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Physiological and transcriptome analyses of Kluyveromyces marxianus reveal adaptive traits in stress response

  • Applied Microbial and Cell Physiology
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Abstract

Kluyveromyces marxianus is a non-conventional yeast with outstanding physiological characteristics and a high potential for lignocellulosic ethanol production. However, achieving high ethanol productivity requires overcoming several biotechnological challenges due to the cellular inhibition caused by the inhibitors present in the medium. In this work, K. marxianus SLP1 was adapted to increase its tolerance to a mix of inhibitory compounds using the adaptive laboratory evolution strategy to study the adaptation and stress response mechanisms used by this non-Saccharomyces yeast. The fermentative and physiological parameters demonstrated that the adapted K. marxianus P8 had a better response against the synergistic effects of multiple inhibitors because it reduced the lag phase from 12 to 4 h, increasing the biomass by 40% and improving the volumetric ethanol productivity 16-fold than the parental K. marxianus SLP1. To reveal the effect of adaptation process in P8, transcriptome analysis was carried out; the result showed that the basal gene expression in P8 changed, suggesting the biological capability of K. marxianus to activate the adaptative prediction mechanism. Similarly, we carried out physiologic and transcriptome analyses to reveal the mechanisms involved in the stress response triggered by furfural, the most potent inhibitor in K. marxianus. Stress response studies demonstrated that P8 had a better physiologic response than SLP1, since key genes related to furfural transformation (ALD4 and ALD6) and stress response (STL1) were upregulated. Our study demonstrates the rapid adaptability of K. marxianus to stressful environments, making this yeast a promising candidate to produce lignocellulosic ethanol.

Key points

K. marxianus was adapted to increase its tolerance to a mix of inhibitory compounds

The basal gene expression of K. marxianus changed after the adaptation process

Adapted K. marxianus showed a better physiological response to stress by inhibitors

Transcriptome analyses revealed key genes involved in the stress response

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Data availability

The RNA-seq data and expression profiles were deposited in the Gene Expression Omnibus (GEO) repository belonging to NCBI under the bioproject PRJNA714250. The accession number of the K. marxianus SLP1 and P8 reads and their replicates is GSE176040. The expression profiles and metadata files are provided in the same bioproject.

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Acknowledgements

The author deeply appreciates the CONACYT-SENER and COECyTJAL for financial support for this study. Sandoval-Nuñez Dania received a grant from CONACYT, Mexico.

Funding

The author sincerely appreciated the financial support from CONACYT-SENER (Fondo de Sustentabilidad Energética, projects 245750 and 250014). Sandoval Nuñez Dania and Gómez Márquez Carolina received a scholarship from CONACYT, Mexico (scholarship number 436599 and 738133, respectively).

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Contributions

LAD and AGM project conceptualization. TRG, CGM, and DSN data curation and formal transcriptomic analysis. LAD funding acquisition and project administration. DSN conducted experiments. LAD, DSN, and MAP designed the methodology. TRG and CGM analyzed the data from bioinformatic analysis. LAD and AGM: supervision and validation. DSN wrote the original draft. DSN, TRG, CGM, and LAD wrote reviews and editing. All authors read and approved the manuscript.

Corresponding author

Correspondence to Lorena Amaya-Delgado.

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This article does not contain any studies with human participants or animals performed by any of the authors.

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The authors declare no competing interests.

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Sandoval-Nuñez, D., Romero-Gutiérrez, T., Gómez-Márquez, C. et al. Physiological and transcriptome analyses of Kluyveromyces marxianus reveal adaptive traits in stress response. Appl Microbiol Biotechnol 107, 1421–1438 (2023). https://doi.org/10.1007/s00253-022-12354-7

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  • DOI: https://doi.org/10.1007/s00253-022-12354-7

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