Academic CentrePurine metabolism is functionally the same across many eukaryotes (fungi, animals). Inability to synthesize purine de novo (purine auxotrophy) is typical trait of many single cell parasites (malaria plasmodium, toxoplasma, leishmania, etc.). Already now nucleotide metabolism is target immunosuppressant therapies, and it is foreseen to become promising target for eukaryotic parasite control. Budding yeast Saccharomyces cerevisiae is excellent model for eukaryotic cells and metabolism.
Our group focuses on the fundamental and applied aspects of purine auxotrophic yeast metabolism. yeast physiology. Currently we are working on to clarify mechanisms involved in formation of purine auxotrophic starvation specific phenotype in the budding yeast Saccharomyces cerevisiae.
Understanding mechanism of yeast cell reaction to depletion of specific nucleotide base would facilitate yeast application in specific drug screens, developing strategies for control of biotechnological relevant auxotrophic strains, parasitic organisms, etc.
We have HANDS ON EXPERTISE with the following methods:
- microbial cultivation (from micro cultivation in 96 well plates to laboratory scale fermenters of several liters)
- yeast protein tagging and immunofluorescence
- yeast stress tolerance assays (heat shock, oxidative tolerance, desiccation, weak acid)
- enzymatic assays (photometric, fluorometric or luminescent detection)
- qPCR
- transcriptome analyses
Team
From left to right, Stivens Zolins, Anitra Zile, Agnese Kokina, Zane Ozolina, Jana Kasaliete, Ernests Auzins, Janis Liepins. (2020)
Reaserch staff
Agnese Kokina, PhD
Current undergraduate students:
Ernests Tomass Auzins
Krista Mehaņikova
Jānis Daugavietis,
Kristaps Čivkulis
Ričards Krastiņš
Current graduate students:
Zane Ozoliņa
Ieva Bērziņa
Our alumni students:
Līva Kristiāna Lukša (University of Tartu, EE)
Anitra Zile (KU Leuven, BE)
Stivens Zolins (expert, Latvia MGI Tech, LV)
Jana Kasaliete (research assistant, Lund University, SE)
Signe Kibilda (geneticist, Central Laboratory, LV)
Juris Kibilds (Senior expert, Institute of Food Safety, Animal Health and Environment, BIOR, LV)
Katrina Daila Neiburga (research fellow, University of Tartu, EE)
Reinis Vangravs (Senior Bioinformatician, Riga East University Hospital, LV)
Joanna Jarzyna (University Lodz, Poland)
Projects
- From purine depletion to resilient phenotype: disecting the mechanisms (Latvian Science Council, 2022-2024)
- Fast and cost-effective machine learning based system for microbial growth analysis (ERDF funded project, 2020-2023)
- Sustainable microbial valorisation of waste lipids into biosurfactants (WASTE2SURF) (ERDF funded project, 2020-2023)
- “Purine auxotrophy – is this Your next superpower?” (Latvian Science Council, 2018-2020)
- “Fast and non-contact optical estimation of micro-organisms activity” (Latvian Science Council 2018-2020)
- Postdoctoral grant “Molecular mechanisms of purine and pyrimidine auxotrophic starvation in budding yeast“ YEAUX (EU Structural Fund, 2017 - 2020)
- “Bacterial intracellular microcompartments as synthetic nanoreactors” (funded by Mikrotik Ltd, administered by Charity Fund of University of Latvia, 2018 - 2019)
- Nacionāla un starptautiska mēroga pasākumu īstenošana izglītojamo talantu attīstībai. SAM 8.3.2. "Palielināt atbalstu vispārējās izglītības iestādēm izglītojamo individuālo kompetenču attīstībai". Projekta numurs: 8.3.2.1/16/I/002.
- COST Action CA18229 “Nonconventional Yeasts for the Production of Bioproducts" (YEAST4BIO)
- COST Action CA16120 (European Epitranscriptomics Network, 2017 - 2021)
Publications
2023
Balmages, I., Liepins, J., Auzins, E.T., Bliznuks, D., Baranovics, E., Lihacova, I. and Lihachev, A., 2023. Use of the speckle imaging sub-pixel correlation analysis in revealing a mechanism of microbial colony growth. Scientific Reports, 13(1), p.2613.
2022
Antone, U., Ciprovica, I., Zolovs, M., Scerbaka, R. and Liepins, J., 2022. Propionic Acid Fermentation—Study of Substrates, Strains, and Antimicrobial Properties. Fermentation, 9(1), p.26
Kokina, A., Tanilas, K., Ozolina, Z., Pleiko, K., Shvirksts, K., Vamza, I. and Liepins, J., 2022. Purine Auxotrophic Starvation Evokes Phenotype Similar to Stationary Phase Cells in Budding Yeast. Journal of Fungi, 8(1), p.29.
2021
Liepins, J., Balina, K., Soloha, R., Berzina, I., Lukasa, L.K. and Dace, E., 2021. Glycolipid biosurfactant production from waste cooking oils by yeast: Review of substrates, producers and products. Fermentation, 7(3), p.136.
Dubencovs, K., Liepins, J., Suleiko, A., Suleiko, A., Vangravs, R., Kassaliete, J., Scerbaka, R., Grigs, O. 2021. Optimization of synthetic media composition for Kluyveromyces marxianus fed-batch cultivation. - Fermentation, 7(2), 62 (21 p.). doi:10.3390/fermentation7020062
Balmages, I., Liepins, J., Zolins, S., Bliznuks, D., Lihacova, I. and Lihachev, A., 2021. Laser speckle imaging for early detection of microbial colony forming units. Biomedical Optics Express, 12(3), pp.1609-1620.
2020
Kuka, J., Videja, M., Makrecka-Kuka, M., Liepins, J., Grinberga, S., Sevostjanovs, E., Vilks, K., Liepinsh, E. and Dambrova, M., 2020. Metformin decreases bacterial trimethylamine production and trimethylamine N-oxide levels in db/db mice. Scientific Reports, 10(1), 1-9.
G Kalnins, EE Cesle, J Jansons, J Liepins, A Filimonenko, K Tars 2020. Encapsulation mechanisms and structural studies of GRM2 bacterial microcompartment particles. Nature communications 11 (1), 1-13
Balmages, I, Bliznuks D, Liepins J, Zolins S., Lihachev A.. 2020. Laser speckle time-series correlation analysis for bacteria activity detection. In Biomedical Spectroscopy, Microscopy, and Imaging, vol. 11359, p. 113591D. International Society for Optics and Photonics, 2020.
Laganovska, K., Zolotarjovs, A., Vázquez, M., Mc Donnell, K., Liepins, J., Ben-Yoav, H., Karitans, V. and Smits, K., 2020. Portable low-cost open-source wireless spectrophotometer for fast and reliable measurements. HardwareX, p.e00108.
2019
Kokina, A., Ozolina, Z. and Liepins, J., 2019. Purine auxotrophy: Possible applications beyond genetic marker. Yeast, 36(11), pp.649-656.
Stivrins N, Aakala T, Ilvonen L, Pasanen L, Kuuluvainen, J. Liepins, et al., and H. Seppa 2019. Integrating fire-scar, charcoal and fungal spore data to study fire-events in the boreal forest of northern Europe., Holocene, 29(9), pp.1480-1490.
Rucins, M., Dimitrijevs, P., Pajuste, K., Petrichenko, O., Jackevica, L., Gulbe, A., Kibilda, S., Smits, K., Plotniece, M., Liepins J., Tirzite, D. and Pajuste, K., 2019. Contribution of Molecular Structure to Self-Assembling and Biological Properties of Bifunctional Lipid-Like 4-(N-Alkylpyridinium)-1, 4-Dihydropyridines. Pharmaceutics, 11(3), p.115.
2018
Jantsch, M.F., Quattrone, A., O'Connell, M., Helm, M., Frye, Liepins J., M., Macias-Gonzales, M., Ohman, M., Ameres, S., Willems, L., Fuks, F. and Oulas, A., 2018. Positioning Europe for the EPITRANSCRIPTOMICS challenge. RNA biology, pp.1-3
2017
Ozolina Z, Kokina A, Liepins J, 2017. Adenine starvation is signalled through environmental stress response system in budding yeast Saccharomyces cerevisiae Environm Experim Biol 15, 283 - 286
Rungis, D.E., Voronova, A., Kokina, A., Veinberga, I., Skrabule, I. and Rostoks, N., 2017. Assessment of genetic diversity and relatedness in the Latvian potato genetic resources collection by DArT genotyping. Plant Genetic Resources, 15(1), pp.72-78.
Pentjuss, A., Stalidzans, E., Liepins, J., Kokina, A., Martynova, J., Zikmanis, P., Mozga, I., Scherbaka, R., Hartman, H., Poolman, M.G., Fell, D.A., Vigants, A., (2017). Model-based biotechnological potential analysis of Kluyveromyces marxianus central metabolism. J. Ind. Microbiol. Biotechnol. Vol. 44, p. 1177–1190.
2016
Martynova J., Kokina A, Liepins J, Scerbaka R, Vigants A, 2016. Effects of acetate on Kluyveromyces marxianus DSM 5422 growth and metabolism. Appl. Microb. and Biotechn., 100 (10), 4585-94 [0]
2015
Liepins J, Kovačova E, Shvirksts K, Grube M, Rapoport A, Kogan G. 2015. Drying enhances immunoactivity of spent brewer's yeast cell wall β-D-glucans. J. Biotechnol. 206: 12-6. [2]
Rungis, D.E., Voronova, A., Kokina, A., Veinberga, I., Skrabule, I. and Rostoks, N. 2015. Assessment of genetic diversity and relatedness in the Latvian potato genetic resources collection by DArT genotyping. Plant Genetic Resources, pp.1-7.
2014
Kuka J, Liepinsh E, Makrecka-Kuka M, Liepins J, Cirule H, Gustina D, Loza E, Zharkova-Malkova O, Grinberga S, Pugovics O, Dambrova M, 2014. Suppression of intestinal microbiota-dependent production of pro-atherogenic trimethylamine N-oxide by shifting L-carnitine microbial degradation. Life. Sci. 117(2): 84-92 [12]
Kokina A, Kibilds J, Liepins J, 2014. Adenine auxotrophy – be aware. Some effects of adenine auxotrophy in Saccharomyces cerevisiae strain W303-1A, FEMS Yeast Res., 14(5): 697-707 [3]
Makrecka M, Svalbe B, Volska K, Sevostjanovs E, Liepins J, Grinberga S, Pugovics O, Liepinsh E, Dambrova M, 2014. Mildronate, the inhibitor of L-carnitine transport, induces brain mitochondrial uncoupling and protects against anoxia-reoxygenation, Eur. J. Pharmacol., 723: 55-61 [6]
2013
Grube M, Dimanta I, Gavare M, Strazdina I, Liepins J, Juhna T, Kalnenieks U, 2013. Hydrogen-producing Escherichia coli strains, overexpressing lactose permease: FT-IR analysis of the lactose-induced stress, Biotechnol. Appl. Biochem., 61(2): 111-7 [1]
2012
Smits K, Liepins J, Gavare M, Patmalnieks A, Gruduls A, Jankovica Dz, 2012. Zirconia nanocrystals as submicron level biological label, IOP Conf. Ser.: Mater. Sci. Eng. 38, 012050 [2]
2011
Rapoport, A., Borovikova, D., Kokina, A., Patmalnieks, A., Polyak, N., Pavlovska, I., Mezinskis, G. and Dekhtyar, Y., 2011. Immobilisation of yeast cells on the surface of hydroxyapatite ceramics. Process Biochemistry, 46(3), pp.665-670.
2010
Brusbardis V, Liepins J, 2010. Mathematical modeling of glycerol cycle in baker’s yeast, Research for Rural Development, Annual 16th, International Scientific Conference Proceedings, Jelgava, LLU, 214 – 220, ISSN 1691-4031 [0]
2008
Kokina, A. and Rostoks, N., 2008, January. Genome-Wide and Mla Locus-Specific Characterisation of Latvian Barley Varieties. In Proceedings of the Latvian Academy of Sciences. Section B. Natural, Exact, and Applied Sciences. (Vol. 62, No. 3, pp. 103-109).
Kokina, A., Legzdina, L., Berzina, I., Bleidere, M., Rashal, I., Rostoks, N. and Šterne, D., 2008. Molecular marker-based characterization of barley powdery mildew Mlo resistance locus in European varieties and breeding lines. Agronomijas Vēstis, (11), pp.77-83.
2006
Liepins J, Kuorelahti S, Penttilä M, Richard P, 2006. Enzymes for the NADPH-dependent reduction of dihydroxyacetone and D-glyceraldehyde and L-glyceraldehyde in the mould Hypocrea jecorina. FEBS J. 2006, 273(18): 4229-35.
Conference thesis
Auzins E, Kokina A, Ozolina Z, Liepins J, 2021. Purine and nitrogen starvation effects on central carbon metabolism in budding yeast purine auxotrophic mutants (February, 2021, Riga, University of Latvia Scientific conference 79th)
Kokina A, Ozolina Z, Pleiko K, Liepins J, 2021. Transcriptional response to purine starvation in budding yeast ade8 knockout (February, 2021, Riga, University of Latvia Scientific conference 79th)
Kassaliete, J., Zile, A., Ozolina, Z., Kokina, A. Liepins, J. (2020). Use of baker’s yeast purine auxotrophs for adenine quantification. (February, 2020, Riga, University of Latvia Scientific conference 78th)
Kokina A, Pleiko K, Ozolina Z, Liepins J, 2019. Role of mutations in purine de novo synthesis pathway in cell cycle arrest and stress resistance phenotype during purine starvation. 29th International Conference on Yeast Genetics and Molecular Biology (ICYGMB 2019), Gothenburg, Sweden 18th - 22th August.
Ozolina Z, Zolins S, Kokina A, Liepins J , 2019. The Role of Cross feeding in the Emergence of Purine Auxotrophs. 29th International Conference on Yeast Genetics and Molecular Biology (ICYGMB 2019), Gothenburg, Sweden 18th - 22th August.
Ozoliņa Z., Kokina A., Martynova J., Liepins J. 2017. How purine starvation is communicated inside the baker’s yeast cell. 28th International Conference on Yeast Genetics and Molecular Biology (ICYGMB 2017), Prague, Czech Republic, 27th August – 1st September.
Kokina A., Ozoliņa Z., Vamža I., Liepiņš J. 2017. Guanine plays critical role in the development of stress resistance phenotype in adenine auxotrophic strains during purine starvation in budding yeast. 28th International Conference on Yeast Genetics and Molecular Biology (ICYGMB 2017), Prague, Czech Republic, 27th August – 1st September.
Liepins J, Kokina A, 2014. Nutritional effects on baker’s yeast desiccation tolerance. CBM2014, Tartu, Estonia, 16- 19.10
Kokina A, Kibilds J, Liepins J, 2013. Some adenine auxotrophy effects in yeast Saccharomyces cerevisiae, 26th International Conference on Yeast Genetics and Molecular Biology, Frankfurt, Germany, 29. August- 04. September
TEACHING UNIVERSITY
Biol2058 Gene and cell technology II (Biotechnology and biongineering, bachelor program, 6 ECT points)
Biol3056 Eucariotic gene engineering (Biotechnology and biongineering, bachelor program 8 ECT points)
Biol3122 Microorganism genetics (Biology bachelor program, 6 ECT points)
Biol5150 Producents biotechnology (Biology master’s program 6 ECT points)
iGEM team hosting (iGEM Latvia 2022, 2023)
HIGH SCHOOL
National biology olimpiad - organisation of regional and national rounds, participant selection for national team in annual international biology olimpiad competition (IBO) [https://www.ibo-info.org/en/countries/nbo/lv-latvian-state-biology-olympiad-53.html]
Hands on course for high school teachers (Biology II), under programm Skola-2030, (2022 August)
SCIENCE POPULARISATION
Radio broadcasts in National Radio ( program "Zināmais Nezināmajā" https://tinyurl.com/yeastLR1)
Art and science projects, like "Close Encounter' (Jan Glockner, DE, RIXC.LV, rixc.org/en/exhibitions/2015/684/)
Science Night 2021 www.youtube.com/watch
Merry Christmas 2020 (yeast painting, auth. Zane Ozolina & Stivens Zolins) tinyurl.com/MChr2020
Cooperation
International
University of Tartu (Estonia)
Center of Food and Fermentation Technologies (TFTAK, Estonia)
National
Institute of Solid State Physics
Institute of Organic Synthesis of Latvia
Latvian Biomedical Research and Study Centre.
National Centre for Education (NCE)
Contacts
Head of the group
Dr.biol. Janis Liepins
twitter @j_liepins