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Reconstruction and analysis of a Kluyveromyces marxianus genome-scale metabolic model.
BMC Bioinformatics. 2019 Nov 06; 20(1):551.BB

Abstract

BACKGROUND

Kluyveromyces marxianus is a thermotolerant yeast with multiple biotechnological potentials for industrial applications, which can metabolize a broad range of carbon sources, including less conventional sugars like lactose, xylose, arabinose and inulin. These phenotypic traits are sustained even up to 45 °C, what makes it a relevant candidate for industrial biotechnology applications, such as ethanol production. It is therefore of much interest to get more insight into the metabolism of this yeast. Recent studies suggested, that thermotolerance is achieved by reducing the number of growth-determining proteins or suppressing oxidative phosphorylation. Here we aimed to find related factors contributing to the thermotolerance of K. marxianus.

RESULTS

Here, we reported the first genome-scale metabolic model of Kluyveromyces marxianus, iSM996, using a publicly available Kluyveromyces lactis model as template. The model was manually curated and refined to include the missing species-specific metabolic capabilities. The iSM996 model includes 1913 reactions, associated with 996 genes and 1531 metabolites. It performed well to predict the carbon source utilization and growth rates under different growth conditions. Moreover, the model was coupled with transcriptomics data and used to perform simulations at various growth temperatures.

CONCLUSIONS

K. marxianus iSM996 represents a well-annotated metabolic model of thermotolerant yeast, which provides a new insight into theoretical metabolic profiles at different temperatures of K. marxianus. This could accelerate the integrative analysis of multi-omics data, leading to model-driven strain design and improvement.

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Authors+Show Affiliations

Marcišauskas S
Department of Biology and Biological Engineering, Chalmers University of Technology, Kemivägen 10, SE412 96, Gothenburg, Sweden.
Ji B
Department of Biology and Biological Engineering, Chalmers University of Technology, Kemivägen 10, SE412 96, Gothenburg, Sweden.
Nielsen J
Department of Biology and Biological Engineering, Chalmers University of Technology, Kemivägen 10, SE412 96, Gothenburg, Sweden. nielsenj@chalmers.se. Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, DK2800, Lyngby, Denmark. nielsenj@chalmers.se. BioInnovation Institute, Ole Måløes Vej 3, DK2200, Copenhagen N, Denmark. nielsenj@chalmers.se.

MeSH

BiomassBiosynthetic PathwaysFermentationGenome, BacterialKluyveromycesModels, BiologicalReproducibility of ResultsRiboflavinSaccharomyces cerevisiaeStress, PhysiologicalTemperature

Pub Type(s)

Journal Article

Language

eng

PubMed ID

31694544

Citation

Marcišauskas, Simonas, et al. "Reconstruction and Analysis of a Kluyveromyces Marxianus Genome-scale Metabolic Model." BMC Bioinformatics, vol. 20, no. 1, 2019, p. 551.
Marcišauskas S, Ji B, Nielsen J. Reconstruction and analysis of a Kluyveromyces marxianus genome-scale metabolic model. BMC Bioinformatics. 2019;20(1):551.
Marcišauskas, S., Ji, B., & Nielsen, J. (2019). Reconstruction and analysis of a Kluyveromyces marxianus genome-scale metabolic model. BMC Bioinformatics, 20(1), 551. https://doi.org/10.1186/s12859-019-3134-5
Marcišauskas S, Ji B, Nielsen J. Reconstruction and Analysis of a Kluyveromyces Marxianus Genome-scale Metabolic Model. BMC Bioinformatics. 2019 Nov 6;20(1):551. PubMed PMID: 31694544.
* Article titles in AMA citation format should be in sentence-case
TY - JOUR T1 - Reconstruction and analysis of a Kluyveromyces marxianus genome-scale metabolic model. AU - Marcišauskas,Simonas, AU - Ji,Boyang, AU - Nielsen,Jens, Y1 - 2019/11/06/ PY - 2019/03/20/received PY - 2019/10/09/accepted PY - 2019/11/8/entrez PY - 2019/11/7/pubmed PY - 2020/1/11/medline KW - Constraint-based flux analysis KW - Genome-scale metabolic model KW - Kluyveromyces marxianus KW - Thermotolerant yeast SP - 551 EP - 551 JF - BMC bioinformatics JO - BMC Bioinformatics VL - 20 IS - 1 N2 - BACKGROUND: Kluyveromyces marxianus is a thermotolerant yeast with multiple biotechnological potentials for industrial applications, which can metabolize a broad range of carbon sources, including less conventional sugars like lactose, xylose, arabinose and inulin. These phenotypic traits are sustained even up to 45 °C, what makes it a relevant candidate for industrial biotechnology applications, such as ethanol production. It is therefore of much interest to get more insight into the metabolism of this yeast. Recent studies suggested, that thermotolerance is achieved by reducing the number of growth-determining proteins or suppressing oxidative phosphorylation. Here we aimed to find related factors contributing to the thermotolerance of K. marxianus. RESULTS: Here, we reported the first genome-scale metabolic model of Kluyveromyces marxianus, iSM996, using a publicly available Kluyveromyces lactis model as template. The model was manually curated and refined to include the missing species-specific metabolic capabilities. The iSM996 model includes 1913 reactions, associated with 996 genes and 1531 metabolites. It performed well to predict the carbon source utilization and growth rates under different growth conditions. Moreover, the model was coupled with transcriptomics data and used to perform simulations at various growth temperatures. CONCLUSIONS: K. marxianus iSM996 represents a well-annotated metabolic model of thermotolerant yeast, which provides a new insight into theoretical metabolic profiles at different temperatures of K. marxianus. This could accelerate the integrative analysis of multi-omics data, leading to model-driven strain design and improvement. SN - 1471-2105 UR - https://www.unboundmedicine.com/medline/citation/31694544/Reconstruction_and_analysis_of_a_Kluyveromyces_marxianus_genome_scale_metabolic_model_ DB - PRIME DP - Unbound Medicine ER -