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Identifying carbohydrate-active enzymes of Cutaneotrichosporon oleaginosus using systems biology

BACKGROUND: The oleaginous yeast Cutaneotrichosporon oleaginosus represents one of the most promising microbial platforms for resource-efficient and scalable lipid production, with the capacity to accept a wide range of carbohydrates encapsulated in complex biomass waste or lignocellulosic hydrolysa...

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Autores principales: Fuchs, Tobias, Melcher, Felix, Rerop, Zora Selina, Lorenzen, Jan, Shaigani, Pariya, Awad, Dania, Haack, Martina, Prem, Sophia Alice, Masri, Mahmoud, Mehlmer, Norbert, Brueck, Thomas B.
Formato: Online Artículo Texto
Lenguaje:English
Publicado: BioMed Central 2021
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8555327/
https://www.ncbi.nlm.nih.gov/pubmed/34711240
http://dx.doi.org/10.1186/s12934-021-01692-2
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author Fuchs, Tobias
Melcher, Felix
Rerop, Zora Selina
Lorenzen, Jan
Shaigani, Pariya
Awad, Dania
Haack, Martina
Prem, Sophia Alice
Masri, Mahmoud
Mehlmer, Norbert
Brueck, Thomas B.
author_facet Fuchs, Tobias
Melcher, Felix
Rerop, Zora Selina
Lorenzen, Jan
Shaigani, Pariya
Awad, Dania
Haack, Martina
Prem, Sophia Alice
Masri, Mahmoud
Mehlmer, Norbert
Brueck, Thomas B.
author_sort Fuchs, Tobias
collection PubMed
description BACKGROUND: The oleaginous yeast Cutaneotrichosporon oleaginosus represents one of the most promising microbial platforms for resource-efficient and scalable lipid production, with the capacity to accept a wide range of carbohydrates encapsulated in complex biomass waste or lignocellulosic hydrolysates. Currently, data related to molecular aspects of the metabolic utilisation of oligomeric carbohydrates are sparse. In addition, comprehensive proteomic information for C. oleaginosus focusing on carbohydrate metabolism is not available. RESULTS: In this study, we conducted a systematic analysis of carbohydrate intake and utilisation by C. oleaginosus and investigated the influence of different di- and trisaccharide as carbon sources. Changes in the cellular growth and morphology could be observed, depending on the selected carbon source. The greatest changes in morphology were observed in media containing trehalose. A comprehensive proteomic analysis of secreted, cell wall-associated, and cytoplasmatic proteins was performed, which highlighted differences in the composition and quantity of secreted proteins, when grown on different disaccharides. Based on the proteomic data, we performed a relative quantitative analysis of the identified proteins (using glucose as the reference carbon source) and observed carbohydrate-specific protein distributions. When using cellobiose or lactose as the carbon source, we detected three- and five-fold higher diversity in terms of the respective hydrolases released. Furthermore, the analysis of the secreted enzymes enabled identification of the motif with the consensus sequence LALL[LA]L[LA][LA]AAAAAAA as a potential signal peptide. CONCLUSIONS: Relative quantification of spectral intensities from crude proteomic datasets enabled the identification of new enzymes and provided new insights into protein secretion, as well as the molecular mechanisms of carbo-hydrolases involved in the cleavage of the selected carbon oligomers. These insights can help unlock new substrate sources for C. oleaginosus, such as low-cost by-products containing difficult to utilize carbohydrates. In addition, information regarding the carbo-hydrolytic potential of C. oleaginosus facilitates a more precise engineering approach when using targeted genetic approaches. This information could be used to find new and more cost-effective carbon sources for microbial lipid production by the oleaginous yeast C. oleaginosus. SUPPLEMENTARY INFORMATION: The online version contains supplementary material available at 10.1186/s12934-021-01692-2.
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spelling pubmed-85553272021-10-29 Identifying carbohydrate-active enzymes of Cutaneotrichosporon oleaginosus using systems biology Fuchs, Tobias Melcher, Felix Rerop, Zora Selina Lorenzen, Jan Shaigani, Pariya Awad, Dania Haack, Martina Prem, Sophia Alice Masri, Mahmoud Mehlmer, Norbert Brueck, Thomas B. Microb Cell Fact Research BACKGROUND: The oleaginous yeast Cutaneotrichosporon oleaginosus represents one of the most promising microbial platforms for resource-efficient and scalable lipid production, with the capacity to accept a wide range of carbohydrates encapsulated in complex biomass waste or lignocellulosic hydrolysates. Currently, data related to molecular aspects of the metabolic utilisation of oligomeric carbohydrates are sparse. In addition, comprehensive proteomic information for C. oleaginosus focusing on carbohydrate metabolism is not available. RESULTS: In this study, we conducted a systematic analysis of carbohydrate intake and utilisation by C. oleaginosus and investigated the influence of different di- and trisaccharide as carbon sources. Changes in the cellular growth and morphology could be observed, depending on the selected carbon source. The greatest changes in morphology were observed in media containing trehalose. A comprehensive proteomic analysis of secreted, cell wall-associated, and cytoplasmatic proteins was performed, which highlighted differences in the composition and quantity of secreted proteins, when grown on different disaccharides. Based on the proteomic data, we performed a relative quantitative analysis of the identified proteins (using glucose as the reference carbon source) and observed carbohydrate-specific protein distributions. When using cellobiose or lactose as the carbon source, we detected three- and five-fold higher diversity in terms of the respective hydrolases released. Furthermore, the analysis of the secreted enzymes enabled identification of the motif with the consensus sequence LALL[LA]L[LA][LA]AAAAAAA as a potential signal peptide. CONCLUSIONS: Relative quantification of spectral intensities from crude proteomic datasets enabled the identification of new enzymes and provided new insights into protein secretion, as well as the molecular mechanisms of carbo-hydrolases involved in the cleavage of the selected carbon oligomers. These insights can help unlock new substrate sources for C. oleaginosus, such as low-cost by-products containing difficult to utilize carbohydrates. In addition, information regarding the carbo-hydrolytic potential of C. oleaginosus facilitates a more precise engineering approach when using targeted genetic approaches. This information could be used to find new and more cost-effective carbon sources for microbial lipid production by the oleaginous yeast C. oleaginosus. SUPPLEMENTARY INFORMATION: The online version contains supplementary material available at 10.1186/s12934-021-01692-2. BioMed Central 2021-10-28 /pmc/articles/PMC8555327/ /pubmed/34711240 http://dx.doi.org/10.1186/s12934-021-01692-2 Text en © The Author(s) 2021 https://creativecommons.org/licenses/by/4.0/Open AccessThis article is licensed under a Creative Commons Attribution 4.0 International License, which permits use, sharing, adaptation, distribution and reproduction in any medium or format, as long as you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons licence, and indicate if changes were made. The images or other third party material in this article are included in the article's Creative Commons licence, unless indicated otherwise in a credit line to the material. If material is not included in the article's Creative Commons licence and your intended use is not permitted by statutory regulation or exceeds the permitted use, you will need to obtain permission directly from the copyright holder. To view a copy of this licence, visit http://creativecommons.org/licenses/by/4.0/ (https://creativecommons.org/licenses/by/4.0/) . The Creative Commons Public Domain Dedication waiver (http://creativecommons.org/publicdomain/zero/1.0/ (https://creativecommons.org/publicdomain/zero/1.0/) ) applies to the data made available in this article, unless otherwise stated in a credit line to the data.
spellingShingle Research
Fuchs, Tobias
Melcher, Felix
Rerop, Zora Selina
Lorenzen, Jan
Shaigani, Pariya
Awad, Dania
Haack, Martina
Prem, Sophia Alice
Masri, Mahmoud
Mehlmer, Norbert
Brueck, Thomas B.
Identifying carbohydrate-active enzymes of Cutaneotrichosporon oleaginosus using systems biology
title Identifying carbohydrate-active enzymes of Cutaneotrichosporon oleaginosus using systems biology
title_full Identifying carbohydrate-active enzymes of Cutaneotrichosporon oleaginosus using systems biology
title_fullStr Identifying carbohydrate-active enzymes of Cutaneotrichosporon oleaginosus using systems biology
title_full_unstemmed Identifying carbohydrate-active enzymes of Cutaneotrichosporon oleaginosus using systems biology
title_short Identifying carbohydrate-active enzymes of Cutaneotrichosporon oleaginosus using systems biology
title_sort identifying carbohydrate-active enzymes of cutaneotrichosporon oleaginosus using systems biology
topic Research
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8555327/
https://www.ncbi.nlm.nih.gov/pubmed/34711240
http://dx.doi.org/10.1186/s12934-021-01692-2
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