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Tengölics R, Szappanos B, Mülleder M, Kalapis D, Grézal G, Sajben C, Agostini F, Mokochinski JB, Bálint B, Nagy LG, Ralser M, Papp B. The metabolic domestication syndrome of budding yeast. Proc Natl Acad Sci U S A 2024; 121:e2313354121. [PMID: 38457520 PMCID: PMC10945815 DOI: 10.1073/pnas.2313354121] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [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: 08/08/2023] [Accepted: 12/11/2023] [Indexed: 03/10/2024] Open
Abstract
Cellular metabolism evolves through changes in the structure and quantitative states of metabolic networks. Here, we explore the evolutionary dynamics of metabolic states by focusing on the collection of metabolite levels, the metabolome, which captures key aspects of cellular physiology. Using a phylogenetic framework, we profiled metabolites in 27 populations of nine budding yeast species, providing a graduated view of metabolic variation across multiple evolutionary time scales. Metabolite levels evolve more rapidly and independently of changes in the metabolic network's structure, providing complementary information to enzyme repertoire. Although metabolome variation accumulates mainly gradually over time, it is profoundly affected by domestication. We found pervasive signatures of convergent evolution in the metabolomes of independently domesticated clades of Saccharomyces cerevisiae. Such recurring metabolite differences between wild and domesticated populations affect a substantial part of the metabolome, including rewiring of the TCA cycle and several amino acids that influence aroma production, likely reflecting adaptation to human niches. Overall, our work reveals previously unrecognized diversity in central metabolism and the pervasive influence of human-driven selection on metabolite levels in yeasts.
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Affiliation(s)
- Roland Tengölics
- Hungarian Centre of Excellence for Molecular Medicine - Biological Research Centre Metabolic Systems Biology Lab, Szeged6726, Hungary
- Synthetic and System Biology Unit, National Laboratory of Biotechnology, Institute of Biochemistry, Biological Research Centre, Hungarian Research Network, Szeged6726, Hungary
- Metabolomics Lab, Core facilities, Biological Research Centre, Hungarian Research Network, Szeged6726, Hungary
| | - Balázs Szappanos
- Hungarian Centre of Excellence for Molecular Medicine - Biological Research Centre Metabolic Systems Biology Lab, Szeged6726, Hungary
- Synthetic and System Biology Unit, National Laboratory of Biotechnology, Institute of Biochemistry, Biological Research Centre, Hungarian Research Network, Szeged6726, Hungary
- Department of Biotechnology, University of Szeged, Szeged6726, Hungary
| | - Michael Mülleder
- Charité Universitätsmedizin, Core Facility High-Throughput Mass Spectrometry, Berlin10117, Germany
| | - Dorottya Kalapis
- Hungarian Centre of Excellence for Molecular Medicine - Biological Research Centre Metabolic Systems Biology Lab, Szeged6726, Hungary
- Synthetic and System Biology Unit, National Laboratory of Biotechnology, Institute of Biochemistry, Biological Research Centre, Hungarian Research Network, Szeged6726, Hungary
| | - Gábor Grézal
- Hungarian Centre of Excellence for Molecular Medicine - Biological Research Centre Metabolic Systems Biology Lab, Szeged6726, Hungary
- Synthetic and System Biology Unit, National Laboratory of Biotechnology, Institute of Biochemistry, Biological Research Centre, Hungarian Research Network, Szeged6726, Hungary
| | - Csilla Sajben
- Metabolomics Lab, Core facilities, Biological Research Centre, Hungarian Research Network, Szeged6726, Hungary
| | - Federica Agostini
- Department of Biochemistry, Charité Universitätsmedizin, Berlin10117, Germany
| | - João Benhur Mokochinski
- Synthetic and System Biology Unit, National Laboratory of Biotechnology, Institute of Biochemistry, Biological Research Centre, Hungarian Research Network, Szeged6726, Hungary
| | - Balázs Bálint
- Institute of Biochemistry, Biological Research Centre, Hungarian Research Network, Szeged6726, Hungary
| | - László G. Nagy
- Institute of Biochemistry, Biological Research Centre, Hungarian Research Network, Szeged6726, Hungary
| | - Markus Ralser
- Department of Biochemistry, Charité Universitätsmedizin, Berlin10117, Germany
- The Francis Crick Institute, Molecular Biology of Metabolism Laboratory, LondonNW11AT, United Kingdom
| | - Balázs Papp
- Hungarian Centre of Excellence for Molecular Medicine - Biological Research Centre Metabolic Systems Biology Lab, Szeged6726, Hungary
- Synthetic and System Biology Unit, National Laboratory of Biotechnology, Institute of Biochemistry, Biological Research Centre, Hungarian Research Network, Szeged6726, Hungary
- National Laboratory for Health Security, Biological Research Centre, Hungarian Research Network, Szeged6726, Hungary
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Fabio Turco J, Benhur Mokochinski J, Reyes Torres Y. Lipidomic Analysis of Geopropolis of Brazilian Stingless Bees by LC-HRMS. Food Res Int 2023; 167:112640. [PMID: 37087233 DOI: 10.1016/j.foodres.2023.112640] [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] [Received: 12/03/2022] [Revised: 02/07/2023] [Accepted: 02/21/2023] [Indexed: 02/26/2023]
Abstract
Stingless bees (Meliponini) represent over than 500 species, found in tropical and sub-tropical regions of the world. They produce geopropolis, a resinous natural product containing bioactive compounds, which is commonly used in folk medicine. In the current study, LC-HRMS and bioinformatic tools were used to carry out for the first time the lipidomic analysis of geopropolis from indigenous Brazilian stingless bees. As a result, 61 compounds of several lipid classes were identified with elevated degree of confidence. Then, we demonstrated that lipids in geopropolis are not restricted to waxes and fatty acids; but fatty amides and amines, phenolic lipids, resorcinols, retinoids, abietanoids, diterpenoids, pentacyclic triterpenoids, prostaglandins, retinoids, and steroids were found. In addition, multivariate analysis, based on the lipidomic profile of extracts, reinforces the assumption that the species of stingless bees, as well as the geographical origin are relevant factors to affect geopropolis composition once that the lipidic profile allowed the discrimination of geopropolis in groups related to the geographical origin, bee specie or bee genus. The lipidic profile also suggest a selective forage habits of T. angustula, which seems to collect resins from more specific vegetal sources regardless geographic origin, while other stingless bees, such as M. marginata and M. quadrifasciata, are less selective and may adapt to collect resins from a wider variety of plants.
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Affiliation(s)
- João Fabio Turco
- Department of Chemistry, State University of Midwest (UNICENTRO), Guarapuava, Parana, Brazil
| | - João Benhur Mokochinski
- Proteomics and Metabolomics Facility, Faculty of Medicine, Hammersmith Hospital Campus, Imperial College London, United Kingdom
| | - Yohandra Reyes Torres
- Department of Chemistry, State University of Midwest (UNICENTRO), Guarapuava, Parana, Brazil.
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de Oliveira FM, Mokochinski JB, Reyes Torres Y, Dalla Santa HS, González-Borrero PP. Photoacoustic spectroscopy applied to the direct detection of bioactive compounds in Agaricus brasiliensis mycelium. J Biol Phys 2017; 44:93-100. [PMID: 29210029 DOI: 10.1007/s10867-017-9478-z] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2017] [Accepted: 11/10/2017] [Indexed: 10/18/2022] Open
Abstract
This paper describes the application of the photoacoustic spectroscopic (PAS) for detection of bioactive compounds in Agaricus brasiliensis mycelium. The mycelium was cultivated by solid-state fermentation and by submerged fermentation. Vegetal residues from food industry were used as substrates for fermentation: apple pomace (Malus domestica), wheat (Triticum aestivum), peel and pomace of pineapple (Ananas comosus), malt (Hordeum vulgare) and grape pomace (Vitis vinifera). Dry and ground samples of biomass were directly put into the PA cell. The optical absorption spectra indicated the existence of three main absorption bands: one around 280 nm related to phytosterols (ergosterol), phenolic acids, flavonoids and aromatic amino acids, another at 340 nm, due to phenolic and flavonoid compounds, and the third one at around 550 nm associated with anthocyanins and anthocyanidins. A correlation between the PA signal and the total phenolic content was satisfactory, as well as for the analyzed spectrum region (270 nm up to 1000 nm), using multivariate methods. Our results indicated that PA technique may be considered as an analytical tool to quickly detect bioactive compounds in mushrooms without the need of sample pretreatment.
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Affiliation(s)
- Fernando Maia de Oliveira
- Department of Physics, State University of Midwest (UNICENTRO), 85040-080, Guarapuava, Paraná, Brazil
| | - João Benhur Mokochinski
- Department of Chemistry, State University of Midwest (UNICENTRO), 85040-080, Guarapuava, Paraná, Brazil
| | - Yohandra Reyes Torres
- Department of Chemistry, State University of Midwest (UNICENTRO), 85040-080, Guarapuava, Paraná, Brazil
| | - Herta Stutz Dalla Santa
- Department of Food Engineering, State University of Midwest (UNICENTRO), 85040-080, Guarapuava, Paraná, Brazil
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Soares KCN, Pianoski KE, Mokochinski JB, Finger D, Sawaya ACHF, da Rosa EA, Quináia SP, Torres YR. Variability and Chemical Composition of Aerials Parts of Verbena minutiflora. J FOOD PROCESS PRES 2015. [DOI: 10.1111/jfpp.12687] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Kelly Cristina Nogueira Soares
- Departamento de Química; Universidade Estadual do Centro-Oeste - UNICENTRO; Rua Simeão Camargo Varela de Sá, 03, Vila Carli Guarapuava Paraná 85040-080 Brazil
| | - Karlos Eduardo Pianoski
- Departamento de Química; Universidade Estadual do Centro-Oeste - UNICENTRO; Rua Simeão Camargo Varela de Sá, 03, Vila Carli Guarapuava Paraná 85040-080 Brazil
| | - João Benhur Mokochinski
- Programa BTPB; Departamento de Biologia Vegetal; Instituto de Biologia; Universidade Estadual de Campinas (UNICAMP); Campinas São Paulo Brazil
| | - Daiane Finger
- Departamento de Química; Universidade Estadual do Centro-Oeste - UNICENTRO; Rua Simeão Camargo Varela de Sá, 03, Vila Carli Guarapuava Paraná 85040-080 Brazil
| | | | - Elisa Aguayo da Rosa
- Departamento de Química; Universidade Estadual do Centro-Oeste - UNICENTRO; Rua Simeão Camargo Varela de Sá, 03, Vila Carli Guarapuava Paraná 85040-080 Brazil
| | - Sueli Pércio Quináia
- Departamento de Química; Universidade Estadual do Centro-Oeste - UNICENTRO; Rua Simeão Camargo Varela de Sá, 03, Vila Carli Guarapuava Paraná 85040-080 Brazil
| | - Yohandra Reyes Torres
- Departamento de Química; Universidade Estadual do Centro-Oeste - UNICENTRO; Rua Simeão Camargo Varela de Sá, 03, Vila Carli Guarapuava Paraná 85040-080 Brazil
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Vieira RP, Mokochinski JB, Sawaya AC. Mathematical Modeling of Ascorbic Acid Thermal Degradation in Orange Juice during Industrial Pasteurizations. J FOOD PROCESS ENG 2015. [DOI: 10.1111/jfpe.12260] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023]
Affiliation(s)
- Roniérik Pioli Vieira
- Department of Chemistry and Chemical Engineering; Federal Institute of South of Minas Gerais; 1730 Aeroporto av. 37550-000 Pouso Alegre Minas Gerais Brazil
- School of Chemical Engineering; University of Campinas; Campinas São Paulo Brazil
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Mokochinski JB, Sovrani V, Dalla Santa HS, Felsner ML, Sawaya ACHF, González-Borrero PP, Bataglion GA, Eberlin MN, Torres YR. Biomass and Sterol Production from Vegetal Substrate Fermentation Using A
garicus brasiliensis. J FOOD QUALITY 2015. [DOI: 10.1111/jfq.12137] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/16/2023] Open
Affiliation(s)
- João Benhur Mokochinski
- Departamento de Química; Universidade Estadual do Centro-Oeste (UNICENTRO); Guarapuava Paraná Brazil
| | - Vanessa Sovrani
- Departamento de Engenharia de Alimentos; Universidade Estadual do Centro-Oeste (UNICENTRO); Guarapuava Paraná Brazil
| | - Herta Stutz Dalla Santa
- Departamento de Engenharia de Alimentos; Universidade Estadual do Centro-Oeste (UNICENTRO); Guarapuava Paraná Brazil
| | - Maria Lurdes Felsner
- Departamento de Química; Universidade Estadual do Centro-Oeste (UNICENTRO); Guarapuava Paraná Brazil
| | | | | | - Giovana Anceski Bataglion
- Laboratório ThoMSom de Espectrometria de Massas; Instituto de Química; Universidade Estadual de Campinas (UNICAMP); Campinas São Paulo Brazil
| | - Marcos Nogueira Eberlin
- Laboratório ThoMSom de Espectrometria de Massas; Instituto de Química; Universidade Estadual de Campinas (UNICAMP); Campinas São Paulo Brazil
| | - Yohandra Reyes Torres
- Departamento de Química; Universidade Estadual do Centro-Oeste (UNICENTRO); Guarapuava Paraná Brazil
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