Optogenetic control of horizontally acquired genes prevent stuck fermentations in yeast
ABSTRACT Nitrogen limitations in the grape must be the main cause of stuck fermentations during the winemaking process. In Saccharomyces cerevisiae, a genetic segment known as region A, which harbors 12 protein-coding genes, was acquired horizontally from a phylogenetically distant yeast species. Th...
Saved in:
| Main Authors: | , , , , , , , , , |
|---|---|
| Format: | Article |
| Language: | English |
| Published: |
American Society for Microbiology
2025-02-01
|
| Series: | Microbiology Spectrum |
| Subjects: | |
| Online Access: | https://journals.asm.org/doi/10.1128/spectrum.01794-24 |
| Tags: |
Add Tag
No Tags, Be the first to tag this record!
|
| _version_ | 1832540844653019136 |
|---|---|
| author | David Figueroa Diego Ruiz Nicolò Tellini Matteo De Chiara Eduardo I. Kessi-Pérez Claudio Martínez Gianni Liti Amparo Querol José M. Guillamón Francisco Salinas |
| author_facet | David Figueroa Diego Ruiz Nicolò Tellini Matteo De Chiara Eduardo I. Kessi-Pérez Claudio Martínez Gianni Liti Amparo Querol José M. Guillamón Francisco Salinas |
| author_sort | David Figueroa |
| collection | DOAJ |
| description | ABSTRACT Nitrogen limitations in the grape must be the main cause of stuck fermentations during the winemaking process. In Saccharomyces cerevisiae, a genetic segment known as region A, which harbors 12 protein-coding genes, was acquired horizontally from a phylogenetically distant yeast species. This region is mainly present in the genome of wine yeast strains, carrying genes that have been associated with nitrogen utilization. Despite the putative importance of region A in yeast fermentation, its contribution to the fermentative process is largely unknown. In this work, we used a wine yeast strain to evaluate the contribution of region A to the fermentation process. To do this, we first sequenced the genome of the wine yeast strain using long-read sequencing and determined that region A is present in a single copy. We then implemented an optogenetic system in this wine yeast strain to precisely regulate the expression of each gene, generating a collection of 12 strains that allow for light-activated gene expression. To evaluate the role of these genes during fermentation, we assayed this collection using microculture and fermentation experiments in synthetic must with varying amounts of nitrogen concentration. Our results show that changes in gene expression for genes within this region can impact growth parameters and fermentation rate. We additionally found that the expression of various genes in region A is necessary to complete the fermentation process and prevent stuck fermentations under low nitrogen conditions. Altogether, our optogenetics-based approach demonstrates the importance of region A in completing fermentation under nitrogen-limited conditions.IMPORTANCEStuck fermentations due to limited nitrogen availability in grape must represent one of the main problems in the winemaking industry. Nitrogen limitation in grape must reduces yeast biomass and fermentation rate, resulting in incomplete fermentations with high levels of residual sugar, undesired by-products, and microbiological instability. Here, we used an optogenetic approach to demonstrate that expression of genes within region A is necessary to complete fermentations under low nitrogen availability. Overall, our results suggest that region A is a genetic signature for adaptation to low nitrogen conditions. |
| format | Article |
| id | doaj-art-b246f6263a2645a7b5fc10895b2fe66a |
| institution | Kabale University |
| issn | 2165-0497 |
| language | English |
| publishDate | 2025-02-01 |
| publisher | American Society for Microbiology |
| record_format | Article |
| series | Microbiology Spectrum |
| spelling | doaj-art-b246f6263a2645a7b5fc10895b2fe66a2025-02-04T14:03:40ZengAmerican Society for MicrobiologyMicrobiology Spectrum2165-04972025-02-0113210.1128/spectrum.01794-24Optogenetic control of horizontally acquired genes prevent stuck fermentations in yeastDavid Figueroa0Diego Ruiz1Nicolò Tellini2Matteo De Chiara3Eduardo I. Kessi-Pérez4Claudio Martínez5Gianni Liti6Amparo Querol7José M. Guillamón8Francisco Salinas9Laboratorio de Genómica Funcional, Instituto de Bioquímica y Microbiología, Facultad de Ciencias, Universidad Austral de Chile, Valdivia, ChileLaboratorio de Genómica Funcional, Instituto de Bioquímica y Microbiología, Facultad de Ciencias, Universidad Austral de Chile, Valdivia, ChileUniversité Côte d'Azur, CNRS, INSERM, IRCAN, Nice, FranceUniversité Côte d'Azur, CNRS, INSERM, IRCAN, Nice, FranceCentro de Estudios en Ciencia y Tecnología de Alimentos (CECTA), Universidad de Santiago de Chile (USACH), Santiago, ChileCentro de Estudios en Ciencia y Tecnología de Alimentos (CECTA), Universidad de Santiago de Chile (USACH), Santiago, ChileUniversité Côte d'Azur, CNRS, INSERM, IRCAN, Nice, FranceDepartamento de Biotecnología de los Alimentos, Instituto de Agroquímica y Tecnología de los Alimentos – Consejo Superior de Investigaciones Científicas (CSIC), Valencia, SpainDepartamento de Biotecnología de los Alimentos, Instituto de Agroquímica y Tecnología de los Alimentos – Consejo Superior de Investigaciones Científicas (CSIC), Valencia, SpainLaboratorio de Genómica Funcional, Instituto de Bioquímica y Microbiología, Facultad de Ciencias, Universidad Austral de Chile, Valdivia, ChileABSTRACT Nitrogen limitations in the grape must be the main cause of stuck fermentations during the winemaking process. In Saccharomyces cerevisiae, a genetic segment known as region A, which harbors 12 protein-coding genes, was acquired horizontally from a phylogenetically distant yeast species. This region is mainly present in the genome of wine yeast strains, carrying genes that have been associated with nitrogen utilization. Despite the putative importance of region A in yeast fermentation, its contribution to the fermentative process is largely unknown. In this work, we used a wine yeast strain to evaluate the contribution of region A to the fermentation process. To do this, we first sequenced the genome of the wine yeast strain using long-read sequencing and determined that region A is present in a single copy. We then implemented an optogenetic system in this wine yeast strain to precisely regulate the expression of each gene, generating a collection of 12 strains that allow for light-activated gene expression. To evaluate the role of these genes during fermentation, we assayed this collection using microculture and fermentation experiments in synthetic must with varying amounts of nitrogen concentration. Our results show that changes in gene expression for genes within this region can impact growth parameters and fermentation rate. We additionally found that the expression of various genes in region A is necessary to complete the fermentation process and prevent stuck fermentations under low nitrogen conditions. Altogether, our optogenetics-based approach demonstrates the importance of region A in completing fermentation under nitrogen-limited conditions.IMPORTANCEStuck fermentations due to limited nitrogen availability in grape must represent one of the main problems in the winemaking industry. Nitrogen limitation in grape must reduces yeast biomass and fermentation rate, resulting in incomplete fermentations with high levels of residual sugar, undesired by-products, and microbiological instability. Here, we used an optogenetic approach to demonstrate that expression of genes within region A is necessary to complete fermentations under low nitrogen availability. Overall, our results suggest that region A is a genetic signature for adaptation to low nitrogen conditions.https://journals.asm.org/doi/10.1128/spectrum.01794-24horizontal gene transferoptogeneticsyeastgene expressionfermentation |
| spellingShingle | David Figueroa Diego Ruiz Nicolò Tellini Matteo De Chiara Eduardo I. Kessi-Pérez Claudio Martínez Gianni Liti Amparo Querol José M. Guillamón Francisco Salinas Optogenetic control of horizontally acquired genes prevent stuck fermentations in yeast Microbiology Spectrum horizontal gene transfer optogenetics yeast gene expression fermentation |
| title | Optogenetic control of horizontally acquired genes prevent stuck fermentations in yeast |
| title_full | Optogenetic control of horizontally acquired genes prevent stuck fermentations in yeast |
| title_fullStr | Optogenetic control of horizontally acquired genes prevent stuck fermentations in yeast |
| title_full_unstemmed | Optogenetic control of horizontally acquired genes prevent stuck fermentations in yeast |
| title_short | Optogenetic control of horizontally acquired genes prevent stuck fermentations in yeast |
| title_sort | optogenetic control of horizontally acquired genes prevent stuck fermentations in yeast |
| topic | horizontal gene transfer optogenetics yeast gene expression fermentation |
| url | https://journals.asm.org/doi/10.1128/spectrum.01794-24 |
| work_keys_str_mv | AT davidfigueroa optogeneticcontrolofhorizontallyacquiredgenespreventstuckfermentationsinyeast AT diegoruiz optogeneticcontrolofhorizontallyacquiredgenespreventstuckfermentationsinyeast AT nicolotellini optogeneticcontrolofhorizontallyacquiredgenespreventstuckfermentationsinyeast AT matteodechiara optogeneticcontrolofhorizontallyacquiredgenespreventstuckfermentationsinyeast AT eduardoikessiperez optogeneticcontrolofhorizontallyacquiredgenespreventstuckfermentationsinyeast AT claudiomartinez optogeneticcontrolofhorizontallyacquiredgenespreventstuckfermentationsinyeast AT gianniliti optogeneticcontrolofhorizontallyacquiredgenespreventstuckfermentationsinyeast AT amparoquerol optogeneticcontrolofhorizontallyacquiredgenespreventstuckfermentationsinyeast AT josemguillamon optogeneticcontrolofhorizontallyacquiredgenespreventstuckfermentationsinyeast AT franciscosalinas optogeneticcontrolofhorizontallyacquiredgenespreventstuckfermentationsinyeast |