Functional genomics and optogenetics lab

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Francisco Salinas (team leader, assistant professor, Austral University of Chile)

Camila Baeza (PhD student, Austral University of Chile)

David Figueroa (PhD student, Austral University of Chile)

Gonzalo Monsalves (undergrad student, Austral University of Chile)

Rodrigo Toro (undergrad student, Austral University of Chile)

Diego Ruiz (undergrad student, Austral University of Chile)

Previous members

Camila Bastias (research assistant, 2017-2019)

David Figueroa (undergrad thesis, 2017-2018)

Joaquín Devia (undergrad thesis, 2017-2018)

Camila Baeza (undergrad thesis, 2018-2019)

Constanza Poblete (undergrad thesis, 2018-2019)

Research interest

The research interest of our group is focus on the functional characterization of horizontally acquired genes in the yeast species Saccharomyces cerevisiae. Horizontal Gene Transfer (HGT) is a fundamental biological process that shapes the eukaryotic genomes. In yeasts, HGT process improves adaptation to different ecological niches. Thereby, we are systematically studying gene expression and protein levels for a set of horizontally acquired genes in yeasts. We are tackling this challenge using different molecular biology methods (gene deletions, reporter genes and fluorescent proteins), as well as, synthetic biology tools such as CRISPR-Cas9 and optogenetic switches.

On the other hand, our research group is also interested in the development of new molecular biology tools to control gene expression using light. These synthetic systems, known as optogenetic switches, allows the spatiotemporal control of multiple yeast phenotypes, such as: cell cycle, flocculation, protein stability, heterologous protein production and metabolic pathways. In conclusion, our research interests range from basic to applied topics using yeast as eukaryotic model organism.

List of publications

  • Devia, J., Bastias, C., Kessi-Perés, EI., Villarroel, CA., De Chiara, M., Cubillos, FA., Liti, G., Martinez, C., Salinas, F. (2020). Transcriptional activity and protein levels of horizontally acquired genes in yeast reveal hallmarks of adaptation to fermentative environments. Frontiers in Genetics, 11: 293.
  • Villalobos-Cid, M., Salinas, F., Kessi-Pérez, EI., De Chiara, M., Liti, G., Inostroza-Ponta, M., Martinez, C. (2020). Comparison of phylogenetic tree topologies for nitrogen associated genes partially reconstruct the evolutionary history of Saccharomyces cerevisiae. Microorganisms, 8(1), 32–12.
  • Kessi-Pérez, EI., Salinas, F., González, A., Su, Y., Guillamón, J. M., Hall, M. N., Larrondo, LF., Martinez, C. (2019). KAE1 Allelic variants affect TORC1 activation and fermentation kinetics in Saccharomyces cerevisiae. Frontiers in Microbiology, 10: 1686.
  • Molinet, J., Cubillos, F. A., Salinas, F., Liti, G., Martinez, C. (2019). Genetic variants of TORC1 signaling pathway affect nitrogen consumption in Saccharomyces cerevisiae during alcoholic fermentation. PloS One, 14(7): e0220515–24.
  • Kessi-Pérez, EI., Salinas, F., Molinet, J., González, A., Muñiz, S., Guillamón, J. M., Hall, MN., Larrondo, LF., Martinez, C. (2019). Indirect monitoring of TORC1 signalling pathway reveals molecular diversity among different yeast strains. Yeast, 36(1), 65–74.
  • Salinas, F., Rojas, V., Delgado, V., López, J., Agosin, E., Larrondo, L. F. (2018). Fungal Light-Oxygen-Voltage domains for optogenetic control of gene expression and flocculation in yeast. mBio, 9(4), e00626-18.
  • Tapia, SM., Cuevas, M., Abarca, V., Delgado, V., Rojas, V., Garcia, V., Brice, C., Martinez, C., Salinas, F., Larrondo, LF., Cubillos, FA. (2018). GPD1 and ADH3 natural variants underlie glycerol yield differences in wine fermentation. Frontiers in Microbiology, 9: 1460.
  • Vázquez-García, I., Salinas, F., Li, J., Fischer, A., Barré, B., Hallin, J., Bergström, A., Alonso-Perez, E., Warringer, , Mustonen, V., Liti, G. (2017). Clonal heterogeneity influences the fate of new adaptive mutations. Cell Reports, 21(3), 732–744.
  • Salinas, F., Rojas, V., Delgado, V., Agosin, E., Larrondo, LF. (2017). Optogenetic switches for light-controlled gene expression in yeast. Applied Microbiology and Biotechnology. 101(7): 2629-2640.
  • Hallin, J., rtens, K. M. A., Young, A. I., Zackrisson, M., Salinas, F., Parts, L., Warringer, J., Liti, G. (2016). Powerful decomposition of complex traits in a diploid model. Nature Communications, 7: 13311.
  • Kessi-Pérez, EI., Araos, S., Garcia, V., Salinas, F., Abarca, V., Larrondo, LF., Martinez, C., Cubillos, FA. (2016). RIM15 antagonistic pleiotropy is responsible for differences in fermentation and stress response kinetics in budding yeast. FEMS Yeast Research, 16(3): fow021.
  • Salinas, F., de Boer, C. G., Abarca, V., Garcia, V., Cuevas, M., Araos, S., Larrondo, LF., Martínez, C., Cubillos, FA. (2016). Natural variation in non-coding regions underlying phenotypic diversity in budding yeast. Scientific Reports, 6: 21849.
  • Laureau, R., Loeillet, S., Salinas, F., Bergström, A., Legoix-Né, P., Liti, G., Nicolas, A. (2016). Extensive recombination of a yeast diploid hybrid through meiotic reversion. PLoS Genetics, 12(2), e1005781–30.
  • López-Martínez, G., Margalef-Català, M., Salinas, F., Liti, G., Cordero-Otero, R. (2015). ATG18 and FAB1 are involved in dehydration stress tolerance in Saccharomyces cerevisiae. PloS One, 10(3), e0119606.
  • Ibstedt, S., Stenberg, S., Bagés, S., Gjuvsland, A. B., Salinas, F., Kourtchenko, O., Samy, JK., Blomberg, A., Omholt, SW., Liti, G., Beltran, G., Warringer, J. (2015). Concerted evolution of life stage performances signals recent selection on yeast nitrogen use. Molecular Biology and Evolution, 32(1), 153–161.
  • Jara, M., Cubillos, F. A., Garcia, V., Salinas, F., Aguilera, O., Liti, G., Martinez, C. (2014). Mapping genetic variants underlying differences in the central nitrogen metabolism in fermenter yeasts. PloS One, 9(1), e86533.
  • Bergstrom, A., Simpson, J. T., Salinas, F., Barre, B., Parts, L., Zia, A., Nguyen Ba, AN., Moses, AM., Louis, EJ., Mustonen, V., Warringer, J., Durbin, R., Liti, G. (2014). A high-definition view of functional genetic variation from natural yeast genomes. Molecular Biology and Evolution, 31(4), 872–888.
  • Cubillos, FA., Parts, L., Salinas, F., Bergström, A., Scovacricchi, E., Zia, A., Illingworth, CJ., Mustonen, V., Ibstedt, , Warringer, J., Louis, EJ., Durbin, R., Liti, G. (2013). High-resolution mapping of complex traits with a four-parent advanced intercross yeast population. Genetics, 195(3), 1141–1155.
  • Contreras, A., García, V., Salinas, F., Urzúa, U., Ganga, M. A., Martinez, C. (2012). Identification of genes related to nitrogen uptake in wine strains of Saccharomyces cerevisiae. World Journal of Microbiology & Biotechnology, 28(3), 1107–1113.
  • Salinas, F., Cubillos, FA., Soto, D., Garcia, V., Bergström, A., Warringer, J., Ganga, MA., Louis, EJ., Liti, G., Martinez, C. (2012). The genetic basis of natural variation in oenological traits in Saccharomyces cerevisiae. PloS One, 7(11), e49640.
  • Parts, L., Cubillos, FA., Warringer, J., Jain, K., Salinas, F., Bumpstead, S. J., Molin, M., Zia, A., Simpson, JT., Quail, , Moses, A., Louis, EJ., Durbin, R., Liti, G. (2011). Revealing the genetic structure of a trait by sequencing a population under selection. Genome Research, 21(7), 1131–1138.
  • Ganga, M. A., Salinas, F., Ravanal, C., Garcia, V., Carrasco, C., Martinez, C., Saavedra, J. (2011). Cinnamic acid, ethanol and temperature interaction on coumarate decarboxylase activity and the relative expression of the putative cd gene in bruxellensis. Electronic Journal of Biotechnology, 14(5), 2–2.
  • Salinas, F., Mandakovi?, D., Urzúa, U., Massera, A., Miras, S., Combina, M., Ganga, MA., Martinez, C. (2010). Genomic and phenotypic comparison between similar wine yeast strains of Saccharomyces cerevisiae from different geographic origins. Journal of Applied Microbiology, 108(5), 1850–1858.
  • Salinas, F., Garrido, D., Ganga, A., Veliz, G., Martinez, C. (2009). Taqman real-time PCR for the detection and enumeration of Saccharomyces cerevisiae in wine. Food Microbiology, 26(3), 328–332.
  • Contreras, A., Salinas, F., Ganga, A., Martinez, C. (2008). Polymerase chain reaction confirmatory method for microbiological detection of Brettanomyces bruxellensis in wines. Journal of Rapid Methods & Automation in Microbiology, 16(4), 308–319.
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