Saccharomyces boulardii promoters for control of gene expression in vivo.


Journal

Microbial cell factories
ISSN: 1475-2859
Titre abrégé: Microb Cell Fact
Pays: England
ID NLM: 101139812

Informations de publication

Date de publication:
07 Jan 2024
Historique:
received: 04 10 2023
accepted: 26 12 2023
medline: 8 1 2024
pubmed: 8 1 2024
entrez: 7 1 2024
Statut: epublish

Résumé

Interest in the use of engineered microbes to deliver therapeutic activities has increased in recent years. The probiotic yeast Saccharomyces boulardii has been investigated for production of therapeutics in the gastrointestinal tract. Well-characterised promoters are a prerequisite for robust therapeutic expression in the gut; however, S. boulardii promoters have not yet been thoroughly characterised in vitro and in vivo. We present a thorough characterisation of the expression activities of 12 S. boulardii promoters in vitro in glucose, fructose, sucrose, inulin and acetate, under both aerobic and anaerobic conditions, as well as in the murine gastrointestinal tract. Green fluorescent protein was used to report on promoter activity. Promoter expression was found to be carbon-source dependent, with inulin emerging as a favourable carbon source. Furthermore, relative promoter expression in vivo was highly correlated with expression in sucrose (R = 0.99). These findings provide insights into S. boulardii promoter activity and aid in promoter selection in future studies utilising S. boulardii to produce therapeutics in the gut.

Sections du résumé

BACKGROUND BACKGROUND
Interest in the use of engineered microbes to deliver therapeutic activities has increased in recent years. The probiotic yeast Saccharomyces boulardii has been investigated for production of therapeutics in the gastrointestinal tract. Well-characterised promoters are a prerequisite for robust therapeutic expression in the gut; however, S. boulardii promoters have not yet been thoroughly characterised in vitro and in vivo.
RESULTS RESULTS
We present a thorough characterisation of the expression activities of 12 S. boulardii promoters in vitro in glucose, fructose, sucrose, inulin and acetate, under both aerobic and anaerobic conditions, as well as in the murine gastrointestinal tract. Green fluorescent protein was used to report on promoter activity. Promoter expression was found to be carbon-source dependent, with inulin emerging as a favourable carbon source. Furthermore, relative promoter expression in vivo was highly correlated with expression in sucrose (R = 0.99).
CONCLUSIONS CONCLUSIONS
These findings provide insights into S. boulardii promoter activity and aid in promoter selection in future studies utilising S. boulardii to produce therapeutics in the gut.

Identifiants

pubmed: 38185666
doi: 10.1186/s12934-023-02288-8
pii: 10.1186/s12934-023-02288-8
doi:

Types de publication

Journal Article

Langues

eng

Sous-ensembles de citation

IM

Pagination

16

Subventions

Organisme : Novo Nordisk Fonden
ID : NNF19SA0035438
Organisme : Novo Nordisk Fonden
ID : NNF20CC0035580
Organisme : European Commission
ID : 813781

Informations de copyright

© 2024. The Author(s).

Références

Pulikkan J, Mazumder A, Grace T. Role of the gut microbiome in autism spectrum disorders BT. In: Guest PC, editor. Reviews on biomarker studies in psychiatric and neurodegenerative disorders. Cham: Springer International Publishing; 2019.
Aoun A, Darwish F, Hamod N. The influence of the gut microbiome on obesity in adults and the role of probiotics, prebiotics, and synbiotics for weight loss. Prev Nutr Food Sci. 2020;25(2):113–23.
doi: 10.3746/pnf.2020.25.2.113 pubmed: 32676461 pmcid: 7333005
Qiu P, Ishimoto T, Fu L, Zhang J, Zhang Z, Liu Y. The gut microbiota in inflammatory bowel disease. Front Cell Infect Microbiol. 2022. https://doi.org/10.3389/fcimb.2022.733992 .
doi: 10.3389/fcimb.2022.733992 pubmed: 36699726 pmcid: 9703976
Kelesidis T, Pothoulakis C. Efficacy and safety of the probiotic Saccharomyces boulardii for the prevention and therapy of gastrointestinal disorders. Therap Adv Gastroenterol. 2012;5(2):111–25. https://doi.org/10.1177/1756283X11428502 .
doi: 10.1177/1756283X11428502 pubmed: 22423260 pmcid: 3296087
Liu J-J, Kong II, Zhang G-C, Jayakody LN, Kim H, Xia P-F, et al. Metabolic engineering of probiotic Saccharomyces boulardii. Appl Environ Microbiol. 2016;82(8):2280.
doi: 10.1128/AEM.00057-16 pubmed: 26850302 pmcid: 4959471
Durmusoglu D, Al’Abri IS, Collins SP, Cheng J, Eroglu A, Beisel CL, et al. In situ biomanufacturing of small molecules in the mammalian gut by probiotic Saccharomyces boulardii. ACS Synth Biol. 2021;10(5):1039–52. https://doi.org/10.1021/acssynbio.0c00562 .
doi: 10.1021/acssynbio.0c00562 pubmed: 33843197
Kwak S, Mahmud B, Dantas G. A tunable and expandable transactivation system in probiotic yeast Saccharomyces boulardii. ACS Synth Biol. 2022;11(1):508–14. https://doi.org/10.1021/acssynbio.1c00384 .
doi: 10.1021/acssynbio.1c00384 pubmed: 34939781
Hedin KA, Zhang H, Kruse V, Rees VE, Bäckhed F, Greiner TU, et al. Cold exposure and oral delivery of GLP-1R agonists by an engineered probiotic yeast strain have antiobesity effects in mice. ACS Synth Biol. 2023;12(11):3433–42. https://doi.org/10.1021/acssynbio.3c00455 .
doi: 10.1021/acssynbio.3c00455 pubmed: 37827516 pmcid: 10661039
Hedin KA, Kruse V, Vazquez-Uribe R, Sommer MOA. Biocontainment strategies for in vivo applications of Saccharomyces boulardii. Front Bioeng Biotechnol. 2023. https://doi.org/10.3389/fbioe.2023.1136095 .
doi: 10.3389/fbioe.2023.1136095 pubmed: 36890914 pmcid: 9986445
Nielsen J. Yeast systems biology: model organism and cell factory. Biotechnol J. 2019;14(9):e1800421.
doi: 10.1002/biot.201800421 pubmed: 30925027
Riglar DT, Silver PA. Engineering bacteria for diagnostic and therapeutic applications. Nat Rev Microbiol. 2018;16:214–25.
doi: 10.1038/nrmicro.2017.172 pubmed: 29398705
Shaw WM, Yamauchi H, Mead J, Gowers GOF, Bell DJ, Öling D, et al. Engineering a model cell for rational tuning of GPCR signaling. Cell. 2019;177(3):782-796.e27.
doi: 10.1016/j.cell.2019.02.023 pubmed: 30955892 pmcid: 6476273
Peng B, Williams TC, Henry M, Nielsen LK, Vickers CE. Controlling heterologous gene expression in yeast cell factories on different carbon substrates and across the diauxic shift: acomparison of yeast promoter activities. Microb Cell Fact. 2015;14(1):91. https://doi.org/10.1186/s12934-015-0278-5 .
doi: 10.1186/s12934-015-0278-5 pubmed: 26112740 pmcid: 4480987
Partow S, Siewers V, Bjørn S, Nielsen J, Maury J. Characterization of different promoters for designing a new expression vector in Saccharomyces cerevisiae. Yeast. 2010;27(11):955–64. https://doi.org/10.1002/yea.1806 .
doi: 10.1002/yea.1806 pubmed: 20625983
Apel AR, D’Espaux L, Wehrs M, Sachs D, Li RA, Tong GJ, et al. A Cas9-based toolkit to program gene expression in Saccharomyces cerevisiae. Nucleic Acids Res. 2017;45(1):496–508.
doi: 10.1093/nar/gkw1023
Maury J, Kannan S, Jensen NB, Öberg FK, Kildegaard KR, Forster J, et al. Glucose-dependent promoters for dynamic regulation of metabolic pathways. Front Bioeng Biotechnol. 2018;6:63.
doi: 10.3389/fbioe.2018.00063 pubmed: 29872655 pmcid: 5972318
Rintala E, Toivari M, Pitkänen J-P, Wiebe MG, Ruohonen L, Penttilä M. Low oxygen levels as a trigger for enhancement of respiratory metabolism in Saccharomyces cerevisiae. BMC Genomics. 2009;10(1):461. https://doi.org/10.1186/1471-2164-10-461 .
doi: 10.1186/1471-2164-10-461 pubmed: 19804647 pmcid: 2767370
Xiong L, Zeng Y, Tang RQ, Alper HS, Bai FW, Zhao XQ. Condition-specific promoter activities in Saccharomyces cerevisiae. Microb Cell Fact. 2018. https://doi.org/10.1186/s12934-018-0899-6 .
doi: 10.1186/s12934-018-0899-6 pubmed: 29631591 pmcid: 5891911
Keren L, Zackay O, Lotan-Pompan M, Barenholz U, Dekel E, Sasson V, et al. Promoters maintain their relative activity levels under different growth conditions. Mol Syst Biol. 2013;9:701.
doi: 10.1038/msb.2013.59 pubmed: 24169404 pmcid: 3817408
Armetta J, Schantz-Klausen M, Shepelin D, Vazquez-Uribe R, Bahl MI, Laursen MF, et al. Escherichia coli promoters with consistent expression throughout the murine gut. ACS Synth Biol. 2021;10(12):3359–68. https://doi.org/10.1021/acssynbio.1c00325 .
doi: 10.1021/acssynbio.1c00325 pubmed: 34842418
Crook N, Ferreiro A, Condiotte Z, Dantas G. Transcript barcoding illuminates the expression level of synthetic constructs in E. coli nissle residing in the mammalian gut. ACS Synth Biol. 2020;9(5):1010–21.
doi: 10.1021/acssynbio.0c00040 pubmed: 32324995 pmcid: 7293544
McConnell EL, Basit AW, Murdan S. Measurements of rat and mouse gastrointestinal pH, fluid and lymphoid tissue, and implications for in-vivo experiments. J Pharm Pharmacol. 2008;60(1):63–70. https://doi.org/10.1211/jpp.60.1.0008 .
doi: 10.1211/jpp.60.1.0008 pubmed: 18088506
Albenberg L, Esipova TV, Judge CP, Bittinger K, Chen J, Laughlin A, et al. Correlation between intraluminal oxygen gradient and radial partitioning of intestinal microbiota. Gastroenterology. 2014;147(5):1055–63.
doi: 10.1053/j.gastro.2014.07.020 pubmed: 25046162
Hatton GB, Yadav V, Basit AW, Merchant HA. Animal farm: considerations in animal gastrointestinal physiology and relevance to drug delivery in humans. J Pharm Sci. 2015;104(9):2747–76. https://doi.org/10.1002/jps.24365 .
doi: 10.1002/jps.24365 pubmed: 25712759
Williams CF, Walton GE, Jiang L, Plummer S, Garaiova I, Gibson GR. Comparative analysis of intestinal tract models. Annu Rev Food Sci Technol. 2015;6(1):329–50. https://doi.org/10.1146/annurev-food-022814-015429 .
doi: 10.1146/annurev-food-022814-015429 pubmed: 25705934
Holst JJ, Gribble F, Horowitz M, Rayner CK. Roles of the gut in glucose homeostasis. Diabetes Care. 2016;39(6):884–92. https://doi.org/10.2337/dc16-0351 .
doi: 10.2337/dc16-0351 pubmed: 27222546
Kaishima M, Ishii J, Matsuno T, Fukuda N, Kondo A. Expression of varied GFPs in Saccharomyces cerevisiae: codon optimization yields stronger than expected expression and fluorescence intensity. Sci Rep. 2016;6:35932.
doi: 10.1038/srep35932 pubmed: 27782154 pmcid: 5080575
Tsien RY. The green fluorescent protein. Annu Rev Biochem. 1998;67(1):509–44. https://doi.org/10.1146/annurev.biochem.67.1.509 .
doi: 10.1146/annurev.biochem.67.1.509 pubmed: 9759496
Guerra P, Vuillemenot L-A, Rae B, Ladyhina V, Milias-Argeitis A. Systematic in vivo characterization of fluorescent protein maturation in budding yeast. ACS Synth Biol. 2022;11(3):1129–41. https://doi.org/10.1021/acssynbio.1c00387 .
doi: 10.1021/acssynbio.1c00387 pubmed: 35180343 pmcid: 8938947
Chia HE, Marsh ENG, Biteen JS. Extending fluorescence microscopy into anaerobic environments. Curr Opin Chem Biol. 2019;51:98–104.
doi: 10.1016/j.cbpa.2019.05.008 pubmed: 31252372
Jessop-Fabre MM, Jakočiūnas T, Stovicek V, Dai Z, Jensen MK, Keasling JD, et al. EasyClone-MarkerFree: a vector toolkit for marker-less integration of genes into Saccharomyces cerevisiae via CRISPR-Cas9. Biotechnol J. 2016;11(8):1110–7. https://doi.org/10.1002/biot.201600147 .
doi: 10.1002/biot.201600147 pubmed: 27166612 pmcid: 5094547
Cooper TG, Bossinger J. Selective inhibition of protein synthesis initiation in Saccharomyces cerevisiae by low concentrations of cycloheximide. J Biol Chem. 1976;251(22):7278–80.
doi: 10.1016/S0021-9258(17)32970-8 pubmed: 791949
Macfarlane GT, Gibson GR, Cummings JH. Comparison of fermentation reactions in different regions of the human colon. J Appl Bacteriol. 1992;72(1):57–64.
pubmed: 1541601
Segú H, Jalševac F, Pinent M, Ardévol A, Terra X, Blay MT. Intestinal morphometric changes induced by a western-style diet in wistar rats and GSPE counter-regulatory effect. Nutrients. 2022. https://doi.org/10.3390/nu14132608 .
doi: 10.3390/nu14132608 pubmed: 35807788 pmcid: 9268310
Mitterdorfer G, Kneifel W, Viernstein H. Utilization of prebiotic carbohydrates by yeasts of therapeutic relevance. Lett Appl Microbiol. 2001;33(4):251–5.
doi: 10.1046/j.1472-765X.2001.00991.x pubmed: 11559396
Shcherbo D, Murphy CS, Ermakova GV, Solovieva EA, Chepurnykh TV, Shcheglov AS, et al. Far-red fluorescent tags for protein imaging in living tissues. Biochem J. 2009;418(3):567–74.
doi: 10.1042/BJ20081949 pubmed: 19143658
Hedin KA, Rees VE, Zhang H, Kruse V, Vazquez-Uribe R, Sommer MOA. Effects of broad-spectrum antibiotics on the colonisation of probiotic yeast Saccharomyces boulardii in the murine gastrointestinal tract. Sci Rep. 2022;12(1):8862. https://doi.org/10.1038/s41598-022-12806-0 .
doi: 10.1038/s41598-022-12806-0 pubmed: 35614092 pmcid: 9133042
Chen K, Zhu Y, Zhang Y, Hamza T, Yu H, Saint Fleur A, et al. A probiotic yeast-based immunotherapy against clostridioides difficile infection. Sci Transl Med. 2020. https://doi.org/10.1126/scitranslmed.aax4905 .
doi: 10.1126/scitranslmed.aax4905 pubmed: 33328330 pmcid: 9719290
Cohen BD, Sertil O, Abramova NE, Davies KJ, Lowry CV. Induction and repression of DAN1 and the family of anaerobic mannoprotein genes in Saccharomyces cerevisiae occurs through a complex array of regulatory sites. Nucleic Acids Res. 2001;29(3):799–808.
doi: 10.1093/nar/29.3.799 pubmed: 11160904 pmcid: 30382
Marteyn B, West NP, Browning DF, Cole JA, Shaw JG, Palm F, et al. Modulation of Shigella virulence in response to available oxygen in vivo. Nature. 2010;465(7296):355–8. https://doi.org/10.1038/nature08970 .
doi: 10.1038/nature08970 pubmed: 20436458 pmcid: 3750455
Nour-Eldin HH, Hansen BG, Nørholm MHH, Jensen JK, Halkier BA. Advancing uracil-excision based cloning towards an ideal technique for cloning PCR fragments. Nucleic Acids Res. 2006;34(18):e122–e122. https://doi.org/10.1093/nar/gkl635 .
doi: 10.1093/nar/gkl635 pubmed: 17000637 pmcid: 1635280
Gibson DG, Young L, Chuang R-Y, Venter JC, Hutchison CA, Smith HO. Enzymatic assembly of DNA molecules up to several hundred kilobases. Nat Methods. 2009;6(5):343–5. https://doi.org/10.1038/nmeth.1318 .
doi: 10.1038/nmeth.1318 pubmed: 19363495
Wirth NT, Funk J, Donati S, Nikel PI. QurvE: user-friendly software for the analysis of biological growth and fluorescence data. Nat Protoc. 2023. https://doi.org/10.1038/s41596-023-00850-7 .
doi: 10.1038/s41596-023-00850-7 pubmed: 37380826
Percie du Sert N, Ahluwalia A, Alam S, Avey MT, Baker M, Browne WJ, et al. Reporting animal research: explanation and elaboration for the ARRIVE guidelines 2.0. PLOS Biol. 2020;18(7):e3000411. https://doi.org/10.1371/journal.pbio.3000411 .
doi: 10.1371/journal.pbio.3000411 pubmed: 32663221 pmcid: 7360025

Auteurs

Carmen Sands (C)

Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, 2800, Kgs. Lyngby, Denmark.

Karl Alex Hedin (KA)

Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, 2800, Kgs. Lyngby, Denmark.

Ruben Vazquez-Uribe (R)

Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, 2800, Kgs. Lyngby, Denmark. ruvas@biosustain.dtu.dk.

Morten Otto Alexander Sommer (MOA)

Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, 2800, Kgs. Lyngby, Denmark. msom@bio.dtu.dk.

Classifications MeSH