Identifying carbohydrate-active enzymes of Cutaneotrichosporon oleaginosus using systems biology.
Carbohydrate metabolism
Carbohydrate uptake
Cutaneotrichosporon oleaginosus
Protein secretion
Proteomics
Journal
Microbial cell factories
ISSN: 1475-2859
Titre abrégé: Microb Cell Fact
Pays: England
ID NLM: 101139812
Informations de publication
Date de publication:
28 Oct 2021
28 Oct 2021
Historique:
received:
23
06
2021
accepted:
05
10
2021
entrez:
29
10
2021
pubmed:
30
10
2021
medline:
1
2
2022
Statut:
epublish
Résumé
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. 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. 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.
Sections du résumé
BACKGROUND
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
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
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.
Identifiants
pubmed: 34711240
doi: 10.1186/s12934-021-01692-2
pii: 10.1186/s12934-021-01692-2
pmc: PMC8555327
doi:
Substances chimiques
Fungal Proteins
0
Proteome
0
Hydrolases
EC 3.-
Types de publication
Journal Article
Langues
eng
Sous-ensembles de citation
IM
Pagination
205Subventions
Organisme : bundesministerium für bildung und forschung
ID : 033RC012B
Informations de copyright
© 2021. The Author(s).
Références
FEMS Microbiol Lett. 2004 Feb 16;231(2):165-9
pubmed: 14987760
Microbiology (Reading). 2012 Jan;158(Pt 1):46-57
pubmed: 22053009
J Mol Biol. 2004 May 14;338(5):1027-36
pubmed: 15111065
Nucleic Acids Res. 2019 Jan 8;47(D1):D506-D515
pubmed: 30395287
Bioprocess Biosyst Eng. 2020 Sep;43(9):1629-1638
pubmed: 32347408
Stud Mycol. 2015 Jun;81:85-147
pubmed: 26955199
Yeast. 1994 Jan;10(1):67-79
pubmed: 8203153
J Environ Manage. 2008 Feb;86(3):481-97
pubmed: 17293023
EMBO Rep. 2004 May;5(5):532-7
pubmed: 15071495
Appl Microbiol Biotechnol. 2006 Dec;73(4):807-14
pubmed: 16896601
Chimia (Aarau). 2015;69(10):572-81
pubmed: 26598400
J Bacteriol. 1986 Nov;168(2):734-8
pubmed: 3782022
J Proteome Res. 2011 Aug 5;10(8):3324-31
pubmed: 21815691
Front Bioeng Biotechnol. 2020 Jan 21;7:481
pubmed: 32039182
FEMS Microbiol Rev. 2000 Oct;24(4):507-29
pubmed: 10978549
Acta Crystallogr D Biol Crystallogr. 2015 Jun;71(Pt 6):1382-91
pubmed: 26057678
Proc Natl Acad Sci U S A. 2017 Aug 1;114(31):8247-8252
pubmed: 28720701
Sci Rep. 2016 Aug 26;6:31730
pubmed: 27562653
Proc Natl Acad Sci U S A. 2017 Nov 14;114(46):E9811-E9820
pubmed: 29087344
Sci Rep. 2017 Sep 5;7(1):10480
pubmed: 28874689
Microb Biotechnol. 2020 Mar;13(2):479-494
pubmed: 31692260
Biochem J. 1993 May 1;291 ( Pt 3):765-71
pubmed: 8489504
Appl Biochem Biotechnol. 2013 May;170(2):420-35
pubmed: 23536251
Biochim Biophys Acta Proteins Proteom. 2019 Sep;1867(9):776-786
pubmed: 31195142
Microb Cell Fact. 2017 Nov 17;16(1):206
pubmed: 29149902
Protein J. 2019 Jun;38(3):200-216
pubmed: 31119599
BMC Syst Biol. 2013 Feb 28;7:17
pubmed: 23448228
Acta Crystallogr Sect F Struct Biol Cryst Commun. 2006 Sep 1;62(Pt 9):849-54
pubmed: 16946462
Lipids. 2010 Nov;45(11):1053-60
pubmed: 20820931
Microbiol Mol Biol Rev. 2002 Sep;66(3):506-77, table of contents
pubmed: 12209002
Biotechnol Biofuels. 2011 Aug 24;4(1):25
pubmed: 21864398
Microb Cell Fact. 2019 Oct 10;18(1):167
pubmed: 31601223
Science. 2010 Oct 1;330(6000):84-6
pubmed: 20829451
Electrophoresis. 2009 Jun;30 Suppl 1:S162-73
pubmed: 19517507
FEMS Yeast Res. 2002 Aug;2(3):371-9
pubmed: 12702287
Protein Eng. 2000 Oct;13(10):735-8
pubmed: 11112513
J Cell Biol. 1985 Mar;100(3):965-73
pubmed: 3972906
Proc Natl Acad Sci U S A. 2006 Jul 25;103(30):11417-22
pubmed: 16844780
Mol Cell Proteomics. 2018 Dec;17(12):2534-2545
pubmed: 30385480
Biochim Biophys Acta. 2013 Nov;1830(11):5204-10
pubmed: 23911748
Genomics. 1992 Dec;14(4):897-911
pubmed: 1478671
Appl Environ Microbiol. 2005 Dec;71(12):7846-57
pubmed: 16332759
Metab Eng. 2011 Nov;13(6):694-703
pubmed: 21963484
FEMS Yeast Res. 2009 Mar;9(2):161-77
pubmed: 19220864
Bioresour Technol. 2013 Jan;128:385-91
pubmed: 23201519
J Biol Chem. 1988 May 5;263(13):6209-14
pubmed: 3283123
Anal Bioanal Chem. 2020 Jan;412(2):449-462
pubmed: 31797019
Antonie Van Leeuwenhoek. 2006 Nov;90(4):391-418
pubmed: 17033882
J Mol Biol. 1997 May 30;269(1):142-53
pubmed: 9193006
FEMS Yeast Res. 2018 Sep 1;18(6):
pubmed: 29718340
Bioinformatics. 2020 Mar 1;36(6):1765-1771
pubmed: 31697312
Mol Cell Biol. 1997 Nov;17(11):6283-93
pubmed: 9343389
FEMS Microbiol Lett. 2000 Sep 1;190(1):9-12
pubmed: 10981682
Biochim Biophys Acta. 2014 Feb;1844(2):366-73
pubmed: 24262091
Yeast. 2005 Mar;22(4):249-70
pubmed: 15704221
Anal Chem. 1996 Mar 1;68(5):850-8
pubmed: 8779443
Nucleic Acids Res. 2018 Jul 2;46(W1):W296-W303
pubmed: 29788355
Appl Biochem Biotechnol. 2014 Aug;173(8):2086-98
pubmed: 24928546
J Biotechnol. 2018 Sep 10;281:81-86
pubmed: 29925036
Antonie Van Leeuwenhoek. 1990 Feb;57(2):77-81
pubmed: 2321931
Sci Rep. 2016 Feb 05;6:20575
pubmed: 26847925
FEMS Yeast Res. 2008 Nov;8(7):1155-63
pubmed: 18752628
Science. 2018 Feb 9;359(6376):689-692
pubmed: 29348368
Nat Methods. 2019 Jan;16(1):63-66
pubmed: 30573815
Biotechnol Biofuels. 2019 Oct 8;12:238
pubmed: 31624500
Biochemistry (Mosc). 2012 Nov;77(11):1303-11
pubmed: 23240568
Bioinformatics. 2011 Feb 1;27(3):343-50
pubmed: 21134891
Eur J Cell Biol. 2018 Aug;97(6):422-441
pubmed: 29958716
Proteomics. 2007 Mar;7(5):642-54
pubmed: 17340585
Front Bioeng Biotechnol. 2019 Mar 26;7:54
pubmed: 30984750
Crit Rev Biochem Mol Biol. 1993;28(4):259-308
pubmed: 8403984
Nucleic Acids Res. 2009 Jul;37(Web Server issue):W202-8
pubmed: 19458158
J Biotechnol. 2006 May 29;123(3):304-13
pubmed: 16446002