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Berg HY, Arju G, Becerra-Rodríguez C, Galeote V, Nisamedtinov I. Unlocking the secrets of peptide transport in wine yeast: insights into oligopeptide transporter functions and nitrogen source preferences. Appl Environ Microbiol 2023; 89:e0114123. [PMID: 37843270 PMCID: PMC10686055 DOI: 10.1128/aem.01141-23] [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: 07/12/2023] [Accepted: 08/27/2023] [Indexed: 10/17/2023] Open
Abstract
IMPORTANCE Limited nitrogen supply can prevent the completion of alcoholic fermentation. Supplementation through peptides as an alternative, natural source of nitrogen for yeast offers an interesting solution for this issue. In this work, the S. cerevisiae peptide transporters of the Opt and Fot families were studied. We demonstrated that Fot and Opt2 have a broader peptide length preference than previously reported, enabling yeasts to acquire sufficient nitrogen from peptides without requiring additional ammonia or amino acids to complete fermentation. On the contrary, Opt1 was unable to consume any peptide in the given conditions, whereas it has been described elsewhere as the main peptide transporter for peptides longer than three amino acid residues in experiments in laboratory conditions. This controversy signifies the need in applied sciences for approaching experimental conditions to those prevalent in the industry for its more accurate characterization. Altogether, this work provides further evidence of the importance of peptides as a nitrogen source for yeast and their consequent positive impact on fermentation kinetics.
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Affiliation(s)
- Hidde Yaël Berg
- Department of Chemistry and Biotechnology, School of Science, Tallinn University of Technology, Tallinn, Estonia
- Center of Food and Fermentation Technologies, Tallinn, Estonia
| | - Georg Arju
- Institute of Chemistry, University of Tartu, Tartu, Estonia
| | | | - Virginie Galeote
- SPO, Univ. Montpellier, INRAE, Institut Agro, Montpellier, France
| | - Ildar Nisamedtinov
- Department of Chemistry and Biotechnology, School of Science, Tallinn University of Technology, Tallinn, Estonia
- Lallemand, Inc., Montreal, Canada
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Leborgne C, Meudec E, Sommerer N, Masson G, Mouret JR, Cheynier V. Untargeted Metabolomics Approach Using UHPLC-HRMS to Unravel the Impact of Fermentation on Color and Phenolic Composition of Rosé Wines. Molecules 2023; 28:5748. [PMID: 37570718 PMCID: PMC10421246 DOI: 10.3390/molecules28155748] [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: 06/15/2023] [Revised: 07/17/2023] [Accepted: 07/25/2023] [Indexed: 08/13/2023] Open
Abstract
Color is a major quality trait of rosé wines due to their packaging in clear glass bottles. This color is due to the presence of phenolic pigments extracted from grapes to wines and products of reactions taking place during the wine-making process. This study focuses on changes occurring during the alcoholic fermentation of Syrah, Grenache and Cinsault musts, which were conducted at laboratory (250 mL) and pilot (100 L) scales. The color and phenolic composition of the musts and wines were analyzed using UV-visible spectrophotometry, and metabolomics fingerprints were acquired by ultra-high performance liquid chromatography-high-resolution mass spectrometry. Untargeted metabolomics data highlighted markers of fermentation stage (must or wine) and markers related to the grape variety (e.g., anthocyanins in Syrah, hydroxycinnamates and tryptophan derivatives in Grenache, norisoprenoids released during fermentation in Cinsault). Cinsault wines contained higher molecular weight compounds possibly resulting from the oxidation of phenolics, which may contribute to their high absorbance values.
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Affiliation(s)
- Cécile Leborgne
- UE PR, INRAE, Domaine de Pech Rouge, F-11430 Gruissan, France
- SPO, INRAE, Univ de Montpellier, Institut Agro, F-34060 Montpellier, France; (E.M.); (N.S.); (J.-R.M.); (V.C.)
- INRAE, PROBE Research Infrastructure, Polyphenol Analytical Facility, F-34060 Montpellier, France
- Institut Français de la Vigne et du Vin, Centre du Rosé, F-83550 Vidauban, France;
| | - Emmanuelle Meudec
- SPO, INRAE, Univ de Montpellier, Institut Agro, F-34060 Montpellier, France; (E.M.); (N.S.); (J.-R.M.); (V.C.)
- INRAE, PROBE Research Infrastructure, Polyphenol Analytical Facility, F-34060 Montpellier, France
| | - Nicolas Sommerer
- SPO, INRAE, Univ de Montpellier, Institut Agro, F-34060 Montpellier, France; (E.M.); (N.S.); (J.-R.M.); (V.C.)
- INRAE, PROBE Research Infrastructure, Polyphenol Analytical Facility, F-34060 Montpellier, France
| | - Gilles Masson
- Institut Français de la Vigne et du Vin, Centre du Rosé, F-83550 Vidauban, France;
| | - Jean-Roch Mouret
- SPO, INRAE, Univ de Montpellier, Institut Agro, F-34060 Montpellier, France; (E.M.); (N.S.); (J.-R.M.); (V.C.)
| | - Véronique Cheynier
- SPO, INRAE, Univ de Montpellier, Institut Agro, F-34060 Montpellier, France; (E.M.); (N.S.); (J.-R.M.); (V.C.)
- INRAE, PROBE Research Infrastructure, Polyphenol Analytical Facility, F-34060 Montpellier, France
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Guerillot P, Salamov A, Louet C, Morin E, Frey P, Grigoriev IV, Duplessis S. A Remarkable Expansion of Oligopeptide Transporter Genes in Rust Fungi (Pucciniales) Suggests a Specialization in Nutrient Acquisition for Obligate Biotrophy. PHYTOPATHOLOGY 2023; 113:252-264. [PMID: 36044359 DOI: 10.1094/phyto-04-22-0128-r] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/15/2023]
Abstract
Nutrient acquisition by rust fungi during their biotrophic growth has been assigned to a few transporters expressed in haustorial infection structures. We performed a comparative genomic analysis of all transporter genes (hereafter termed transportome) classified according to the Transporter Classification Database, focusing specifically on rust fungi (order Pucciniales) versus other species in the Dikarya. We also surveyed expression of transporter genes in the poplar rust fungus for which transcriptomics data are available across the whole life cycle. Despite a significant increase in gene number, rust fungi presented a reduced transportome compared with most fungi in the Dikarya. However, a few transporter families in the subclass Porters showed significant expansions. Notably, three metal transport-related families involved in the import, export, and sequestration of metals were expanded in Pucciniales and expressed at various stages of the rust life cycle, suggesting a tight regulation of metal homeostasis. The most remarkable gene expansion in the Pucciniales was observed for the oligopeptide transporter (OPT) family, with 25 genes on average compared with seven to 14 genes in the other surveyed taxonomical ranks. A phylogenetic analysis showed several specific expansion events at the root of the order Pucciniales with subsequent expansions in rust taxonomical families. The OPT genes showed dynamic expression patterns along the rust life cycle and more particularly during infection of the poplar host tree, suggesting a possible specialization for the acquisition of nitrogen and sulfur through the transport of oligopeptides from the host during biotrophic growth.
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Affiliation(s)
- Pamela Guerillot
- Université de Lorraine, INRAE, UMR 1136 IAM, 54000 Nancy, France
| | - Asaf Salamov
- US Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, U.S.A
| | - Clémentine Louet
- Université de Lorraine, INRAE, UMR 1136 IAM, 54000 Nancy, France
| | - Emmanuelle Morin
- Université de Lorraine, INRAE, UMR 1136 IAM, 54000 Nancy, France
- US Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, U.S.A
| | - Pascal Frey
- Université de Lorraine, INRAE, UMR 1136 IAM, 54000 Nancy, France
| | - Igor V Grigoriev
- US Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, U.S.A
- Department of Plant and Microbial Biology, University of California Berkeley, Berkeley, CA, U.S.A
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García-Ríos E, Guillamón JM. Genomic Adaptations of Saccharomyces Genus to Wine Niche. Microorganisms 2022; 10:microorganisms10091811. [PMID: 36144411 PMCID: PMC9500811 DOI: 10.3390/microorganisms10091811] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2022] [Revised: 09/05/2022] [Accepted: 09/08/2022] [Indexed: 11/16/2022] Open
Abstract
Wine yeast have been exposed to harsh conditions for millennia, which have led to adaptive evolutionary strategies. Thus, wine yeasts from Saccharomyces genus are considered an interesting and highly valuable model to study human-drive domestication processes. The rise of whole-genome sequencing technologies together with new long reads platforms has provided new understanding about the population structure and the evolution of wine yeasts. Population genomics studies have indicated domestication fingerprints in wine yeast, including nucleotide variations, chromosomal rearrangements, horizontal gene transfer or hybridization, among others. These genetic changes contribute to genetically and phenotypically distinct strains. This review will summarize and discuss recent research on evolutionary trajectories of wine yeasts, highlighting the domestication hallmarks identified in this group of yeast.
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Affiliation(s)
- Estéfani García-Ríos
- Department of Food Biotechnology, Instituto de Agroquímica y Tecnología de los Alimentos (CSIC), Avda. Agustín Escardino, 7, 46980 Paterna, Spain
- Department of Science, Universidad Internacional de Valencia-VIU, Pintor Sorolla 21, 46002 Valencia, Spain
- Correspondence:
| | - José Manuel Guillamón
- Department of Food Biotechnology, Instituto de Agroquímica y Tecnología de los Alimentos (CSIC), Avda. Agustín Escardino, 7, 46980 Paterna, Spain
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Methodology for Analysis of Peptide Consumption by Yeast during Fermentation of Enzymatic Protein Hydrolysate Supplemented Synthetic Medium Using UPLC-IMS-HRMS. FERMENTATION 2022. [DOI: 10.3390/fermentation8040145] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022] Open
Abstract
Several studies have shown the ability of yeast to consume peptides as a nitrogen source in single-peptide containing media. However, a suitable and cost-effective methodology to study the utilization of peptides by yeast and other microorganisms in a complex peptide mixture has yet to be put forward. This article addresses this issue by presenting a screening methodology for tracking the consumption of peptides by yeast during alcoholic fermentation. As a peptide source, the methodology makes use of an in-house prepared peptide-mapped bovine serum albumin (BSA) proteolytic digest, which was applied to a synthetic grape must. The peptide uptake was analyzed using high-throughput ultra-high-pressure liquid chromatography coupled to data-independent acquisition-based ion mobility separation-enabled high-resolution mass spectrometry (UPLC-DIA-IMS-HRMS) analysis. The relative changes of abundance of 123 di- to hexapeptides were monitored and reported during fermentations with three commercial wine strains, demonstrating different uptake kinetics for individual peptides. Using the same peptide-mapped BSA hydrolysate, the applicability of an untargeted workflow was additionally assessed for peptide profiling in unelucidated matrixes. The comparison of the results from peptide mapping and untargeted analysis experiments highlighted the ability of untargeted analysis to consistently identify small molecular weight peptides on the length and amino acid composition. The proposed method, in combination with other analytical techniques, such as gene or protein expression analysis, can be a useful tool for different metabolic studies related to the consumption of complex nitrogen sources by yeast or other microorganisms.
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