1
|
Schalamun M, Beier S, Hinterdobler W, Wanko N, Schinnerl J, Brecker L, Engl DE, Schmoll M. MAPkinases regulate secondary metabolism, sexual development and light dependent cellulase regulation in Trichoderma reesei. Sci Rep 2023; 13:1912. [PMID: 36732590 PMCID: PMC9894936 DOI: 10.1038/s41598-023-28938-w] [Citation(s) in RCA: 9] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2022] [Accepted: 01/27/2023] [Indexed: 02/04/2023] Open
Abstract
The filamentous fungus Trichoderma reesei is a prolific producer of plant cell wall degrading enzymes, which are regulated in response to diverse environmental signals for optimal adaptation, but also produces a wide array of secondary metabolites. Available carbon source and light are the strongest cues currently known to impact secreted enzyme levels and an interplay with regulation of secondary metabolism became increasingly obvious in recent years. While cellulase regulation is already known to be modulated by different mitogen activated protein kinase (MAPK) pathways, the relevance of the light signal, which is transmitted by this pathway in other fungi as well, is still unknown in T. reesei as are interconnections to secondary metabolism and chemical communication under mating conditions. Here we show that MAPkinases differentially influence cellulase regulation in light and darkness and that the Hog1 homologue TMK3, but not TMK1 or TMK2 are required for the chemotropic response to glucose in T. reesei. Additionally, MAPkinases regulate production of specific secondary metabolites including trichodimerol and bisorbibutenolid, a bioactive compound with cytostatic effect on cancer cells and deterrent effect on larvae, under conditions facilitating mating, which reflects a defect in chemical communication. Strains lacking either of the MAPkinases become female sterile, indicating the conservation of the role of MAPkinases in sexual fertility also in T. reesei. In summary, our findings substantiate the previously detected interconnection of cellulase regulation with regulation of secondary metabolism as well as the involvement of MAPkinases in light dependent gene regulation of cellulase and secondary metabolite genes in fungi.
Collapse
Affiliation(s)
- Miriam Schalamun
- Center for Health and Bioresources, Bioresources Unit, AIT Austrian Institute of Technology GmbH, Konrad Lorenz Strasse 24, 3430, Tulln, Austria
| | - Sabrina Beier
- Center for Health and Bioresources, Bioresources Unit, AIT Austrian Institute of Technology GmbH, Konrad Lorenz Strasse 24, 3430, Tulln, Austria
| | - Wolfgang Hinterdobler
- Center for Health and Bioresources, Bioresources Unit, AIT Austrian Institute of Technology GmbH, Konrad Lorenz Strasse 24, 3430, Tulln, Austria
- MyPilz GmbH, Wienerbergstrasse 55/13-15, 1120, Vienna, Austria
| | - Nicole Wanko
- Center for Health and Bioresources, Bioresources Unit, AIT Austrian Institute of Technology GmbH, Konrad Lorenz Strasse 24, 3430, Tulln, Austria
| | - Johann Schinnerl
- Department of Botany and Biodiversity Research, University of Vienna, Rennweg 14, 1030, Vienna, Austria
| | - Lothar Brecker
- Department of Organic Chemistry, University of Vienna, Währinger Strasse 38, 1090, Vienna, Austria
| | - Dorothea Elisa Engl
- Department of Organic Chemistry, University of Vienna, Währinger Strasse 38, 1090, Vienna, Austria
| | - Monika Schmoll
- Center for Health and Bioresources, Bioresources Unit, AIT Austrian Institute of Technology GmbH, Konrad Lorenz Strasse 24, 3430, Tulln, Austria.
- Division of Terrestrial Ecosystem Research, Department of Microbiology and Ecosystem Science, University of Vienna, Djerassiplatz 1, 1030, Vienna, Austria.
| |
Collapse
|
2
|
Henríquez-Urrutia M, Spanner R, Olivares-Yánez C, Seguel-Avello A, Pérez-Lara R, Guillén-Alonso H, Winkler R, Herrera-Estrella AH, Canessa P, Larrondo LF. Circadian oscillations in Trichoderma atroviride and the role of core clock components in secondary metabolism, development, and mycoparasitism against the phytopathogen Botrytis cinerea. eLife 2022; 11:71358. [PMID: 35950750 PMCID: PMC9427114 DOI: 10.7554/elife.71358] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2021] [Accepted: 08/10/2022] [Indexed: 11/13/2022] Open
Abstract
Circadian clocks are important for an individual’s fitness, and recent studies have underlined their role in the outcome of biological interactions. However, the relevance of circadian clocks in fungal–fungal interactions remains largely unexplored. We sought to characterize a functional clock in the biocontrol agent Trichoderma atroviride to assess its importance in the mycoparasitic interaction against the phytopathogen Botrytis cinerea. Thus, we confirmed the existence of circadian rhythms in T. atroviride, which are temperature-compensated and modulated by environmental cues such as light and temperature. Nevertheless, the presence of such molecular rhythms appears to be highly dependent on the nutritional composition of the media. Complementation of a clock null (Δfrq) Neurospora crassa strain with the T. atroviride-negative clock component (tafrq) restored core clock function, with the same period observed in the latter fungus, confirming the role of tafrq as a bona fide core clock component. Confrontation assays between wild-type and clock mutant strains of T. atroviride and B. cinerea, in constant light or darkness, revealed an inhibitory effect of light on T. atroviride’s mycoparasitic capabilities. Interestingly, when confrontation assays were performed under light/dark cycles, T. atroviride’s overgrowth capacity was enhanced when inoculations were at dawn compared to dusk. Deleting the core clock-negative element FRQ in B. cinerea, but not in T. atroviride, was vital for the daily differential phenotype, suggesting that the B. cinerea clock has a more significant influence on the result of this interaction. Additionally, we observed that T. atroviride clock components largely modulate development and secondary metabolism in this fungus, including the rhythmic production of distinct volatile organic compounds (VOCs). Thus, this study provides evidence on how clock components impact diverse aspects of T. atroviride lifestyle and how daily changes modulate fungal interactions and dynamics.
Collapse
Affiliation(s)
- Marlene Henríquez-Urrutia
- Molecular Genetics and Microbiology department, Pontificia Universidad Católica de Chile, Santiago, Chile
| | - Rebecca Spanner
- Molecular Genetics and Microbiology department, Pontificia Universidad Católica de Chile, Santiago, Chile
| | - Consuelo Olivares-Yánez
- Millennium Science Initiative Program, Millennium Institute for Integrative Biology, Santiago, Chile
| | - Aldo Seguel-Avello
- Molecular Genetics and Microbiology department, Pontificia Universidad Católica de Chile, Santiago, Chile
| | - Rodrigo Pérez-Lara
- Molecular Genetics and Microbiology department, Pontificia Universidad Católica de Chile, Santiago, Chile
| | - Hector Guillén-Alonso
- Department of Biotechnology and Biochemistry, Cinvestav Unidad Irapuato, Irapuato, Mexico
| | - Robert Winkler
- Department of Biotechnology and Biochemistry, Cinvestav Unidad Irapuato, Irapuato, Mexico
| | | | - Paulo Canessa
- Centro de Biotecnología Vegetal, Universidad Andrés Bello, Santiago, Chile
| | - Luis F Larrondo
- Molecular Genetics and Microbiology department, Pontificia Universidad Católica de Chile, Santiago, Chile
| |
Collapse
|
3
|
Schmoll M, Sanz C, Zhang W. Editorial: Light Regulation of Metabolic Networks in Microbes. Front Microbiol 2022; 13:829106. [PMID: 35197956 PMCID: PMC8859093 DOI: 10.3389/fmicb.2022.829106] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2021] [Accepted: 01/10/2022] [Indexed: 11/17/2022] Open
Affiliation(s)
- Monika Schmoll
- AIT Austrian Institute of Technology GmbH, Center for Health and Bioresources, Tulln, Austria
- *Correspondence: Monika Schmoll
| | - Catalina Sanz
- Department of Microbiology and Genetics, University of Salamanca, Salamanca, Spain
| | - Weiwen Zhang
- Laboratory of Synthetic Microbiology, School of Chemical Engineering and Technology, Tianjin University, Tianjin, China
| |
Collapse
|
4
|
Burt P, Grabe S, Madeti C, Upadhyay A, Merrow M, Roenneberg T, Herzel H, Schmal C. Principles underlying the complex dynamics of temperature entrainment by a circadian clock. iScience 2021; 24:103370. [PMID: 34816105 PMCID: PMC8593569 DOI: 10.1016/j.isci.2021.103370] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2021] [Revised: 09/01/2021] [Accepted: 10/25/2021] [Indexed: 01/20/2023] Open
Abstract
Autonomously oscillating circadian clocks resonate with daily environmental (zeitgeber) rhythms to organize physiology around the solar day. Although entrainment properties and mechanisms have been studied widely and in great detail for light-dark cycles, entrainment to daily temperature rhythms remains poorly understood despite that they are potent zeitgebers. Here we investigate the entrainment of the chronobiological model organism Neurospora crassa, subject to thermocycles of different periods and fractions of warm versus cold phases, mimicking seasonal variations. Depending on the properties of these thermocycles, regularly entrained rhythms, period-doubling (frequency demultiplication) but also irregular aperiodic behavior occurs. We demonstrate that the complex nonlinear phenomena of experimentally observed entrainment dynamics can be understood by molecular mathematical modeling.
Collapse
Affiliation(s)
- Philipp Burt
- Institute for Theoretical Biology, Faculty of Life Sciences, Humboldt-Universität zu Berlin, Unter den Linden 6, 10117 Berlin, Germany
- Institute for Theoretical Biology, Charité Universitätsmedizin Berlin, Charitéplatz 1, 10117 Berlin, Germany
| | - Saskia Grabe
- Institute for Theoretical Biology, Faculty of Life Sciences, Humboldt-Universität zu Berlin, Unter den Linden 6, 10117 Berlin, Germany
- Institute for Theoretical Biology, Charité Universitätsmedizin Berlin, Charitéplatz 1, 10117 Berlin, Germany
| | - Cornelia Madeti
- Institute of Medical Psychology, Faculty of Medicine, LMU Munich, Goethestrasse 31, 80336 Munich, Germany
| | - Abhishek Upadhyay
- Institute for Theoretical Biology, Faculty of Life Sciences, Humboldt-Universität zu Berlin, Unter den Linden 6, 10117 Berlin, Germany
- Institute for Theoretical Biology, Charité Universitätsmedizin Berlin, Charitéplatz 1, 10117 Berlin, Germany
- Friedrich Miescher Institute for Biomedical Research, Maulbeerstrasse 66, 4058 Basel, Switzerland
| | - Martha Merrow
- Institute of Medical Psychology, Faculty of Medicine, LMU Munich, Goethestrasse 31, 80336 Munich, Germany
| | - Till Roenneberg
- Institute of Medical Psychology, Faculty of Medicine, LMU Munich, Goethestrasse 31, 80336 Munich, Germany
| | - Hanspeter Herzel
- Institute for Theoretical Biology, Faculty of Life Sciences, Humboldt-Universität zu Berlin, Unter den Linden 6, 10117 Berlin, Germany
- Institute for Theoretical Biology, Charité Universitätsmedizin Berlin, Charitéplatz 1, 10117 Berlin, Germany
| | - Christoph Schmal
- Institute for Theoretical Biology, Faculty of Life Sciences, Humboldt-Universität zu Berlin, Unter den Linden 6, 10117 Berlin, Germany
- Institute for Theoretical Biology, Charité Universitätsmedizin Berlin, Charitéplatz 1, 10117 Berlin, Germany
| |
Collapse
|
5
|
Veronda AC, Kline CE, Irish LA. The impact of circadian timing on energy balance: an extension of the energy balance model. Health Psychol Rev 2021; 16:161-203. [PMID: 34387140 DOI: 10.1080/17437199.2021.1968310] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Abstract
A significant proportion of the population is classified as having overweight or obesity. One framework which has attempted to explain biobehavioral mechanisms influencing the development of overweight and obesity is the energy balance model. According to this model, the body continually attempts to balance energy intake with energy expenditure. When energy intake and energy expenditure become imbalanced, there is an increase in homeostatic and allostatic pressure, generally to either increase energy intake or decrease energy expenditure, so as to restore energy homeostasis.Recent research has indicated that circadian aspects of energy intake and energy expenditure may influence energy balance. This paper provides a narrative review of existing evidence of the role of circadian timing on components of energy balance. Research on the timing of food intake, physical activity, and sleep indicates that unhealthy timing is likely to increase risk of weight gain. Public health guidelines focus on how much individuals eat and sleep, what foods are consumed, and the type and frequency of exercise, but the field of circadian science has begun to demonstrate that when these behaviors occur may also influence overweight and obesity prevention and treatment efforts.
Collapse
Affiliation(s)
- Allison C Veronda
- Department of Psychology, North Dakota State University, Fargo, ND, USA
| | - Christopher E Kline
- Department of Health and Human Development, University of Pittsburgh, Pittsburgh, PA, USA
| | - Leah A Irish
- Department of Psychology, North Dakota State University, Fargo, ND, USA.,Sanford Center for Biobehavioral Research, Sanford Research, Fargo, ND, USA
| |
Collapse
|
6
|
Wang T, Guan W, Du Y, Xu Y, He Z, Zhang Y, Kang C, Wan X, Chi X, Sun K, Zhang X. Proteome-wide analyses reveal diverse functions of acetylation proteins in Neurospora crassa. Proteomics 2021; 21:e2000212. [PMID: 33491270 DOI: 10.1002/pmic.202000212] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2020] [Revised: 12/15/2020] [Accepted: 01/12/2021] [Indexed: 11/07/2022]
Abstract
Quantitative acetyl-proteomics, a newly identified post-translational modification, is known to regulate transcriptional activity in different organisms. Neurospora crassa is a model ascomycete fungus maintained for biochemistry and molecular biology research; however, extensive studies of the functions of its acylation proteins have yet to be performed. In this study, using LC-MS/MS qualitative proteomics strategies, we identified 1909 modification sites on 940 proteins in N. crassa and analysed the functions of these proteins using GO enrichment, KEGG pathway, and subcellular location experiments. We classified the acetylation protein involvement in diverse pathways, and protein-protein interaction (PPI) network analysis further demonstrated that these proteins participate in diverse biological processes. In summary, our study comprehensively profiles the crosstalk of modified sites, and PPI among these proteins may form a complex network with both similar and distinct regulatory mechanisms, providing improved understanding of their biological functions in N. crassa.
Collapse
Affiliation(s)
- Tielin Wang
- State Key Laboratory Breeding Base of Dao-di Herbs, National Resource Center for Chinese Materia Medica, China Academy of Chinese Medical Sciences, Beijing, China
| | - Wei Guan
- State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Yongxi Du
- State Key Laboratory Breeding Base of Dao-di Herbs, National Resource Center for Chinese Materia Medica, China Academy of Chinese Medical Sciences, Beijing, China
| | - Yang Xu
- State Key Laboratory Breeding Base of Dao-di Herbs, National Resource Center for Chinese Materia Medica, China Academy of Chinese Medical Sciences, Beijing, China
| | - Zhen He
- School of Horticulture and Plant Protection, Yangzhou University, Yangzhou, Jiangsu Province, P. R. China
| | - Yan Zhang
- State Key Laboratory Breeding Base of Dao-di Herbs, National Resource Center for Chinese Materia Medica, China Academy of Chinese Medical Sciences, Beijing, China
| | - Chuanzhi Kang
- State Key Laboratory Breeding Base of Dao-di Herbs, National Resource Center for Chinese Materia Medica, China Academy of Chinese Medical Sciences, Beijing, China
| | - Xiufu Wan
- State Key Laboratory Breeding Base of Dao-di Herbs, National Resource Center for Chinese Materia Medica, China Academy of Chinese Medical Sciences, Beijing, China
| | - Xiulian Chi
- State Key Laboratory Breeding Base of Dao-di Herbs, National Resource Center for Chinese Materia Medica, China Academy of Chinese Medical Sciences, Beijing, China
| | - Kai Sun
- State Key Laboratory Breeding Base of Dao-di Herbs, National Resource Center for Chinese Materia Medica, China Academy of Chinese Medical Sciences, Beijing, China
| | - Xiaobo Zhang
- State Key Laboratory Breeding Base of Dao-di Herbs, National Resource Center for Chinese Materia Medica, China Academy of Chinese Medical Sciences, Beijing, China
| |
Collapse
|
7
|
Díaz RD, Larrondo LF. A circadian clock in Neurospora crassa functions during plant cell wall deconstruction. Fungal Biol 2020; 124:501-508. [PMID: 32389313 DOI: 10.1016/j.funbio.2020.03.003] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2019] [Revised: 03/05/2020] [Accepted: 03/07/2020] [Indexed: 01/24/2023]
Abstract
Circadian clocks are autonomous timers that are believed to confer organisms a selective advantage by enabling processes to occur at appropriate times of the day. In the model fungus Neurospora crassa, 20-40 % of its genes are reported to be under circadian regulation, as assayed in simple sugar media. Although it has been well-described that Neurospora efficiently deconstructs plant cell wall components, little is known regarding the status of the clock when Neurospora grows on cellulosic material, or whether such a clock has an impact on any of the genes involved in this process. Through luciferase-based reporters and fluorescent detection assays, we show that a clock is functioning when Neurospora grows on cellulose-containing wheat straw as the only carbon and nitrogen source. Additionally, we found that the major cellobiohydrolase encoding gene involved in plant cell wall deconstruction, cbh-1, is rhythmically regulated by the Neurospora clock, in a manner that depends on cellulose concentration and on the transcription factor CRE-1, known as a key player in carbon-catabolite repression in this fungus. Our findings are a step towards a more comprehensive understanding on how clock regulation modulates cellulose degradation, and thus Neurospora's physiology.
Collapse
Affiliation(s)
- Rodrigo D Díaz
- Millennium Institute for Integrative Biology, Departamento de Genética Molecular y Microbiología, Facultad de Ciencias Biológicas, Pontificia Universidad Católica de Chile, Casilla 114-D, Santiago, Chile
| | - Luis F Larrondo
- Millennium Institute for Integrative Biology, Departamento de Genética Molecular y Microbiología, Facultad de Ciencias Biológicas, Pontificia Universidad Católica de Chile, Casilla 114-D, Santiago, Chile.
| |
Collapse
|
8
|
Diernfellner AC, Brunner M. Phosphorylation Timers in the Neurospora crassa Circadian Clock. J Mol Biol 2020; 432:3449-3465. [DOI: 10.1016/j.jmb.2020.04.004] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2019] [Revised: 03/10/2020] [Accepted: 04/05/2020] [Indexed: 02/08/2023]
|
9
|
Refinetti R. Circadian rhythmicity of body temperature and metabolism. Temperature (Austin) 2020; 7:321-362. [PMID: 33251281 PMCID: PMC7678948 DOI: 10.1080/23328940.2020.1743605] [Citation(s) in RCA: 44] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2020] [Revised: 03/11/2020] [Accepted: 03/12/2020] [Indexed: 12/19/2022] Open
Abstract
This article reviews the literature on the circadian rhythms of body temperature and whole-organism metabolism. The two rhythms are first described separately, each description preceded by a review of research methods. Both rhythms are generated endogenously but can be affected by exogenous factors. The relationship between the two rhythms is discussed next. In endothermic animals, modulation of metabolic activity can affect body temperature, but the rhythm of body temperature is not a mere side effect of the rhythm of metabolic thermogenesis associated with general activity. The circadian system modulates metabolic heat production to generate the body temperature rhythm, which challenges homeothermy but does not abolish it. Individual cells do not regulate their own temperature, but the relationship between circadian rhythms and metabolism at the cellular level is also discussed. Metabolism is both an output of and an input to the circadian clock, meaning that circadian rhythmicity and metabolism are intertwined in the cell.
Collapse
Affiliation(s)
- Roberto Refinetti
- Department of Psychology, University of New Orleans, New Orleans, LA, USA
| |
Collapse
|
10
|
Horta MAC, Thieme N, Gao Y, Burnum-Johnson KE, Nicora CD, Gritsenko MA, Lipton MS, Mohanraj K, de Assis LJ, Lin L, Tian C, Braus GH, Borkovich KA, Schmoll M, Larrondo LF, Samal A, Goldman GH, Benz JP. Broad Substrate-Specific Phosphorylation Events Are Associated With the Initial Stage of Plant Cell Wall Recognition in Neurospora crassa. Front Microbiol 2019; 10:2317. [PMID: 31736884 PMCID: PMC6838226 DOI: 10.3389/fmicb.2019.02317] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2019] [Accepted: 09/23/2019] [Indexed: 12/26/2022] Open
Abstract
Fungal plant cell wall degradation processes are governed by complex regulatory mechanisms, allowing the organisms to adapt their metabolic program with high specificity to the available substrates. While the uptake of representative plant cell wall mono- and disaccharides is known to induce specific transcriptional and translational responses, the processes related to early signal reception and transduction remain largely unknown. A fast and reversible way of signal transmission are post-translational protein modifications, such as phosphorylations, which could initiate rapid adaptations of the fungal metabolism to a new condition. To elucidate how changes in the initial substrate recognition phase of Neurospora crassa affect the global phosphorylation pattern, phospho-proteomics was performed after a short (2 min) induction period with several plant cell wall-related mono- and disaccharides. The MS/MS-based peptide analysis revealed large-scale substrate-specific protein phosphorylation and de-phosphorylations. Using the proteins identified by MS/MS, a protein-protein-interaction (PPI) network was constructed. The variance in phosphorylation of a large number of kinases, phosphatases and transcription factors indicate the participation of many known signaling pathways, including circadian responses, two-component regulatory systems, MAP kinases as well as the cAMP-dependent and heterotrimeric G-protein pathways. Adenylate cyclase, a key component of the cAMP pathway, was identified as a potential hub for carbon source-specific differential protein interactions. In addition, four phosphorylated F-Box proteins were identified, two of which, Fbx-19 and Fbx-22, were found to be involved in carbon catabolite repression responses. Overall, these results provide unprecedented and detailed insights into a so far less well known stage of the fungal response to environmental cues and allow to better elucidate the molecular mechanisms of sensory perception and signal transduction during plant cell wall degradation.
Collapse
Affiliation(s)
- Maria Augusta C. Horta
- Holzforschung München, TUM School of Life Sciences Weihenstephan, Technical University of Munich, Freising, Germany
| | - Nils Thieme
- Holzforschung München, TUM School of Life Sciences Weihenstephan, Technical University of Munich, Freising, Germany
| | - Yuqian Gao
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, WA, United States
| | | | - Carrie D. Nicora
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, WA, United States
| | - Marina A. Gritsenko
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, WA, United States
| | - Mary S. Lipton
- Environmental Molecular Sciences Laboratory, Pacific Northwest National Laboratory, Richland, WA, United States
| | - Karthikeyan Mohanraj
- The Institute of Mathematical Sciences (IMSc), Homi Bhabha National Institute (HBNI), Chennai, India
| | - Leandro José de Assis
- Faculdade de Ciências Farmacêuticas de Ribeirão Preto, Universidade de São Paulo, Ribeirão Preto, Brazil
| | - Liangcai Lin
- Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, China
| | - Chaoguang Tian
- Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, China
| | - Gerhard H. Braus
- Department of Molecular Microbiology and Genetics, Institute of Microbiology and Genetics, Göttingen Center for Molecular Biosciences, University of Göttingen, Göttingen, Germany
| | - Katherine A. Borkovich
- Department of Microbiology & Plant Pathology, Institute for Integrative Genome Biology, University of California, Riverside, Riverside, CA, United States
| | - Monika Schmoll
- AIT - Austrian Institute of Technology GmbH, Center for Health & Bioresources, Tulln, Austria
| | - Luis F. Larrondo
- Millennium Institute for Integrative Biology (iBio), Departamento Genética Molecular y Microbiología, Facultad de Ciencias Biológicas, Pontificia Universidad Católica de Chile, Santiago, Chile
| | - Areejit Samal
- The Institute of Mathematical Sciences (IMSc), Homi Bhabha National Institute (HBNI), Chennai, India
| | - Gustavo H. Goldman
- Faculdade de Ciências Farmacêuticas de Ribeirão Preto, Universidade de São Paulo, Ribeirão Preto, Brazil
- Institute for Advanced Study, Technical University of Munich, Garching, Germany
| | - J. Philipp Benz
- Holzforschung München, TUM School of Life Sciences Weihenstephan, Technical University of Munich, Freising, Germany
- Institute for Advanced Study, Technical University of Munich, Garching, Germany
| |
Collapse
|
11
|
Lee SJ, Morse D, Hijri M. Holobiont chronobiology: mycorrhiza may be a key to linking aboveground and underground rhythms. MYCORRHIZA 2019; 29:403-412. [PMID: 31190278 DOI: 10.1007/s00572-019-00903-4] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/15/2019] [Accepted: 06/05/2019] [Indexed: 06/09/2023]
Abstract
Circadian clocks are nearly ubiquitous timing mechanisms that can orchestrate rhythmic behavior and gene expression in a wide range of organisms. Clock mechanisms are becoming well understood in fungal, animal, and plant model systems, yet many of these organisms are surrounded by a complex and diverse microbiota which should be taken into account when examining their biology. Of particular interest are the symbiotic relationships between organisms that have coevolved over time, forming a unit called a holobiont. Several studies have now shown linkages between the circadian rhythms of symbiotic partners. Interrelated regulation of holobiont circadian rhythms seems thus important to coordinate shifts in activity over the day for all the partners. Therefore, we suggest that the classical view of "chronobiological individuals" should include "a holobiont" rather than an organism. Unfortunately, mechanisms that may regulate interspecies temporal acclimation and the evolution of the circadian clock in holobionts are far from being understood. For the plant holobiont, our understanding is particularly limited. In this case, the holobiont encompasses two different ecosystems, one above and the other below the ground, with the two potentially receiving timing information from different synchronizing signals (Zeitgebers). The arbuscular mycorrhizal (AM) symbiosis, formed by plant roots and fungi, is one of the oldest and most widespread associations between organisms. By mediating the nutritional flux between the plant and the many microbes in the soil, AM symbiosis constitutes the backbone of the plant holobiont. Even though the importance of the AM symbiosis has been well recognized in agricultural and environmental sciences, its circadian chronobiology remains almost completely unknown. We have begun to study the circadian clock of arbuscular mycorrhizal fungi, and we compile and here discuss the available information on the subject. We propose that analyzing the interrelated temporal organization of the AM symbiosis and determining its underlying mechanisms will advance our understanding of the role and coordination of circadian clocks in holobionts in general.
Collapse
Affiliation(s)
- Soon-Jae Lee
- Institut de Recherche en Biologie Végétale (IRBV), Université de Montréal, 4101 Rue Sherbrooke Est, Montréal, Québec, H1X 2B2, Canada
- Department of Ecology and Evolution, University of Lausanne, 1015, Lausanne, Switzerland
| | - David Morse
- Institut de Recherche en Biologie Végétale (IRBV), Université de Montréal, 4101 Rue Sherbrooke Est, Montréal, Québec, H1X 2B2, Canada
| | - Mohamed Hijri
- Institut de Recherche en Biologie Végétale (IRBV), Université de Montréal, 4101 Rue Sherbrooke Est, Montréal, Québec, H1X 2B2, Canada.
| |
Collapse
|
12
|
Causton HC. Metabolic rhythms: A framework for coordinating cellular function. Eur J Neurosci 2018; 51:1-12. [PMID: 30548718 DOI: 10.1111/ejn.14296] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2018] [Revised: 11/13/2018] [Accepted: 11/19/2018] [Indexed: 01/02/2023]
Abstract
Circadian clocks are widespread among eukaryotes and generally involve feedback loops coupled with metabolic processes and redox balance. The organising power of these oscillations has not only allowed organisms to anticipate day-night cycles, but also acts to temporally compartmentalise otherwise incompatible processes, enhance metabolic efficiency, make the system more robust to noise and propagate signals among cells. While daily rhythms and the function of the circadian transcription-translation loop have been the subject of extensive research over the past four decades, cycles of shorter period and respiratory oscillations, with which they are intertwined, have received less attention. Here, we describe features of yeast respiratory oscillations, which share many features with daily and 12 hr cellular oscillations in animal cells. This relatively simple system enables the analysis of dynamic rhythmic changes in metabolism, independent of cellular oscillations that are a product of the circadian transcription-translation feedback loop. Knowledge gained from studying ultradian oscillations in yeast will lead to a better understanding of the basic mechanistic principles and evolutionary origins of oscillatory behaviour among eukaryotes.
Collapse
Affiliation(s)
- Helen C Causton
- Department of Pathology and Cell Biology, Columbia University Medical Center, New York City, New York
| |
Collapse
|
13
|
Circadian rhythms, metabolic oscillators, and the target of rapamycin (TOR) pathway: the Neurospora connection. Curr Genet 2018; 65:339-349. [DOI: 10.1007/s00294-018-0897-6] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2018] [Revised: 10/09/2018] [Accepted: 10/20/2018] [Indexed: 01/25/2023]
|
14
|
Mwimba M, Karapetyan S, Liu L, Marqués J, McGinnis EM, Buchler NE, Dong X. Daily humidity oscillation regulates the circadian clock to influence plant physiology. Nat Commun 2018; 9:4290. [PMID: 30327472 PMCID: PMC6191426 DOI: 10.1038/s41467-018-06692-2] [Citation(s) in RCA: 27] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2017] [Accepted: 09/20/2018] [Indexed: 01/27/2023] Open
Abstract
Early circadian studies in plants by de Mairan and de Candolle alluded to a regulation of circadian clocks by humidity. However, this regulation has not been described in detail, nor has its influence on physiology been demonstrated. Here we report that, under constant light, circadian humidity oscillation can entrain the plant circadian clock to a period of 24 h probably through the induction of clock genes such as CIRCADIAN CLOCK ASSOCIATED 1. Under simulated natural light and humidity cycles, humidity oscillation increases the amplitude of the circadian clock and further improves plant fitness-related traits. In addition, humidity oscillation enhances effector-triggered immunity at night possibly to counter increased pathogen virulence under high humidity. These results indicate that the humidity oscillation regulates specific circadian outputs besides those co-regulated with the light-dark cycle.
Collapse
Affiliation(s)
- Musoki Mwimba
- Howard Hughes Medical Institute, Duke University, Durham, NC, 27708, USA.,Department of Biology, Duke University, PO Box 90338, Durham, NC, 27708, USA
| | - Sargis Karapetyan
- Department of Biology, Duke University, PO Box 90338, Durham, NC, 27708, USA.,Department of Physics, Duke University, Durham, NC, 27708, USA
| | - Lijing Liu
- Howard Hughes Medical Institute, Duke University, Durham, NC, 27708, USA.,Department of Biology, Duke University, PO Box 90338, Durham, NC, 27708, USA
| | - Jorge Marqués
- Howard Hughes Medical Institute, Duke University, Durham, NC, 27708, USA.,Department of Biology, Duke University, PO Box 90338, Durham, NC, 27708, USA
| | - Erin M McGinnis
- Howard Hughes Medical Institute, Duke University, Durham, NC, 27708, USA.,Department of Biology, Duke University, PO Box 90338, Durham, NC, 27708, USA
| | - Nicolas E Buchler
- Department of Biology, Duke University, PO Box 90338, Durham, NC, 27708, USA.,Department of Physics, Duke University, Durham, NC, 27708, USA.,Department of Molecular Biomedical Sciences, North Carolina State University, Raleigh, NC, 27606, USA
| | - Xinnian Dong
- Howard Hughes Medical Institute, Duke University, Durham, NC, 27708, USA. .,Department of Biology, Duke University, PO Box 90338, Durham, NC, 27708, USA.
| |
Collapse
|
15
|
Lee SJ, Kong M, Morse D, Hijri M. Expression of putative circadian clock components in the arbuscular mycorrhizal fungus Rhizoglomus irregulare. MYCORRHIZA 2018; 28:523-534. [PMID: 29931403 DOI: 10.1007/s00572-018-0843-y] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/04/2018] [Accepted: 06/11/2018] [Indexed: 06/08/2023]
Abstract
Arbuscular mycorrhizal fungi (AMF) are obligatory plant symbionts that live underground, so few studies have examined their response to light. Responses to blue light by other fungi can be mediated by White Collar-1 (WC-1) and WC-2 proteins. These wc genes, together with the frequency gene (frq), also form part of the endogenous circadian clock. The clock mechanism has never been studied in AMF, although circadian growth of their hyphae in the field has been reported. Using both genomic and transcriptomic data, we have found homologs of wc-1, wc-2, and frq and related circadian clock genes in the arbuscular mycorrhizal fungus Rhizoglomus irregulare (synonym Rhizophagus irregularis). Gene expression of wc-1, wc-2, and frq was analyzed using RT-qPCR on RNA extracted from germinating spores and from fungal material cultivated in vitro with transformed carrot roots. We found that all three core clock genes were expressed in both pre- and post-mycorrhizal stages of R. irregulare growth. Similar to the model fungus Neurospora crassa, the core circadian oscillator gene frq was induced by brief light stimulation. The presence of circadian clock and output genes in R. irregulare opens the door to the study of circadian clocks in the fungal partner of plant-AMF symbiosis. Our finding also provides new insight into the evolution of the circadian frq gene in fungi.
Collapse
Affiliation(s)
- Soon-Jae Lee
- Institut de Recherche en Biologie Végétale, Université de Montréal, 4101 Rue Sherbrooke Est, Montréal, Québec, H1X 2B2, Canada
| | - Mengxuan Kong
- Institut de Recherche en Biologie Végétale, Université de Montréal, 4101 Rue Sherbrooke Est, Montréal, Québec, H1X 2B2, Canada
| | - David Morse
- Institut de Recherche en Biologie Végétale, Université de Montréal, 4101 Rue Sherbrooke Est, Montréal, Québec, H1X 2B2, Canada
| | - Mohamed Hijri
- Institut de Recherche en Biologie Végétale, Université de Montréal, 4101 Rue Sherbrooke Est, Montréal, Québec, H1X 2B2, Canada.
| |
Collapse
|
16
|
Ratnayake L, Adhvaryu KK, Kafes E, Motavaze K, Lakin-Thomas P. A component of the TOR (Target Of Rapamycin) nutrient-sensing pathway plays a role in circadian rhythmicity in Neurospora crassa. PLoS Genet 2018; 14:e1007457. [PMID: 29924817 PMCID: PMC6028147 DOI: 10.1371/journal.pgen.1007457] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2017] [Revised: 07/02/2018] [Accepted: 05/31/2018] [Indexed: 01/06/2023] Open
Abstract
The TOR (Target of Rapamycin) pathway is a highly-conserved signaling pathway in eukaryotes that regulates cellular growth and stress responses. The cellular response to amino acids or carbon sources such as glucose requires anchoring of the TOR kinase complex to the lysosomal/vacuolar membrane by the Ragulator (mammals) or EGO (yeast) protein complex. Here we report a connection between the TOR pathway and circadian (daily) rhythmicity. The molecular mechanism of circadian rhythmicity in all eukaryotes has long been thought to be transcription/translation feedback loops (TTFLs). In the model eukaryote Neurospora crassa, a TTFL including FRQ (frequency) and WCC (white collar complex) has been intensively studied. However, it is also well-known that rhythmicity can be seen in the absence of TTFL functioning. We previously isolated uv90 as a mutation that compromises FRQ-less rhythms and also damps the circadian oscillator when FRQ is present. We have now mapped the uv90 gene and identified it as NCU05950, homologous to the TOR pathway proteins EGO1 (yeast) and LAMTOR1 (mammals), and we have named the N. crassa protein VTA (vacuolar TOR-associated protein). The protein is anchored to the outer vacuolar membrane and deletion of putative acylation sites destroys this localization as well as the protein’s function in rhythmicity. A deletion of VTA is compromised in its growth responses to amino acids and glucose. We conclude that a key protein in the complex that anchors TOR to the vacuole plays a role in maintaining circadian (daily) rhythmicity. Our results establish a connection between the TOR pathway and circadian rhythms and point towards a network integrating metabolism and the circadian system. Circadian clocks drive 24-hour rhythms in living things at all levels of organization, from single cells to whole organisms. In spite of the importance of daily clocks for organizing the activities and internal functions of organisms, there are still many unsolved problems concerning the molecular mechanisms. In eukaryotes, a set of “clock proteins” turns on and off specific genes in a 24-hour feedback loop. This “clock gene feedback loop” has been the dominant idea about how clocks work for many years. However, some rhythms can still be seen when these feedback loops are not functioning. Using the fungus Neurospora crassa as a model organism, we have discovered a gene that is important for maintaining rhythms that continue without the known feedback loop. We have found that this gene codes for a protein that was already known to be important in helping cells to adjust their growth rate to adapt to varying availability of nutrients. Because the same gene is found in all eukaryotes, including mammals, this finding may point towards a universal clock mechanism that integrates nutritional needs with daily rhythms.
Collapse
|
17
|
Wohlgemuth R. Horizons of Systems Biocatalysis and Renaissance of Metabolite Synthesis. Biotechnol J 2018; 13:e1700620. [DOI: 10.1002/biot.201700620] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2018] [Revised: 04/26/2018] [Indexed: 12/12/2022]
Affiliation(s)
- Roland Wohlgemuth
- European Federation of Biotechnology; Section on Applied Biocatalysis (ESAB); Theodor-Heuss-Allee 25,Frankfurt am Main 60486 Germany
- Sigma-Aldrich; Member of Merck Group; Industriestrasse 25,Buchs 9470 Switzerland
| |
Collapse
|
18
|
Schmoll M. Regulation of plant cell wall degradation by light in Trichoderma. Fungal Biol Biotechnol 2018; 5:10. [PMID: 29713489 PMCID: PMC5913809 DOI: 10.1186/s40694-018-0052-7] [Citation(s) in RCA: 54] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2018] [Accepted: 03/27/2018] [Indexed: 12/22/2022] Open
Abstract
Trichoderma reesei (syn. Hypocrea jecorina) is the model organism for industrial production of plant cell wall degradating enzymes. The integration of light and nutrient signals for adaptation of enzyme production in T. reesei emerged as an important regulatory mechanism to be tackled for strain improvement. Gene regulation specific for cellulase inducing conditions is different in light and darkness with substantial regulation by photoreceptors. Genes regulated by light are clustered in the genome, with several of the clusters overlapping with CAZyme clusters. Major cellulase transcription factor genes and at least 75% of glycoside hydrolase encoding genes show the potential of light dependent regulation. Accordingly, light dependent protein complex formation occurs within the promoters of cellulases and their regulators. Additionally growth on diverse carbon sources is different between light and darkness and dependent on the presence of photoreceptors in several cases. Thereby, also light intensity plays a regulatory role, with cellulase levels dropping at higher light intensities dependent in the strain background. The heterotrimeric G-protein pathway is the most important nutrient signaling pathway in the connection with light response and triggers posttranscriptional regulation of cellulase expression. All G-protein alpha subunits impact cellulase regulation in a light dependent manner. The downstream cAMP pathway is involved in light dependent regulation as well. Connections between the regulatory pathways are mainly established via the photoreceptor ENV1. The effect of photoreceptors on plant cell wall degradation also occurs in the model filamentous fungus Neurospora crassa. In the currently proposed model, T. reesei senses the presence of plant biomass in its environment by detection of building blocks of cellulose and hemicellulose. Interpretation of the respective signals is subsequently adjusted to the requirements in light and darkness (or on the surface versus within the substrate) by an interconnection of nutrient signaling with light response. This review provides an overview on the importance of light, photoreceptors and related signaling pathways for formation of plant cell wall degrading enzymes in T. reesei. Additionally, the relevance of light dependent gene regulation for industrial fermentations with Trichoderma as well as strategies for exploitation of the observed effects are discussed.
Collapse
Affiliation(s)
- Monika Schmoll
- Center for Health and Bioresources, AIT Austrian Institute of Technology GmbH, Konrad Lorenz Straße 24, 3430 Tulln, Austria
| |
Collapse
|
19
|
Pelham JF, Mosier AE, Hurley JM. Characterizing Time-of-Day Conformational Changes in the Intrinsically Disordered Proteins of the Circadian Clock. Methods Enzymol 2018; 611:503-529. [DOI: 10.1016/bs.mie.2018.08.024] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
|
20
|
de Bekker C, Will I, Hughes DP, Brachmann A, Merrow M. Daily rhythms and enrichment patterns in the transcriptome of the behavior-manipulating parasite Ophiocordyceps kimflemingiae. PLoS One 2017; 12:e0187170. [PMID: 29099875 PMCID: PMC5669440 DOI: 10.1371/journal.pone.0187170] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2017] [Accepted: 10/13/2017] [Indexed: 12/22/2022] Open
Abstract
Various parasite-host interactions that involve adaptive manipulation of host behavior display time-of-day synchronization of certain events. One example is the manipulated biting behavior observed in Carpenter ants infected with Ophiocordyceps unilateralis sensu lato. We hypothesized that biological clocks play an important role in this and other parasite-host interactions. In order to identify candidate molecular clock components, we used two general strategies: bioinformatics and transcriptional profiling. The bioinformatics approach was used to identify putative homologs of known clock genes. For transcriptional profiling, RNA-Seq was performed on 48 h time courses of Ophiocordyceps kimflemingiae (a recently named species of the O. unilateralis complex), whose genome has recently been sequenced. Fungal blastospores were entrained in liquid media under 24 h light-dark (LD) cycles and were harvested at 4 h intervals either under LD or continuous darkness. Of all O. kimflemingiae genes, 5.3% had rhythmic mRNAs under these conditions (JTK Cycle, ≤ 0.057 statistical cutoff). Our data further indicates that a significant number of transcription factors have a peaked activity during the light phase (day time). The expression levels of a significant number of secreted enzymes, proteases, toxins and small bioactive compounds peaked during the dark phase or subjective night. These findings support a model whereby this fungal parasite uses its biological clock for phase-specific activity. We further suggest that this may be a general mechanism involved in parasite-host interactions.
Collapse
Affiliation(s)
- Charissa de Bekker
- University of Central Florida, Department of Biology, Orlando, Florida, United States of America
- LMU Munich, Institute of Medical Psychology, Faculty of Medicine, Munich, Germany
- LMU Munich, Genetics, Faculty of Biology, Planegg-Martinsried, Germany
- * E-mail:
| | - Ian Will
- University of Central Florida, Department of Biology, Orlando, Florida, United States of America
- LMU Munich, Institute of Medical Psychology, Faculty of Medicine, Munich, Germany
| | - David P. Hughes
- Pennsylvania State University, Departments of Biology and Entomology, University Park, Pennsylvania, United States of America
| | - Andreas Brachmann
- LMU Munich, Genetics, Faculty of Biology, Planegg-Martinsried, Germany
| | - Martha Merrow
- LMU Munich, Institute of Medical Psychology, Faculty of Medicine, Munich, Germany
| |
Collapse
|
21
|
Franco DL, Canessa P, Bellora N, Risau-Gusman S, Olivares-Yañez C, Pérez-Lara R, Libkind D, Larrondo LF, Marpegan L. Spontaneous circadian rhythms in a cold-adapted natural isolate of Aureobasidium pullulans. Sci Rep 2017; 7:13837. [PMID: 29062053 PMCID: PMC5653790 DOI: 10.1038/s41598-017-14085-6] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2017] [Accepted: 09/15/2017] [Indexed: 01/01/2023] Open
Abstract
Circadian systems enable organisms to synchronize their physiology to daily and seasonal environmental changes relying on endogenous pacemakers that oscillate with a period close to 24 h even in the absence of external timing cues. The oscillations are achieved by intracellular transcriptional/translational feedback loops thoroughly characterized for many organisms, but still little is known about the presence and characteristics of circadian clocks in fungi other than Neurospora crassa. We sought to characterize the circadian system of a natural isolate of Aureobasidium pullulans, a cold-adapted yeast bearing great biotechnological potential. A. pullulans formed daily concentric rings that were synchronized by light/dark cycles and were also formed in constant darkness with a period of 24.5 h. Moreover, these rhythms were temperature compensated, as evidenced by experiments conducted at temperatures as low as 10 °C. Finally, the expression of clock-essential genes, frequency, white collar-1, white collar-2 and vivid was confirmed. In summary, our results indicate the existence of a functional circadian clock in A. pullulans, capable of sustaining rhythms at very low temperatures and, based on the presence of conserved clock-gene homologues, suggest a molecular and functional relationship to well-described circadian systems.
Collapse
Affiliation(s)
- Diana L Franco
- Instituto de Investigaciones en Biodiversidad y Medio Ambiente (INIBIOMA), Universidad Nacional del Comahue, CONICET, CRUB, San Carlos de Bariloche, Río Negro, Argentina.,Departamento de Física Médica Centro Atómico Bariloche and Instituto Balseiro, CONICET, San Carlos de Bariloche, Río Negro, Argentina
| | - Paulo Canessa
- Centro de Biotecnologia Vegetal, Facultad de Ciencias Biologicas, Universidad Andres Bello, Santiago, Chile.,Millennium Nucleus for Fungal Integrative and Synthetic Biology (MN-FISB), Santiago, Chile
| | - Nicolás Bellora
- Instituto de Investigaciones en Biodiversidad y Medio Ambiente (INIBIOMA), Universidad Nacional del Comahue, CONICET, CRUB, San Carlos de Bariloche, Río Negro, Argentina
| | | | - Consuelo Olivares-Yañez
- Millennium Nucleus for Fungal Integrative and Synthetic Biology (MN-FISB), Santiago, Chile.,Departamento de Genética Molecular y Microbiología, Facultad de Ciencias Biológicas, Pontificia Universidad Católica de Chile, Santiago, Chile
| | - Rodrigo Pérez-Lara
- Millennium Nucleus for Fungal Integrative and Synthetic Biology (MN-FISB), Santiago, Chile.,Departamento de Genética Molecular y Microbiología, Facultad de Ciencias Biológicas, Pontificia Universidad Católica de Chile, Santiago, Chile
| | - Diego Libkind
- Instituto de Investigaciones en Biodiversidad y Medio Ambiente (INIBIOMA), Universidad Nacional del Comahue, CONICET, CRUB, San Carlos de Bariloche, Río Negro, Argentina
| | - Luis F Larrondo
- Millennium Nucleus for Fungal Integrative and Synthetic Biology (MN-FISB), Santiago, Chile.,Departamento de Genética Molecular y Microbiología, Facultad de Ciencias Biológicas, Pontificia Universidad Católica de Chile, Santiago, Chile
| | - Luciano Marpegan
- Departamento de Ciencia y Tecnología, Universidad Nacional de Quilmes, Bernal, Buenos Aires, Argentina.
| |
Collapse
|
22
|
Gyöngyösi N, Szőke A, Ella K, Káldi K. The small G protein RAS2 is involved in the metabolic compensation of the circadian clock in the circadian model Neurospora crassa. J Biol Chem 2017; 292:14929-14939. [PMID: 28729421 DOI: 10.1074/jbc.m117.804922] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2017] [Indexed: 11/06/2022] Open
Abstract
Accumulating evidence from both experimental and clinical investigations indicates a tight interaction between metabolism and circadian timekeeping; however, knowledge of the underlying mechanism is still incomplete. Metabolic compensation allows circadian oscillators to run with a constant speed at different substrate levels and, therefore, is a substantial criterion of a robust rhythm in a changing environment. Because previous data have suggested a central role of RAS2-mediated signaling in the adaptation of yeast to different nutritional environments, we examined the involvement of RAS2 in the metabolic regulation of the clock in the circadian model organism Neurospora crassa We show that, in a ras2-deficient strain, the period is longer than in the control. Moreover, unlike in the WT, in Δras2, operation of the circadian clock was affected by glucose; compared with starvation conditions, the period was longer and the oscillation of expression of the frequency (frq) gene was dampened. In constant darkness, the delayed phosphorylation of the FRQ protein and the long-lasting accumulation of FRQ in the nucleus were in accordance with the longer period and the less robust rhythm in the mutant. Although glucose did not affect the subcellular distribution of FRQ in the WT, highly elevated FRQ levels were detected in the nucleus in Δras2 RAS2 interacted with the RAS-binding domain of the adenylate cyclase in vitro, and the cAMP analogue 8-bromo-cyclic AMP partially rescued the circadian phenotype in vivo We therefore propose that RAS2 acts via a cAMP-dependent pathway and exerts significant metabolic control on the Neurospora circadian clock.
Collapse
Affiliation(s)
- Norbert Gyöngyösi
- From the Department of Physiology, Semmelweis University, Tűzoltó u. 37-47, 1094 Budapest, Hungary
| | - Anita Szőke
- From the Department of Physiology, Semmelweis University, Tűzoltó u. 37-47, 1094 Budapest, Hungary
| | - Krisztina Ella
- From the Department of Physiology, Semmelweis University, Tűzoltó u. 37-47, 1094 Budapest, Hungary
| | - Krisztina Káldi
- From the Department of Physiology, Semmelweis University, Tűzoltó u. 37-47, 1094 Budapest, Hungary
| |
Collapse
|
23
|
Mellor J. The molecular basis of metabolic cycles and their relationship to circadian rhythms. Nat Struct Mol Biol 2017; 23:1035-1044. [PMID: 27922609 DOI: 10.1038/nsmb.3311] [Citation(s) in RCA: 33] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2016] [Accepted: 09/23/2016] [Indexed: 12/12/2022]
Abstract
Metabolic cycles result from the partitioning of oxidative and reductive metabolism into rhythmic phases of gene expression and oscillating post-translational protein modifications. Relatively little is known about how these switches in gene expression are controlled, although recent studies have suggested that transcription itself may play a central role. This review explores the molecular basis of the metabolic and gene-expression oscillations in the yeast Saccharomyces cerevisiae, as well as how they relate to other biological time-keeping mechanisms, such as circadian rhythms.
Collapse
Affiliation(s)
- Jane Mellor
- Department of Biochemistry, University of Oxford, Oxford, UK
| |
Collapse
|
24
|
Dunlap JC, Loros JJ. Making Time: Conservation of Biological Clocks from Fungi to Animals. Microbiol Spectr 2017; 5:10.1128/microbiolspec.FUNK-0039-2016. [PMID: 28527179 PMCID: PMC5446046 DOI: 10.1128/microbiolspec.funk-0039-2016] [Citation(s) in RCA: 81] [Impact Index Per Article: 11.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2016] [Indexed: 01/03/2023] Open
Abstract
The capacity for biological timekeeping arose at least three times through evolution, in prokaryotic cyanobacteria, in cells that evolved into higher plants, and within the group of organisms that eventually became the fungi and the animals. Neurospora is a tractable model system for understanding the molecular bases of circadian rhythms in the last of these groups, and is perhaps the most intensively studied circadian cell type. Rhythmic processes described in fungi include growth rate, stress responses, developmental capacity, and sporulation, as well as much of metabolism; fungi use clocks to anticipate daily environmental changes. A negative feedback loop comprises the core of the circadian system in fungi and animals. In Neurospora, the best studied fungal model, it is driven by two transcription factors, WC-1 and WC-2, that form the White Collar Complex (WCC). WCC elicits expression of the frq gene. FRQ complexes with other proteins, physically interacts with the WCC, and reduces its activity; the kinetics of these processes is strongly influenced by progressive phosphorylation of FRQ. When FRQ becomes sufficiently phosphorylated that it loses the ability to influence WCC activity, the circadian cycle starts again. Environmental cycles of light and temperature influence frq and FRQ expression and thereby reset the internal circadian clocks. The molecular basis of circadian output is also becoming understood. Taken together, molecular explanations are emerging for all the canonical circadian properties, providing a molecular and regulatory framework that may be extended to many members of the fungal and animal kingdoms, including humans.
Collapse
Affiliation(s)
- Jay C Dunlap
- Department of Molecular and Systems Biology, Geisel School of Medicine at Dartmouth, Hanover, NH 03755
| | - Jennifer J Loros
- Department of Molecular and Systems Biology, Geisel School of Medicine at Dartmouth, Hanover, NH 03755
- Department of Biochemistry and Cell Biology, Geisel School of Medicine at Dartmouth, Hanover, NH 03755
| |
Collapse
|
25
|
Vinod C, Jagota A. Daily Socs1 rhythms alter with aging differentially in peripheral clocks in male Wistar rats: therapeutic effects of melatonin. Biogerontology 2017; 18:333-345. [DOI: 10.1007/s10522-017-9687-7] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2016] [Accepted: 02/22/2017] [Indexed: 12/12/2022]
|
26
|
Benocci T, Aguilar-Pontes MV, Zhou M, Seiboth B, de Vries RP. Regulators of plant biomass degradation in ascomycetous fungi. BIOTECHNOLOGY FOR BIOFUELS 2017; 10:152. [PMID: 28616076 PMCID: PMC5468973 DOI: 10.1186/s13068-017-0841-x] [Citation(s) in RCA: 122] [Impact Index Per Article: 17.4] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/27/2017] [Accepted: 06/06/2017] [Indexed: 05/05/2023]
Abstract
Fungi play a major role in the global carbon cycle because of their ability to utilize plant biomass (polysaccharides, proteins, and lignin) as carbon source. Due to the complexity and heterogenic composition of plant biomass, fungi need to produce a broad range of degrading enzymes, matching the composition of (part of) the prevalent substrate. This process is dependent on a network of regulators that not only control the extracellular enzymes that degrade the biomass, but also the metabolic pathways needed to metabolize the resulting monomers. This review will summarize the current knowledge on regulation of plant biomass utilization in fungi and compare the differences between fungal species, focusing in particular on the presence or absence of the regulators involved in this process.
Collapse
Affiliation(s)
- Tiziano Benocci
- Fungal Physiology, Westerdijk Fungal Biodiversity Institute & Fungal Molecular Physiology, Utrecht University, Uppsalalaan 8, 3584 CT Utrecht, The Netherlands
| | - Maria Victoria Aguilar-Pontes
- Fungal Physiology, Westerdijk Fungal Biodiversity Institute & Fungal Molecular Physiology, Utrecht University, Uppsalalaan 8, 3584 CT Utrecht, The Netherlands
| | - Miaomiao Zhou
- Fungal Physiology, Westerdijk Fungal Biodiversity Institute & Fungal Molecular Physiology, Utrecht University, Uppsalalaan 8, 3584 CT Utrecht, The Netherlands
| | - Bernhard Seiboth
- Research Area Biochemical Technology, Institute of Chemical and Biological Engineering, TU Wien, 1060 Vienna, Austria
| | - Ronald P. de Vries
- Fungal Physiology, Westerdijk Fungal Biodiversity Institute & Fungal Molecular Physiology, Utrecht University, Uppsalalaan 8, 3584 CT Utrecht, The Netherlands
| |
Collapse
|
27
|
Keller N. Plenary reviews of the 28th Fungal Genetics Conference. Fungal Genet Biol 2016; 90:23. [DOI: 10.1016/j.fgb.2016.03.005] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
|
28
|
Wang L, Li L, Zhao L, Liu C, Liu J, Liu L, Lin P, Liu B, Li M. Chronopharmacokinetics and mechanisms of gefitinib in a nude mice model of non-small cell lung cancer. RSC Adv 2016. [DOI: 10.1039/c6ra13854c] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022] Open
Abstract
Circadian rhythms may influence the pharmacokinetics of drugs.
Collapse
Affiliation(s)
- Le Wang
- Department of Pharmacy
- Pharmaceutical College of Qingdao University
- Qingdao 266021
- China
| | - Lujia Li
- Department of Oncology
- No. 401 Hospital of Chinese People's Liberation Army
- Qingdao 266071
- China
| | - Liyan Zhao
- Department of Pharmacy
- No. 401 Hospital of Chinese People's Liberation Army
- Qingdao 266071
- China
| | - Changjiao Liu
- Pharmaceutical College of Dalian Medical University
- Dalian 116000
- China
| | - Jiao Liu
- Department of Pharmacy
- Affiliate Hospital of Weifang Medical University
- Weifang
- 261000 China
| | - Liang Liu
- Department of Pharmacy
- Pharmaceutical College of Qingdao University
- Qingdao 266021
- China
| | - Pingping Lin
- Department of Clinical Pharmacology
- Zhongshan Hospital
- Fudan University
- Shanghai 200032
- China
| | - Bo Liu
- Department of Pharmacy
- No. 401 Hospital of Chinese People's Liberation Army
- Qingdao 266071
- China
| | - Mingchun Li
- Department of Pharmacy
- No. 401 Hospital of Chinese People's Liberation Army
- Qingdao 266071
- China
| |
Collapse
|
29
|
Fuller K, Dunlap J, Loros J. Fungal Light Sensing at the Bench and Beyond. ADVANCES IN GENETICS 2016; 96:1-51. [DOI: 10.1016/bs.adgen.2016.08.002] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
|