1
|
Calderan-Rodrigues MJ, Caldana C. Impact of the TOR pathway on plant growth via cell wall remodeling. J Plant Physiol 2024; 294:154202. [PMID: 38422631 DOI: 10.1016/j.jplph.2024.154202] [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] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/01/2023] [Revised: 02/12/2024] [Accepted: 02/13/2024] [Indexed: 03/02/2024]
Abstract
Plant growth is intimately linked to the availability of carbon and energy status. The Target of rapamycin (TOR) pathway is a highly relevant metabolic sensor and integrator of plant-assimilated C into development and growth. The cell wall accounts for around a third of the cell biomass, and the investment of C into this structure should be finely tuned for optimal growth. The plant C status plays a significant role in controlling the rate of cell wall synthesis. TOR signaling regulates cell growth and expansion, which are fundamental processes for plant development. The availability of nutrients and energy, sensed and integrated by TOR, influences cell division and elongation, ultimately impacting the synthesis and deposition of cell wall components. The plant cell wall is crucial in environmental adaptation and stress responses. TOR senses and internalizes various environmental cues, such as nutrient availability and stresses. These environmental factors influence TOR activity, which modulates cell wall remodeling to cope with changing conditions. Plant hormones, including auxins, gibberellins, and brassinosteroids, also regulate TOR signaling and cell wall-related processes. The connection between nutrients and cell wall pathways modulated by TOR are discussed.
Collapse
Affiliation(s)
- Maria Juliana Calderan-Rodrigues
- Max-Planck Institut für Molekulare Pflanzenphysiologie, 14476, Potsdam-Golm, Germany; Universidade de São Paulo, Escola Superior de Agricultura "Luiz de Queiroz", 13418-900, Piracicaba, SP, Brazil.
| | - Camila Caldana
- Max-Planck Institut für Molekulare Pflanzenphysiologie, 14476, Potsdam-Golm, Germany
| |
Collapse
|
2
|
Artins A, Martins MCM, Meyer C, Fernie AR, Caldana C. Sensing and regulation of C and N metabolism - novel features and mechanisms of the TOR and SnRK1 signaling pathways. Plant J 2024. [PMID: 38349940 DOI: 10.1111/tpj.16684] [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] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/16/2022] [Revised: 01/25/2024] [Accepted: 02/02/2024] [Indexed: 02/15/2024]
Abstract
Carbon (C) and nitrogen (N) metabolisms are tightly integrated to allow proper plant growth and development. Photosynthesis is dependent on N invested in chlorophylls, enzymes, and structural components of the photosynthetic machinery, while N uptake and assimilation rely on ATP, reducing equivalents, and C-skeletons provided by photosynthesis. The direct connection between N availability and photosynthetic efficiency allows the synthesis of precursors for all metabolites and building blocks in plants. Thus, the capacity to sense and respond to sudden changes in C and N availability is crucial for plant survival and is mediated by complex yet efficient signaling pathways such as TARGET OF RAPAMYCIN (TOR) and SUCROSE-NON-FERMENTING-1-RELATED PROTEIN KINASE 1 (SnRK1). In this review, we present recent advances in mechanisms involved in sensing C and N status as well as identifying current gaps in our understanding. We finally attempt to provide new perspectives and hypotheses on the interconnection of diverse signaling pathways that will allow us to understand the integration and orchestration of the major players governing the regulation of the CN balance.
Collapse
Affiliation(s)
- Anthony Artins
- Max-Planck-Institute of Molecular Plant Physiology, Am Mühlenberg 1, 14476, Potsdam, Golm, Germany
| | - Marina C M Martins
- in Press - Scientific Consulting and Communication Services, 05089-030, São Paulo, São Paulo, Brazil
| | - Christian Meyer
- Institut Jean-Pierre Bourgin (IJPB), INRAE, AgroParisTech, Université Paris-Saclay, 78000, Versailles, France
| | - Alisdair R Fernie
- Max-Planck-Institute of Molecular Plant Physiology, Am Mühlenberg 1, 14476, Potsdam, Golm, Germany
| | - Camila Caldana
- Max-Planck-Institute of Molecular Plant Physiology, Am Mühlenberg 1, 14476, Potsdam, Golm, Germany
| |
Collapse
|
3
|
Kudo SN, Bello CCM, Artins A, Caldana C, Satake A. Assessing the impacts of genetic defects on starch metabolism in Arabidopsis plants using the carbon homeostasis model. J R Soc Interface 2023; 20:20230426. [PMID: 38016639 PMCID: PMC10684347 DOI: 10.1098/rsif.2023.0426] [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: 07/26/2023] [Accepted: 10/30/2023] [Indexed: 11/30/2023] Open
Abstract
Starch serves as an important carbon storage mechanism for many plant species, facilitating their adaptation to the cyclic variations in the light environment, including day-night cycles as well as seasonal changes in photoperiod. By dynamically adjusting starch accumulation and degradation rates, plants maintain carbon homeostasis, enabling continuous growth under fluctuating environmental conditions. To understand dynamic nature of starch metabolism at the molecular level, it is necessary to integrate empirical knowledge from genetic defects in specific regulatory pathways into the dynamical system of starch metabolism. To achieve this, we evaluated the impact of genetic defects in the circadian clock, sugar sensing and starch degradation pathways using the carbon homeostasis model that encompasses the interplay between these pathways. Through the collection of starch metabolism data from 10 Arabidopsis mutants, we effectively fitted the experimental data to the model. The system-level assessment revealed that genetic defects in both circadian clock components and sugar sensing pathway hindered the appropriate adjustment of the starch degradation rate, particularly under long-day conditions. These findings not only confirmed the previous empirical findings but also provide the novel insights into the role of each gene within the gene regulatory network on the emergence of carbon homeostasis.
Collapse
Affiliation(s)
- Shuichi N. Kudo
- Graduate School of Systems Life Science, Kyushu University, Fukuoka 819-0395, Japan
| | | | - Anthony Artins
- Max Planck Institute of Molecular Plant Physiology, Golm/Postdam 14476, Germany
| | - Camila Caldana
- Max Planck Institute of Molecular Plant Physiology, Golm/Postdam 14476, Germany
| | - Akiko Satake
- Department of Biology, Faculty of Science, Kyushu University, Fukuoka 819-0395, Japan
| |
Collapse
|
4
|
Caldana C, Carrari F, Fernie AR, Sampathkumar A. How metabolism and development are intertwined in space and time. Plant J 2023; 116:347-359. [PMID: 37433681 DOI: 10.1111/tpj.16391] [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] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/21/2022] [Revised: 07/05/2023] [Accepted: 07/07/2023] [Indexed: 07/13/2023]
Abstract
Developmental transitions, occurring throughout the life cycle of plants, require precise regulation of metabolic processes to generate the energy and resources necessary for the committed growth processes. In parallel, the establishment of new cells, tissues, and even organs, alongside their differentiation provoke profound changes in metabolism. It is increasingly being recognized that there is a certain degree of feedback regulation between the components and products of metabolic pathways and developmental regulators. The generation of large-scale metabolomics datasets during developmental transitions, in combination with molecular genetic approaches has helped to further our knowledge on the functional importance of metabolic regulation of development. In this perspective article, we provide insights into studies that elucidate interactions between metabolism and development at the temporal and spatial scales. We additionally discuss how this influences cell growth-related processes. We also highlight how metabolic intermediates function as signaling molecules to direct plant development in response to changing internal and external conditions.
Collapse
Affiliation(s)
- Camila Caldana
- Max-Planck-Institute of Molecular Plant Physiology, Am Mühlenberg 1, 14476, Potsdam-Golm, Germany
| | - Fernando Carrari
- Facultad de Agronomía, Cátedra de Genética, Universidad de Buenos Aires, Buenos Aires, Argentina
- Instituto de Fisiología, Biología Molecular y Neurociencias (IFIBYNE-UBA-CONICET), Ciudad Universitaria, C1428EHA, Buenos Aires, Argentina
| | - Alisdair R Fernie
- Max-Planck-Institute of Molecular Plant Physiology, Am Mühlenberg 1, 14476, Potsdam-Golm, Germany
| | - Arun Sampathkumar
- Max-Planck-Institute of Molecular Plant Physiology, Am Mühlenberg 1, 14476, Potsdam-Golm, Germany
| |
Collapse
|
5
|
Caldana C, Fernie AR. Plant biology: Identification of the connecTOR linking metabolism, epigenetics and development. Curr Biol 2022; 32:R1272-R1274. [PMID: 36413970 DOI: 10.1016/j.cub.2022.10.002] [Citation(s) in RCA: 0] [Impact Index Per Article: 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: 11/23/2022]
Abstract
While metabolism has been recognized as a key regulator of plant development, exactly how this is achieved is unknown. A new study identifies a component of the Polycomb repressor complex 2 as linking these processes via histone modification.
Collapse
Affiliation(s)
- Camila Caldana
- Max-Planck-Institute of Molecular Plant Physiology, 14467 Potsdam-Golm, Germany
| | - Alisdair R Fernie
- Max-Planck-Institute of Molecular Plant Physiology, 14467 Potsdam-Golm, Germany.
| |
Collapse
|
6
|
Urrea-Castellanos R, Caldana C, Henriques R. Growing at the right time: interconnecting the TOR pathway with photoperiod and circadian regulation. J Exp Bot 2022; 73:7006-7015. [PMID: 35738873 PMCID: PMC9664226 DOI: 10.1093/jxb/erac279] [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] [Figures] [Subscribe] [Scholar Register] [Received: 02/20/2022] [Accepted: 06/23/2022] [Indexed: 06/15/2023]
Abstract
Plants can adjust their growth to specific times of the day and season. Different photoperiods result in distinct growth patterns, which correlate with specific carbon-partitioning strategies in source (leaves) and sink (roots) organs. Therefore, external cues such as light, day length, and temperature need to be integrated with intracellular processes controlling overall carbon availability and anabolism. The target of rapamycin (TOR) pathway is a signalling hub where environmental signals, circadian information, and metabolic processes converge to regulate plant growth. TOR complex mutants display altered patterns of root growth and starch levels. Moreover, depletion of TOR or reduction in cellular energy levels affect the pace of the clock by extending the period length, suggesting that this pathway could participate in circadian metabolic entrainment. However, this seems to be a mutual interaction, since the TOR pathway components are also under circadian regulation. These results strengthen the role of this signalling pathway as a master sensor of metabolic status, integrating day length and circadian cues to control anabolic processes in the cell, thus promoting plant growth and development. Expanding this knowledge from Arabidopsis thaliana to crops will improve our understanding of the molecular links connecting environmental perception and growth regulation under field conditions.
Collapse
Affiliation(s)
| | - Camila Caldana
- Max Planck Institute of Molecular Plant Physiology, Am Mühlenberg, Potsdam-Golm, Germany
| | | |
Collapse
|
7
|
Henriques R, Calderan-Rodrigues MJ, Luis Crespo J, Baena-González E, Caldana C. Growing of the TOR world. J Exp Bot 2022; 73:6987-6992. [PMID: 36377640 PMCID: PMC9664224 DOI: 10.1093/jxb/erac401] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/07/2022] [Indexed: 06/16/2023]
Affiliation(s)
| | | | - José Luis Crespo
- Instituto de Bioquimica Vegetal y Fotosintesis, Consejo Superior de Investigaciones Cientificas (CSIC)-Universidad de Sevilla, Sevilla, Spain
| | - Elena Baena-González
- Instituto Gulbenkian de Ciência, 2780-156 Oeiras, Portugal and GREEN-IT Bioresources for Sustainability, ITQB-NOVA, 2780-157 Oeiras, Portugal
| | - Camila Caldana
- Max Planck Institute of Molecular Plant Physiology, Am Mühlenberg 1, 14476, Potsdam-Golm, Germany
| |
Collapse
|
8
|
Li X, Deng D, Cataltepe G, Román Á, Buckley CR, Cassano Monte‐Bello C, Skirycz A, Caldana C, Haydon MJ. A reactive oxygen species Ca 2+ signalling pathway identified from a chemical screen for modifiers of sugar-activated circadian gene expression. New Phytol 2022; 236:1027-1041. [PMID: 35842791 PMCID: PMC9804775 DOI: 10.1111/nph.18380] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/16/2022] [Accepted: 07/13/2022] [Indexed: 06/10/2023]
Abstract
Sugars are essential metabolites for energy and anabolism that can also act as signals to regulate plant physiology and development. Experimental tools to disrupt major sugar signalling pathways are limited. We performed a chemical screen for modifiers of activation of circadian gene expression by sugars to discover pharmacological tools to investigate and manipulate plant sugar signalling. Using a library of commercially available bioactive compounds, we identified 75 confident hits that modified the response of a circadian luciferase reporter to sucrose in dark-adapted Arabidopsis thaliana seedlings. We validated the transcriptional effect on a subset of the hits and measured their effects on a range of sugar-dependent phenotypes for 13 of these chemicals. Chemicals were identified that appear to influence known and unknown sugar signalling pathways. Pentamidine isethionate was identified as a modifier of a sugar-activated Ca2+ signal that acts as a calmodulin inhibitor downstream of superoxide in a metabolic signalling pathway affecting circadian rhythms, primary metabolism and plant growth. Our data provide a resource of new experimental tools to manipulate plant sugar signalling and identify novel components of these pathways.
Collapse
Affiliation(s)
- Xiang Li
- School of BioSciencesUniversity of MelbourneParkvilleVic.3010Australia
| | - Dongjing Deng
- School of BioSciencesUniversity of MelbourneParkvilleVic.3010Australia
| | - Gizem Cataltepe
- School of BioSciencesUniversity of MelbourneParkvilleVic.3010Australia
- Max Planck Institute of Molecular Plant Physiology14476PotsdamGermany
| | - Ángela Román
- School of BioSciencesUniversity of MelbourneParkvilleVic.3010Australia
| | | | | | | | - Camila Caldana
- Max Planck Institute of Molecular Plant Physiology14476PotsdamGermany
| | - Michael J. Haydon
- School of BioSciencesUniversity of MelbourneParkvilleVic.3010Australia
| |
Collapse
|
9
|
Silva FMDO, Bulgarelli RG, Mubeen U, Caldana C, Andrade SAL, Mazzafera P. Low phosphorus induces differential metabolic responses in eucalyptus species improving nutrient use efficiency. Front Plant Sci 2022; 13:989827. [PMID: 36186027 PMCID: PMC9520260 DOI: 10.3389/fpls.2022.989827] [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] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/08/2022] [Accepted: 08/11/2022] [Indexed: 06/16/2023]
Abstract
Phosphorus (P) is a vital nutrient for plant growth. P availability is generally low in soils, and plant responses to low P availability need to be better understood. In a previous study, we studied the growth and physiological responses of 24 species to low P availability in the soil and verified of eucalypts, five (Eucalyptus acmenoides, E. grandis, E. globulus, E. tereticornis, and Corymbia maculata) contrasted regarding their efficiency and responsiveness to soil P availability. Here, we obtained the metabolomic and lipidomic profile of leaves, stems, and roots from these species growing under low (4.5 mg dm-3) and sufficient (10.8 mg dm-3) P in the soil. Disregarding the level of P in the soils, P allocation was always higher in the stems. However, when grown in the P-sufficient soil, the stems steadily were the largest compartment of the total plant P. Under low P, the relative contents of primary metabolites, such as amino acids, TCA cycle intermediates, organic acids and carbohydrates, changed differently depending on the species. Additionally, phosphorylated metabolites showed enhanced turnover or reductions. While photosynthetic efficiencies were not related to higher biomass production, A/Ci curves showed that reduced P availability increased the eucalypt species' Vcmax, Jmax and photosynthetic P-use efficiency. Plants of E. acmenoides increased galactolipids and sulfolipids in leaves more than other eucalypt species, suggesting that lipid remodelling can be a strategy to cope with the P shortage in this species. Our findings offer insights to understand genotypic efficiency among eucalypt species to accommodate primary metabolism under low soil P availability and eventually be used as biochemical markers for breeding programs.
Collapse
Affiliation(s)
| | | | - Umarah Mubeen
- Department of Molecular Physiology, Max Planck Institute of Molecular Plant Physiology, Potsdam, Germany
| | - Camila Caldana
- Department of Molecular Physiology, Max Planck Institute of Molecular Plant Physiology, Potsdam, Germany
| | - Sara Adrian L. Andrade
- Department of Plant Biology, Institute of Biology, State University of Campinas, Campinas, Brazil
| | - Paulo Mazzafera
- Department of Plant Biology, Institute of Biology, State University of Campinas, Campinas, Brazil
- Department of Crop Production, Luiz de Queiroz College of Agriculture, University of São Paulo, São Paulo, Brazil
| |
Collapse
|
10
|
Paschoal D, Costa JL, da Silva EM, da Silva FB, Capelin D, Ometto V, Aricetti JA, Carvalho GG, Pimpinato RF, de Oliveira RF, Carrera E, López-Díaz I, Rossi ML, Tornisielo V, Caldana C, Riano-Pachon DM, Cesarino I, Teixeira PJPL, Figueira A. Infection by Moniliophthora perniciosa reprograms tomato Micro-Tom physiology, establishes a sink, and increases secondary cell wall synthesis. J Exp Bot 2022; 73:3651-3670. [PMID: 35176760 DOI: 10.1093/jxb/erac057] [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] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/26/2021] [Accepted: 02/15/2022] [Indexed: 06/14/2023]
Abstract
Witches' broom disease of cacao is caused by the pathogenic fungus Moniliophthora perniciosa. By using tomato (Solanum lycopersicum) cultivar Micro-Tom (MT) as a model system, we investigated the physiological and metabolic consequences of M. perniciosa infection to determine whether symptoms result from sink establishment during infection. Infection of MT by M. perniciosa caused reductions in root biomass and fruit yield, a decrease in leaf gas exchange, and down-regulation of photosynthesis-related genes. The total leaf area and water potential decreased, while ABA levels, water conductance/conductivity, and ABA-related gene expression increased. Genes related to sugar metabolism and those involved in secondary cell wall deposition were up-regulated upon infection, and the concentrations of sugars, fumarate, and amino acids increased. 14C-glucose was mobilized towards infected MT stems, but not in inoculated stems of the MT line overexpressing CYTOKININ OXIDASE-2 (35S::AtCKX2), suggesting a role for cytokinin in establishing a sugar sink. The up-regulation of genes involved in cell wall deposition and phenylpropanoid metabolism in infected MT, but not in 35S::AtCKX2 plants, suggests establishment of a cytokinin-mediated sink that promotes tissue overgrowth with an increase in lignin. Possibly, M. perniciosa could benefit from the accumulation of secondary cell walls during its saprotrophic phase of infection.
Collapse
Affiliation(s)
- Daniele Paschoal
- Centro de Energia Nuclear na Agricultura, Universidade de São Paulo, Piracicaba, SP, 13400-970, Brazil
- Escola Superior de Agricultura "Luiz de Queiroz", Universidade de São Paulo, Piracicaba, SP, 13418-900, Brazil
| | - Juliana L Costa
- Centro de Energia Nuclear na Agricultura, Universidade de São Paulo, Piracicaba, SP, 13400-970, Brazil
| | - Eder M da Silva
- Centro de Energia Nuclear na Agricultura, Universidade de São Paulo, Piracicaba, SP, 13400-970, Brazil
| | - Fábia B da Silva
- Escola Superior de Agricultura "Luiz de Queiroz", Universidade de São Paulo, Piracicaba, SP, 13418-900, Brazil
| | - Diogo Capelin
- Escola Superior de Agricultura "Luiz de Queiroz", Universidade de São Paulo, Piracicaba, SP, 13418-900, Brazil
| | - Vitor Ometto
- Centro de Energia Nuclear na Agricultura, Universidade de São Paulo, Piracicaba, SP, 13400-970, Brazil
| | - Juliana A Aricetti
- Laboratório Nacional de Biorrenováveis, Centro Nacional de Pesquisa em Energia e Materiais, Campinas, SP, 13083-100, Brazil
| | - Gabriel G Carvalho
- Instituto de Biociências, Universidade de São Paulo, São Paulo, SP, 05508-090, Brazil
| | - Rodrigo F Pimpinato
- Centro de Energia Nuclear na Agricultura, Universidade de São Paulo, Piracicaba, SP, 13400-970, Brazil
| | - Ricardo F de Oliveira
- Escola Superior de Agricultura "Luiz de Queiroz", Universidade de São Paulo, Piracicaba, SP, 13418-900, Brazil
| | - Esther Carrera
- Universitat Politècnica de València (UPV), Consejo Superior de Investigaciones Científicas (CSIC), Valencia, Spain
| | - Isabel López-Díaz
- Universitat Politècnica de València (UPV), Consejo Superior de Investigaciones Científicas (CSIC), Valencia, Spain
| | - Mônica L Rossi
- Centro de Energia Nuclear na Agricultura, Universidade de São Paulo, Piracicaba, SP, 13400-970, Brazil
| | - Valdemar Tornisielo
- Centro de Energia Nuclear na Agricultura, Universidade de São Paulo, Piracicaba, SP, 13400-970, Brazil
| | - Camila Caldana
- Max Planck Institute for Molecular Plant Physiology, 14476 Potsdam-Golm, Germany
| | - Diego M Riano-Pachon
- Centro de Energia Nuclear na Agricultura, Universidade de São Paulo, Piracicaba, SP, 13400-970, Brazil
| | - Igor Cesarino
- Instituto de Biociências, Universidade de São Paulo, São Paulo, SP, 05508-090, Brazil
| | - Paulo J P L Teixeira
- Escola Superior de Agricultura "Luiz de Queiroz", Universidade de São Paulo, Piracicaba, SP, 13418-900, Brazil
| | - Antonio Figueira
- Centro de Energia Nuclear na Agricultura, Universidade de São Paulo, Piracicaba, SP, 13400-970, Brazil
| |
Collapse
|
11
|
Artins A, Caldana C. The metabolic homeostaTOR: The balance of holding on or letting grow. Curr Opin Plant Biol 2022; 66:102196. [PMID: 35219142 DOI: 10.1016/j.pbi.2022.102196] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/15/2021] [Revised: 01/18/2022] [Accepted: 01/23/2022] [Indexed: 06/14/2023]
Abstract
Plants, as autotrophic organisms, capture light energy to convert carbon dioxide into ATP, NADPH, and sugars, which are essential for the biosynthesis of building blocks, cell proliferation, biomass accumulation, and reproductive fitness. The Target Of Rapamycin (TOR) signalling pathway is a master regulator in sensing energy and nutrients, adapting the metabolic network and cell behaviour in response to environmental resource availability. In the past years, exciting advances in this endeavour have pointed out this pathway's importance in controlling metabolic homeostasis in various biological processes and systems. In this review, we discuss these recent discoveries highlighting the need for a metabolic threshold for the proper function of this kinase complex at the cellular level and across distinct tissues and organs to control growth and development in plants.
Collapse
Affiliation(s)
- Anthony Artins
- Max Planck Institute of Molecular Plant Physiology, Am Mühlenberg 1, 14476, Potsdam-Golm, Germany
| | - Camila Caldana
- Max Planck Institute of Molecular Plant Physiology, Am Mühlenberg 1, 14476, Potsdam-Golm, Germany.
| |
Collapse
|
12
|
Calderan-Rodrigues MJ, Luzarowski M, Monte-Bello CC, Minen RI, Zühlke BM, Nikoloski Z, Skirycz A, Caldana C. Proteogenic Dipeptides Are Characterized by Diel Fluctuations and Target of Rapamycin Complex-Signaling Dependency in the Model Plant Arabidopsis thaliana. Front Plant Sci 2021; 12:758933. [PMID: 35003157 PMCID: PMC8727597 DOI: 10.3389/fpls.2021.758933] [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] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 08/15/2021] [Accepted: 11/11/2021] [Indexed: 06/14/2023]
Abstract
As autotrophic organisms, plants capture light energy to convert carbon dioxide into ATP, nicotinamide adenine dinucleotide phosphate (NADPH), and sugars, which are essential for the biosynthesis of building blocks, storage, and growth. At night, metabolism and growth can be sustained by mobilizing carbon (C) reserves. In response to changing environmental conditions, such as light-dark cycles, the small-molecule regulation of enzymatic activities is critical for reprogramming cellular metabolism. We have recently demonstrated that proteogenic dipeptides, protein degradation products, act as metabolic switches at the interface of proteostasis and central metabolism in both plants and yeast. Dipeptides accumulate in response to the environmental changes and act via direct binding and regulation of critical enzymatic activities, enabling C flux distribution. Here, we provide evidence pointing to the involvement of dipeptides in the metabolic rewiring characteristics for the day-night cycle in plants. Specifically, we measured the abundance of 13 amino acids and 179 dipeptides over short- (SD) and long-day (LD) diel cycles, each with different light intensities. Of the measured dipeptides, 38 and eight were characterized by day-night oscillation in SD and LD, respectively, reaching maximum accumulation at the end of the day and then gradually falling in the night. Not only the number of dipeptides, but also the amplitude of the oscillation was higher in SD compared with LD conditions. Notably, rhythmic dipeptides were enriched in the glucogenic amino acids that can be converted into glucose. Considering the known role of Target of Rapamycin (TOR) signaling in regulating both autophagy and metabolism, we subsequently investigated whether diurnal fluctuations of dipeptides levels are dependent on the TOR Complex (TORC). The Raptor1b mutant (raptor1b), known for the substantial reduction of TOR kinase activity, was characterized by the augmented accumulation of dipeptides, which is especially pronounced under LD conditions. We were particularly intrigued by the group of 16 dipeptides, which, based on their oscillation under SD conditions and accumulation in raptor1b, can be associated with limited C availability or photoperiod. By mining existing protein-metabolite interaction data, we delineated putative protein interactors for a representative dipeptide Pro-Gln. The obtained list included enzymes of C and amino acid metabolism, which are also linked to the TORC-mediated metabolic network. Based on the obtained results, we speculate that the diurnal accumulation of dipeptides contributes to its metabolic adaptation in response to changes in C availability. We hypothesize that dipeptides would act as alternative respiratory substrates and by directly modulating the activity of the focal enzymes.
Collapse
Affiliation(s)
| | - Marcin Luzarowski
- Max Planck Institute of Molecular Plant Physiology, Potsdam, Germany
| | | | | | - Boris M. Zühlke
- Max Planck Institute of Molecular Plant Physiology, Potsdam, Germany
- Institute for Biochemistry and Biology, University of Potsdam, Potsdam, Germany
| | - Zoran Nikoloski
- Max Planck Institute of Molecular Plant Physiology, Potsdam, Germany
- Institute for Biochemistry and Biology, University of Potsdam, Potsdam, Germany
| | - Aleksandra Skirycz
- Max Planck Institute of Molecular Plant Physiology, Potsdam, Germany
- Boyce Thompson Institute, Ithaca, NY, United States
| | - Camila Caldana
- Max Planck Institute of Molecular Plant Physiology, Potsdam, Germany
| |
Collapse
|
13
|
Dantas LLB, Dourado MM, de Lima NO, Cavaçana N, Nishiyama MY, Souza GM, Carneiro MS, Caldana C, Hotta CT. Field microenvironments regulate crop diel transcript and metabolite rhythms. New Phytol 2021; 232:1738-1749. [PMID: 34312886 DOI: 10.1111/nph.17650] [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] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/30/2021] [Accepted: 07/21/2021] [Indexed: 06/13/2023]
Abstract
Most research in plant chronobiology has been done in laboratory conditions. However, laboratories usually fail to mimic natural conditions and their slight fluctuations, highlighting or obfuscating rhythmicity. High-density crops, such as sugarcane (Saccharum hybrid), generate field microenvironments with specific light and temperature regimes resulting from mutual shading. We measured the metabolic and transcriptional rhythms in the leaves of 4-month-old (4 mo) and 9 mo field-grown sugarcane. Most of the assayed rhythms in 9 mo sugarcane peaked >1 h later than in 4 mo sugarcane, including rhythms of the circadian clock gene, LATE ELONGATED HYPOCOTYL (LHY). We hypothesized that older sugarcane perceives dawn later than younger sugarcane as a consequence of self-shading. As a test, we measured LHY rhythms in plants on the east and the west sides of a field. We also tested if a wooden wall built between lines of sugarcane plants changed their rhythms. The LHY peak was delayed in the plants in the west of the field or beyond the wall; both shaded at dawn. We conclude that plants in the same field may have different phases resulting from field microenvironments, impacting important agronomical traits, such as flowering time, stalk weight and number.
Collapse
Affiliation(s)
- Luíza Lane Barros Dantas
- Departamento de Bioquímica, Instituto de Química, Universidade de São Paulo, São Paulo, SP, 05508-000, Brazil
- John Innes Centre, Norwich Research Park, Norwich, NR4 7UH, UK
| | - Maíra Marins Dourado
- Departamento de Bioquímica, Instituto de Química, Universidade de São Paulo, São Paulo, SP, 05508-000, Brazil
| | - Natalia Oliveira de Lima
- Departamento de Bioquímica, Instituto de Química, Universidade de São Paulo, São Paulo, SP, 05508-000, Brazil
| | - Natale Cavaçana
- Departamento de Bioquímica, Instituto de Química, Universidade de São Paulo, São Paulo, SP, 05508-000, Brazil
| | - Milton Yutaka Nishiyama
- Laboratório Especial de Toxicologia Aplicada, Instituto Butantan, São Paulo, SP, 05503-900, Brazil
| | - Glaucia Mendes Souza
- Departamento de Bioquímica, Instituto de Química, Universidade de São Paulo, São Paulo, SP, 05508-000, Brazil
| | - Monalisa Sampaio Carneiro
- Departamento de Biotecnologia e Produção Vegetal e Animal, Centro de Ciências Agrárias, Universidade Federal de São Carlos, São Carlos, SP, 13600-970, Brazil
| | - Camila Caldana
- Max Planck Institute for Molecular Plant Physiology, Potsdam-Golm, 14476, Germany
| | - Carlos Takeshi Hotta
- Departamento de Bioquímica, Instituto de Química, Universidade de São Paulo, São Paulo, SP, 05508-000, Brazil
| |
Collapse
|
14
|
Viana AJC, Matiolli CC, Newman DW, Vieira JGP, Duarte GT, Martins MCM, Gilbault E, Hotta CT, Caldana C, Vincentz M. The sugar-responsive circadian clock regulator bZIP63 modulates plant growth. New Phytol 2021; 231:1875-1889. [PMID: 34053087 PMCID: PMC9292441 DOI: 10.1111/nph.17518] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/08/2020] [Accepted: 05/18/2021] [Indexed: 05/02/2023]
Abstract
Adjustment to energy starvation is crucial to ensure growth and survival. In Arabidopsis thaliana (Arabidopsis), this process relies in part on the phosphorylation of the circadian clock regulator bZIP63 by SUCROSE non-fermenting RELATED KINASE1 (SnRK1), a key mediator of responses to low energy. We investigated the effects of mutations in bZIP63 on plant carbon (C) metabolism and growth. Results from phenotypic, transcriptomic and metabolomic analysis of bZIP63 mutants prompted us to investigate the starch accumulation pattern and the expression of genes involved in starch degradation and in the circadian oscillator. bZIP63 mutation impairs growth under light-dark cycles, but not under constant light. The reduced growth likely results from the accentuated C depletion towards the end of the night, which is caused by the accelerated starch degradation of bZIP63 mutants. The diel expression pattern of bZIP63 is dictated by both the circadian clock and energy levels, which could determine the changes in the circadian expression of clock and starch metabolic genes observed in bZIP63 mutants. We conclude that bZIP63 composes a regulatory interface between the metabolic and circadian control of starch breakdown to optimize C usage and plant growth.
Collapse
Affiliation(s)
- Américo J. C. Viana
- Centro de Biologia Molecular e Engenharia GenéticaDepartamento de Biologia VegetalInstituto de BiologiaUniversidade Estadual de CampinasCEP 13083‐875, CP 6010CampinasSPBrazil
| | - Cleverson C. Matiolli
- Centro de Biologia Molecular e Engenharia GenéticaDepartamento de Biologia VegetalInstituto de BiologiaUniversidade Estadual de CampinasCEP 13083‐875, CP 6010CampinasSPBrazil
| | - David W. Newman
- Centro de Biologia Molecular e Engenharia GenéticaDepartamento de Biologia VegetalInstituto de BiologiaUniversidade Estadual de CampinasCEP 13083‐875, CP 6010CampinasSPBrazil
| | - João G. P. Vieira
- Centro de Biologia Molecular e Engenharia GenéticaDepartamento de Biologia VegetalInstituto de BiologiaUniversidade Estadual de CampinasCEP 13083‐875, CP 6010CampinasSPBrazil
| | - Gustavo T. Duarte
- Centro de Biologia Molecular e Engenharia GenéticaDepartamento de Biologia VegetalInstituto de BiologiaUniversidade Estadual de CampinasCEP 13083‐875, CP 6010CampinasSPBrazil
| | - Marina C. M. Martins
- Brazilian Bioethanol Science and Technology Laboratory (CTBE/CNPEM)Rua Giuseppe Máximo Scolfaro 10000CampinasSPCEP 13083‐970Brazil
- Max‐Planck Partner GroupBrazilian Bioethanol Science and Technology Laboratory (CTBE/CNPEM)Campinas, SPBrazil
- Laboratory of Plant Physiological EcologyDepartment of BotanyInstitute of BiosciencesUniversity of São PauloSão Paulo, SPCEP 05508‐090Brazil
| | - Elodie Gilbault
- Institut Jean‐Pierre BourginINRAEAgroParisTechUniversité Paris‐SaclayVersailles78000France
| | - Carlos T. Hotta
- Departamento de BioquímicaInstituto de QuímicaUniversidade de São PauloSão Paulo, SPCEP 05508‐000Brazil
| | - Camila Caldana
- Brazilian Bioethanol Science and Technology Laboratory (CTBE/CNPEM)Rua Giuseppe Máximo Scolfaro 10000CampinasSPCEP 13083‐970Brazil
- Max‐Planck Partner GroupBrazilian Bioethanol Science and Technology Laboratory (CTBE/CNPEM)Campinas, SPBrazil
- Max Planck Institute of Molecular Plant PhysiologyAm Mühlenberg 114476 PotsdamGolmGermany
| | - Michel Vincentz
- Centro de Biologia Molecular e Engenharia GenéticaDepartamento de Biologia VegetalInstituto de BiologiaUniversidade Estadual de CampinasCEP 13083‐875, CP 6010CampinasSPBrazil
| |
Collapse
|
15
|
Nascimento VL, Pereira AM, Pereira AS, Silva VF, Costa LC, Bastos CEA, Ribeiro DM, Caldana C, Sulpice R, Nunes-Nesi A, Zsögön A, Araújo WL. Physiological and metabolic bases of increased growth in the tomato ethylene-insensitive mutant Never ripe: extending ethylene signaling functions. Plant Cell Rep 2021; 40:1377-1393. [PMID: 33074436 DOI: 10.1007/s00299-020-02623-y] [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] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/14/2020] [Accepted: 10/03/2020] [Indexed: 06/11/2023]
Abstract
The tomato mutant Never ripe (Nr), a loss-of-function for the ethylene receptor SlETR3, shows enhanced growth, associated with increased carbon assimilation and a rewiring of the central metabolism. Compelling evidence has demonstrated the importance of ethylene during tomato fruit development, yet its role on leaf central metabolism and plant growth remains elusive. Here, we performed a detailed characterization of Never ripe (Nr) tomato, a loss-of-function mutant for the ethylene receptor SlETR3, known for its fruits which never ripe. However, besides fruits, the Nr gene is also constitutively expressed in vegetative tissues. Nr mutant showed a growth enhancement during both the vegetative and reproductive stage, without an earlier onset of leaf senescence, with Nr plants exhibiting a higher number of leaves and an increased dry weight of leaves, stems, roots, and fruits. At metabolic level, Nr also plays a significant role with the mutant showing changes in carbon assimilation, carbohydrates turnover, and an exquisite reprogramming of a large number of metabolite levels. Notably, the expression of genes related to ethylene signaling and biosynthesis are not altered in Nr. We assess our results in the context of those previously published for tomato fruits and of current models of ethylene signal transduction, and conclude that ethylene insensitivity mediated by Nr impacts the whole central metabolism at vegetative stage, leading to increased growth rates.
Collapse
Affiliation(s)
- Vitor L Nascimento
- Departamento de Biologia Vegetal, Universidade Federal de Viçosa, Viçosa, MG, 36570-900, Brazil
| | - Auderlan M Pereira
- Departamento de Biologia Vegetal, Universidade Federal de Viçosa, Viçosa, MG, 36570-900, Brazil
| | - Aurelio S Pereira
- Departamento de Biologia Vegetal, Universidade Federal de Viçosa, Viçosa, MG, 36570-900, Brazil
| | - Victor F Silva
- Departamento de Biologia Vegetal, Universidade Federal de Viçosa, Viçosa, MG, 36570-900, Brazil
| | - Lucas C Costa
- Departamento de Biologia Vegetal, Universidade Federal de Viçosa, Viçosa, MG, 36570-900, Brazil
| | - Carla E A Bastos
- Departamento de Biologia Vegetal, Universidade Federal de Viçosa, Viçosa, MG, 36570-900, Brazil
| | - Dimas M Ribeiro
- Departamento de Biologia Vegetal, Universidade Federal de Viçosa, Viçosa, MG, 36570-900, Brazil
| | - Camila Caldana
- Max Planck Institute of Molecular Plant Physiology, Am Mühlenberg 1, 14476, Potsdam-Golm, Germany
| | - Ronan Sulpice
- Plant Systems Biology Laboratory, Plant and AgriBiosciences Research Centre and Ryan Institute, National University of Ireland Galway, Galway, H91 TK33, Ireland
| | - Adriano Nunes-Nesi
- Departamento de Biologia Vegetal, Universidade Federal de Viçosa, Viçosa, MG, 36570-900, Brazil
| | - Agustin Zsögön
- Departamento de Biologia Vegetal, Universidade Federal de Viçosa, Viçosa, MG, 36570-900, Brazil
| | - Wagner L Araújo
- Departamento de Biologia Vegetal, Universidade Federal de Viçosa, Viçosa, MG, 36570-900, Brazil.
| |
Collapse
|
16
|
Picchi SC, de Souza E Silva M, Saldanha LL, Ferreira H, Takita MA, Caldana C, de Souza AA. GC-TOF/MS-based metabolomics analysis to investigate the changes driven by N-Acetylcysteine in the plant-pathogen Xanthomonas citri subsp. citri. Sci Rep 2021; 11:15558. [PMID: 34330957 PMCID: PMC8324833 DOI: 10.1038/s41598-021-95113-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2021] [Accepted: 07/09/2021] [Indexed: 11/09/2022] Open
Abstract
N-Acetylcysteine (NAC) is an antioxidant, anti-adhesive, and antimicrobial compound. Even though there is much information regarding the role of NAC as an antioxidant and anti-adhesive agent, little is known about its antimicrobial activity. In order to assess its mode of action in bacterial cells, we investigated the metabolic responses triggered by NAC at neutral pH. As a model organism, we chose the Gram-negative plant pathogen Xanthomonas citri subsp. citri (X. citri), the causal agent of citrus canker disease, due to the potential use of NAC as a sustainable molecule against phytopathogens dissemination in citrus cultivated areas. In presence of NAC, cell proliferation was affected after 4 h, but damages to the cell membrane were observed only after 24 h. Targeted metabolite profiling analysis using GC-MS/TOF unravelled that NAC seems to be metabolized by the cells affecting cysteine metabolism. Intriguingly, glutamine, a marker for nitrogen status, was not detected among the cells treated with NAC. The absence of glutamine was followed by a decrease in the levels of the majority of the proteinogenic amino acids, suggesting that the reduced availability of amino acids affect protein synthesis and consequently cell proliferation.
Collapse
Affiliation(s)
- Simone Cristina Picchi
- Centro de Citricultura "Sylvio Moreira" - Instituto Agronômico de Campinas, Cordeirópolis, São Paulo, 13490-970, Brazil
| | - Mariana de Souza E Silva
- Centro de Citricultura "Sylvio Moreira" - Instituto Agronômico de Campinas, Cordeirópolis, São Paulo, 13490-970, Brazil
| | - Luiz Leonardo Saldanha
- Departamento de Bioquímica e Microbiologia, Instituto de Biociências, Universidade Estadual Paulista, Rio Claro, São Paulo, 13506-900, Brazil
| | - Henrique Ferreira
- Departamento de Bioquímica e Microbiologia, Instituto de Biociências, Universidade Estadual Paulista, Rio Claro, São Paulo, 13506-900, Brazil
| | - Marco Aurélio Takita
- Centro de Citricultura "Sylvio Moreira" - Instituto Agronômico de Campinas, Cordeirópolis, São Paulo, 13490-970, Brazil
| | - Camila Caldana
- Laboratório Nacional de Ciência e Tecnologia do Bioetanol - Centro Nacional de Pesquisa em Energia e Materiais, Campinas, São Paulo, 13083-100, Brazil.,Max-Planck-Institut Für Molekulare Pflanzenphysiologie, Wissenschaftspark Golm, Am Mühlenberg 1, 14476, Potsdam, Germany
| | - Alessandra Alves de Souza
- Centro de Citricultura "Sylvio Moreira" - Instituto Agronômico de Campinas, Cordeirópolis, São Paulo, 13490-970, Brazil.
| |
Collapse
|
17
|
Busso-Lopes AF, Carnielli CM, Winck FV, Patroni FMDS, Oliveira AK, Granato DC, E Costa RAP, Domingues RR, Pauletti BA, Riaño-Pachón DM, Aricetti J, Caldana C, Graner E, Coletta RD, Dryden K, Fox JW, Paes Leme AF. A Reductionist Approach Using Primary and Metastatic Cell-Derived Extracellular Vesicles Reveals Hub Proteins Associated with Oral Cancer Prognosis. Mol Cell Proteomics 2021; 20:100118. [PMID: 34186243 PMCID: PMC8350068 DOI: 10.1016/j.mcpro.2021.100118] [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] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2021] [Revised: 05/28/2021] [Accepted: 06/20/2021] [Indexed: 12/12/2022] Open
Abstract
Oral squamous cell carcinoma (OSCC) has high mortality rates that are largely associated with lymph node metastasis. However, the molecular mechanisms that drive OSCC metastasis are unknown. Extracellular vesicles (EVs) are membrane-bound particles that play a role in intercellular communication and impact cancer development and progression. Thus, profiling EVs would be of great significance to decipher their role in OSCC metastasis. For that purpose, we used a reductionist approach to map the proteomic, miRNA, metabolomic, and lipidomic profiles of EVs derived from human primary tumor (SCC-9) cells and matched lymph node metastatic (LN1) cells. Distinct omics profiles were associated with the metastatic phenotype, including 670 proteins, 217 miRNAs, 26 metabolites, and 63 lipids differentially abundant between LN1 cell– and SCC-9 cell–derived EVs. A multi-omics integration identified 11 ‘hub proteins’ significantly decreased at the metastatic site compared with primary tumor–derived EVs. We confirmed the validity of these findings with analysis of data from multiple public databases and found that low abundance of seven ‘hub proteins’ in EVs from metastatic lymph nodes (ALDH7A1, CAD, CANT1, GOT1, MTHFD1, PYGB, and SARS) is correlated with reduced survival and tumor aggressiveness in patients with cancer. In summary, this multi-omics approach identified proteins transported by EVs that are associated with metastasis and which may potentially serve as prognostic markers in OSCC. Proteomic, miRNA, metabolomic, and lipidomic profiles were mapped in oral cancer EVs. The molecular profile of EVs was associated with the lymph node metastatic phenotype. A multi-omics integrative analysis revealed 11 highly connected ‘hub proteins.’ ‘Hub proteins’ from EVs are candidates as prognostic markers in oral cancer.
Collapse
Affiliation(s)
- Ariane Fidelis Busso-Lopes
- Laboratório Nacional de Biociências - LNBio, Centro Nacional de Pesquisa em Energia e Materiais - CNPEM, Campinas, SP, Brazil
| | - Carolina Moretto Carnielli
- Laboratório Nacional de Biociências - LNBio, Centro Nacional de Pesquisa em Energia e Materiais - CNPEM, Campinas, SP, Brazil
| | - Flavia Vischi Winck
- Laboratório de Biologia de Sistemas Regulatórios, Departamento de Bioquímica, Instituto de Química, Universidade de São Paulo, São Paulo, SP, Brazil
| | - Fábio Malta de Sá Patroni
- Laboratório Nacional de Biociências - LNBio, Centro Nacional de Pesquisa em Energia e Materiais - CNPEM, Campinas, SP, Brazil
| | - Ana Karina Oliveira
- Laboratório Nacional de Biociências - LNBio, Centro Nacional de Pesquisa em Energia e Materiais - CNPEM, Campinas, SP, Brazil
| | - Daniela Campos Granato
- Laboratório Nacional de Biociências - LNBio, Centro Nacional de Pesquisa em Energia e Materiais - CNPEM, Campinas, SP, Brazil
| | - Rute Alves Pereira E Costa
- Laboratório Nacional de Biociências - LNBio, Centro Nacional de Pesquisa em Energia e Materiais - CNPEM, Campinas, SP, Brazil
| | - Romênia Ramos Domingues
- Laboratório Nacional de Biociências - LNBio, Centro Nacional de Pesquisa em Energia e Materiais - CNPEM, Campinas, SP, Brazil
| | - Bianca Alves Pauletti
- Laboratório Nacional de Biociências - LNBio, Centro Nacional de Pesquisa em Energia e Materiais - CNPEM, Campinas, SP, Brazil
| | - Diego Mauricio Riaño-Pachón
- Laboratório de Biologia de Sistemas Regulatórios, Departamento de Bioquímica, Instituto de Química, Universidade de São Paulo, São Paulo, SP, Brazil
| | - Juliana Aricetti
- Laboratório Nacional de Biorrenováveis - LNBR, Centro Nacional de Pesquisa em Energia e Materiais - CNPEM, Campinas, SP, Brazil
| | - Camila Caldana
- Max Planck Institute of Molecular Plant Physiology, Am Mühlenberg, Potsdam-Golm, Germany
| | - Edgard Graner
- Departamento de Diagnóstico Oral, Faculdade de Odontologia de Piracicaba, Universidade Estadual de Campinas, Piracicaba, SP, Brazil
| | - Ricardo Della Coletta
- Departamento de Diagnóstico Oral, Faculdade de Odontologia de Piracicaba, Universidade Estadual de Campinas, Piracicaba, SP, Brazil
| | - Kelly Dryden
- Molecular Electron Microscopy Core, University of Virginia, Charlottesville, Virginia, USA
| | - Jay William Fox
- Department of Microbiology, Immunology and Cancer Biology, University of Virginia, Charlottesville, Virginia, USA
| | - Adriana Franco Paes Leme
- Laboratório Nacional de Biociências - LNBio, Centro Nacional de Pesquisa em Energia e Materiais - CNPEM, Campinas, SP, Brazil.
| |
Collapse
|
18
|
da Silva VCH, Martins MCM, Calderan-Rodrigues MJ, Artins A, Monte Bello CC, Gupta S, Sobreira TJP, Riaño-Pachón DM, Mafra V, Caldana C. Shedding Light on the Dynamic Role of the "Target of Rapamycin" Kinase in the Fast-Growing C 4 Species Setaria viridis, a Suitable Model for Biomass Crops. Front Plant Sci 2021; 12:637508. [PMID: 33927734 PMCID: PMC8078139 DOI: 10.3389/fpls.2021.637508] [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] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/03/2020] [Accepted: 03/04/2021] [Indexed: 06/12/2023]
Abstract
The Target of Rapamycin (TOR) kinase pathway integrates energy and nutrient availability into metabolism promoting growth in eukaryotes. The overall higher efficiency on nutrient use translated into faster growth rates in C4 grass plants led to the investigation of differential transcriptional and metabolic responses to short-term chemical TOR complex (TORC) suppression in the model Setaria viridis. In addition to previously described responses to TORC inhibition (i.e., general growth arrest, translational repression, and primary metabolism reprogramming) in Arabidopsis thaliana (C3), the magnitude of changes was smaller in S. viridis, particularly regarding nutrient use efficiency and C allocation and partitioning that promote biosynthetic growth. Besides photosynthetic differences, S. viridis and A. thaliana present several specificities that classify them into distinct lineages, which also contribute to the observed alterations mediated by TOR. Indeed, cell wall metabolism seems to be distinctly regulated according to each cell wall type, as synthesis of non-pectic polysaccharides were affected in S. viridis, whilst assembly and structure in A. thaliana. Our results indicate that the metabolic network needed to achieve faster growth seems to be less stringently controlled by TORC in S. viridis.
Collapse
Affiliation(s)
| | | | | | - Anthony Artins
- Max Planck Institute of Molecular Plant Physiology, Potsdam-Golm, Germany
| | | | - Saurabh Gupta
- Institute of Biochemistry and Biology, University of Potsdam, Potsdam-Golm, Germany
| | | | | | - Valéria Mafra
- National Center for Research in Energy and Materials (CNPEM), Campinas, Brazil
| | - Camila Caldana
- National Center for Research in Energy and Materials (CNPEM), Campinas, Brazil
| |
Collapse
|
19
|
Calderan-Rodrigues MJ, de Barros Dantas LL, Cheavegatti Gianotto A, Caldana C. Applying Molecular Phenotyping Tools to Explore Sugarcane Carbon Potential. Front Plant Sci 2021; 12:637166. [PMID: 33679852 PMCID: PMC7935522 DOI: 10.3389/fpls.2021.637166] [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] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/02/2020] [Accepted: 01/27/2021] [Indexed: 05/21/2023]
Abstract
Sugarcane (Saccharum spp.), a C4 grass, has a peculiar feature: it accumulates, gradient-wise, large amounts of carbon (C) as sucrose in its culms through a complex pathway. Apart from being a sustainable crop concerning C efficiency and bioenergetic yield per hectare, sugarcane is used as feedstock for producing ethanol, sugar, high-value compounds, and products (e.g., polymers and succinate), and bioelectricity, earning the title of the world's leading biomass crop. Commercial cultivars, hybrids bearing high levels of polyploidy, and aneuploidy, are selected from a large number of crosses among suitable parental genotypes followed by the cloning of superior individuals among the progeny. Traditionally, these classical breeding strategies have been favoring the selection of cultivars with high sucrose content and resistance to environmental stresses. A current paradigm change in sugarcane breeding programs aims to alter the balance of C partitioning as a means to provide more plasticity in the sustainable use of this biomass for metabolic engineering and green chemistry. The recently available sugarcane genetic assemblies powered by data science provide exciting perspectives to increase biomass, as the current sugarcane yield is roughly 20% of its predicted potential. Nowadays, several molecular phenotyping tools can be applied to meet the predicted sugarcane C potential, mainly targeting two competing pathways: sucrose production/storage and biomass accumulation. Here we discuss how molecular phenotyping can be a powerful tool to assist breeding programs and which strategies could be adopted depending on the desired final products. We also tackle the advances in genetic markers and mapping as well as how functional genomics and genetic transformation might be able to improve yield and saccharification rates. Finally, we review how "omics" advances are promising to speed up plant breeding and reach the unexplored potential of sugarcane in terms of sucrose and biomass production.
Collapse
Affiliation(s)
| | | | | | - Camila Caldana
- Max Planck Institute of Molecular Plant Physiology, Potsdam, Germany
- *Correspondence: Camila Caldana,
| |
Collapse
|
20
|
Martins MCM, Mafra V, Monte-Bello CC, Caldana C. The Contribution of Metabolomics to Systems Biology: Current Applications Bridging Genotype and Phenotype in Plant Science. Advances in Plant Omics and Systems Biology Approaches 2021; 1346:91-105. [DOI: 10.1007/978-3-030-80352-0_5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
|
21
|
Mubeen U, Giavalisco P, Caldana C. TOR inhibition interrupts the metabolic homeostasis by shifting the carbon-nitrogen balance in Chlamydomonas reinhardtii. Plant Signal Behav 2019; 14:1670595. [PMID: 31583958 PMCID: PMC6804693 DOI: 10.1080/15592324.2019.1670595] [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] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 04/13/2019] [Revised: 09/13/2019] [Accepted: 09/17/2019] [Indexed: 06/10/2023]
Abstract
The allocation of nutrient resources to growth and metabolism is an essential function for controlling biomass accumulation in photoautotrophic organisms. One essential protein complex involved in this process is the target of rapamycin (TOR) kinase. It has been shown that the inhibition of TOR leads to a considerable upsurge in the amino acid levels. This molecular phenotype relies mainly on the availability of light, carbon (C) and nitrogen (N). To validate the time-resolved response of C and N metabolites, we used a targeted gas chromatography mass spectrometery (GC-MS)-based metabolomic approach, where we examined the response of Chlamydomonas reinhardtii upon TOR inhibition under C-limited condition, namely extended darkness. Contrary to C-supplemented conditions, the rapid increase in the amino acid levels is suppressed almost completely 4 h after TOR inhibition, confirming that C supply is essential to raise the amino acid levels mediated by their de novo synthesis. An exception to this observation was the levels of aspartate, which is presumably synthesized via the anaplerotic pathway. In agreement with previous reports, TOR repression, under these C-limited conditions, leads to a significant reduction in the C/N ratio, corroborating with the crucial role of the pathway in maintaining the metabolic balance of the cells and consequently propelling growth.
Collapse
Affiliation(s)
- Umarah Mubeen
- Molecular Physiology Department, Max Planck Institute of Molecular Plant Physiology, Potsdam-Golm, Germany
| | | | - Camila Caldana
- Molecular Physiology Department, Max Planck Institute of Molecular Plant Physiology, Potsdam-Golm, Germany
| |
Collapse
|
22
|
Caldana C, Martins MCM, Mubeen U, Urrea-Castellanos R. The magic 'hammer' of TOR: the multiple faces of a single pathway in the metabolic regulation of plant growth and development. J Exp Bot 2019; 70:2217-2225. [PMID: 30722050 DOI: 10.1093/jxb/ery459] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/03/2018] [Accepted: 12/11/2018] [Indexed: 06/09/2023]
Abstract
The target of rapamycin (TOR) pathway has emerged as a central hub synchronizing plant growth according to the nutrient/energy status and environmental inputs. Molecular mechanisms through which TOR promotes plant growth involve the positive regulation of transcription of cell proliferation-associated genes, mRNA translation initiation and ribosome biogenesis, to cite a few examples. Phytohormones, light, sugars, and sulfur have been found to broadly regulate TOR activity. TOR operates as a metabolic homeostat to fine-tune anabolic processes and efficiently enable plant growth under different circumstances. However, little is known about the multiple effectors that act up- and downstream of TOR. Here, we mainly discuss recent findings related to the TOR pathway in the context of plant metabolism and highlight areas of interest that need to be addressed to keep unravelling the intricate networks governing the regulation of TOR and its function in controlling biosynthetic growth.
Collapse
Affiliation(s)
- Camila Caldana
- Max Planck Institute of Molecular Plant Physiology, Am Mühlenberg, Potsdam-Golm, Germany
| | | | - Umarah Mubeen
- Max Planck Institute of Molecular Plant Physiology, Am Mühlenberg, Potsdam-Golm, Germany
| | | |
Collapse
|
23
|
Alborghetti MR, Correa MEP, Whangbo J, Shi X, Aricetti JA, da Silva AA, Miranda ECM, Sforca ML, Caldana C, Gerszten RE, Ritz J, Zeri ACDM. Clinical Metabolomics Identifies Blood Serum Branched Chain Amino Acids as Potential Predictive Biomarkers for Chronic Graft vs. Host Disease. Front Oncol 2019; 9:141. [PMID: 30949447 PMCID: PMC6436081 DOI: 10.3389/fonc.2019.00141] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2018] [Accepted: 02/18/2019] [Indexed: 12/19/2022] Open
Abstract
The allogeneic hematopoietic stem cell transplantation procedure—the only curative therapy for many types of hematological cancers—is increasing, and graft vs. host disease (GVHD) is the main cause of morbidity and mortality after transplantation. Currently, GVHD diagnosis is clinically performed. Whereas, biomarker panels have been developed for acute GVHD (aGVHD), there is a lack of information about the chronic form (cGVHD). Using nuclear magnetic resonance (NMR) and gas chromatography coupled to time-of-flight (GC-TOF) mass spectrometry, this study prospectively evaluated the serum metabolome of 18 Brazilian patients who had undergone allogeneic hematopoietic stem cell transplantation (HSCT). We identified and quantified 63 metabolites and performed the metabolomic profile on day −10, day 0, day +10 and day +100, in reference to day of transplantation. Patients did not present aGVHD or cGVHD clinical symptoms at sampling times. From 18 patients analyzed, 6 developed cGVHD. The branched-chain amino acids (BCAAs) leucine and isoleucine were reduced and the sulfur-containing metabolite (cystine) was increased at day +10 and day +100. The area under receiver operating characteristics (ROC) curves was higher than 0.79. BCAA findings were validated by liquid chromatography coupled to tandem mass spectrometry (LC-MS/MS) in 49 North American patients at day +100; however, cystine findings were not statistically significant in this patient set. Our results highlight the importance of multi-temporal and multivariate biomarker panels for predicting and understanding cGVHD.
Collapse
Affiliation(s)
| | - Maria Elvira Pizzigatti Correa
- Hematology and Hemotherapy Center, Instituto Nacional de Ciência e Tecnologia do Sangue, University of Campinas, Hemocentro-Unicamp, Campinas, Brazil
| | - Jennifer Whangbo
- Harvard Medical School, Dana-Farber Cancer Institute, Boston, MA, United States
| | - Xu Shi
- Beth Israel Deaconess Hospital, Harvard Medical School, Boston, MA, United States
| | - Juliana Aparecida Aricetti
- Brazilian Bioethanol Science and Technology Laboratory (CTBE)/Brazilian Center for Research in Energy and Materials (CNPEM), Campinas, Brazil
| | - Andreia Aparecida da Silva
- Hematology and Hemotherapy Center, Instituto Nacional de Ciência e Tecnologia do Sangue, University of Campinas, Hemocentro-Unicamp, Campinas, Brazil
| | - Eliana Cristina Martins Miranda
- Hematology and Hemotherapy Center, Instituto Nacional de Ciência e Tecnologia do Sangue, University of Campinas, Hemocentro-Unicamp, Campinas, Brazil
| | - Mauricio Luis Sforca
- Brazilian Biosciences National Laboratory (LNBio), Brazilian Center for Research in Energy and Materials (CNPEM), Campinas, Brazil
| | - Camila Caldana
- Brazilian Bioethanol Science and Technology Laboratory (CTBE)/Brazilian Center for Research in Energy and Materials (CNPEM), Campinas, Brazil
| | - Robert E Gerszten
- Beth Israel Deaconess Hospital, Harvard Medical School, Boston, MA, United States
| | - Jerome Ritz
- Harvard Medical School, Dana-Farber Cancer Institute, Boston, MA, United States
| | - Ana Carolina de Mattos Zeri
- Brazilian Biosciences National Laboratory (LNBio), Brazilian Center for Research in Energy and Materials (CNPEM), Campinas, Brazil
| |
Collapse
|
24
|
Abstract
The clockwork of plant circadian oscillators has been resolved through investigations in Arabidopsis thaliana. The circadian oscillator is an important regulator of much of plant physiology, though many of the mechanisms are unclear. New findings demonstrate that the oscillator adjusts phase and period in response to abiotic and biotic signals, providing insight in to how the plant circadian oscillator integrates with the biology of the cell and entrains to light, dark and temperature cycles. We propose that the plant circadian oscillator is dynamically plastic, in constant adjustment, rather than being an isolated clock impervious to cellular events.
Collapse
Affiliation(s)
- Alex A R Webb
- Department of Plant Sciences, Downing Street, Cambridge, CB3 0LJ, UK.
| | - Motohide Seki
- Faculty of Design, Kyushu University, 4-9-1 Shiobaru, Minamiku, Fukuoka, 815-8540, Japan
| | - Akiko Satake
- Department of Biology, Faculty of Science, Kyushu University, Fukuoka, 819-0395, Japan
| | - Camila Caldana
- Max Planck Institute of Molecular Plant Physiology, Am Mühlenberg 1, 14476, Potsdam-Golm, Germany
| |
Collapse
|
25
|
Mora Salguero DA, Fernández-Niño M, Serrano-Bermúdez LM, Páez Melo DO, Winck FV, Caldana C, González Barrios AF. Development of a Chlamydomonas reinhardtii metabolic network dynamic model to describe distinct phenotypes occurring at different CO 2 levels. PeerJ 2018; 6:e5528. [PMID: 30202653 PMCID: PMC6126472 DOI: 10.7717/peerj.5528] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2018] [Accepted: 08/06/2018] [Indexed: 12/13/2022] Open
Abstract
The increase in atmospheric CO2 due to anthropogenic activities is generating climate change, which has resulted in a subsequent rise in global temperatures with severe environmental impacts. Biological mitigation has been considered as an alternative for environmental remediation and reduction of greenhouse gases in the atmosphere. In fact, the use of easily adapted photosynthetic organisms able to fix CO2 with low-cost operation is revealing its high potential for industry. Among those organism, the algae Chlamydomonas reinhardtii have gain special attention as a model organism for studying CO2 fixation, biomass accumulation and bioenergy production upon exposure to several environmental conditions. In the present study, we studied the Chlamydomonas response to different CO2 levels by comparing metabolomics and transcriptomics data with the predicted results from our new-improved genomic-scale metabolic model. For this, we used in silico methods at steady dynamic state varying the levels of CO2. Our main goal was to improve our capacity for predicting metabolic routes involved in biomass accumulation. The improved genomic-scale metabolic model presented in this study was shown to be phenotypically accurate, predictive, and a significant improvement over previously reported models. Our model consists of 3726 reactions and 2436 metabolites, and lacks any thermodynamically infeasible cycles. It was shown to be highly sensitive to environmental changes under both steady-state and dynamic conditions. As additional constraints, our dynamic model involved kinetic parameters associated with substrate consumption at different growth conditions (i.e., low CO2-heterotrophic and high CO2-mixotrophic). Our results suggest that cells growing at high CO2 (i.e., photoautotrophic and mixotrophic conditions) have an increased capability for biomass production. In addition, we have observed that ATP production also seems to be an important limiting factor for growth under the conditions tested. Our experimental data (metabolomics and transcriptomics) and the results predicted by our model clearly suggest a differential behavior between low CO2-heterotrophic and high CO2-mixotrophic growth conditions. The data presented in the current study contributes to better dissect the biological response of C. reinhardtii, as a dynamic entity, to environmental and genetic changes. These findings are of great interest given the biotechnological potential of this microalga for CO2 fixation, biomass accumulation, and bioenergy production.
Collapse
Affiliation(s)
- Daniela Alejandra Mora Salguero
- Grupo de Diseño de Productos y Procesos (GDPP), Department of Chemical Engineering, Universidad de Los Andes, Bogotá, Colombia
| | - Miguel Fernández-Niño
- Grupo de Diseño de Productos y Procesos (GDPP), Department of Chemical Engineering, Universidad de Los Andes, Bogotá, Colombia
| | | | - David O. Páez Melo
- Grupo de Diseño de Productos y Procesos (GDPP), Department of Chemical Engineering, Universidad de Los Andes, Bogotá, Colombia
| | - Flavia V. Winck
- Laboratory of Regulatory Systems Biology, Department of Biochemistry, Institute of Chemistry, Universidade de São Paulo, São Paulo, Brazil
| | - Camila Caldana
- Brazilian Bioethanol Science and Technology Laboratory, Brazilian Center for Research in Energy and Materials, Campinas, Brazil
- Max Planck Partner Group, Brazilian Bioethanol Science and Technology Laboratory, Brazilian Center for Research in Energy and Materials, Campinas, Brazil
| | | |
Collapse
|
26
|
Monte-Bello CC, Araujo EF, Martins MCM, Mafra V, da Silva VCH, Celente V, Caldana C. A Flexible Low Cost Hydroponic System for Assessing Plant Responses to Small Molecules in Sterile Conditions. J Vis Exp 2018:57800. [PMID: 30199012 PMCID: PMC6231878 DOI: 10.3791/57800] [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] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022] Open
Abstract
A wide range of studies in plant biology are performed using hydroponic cultures. In this work, an in vitro hydroponic growth system designed for assessing plant responses to chemicals and other substances of interest is presented. This system is highly efficient in obtaining homogeneous and healthy seedlings of the C3 and C4 model species Arabidopsis thaliana and Setaria viridis, respectively. The sterile cultivation avoids algae and microorganism contamination, which are known limiting factors for plant normal growth and development in hydroponics. In addition, this system is scalable, enabling the harvest of plant material on a large scale with minor mechanical damage, as well as the harvest of individual parts of a plant if desired. A detailed protocol demonstrating that this system has an easy and low-cost assembly, as it uses pipette racks as the main platform for growing plants, is provided. The feasibility of this system was validated using Arabidopsis seedlings to assess the effect of the drug AZD-8055, a chemical inhibitor of the target of rapamycin (TOR) kinase. TOR inhibition was efficiently detected as early as 30 min after an AZD-8055 treatment in roots and shoots. Furthermore, AZD-8055-treated plants displayed the expected starch-excess phenotype. We proposed this hydroponic system as an ideal method for plant researchers aiming to monitor the action of plant inducers or inhibitors, as well as to assess metabolic fluxes using isotope-labeling compounds which, in general, requires the use of expensive reagents.
Collapse
Affiliation(s)
- Carolina C Monte-Bello
- Brazilian Bioethanol Science and Technology Laboratory (CTBE), Brazilian Center for Research in energy and materials (CNPEM); University of Campinas (UNICAMP)
| | - Elias F Araujo
- Brazilian Bioethanol Science and Technology Laboratory (CTBE), Brazilian Center for Research in energy and materials (CNPEM); University of Viçosa (UFV)
| | - Marina C M Martins
- Brazilian Bioethanol Science and Technology Laboratory (CTBE), Brazilian Center for Research in energy and materials (CNPEM)
| | | | - Viviane C H da Silva
- Brazilian Bioethanol Science and Technology Laboratory (CTBE), Brazilian Center for Research in energy and materials (CNPEM); University of Campinas (UNICAMP)
| | - Viviane Celente
- Brazilian Bioethanol Science and Technology Laboratory (CTBE), Brazilian Center for Research in energy and materials (CNPEM)
| | - Camila Caldana
- Brazilian Bioethanol Science and Technology Laboratory (CTBE), Brazilian Center for Research in energy and materials (CNPEM); Brazilian Bioethanol Science and Technology Laboratory (CTBE/CNPEM), Max Planck Partner Group;
| |
Collapse
|
27
|
Garcia Tavares R, Lakshmanan P, Peiter E, O’Connell A, Caldana C, Vicentini R, Soares JS, Menossi M. ScGAI is a key regulator of culm development in sugarcane. J Exp Bot 2018; 69:3823-3837. [PMID: 29767776 PMCID: PMC6054169 DOI: 10.1093/jxb/ery180] [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] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Revised: 04/03/2018] [Accepted: 05/08/2018] [Indexed: 05/30/2023]
Abstract
Sugarcane contributes more than 70% of sugar production and is the second largest feedstock for ethanol production globally. Since sugar accumulates in sugarcane culms, culm biomass and sucrose content are the most commercially important traits. Despite extensive breeding, progress in both cane yield and sugar content remains very slow in most countries. We hypothesize that manipulating the genetic elements controlling culm growth will alter source-sink regulation and help break down the yield barriers. In this study, we investigate the role of sugarcane ScGAI, an ortholog of SLR1/D8/RHT1/GAI, on culm development and source-sink regulation through a combination of molecular techniques and transgenic strategies. We show that ScGAI is a key molecular regulator of culm growth and development. Changing ScGAI activity created substantial culm growth and carbon allocation changes for structural molecules and storage. ScGAI regulates spatio-temporal growth of sugarcane culm and leaf by interacting with ScPIF3/PIF4 and ethylene signaling elements ScEIN3/ScEIL1, and its action appears to be regulated by SUMOylation in leaf but not in the culm. Collectively, the remarkable culm growth variation observed suggests that ScGAI could be used as an effective molecular breeding target for breaking the slow yield gain in sugarcane.
Collapse
Affiliation(s)
- Rafael Garcia Tavares
- Functional Genome Laboratory, Department of Genetics, Evolution and Bioagents, Institute of Biology, State University of Campinas, Campinas, Brazil
- Sugar Research Australia (SRA), Indooroopilly, Brisbane, Australia
| | | | - Edgar Peiter
- Plant Nutrition Laboratory, Institute of Agricultural and Nutritional Sciences, Faculty of Natural Sciences III, Martin Luther University Halle-Wittenberg, Halle (Saale), Germany
| | | | - Camila Caldana
- Brazilian Bioethanol Science and Technology Laboratory, Brazilian Center for Research in Energy and Materials (CTBE), Campinas, Brazil
- Max Planck Partner Group at CTBE, Campinas, Brazil
| | - Renato Vicentini
- System Biology Laboratory, Department of Genetics, Evolution and Bioagents, Institute of Biology, State University of Campinas, Campinas, Brazil
| | - José Sérgio Soares
- Functional Genome Laboratory, Department of Genetics, Evolution and Bioagents, Institute of Biology, State University of Campinas, Campinas, Brazil
| | - Marcelo Menossi
- Functional Genome Laboratory, Department of Genetics, Evolution and Bioagents, Institute of Biology, State University of Campinas, Campinas, Brazil
| |
Collapse
|
28
|
Busso-Lopes AF, Carnielli CM, Winck F, Riaño-Pachón DM, Oliveira AK, Costa RA, Rivera C, Caldana C, Fox JW, Leme AFP. Abstract 5649: Multi-omics data indicate that primary and lymph node oral cancer cells-derived extracellular vesicles carry cargo molecules with a specific aggressive pattern. Cancer Res 2018. [DOI: 10.1158/1538-7445.am2018-5649] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Abstract
Oral squamous cell carcinoma (OSCC) exhibits high incidence and morbidity, representing 300,000 new cases and 145,000 deaths per year. Moreover, the 5-year survival rate is 50% and this is directly associated with regional lymph node metastases. To explore how the extracellular vesicles (EVs) play a significant role on OSCC lymph node metastasis, we characterized the EVs released by tumor primary site cells and their paired lymph node metastasis cells using nanoparticle tracking analysis, high-resolution microscopy (Cryo-EM), EVs uptake by HUVEC, BJ-5ta and gingival primary fibroblasts recipient cells and the proteins, lipids, metabolites and miRNAs contents. Both cells-derived EVs showed a similar size, morphology, and the presence of annexin-2 and flotillin-1 surface markers. Interesting, only gingival primary recipient cells were more likely to uptake primary OSCC-derived EVs compared with lymph node-derived EVs. This effect is probably associated with the differential abundance of 490 proteins, 316 miRNAs, 63 lipids and 17 metabolites between the oral cancer cells-derived EVs. Markedly, multilevel omic data integration indicates that metabolic processes were over-represented mainly in primary OSCC-derived EVs, suggesting that these EVs carry specific cargo molecules associated with a more aggressive pattern compared with lymph node OSCC-derived EVs.
Financial support: FAPESP (Process number 2016/50005-7).
Citation Format: Ariane F. Busso-Lopes, Carolina M. Carnielli, Flávia Winck, Diego M. Riaño-Pachón, Ana K. Oliveira, Rute A. Costa, César Rivera, Camila Caldana, Jay W. Fox, Adriana F. Paes Leme. Multi-omics data indicate that primary and lymph node oral cancer cells-derived extracellular vesicles carry cargo molecules with a specific aggressive pattern [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2018; 2018 Apr 14-18; Chicago, IL. Philadelphia (PA): AACR; Cancer Res 2018;78(13 Suppl):Abstract nr 5649.
Collapse
Affiliation(s)
| | | | | | | | - Ana K. Oliveira
- 1Brazilian Center for Research in Energy and Materials - CNPEM, Campinas, Brazil
| | - Rute A. Costa
- 1Brazilian Center for Research in Energy and Materials - CNPEM, Campinas, Brazil
| | - César Rivera
- 1Brazilian Center for Research in Energy and Materials - CNPEM, Campinas, Brazil
| | - Camila Caldana
- 1Brazilian Center for Research in Energy and Materials - CNPEM, Campinas, Brazil
| | - Jay W. Fox
- 3University of Virginia, Charlottesville, VA
| | - Adriana F. Paes Leme
- 1Brazilian Center for Research in Energy and Materials - CNPEM, Campinas, Brazil
| |
Collapse
|
29
|
Ferreira DA, Martins MCM, Cheavegatti-Gianotto A, Carneiro MS, Amadeu RR, Aricetti JA, Wolf LD, Hoffmann HP, de Abreu LGF, Caldana C. Metabolite Profiles of Sugarcane Culm Reveal the Relationship Among Metabolism and Axillary Bud Outgrowth in Genetically Related Sugarcane Commercial Cultivars. Front Plant Sci 2018; 9:857. [PMID: 29988592 PMCID: PMC6027322 DOI: 10.3389/fpls.2018.00857] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/03/2017] [Accepted: 06/01/2018] [Indexed: 05/04/2023]
Abstract
Metabolic composition is known to exert influence on several important agronomic traits, and metabolomics, which represents the chemical composition in a cell, has long been recognized as a powerful tool for bridging phenotype-genotype interactions. In this work, sixteen truly representative sugarcane Brazilian varieties were selected to explore the metabolic networks in buds and culms, the tissues involved in the vegetative propagation of this species. Due to the fact that bud sprouting is a key trait determining crop establishment in the field, the sprouting potential among the genotypes was evaluated. The use of partial least square discriminant analysis indicated only mild differences on bud outgrowth potential under controlled environmental conditions. However, primary metabolite profiling provided information on the variability of metabolic features even under a narrow genetic background, typical for modern sugarcane cultivars. Metabolite-metabolite correlations within and between tissues revealed more complex patterns for culms in relation to buds, and enabled the recognition of key metabolites (e.g., sucrose, putrescine, glutamate, serine, and myo-inositol) affecting sprouting ability. Finally, those results were associated with the genetic background of each cultivar, showing that metabolites can be potentially used as indicators for the genetic background.
Collapse
Affiliation(s)
- Danilo A. Ferreira
- Brazilian Bioethanol Science and Technology Laboratory, Centro Nacional de Pesquisa em Energia e Materiais, Campinas, Brazil
- Genetics and Molecular Biology Graduate Program, University of Campinas, Campinas, Brazil
| | - Marina C. M. Martins
- Brazilian Bioethanol Science and Technology Laboratory, Centro Nacional de Pesquisa em Energia e Materiais, Campinas, Brazil
| | - Adriana Cheavegatti-Gianotto
- Brazilian Bioethanol Science and Technology Laboratory, Centro Nacional de Pesquisa em Energia e Materiais, Campinas, Brazil
| | - Monalisa S. Carneiro
- Department of Biotechnology and Plant and Animal Production, Center for Agricultural Sciences, Federal University of São Carlos, São Carlos, Brazil
| | - Rodrigo R. Amadeu
- Department of Genetics, Luiz de Queiroz College of Agriculture, University of São Paulo, Piracicaba, Brazil
| | - Juliana A. Aricetti
- Brazilian Bioethanol Science and Technology Laboratory, Centro Nacional de Pesquisa em Energia e Materiais, Campinas, Brazil
| | - Lucia D. Wolf
- Brazilian Bioethanol Science and Technology Laboratory, Centro Nacional de Pesquisa em Energia e Materiais, Campinas, Brazil
| | - Hermann P. Hoffmann
- Department of Biotechnology and Plant and Animal Production, Center for Agricultural Sciences, Federal University of São Carlos, São Carlos, Brazil
| | - Luis G. F. de Abreu
- Brazilian Bioethanol Science and Technology Laboratory, Centro Nacional de Pesquisa em Energia e Materiais, Campinas, Brazil
| | - Camila Caldana
- Brazilian Bioethanol Science and Technology Laboratory, Centro Nacional de Pesquisa em Energia e Materiais, Campinas, Brazil
- Max-Planck Partner Group, Brazilian Bioethanol Science and Technology Laboratory, Centro Nacional de Pesquisa em Energia e Materiais, Campinas, Brazil
| |
Collapse
|
30
|
Moraes EC, Alvarez TM, Persinoti GF, Tomazetto G, Brenelli LB, Paixão DAA, Ematsu GC, Aricetti JA, Caldana C, Dixon N, Bugg TDH, Squina FM. Lignolytic-consortium omics analyses reveal novel genomes and pathways involved in lignin modification and valorization. Biotechnol Biofuels 2018; 11:75. [PMID: 29588660 PMCID: PMC5863372 DOI: 10.1186/s13068-018-1073-4] [Citation(s) in RCA: 36] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/23/2017] [Accepted: 03/09/2018] [Indexed: 05/19/2023]
Abstract
BACKGROUND Lignin is a heterogeneous polymer representing a renewable source of aromatic and phenolic bio-derived products for the chemical industry. However, the inherent structural complexity and recalcitrance of lignin makes its conversion into valuable chemicals a challenge. Natural microbial communities produce biocatalysts derived from a large number of microorganisms, including those considered unculturable, which operate synergistically to perform a variety of bioconversion processes. Thus, metagenomic approaches are a powerful tool to reveal novel optimized metabolic pathways for lignin conversion and valorization. RESULTS The lignin-degrading consortium (LigMet) was obtained from a sugarcane plantation soil sample. The LigMet taxonomical analyses (based on 16S rRNA) indicated prevalence of Proteobacteria, Actinobacteria and Firmicutes members, including the Alcaligenaceae and Micrococcaceae families, which were enriched in the LigMet compared to sugarcane soil. Analysis of global DNA sequencing revealed around 240,000 gene models, and 65 draft bacterial genomes were predicted. Along with depicting several peroxidases, dye-decolorizing peroxidases, laccases, carbohydrate esterases, and lignocellulosic auxiliary (redox) activities, the major pathways related to aromatic degradation were identified, including benzoate (or methylbenzoate) degradation to catechol (or methylcatechol), catechol ortho-cleavage, catechol meta-cleavage, and phthalate degradation. A novel Paenarthrobacter strain harboring eight gene clusters related to aromatic degradation was isolated from LigMet and was able to grow on lignin as major carbon source. Furthermore, a recombinant pathway for vanillin production was designed based on novel gene sequences coding for a feruloyl-CoA synthetase and an enoyl-CoA hydratase/aldolase retrieved from the metagenomic data set. CONCLUSION The enrichment protocol described in the present study was successful for a microbial consortium establishment towards the lignin and aromatic metabolism, providing pathways and enzyme sets for synthetic biology engineering approaches. This work represents a pioneering study on lignin conversion and valorization strategies based on metagenomics, revealing several novel lignin conversion enzymes, aromatic-degrading bacterial genomes, and a novel bacterial strain of potential biotechnological interest. The validation of a biosynthetic route for vanillin synthesis confirmed the applicability of the targeted metagenome discovery approach for lignin valorization strategies.
Collapse
Affiliation(s)
- Eduardo C. Moraes
- Laboratório Nacional de Ciência e Tecnologia do Bioetanol, Centro Nacional de Pesquisa em Energia e Materiais, Campinas, Brazil
| | - Thabata M. Alvarez
- Master Program in Industrial Biotechnology, Universidade Positivo (UP), Curitiba, Brazil
| | - Gabriela F. Persinoti
- Laboratório Nacional de Ciência e Tecnologia do Bioetanol, Centro Nacional de Pesquisa em Energia e Materiais, Campinas, Brazil
| | - Geizecler Tomazetto
- Laboratório Nacional de Ciência e Tecnologia do Bioetanol, Centro Nacional de Pesquisa em Energia e Materiais, Campinas, Brazil
| | - Livia B. Brenelli
- Laboratório Nacional de Ciência e Tecnologia do Bioetanol, Centro Nacional de Pesquisa em Energia e Materiais, Campinas, Brazil
| | - Douglas A. A. Paixão
- Laboratório Nacional de Ciência e Tecnologia do Bioetanol, Centro Nacional de Pesquisa em Energia e Materiais, Campinas, Brazil
| | - Gabriela C. Ematsu
- Laboratório Nacional de Ciência e Tecnologia do Bioetanol, Centro Nacional de Pesquisa em Energia e Materiais, Campinas, Brazil
| | - Juliana A. Aricetti
- Laboratório Nacional de Ciência e Tecnologia do Bioetanol, Centro Nacional de Pesquisa em Energia e Materiais, Campinas, Brazil
| | - Camila Caldana
- Laboratório Nacional de Ciência e Tecnologia do Bioetanol, Centro Nacional de Pesquisa em Energia e Materiais, Campinas, Brazil
| | - Neil Dixon
- Manchester Institute of Biotechnology, School of Chemistry, University of Manchester, Manchester, UK
| | | | - Fabio M. Squina
- Programa de Processos Tecnológicos e Ambientais, Universidade de Sorocaba, Sorocaba, Brazil
| |
Collapse
|
31
|
Jüppner J, Mubeen U, Leisse A, Caldana C, Wiszniewski A, Steinhauser D, Giavalisco P. The target of rapamycin kinase affects biomass accumulation and cell cycle progression by altering carbon/nitrogen balance in synchronized Chlamydomonas reinhardtii cells. Plant J 2018; 93:355-376. [PMID: 29172247 DOI: 10.1111/tpj.13787] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/17/2017] [Revised: 10/31/2017] [Accepted: 11/15/2017] [Indexed: 05/19/2023]
Abstract
Several metabolic processes tightly regulate growth and biomass accumulation. A highly conserved protein complex containing the target of rapamycin (TOR) kinase is known to integrate intra- and extracellular stimuli controlling nutrient allocation and hence cellular growth. Although several functions of TOR have been described in various heterotrophic eukaryotes, our understanding lags far behind in photosynthetic organisms. In the present investigation, we used the model alga Chlamydomonas reinhardtii to conduct a time-resolved analysis of molecular and physiological features throughout the diurnal cycle after TOR inhibition. Detailed examination of the cell cycle phases revealed that growth is not only repressed by 50%, but also that significant, non-linear delays in the progression can be observed. By using metabolomics analysis, we elucidated that the growth repression was mainly driven by differential carbon partitioning between anabolic and catabolic processes. Accordingly, the time-resolved analysis illustrated that metabolic processes including amino acid-, starch- and triacylglycerol synthesis, as well RNA degradation, were redirected within minutes of TOR inhibition. Here especially the high accumulation of nitrogen-containing compounds indicated that an active TOR kinase controls the carbon to nitrogen balance of the cell, which is responsible for biomass accumulation, growth and cell cycle progression.
Collapse
Affiliation(s)
- Jessica Jüppner
- Max Planck Institute of Molecular Plant Physiology, Am Mühlenberg 1, 14476, Potsdam-Golm, Germany
| | - Umarah Mubeen
- Max Planck Institute of Molecular Plant Physiology, Am Mühlenberg 1, 14476, Potsdam-Golm, Germany
| | - Andrea Leisse
- Max Planck Institute of Molecular Plant Physiology, Am Mühlenberg 1, 14476, Potsdam-Golm, Germany
| | - Camila Caldana
- Max Planck Institute of Molecular Plant Physiology, Am Mühlenberg 1, 14476, Potsdam-Golm, Germany
- Brazilian Bioethanol Science and Technology Laboratory/CNPEM, Rua Giuseppe Máximo Scolfano 10000, 13083-970, Campinas, Brazil
| | - Andrew Wiszniewski
- Max Planck Institute of Molecular Plant Physiology, Am Mühlenberg 1, 14476, Potsdam-Golm, Germany
| | - Dirk Steinhauser
- Max Planck Institute of Molecular Plant Physiology, Am Mühlenberg 1, 14476, Potsdam-Golm, Germany
| | - Patrick Giavalisco
- Max Planck Institute of Molecular Plant Physiology, Am Mühlenberg 1, 14476, Potsdam-Golm, Germany
| |
Collapse
|
32
|
Rocha RP, Machado M, Vaz MGMV, Vinson CC, Leite M, Richard R, Mendes LBB, Araujo WL, Caldana C, Martins MA, Williams TC, Nunes-Nesi A. Exploring the metabolic and physiological diversity of native microalgal strains (Chlorophyta) isolated from tropical freshwater reservoirs. ALGAL RES 2017. [DOI: 10.1016/j.algal.2017.10.021] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
|
33
|
Jüppner J, Mubeen U, Leisse A, Caldana C, Brust H, Steup M, Herrmann M, Steinhauser D, Giavalisco P. Dynamics of lipids and metabolites during the cell cycle of Chlamydomonas reinhardtii. Plant J 2017; 92:331-343. [PMID: 28742931 DOI: 10.1111/tpj.13642] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/13/2017] [Revised: 07/17/2017] [Accepted: 07/19/2017] [Indexed: 05/12/2023]
Abstract
Metabolites and lipids are the final products of enzymatic processes, distinguishing the different cellular functions and activities of single cells or whole tissues. Understanding these cellular functions within a well-established model system requires a systemic collection of molecular and physiological information. In the current report, the green alga Chlamydomonas reinhardtii was selected to establish a comprehensive workflow for the detailed multi-omics analysis of a synchronously growing cell culture system. After implementation and benchmarking of the synchronous cell culture, a two-phase extraction method was adopted for the analysis of proteins, lipids, metabolites and starch from a single sample aliquot of as little as 10-15 million Chlamydomonas cells. In a proof of concept study, primary metabolites and lipids were sampled throughout the diurnal cell cycle. The results of these time-resolved measurements showed that single compounds were not only coordinated with each other in different pathways, but that these complex metabolic signatures have the potential to be used as biomarkers of various cellular processes. Taken together, the developed workflow, including the synchronized growth of the photoautotrophic cell culture, in combination with comprehensive extraction methods and detailed metabolic phenotyping has the potential for use in in-depth analysis of complex cellular processes, providing essential information for the understanding of complex biological systems.
Collapse
Affiliation(s)
- Jessica Jüppner
- Max Planck Institute of Molecular Plant Physiology, Am Mühlenberg 1, 14476, Potsdam-Golm, Germany
| | - Umarah Mubeen
- Max Planck Institute of Molecular Plant Physiology, Am Mühlenberg 1, 14476, Potsdam-Golm, Germany
| | - Andrea Leisse
- Max Planck Institute of Molecular Plant Physiology, Am Mühlenberg 1, 14476, Potsdam-Golm, Germany
| | - Camila Caldana
- Max Planck Institute of Molecular Plant Physiology, Am Mühlenberg 1, 14476, Potsdam-Golm, Germany
- Brazilian Bioethanol Science and Technology Laboratory/CNPEM, Rua Giuseppe Máximo Scolfano 10000, 13083-970, Campinas, Brazil
| | - Henrike Brust
- Institute for Biochemistry and Biology, University of Potsdam, 14476, Potsdam-Golm, Germany
| | - Martin Steup
- Institute for Biochemistry and Biology, University of Potsdam, 14476, Potsdam-Golm, Germany
- University of Toronto c/o Hospital for Sick Children, PGCRL 14.9420, 72 Elm St, Toronto, ON M561H3, Canada
| | - Marion Herrmann
- Institute for Human Genetics, Humboldt University Berlin, Charité, Augustenburger Platz 1, 13353, Berlin, Germany
| | - Dirk Steinhauser
- Max Planck Institute of Molecular Plant Physiology, Am Mühlenberg 1, 14476, Potsdam-Golm, Germany
| | - Patrick Giavalisco
- Max Planck Institute of Molecular Plant Physiology, Am Mühlenberg 1, 14476, Potsdam-Golm, Germany
| |
Collapse
|
34
|
Benedetti D, Tissino E, Pozzo F, Bittolo T, Caldana C, Perini C, Martorelli D, Bravin V, D’Agaro T, Rossi FM, Bomben R, Santinelli E, Zaja F, Pozzato G, Chiarenza A, Di Raimondo F, Del Poeta G, Rossi D, Gaidano G, Dal Bo M, Gattei V, Zucchetto A. NOTCH1 mutations are associated with high CD49d expression in chronic lymphocytic leukemia: link between the NOTCH1 and the NF-κB pathways. Leukemia 2017; 32:654-662. [DOI: 10.1038/leu.2017.296] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2017] [Revised: 08/23/2017] [Accepted: 09/08/2017] [Indexed: 12/16/2022]
|
35
|
Seki M, Ohara T, Hearn TJ, Frank A, da Silva VCH, Caldana C, Webb AAR, Satake A. Adjustment of the Arabidopsis circadian oscillator by sugar signalling dictates the regulation of starch metabolism. Sci Rep 2017; 7:8305. [PMID: 28814797 PMCID: PMC5559614 DOI: 10.1038/s41598-017-08325-y] [Citation(s) in RCA: 35] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2017] [Accepted: 07/20/2017] [Indexed: 02/02/2023] Open
Abstract
Arabidopsis plants store part of the carbon fixed by photosynthesis as starch to sustain growth at night. Two competing hypotheses have been proposed to explain this diel starch turnover based on either the measurement of starch abundance with respect to circadian time, or the sensing of sugars to feedback to the circadian oscillator to dynamically adjust the timing of starch turnover. We report a phase oscillator model that permitted derivation of the ideal responses of the circadian regulation of starch breakdown to maintain sucrose homeostasis. Testing the model predictions using a sugar-unresponsive mutant of Arabidopsis demonstrated that the dynamics of starch turnover arise from the circadian clock measuring and responding to the rate of change of cellular sucrose. Our theory and experiments suggest that starch turnover is controlled by the circadian clock acting as a dynamic homeostat responding to sucrose signals to maintain carbon homeostasis.
Collapse
Affiliation(s)
- Motohide Seki
- 0000 0001 2242 4849grid.177174.3Department of Biology, Faculty of Science, Kyushu University, 744 Motooka, Nishi-ku, Fukuoka 819-0395 Japan
| | - Takayuki Ohara
- 0000 0001 2242 4849grid.177174.3Department of Biology, Faculty of Science, Kyushu University, 744 Motooka, Nishi-ku, Fukuoka 819-0395 Japan ,0000 0001 2173 7691grid.39158.36Graduate School of Environmental Science, Hokkaido University, N10W5, Sapporo, 060-0810 Japan
| | - Timothy J. Hearn
- 0000000121885934grid.5335.0Department of Plant Sciences, University of Cambridge, Cambridge, CB2 3EA United Kingdom
| | - Alexander Frank
- 0000000121885934grid.5335.0Department of Plant Sciences, University of Cambridge, Cambridge, CB2 3EA United Kingdom
| | - Viviane C. H. da Silva
- Brazilian Bioethanol Science and Technology Laboratory (CTBE), Rua Giuseppe Máximo Scolfaro 10.000 CEP 13083-100 Campinas, São Paulo, Brazil
| | - Camila Caldana
- Brazilian Bioethanol Science and Technology Laboratory (CTBE), Rua Giuseppe Máximo Scolfaro 10.000 CEP 13083-100 Campinas, São Paulo, Brazil ,Max Planck Partner Group at Brazilian Bioethanol Science and Technology Laboratory, Campinas, SP Brazil
| | - Alex A. R. Webb
- 0000000121885934grid.5335.0Department of Plant Sciences, University of Cambridge, Cambridge, CB2 3EA United Kingdom
| | - Akiko Satake
- 0000 0001 2242 4849grid.177174.3Department of Biology, Faculty of Science, Kyushu University, 744 Motooka, Nishi-ku, Fukuoka 819-0395 Japan
| |
Collapse
|
36
|
Mandelli F, Couger MB, Paixão DAA, Machado CB, Carnielli CM, Aricetti JA, Polikarpov I, Prade R, Caldana C, Paes Leme AF, Mercadante AZ, Riaño-Pachón DM, Squina FM. Thermal adaptation strategies of the extremophile bacterium Thermus filiformis based on multi-omics analysis. Extremophiles 2017; 21:775-788. [DOI: 10.1007/s00792-017-0942-2] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2017] [Accepted: 04/29/2017] [Indexed: 12/25/2022]
|
37
|
de Vries RP, Riley R, Wiebenga A, Aguilar-Osorio G, Amillis S, Uchima CA, Anderluh G, Asadollahi M, Askin M, Barry K, Battaglia E, Bayram Ö, Benocci T, Braus-Stromeyer SA, Caldana C, Cánovas D, Cerqueira GC, Chen F, Chen W, Choi C, Clum A, dos Santos RAC, Damásio ARDL, Diallinas G, Emri T, Fekete E, Flipphi M, Freyberg S, Gallo A, Gournas C, Habgood R, Hainaut M, Harispe ML, Henrissat B, Hildén KS, Hope R, Hossain A, Karabika E, Karaffa L, Karányi Z, Kraševec N, Kuo A, Kusch H, LaButti K, Lagendijk EL, Lapidus A, Levasseur A, Lindquist E, Lipzen A, Logrieco AF, MacCabe A, Mäkelä MR, Malavazi I, Melin P, Meyer V, Mielnichuk N, Miskei M, Molnár ÁP, Mulé G, Ngan CY, Orejas M, Orosz E, Ouedraogo JP, Overkamp KM, Park HS, Perrone G, Piumi F, Punt PJ, Ram AFJ, Ramón A, Rauscher S, Record E, Riaño-Pachón DM, Robert V, Röhrig J, Ruller R, Salamov A, Salih NS, Samson RA, Sándor E, Sanguinetti M, Schütze T, Sepčić K, Shelest E, Sherlock G, Sophianopoulou V, Squina FM, Sun H, Susca A, Todd RB, Tsang A, Unkles SE, van de Wiele N, van Rossen-Uffink D, Oliveira JVDC, Vesth TC, Visser J, Yu JH, Zhou M, Andersen MR, Archer DB, Baker SE, Benoit I, Brakhage AA, Braus GH, Fischer R, Frisvad JC, Goldman GH, Houbraken J, Oakley B, Pócsi I, Scazzocchio C, Seiboth B, vanKuyk PA, Wortman J, Dyer PS, Grigoriev IV. Comparative genomics reveals high biological diversity and specific adaptations in the industrially and medically important fungal genus Aspergillus. Genome Biol 2017; 18:28. [PMID: 28196534 PMCID: PMC5307856 DOI: 10.1186/s13059-017-1151-0] [Citation(s) in RCA: 311] [Impact Index Per Article: 44.4] [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: 07/05/2016] [Accepted: 01/10/2017] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND The fungal genus Aspergillus is of critical importance to humankind. Species include those with industrial applications, important pathogens of humans, animals and crops, a source of potent carcinogenic contaminants of food, and an important genetic model. The genome sequences of eight aspergilli have already been explored to investigate aspects of fungal biology, raising questions about evolution and specialization within this genus. RESULTS We have generated genome sequences for ten novel, highly diverse Aspergillus species and compared these in detail to sister and more distant genera. Comparative studies of key aspects of fungal biology, including primary and secondary metabolism, stress response, biomass degradation, and signal transduction, revealed both conservation and diversity among the species. Observed genomic differences were validated with experimental studies. This revealed several highlights, such as the potential for sex in asexual species, organic acid production genes being a key feature of black aspergilli, alternative approaches for degrading plant biomass, and indications for the genetic basis of stress response. A genome-wide phylogenetic analysis demonstrated in detail the relationship of the newly genome sequenced species with other aspergilli. CONCLUSIONS Many aspects of biological differences between fungal species cannot be explained by current knowledge obtained from genome sequences. The comparative genomics and experimental study, presented here, allows for the first time a genus-wide view of the biological diversity of the aspergilli and in many, but not all, cases linked genome differences to phenotype. Insights gained could be exploited for biotechnological and medical applications of fungi.
Collapse
Affiliation(s)
- Ronald P. de Vries
- Westerdijk Fungal Biodiversity Institute, Uppsalalaan 8, 3584 CT Utrecht, The Netherlands
- Fungal Molecular Physiology, Utrecht University, Uppsalalaan 8, 3584 CT Utrecht, The Netherlands
| | - Robert Riley
- US Department of Energy Joint Genome Institute, 2800 Mitchell Drive, Walnut Creek, CA 94598 USA
| | - Ad Wiebenga
- Westerdijk Fungal Biodiversity Institute, Uppsalalaan 8, 3584 CT Utrecht, The Netherlands
- Fungal Molecular Physiology, Utrecht University, Uppsalalaan 8, 3584 CT Utrecht, The Netherlands
| | - Guillermo Aguilar-Osorio
- Department of Food Science and Biotechnology, Faculty of Chemistry, National University of Mexico, Ciudad Universitaria, D.F. C.P. 04510 Mexico
| | - Sotiris Amillis
- Department of Biology, National and Kapodistrian University of Athens, Panepistimioupolis, 15781 Athens, Greece
| | - Cristiane Akemi Uchima
- Laboratório Nacional de Ciência e Tecnologia do Bioetanol (CTBE), Centro Nacional de Pesquisa em Energia e Materiais (CNPEM), Caixa Postal 6192 CEP 13083-970, Campinas, São Paulo Brasil
- Present address: VTT Brasil, Alameda Inajá, 123, CEP 06460-055 Barueri, São Paulo Brazil
| | - Gregor Anderluh
- Laboratory for Molecular Biology and Nanobiotechnology, National Institute of Chemistry, Hajdrihova 19, 1000 Ljubljana, Slovenia
| | - Mojtaba Asadollahi
- Department of Biochemical Engineering, Faculty of Science and Technology, University of Debrecen, 4032 Debrecen, Hungary
| | - Marion Askin
- Institute of Biology Leiden, Molecular Microbiology and Biotechnology, Leiden University, Sylviusweg 72, 2333 BE Leiden, The Netherlands
- Present address: CSIRO Publishing, Unipark, Building 1 Level 1, 195 Wellington Road, Clayton, VIC 3168 Australia
| | - Kerrie Barry
- US Department of Energy Joint Genome Institute, 2800 Mitchell Drive, Walnut Creek, CA 94598 USA
| | - Evy Battaglia
- Westerdijk Fungal Biodiversity Institute, Uppsalalaan 8, 3584 CT Utrecht, The Netherlands
- Fungal Molecular Physiology, Utrecht University, Uppsalalaan 8, 3584 CT Utrecht, The Netherlands
| | - Özgür Bayram
- Department of Molecular Microbiology and Genetics, Institute for Microbiology and Genetics, Georg August University Göttingen, Grisebachstr. 8, 37077 Göttingen, Germany
- Department of Biology, Maynooth University, Maynooth, Co. Kildare Ireland
| | - Tiziano Benocci
- Westerdijk Fungal Biodiversity Institute, Uppsalalaan 8, 3584 CT Utrecht, The Netherlands
- Fungal Molecular Physiology, Utrecht University, Uppsalalaan 8, 3584 CT Utrecht, The Netherlands
| | - Susanna A. Braus-Stromeyer
- Department of Molecular Microbiology and Genetics, Institute for Microbiology and Genetics, Georg August University Göttingen, Grisebachstr. 8, 37077 Göttingen, Germany
| | - Camila Caldana
- Laboratório Nacional de Ciência e Tecnologia do Bioetanol (CTBE), Centro Nacional de Pesquisa em Energia e Materiais (CNPEM), Caixa Postal 6192 CEP 13083-970, Campinas, São Paulo Brasil
- Max Planck Partner Group, Brazilian Bioethanol Science and Technology Laboratory, CEP 13083-100 Campinas, Sao Paulo Brazil
| | - David Cánovas
- Department of Genetics, Faculty of Biology, University of Seville, Avda de Reina Mercedes 6, 41012 Sevilla, Spain
- Fungal Genetics and Genomics Unit, Department of Applied Genetics and Cell Biology, University of Natural Resources and Life Sciences (BOKU) Vienna, Vienna, Austria
| | | | - Fusheng Chen
- College of Food Science and Technology, Huazhong Agricultural University, Wuhan, 430070 China
| | - Wanping Chen
- College of Food Science and Technology, Huazhong Agricultural University, Wuhan, 430070 China
| | - Cindy Choi
- US Department of Energy Joint Genome Institute, 2800 Mitchell Drive, Walnut Creek, CA 94598 USA
| | - Alicia Clum
- US Department of Energy Joint Genome Institute, 2800 Mitchell Drive, Walnut Creek, CA 94598 USA
| | - Renato Augusto Corrêa dos Santos
- Laboratório Nacional de Ciência e Tecnologia do Bioetanol (CTBE), Centro Nacional de Pesquisa em Energia e Materiais (CNPEM), Caixa Postal 6192 CEP 13083-970, Campinas, São Paulo Brasil
| | - André Ricardo de Lima Damásio
- Laboratório Nacional de Ciência e Tecnologia do Bioetanol (CTBE), Centro Nacional de Pesquisa em Energia e Materiais (CNPEM), Caixa Postal 6192 CEP 13083-970, Campinas, São Paulo Brasil
- Department of Biochemistry and Tissue Biology, Institute of Biology, University of Campinas, CEP 13083-862 Campinas, SP Brazil
| | - George Diallinas
- Department of Biology, National and Kapodistrian University of Athens, Panepistimioupolis, 15781 Athens, Greece
| | - Tamás Emri
- Department of Biotechnology and Microbiology, Faculty of Science and Technology, University of Debrecen, Egyetem tér 1, 4032 Debrecen, Hungary
| | - Erzsébet Fekete
- Department of Biochemical Engineering, Faculty of Science and Technology, University of Debrecen, 4032 Debrecen, Hungary
| | - Michel Flipphi
- Department of Biochemical Engineering, Faculty of Science and Technology, University of Debrecen, 4032 Debrecen, Hungary
| | - Susanne Freyberg
- Department of Molecular Microbiology and Genetics, Institute for Microbiology and Genetics, Georg August University Göttingen, Grisebachstr. 8, 37077 Göttingen, Germany
| | - Antonia Gallo
- Institute of Sciences of Food Production (ISPA), National Research Council (CNR), via Provinciale Lecce-Monteroni, 73100 Lecce, Italy
| | - Christos Gournas
- Institute of Biosciences and Applications, Microbial Molecular Genetics Laboratory, National Center for Scientific Research, Demokritos (NCSRD), Athens, Greece
- Present address: Université Libre de Bruxelles Institute of Molecular Biology and Medicine (IBMM), Brussels, Belgium
| | - Rob Habgood
- School of Life Sciences, University of Nottingham, University Park, Nottingham, NG7 2RD UK
| | | | - María Laura Harispe
- Institut Pasteur de Montevideo, Unidad Mixta INIA-IPMont, Mataojo 2020, CP11400 Montevideo, Uruguay
- Present address: Instituto de Profesores Artigas, Consejo de Formación en Educación, ANEP, CP 11800, Av. del Libertador 2025, Montevideo, Uruguay
| | - Bernard Henrissat
- CNRS, Aix-Marseille Université, Marseille, France
- INRA, USC 1408 AFMB, 13288 Marseille, France
- Department of Biological Sciences, King Abdulaziz University, Jeddah, Saudi Arabia
| | - Kristiina S. Hildén
- Department of Food and Environmental Sciences, University of Helsinki, Viikinkaari 9, Helsinki, Finland
| | - Ryan Hope
- School of Life Sciences, University of Nottingham, University Park, Nottingham, NG7 2RD UK
| | - Abeer Hossain
- Dutch DNA Biotech BV, Utrechtseweg 48, 3703AJ Zeist, The Netherlands
- Swammerdam Institute for Life Sciences, University of Amsterdam, Amsterdam, The Netherlands
| | - Eugenia Karabika
- School of Biology, University of St Andrews, St Andrews, Fife KY16 9TH UK
- Present Address: Department of Chemistry, University of Ioannina, Ioannina, 45110 Greece
| | - Levente Karaffa
- Department of Biochemical Engineering, Faculty of Science and Technology, University of Debrecen, 4032 Debrecen, Hungary
| | - Zsolt Karányi
- Department of Medicine, Faculty of Medicine, University of Debrecen, Nagyerdei krt. 98, 4032 Debrecen, Hungary
| | - Nada Kraševec
- Laboratory for Molecular Biology and Nanobiotechnology, National Institute of Chemistry, Hajdrihova 19, 1000 Ljubljana, Slovenia
| | - Alan Kuo
- US Department of Energy Joint Genome Institute, 2800 Mitchell Drive, Walnut Creek, CA 94598 USA
| | - Harald Kusch
- Department of Molecular Microbiology and Genetics, Institute for Microbiology and Genetics, Georg August University Göttingen, Grisebachstr. 8, 37077 Göttingen, Germany
- Department of Medical Informatics, University Medical Centre, Robert-Koch-Str.40, 37075 Göttingen, Germany
- Department of Molecular Biology, Universitätsmedizin Göttingen, Humboldtallee 23, Göttingen, 37073 Germany
| | - Kurt LaButti
- US Department of Energy Joint Genome Institute, 2800 Mitchell Drive, Walnut Creek, CA 94598 USA
| | - Ellen L. Lagendijk
- Institute of Biology Leiden, Molecular Microbiology and Biotechnology, Leiden University, Sylviusweg 72, 2333 BE Leiden, The Netherlands
| | - Alla Lapidus
- US Department of Energy Joint Genome Institute, 2800 Mitchell Drive, Walnut Creek, CA 94598 USA
- Present address: Center for Algorithmic Biotechnology, St.Petersburg State University, St. Petersburg, Russia
| | - Anthony Levasseur
- INRA, Aix-Marseille Univ, BBF, Biodiversité et Biotechnologie Fongiques, Marseille, France
- Present address: Aix-Marseille Université, Unité de Recherche sur les Maladies Infectieuses et Tropicales Emergentes (URMITE), UM63, CNRS 7278, IRD 198, INSERM U1095, IHU Méditerranée Infection, Pôle des Maladies Infectieuses, Assistance Publique-Hôpitaux de Marseille, Faculté de Médecine, 27 Bd Jean Moulin, 13005 Marseille, France
| | - Erika Lindquist
- US Department of Energy Joint Genome Institute, 2800 Mitchell Drive, Walnut Creek, CA 94598 USA
| | - Anna Lipzen
- US Department of Energy Joint Genome Institute, 2800 Mitchell Drive, Walnut Creek, CA 94598 USA
| | - Antonio F. Logrieco
- Institute of Sciences of Food Production (ISPA), National Research Council (CNR), Via Amendola 122/O, 70126 Bari, Italy
| | - Andrew MacCabe
- Departamento de Biotecnología, Instituto de Agroquímica y Tecnología de Alimentos, Consejo Superior de Investigaciones Científicas (CSIC), Paterna, Valencia, Spain
| | - Miia R. Mäkelä
- Department of Food and Environmental Sciences, University of Helsinki, Viikinkaari 9, Helsinki, Finland
| | - Iran Malavazi
- Departamento de Genética e Evolução, Centro de Ciências Biológicas e da Saúde, Universidade Federal de São Carlos, São Carlos, São Paulo Brazil
| | - Petter Melin
- Uppsala BioCenter, Department of Microbiology, Swedish University of Agricultural Sciences, P.O. Box 7025, 750 07 Uppsala, Sweden
- Present address: Swedish Chemicals Agency, Box 2, 172 13 Sundbyberg, Sweden
| | - Vera Meyer
- Institute of Biotechnology, Department Applied and Molecular Microbiology, Berlin University of Technology, Gustav-Meyer-Allee 25, 13355 Berlin, Germany
| | - Natalia Mielnichuk
- Department of Genetics, Faculty of Biology, University of Seville, Avda de Reina Mercedes 6, 41012 Sevilla, Spain
- Present address: Instituto de Ciencia y Tecnología Dr. César Milstein, Fundación Pablo Cassará, CONICET, Saladillo 2468 C1440FFX, Ciudad de Buenos Aires, Argentina
| | - Márton Miskei
- Department of Biotechnology and Microbiology, Faculty of Science and Technology, University of Debrecen, Egyetem tér 1, 4032 Debrecen, Hungary
- MTA-DE Momentum, Laboratory of Protein Dynamics, Department of Biochemistry and Molecular Biology, University of Debrecen, Nagyerdei krt.98., 4032 Debrecen, Hungary
| | - Ákos P. Molnár
- Department of Biochemical Engineering, Faculty of Science and Technology, University of Debrecen, 4032 Debrecen, Hungary
| | - Giuseppina Mulé
- Institute of Sciences of Food Production (ISPA), National Research Council (CNR), Via Amendola 122/O, 70126 Bari, Italy
| | - Chew Yee Ngan
- US Department of Energy Joint Genome Institute, 2800 Mitchell Drive, Walnut Creek, CA 94598 USA
| | - Margarita Orejas
- Departamento de Biotecnología, Instituto de Agroquímica y Tecnología de Alimentos, Consejo Superior de Investigaciones Científicas (CSIC), Paterna, Valencia, Spain
| | - Erzsébet Orosz
- Westerdijk Fungal Biodiversity Institute, Uppsalalaan 8, 3584 CT Utrecht, The Netherlands
- Department of Biotechnology and Microbiology, Faculty of Science and Technology, University of Debrecen, Egyetem tér 1, 4032 Debrecen, Hungary
| | - Jean Paul Ouedraogo
- Institute of Biology Leiden, Molecular Microbiology and Biotechnology, Leiden University, Sylviusweg 72, 2333 BE Leiden, The Netherlands
- Present address: Centre for Structural and Functional Genomics, Concordia University, 7141 Sherbrooke Street West, Montreal, QC H4B 1R6 Canada
| | - Karin M. Overkamp
- Dutch DNA Biotech BV, Utrechtseweg 48, 3703AJ Zeist, The Netherlands
| | - Hee-Soo Park
- School of Food Science and Biotechnology, Kyungpook National University, Daegu, 702-701 Republic of Korea
| | - Giancarlo Perrone
- Institute of Sciences of Food Production (ISPA), National Research Council (CNR), Via Amendola 122/O, 70126 Bari, Italy
| | - Francois Piumi
- INRA, Aix-Marseille Univ, BBF, Biodiversité et Biotechnologie Fongiques, Marseille, France
- Present address: INRA UMR1198 Biologie du Développement et de la Reproduction - Domaine de Vilvert, Jouy en Josas, 78352 Cedex France
| | - Peter J. Punt
- Institute of Biology Leiden, Molecular Microbiology and Biotechnology, Leiden University, Sylviusweg 72, 2333 BE Leiden, The Netherlands
- Dutch DNA Biotech BV, Utrechtseweg 48, 3703AJ Zeist, The Netherlands
| | - Arthur F. J. Ram
- Institute of Biology Leiden, Molecular Microbiology and Biotechnology, Leiden University, Sylviusweg 72, 2333 BE Leiden, The Netherlands
| | - Ana Ramón
- Sección Bioquímica, Departamento de Biología Celular y Molecular, Facultad de Ciencias, Universidad de la República, Montevideo, Uruguay
| | - Stefan Rauscher
- Department of Microbiology, Karlsruhe Institute of Technology, Institute for Applied Biosciences, Hertzstrasse 16,, 76187 Karlsruhe, Germany
| | - Eric Record
- INRA, Aix-Marseille Univ, BBF, Biodiversité et Biotechnologie Fongiques, Marseille, France
| | - Diego Mauricio Riaño-Pachón
- Laboratório Nacional de Ciência e Tecnologia do Bioetanol (CTBE), Centro Nacional de Pesquisa em Energia e Materiais (CNPEM), Caixa Postal 6192 CEP 13083-970, Campinas, São Paulo Brasil
| | - Vincent Robert
- Westerdijk Fungal Biodiversity Institute, Uppsalalaan 8, 3584 CT Utrecht, The Netherlands
| | - Julian Röhrig
- Department of Microbiology, Karlsruhe Institute of Technology, Institute for Applied Biosciences, Hertzstrasse 16,, 76187 Karlsruhe, Germany
| | - Roberto Ruller
- Laboratório Nacional de Ciência e Tecnologia do Bioetanol (CTBE), Centro Nacional de Pesquisa em Energia e Materiais (CNPEM), Caixa Postal 6192 CEP 13083-970, Campinas, São Paulo Brasil
| | - Asaf Salamov
- US Department of Energy Joint Genome Institute, 2800 Mitchell Drive, Walnut Creek, CA 94598 USA
| | - Nadhira S. Salih
- School of Life Sciences, University of Nottingham, University Park, Nottingham, NG7 2RD UK
- Department of Biology, School of Science, University of Sulaimani, Al Sulaymaneyah, Iraq
| | - Rob A. Samson
- Westerdijk Fungal Biodiversity Institute, Uppsalalaan 8, 3584 CT Utrecht, The Netherlands
| | - Erzsébet Sándor
- Institute of Food Science, Faculty of Agricultural and Food Sciences and Environmental Management, University of Debrecen, 4032 Debrecen, Hungary
| | - Manuel Sanguinetti
- Sección Bioquímica, Departamento de Biología Celular y Molecular, Facultad de Ciencias, Universidad de la República, Montevideo, Uruguay
| | - Tabea Schütze
- Institute of Biology Leiden, Molecular Microbiology and Biotechnology, Leiden University, Sylviusweg 72, 2333 BE Leiden, The Netherlands
- Present address: Department Applied and Molecular Microbiology, Institute of Biotechnology, Berlin University of Technology, Gustav-Meyer-Allee 25, 13355 Berlin, Germany
| | - Kristina Sepčić
- Department of Biology, Biotechnical Faculty, University of Ljubljana, Jamnikarjeva 101, 1000 Ljubljana, Slovenia
| | - Ekaterina Shelest
- Systems Biology/Bioinformatics group, Leibniz Institute for Natural Product Research and Infection Biology, Hans Knoell Institute, (HKI), Beutenbergstr. 11a, 07745 Jena, Germany
| | - Gavin Sherlock
- Department of Genetics, Stanford University, Stanford, CA 94305-5120 USA
| | - Vicky Sophianopoulou
- Institute of Biosciences and Applications, Microbial Molecular Genetics Laboratory, National Center for Scientific Research, Demokritos (NCSRD), Athens, Greece
| | - Fabio M. Squina
- Laboratório Nacional de Ciência e Tecnologia do Bioetanol (CTBE), Centro Nacional de Pesquisa em Energia e Materiais (CNPEM), Caixa Postal 6192 CEP 13083-970, Campinas, São Paulo Brasil
| | - Hui Sun
- US Department of Energy Joint Genome Institute, 2800 Mitchell Drive, Walnut Creek, CA 94598 USA
| | - Antonia Susca
- Institute of Sciences of Food Production (ISPA), National Research Council (CNR), Via Amendola 122/O, 70126 Bari, Italy
| | - Richard B. Todd
- Department of Plant Pathology, Kansas State University, Manhattan, KS 66506 USA
| | - Adrian Tsang
- Centre for Structural and Functional Genomics, Concordia University, 7141 Sherbrooke Street West, Montreal, QC H4B 1R6 Canada
| | - Shiela E. Unkles
- School of Biology, University of St Andrews, St Andrews, Fife KY16 9TH UK
| | - Nathalie van de Wiele
- Westerdijk Fungal Biodiversity Institute, Uppsalalaan 8, 3584 CT Utrecht, The Netherlands
| | - Diana van Rossen-Uffink
- Institute of Biology Leiden, Molecular Microbiology and Biotechnology, Leiden University, Sylviusweg 72, 2333 BE Leiden, The Netherlands
- Present address: BaseClear B.V., Einsteinweg 5, 2333 CC Leiden, The Netherlands
| | - Juliana Velasco de Castro Oliveira
- Laboratório Nacional de Ciência e Tecnologia do Bioetanol (CTBE), Centro Nacional de Pesquisa em Energia e Materiais (CNPEM), Caixa Postal 6192 CEP 13083-970, Campinas, São Paulo Brasil
| | - Tammi C. Vesth
- Department of Biotechnology and Biomedicine, Technical University of Denmark, Søltofts Plads 223, 2800 Kongens Lyngby, Denmark
| | - Jaap Visser
- Westerdijk Fungal Biodiversity Institute, Uppsalalaan 8, 3584 CT Utrecht, The Netherlands
| | - Jae-Hyuk Yu
- Departments of Bacteriology and Genetics, University of Wisconsin-Madison, 1550 Linden Drive, Madison, WI 53706 USA
| | - Miaomiao Zhou
- Westerdijk Fungal Biodiversity Institute, Uppsalalaan 8, 3584 CT Utrecht, The Netherlands
- Fungal Molecular Physiology, Utrecht University, Uppsalalaan 8, 3584 CT Utrecht, The Netherlands
| | - Mikael R. Andersen
- Department of Biotechnology and Biomedicine, Technical University of Denmark, Søltofts Plads 223, 2800 Kongens Lyngby, Denmark
| | - David B. Archer
- School of Life Sciences, University of Nottingham, University Park, Nottingham, NG7 2RD UK
| | - Scott E. Baker
- Fungal Biotechnology Team, Pacific Northwest National Laboratory, Richland, Washington, 99352 USA
| | - Isabelle Benoit
- Westerdijk Fungal Biodiversity Institute, Uppsalalaan 8, 3584 CT Utrecht, The Netherlands
- Fungal Molecular Physiology, Utrecht University, Uppsalalaan 8, 3584 CT Utrecht, The Netherlands
- Present address: Centre of Functional and Structure Genomics Biology Department Concordia University, 7141 Sherbrooke St. W., Montreal, QC H4B 1R6 Canada
| | - Axel A. Brakhage
- Department of Molecular and Applied Microbiology, Leibniz-Institute for Natural Product Research and Infection Biology - Hans Knoell Institute (HKI) and Institute for Microbiology, Friedrich Schiller University Jena, Beutenbergstr. 11a, 07745 Jena, Germany
| | - Gerhard H. Braus
- Department of Molecular Microbiology and Genetics, Institute for Microbiology and Genetics, Georg August University Göttingen, Grisebachstr. 8, 37077 Göttingen, Germany
| | - Reinhard Fischer
- Department of Microbiology, Karlsruhe Institute of Technology, Institute for Applied Biosciences, Hertzstrasse 16,, 76187 Karlsruhe, Germany
| | - Jens C. Frisvad
- Department of Biotechnology and Biomedicine, Technical University of Denmark, Søltofts Plads 223, 2800 Kongens Lyngby, Denmark
| | - Gustavo H. Goldman
- Faculdade de Ciências Farmacêuticas de Ribeirão Preto, Universidade de São Paulo, Av. do Café S/N, CEP 14040-903 Ribeirão Preto, São Paulo Brazil
| | - Jos Houbraken
- Westerdijk Fungal Biodiversity Institute, Uppsalalaan 8, 3584 CT Utrecht, The Netherlands
| | - Berl Oakley
- Department of Molecular Biosciences, University of Kansas, Lawrence, Kansas 66045 USA
| | - István Pócsi
- Department of Biotechnology and Microbiology, Faculty of Science and Technology, University of Debrecen, Egyetem tér 1, 4032 Debrecen, Hungary
| | - Claudio Scazzocchio
- Department of Microbiology, Imperial College, London, SW7 2AZ UK
- Institute for Integrative Biology of the Cell (I2BC), CEA, CNRS, University Paris‐Sud, Université Paris‐Saclay, 91198 Gif‐sur‐Yvette cedex, France
| | - Bernhard Seiboth
- Research Division Biochemical Technology, Institute of Chemical Engineering, TU Wien, Gumpendorferstraße 1a, 1060 Vienna, Austria
| | - Patricia A. vanKuyk
- Westerdijk Fungal Biodiversity Institute, Uppsalalaan 8, 3584 CT Utrecht, The Netherlands
- Institute of Biology Leiden, Molecular Microbiology and Biotechnology, Leiden University, Sylviusweg 72, 2333 BE Leiden, The Netherlands
| | - Jennifer Wortman
- Broad Institute, 415 Main St, Cambridge, MA 02142 USA
- Present address: Seres Therapeutics, 200 Sidney St, Cambridge, MA 02139 USA
| | - Paul S. Dyer
- School of Life Sciences, University of Nottingham, University Park, Nottingham, NG7 2RD UK
| | - Igor V. Grigoriev
- US Department of Energy Joint Genome Institute, 2800 Mitchell Drive, Walnut Creek, CA 94598 USA
| |
Collapse
|
38
|
Schaker PDC, Peters LP, Cataldi TR, Labate CA, Caldana C, Monteiro-Vitorello CB. Metabolome Dynamics of Smutted Sugarcane Reveals Mechanisms Involved in Disease Progression and Whip Emission. Front Plant Sci 2017; 8:882. [PMID: 28620397 PMCID: PMC5450380 DOI: 10.3389/fpls.2017.00882] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/03/2017] [Accepted: 05/10/2017] [Indexed: 05/02/2023]
Abstract
Sugarcane smut disease, caused by the biotrophic fungus Sporisorium scitamineum, is characterized by the development of a whip-like structure from the plant meristem. The disease causes negative effects on sucrose accumulation, fiber content and juice quality. The aim of this study was to exam whether the transcriptomic changes already described during the infection of sugarcane by S. scitamineum result in changes at the metabolomic level. To address this question, an analysis was conducted during the initial stage of the interaction and through disease progression in a susceptible sugarcane genotype. GC-TOF-MS allowed the identification of 73 primary metabolites. A set of these compounds was quantitatively altered at each analyzed point as compared with healthy plants. The results revealed that energetic pathways and amino acid pools were affected throughout the interaction. Raffinose levels increased shortly after infection but decreased remarkably after whip emission. Changes related to cell wall biosynthesis were characteristic of disease progression and suggested a loosening of its structure to allow whip growth. Lignin biosynthesis related to whip formation may rely on Tyr metabolism through the overexpression of a bifunctional PTAL. The altered levels of Met residues along with overexpression of SAM synthetase and ACC synthase genes suggested a role for ethylene in whip emission. Moreover, unique secondary metabolites antifungal-related were identified using LC-ESI-MS approach, which may have potential biomarker applications. Lastly, a putative toxin was the most important fungal metabolite identified whose role during infection remains to be established.
Collapse
Affiliation(s)
- Patricia D. C. Schaker
- Department of Genetics, “Luiz de Queiroz”' College of Agriculture, University of São PauloSão Paulo, Brazil
| | - Leila P. Peters
- Department of Genetics, “Luiz de Queiroz”' College of Agriculture, University of São PauloSão Paulo, Brazil
| | - Thais R. Cataldi
- Department of Genetics, “Luiz de Queiroz”' College of Agriculture, University of São PauloSão Paulo, Brazil
| | - Carlos A. Labate
- Department of Genetics, “Luiz de Queiroz”' College of Agriculture, University of São PauloSão Paulo, Brazil
| | - Camila Caldana
- Brazilian Bioethanol Science and Technology LaboratorySão Paulo, Brazil
- Max Planck Partner Group at Brazilian Bioethanol Science and Technology LaboratorySão Paulo, Brazil
| | - Claudia B. Monteiro-Vitorello
- Department of Genetics, “Luiz de Queiroz”' College of Agriculture, University of São PauloSão Paulo, Brazil
- *Correspondence: Claudia B. Monteiro-Vitorello
| |
Collapse
|
39
|
Alves de Castro P, Dos Reis TF, Dolan SK, Oliveira Manfiolli A, Brown NA, Jones GW, Doyle S, Riaño-Pachón DM, Squina FM, Caldana C, Singh A, Del Poeta M, Hagiwara D, Silva-Rocha R, Goldman GH. The Aspergillus fumigatus SchA SCH9 kinase modulates SakA HOG1 MAP kinase activity and it is essential for virulence. Mol Microbiol 2016; 102:642-671. [PMID: 27538790 DOI: 10.1111/mmi.13484] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 08/17/2016] [Indexed: 02/06/2023]
Abstract
The serine-threonine kinase TOR, the Target of Rapamycin, is an important regulator of nutrient, energy and stress signaling in eukaryotes. Sch9, a Ser/Thr kinase of AGC family (the cAMP-dependent PKA, cGMP- dependent protein kinase G and phospholipid-dependent protein kinase C family), is a substrate of TOR. Here, we characterized the fungal opportunistic pathogen Aspergillus fumigatus Sch9 homologue (SchA). The schA null mutant was sensitive to rapamycin, high concentrations of calcium, hyperosmotic stress and SchA was involved in iron metabolism. The ΔschA null mutant showed increased phosphorylation of SakA, the A. fumigatus Hog1 homologue. The schA null mutant has increased and decreased trehalose and glycerol accumulation, respectively, suggesting SchA performs different roles for glycerol and trehalose accumulation during osmotic stress. The schA was transcriptionally regulated by osmotic stress and this response was dependent on SakA and MpkC. The double ΔschA ΔsakA and ΔschA ΔmpkC mutants were more sensitive to osmotic stress than the corresponding parental strains. Transcriptomics and proteomics identified direct and indirect targets of SchA post-exposure to hyperosmotic stress. Finally, ΔschA was avirulent in a low dose murine infection model. Our results suggest there is a complex network of interactions amongst the A. fumigatus TOR, SakA and SchA pathways.
Collapse
Affiliation(s)
- Patrícia Alves de Castro
- Faculdade de Ciências Farmacêuticas de Ribeirão Preto, Universidade de São Paulo, Ribeirão Preto, Brazil
| | - Thaila Fernanda Dos Reis
- Faculdade de Ciências Farmacêuticas de Ribeirão Preto, Universidade de São Paulo, Ribeirão Preto, Brazil
| | - Stephen K Dolan
- Department of Biology, Maynooth University, Maynooth, Co. Kildare, Ireland
| | - Adriana Oliveira Manfiolli
- Faculdade de Ciências Farmacêuticas de Ribeirão Preto, Universidade de São Paulo, Ribeirão Preto, Brazil
| | - Neil Andrew Brown
- Plant Biology and Crop Science, Rothamsted Research, Harpenden, Herts, AL5 2JQ, UK
| | - Gary W Jones
- Department of Biology, Maynooth University, Maynooth, Co. Kildare, Ireland
| | - Sean Doyle
- Department of Biology, Maynooth University, Maynooth, Co. Kildare, Ireland
| | - Diego M Riaño-Pachón
- Laboratório Nacional de Ciência e Tecnologia do Bioetanol (CTBE), Centro Nacional de Pesquisa em Energia e Materiais (CNPEM), Caixa Postal 6192, Campinas, São Paulo, CEP 13083-970, Brasil
| | - Fábio Márcio Squina
- Laboratório Nacional de Ciência e Tecnologia do Bioetanol (CTBE), Centro Nacional de Pesquisa em Energia e Materiais (CNPEM), Caixa Postal 6192, Campinas, São Paulo, CEP 13083-970, Brasil
| | - Camila Caldana
- Laboratório Nacional de Ciência e Tecnologia do Bioetanol (CTBE), Centro Nacional de Pesquisa em Energia e Materiais (CNPEM), Caixa Postal 6192, Campinas, São Paulo, CEP 13083-970, Brasil.,Max Planck Partner Group at Brazilian Bioethanol Science and Technology Laboratory, Brazilian Center for Research in Energy and Materials, São Paulo, Brazil
| | - Ashutosh Singh
- Department of Molecular Genetics and Microbiology, Stony Brook University, Stony Brook, NY, USA
| | - Maurizio Del Poeta
- Department of Molecular Genetics and Microbiology, Stony Brook University, Stony Brook, NY, USA
| | - Daisuke Hagiwara
- Medical Mycology Research Center, Chiba University, Chiba, Japan
| | - Rafael Silva-Rocha
- Faculdade de Medicina de Ribeirão Preto, Universidade de São Paulo, Ribeirão Preto, Brazil
| | - Gustavo H Goldman
- Faculdade de Ciências Farmacêuticas de Ribeirão Preto, Universidade de São Paulo, Ribeirão Preto, Brazil
| |
Collapse
|
40
|
Jorge TF, Rodrigues JA, Caldana C, Schmidt R, van Dongen JT, Thomas-Oates J, António C. Mass spectrometry-based plant metabolomics: Metabolite responses to abiotic stress. Mass Spectrom Rev 2016; 35:620-49. [PMID: 25589422 DOI: 10.1002/mas.21449] [Citation(s) in RCA: 145] [Impact Index Per Article: 18.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/22/2014] [Revised: 10/02/2014] [Accepted: 10/14/2014] [Indexed: 05/08/2023]
Abstract
Metabolomics is one omics approach that can be used to acquire comprehensive information on the composition of a metabolite pool to provide a functional screen of the cellular state. Studies of the plant metabolome include analysis of a wide range of chemical species with diverse physical properties, from ionic inorganic compounds to biochemically derived hydrophilic carbohydrates, organic and amino acids, and a range of hydrophobic lipid-related compounds. This complexitiy brings huge challenges to the analytical technologies employed in current plant metabolomics programs, and powerful analytical tools are required for the separation and characterization of this extremely high compound diversity present in biological sample matrices. The use of mass spectrometry (MS)-based analytical platforms to profile stress-responsive metabolites that allow some plants to adapt to adverse environmental conditions is fundamental in current plant biotechnology research programs for the understanding and development of stress-tolerant plants. In this review, we describe recent applications of metabolomics and emphasize its increasing application to study plant responses to environmental (stress-) factors, including drought, salt, low oxygen caused by waterlogging or flooding of the soil, temperature, light and oxidative stress (or a combination of them). Advances in understanding the global changes occurring in plant metabolism under specific abiotic stress conditions are fundamental to enhance plant fitness and increase stress tolerance. © 2015 Wiley Periodicals, Inc. Mass Spec Rev 35:620-649, 2016.
Collapse
Affiliation(s)
- Tiago F Jorge
- Plant Metabolomics Laboratory, Instituto de Tecnologia Química e Biológica António Xavier-Universidade Nova de Lisboa (ITQB-UNL), Avenida República, 2780-157, Oeiras, Portugal
| | - João A Rodrigues
- Instituto de Medicina Molecular, Faculdade de Medicina da Universidade de Lisboa, Avenida Professor Egas Moniz, 1649-028, Lisboa, Portugal
| | - Camila Caldana
- Max-Planck-partner group at the Brazilian Bioethanol Science and Technology Laboratory/CNPEM, 13083-970, Campinas-SP, Brazil
| | - Romy Schmidt
- Institute of Biology I, RWTH Aachen University, Worringerweg 1, 52074, Aachen, Germany
| | - Joost T van Dongen
- Institute of Biology I, RWTH Aachen University, Worringerweg 1, 52074, Aachen, Germany
| | - Jane Thomas-Oates
- Jane Thomas-Oates, Centre of Excellence in Mass Spectrometry, and Department of Chemistry, University of York, Heslington, York, YO10 5DD, UK
| | - Carla António
- Plant Metabolomics Laboratory, Instituto de Tecnologia Química e Biológica António Xavier-Universidade Nova de Lisboa (ITQB-UNL), Avenida República, 2780-157, Oeiras, Portugal
| |
Collapse
|
41
|
Abstract
All living organisms rely on nutrients to sustain cell metabolism and energy production, which in turn need to be adjusted based on available resources. The evolutionarily conserved target of rapamycin (TOR) protein kinase is a central regulatory hub that connects environmental information about the quantity and quality of nutrients to developmental and metabolic processes in order to maintain cellular homeostasis. TOR is activated by both nitrogen and carbon metabolites and promotes energy-consuming processes such as cell division, mRNA translation, and anabolism in times of abundance while repressing nutrient remobilization through autophagy. In animals and yeasts, TOR acts antagonistically to the starvation-induced AMP-activated kinase (AMPK)/sucrose nonfermenting 1 (Snf1) kinase, called Snf1-related kinase 1 (SnRK1) in plants. This review summarizes the immense knowledge on the relationship between TOR signaling and nutrients in nonphotosynthetic organisms and presents recent findings in plants that illuminate the crucial role of this pathway in conveying nutrient-derived signals and regulating many aspects of metabolism and growth.
Collapse
Affiliation(s)
- Thomas Dobrenel
- Institut Jean-Pierre Bourgin, UMR 1318 INRA AgroParisTech, ERL CNRS 3559, Saclay Plant Sciences, Versailles 78026, France;
- Umeå Plant Science Center, Department of Plant Physiology, Umeå University, Umeå 90187, Sweden
| | - Camila Caldana
- Molecular Physiology of Plant Biomass Production Group, Max Planck Partner Group, Brazilian Bioethanol Science and Technology Laboratory, CEP 13083-100 Campinas, São Paulo, Brazil
| | - Johannes Hanson
- Umeå Plant Science Center, Department of Plant Physiology, Umeå University, Umeå 90187, Sweden
| | - Christophe Robaglia
- Laboratoire de Génétique et Biophysique des Plantes, UMR 7265, DSV, IBEB, SBVME, CEA, CNRS, Aix Marseille Université, Faculté des Sciences de Luminy, Marseille 13009, France
| | - Michel Vincentz
- Laboratório de Genética de Plantas, Centro de Biologia Molecular e Engenharia Genética, Universidade Estadual de Campinas, CEP 13083-875 Campinas, São Paulo, Brazil
| | - Bruce Veit
- Forage Improvement, AgResearch, Institute of Fundamental Sciences, Massey University, Palmerston North 4442, New Zealand
| | - Christian Meyer
- Institut Jean-Pierre Bourgin, UMR 1318 INRA AgroParisTech, ERL CNRS 3559, Saclay Plant Sciences, Versailles 78026, France;
| |
Collapse
|
42
|
Abstract
All living organisms rely on nutrients to sustain cell metabolism and energy production, which in turn need to be adjusted based on available resources. The evolutionarily conserved target of rapamycin (TOR) protein kinase is a central regulatory hub that connects environmental information about the quantity and quality of nutrients to developmental and metabolic processes in order to maintain cellular homeostasis. TOR is activated by both nitrogen and carbon metabolites and promotes energy-consuming processes such as cell division, mRNA translation, and anabolism in times of abundance while repressing nutrient remobilization through autophagy. In animals and yeasts, TOR acts antagonistically to the starvation-induced AMP-activated kinase (AMPK)/sucrose nonfermenting 1 (Snf1) kinase, called Snf1-related kinase 1 (SnRK1) in plants. This review summarizes the immense knowledge on the relationship between TOR signaling and nutrients in nonphotosynthetic organisms and presents recent findings in plants that illuminate the crucial role of this pathway in conveying nutrient-derived signals and regulating many aspects of metabolism and growth.
Collapse
Affiliation(s)
- Thomas Dobrenel
- Institut Jean-Pierre Bourgin, UMR 1318 INRA AgroParisTech, ERL CNRS 3559, Saclay Plant Sciences, Versailles 78026, France;
- Umeå Plant Science Center, Department of Plant Physiology, Umeå University, Umeå 90187, Sweden
| | - Camila Caldana
- Molecular Physiology of Plant Biomass Production Group, Max Planck Partner Group, Brazilian Bioethanol Science and Technology Laboratory, CEP 13083-100 Campinas, São Paulo, Brazil
| | - Johannes Hanson
- Umeå Plant Science Center, Department of Plant Physiology, Umeå University, Umeå 90187, Sweden
| | - Christophe Robaglia
- Laboratoire de Génétique et Biophysique des Plantes, UMR 7265, DSV, IBEB, SBVME, CEA, CNRS, Aix Marseille Université, Faculté des Sciences de Luminy, Marseille 13009, France
| | - Michel Vincentz
- Laboratório de Genética de Plantas, Centro de Biologia Molecular e Engenharia Genética, Universidade Estadual de Campinas, CEP 13083-875 Campinas, São Paulo, Brazil
| | - Bruce Veit
- Forage Improvement, AgResearch, Institute of Fundamental Sciences, Massey University, Palmerston North 4442, New Zealand
| | - Christian Meyer
- Institut Jean-Pierre Bourgin, UMR 1318 INRA AgroParisTech, ERL CNRS 3559, Saclay Plant Sciences, Versailles 78026, France;
| |
Collapse
|
43
|
Winck FV, Melo DOP, Riaño-Pachón DM, Martins MCM, Caldana C, Barrios AFG. Analysis of Sensitive CO2 Pathways and Genes Related to Carbon Uptake and Accumulation in Chlamydomonas reinhardtii through Genomic Scale Modeling and Experimental Validation. Front Plant Sci 2016; 7:43. [PMID: 26904035 PMCID: PMC4746324 DOI: 10.3389/fpls.2016.00043] [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] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/11/2015] [Accepted: 01/11/2016] [Indexed: 05/25/2023]
Abstract
The development of microalgae sustainable applications needs better understanding of microalgae biology. Moreover, how cells coordinate their metabolism toward biomass accumulation is not fully understood. In this present study, flux balance analysis (FBA) was performed to identify sensitive metabolic pathways of Chlamydomonas reinhardtii under varied CO2 inputs. The metabolic network model of Chlamydomonas was updated based on the genome annotation data and sensitivity analysis revealed CO2 sensitive reactions. Biological experiments were performed with cells cultivated at 0.04% (air), 2.5, 5, 8, and 10% CO2 concentration under controlled conditions and cell growth profiles and biomass content were measured. Pigments, lipids, proteins, and starch were further quantified for the reference low (0.04%) and high (10%) CO2 conditions. The expression level of candidate genes of sensitive reactions was measured and validated by quantitative real time PCR. The sensitive analysis revealed mitochondrial compartment as the major affected by changes on the CO2 concentrations and glycolysis/gluconeogenesis, glyoxylate, and dicarboxylate metabolism among the affected metabolic pathways. Genes coding for glycerate kinase (GLYK), glycine cleavage system, H-protein (GCSH), NAD-dependent malate dehydrogenase (MDH3), low-CO2 inducible protein A (LCIA), carbonic anhydrase 5 (CAH5), E1 component, alpha subunit (PDC3), dual function alcohol dehydrogenase/acetaldehyde dehydrogenase (ADH1), and phosphoglucomutase (GPM2), were defined, among other genes, as sensitive nodes in the metabolic network simulations. These genes were experimentally responsive to the changes in the carbon fluxes in the system. We performed metabolomics analysis using mass spectrometry validating the modulation of carbon dioxide responsive pathways and metabolites. The changes on CO2 levels mostly affected the metabolism of amino acids found in the photorespiration pathway. Our updated metabolic network was compared to previous model and it showed more consistent results once considering the experimental data. Possible roles of the sensitive pathways in the biomass metabolism are discussed.
Collapse
Affiliation(s)
- Flavia V. Winck
- Grupo de Diseño de Productos y Procesos, Department of Chemical Engineering, Universidad de los AndesBogotá, Colombia
| | - David O. Páez Melo
- Grupo de Diseño de Productos y Procesos, Department of Chemical Engineering, Universidad de los AndesBogotá, Colombia
| | - Diego M. Riaño-Pachón
- Group of Computational and Evolutionary Biology, Department of Biological Sciences, Universidad de los AndesBogotá, Colombia
| | - Marina C. M. Martins
- Brazilian Bioethanol Science and Technology Laboratory, Brazilian Center for Research in Energy and MaterialsCampinas, Brazil
| | - Camila Caldana
- Brazilian Bioethanol Science and Technology Laboratory, Brazilian Center for Research in Energy and MaterialsCampinas, Brazil
- Max Planck Partner Group, Brazilian Bioethanol Science and Technology Laboratory, Brazilian Center for Research in Energy and MaterialsCampinas, Brazil
| | - Andrés F. González Barrios
- Grupo de Diseño de Productos y Procesos, Department of Chemical Engineering, Universidad de los AndesBogotá, Colombia
| |
Collapse
|
44
|
Brown NA, Dos Reis TF, Ries LNA, Caldana C, Mah JH, Yu JH, Macdonald JM, Goldman GH. G-protein coupled receptor-mediated nutrient sensing and developmental control in Aspergillus nidulans. Mol Microbiol 2015; 98:420-39. [PMID: 26179439 DOI: 10.1111/mmi.13135] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 07/14/2015] [Indexed: 12/31/2022]
Abstract
Nutrient sensing and utilisation are fundamental for all life forms. As heterotrophs, fungi have evolved a diverse range of mechanisms for sensing and taking up various nutrients. Despite its importance, only a limited number of nutrient receptors and their corresponding ligands have been identified in fungi. G-protein coupled receptors (GPCRs) are the largest family of transmembrane receptors. The Aspergillus nidulans genome encodes 16 putative GPCRs, but only a few have been functionally characterised. Our previous study showed the increased expression of an uncharacterised putative GPCR, gprH, during carbon starvation. GprH appears conserved throughout numerous filamentous fungi. Here, we reveal that GprH is a putative receptor involved in glucose and tryptophan sensing. The absence of GprH results in a reduction in cAMP levels and PKA activity upon adding glucose or tryptophan to starved cells. GprH is pre-formed in conidia and is increasingly active during carbon starvation, where it plays a role in glucose uptake and the recovery of hyphal growth. GprH also represses sexual development under conditions favouring sexual fruiting and during carbon starvation in submerged cultures. In summary, the GprH nutrient-sensing system functions upstream of the cAMP-PKA pathway, influences primary metabolism and hyphal growth, while represses sexual development in A. nidulans.
Collapse
Affiliation(s)
- Neil Andrew Brown
- Plant Biology and Crop Science, Rothamsted Research, Harpenden, Herts, AL5 2JQ, UK
| | - Thaila Fernanda Dos Reis
- Faculdade de Ciências Farmacêuticas de Ribeirão Preto, Universidade de São Paulo, São Paulo, Brazil
| | | | - Camila Caldana
- Laboratório Nacional de Ciência e Tecnologia do Bioetanol - CTBE, Campinas, São Paulo, Brazil.,Max Planck Partnergroup at CTBE/CNPEM, Campinas, São Paulo, Brazil
| | - Jae-Hyung Mah
- Department of Food and Biotechnology, Korea University, Sejong, South Korea
| | - Jae-Hyuk Yu
- Department of Bacteriology, University of Wisconsin, Madison, WI, USA
| | - Jeffrey M Macdonald
- UNC Metabolomic Facility, University of North Carolina, Chapel Hill, NC, 27599, USA
| | - Gustavo Henrique Goldman
- Faculdade de Ciências Farmacêuticas de Ribeirão Preto, Universidade de São Paulo, São Paulo, Brazil.,Laboratório Nacional de Ciência e Tecnologia do Bioetanol - CTBE, Campinas, São Paulo, Brazil
| |
Collapse
|
45
|
Fala AM, Oliveira JF, Adamoski D, Aricetti JA, Dias MM, Dias MVB, Sforça ML, Lopes-de-Oliveira PS, Rocco SA, Caldana C, Dias SMG, Ambrosio ALB. Unsaturated fatty acids as high-affinity ligands of the C-terminal Per-ARNT-Sim domain from the Hypoxia-inducible factor 3α. Sci Rep 2015; 5:12698. [PMID: 26237540 PMCID: PMC4522956 DOI: 10.1038/srep12698] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2015] [Accepted: 07/07/2015] [Indexed: 01/09/2023] Open
Abstract
Hypoxia-inducible transcription factors (HIF) form heterodimeric complexes that mediate cell responses to hypoxia. The oxygen-dependent stability and activity of the HIF-α subunits is traditionally associated to post-translational modifications such as hydroxylation, acetylation, ubiquitination, and phosphorylation. Here we report novel evidence showing that unsaturated fatty acids are naturally occurring, non-covalent structural ligands of HIF-3α, thus providing the initial framework for exploring its exceptional role as a lipid sensor under hypoxia.
Collapse
Affiliation(s)
- Angela M Fala
- Laboratório Nacional de Biociências, Centro Nacional de Pesquisa em Energia e Materiais, Campinas, SP, Brazil, 13083-100
| | - Juliana F Oliveira
- Laboratório Nacional de Biociências, Centro Nacional de Pesquisa em Energia e Materiais, Campinas, SP, Brazil, 13083-100
| | - Douglas Adamoski
- Laboratório Nacional de Biociências, Centro Nacional de Pesquisa em Energia e Materiais, Campinas, SP, Brazil, 13083-100
| | - Juliana A Aricetti
- Laboratório Nacional de Ciência e Tecnologia do Bioetanol, Centro Nacional de Pesquisa em Energia e Materiais,, Campinas, SP, Brazil, 13083-100
| | - Marilia M Dias
- Laboratório Nacional de Biociências, Centro Nacional de Pesquisa em Energia e Materiais, Campinas, SP, Brazil, 13083-100
| | - Marcio V B Dias
- Laboratório Nacional de Biociências, Centro Nacional de Pesquisa em Energia e Materiais, Campinas, SP, Brazil, 13083-100
| | - Maurício L Sforça
- Laboratório Nacional de Biociências, Centro Nacional de Pesquisa em Energia e Materiais, Campinas, SP, Brazil, 13083-100
| | - Paulo S Lopes-de-Oliveira
- Laboratório Nacional de Biociências, Centro Nacional de Pesquisa em Energia e Materiais, Campinas, SP, Brazil, 13083-100
| | - Silvana A Rocco
- Laboratório Nacional de Biociências, Centro Nacional de Pesquisa em Energia e Materiais, Campinas, SP, Brazil, 13083-100
| | - Camila Caldana
- Laboratório Nacional de Ciência e Tecnologia do Bioetanol, Centro Nacional de Pesquisa em Energia e Materiais,, Campinas, SP, Brazil, 13083-100.,Max Plack-partner group at the Laboratório Nacional de Ciência e Tecnologia do Bioetanol
| | - Sandra M G Dias
- Laboratório Nacional de Biociências, Centro Nacional de Pesquisa em Energia e Materiais, Campinas, SP, Brazil, 13083-100
| | - Andre L B Ambrosio
- Laboratório Nacional de Biociências, Centro Nacional de Pesquisa em Energia e Materiais, Campinas, SP, Brazil, 13083-100
| |
Collapse
|
46
|
Schmidt R, Caldana C, Mueller-Roeber B, Schippers JHM. The contribution of SERF1 to root-to-shoot signaling during salinity stress in rice. Plant Signal Behav 2014; 9:e27540. [PMID: 24451326 PMCID: PMC4091250 DOI: 10.4161/psb.27540] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/06/2013] [Revised: 12/15/2013] [Accepted: 12/16/2013] [Indexed: 05/20/2023]
Abstract
Stress perception and communication play important roles in the adaptation of plants to changing environmental conditions. Plant roots are the first organs to detect changes in the soil water potential induced by salt stress. In the presence of salinity stress, root-to-shoot communication occurs to adjust the growth of the whole plant. So far, the phytohormone abscisic acid (ABA), hydraulic signals and reactive oxygen species (ROS) have been proposed to mediate this communication under salt stress. Recently, we identified the rice transcription factor SALT-RESPONSIVE ERF1 (SERF1), which regulates a ROS-dependent transcriptional cascade in roots required for salinity tolerance. Upon salt stress, SERF1 knockout mutant plants show an increased leaf temperature as compared with wild type. As this occurs within the first 20 min of salt stress, we here evaluated the involvement of SERF1 in the perception of salt stress in the shoot. By metabolic profiling and expression analysis we show that the action of SERF1 in signal communication to the shoot is independent from ABA, but does affect the accumulation of ROS-related metabolites and transcripts under short-term salt stress.
Collapse
Affiliation(s)
- Romy Schmidt
- Institute of Biochemistry and Biology; University of Potsdam; Potsdam, Germany
- Max Planck Institute of Molecular Plant Physiology; Potsdam, Germany
| | - Camila Caldana
- Max Planck Institute of Molecular Plant Physiology; Potsdam, Germany
| | - Bernd Mueller-Roeber
- Institute of Biochemistry and Biology; University of Potsdam; Potsdam, Germany
- Max Planck Institute of Molecular Plant Physiology; Potsdam, Germany
| | - Jos HM Schippers
- Institute of Biochemistry and Biology; University of Potsdam; Potsdam, Germany
- Max Planck Institute of Molecular Plant Physiology; Potsdam, Germany
| |
Collapse
|
47
|
Pérez-Pérez JM, Esteve-Bruna D, González-Bayón R, Kangasjärvi S, Caldana C, Hannah MA, Willmitzer L, Ponce MR, Micol JL. Functional Redundancy and Divergence within the Arabidopsis RETICULATA-RELATED Gene Family. Plant Physiol 2013; 162:589-603. [PMID: 23596191 PMCID: PMC3668055 DOI: 10.1104/pp.113.217323] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/06/2013] [Accepted: 04/17/2013] [Indexed: 05/20/2023]
Abstract
A number of Arabidopsis (Arabidopsis thaliana) mutants exhibit leaf reticulation, having green veins that stand out against paler interveinal tissues, fewer cells in the interveinal mesophyll, and normal perivascular bundle sheath cells. Here, to examine the basis of leaf reticulation, we analyzed the Arabidopsis RETICULATA-RELATED (RER) gene family, several members of which cause leaf reticulation when mutated. Although transcripts of RE, RER1, and RER3 were mainly detected in the bundle sheath cells of expanded leaves, functional RER3:GREEN FLUORESCENT PROTEIN was visualized in the chloroplast membranes of all photosynthetic cells. Leaf reticulation in the re and rer3 loss-of-function mutants occurred, along with accumulation of reactive oxygen species, in a photoperiod-dependent manner. A comparison of re and rer3 leaf messenger RNA expression profiles showed more than 200 genes were similarly misexpressed in both mutants. In addition, metabolic profiles of mature leaves revealed that several biosynthetic pathways downstream of pyruvate are altered in re and rer3. Double mutant analysis showed that only re rer1 and rer5 rer6 exhibited synergistic phenotypes, indicating functional redundancy. The redundancy between RE and its closest paralog, RER1, was confirmed by overexpressing RER1 in re mutants, which partially suppressed leaf reticulation. Our results show that RER family members can be divided into four functional modules with divergent functions. Moreover, these results provide insights into the origin of the reticulated phenotype, suggesting that the RER proteins functionally interconnect photoperiodic growth, amino acid homeostasis, and reactive oxygen species metabolism during Arabidopsis leaf growth.
Collapse
|
48
|
Töpfer N, Caldana C, Grimbs S, Willmitzer L, Fernie AR, Nikoloski Z. Integration of genome-scale modeling and transcript profiling reveals metabolic pathways underlying light and temperature acclimation in Arabidopsis. Plant Cell 2013; 25:1197-211. [PMID: 23613196 PMCID: PMC3663262 DOI: 10.1105/tpc.112.108852] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/22/2012] [Revised: 03/18/2013] [Accepted: 04/05/2013] [Indexed: 05/21/2023]
Abstract
Understanding metabolic acclimation of plants to challenging environmental conditions is essential for dissecting the role of metabolic pathways in growth and survival. As stresses involve simultaneous physiological alterations across all levels of cellular organization, a comprehensive characterization of the role of metabolic pathways in acclimation necessitates integration of genome-scale models with high-throughput data. Here, we present an integrative optimization-based approach, which, by coupling a plant metabolic network model and transcriptomics data, can predict the metabolic pathways affected in a single, carefully controlled experiment. Moreover, we propose three optimization-based indices that characterize different aspects of metabolic pathway behavior in the context of the entire metabolic network. We demonstrate that the proposed approach and indices facilitate quantitative comparisons and characterization of the plant metabolic response under eight different light and/or temperature conditions. The predictions of the metabolic functions involved in metabolic acclimation of Arabidopsis thaliana to the changing conditions are in line with experimental evidence and result in a hypothesis about the role of homocysteine-to-Cys interconversion and Asn biosynthesis. The approach can also be used to reveal the role of particular metabolic pathways in other scenarios, while taking into consideration the entirety of characterized plant metabolism.
Collapse
Affiliation(s)
- Nadine Töpfer
- Systems Biology and Mathematical Modeling Group, Max Planck Institute of Molecular Plant Physiology, 14476 Potsdam-Golm, Germany
| | - Camila Caldana
- Brazilian Bioethanol Science and Technology Laboratory, Integrate Brazilian Center of Research in Energy and Materials, Associated Centers to the Brazilian Association for Synchrotron Light Technology, 13083-970 Campinas, Brazil
| | - Sergio Grimbs
- Institute of Biochemistry and Biology, University of Potsdam, 14476 Potsdam-Golm, Germany
| | - Lothar Willmitzer
- Genes and Small Molecules Group, Max Planck Institute of Molecular Plant Physiology, 14476 Potsdam-Golm, Germany
| | - Alisdair R. Fernie
- Central Metabolism Group, Max Planck Institute of Molecular Plant Physiology, 14476 Potsdam-Golm, Germany
| | - Zoran Nikoloski
- Systems Biology and Mathematical Modeling Group, Max Planck Institute of Molecular Plant Physiology, 14476 Potsdam-Golm, Germany
- Address correspondence to
| |
Collapse
|
49
|
Caldana C, Li Y, Leisse A, Zhang Y, Bartholomaeus L, Fernie AR, Willmitzer L, Giavalisco P. Systemic analysis of inducible target of rapamycin mutants reveal a general metabolic switch controlling growth in Arabidopsis thaliana. Plant J 2013; 73:897-909. [PMID: 23173928 DOI: 10.1111/tpj.12080] [Citation(s) in RCA: 152] [Impact Index Per Article: 13.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/23/2012] [Revised: 11/18/2012] [Accepted: 11/20/2012] [Indexed: 05/19/2023]
Abstract
The target of rapamycin (TOR) pathway is a major regulator of growth in all eukaryotes, integrating energy, nutrient and stress signals into molecular decisions. By using large-scale MS-based metabolite profiling of primary, secondary and lipid compounds in combination with array-based transcript profiling, we show that the TOR protein not only regulates growth but also influences nutrient partitioning and central energy metabolism. The study was performed on plants exhibiting conditional down-regulation of AtTOR expression, revealing strong regulation of genes involved in pathways such as the cell cycle, cell-wall modifications and senescence, together with major changes in transcripts and metabolites of the primary and secondary metabolism. In agreement with these results, our morphological and metabolic analyses disclosed major metabolic changes leading to massive accumulations of storage lipids and starch. The implications of these data in the context of the general role of TOR in eukaryotic systems are discussed in parallel with the plant-specific aspects of TOR function. Finally, we propose a role for harnessing the plant TOR pathway by utilizing it as a potent metabolic switch, offering a possible route for biotechnological optimization of plant energy content and carbon partitioning for the production of bioenergy.
Collapse
Affiliation(s)
- Camila Caldana
- Max Planck Institute of Molecular Plant Physiology, Am Mühlenberg 1, 14476, Potsdam, Germany.
| | | | | | | | | | | | | | | |
Collapse
|
50
|
Hubberten HM, Klie S, Caldana C, Degenkolbe T, Willmitzer L, Hoefgen R. Additional role of O-acetylserine as a sulfur status-independent regulator during plant growth. Plant J 2012; 70:666-77. [PMID: 22243437 DOI: 10.1111/j.1365-313x.2012.04905.x] [Citation(s) in RCA: 65] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/18/2023]
Abstract
O-acetylserine (OAS) is one of the most prominent metabolites whose levels are altered upon sulfur starvation. However, its putative role as a signaling molecule in higher plants is controversial. This paper provides further evidence that OAS is a signaling molecule, based on computational analysis of time-series experiments and on studies of transgenic plants conditionally displaying increased OAS levels. Transcripts whose levels correlated with the transient and specific increase in OAS levels observed in leaves of Arabidopsis thaliana plants 5-10 min after transfer to darkness and with diurnal oscillation of the OAS content, showing a characteristic peak during the night, were identified. Induction of a serine-O-acetyltransferase gene (SERAT) in transgenic A. thaliana plants expressing the genes under the control of an inducible promoter resulted in a specific time-dependent increase in OAS levels. Monitoring the transcriptome response at time points at which no changes in sulfur-related metabolites except OAS were observed and correlating this with the light/dark transition and diurnal experiments resulted in identification of six genes whose expression was highly correlated with that of OAS (adenosine-5'-phosphosulfate reductase 3, sulfur-deficiency-induced 1, sulfur-deficiency-induced 2, low-sulfur-induced 1, serine hydroxymethyltransferase 7 and ChaC-like protein). These data suggest that OAS displays a signalling function leading to changes in transcript levels of a specific gene set irrespective of the sulfur status of the plant. Additionally, a role for OAS in a specific part of the sulfate response can be deduced.
Collapse
Affiliation(s)
- Hans-Michael Hubberten
- Max Planck Institut für Molekulare Pflanzenphysiologie, Am Mühlenberg 1, Potsdam-Golm, Germany.
| | | | | | | | | | | |
Collapse
|