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Ziegler AL, Ullmann L, Boßmann M, Stein KL, Liebal UW, Mitsos A, Blank LM. Itaconic acid production by co-feeding of Ustilago maydis: A combined approach of experimental data, design of experiments, and metabolic modeling. Biotechnol Bioeng 2024; 121:1846-1858. [PMID: 38494797 DOI: 10.1002/bit.28693] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2023] [Revised: 02/26/2024] [Accepted: 02/29/2024] [Indexed: 03/19/2024]
Abstract
Itaconic acid is a platform chemical with a range of applications in polymer synthesis and is also discussed for biofuel production. While produced in industry from glucose or sucrose, co-feeding of glucose and acetate was recently discussed to increase itaconic acid production by the smut fungus Ustilago maydis. In this study, we investigate the optimal co-feeding conditions by interlocking experimental and computational methods. Flux balance analysis indicates that acetate improves the itaconic acid yield up to a share of 40% acetate on a carbon molar basis. A design of experiment results in the maximum yield of 0.14 itaconic acid per carbon source from 100 g L - 1 $\,\text{g L}{}^{-1}$ glucose and 12 g L - 1 $\,\text{g L}{}^{-1}$ acetate. The yield is improved by around 22% when compared to feeding of glucose as sole carbon source. To further improve the yield, gene deletion targets are discussed that were identified using the metabolic optimization tool OptKnock. The study contributes ideas to reduce land use for biotechnology by incorporating acetate as co-substrate, a C2-carbon source that is potentially derived from carbon dioxide.
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Affiliation(s)
- Anita L Ziegler
- Aachener Verfahrenstechnik - Process Systems Engineering (AVT.SVT), RWTH Aachen University, Aachen, Germany
| | - Lena Ullmann
- Institute of Applied Microbiology (iAMB), Aachen Biology and Biotechnology (ABBt), RWTH Aachen University, Aachen, Germany
| | - Manuel Boßmann
- Aachener Verfahrenstechnik - Process Systems Engineering (AVT.SVT), RWTH Aachen University, Aachen, Germany
| | - Karla L Stein
- Institute of Applied Microbiology (iAMB), Aachen Biology and Biotechnology (ABBt), RWTH Aachen University, Aachen, Germany
| | - Ulf W Liebal
- Institute of Applied Microbiology (iAMB), Aachen Biology and Biotechnology (ABBt), RWTH Aachen University, Aachen, Germany
| | - Alexander Mitsos
- Aachener Verfahrenstechnik - Process Systems Engineering (AVT.SVT), RWTH Aachen University, Aachen, Germany
- JARA-ENERGY, Aachen, Germany
- Institute of Energy and Climate Research: Energy Systems Engineering (IEK-10), Forschungszentrum Jü lich GmbH, Jü lich, Germany
| | - Lars M Blank
- Institute of Applied Microbiology (iAMB), Aachen Biology and Biotechnology (ABBt), RWTH Aachen University, Aachen, Germany
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McCotter SW, Kretschmer M, Lee CWJ, Heimel K, Kronstad JW. The Monothiol Glutaredoxin Grx4 Influences Iron Homeostasis and Virulence in Ustilago maydis. J Fungi (Basel) 2023; 9:1112. [PMID: 37998917 PMCID: PMC10672361 DOI: 10.3390/jof9111112] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2023] [Revised: 11/12/2023] [Accepted: 11/13/2023] [Indexed: 11/25/2023] Open
Abstract
The corn smut fungus, Ustilago maydis, is an excellent model for studying biotrophic plant-pathogen interactions, including nutritional adaptation to the host environment. Iron acquisition during host colonization is a key aspect of microbial pathogenesis yet less is known about this process for fungal pathogens of plants. Monothiol glutaredoxins are central regulators of key cellular functions in fungi, including iron homeostasis, cell wall integrity, and redox status via interactions with transcription factors, iron-sulfur clusters, and glutathione. In this study, the roles of the monothiol glutaredoxin Grx4 in the biology of U. maydis were investigated by constructing strains expressing a conditional allele of grx4 under the control of the arabinose-inducible, glucose-repressible promoter Pcrg1. The use of conditional expression was necessary because Grx4 appeared to be essential for U. maydis. Transcriptome and genetic analyses with strains depleted in Grx4 revealed that the protein participates in the regulation of iron acquisition functions and is necessary for the ability of U. maydis to cause disease on maize seedlings. Taken together, this study supports the growing appreciation of monothiol glutaredoxins as key regulators of virulence-related phenotypes in pathogenic fungi.
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Affiliation(s)
- Sean W. McCotter
- Michael Smith Laboratories, Department of Microbiology and Immunology, University of British Columbia, 301-2185 East Mall, Vancouver, BC V6T 1Z4, Canada; (S.W.M.); (M.K.); (C.W.J.L.)
| | - Matthias Kretschmer
- Michael Smith Laboratories, Department of Microbiology and Immunology, University of British Columbia, 301-2185 East Mall, Vancouver, BC V6T 1Z4, Canada; (S.W.M.); (M.K.); (C.W.J.L.)
| | - Christopher W. J. Lee
- Michael Smith Laboratories, Department of Microbiology and Immunology, University of British Columbia, 301-2185 East Mall, Vancouver, BC V6T 1Z4, Canada; (S.W.M.); (M.K.); (C.W.J.L.)
| | - Kai Heimel
- Institute of Microbiology and Genetics, Department of Microbial Cell Biology, Göttingen Center for Molecular Biosciences (GZMB), University of Göttingen, Grisebachstr. 8, D-37077 Göttingen, Germany
| | - James W. Kronstad
- Michael Smith Laboratories, Department of Microbiology and Immunology, University of British Columbia, 301-2185 East Mall, Vancouver, BC V6T 1Z4, Canada; (S.W.M.); (M.K.); (C.W.J.L.)
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3
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Romero-Aguilar L, Hernández-Morfín KD, Guerra-Sánchez G, Pardo JP. Metabolic Changes and Antioxidant Response in Ustilago maydis Grown in Acetate. J Fungi (Basel) 2023; 9:749. [PMID: 37504737 PMCID: PMC10381545 DOI: 10.3390/jof9070749] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2023] [Revised: 06/29/2023] [Accepted: 07/06/2023] [Indexed: 07/29/2023] Open
Abstract
Ustilago maydis is an important model to study intermediary and mitochondrial metabolism, among other processes. U. maydis can grow, at very different rates, on glucose, lactate, glycerol, and ethanol as carbon sources. Under nitrogen starvation and glucose as the only carbon source, this fungus synthesizes and accumulates neutral lipids in the form of lipid droplets (LD). In this work, we studied the accumulation of triacylglycerols in cells cultured in a medium containing acetate, a direct precursor of the acetyl-CoA required for the synthesis of fatty acids. The metabolic adaptation of cells to acetate was studied by measuring the activities of key enzymes involved in glycolysis, gluconeogenesis, and the pentose phosphate pathways. Since growth on acetate induces oxidative stress, the activities of some antioxidant enzymes were also assayed. The results show that cells grown in acetate plus nitrate did not increase the amount of LD, but increased the activities of glutathione reductase, glutathione peroxidase, catalase, and superoxide dismutase, suggesting a higher production of reactive oxygen species in cells growing in acetate. The phosphofructokinase-1 (PFK1) was the enzyme with the lowest specific activity in the glycolytic pathway, suggesting that PFK1 controls the flux of glycolysis. As expected, the activity of the phosphoenolpyruvate carboxykinase, a gluconeogenic enzyme, was present only in the acetate condition. In summary, in the presence of acetate as the only carbon source, U. maydis synthesized fatty acids, which were directed into the production of phospholipids and neutral lipids for biomass generation, but without any excessive accumulation of LD.
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Affiliation(s)
- Lucero Romero-Aguilar
- Departamento de Bioquímica, Facultad de Medicina, Universidad Nacional Autónoma de México, Circuito Interior, Ciudad Universitaria, Coyoacán, Ciudad de México C.P. 04510, Mexico
| | - Katia Daniela Hernández-Morfín
- Departamento de Microbiología, Escuela Nacional de Ciencias Biológicas, Instituto Politécnico Nacional, Carpio y Plan de Ayala S/N Santo Tomás, Miguel Hidalgo, Ciudad de México C.P. 11340, Mexico
| | - Guadalupe Guerra-Sánchez
- Departamento de Microbiología, Escuela Nacional de Ciencias Biológicas, Instituto Politécnico Nacional, Carpio y Plan de Ayala S/N Santo Tomás, Miguel Hidalgo, Ciudad de México C.P. 11340, Mexico
| | - Juan Pablo Pardo
- Departamento de Bioquímica, Facultad de Medicina, Universidad Nacional Autónoma de México, Circuito Interior, Ciudad Universitaria, Coyoacán, Ciudad de México C.P. 04510, Mexico
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4
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Romero-Aguilar L, Vázquez-Meza H, Guerra-Sánchez G, Luqueño-Bocardo OI, Pardo JP. The Mitochondrial Alternative Oxidase in Ustilago maydis Is Not Involved in Response to Oxidative Stress Induced by Paraquat. J Fungi (Basel) 2022; 8:1221. [PMID: 36422042 PMCID: PMC9693204 DOI: 10.3390/jof8111221] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2022] [Revised: 11/10/2022] [Accepted: 11/17/2022] [Indexed: 07/29/2023] Open
Abstract
It has been shown that the alternative oxidase in mitochondria of fungi and plants has important functions in the response against stress conditions, although their role in some organisms is still unknown. This is the case of Ustilago maydis. There is no evidence of the participation of the U. maydis Aox1 in stressful conditions such as desiccation, high or low temperature, and low pH, among others. Therefore, in this work, we studied the role of the U. maydis Aox1 in cells exposed to oxidative stress induced by methyl viologen (paraquat). To gain insights into the role of this enzyme, we took advantage of four strains: the FB2 wild-type, a strain without the alternative oxidase (FB2aox1Δ), other with the Aox1 fused to the Gfp under the control of the original promoter (FB2aox1-Gfp), and one expressing constitutively de Aox1-Gfp (FB2Potef:aox1-Gfp). Cells were incubated for various times in the presence of 1 mM paraquat and growth, replicative capacities, mitochondrial respiratory activity, Aox1 capacity, and the activities of several antioxidant enzymes (catalase, glutathione peroxidase, glutathione reductase, and superoxide dismutase) were assayed. The results show that (1) the response of U. maydis against oxidative stress was the same in the presence or absence of the Aox1; (2) the activities of the antioxidant enzymes remained constant despite the oxidative stress; and (3) there was a decrease in the GSH/GSSG ratio in U. maydis cells incubated with paraquat.
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Affiliation(s)
- Lucero Romero-Aguilar
- Departamento de Bioquímica, Facultad de Medicina, Universidad Nacional Autónoma de México, Circuito Interior, Ciudad Universitaria, Coyoacán, Ciudad de México C.P. 04510, Mexico
| | - Héctor Vázquez-Meza
- Departamento de Bioquímica, Facultad de Medicina, Universidad Nacional Autónoma de México, Circuito Interior, Ciudad Universitaria, Coyoacán, Ciudad de México C.P. 04510, Mexico
| | - Guadalupe Guerra-Sánchez
- Instituto Politécnico Nacional, Escuela Nacional de Ciencias Biológicas, Departamento de Microbiología, Plan de Carpio y Plan de Ayala S/N Santo Tomás, Miguel Hidalgo, Ciudad de México C.P. 11340, Mexico
| | - Oscar Ivan Luqueño-Bocardo
- Departamento de Bioquímica, Facultad de Medicina, Universidad Nacional Autónoma de México, Circuito Interior, Ciudad Universitaria, Coyoacán, Ciudad de México C.P. 04510, Mexico
| | - Juan Pablo Pardo
- Departamento de Bioquímica, Facultad de Medicina, Universidad Nacional Autónoma de México, Circuito Interior, Ciudad Universitaria, Coyoacán, Ciudad de México C.P. 04510, Mexico
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5
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Cuervo-Zanatta D, Syeda T, Sánchez-Valle V, Irene-Fierro M, Torres-Aguilar P, Torres-Ramos MA, Shibayama-Salas M, Silva-Olivares A, Noriega LG, Torres N, Tovar AR, Ruminot I, Barros LF, García-Mena J, Perez-Cruz C. Dietary Fiber Modulates the Release of Gut Bacterial Products Preventing Cognitive Decline in an Alzheimer's Mouse Model. Cell Mol Neurobiol 2022; 43:1595-1618. [PMID: 35953741 DOI: 10.1007/s10571-022-01268-7] [Citation(s) in RCA: 18] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2022] [Accepted: 07/28/2022] [Indexed: 12/11/2022]
Abstract
Fiber intake is associated with a lower risk for Alzheimer´s disease (AD) in older adults. Intake of plant-based diets rich in soluble fiber promotes the production of short-chain fatty acids (SCFAs: butyrate, acetate, propionate) by gut bacteria. Butyrate administration has antiinflammatory actions, but propionate promotes neuroinflammation. In AD patients, gut microbiota dysbiosis is a common feature even in the prodromal stages of the disease. It is unclear whether the neuroprotective effects of fiber intake rely on gut microbiota modifications and specific actions of SCFAs in brain cells. Here, we show that restoration of the gut microbiota dysbiosis through the intake of soluble fiber resulted in lower propionate and higher butyrate production, reduced astrocyte activation and improved cognitive function in 6-month-old male APP/PS1 mice. The neuroprotective effects were lost in antibiotic-treated mice. Moreover, propionate promoted higher glycolysis and mitochondrial respiration in astrocytes, while butyrate induced a more quiescent metabolism. Therefore, fiber intake neuroprotective action depends on the modulation of butyrate/propionate production by gut bacteria. Our data further support and provide a mechanism to explain the beneficial effects of dietary interventions rich in soluble fiber to prevent dementia and AD. Fiber intake restored the concentration of propionate and butyrate by modulating the composition of gut microbiota in male transgenic (Tg) mice with Alzheimer´s disease. Gut dysbiosis was associated with intestinal damage and high propionate levels in control diet fed-Tg mice. Fiber-rich diet restored intestinal integrity and promoted the abundance of butyrate-producing bacteria. Butyrate concentration was associated with better cognitive performance in fiber-fed Tg mice. A fiber-rich diet may prevent the development of a dysbiotic microbiome and the related cognitive dysfunction in people at risk of developing Alzheimer´s disease.
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Affiliation(s)
- Daniel Cuervo-Zanatta
- Laboratorio de Neuroplasticidad y Neurodegeneración, Departamento de Farmacologia, Centro de Investigación y de Estudios Avanzados del I.P.N. (Cinvestav), Av. IPN 2508, Ciudad de Mexico, 07360, México.,Laboratorio de Referencia y Soporte Para Genomas, Transcriptomas y Caracterización de Microbiomas, Departamento de Genética y Biología Molecular, Centro de Investigación y de Estudios Avanzados del I.P.N. (Cinvestav), Av. IPN 2508, Ciudad de Mexico, 07360, México
| | - Tauqeerunnisa Syeda
- Laboratorio de Neuroplasticidad y Neurodegeneración, Departamento de Farmacologia, Centro de Investigación y de Estudios Avanzados del I.P.N. (Cinvestav), Av. IPN 2508, Ciudad de Mexico, 07360, México
| | - Vicente Sánchez-Valle
- Laboratorio de Neuroplasticidad y Neurodegeneración, Departamento de Farmacologia, Centro de Investigación y de Estudios Avanzados del I.P.N. (Cinvestav), Av. IPN 2508, Ciudad de Mexico, 07360, México
| | - Mariangel Irene-Fierro
- Laboratorio de Neuroplasticidad y Neurodegeneración, Departamento de Farmacologia, Centro de Investigación y de Estudios Avanzados del I.P.N. (Cinvestav), Av. IPN 2508, Ciudad de Mexico, 07360, México
| | - Pablo Torres-Aguilar
- Unidad Periférica de Neurociencias, Instituto de Neurología y Neurocirugía Manuel Velasco Suárez (INNNMVS), Ciudad de Mexico, 14269, México
| | - Mónica Adriana Torres-Ramos
- Unidad Periférica de Neurociencias, Instituto de Neurología y Neurocirugía Manuel Velasco Suárez (INNNMVS), Ciudad de Mexico, 14269, México
| | - Mineko Shibayama-Salas
- Departmento de Infectómica y Patogénesis Molecular, Centro de Investigación y de Estudios Avanzados del I.P.N. (Cinvestav), Av. IPN 2508, 07360, Ciudad de Mexico, Mexico
| | - Angélica Silva-Olivares
- Departmento de Infectómica y Patogénesis Molecular, Centro de Investigación y de Estudios Avanzados del I.P.N. (Cinvestav), Av. IPN 2508, 07360, Ciudad de Mexico, Mexico
| | - Lilia G Noriega
- Departamento de Fisiología de la Nutrición, Instituto Nacional de Ciencias Médicas y de la Nutrición "Salvador Zubiran" (INCMNSZ), 14080, Ciudad de México, Mexico
| | - Nimbe Torres
- Departamento de Fisiología de la Nutrición, Instituto Nacional de Ciencias Médicas y de la Nutrición "Salvador Zubiran" (INCMNSZ), 14080, Ciudad de México, Mexico
| | - Armando R Tovar
- Departamento de Fisiología de la Nutrición, Instituto Nacional de Ciencias Médicas y de la Nutrición "Salvador Zubiran" (INCMNSZ), 14080, Ciudad de México, Mexico
| | - Iván Ruminot
- Universidad San Sebastián, Facultad de Medicina y Ciencia, Centro de Estudios Científicos-CECs, Valdivia, Chile
| | - L Felipe Barros
- Universidad San Sebastián, Facultad de Medicina y Ciencia, Centro de Estudios Científicos-CECs, Valdivia, Chile
| | - Jaime García-Mena
- Laboratorio de Referencia y Soporte Para Genomas, Transcriptomas y Caracterización de Microbiomas, Departamento de Genética y Biología Molecular, Centro de Investigación y de Estudios Avanzados del I.P.N. (Cinvestav), Av. IPN 2508, Ciudad de Mexico, 07360, México.
| | - Claudia Perez-Cruz
- Laboratorio de Neuroplasticidad y Neurodegeneración, Departamento de Farmacologia, Centro de Investigación y de Estudios Avanzados del I.P.N. (Cinvestav), Av. IPN 2508, Ciudad de Mexico, 07360, México.
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6
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Kretschmer M, Damoo D, Sun S, Lee CWJ, Croll D, Brumer H, Kronstad J. Organic acids and glucose prime late-stage fungal biotrophy in maize. Science 2022; 376:1187-1191. [PMID: 35679407 DOI: 10.1126/science.abo2401] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
Many plant-associated fungi are obligate biotrophs that depend on living hosts to proliferate. However, little is known about the molecular basis of the biotrophic lifestyle, despite the impact of fungi on the environment and food security. In this work, we show that combinations of organic acids and glucose trigger phenotypes that are associated with the late stage of biotrophy for the maize pathogen Ustilago maydis. These phenotypes include the expression of a set of effectors normally observed only during biotrophic development, as well as the formation of melanin associated with sporulation in plant tumors. U. maydis and other hemibiotrophic fungi also respond to a combination of carbon sources with enhanced proliferation. Thus, the response to combinations of nutrients from the host may be a conserved feature of fungal biotrophy.
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Affiliation(s)
- Matthias Kretschmer
- Michael Smith Laboratories and Department of Microbiology and Immunology, University of British Columbia, Vancouver, BC, Canada
| | - Djihane Damoo
- Michael Smith Laboratories and Department of Microbiology and Immunology, University of British Columbia, Vancouver, BC, Canada
| | - Sherry Sun
- Michael Smith Laboratories and Department of Microbiology and Immunology, University of British Columbia, Vancouver, BC, Canada
| | - Christopher W J Lee
- Michael Smith Laboratories and Department of Microbiology and Immunology, University of British Columbia, Vancouver, BC, Canada
| | - Daniel Croll
- Laboratory of Evolutionary Genetics, Institute of Biology, Université de Neuchâtel, Neuchâtel, Switzerland
| | - Harry Brumer
- Michael Smith Laboratories and Department of Chemistry, University of British Columbia, Vancouver, BC, Canada
| | - James Kronstad
- Michael Smith Laboratories and Department of Microbiology and Immunology, University of British Columbia, Vancouver, BC, Canada
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7
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Soberanes-Gutiérrez CV, León-Ramírez C, Sánchez-Segura L, Cordero-Martínez E, Vega-Arreguín JC, Ruiz-Herrera J. Cell death in Ustilago maydis: comparison with other fungi and the effect of metformin and curcumin on its chronological lifespan. FEMS Yeast Res 2021; 20:5908381. [PMID: 32945857 DOI: 10.1093/femsyr/foaa051] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2019] [Accepted: 09/14/2020] [Indexed: 12/11/2022] Open
Abstract
Ustilago maydis is a Basidiomycota fungus, in which very little is known about its mechanisms of cell survival and death. To date, only the role of metacaspase1, acetate and hydrogen peroxide as inducers of cell death has been investigated. In the present work, we analyzed the lifespan of U. maydis compared with other species like Sporisorium reilianum, Saccharomyces cerevisiae and Yarrowia lipolytica, and we observed that U. maydis has a minor lifespan. We probe the addition of low concentrations metformin and curcumin to the culture media, and we observed that both prolonged the lifespan of U. maydis, a result observed for the first time in a phytopathogen fungus. However, higher concentrations of curcumin were toxic for the cells, and interestingly induced the yeast-to-mycelium dimorphic transition. The positive effect of metformin and curcumin appears to be related to an inhibition of the mechanistic Target of Rapamycin (mTOR) pathway, increase expression of autophagy genes and reducing of reactive oxygen species. These data indicate that U. maydis may be a eukaryotic model organism to elucidate the molecular mechanism underlying apoptotic and necrosis pathways, and the lifespan increase caused by metformin and curcumin.
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Affiliation(s)
- Cinthia V Soberanes-Gutiérrez
- Laboratorio de Ciencias Agrogenómicas, de la Escuela Nacional de Estudios Superiores Unidad León, Universidad Nacional Autónoma de México, Blv. UNAM 2011, Col. Predio el Saucillo y El Potrero, Comunidad de Los Tepetates, 37684, León Gto., México.,Departamento de Ingeniería Genética, Unidad Irapuato, Centro de Investigación y de Estudios Avanzados del Instituto Politécnico Nacional, Km. 9.6 Libramiento Norte Carr. Irapuato-León 36824 Irapuato Gto., México
| | - Claudia León-Ramírez
- Departamento de Ingeniería Genética, Unidad Irapuato, Centro de Investigación y de Estudios Avanzados del Instituto Politécnico Nacional, Km. 9.6 Libramiento Norte Carr. Irapuato-León 36824 Irapuato Gto., México
| | - Lino Sánchez-Segura
- Departamento de Ingeniería Genética, Unidad Irapuato, Centro de Investigación y de Estudios Avanzados del Instituto Politécnico Nacional, Km. 9.6 Libramiento Norte Carr. Irapuato-León 36824 Irapuato Gto., México
| | - Emmanuel Cordero-Martínez
- Laboratorio de Ciencias Agrogenómicas, de la Escuela Nacional de Estudios Superiores Unidad León, Universidad Nacional Autónoma de México, Blv. UNAM 2011, Col. Predio el Saucillo y El Potrero, Comunidad de Los Tepetates, 37684, León Gto., México
| | - Julio C Vega-Arreguín
- Laboratorio de Ciencias Agrogenómicas, de la Escuela Nacional de Estudios Superiores Unidad León, Universidad Nacional Autónoma de México, Blv. UNAM 2011, Col. Predio el Saucillo y El Potrero, Comunidad de Los Tepetates, 37684, León Gto., México
| | - José Ruiz-Herrera
- Departamento de Ingeniería Genética, Unidad Irapuato, Centro de Investigación y de Estudios Avanzados del Instituto Politécnico Nacional, Km. 9.6 Libramiento Norte Carr. Irapuato-León 36824 Irapuato Gto., México
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8
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de Almeida JR, Riaño Pachón DM, Franceschini LM, dos Santos IB, Ferrarezi JA, de Andrade PAM, Monteiro-Vitorello CB, Labate CA, Quecine MC. Revealing the high variability on nonconserved core and mobile elements of Austropuccinia psidii and other rust mitochondrial genomes. PLoS One 2021; 16:e0248054. [PMID: 33705433 PMCID: PMC7951889 DOI: 10.1371/journal.pone.0248054] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2020] [Accepted: 02/18/2021] [Indexed: 01/12/2023] Open
Abstract
Mitochondrial genomes are highly conserved in many fungal groups, and they can help characterize the phylogenetic relationships and evolutionary biology of plant pathogenic fungi. Rust fungi are among the most devastating diseases for economically important crops around the world. Here, we report the complete sequence and annotation of the mitochondrial genome of Austropuccinia psidii (syn. Puccinia psidii), the causal agent of myrtle rust. We performed a phylogenomic analysis including the complete mitochondrial sequences from other rust fungi. The genome composed of 93.299 bp has 73 predicted genes, 33 of which encoded nonconserved proteins (ncORFs), representing almost 45% of all predicted genes. A. psidii mtDNA is one of the largest rust mtDNA sequenced to date, most likely due to the abundance of ncORFs. Among them, 33% were within intronic regions of diverse intron groups. Mobile genetic elements invading intron sequences may have played significant roles in size but not shaping of the rust mitochondrial genome structure. The mtDNAs from rust fungi are highly syntenic. Phylogenetic inferences with 14 concatenated mitochondrial proteins encoded by the core genes placed A. psidii according to phylogenetic analysis based on 18S rDNA. Interestingly, cox1, the gene with the greatest number of introns, provided phylogenies not congruent with the core set. For the first time, we identified the proteins encoded by three A. psidii ncORFs using proteomics analyses. Also, the orf208 encoded a transmembrane protein repressed during in vitro morphogenesis. To the best of our knowledge, we presented the first report of a complete mtDNA sequence of a member of the family Sphaerophragmiacea.
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Affiliation(s)
- Jaqueline Raquel de Almeida
- Department of Genetics, “Luiz de Queiroz” College of Agriculture (ESALQ), University of São Paulo, Piracicaba, São Paulo, Brazil
| | | | - Livia Maria Franceschini
- Department of Genetics, “Luiz de Queiroz” College of Agriculture (ESALQ), University of São Paulo, Piracicaba, São Paulo, Brazil
| | - Isaneli Batista dos Santos
- Department of Genetics, “Luiz de Queiroz” College of Agriculture (ESALQ), University of São Paulo, Piracicaba, São Paulo, Brazil
| | - Jessica Aparecida Ferrarezi
- Department of Genetics, “Luiz de Queiroz” College of Agriculture (ESALQ), University of São Paulo, Piracicaba, São Paulo, Brazil
| | - Pedro Avelino Maia de Andrade
- Department of Genetics, “Luiz de Queiroz” College of Agriculture (ESALQ), University of São Paulo, Piracicaba, São Paulo, Brazil
| | | | - Carlos Alberto Labate
- Department of Genetics, “Luiz de Queiroz” College of Agriculture (ESALQ), University of São Paulo, Piracicaba, São Paulo, Brazil
| | - Maria Carolina Quecine
- Department of Genetics, “Luiz de Queiroz” College of Agriculture (ESALQ), University of São Paulo, Piracicaba, São Paulo, Brazil
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9
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Ullmann L, Phan ANT, Kaplan DKP, Blank LM. Ustilaginaceae Biocatalyst for Co-Metabolism of CO 2-Derived Substrates toward Carbon-Neutral Itaconate Production. J Fungi (Basel) 2021; 7:jof7020098. [PMID: 33573033 PMCID: PMC7911105 DOI: 10.3390/jof7020098] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/26/2020] [Revised: 01/26/2021] [Accepted: 01/27/2021] [Indexed: 12/14/2022] Open
Abstract
The family Ustilaginaceae (belonging to the smut fungi) are known for their plant pathogenicity. Despite the fact that these plant diseases cause agricultural yield reduction, smut fungi attracted special attention in the field of industrial biotechnology. Ustilaginaceae show a versatile product spectrum such as organic acids (e.g., itaconate, malate, succinate), polyols (e.g., erythritol, mannitol), and extracellular glycolipids, which are considered value-added chemicals with potential applications in the pharmaceutical, food, and chemical industries. This study focused on itaconate as a platform chemical for the production of resins, plastics, adhesives, and biofuels. During this work, 72 different Ustilaginaceae strains from 36 species were investigated for their ability to (co-) consume the CO2-derived substrates acetate and formate, potentially contributing toward a carbon-neutral itaconate production. The fungal growth and product spectrum with special interest in itaconate was characterized. Ustilago maydis MB215 and Ustilago rabenhorstiana NBRC 8995 were identified as promising candidates for acetate metabolization whereas Ustilago cynodontis NBRC 7530 was identified as a potential production host using formate as a co-substrate enhancing the itaconate production. Selected strains with the best itaconate production were characterized in more detail in controlled-batch bioreactor experiments confirming the co-substrate utilization. Thus, a proof-of-principle study was performed resulting in the identification and characterization of three promising Ustilaginaceae biocatalyst candidates for carbon-neutral itaconate production contributing to the biotechnological relevance of Ustilaginaceae.
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Petkovic J, Kojic M, Milisavljevic M. Self-Generated Hypoxia Leads to Oxidative Stress and Massive Death in Ustilago maydis Populations under Extreme Starvation and Oxygen-Limited Conditions. J Fungi (Basel) 2021; 7:jof7020092. [PMID: 33525319 PMCID: PMC7912166 DOI: 10.3390/jof7020092] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2020] [Revised: 01/21/2021] [Accepted: 01/26/2021] [Indexed: 12/02/2022] Open
Abstract
Ustilago maydis and Saccharomyces cerevisiae differ considerably in their response to water-transfer treatments. When stationary phase cells were transferred to pure water and incubated under limited supply of oxygen, the U. maydis cells suffered a catastrophic loss of viability while the S. cerevisiae population was virtually unaffected by the treatment. The major factor underlying the death of the U. maydis cells under those conditions was an oxygen-consuming cellular activity that generated a hypoxic environment, thereby inducing oxidative stress and accumulation of reactive oxygen species, which resulted in lethality. Importantly, a small residue of U. maydis cells that did survive was able to resume growth and repopulate up to the initial culture density when sufficient aeration was restored. The regrowth was dependent on the cellular factors (Adr1, Did4, Kel1, and Tbp1), previously identified as required for repopulation, after killing with hydrogen peroxide. Surprisingly, the survivors were also able to resume growth under apparently hypoxic conditions, indicating that these remnant cells likely switched to a fermentative mode of growth. We discuss the findings in terms of their possible relevance to the eco-evolutionary adaptation of U. maydis to risky environments.
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Ruiz-Herrera J, Pérez-Rodríguez F, Velez-Haro J. The signaling mechanisms involved in the dimorphic phenomenon of the Basidiomycota fungus Ustilago maydis. Int Microbiol 2020; 23:121-126. [PMID: 31915950 DOI: 10.1007/s10123-019-00100-5] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2019] [Revised: 09/02/2019] [Accepted: 09/12/2019] [Indexed: 12/24/2022]
Abstract
In the present manuscript, we describe the mechanisms involved in the yeast-to-hypha dimorphic transition of the plant pathogenic Basidiomycota fungus Ustilago maydis. During its life cycle, U. maydis presents two stages: one in the form of haploid saprophytic yeasts that divide by budding and the other that is the product of the mating of sexually compatible yeast cells (sporidia), in the form of mycelial dikaryons that invade the plant host. The occurrence of the involved dimorphic transition is controlled by the two mating loci a and b. In addition, the dimorphic event can be obtained in vitro by different stimuli: change in the pH of the growth medium, use of different carbon sources, and by nitrogen depletion. The presence of other factors and mechanisms may affect this phenomenon; among these, we may cite the PKA and MAPK signal transduction pathways, polyamines, and factors that affect the structure of the nucleosomes. Some of these factors and conditions may affect all these dimorphic events, or they may be specific for only one or more but not all the processes involved. The conclusion reached by these experiments is that U. maydis has constituted a useful model for the analysis of the mechanisms involved in cell differentiation of fungi in general.
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Affiliation(s)
- José Ruiz-Herrera
- Departamento de Ingeniería Genética, Unidad Irapuato, Centro de Investigación y de Estudios Avanzados del IPN, Km. 9.4 Carretera Irapuato-León, Irapuato, Gto., Mexico.
| | - Fernando Pérez-Rodríguez
- Departamento de Ingeniería Genética, Unidad Irapuato, Centro de Investigación y de Estudios Avanzados del IPN, Km. 9.4 Carretera Irapuato-León, Irapuato, Gto., Mexico
| | - John Velez-Haro
- Departamento de Ingeniería Genética, Unidad Irapuato, Centro de Investigación y de Estudios Avanzados del IPN, Km. 9.4 Carretera Irapuato-León, Irapuato, Gto., Mexico.,Instituto Tecnológico de Celaya, Celaya, Gto., Mexico
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Vijayakrishnapillai LMK, Desmarais JS, Groeschen MN, Perlin MH. Deletion of ptn1, a PTEN/ TEP1 Orthologue, in Ustilago maydis Reduces Pathogenicity and Teliospore Development. J Fungi (Basel) 2018; 5:E1. [PMID: 30577430 PMCID: PMC6462984 DOI: 10.3390/jof5010001] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2018] [Revised: 12/13/2018] [Accepted: 12/19/2018] [Indexed: 01/23/2023] Open
Abstract
The PTEN/PI3K/mTOR signal transduction pathway is involved in the regulation of biological processes such as metabolism, cell growth, cell proliferation, and apoptosis. This pathway has been extensively studied in mammals, leading to the conclusion that PTEN is a major tumor suppressor gene. PTEN orthologues have been characterized in a variety of organisms, both vertebrates and non-vertebrates, and studies of the associated PTEN/PI3K/mTOR pathway indicate that it is widely conserved. Studies in fungal systems indicated a role of PTEN in fungal defense mechanisms in Candida albicans, and in the developmental process of sporulation in Saccharomyces cerevisiae. The present study was aimed at investigating the role of the PTEN ortholog, ptn1, in Ustilago maydis, the pathogen of maize. U. maydis ptn1 mutant strains where ptn1 gene is deleted or overexpressed were examined for phenotypes associate with mating, virulence and spore formation. While the overexpression of ptn1 had no substantial effects on virulence, ptn1 deletion strains showed slight reductions in mating efficiency and significant reductions in virulence; tumor formation on stem and/or leaves were severely reduced. Moreover, tumors, when present, had significantly lower levels of mature teliospores, and the percent germination of such spores was similarly reduced. Thus, ptn1 is required for these important aspects of virulence in this fungus.
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Affiliation(s)
| | - John S Desmarais
- Department of Biology, Program on Disease Evolution, University of Louisville, Louisville, KY 40292, USA.
| | - Michael N Groeschen
- Department of Biology, Program on Disease Evolution, University of Louisville, Louisville, KY 40292, USA.
| | - Michael H Perlin
- Department of Biology, Program on Disease Evolution, University of Louisville, Louisville, KY 40292, USA.
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Schmitz L, McCotter S, Kretschmer M, Kronstad JW, Heimel K. Transcripts and tumors: regulatory and metabolic programming during biotrophic phytopathogenesis. F1000Res 2018; 7. [PMID: 30519451 PMCID: PMC6248262 DOI: 10.12688/f1000research.16404.1] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 11/12/2018] [Indexed: 01/05/2023] Open
Abstract
Biotrophic fungal pathogens of plants must sense and adapt to the host environment to complete their life cycles. Recent transcriptome studies of the infection of maize by the biotrophic pathogen
Ustilago maydis are providing molecular insights into an ordered program of changes in gene expression and the deployment of effectors as well as key features of nutrient acquisition. In particular, the transcriptome data provide a deeper appreciation of the complexity of the transcription factor network that controls the biotrophic program of invasion, proliferation, and sporulation. Additionally, transcriptome analysis during tumor formation, a key late stage in the life cycle, revealed features of the remodeling of host and pathogen metabolism that may support the formation of tremendous numbers of spores. Transcriptome studies are also appearing for other smut species during interactions with their hosts, thereby providing opportunities for comparative approaches to understand biotrophic adaptation.
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Affiliation(s)
- Lara Schmitz
- Institute for Microbiology and Genetics, Department of Molecular Microbiology and Genetics, Georg-August-University-Göttingen, Göttingen, Lower Saxony, D-37077, Germany
| | - Sean McCotter
- Michael Smith Laboratories, Department of Microbiology and Immunology, University of British Columbia, Vancouver, BC, V6T 1Z4, Canada
| | - Matthias Kretschmer
- Michael Smith Laboratories, Department of Microbiology and Immunology, University of British Columbia, Vancouver, BC, V6T 1Z4, Canada
| | - James W Kronstad
- Michael Smith Laboratories, Department of Microbiology and Immunology, University of British Columbia, Vancouver, BC, V6T 1Z4, Canada
| | - Kai Heimel
- Institute for Microbiology and Genetics, Department of Molecular Microbiology and Genetics, Georg-August-University-Göttingen, Göttingen, Lower Saxony, D-37077, Germany
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