Cell wall alterations occurring in an evolved multi-stress tolerant strain of the oleaginous yeast Rhodotorula toruloides.
Journal
Scientific reports
ISSN: 2045-2322
Titre abrégé: Sci Rep
Pays: England
ID NLM: 101563288
Informations de publication
Date de publication:
08 Oct 2024
08 Oct 2024
Historique:
received:
26
07
2024
accepted:
30
09
2024
medline:
8
10
2024
pubmed:
8
10
2024
entrez:
7
10
2024
Statut:
epublish
Résumé
The oleaginous yeast species Rhodotorula toruloides is a promising candidate for applications in circular bioeconomy due to its ability to efficiently utilize diverse carbon sources being tolerant to cellular stress in bioprocessing. Previous studies including genome-wide analyses of the multi-stress tolerant strain IST536 MM15, derived through adaptive laboratory evolution from a promising IST536 strain for lipid production from sugar beet hydrolysates, suggested the occurrence of significant modifications in the cell wall. In this study, the cell wall integrity and carbohydrate composition of those strains was characterized to gain insights into the physicochemical changes associated to the remarkable multi-stress tolerance phenotype of the evolved strain. Compared to the original strain, the evolved strain exhibited a higher proportion of glucomannans, fucogalactomannans, and chitin relative to (1→4)-linked glucans, and an increased presence of glycoproteins with short glucosamine derived oligosaccharides, which have been found to be associated to ethanol stress tolerance and physical strength of the cell wall. Furthermore, the evolved strain cells were found to be significantly smaller than the original strain and more resistant to thermal and mechanical disruption, consistent with higher proportion of beta-linked polymers instead of glycogen, conferring a more rigid and robust cell wall. These findings provide further insights into the cell wall composition of this basidiomycetous red yeast species and into the alterations occurring in a multi-stress tolerant evolved strain. This new information can guide yeast genome engineering towards more robust strains of biotechnological relevance.
Identifiants
pubmed: 39375422
doi: 10.1038/s41598-024-74919-y
pii: 10.1038/s41598-024-74919-y
doi:
Types de publication
Journal Article
Langues
eng
Sous-ensembles de citation
IM
Pagination
23366Subventions
Organisme : Fundação para a Ciência e a Tecnologia
ID : PD/BD142944/2018
Organisme : Fundação para a Ciência e a Tecnologia
ID : PD/BD146167/2019
Organisme : Fundação para a Ciência e a Tecnologia
ID : LA/P/0008/2020
Organisme : Fundação para a Ciência e a Tecnologia
ID : LA/P/0008/2020
Organisme : Fundação para a Ciência e a Tecnologia
ID : LA/P/0008/2020
Organisme : Fundação para a Ciência e a Tecnologia
ID : 2022.01501.PTDC
Organisme : European Cooperation in Science and Technology
ID : CA18229
Organisme : European Cooperation in Science and Technology
ID : CA18229
Informations de copyright
© 2024. The Author(s).
Références
Osorio-González, C. S., Hegde, K., Brar, S. K. & Kermanshahipour, A. Avalos-Ramírez, A. Challenges in lipid production from lignocellulosic biomass using Rhodosporidium sp.; a look at the role of lignocellulosic inhibitors. Biofuels, Bioprod. Biorefin. 13, 740–759 (2019).
doi: 10.1002/bbb.1954
Mota, M. N. & Múgica, P. & Sá-Correia, I. Exploring yeast diversity to produce lipid-based biofuels from agro-forestry and industrial organic residues. J. Fungi. 8, (2022).
Yu, Y. & Shi, S. Development and perspective of Rhodotorula toruloides as an efficient cell factory. J. Agric. Food Chem. 71, 1802–1819 (2023).
doi: 10.1021/acs.jafc.2c07361
pubmed: 36688927
Zhao, Y., Song, B., Li, J. & Zhang, J. Rhodotorula toruloides: an ideal microbial cell factory to produce oleochemicals, carotenoids, and other products. World J. Microbiol. Biotechnol. 38, 1–19 (2022).
doi: 10.1007/s11274-021-03201-4
Martins, L. C. et al. Complete utilization of the major carbon sources present in sugar beet pulp hydrolysates by the oleaginous red yeasts. Rhodotorula toruloides and R. mucilaginosa. J. Fungi. 7, 215 (2021).
Fernandes, M. A., Mota, M. N. & Faria, N. T. & Sá-Correia, I. An evolved strain of the oleaginous yeast Rhodotorula toruloides, multi-tolerant to the major inhibitors present in lignocellulosic hydrolysates, exhibits an altered cell envelope. J. Fungi. 9, (2023).
Antunes, M., Mota, M. N. & Sá-Correia, I. Cell envelope and stress-responsive pathways underlie an evolved oleaginous Rhodotorula toruloides strain multi-stress tolerance. Biotechnol. Biofuels Bioprod. 17, 71 (2024).
doi: 10.1186/s13068-024-02518-0
pubmed: 38807231
Kumar, L. R., Yellapu, S. K., Tyagi, R. D. & Zhang, X. A review on variation in crude glycerol composition, bio-valorization of crude and purified glycerol as carbon source for lipid production. Bioresour. Technol. 293, 122155 (2019).
doi: 10.1016/j.biortech.2019.122155
pubmed: 31561979
Ribeiro, R. A., Bourbon-Melo, N. & Sá-Correia, I. The cell wall and the response and tolerance to stresses of biotechnological relevance in yeasts. Front. Microbiol. 13, 2900 (2022).
doi: 10.3389/fmicb.2022.953479
Gao, L. et al. Deciphering cell wall sensors enabling the construction of robust P. pastoris for single-cell protein production. Biotechnol. Biofuels Bioprod. 16, 178 (2023).
doi: 10.1186/s13068-023-02428-7
pubmed: 37978550
Orlean, P. Architecture and biosynthesis of the Saccharomyces cerevisiae cell wall. Genetics. 192, 775–818 Preprint at https://doi.org/10.1534/genetics.112.144485 (2012).
Bastos, R. et al. Covalent connectivity of glycogen in brewer’s spent yeast cell walls revealed by enzymatic approaches and dynamic nuclear polarization NMR. Carbohydr. Polym. 324, 121475 (2024).
Pratt, P. L., Bryce, J. H. & Stewart, G. G. The effects of osmotic pressure and ethanol on yeast viability and morphology. J. Inst. Brew. 109, 218–228 (2003).
doi: 10.1002/j.2050-0416.2003.tb00162.x
Ribeiro, R. A. et al. Yeast adaptive response to acetic acid stress involves structural alterations and increased stiffness of the cell wall. Sci. Rep. 11, 1–9 (2021).
doi: 10.1038/s41598-021-92069-3
Khot, M. et al. Lipid recovery from oleaginous yeasts: perspectives and challenges for industrial applications. Fuel. 259, 116292 (2020).
Prillinger, H. et al. Analysis of cell wall carbohydrates (neutral sugars) from ascomycetous and basidiomycetous yeasts with and without derivatization. J. Gen. Appl. Microbiol. 39, 1–34 (1993).
doi: 10.2323/jgam.39.1
Sipiczki, M. & Farkaš, V. Morphogenic effect of 2-deoxy-D-arabino-hexose on Rhodosporidium toruloides. Folia Microbiol. (Praha). 24, 389–395 (1979).
doi: 10.1007/BF02927121
pubmed: 527913
Prillinger, H. & Lopandic, K. Yeast-types of the Basidiomycota using cell wall sugars and ribosomal DNA sequences. Prillinger loPandic • Yeast-types Basidiomycota STAPFIA. 103, 81–96 (2015).
Barber, F., Amir, A. & Murray, A. W. Cell-size regulation in budding yeast does not depend on linear accumulation of Whi5. Proceedings of the National Academy of Sciences117, 14243–14250 (2020).
Lee, T. H., Arai, M. & Murao, S. Localization of glucomannan and fucogalactomannan in Rhodotorula glutinis cell wall and spheroplast formation of its living cell. Agric. Biol. Chem. 45, 2343–2345 (1981).
Moulki, H., Bonaly, R., Fournet, B. & Montreuil, J. Studies on the cell wall of yeast of the genus Rhodotorula. X. Isolation and purification of cell-wall glycoproteins from Rhodotorula rubra (author’s transl). Biochim. et Biophys. Acta (BBA) - Protein Struct. 420, 279–287 (1976).
Turner, J. J., Ewald, J. C. & Skotheim, J. M. Cell size control in yeast. Curr. Biol. 22, R350–R359 (2012).
doi: 10.1016/j.cub.2012.02.041
pubmed: 22575477
Wu, C. Y., Rolfe, A., Gifford, P. & Fink, G. R. D. K. Control of transcription by cell size. PLoS Biol. 8, e1000523 (2010).
Miettinen, T. P., Caldez, M. J., Kaldis, P. & Björklund, M. Cell size control – a mechanism for maintaining fitness and function. BioEssays. 39, 9 (2017).
Lee, T. H., Arai, M. & Murao, S. Structure of fucogalactomannan of red yeast cell wall. Biol. Chem. 45, 1301–1309 (1981).
Ibe, C. & Munro, C. A. Fungal cell wall proteins and signaling pathways form a cytoprotective network to combat stresses. J. Fungi. 7 Preprint at https://doi.org/10.3390/jof7090739 (2021).
Pittet, M. & Conzelmann, A. Biosynthesis and function of GPI proteins in the yeast Saccharomyces cerevisiae. Biochimica et Biophysica Acta - Molecular and Cell Biology of Lipids vol. 1771 405–420 Preprint at https://doi.org/10.1016/j.bbalip.2006.05.015 (2007).
Yazawa, H., Iwahashi, H. & Uemura, H. Disruption of URA7 and GAL6 improves the ethanol tolerance and fermentation capacity of Saccharomyces cerevisiae. Yeast. 24, 551–560 (2007).
doi: 10.1002/yea.1492
pubmed: 17506111
Udom, N., Chansongkrow, P., Charoensawan, V. & Auesukaree, C. Coordination of the cell wall integrity and highosmolarity glycerol pathways in response to ethanol stress in Saccharomyces cerevisiae. Appl. Environ. Microbiol. 85, 1–16 (2019).
doi: 10.1128/AEM.00551-19
Charoenbhakdi, S., Dokpikul, T., Burphan, T., Techo, T. & Auesukaree, C. Vacuolar H+-ATPase protects Saccharomyces cerevisiae cells against ethanol induced oxidative and cell wall stresses. Appl. Environ. Microbiol. 82, 3121–3130 (2016).
doi: 10.1128/AEM.00376-16
pubmed: 26994074
Rahbar Saadat, Y. & Yari Khosroushahi, A. & Pourghassem Gargari, B. Yeast exopolysaccharides and their physiological functions. Folia Microbiologica. 66, 171–182 Preprint at https://doi.org/10.1007/s12223-021-00856-2 (2021).
Reis, S. F. et al. Structural differences on cell wall polysaccharides of brewer’s spent Saccharomyces and microarray binding profiles with immune receptors. Carbohydr. Polym. 301, 120325 (2023).
Sürmeli, Y. et al. Evolutionary engineering and molecular characterization of a caffeine-resistant Saccharomyces cerevisiae strain. World J. Microbiol. Biotechnol. 35, 183 (2019).
Balaban, B. G. et al. Evolutionary engineering of an iron-resistant Saccharomyces cerevisiae mutant and its physiological and molecular characterization. Microorganisms. 8, 43 (2020).
Terzioğlu, E. et al. Genomic, transcriptomic and physiological analyses of silver-resistant Saccharomyces cerevisiae obtained by evolutionary engineering. Yeast. 37, 413–426 (2020).
doi: 10.1002/yea.3514
pubmed: 33464648
Kocaefe-Özşen, N. et al. Physiological and molecular characterization of an oxidative stress-resistant Saccharomyces cerevisiae strain obtained by evolutionary engineering. Front. Microbiol. 13, (2022).
Holyavkin, C. et al. Genomic, transcriptomic, and metabolic characterization of 2-phenylethanol-resistant Saccharomyces cerevisiae obtained by evolutionary engineering. Front. Microbiol. 14, 1148065 (2023).
Banno, I. Studies on the sexuality of Rhodotorula. J. Gen. Appl. Microbiol. 13, 167–196 (1967).
doi: 10.2323/jgam.13.167
Fernandes, P. A. R. et al. The hydrophobic polysaccharides of apple pomace. Carbohydr. Polym. 223, 115132 (2019).
Blumenkrantz, N. & Asboe-Hansen, G. New method for quantitative determination of uronic acids. Anal. Biochem. 54, 484–489 (1973).
doi: 10.1016/0003-2697(73)90377-1
pubmed: 4269305
Fernandes, P. A. R. et al. Interactions of arabinan-rich pectic polysaccharides with polyphenols. Carbohydr. Polym. 230, 115644 (2020).