonds in the proteins of wc-1 and wc-2 mutants (as compared with the wild type strain) was recorded. These results indicate disrupted transduction in the WCC mutants of stress factor signals that promote ROS (reactive oxygen species) formation.
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43
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Abstract
Circadian clocks drive daily rhythms in physiology and behaviour, and thus allow organisms to better adapt to rhythmic changes in the environment. Circadian oscillators are cell-autonomous systems, which generate via transcriptional, post-transcriptional, translational and post-translational control mechanisms a daily activity-rhythm of a circadian transcription factor complex. According to recent models, this complex of transcription factors controls directly or indirectly expression of a large number of genes, and thus generates the potential to modulate physiological processes in a rhythmic fashion. The basic principles of the generation of circadian oscillation are similar in all eukaryotic systems. The circadian clock of the filamentous fungus Neurospora crassa is well characterized at the molecular level. Focusing on the molecular properties, interactions and post-translational modifications of the core Neurospora clock proteins WHITE COLLAR-1, WHITE COLLAR-2, FREQUENCY and VIVID, this review summarizes our knowledge of the molecular basis of circadian time keeping in Neurospora. Moreover, we discuss the mechanisms by which environmental cues like light and temperature entrain and reset this circadian system.
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Affiliation(s)
- Michael Brunner
- University of Heidelberg Biochemistry Center, Im Neuenheimer Feld 328, 69120 Heidelberg, Germany
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44
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Akman OE, Locke JCW, Tang S, Carré I, Millar AJ, Rand DA. Isoform switching facilitates period control in the Neurospora crassa circadian clock. Mol Syst Biol 2008; 4:164. [PMID: 18277380 PMCID: PMC2267733 DOI: 10.1038/msb.2008.5] [Citation(s) in RCA: 29] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2007] [Accepted: 12/21/2007] [Indexed: 11/09/2022] Open
Abstract
A striking and defining feature of circadian clocks is the small variation in period over a physiological range of temperatures. This is referred to as temperature compensation, although recent work has suggested that the variation observed is a specific, adaptive control of period. Moreover, given that many biological rate constants have a Q(10) of around 2, it is remarkable that such clocks remain rhythmic under significant temperature changes. We introduce a new mathematical model for the Neurospora crassa circadian network incorporating experimental work showing that temperature alters the balance of translation between a short and long form of the FREQUENCY (FRQ) protein. This is used to discuss period control and functionality for the Neurospora system. The model reproduces a broad range of key experimental data on temperature dependence and rhythmicity, both in wild-type and mutant strains. We present a simple mechanism utilising the presence of the FRQ isoforms (isoform switching) by which period control could have evolved, and argue that this regulatory structure may also increase the temperature range where the clock is robustly rhythmic.
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Affiliation(s)
- Ozgur E Akman
- Interdisciplinary Programme for Cellular Regulation, University of Warwick, Coventry, UK
- Systems Biology Centre, University of Warwick, Coventry, UK
- Mathematics Institute, University of Warwick, Coventry, UK
| | - James C W Locke
- Interdisciplinary Programme for Cellular Regulation, University of Warwick, Coventry, UK
- Department of Physics, University of Warwick, Coventry, UK
| | - Sanyi Tang
- Interdisciplinary Programme for Cellular Regulation, University of Warwick, Coventry, UK
- Systems Biology Centre, University of Warwick, Coventry, UK
- Mathematics Institute, University of Warwick, Coventry, UK
| | - Isabelle Carré
- Department of Biological Sciences, University of Warwick, Coventry, UK
| | - Andrew J Millar
- Interdisciplinary Programme for Cellular Regulation, University of Warwick, Coventry, UK
- School of Biological Sciences, University of Edinburgh, Edinburgh, UK
| | - David A Rand
- Interdisciplinary Programme for Cellular Regulation, University of Warwick, Coventry, UK
- Systems Biology Centre, University of Warwick, Coventry, UK
- Mathematics Institute, University of Warwick, Coventry, UK
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45
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Ziv C, Gorovits R, Yarden O. Carbon source affects PKA-dependent polarity of Neurospora crassa in a CRE-1-dependent and independent manner. Fungal Genet Biol 2008; 45:103-16. [PMID: 17625933 DOI: 10.1016/j.fgb.2007.05.005] [Citation(s) in RCA: 40] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2007] [Revised: 05/07/2007] [Accepted: 05/22/2007] [Indexed: 11/21/2022]
Abstract
A defect in mcb, encoding the cAMP-dependent protein kinase A (PKA) regulatory subunit in Neurospora crassa, which confers an apolar growth phenotype, is accompanied by an increase in PKA activity levels. Both PKA and CRE-1 [a key carbon catabolite repression (CCR) regulator] mediate the cellular response to carbon-source availability. Inactivation of the cre-1 gene resulted in reduced growth rate, abnormal hyphal morphology and altered CCR. Both PKA and CRE-1 affected morphology in a carbon-dependent manner, as fructose suppressed the apolar morphology of the mcb strain and enabled faster growth of the Deltacre-1 mutant. An increase in cre-1 transcript abundance was observed in mcb and a reduction in PKA activity levels was measured in Deltacre-1. CRE-1 is involved in determining PKA-dependent polarity, as an mcb;Deltacre-1 strain displayed partial reestablishment of hyphal polarity. Taken together, our results demonstrate regulatory interactions between PKA and CRE-1 that affect cell polarity in a filamentous fungus.
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Affiliation(s)
- Carmit Ziv
- Department of Plant Pathology and Microbiology, The Otto Warburg Minerva Center for Agricultural Biotechnology, Faculty of Agricultural, Food and Environmental Quality Sciences, The Hebrew University of Jerusalem, Rehovot 76100, Israel
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46
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Abstract
The internal hydrostatic pressure (turgor) of fungal cells is maintained at 400-500 kPa. The turgor is regulated by changes in ion flux and by production of the osmotically active metabolite glycerol. In Neurospora crassa, there are at least two genetically distinct pathways that function in adaptation to hyperosmotic shock. One involves a mitogen-activated protein (MAP) kinase cascade (kinases OS-4, OS-5 and OS-2 downstream of the osmosensing OS-1); the other is less understood, but involves the cut gene, which encodes a putative phosphatase. This study examined turgor regulation, electrical responses, ion fluxes and glycerol accumulation in the cut mutant. Turgor recovery after hyperosmotic treatment was similar to that in the wild-type, for both time-course ( approximately 40 min) and magnitude. Prior to turgor recovery, the hyperosmotic shock caused a rapid transient depolarization of the membrane potential, followed by a sustained hyperpolarization that occurred concomitant with increased H(+) efflux, indicating that the plasma membrane H(+)-ATPase was being activated. These changes also occurred in the wild-type. Net fluxes of Ca(2+) and Cl(-) during turgor recovery were similar to those in the wild-type, but K(+) influx was attenuated in the cut mutant. The similar turgor recovery can be explained by the ion uptake, since glycerol did not accumulate in the cut mutant within the time frame of turgor recovery (but did accumulate in the wild-type). The results suggest that turgor regulation involves multi-faceted coordination of both ion flux and glycerol accumulation. Ion uptake is activated by a MAP kinase cascade, while CUT is required for glycerol accumulation.
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Affiliation(s)
- Roger R Lew
- Department of Biology, York University, 4700 Keele Street, Toronto, ON M3J 1P3, Canada
| | - Natalia N Levina
- Department of Biology, York University, 4700 Keele Street, Toronto, ON M3J 1P3, Canada
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47
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Dong W, Tang X, Yu Y, Griffith J, Nilsen R, Choi D, Baldwin J, Hilton L, Kelps K, Mcguire J, Morgan R, Smith M, Case M, Arnold J, Schüttler HB, Wang Q, Liu J, Reeves J, Logan D. Systems biology of the neurospora biological clock. IET Syst Biol 2007; 1:257-65. [PMID: 17907673 DOI: 10.1049/iet-syb:20060080] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022] Open
Abstract
A major challenge of systems biology is explaining complex traits, such as the biological clock, in terms of the kinetics of macromolecules. The clock poses at least four challenges for systems biology: (i) identifying the genetic network to explain the clock mechanism quantitatively; (ii) specifying the clock's functional connection to a thousand or more genes and their products in the genome; (iii) explaining the clock's response to light and other environmental cues; and (iv) explaining how the clock's genetic network evolves. Here, the authors illustrate an approach to these problems by fitting an ensemble of genetic networks to microarray data derived from oligonucleotide arrays with approximately all 11 000 Neurospora crassa genes represented. A promising genetic network for the clock mechanism is identified.
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Affiliation(s)
- W Dong
- Genetics Department, University of Georgia, Athens, GA 30602, USA
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48
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Uchida M, Mouriño-Pérez RR, Freitag M, Bartnicki-García S, Roberson RW. Microtubule dynamics and the role of molecular motors in Neurospora crassa. Fungal Genet Biol 2007; 45:683-92. [PMID: 18069024 DOI: 10.1016/j.fgb.2007.10.013] [Citation(s) in RCA: 29] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2007] [Revised: 10/15/2007] [Accepted: 10/19/2007] [Indexed: 11/17/2022]
Abstract
Live-cell imaging methods were used to study microtubule dynamics in the apical regions of leading hyphae and germ tubes of Neurospora crassa expressing beta-tubulin-GFP. Microtubule polymerization rates in hyphae of N. crassa were much faster than those previously reported in any other eukaryotic organism. In order to address the roles of motor proteins in microtubule dynamic instability in N. crassa, the microtubule-motor mutant strains, Deltankin and ro-1, were examined. Polymerization and depolymerization rates in leading hyphae of these strains were reduced by one half relative to the wild type. Furthermore, microtubules in germ tubes of wild type and microtubule-motor mutants exhibited similar dynamic characteristics as those in hyphae of mutant strains. Small microtubule fragments exhibiting anterograde and retrograde motility were present in leading hyphae of all strains and germ tubes of wild-type strains. Our data suggest that microtubule motors play important roles in regulating microtubule dynamic instability in leading hyphae but not in germ tubes.
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Affiliation(s)
- Maho Uchida
- School of Life Sciences, Arizona State University, Tempe, AZ 85287-4501, USA
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49
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Rensing L, Kallies A, Gebauer G, Mohsenzadeh S. The effects of temperature change on the circadian clock of Neurospora. Ciba Found Symp 2007; 183:26-41; discussion 41-50. [PMID: 7656690 DOI: 10.1002/9780470514597.ch3] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/26/2023]
Abstract
The phase resetting of the circadian oscillatory system by pulses of increased temperature (zeitgebers) and the temperature compensation of its period length during longer exposures are major features of the system, but are not well understood in molecular terms. In Neurospora crassa, the effects of pulses of increased temperature on the circadian rhythm of conidiation were determined and possible inputs to the oscillatory system tested, including changes in cyclic 3',5'-adenosine monophosphate (cAMP), inositol 1,4,5-trisphosphate and H+ concentrations, as well as changes of phosphorylation, synthesis and degradation of proteins. Following the kinetics of these parameters during exposure to increased temperature showed transient changes. Experimental manipulation of cAMP, Ca2+ and H+ levels, and of the synthesis and, possibly, degradation of proteins, resulted in phase shifts of the oscillatory system. It is assumed that the temperature signal affects the oscillator(s) by multiple pathways and shifts the whole state of the oscillatory system. Second messenger levels, protein synthesis and protein degradation show adaptation to longer exposures to elevated temperature which may be involved in the temperature compensation of the period length. The temperature compensation is also proposed to involve a shift in the state of all or most oscillator variables.
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Affiliation(s)
- L Rensing
- Department of Biology, University of Bremen, Germany
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50
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Hunt SM, Elvin M, Crosthwaite SK, Heintzen C. The PAS/LOV protein VIVID controls temperature compensation of circadian clock phase and development in Neurospora crassa. Genes Dev 2007; 21:1964-74. [PMID: 17671094 PMCID: PMC1935033 DOI: 10.1101/gad.437107] [Citation(s) in RCA: 43] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
Abstract
Circadian clocks are cellular timekeepers that regulate aspects of temporal organization on daily and seasonal time scales. To allow accurate time measurement, the period lengths of clocks are conserved in a range of temperatures--a phenomenon known as temperature compensation. Temperature compensation of circadian clock period aids in maintaining a stable "target time" or phase of clock-controlled events. Here we show that the Neurospora protein VIVID (VVD) buffers the circadian system against temperature fluctuations. In vvd-null mutants, the circadian period of clock-controlled events such as asexual sporulation (conidiation) is temperature compensated, but the phase of this clock time marker is not. Consistent with delayed conidiation at lower temperatures in vvd(KO) strains, the levels of vvd gene products in the wild type increase with decreasing temperatures. Moreover, vvd(C108A) mutants that lack the light function of VVD maintain a dark activity that transiently influences the phase of conidiation, indicating that VVD influences the time of conidiation downstream from the clock. FREQUENCY (FRQ) phosphorylation is altered in a vvd(KO) strain, suggesting a mechanism by which VVD can influence the timing of clock-controlled processes in the dark. Thus, temperature compensation of clock-controlled output is a key factor in maintaining temperature compensation of the entire circadian system.
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Affiliation(s)
- Suzanne M. Hunt
- Faculty of Life Sciences, The University of Manchester, Manchester M13 9PT, United Kingdom
| | - Mark Elvin
- Faculty of Life Sciences, The University of Manchester, Manchester M13 9PT, United Kingdom
| | - Susan K. Crosthwaite
- Faculty of Life Sciences, The University of Manchester, Manchester M13 9PT, United Kingdom
| | - Christian Heintzen
- Faculty of Life Sciences, The University of Manchester, Manchester M13 9PT, United Kingdom
- Corresponding author.E-MAIL ; FAX 44-0161-275-5082
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