Engineering of Aspergillus niger for efficient production of D-xylitol from L-arabinose.
Aspergillus niger
l-arabinose conversion
Arabinanase production
Carbon catabolite repression
Xylitol production
Xylitol transporter
Journal
Microbial cell factories
ISSN: 1475-2859
Titre abrégé: Microb Cell Fact
Pays: England
ID NLM: 101139812
Informations de publication
Date de publication:
05 Oct 2024
05 Oct 2024
Historique:
received:
14
06
2024
accepted:
11
09
2024
medline:
5
10
2024
pubmed:
5
10
2024
entrez:
4
10
2024
Statut:
epublish
Résumé
D-Xylitol is a naturally occurring sugar alcohol present in diverse plants that is used as an alternative sweetener based on a sweetness similar to sucrose and several health benefits compared to conventional sugar. However, current industrial methods for D-xylitol production are based on chemical hydrogenation of D-xylose, which is energy-intensive and environmentally harmful. However, efficient conversion of L-arabinose as an additional highly abundant pentose in lignocellulosic materials holds great potential to broaden the range of applicable feedstocks. Both pentoses D-xylose and L-arabinose are converted to D-xylitol as a common metabolic intermediate in the native fungal pentose catabolism.To engineer a strain capable of accumulating D-xylitol from arabinan-rich agricultural residues, pentose catabolism was stopped in the ascomycete filamentous fungus Aspergillus niger at the stage of D-xylitol by knocking out three genes encoding enzymes involved in D-xylitol degradation (ΔxdhA, ΔsdhA, ΔxkiA). Additionally, to facilitate its secretion into the medium, an aquaglyceroporin from Saccharomyces cerevisiae was tested. In S. cerevisiae, Fps1 is known to passively transport glycerol and is regulated to convey osmotic stress tolerance but also exhibits the ability to transport other polyols such as D-xylitol. Thus, a constitutively open version of this transporter was introduced into A. niger, controlled by multiple promoters with varying expression strengths. The strain expressing the transporter under control of the PtvdA promoter in the background of the pentose catabolism-deficient triple knock-out yielded the most favorable outcome, producing up to 45% D-xylitol from L-arabinose in culture supernatants, while displaying minimal side effects during osmotic stress. Due to its additional ability to extract D-xylose and L-arabinose from lignocellulosic material via the production of highly active pectinases and hemicellulases, A. niger emerges as an ideal candidate cell factory for D-xylitol production from lignocellulosic biomasses rich in both pentoses.In summary, we are showing for the first time an efficient biosynthesis of D-xylitol from L-arabinose utilizing a filamentous ascomycete fungus. This broadens the potential resources to include also arabinan-rich agricultural waste streams like sugar beet pulp and could thus help to make alternative sweetener production more environmentally friendly and cost-effective.
Identifiants
pubmed: 39367393
doi: 10.1186/s12934-024-02526-7
pii: 10.1186/s12934-024-02526-7
doi:
Substances chimiques
Arabinose
B40ROO395Z
Xylitol
VCQ006KQ1E
Xylose
A1TA934AKO
Fungal Proteins
0
Types de publication
Journal Article
Langues
eng
Sous-ensembles de citation
IM
Pagination
262Subventions
Organisme : Bundesministerium für Bildung und Forschung
ID : 031B01048A
Informations de copyright
© 2024. The Author(s).
Références
FOA (2023): Sugar beet production. Unter Mitarbeit von Food and Agriculture Organization of the United Nations. Hg. v. Food and Agriculture Organization of the United Nations. https://ourworldindata.org/grapher/sugar-beet-production .
Usmani Z, Sharma M, Diwan D, Tripathi M, Whale E, Jayakody LN, et al. Valorization of sugar beet pulp to value-added products: a review. Biores Technol. 2022;346:126580. https://doi.org/10.1016/j.biortech.2021.126580 .
doi: 10.1016/j.biortech.2021.126580
Tomaszewska J, Bieliński D, Binczarski M, Berlowska J, Dziugan P, Piotrowski J, et al. Products of sugar beet processing as raw materials for chemicals and biodegradable polymers. Royal Soc Chem Adv. 2018;8(6):3161–77. https://doi.org/10.1039/C7RA12782K .
doi: 10.1039/C7RA12782K
Duraisam R, Salelgn K, Berekete AK. Production of beet sugar and bio-ethanol from sugar beet and it bagasse: A review. Int J Eng Trends Technol. 2017;43(4):222–33. https://doi.org/10.14445/22315381/ijett-v43p237 .
doi: 10.14445/22315381/ijett-v43p237
Kühnel S, Schols HA, Gruppen H. Aiming for the complete utilization of sugar-beet pulp: examination of the effects of mild acid and hydrothermal pretreatment followed by enzymatic digestion. Biotechnol Biofuels. 2011;4(1):S14. https://doi.org/10.1186/1754-6834-4-14 .
doi: 10.1186/1754-6834-4-14
Amoah J, Kahar P, Ogino C, Kondo A. Bioenergy and biorefinery: feedstock, biotechnological conversion, and products. Biotechnol J. 2019;14(6):e1800494. https://doi.org/10.1002/biot.201800494 .
doi: 10.1002/biot.201800494
Kumar K, Singh E, Shrivastava S. Microbial xylitol production. Appl Microbiol Biotechnol. 2022;106(3):971–9. https://doi.org/10.1007/s00253-022-11793-6 .
doi: 10.1007/s00253-022-11793-6
Mussatto, Solange Inês (2012): Application of xylitol in food formulations and benefits for health. In: Silvio Silvério Da Silva und Anuj Kumar Chandel (Hg.): D-Xylitol. Fermentative production, application and commercialization. Berlin, Heidelberg: Springer Berlin Heidelberg; Imprint; Springer, S. 309–323. Online verfügbar unter https://doi.org/10.1007/978-3-642-31887-0_14 .
Gasmi Benahmed A, Gasmi A, Arshad M, Shanaida M, Lysiuk R, Peana M, et al. Health benefits of xylitol. Appl Microbiol Biotechnol. 2020;104(17):7225–37. https://doi.org/10.1007/s00253-020-10708-7 .
doi: 10.1007/s00253-020-10708-7
Mathur S, Kumar D, Kumar V, Dantas A, Verma R, Kuca K. Xylitol: production strategies with emphasis on biotechnological approach, scale up, and market trends. Sustain Chem Pharm. 2023;35:101203. https://doi.org/10.1016/j.scp.2023.101203 .
doi: 10.1016/j.scp.2023.101203
Felipe Hernández-Pérez A, de Arruda PV, Sene L, da Silva SS, Kumar Chandel A, de Almeida Felipe MD. Xylitol bioproduction: state-of-the-art, industrial paradigm shift, and opportunities for integrated biorefineries. Critic Rev Biotechnol. 2019;39(7):924–43. https://doi.org/10.1080/07388551.2019.1640658 .
doi: 10.1080/07388551.2019.1640658
Arcaño YD, García OD, Mandelli D, Carvalho WA, Pontes LA. Xylitol: a review on the progress and challenges of its production by chemical route. Catal Today. 2020;344:2–14. https://doi.org/10.1016/j.cattod.2018.07.060 .
doi: 10.1016/j.cattod.2018.07.060
Hou-Rui Z (2012): Key drivers influencing the large scale production of xylitol. In: Silvio Silvério Da Silva und Anuj Kumar Chandel (Hg.): D-Xylitol. Fermentative production, application and commercialization. Berlin, Heidelberg: Springer Berlin Heidelberg; Imprint; Springer, S. 267–289. https://doi.org/10.1007/978-3-642-31887-0_12 .
Regmi P, Knesebeck M, Boles E, Weuster-Botz D, Oreb M. A comparative analysis of NADPH supply strategies in Saccharomyces cerevisiae: production of D-xylitol from D-xylose as a case study. Metabol Eng Commun. 2024;19:e00245. https://doi.org/10.1016/j.mec.2024.e00245 .
doi: 10.1016/j.mec.2024.e00245
Hong Y, Dashtban M, Kepka G, Chen S, Qin W. Overexpression of D-xylose reductase (xyl1) gene and antisense inhibition of D-xylulokinase (xyiH) gene increase xylitol production in Trichoderma reesei. Biomed J Res Int. 2014. https://doi.org/10.1155/2014/169705 .
doi: 10.1155/2014/169705
Mahmud A, Hattori K, Hongwen C, Kitamoto N, Suzuki T, Nakamura K, Takamizawa K. Xylitol production by NAD(+)-dependent xylitol dehydrogenase (xdhA)- and l-arabitol-4-dehydrogenase (ladA)-disrupted mutants of Aspergillus oryzae. J Biosci Bioeng. 2013;115(4):353–9. https://doi.org/10.1016/j.jbiosc.2012.10.017 .
doi: 10.1016/j.jbiosc.2012.10.017
Mäkelä MR, Donofrio N, de Vries RP. Plant biomass degradation by fungi. Fungal Genet Biol. 2014. https://doi.org/10.1016/j.fgb.2014.08.010 .
doi: 10.1016/j.fgb.2014.08.010
Baker SE. Aspergillus niger genomics: past, present and into the future. J Med Mycol. 2006;44(1):S17-21. https://doi.org/10.1080/13693780600921037 .
doi: 10.1080/13693780600921037
Meyer V. Metabolic engineering of filamentous fungi. In: Meyer V, editor. Metabolic engineering. Hoboken: John Wiley & Sons, Ltd; 2021.
Chroumpi T, Peng M, Markillie LM, Mitchell HD, Nicora CD, Hutchinson CM, Chelsea M, et al. Re-routing of sugar catabolism provides a better insight into fungal flexibility in using plant biomass-derived monomers as substrates. Front Bioeng Biotechnol. 2021;9:644216. https://doi.org/10.3389/fbioe.2021.644216 .
doi: 10.3389/fbioe.2021.644216
Meng J, Chroumpi T, Mäkelä MR, de Vries RP. Xylitol production from plant biomass by Aspergillus niger through metabolic engineering. Biores Technol. 2022;344:126199. https://doi.org/10.1016/j.biortech.2021.126199 .
doi: 10.1016/j.biortech.2021.126199
Witteveen CF, Busink R, Van de Vondervoort P, Dijkema C, Swart K, Visser J. L-arabinose and D-xylose catabolism in Aspergillus niger. Microbiology. 1989;135(8):2163–71. https://doi.org/10.1099/00221287-135-8-2163 .
doi: 10.1099/00221287-135-8-2163
Arentshorst M, Ram AF, Meyer V. Using non-homologous end-joining-deficient strains for functional gene analyses in filamentous fungi. Methods Mol Biol. 2012;835:133–50. https://doi.org/10.1007/978-1-61779-501-5_9 .
doi: 10.1007/978-1-61779-501-5_9
Sambrook J, Russell DW. Molecular cloning: a laboratory manual. 3rd edition (Vol. 1). 2021.
Tamás MJ, Karlgren S, Bill RM, Hedfalk K, Allegri L, Ferreira M, et al. A short regulatory domain restricts glycerol transport through yeast Fps1p. J Biol Chem. 2003;278(8):6337–45. https://doi.org/10.1074/jbc.M209792200 .
doi: 10.1074/jbc.M209792200
Blumhoff M, Steiger MG, Marx H, Mattanovich D, Sauer M. Six novel constitutive promoters for metabolic engineering of Aspergillus niger. Appl Microbiol Biotechnol. 2013;97(1):259–67. https://doi.org/10.1007/s00253-012-4207-9 .
doi: 10.1007/s00253-012-4207-9
Lu Y, Zheng X, Wang Y, Zhang L, Wang L, Lei Y, et al. Evaluation of Aspergillus niger six constitutive strong promoters by fluorescent-auxotrophic selection coupled with flow cytometry: a case for citric acid production. J Fungi. 2022. https://doi.org/10.3390/jof8060568 .
doi: 10.3390/jof8060568
Punt PJ, Dingemanse MA, Kuyvenhoven A, Soede RD, Pouwels PH, van den Hondel CA. Functional elements in the promoter region of the Aspergillus nidulans gpdA gene encoding glyceraldehyde-3-phosphate dehydrogenase. Gene. 1990;93(1):101–9. https://doi.org/10.1016/0378-1119(90)90142-e .
doi: 10.1016/0378-1119(90)90142-e
Cesbron F, Brunner M, Diernfellner AC. Light-dependent and circadian transcription dynamics in vivo recorded with a destabilized luciferase reporter in Neurospora. Public LibSci One. 2013;8(12):e83660.
doi: 10.1371/journal.pone.0083660
Leskinen P, Virta M, Karp M. One-step measurement of firefly luciferase activity in yeast. Yeast. 2003;20(13):1109–13. https://doi.org/10.1002/yea.1024 .
doi: 10.1002/yea.1024
Gooch VD, Mehra A, Larrondo LF, Fox J, Touroutoutoudis M, Loros JJ, Dunlap JC. Fully codon-optimized luciferase uncovers novel temperature characteristics of the Neurospora clock. Eukaryot Cell. 2008;7(1):28–37. https://doi.org/10.1128/EC.00257-07 .
doi: 10.1128/EC.00257-07
Lee ME, DeLoache WC, Cervantes B, Dueber JE. A highly characterized yeast toolkit for modular, multipart assembly. Am Chem Soc Syn Biol. 2015;4(9):975–86. https://doi.org/10.1021/sb500366v .
doi: 10.1021/sb500366v
Knesebeck M, Schäfer D, Schmitz K, Rüllke M, Benz JP, Weuster-Botz D. Enzymatic one-pot hydrolysis of extracted sugar beet press pulp after solid-state Fermentation with an Engineered Aspergillus niger Strain. Fermentation. 2023;9(7):582. https://doi.org/10.3390/fermentation9070582 .
doi: 10.3390/fermentation9070582
Leynaud-Kieffer LM, Curran SC, Kim I, Magnuson JK, Gladden JM, Baker SE, Simmons BA. A new approach to Cas9-based genome editing in Aspergillus niger that is precise, efficient and selectable. Pub Lib Sci One. 2019;14(1):e0210243. https://doi.org/10.1371/journal.pone.0210243 .
doi: 10.1371/journal.pone.0210243
Rüllke M, Meyer F, Schmitz K, Blase H, Tamayo E, Benz JP. A novel luciferase-based reporter tool to monitor the dynamics of carbon catabolite repression in filamentous fungi. Microbial Biotechnol. 2024. https://doi.org/10.1111/1751-7915.70012 .
Niu J, Arentshorst M, Seelinger F, Ram AF, Ouedraogo JP. A set of isogenic auxotrophic strains for constructing multiple gene deletion mutants and parasexual crossings in Aspergillus niger. Archiv Microbiol. 2016;198(9):861–8. https://doi.org/10.1007/s00203-016-1240-6 .
doi: 10.1007/s00203-016-1240-6
Meyer V, Arentshorst M, El-Ghezal A, Drews AC, Kooistra R, van den Hondel CA, Ram AF. Highly efficient gene targeting in the Aspergillus niger kusA mutant. J Biotechnol. 2007;128(4):770–5. https://doi.org/10.1016/j.jbiotec.2006.12.021 .
doi: 10.1016/j.jbiotec.2006.12.021
Meyer V, Wu B, Ram AF. Aspergillus as a multi-purpose cell factory: current status and perspectives. Biotechnol Lett. 2011;33(3):469–76. https://doi.org/10.1007/s10529-010-0473-8 .
doi: 10.1007/s10529-010-0473-8
Tamás MJ, Luyten K, Sutherland FC, Hernandez A, Albertyn J, Valadi H, et al. Fps1p controls the accumulation and release of the compatible solute glycerol in yeast osmoregulation. Mol Microbiol. 1999;31(4):1087–104. https://doi.org/10.1046/j.1365-2958.1999.01248.x .
doi: 10.1046/j.1365-2958.1999.01248.x
Wei N, Xu H, Kim SR, Jin YS. Deletion of FPS1, encoding aquaglyceroporin Fps1p, improves xylose fermentation by engineered Saccharomyces cerevisiae. Appl Environ Microbiol. 2013;79(10):3193–201. https://doi.org/10.1128/AEM.00490-13 .
doi: 10.1128/AEM.00490-13
Dunayevich P, Baltanás R, Clemente JA, Couto A, Sapochnik D, Vasen G, Colman-Lerner A. Heat-stress triggers MAPK crosstalk to turn on the hyperosmotic response pathway. Sci Rep. 2018;8(1):15168. https://doi.org/10.1038/s41598-018-33203-6 .
doi: 10.1038/s41598-018-33203-6
Zhang H, Yan JN, Zhang H, Liu TQ, Xu Y, Zhang YY, Li J. Effect of gpd box copy numbers in the gpdA promoter of Aspergillus nidulans on its transcription efficiency in Aspergillus niger. Fed Eur Biochem Soc Lett. 2018. https://doi.org/10.1093/femsle/fny154 .
doi: 10.1093/femsle/fny154
Adnan M, Zheng W, Islam W, Arif M, Abubakar YS, Wang Z, Lu G. Carbon catabolite repression in filamentous fungi. Int J Mol Sci. 2017. https://doi.org/10.3390/ijms19010048 .
doi: 10.3390/ijms19010048
Gancedo JM. Yeast carbon catabolite repression. Microbiol Mol Biol Rev. 1998;62(2):334–61. https://doi.org/10.1128/MMBR.62.2.334-361.1998 .
doi: 10.1128/MMBR.62.2.334-361.1998
Ruijter GJ, Visser J. Carbon repression in Aspergilli. Fed Eur Biochem Soc Lett. 1997;151(2):103–14. https://doi.org/10.1111/j.1574-6968.1997.tb12557.x .
doi: 10.1111/j.1574-6968.1997.tb12557.x
Dowzer CE, Kelly JM. Cloning of the creA gene from Aspergillus nidulans: a gene involved in carbon catabolite repression. Curr Genet. 1989;15(6):457–9. https://doi.org/10.1007/BF00376804 .
doi: 10.1007/BF00376804
Mäkelä MR, Aguilar-Pontes MV, van Rossen-Uffink D, Peng M, de Vries RP. The fungus Aspergillus niger consumes sugars in a sequential manner that is not mediated by the carbon catabolite repressor CreA. Sci Rep. 2018;8(1):6655. https://doi.org/10.1038/s41598-018-25152-x .
doi: 10.1038/s41598-018-25152-x
Ruijter GJ, Vanhanen SA, Gielkens MM, van de Vondervoort PJ, Visser J. Isolation of Aspergillus niger creA mutants and effects of the mutations on expression of arabinases and L-arabinose catabolic enzymes. Microbiology. 1997;143(Pt9):2991–8. https://doi.org/10.1099/00221287-143-9-2991 .
doi: 10.1099/00221287-143-9-2991
Schäfer D, Schmitz K, Weuster-Botz D, Benz JP. Comparative evaluation of Aspergillus niger strains for endogenous pectin-depolymerization capacity and suitability for D-galacturonic acid production. Bioproc Biosyst Eng. 2020;43(9):1549–60. https://doi.org/10.1007/s00449-020-02347-z .
doi: 10.1007/s00449-020-02347-z
Rutten L, Ribot C, Trejo-Aguilar B, Wösten HA, de Vries RP. A single amino acid change (Y318F) in the L-arabitol dehydrogenase (LadA) from Aspergillus niger results in a significant increase in affinity for D-sorbitol. Biomed Central Microbiol. 2009;9:166. https://doi.org/10.1186/1471-2180-9-166 .
doi: 10.1186/1471-2180-9-166
Koivistoinen OM, Richard P, Penttilä M, Ruohonen L, Mojzita D. Sorbitol dehydrogenase of Aspergillus niger, SdhA, is part of the oxido-reductive D-galactose pathway and essential for D-sorbitol catabolism. Fed Eur Biochem Soc Lett. 2012;586(4):378–83. https://doi.org/10.1016/j.febslet.2012.01.004 .
doi: 10.1016/j.febslet.2012.01.004
Karlgren S, Pettersson N, Nordlander B, Mathai JC, Brodsky JL, Zeidel ML, et al. Conditional osmotic stress in yeast: a system to study transport through aquaglyceroporins and osmostress signaling. J Biol Chem. 2005;280(8):7186–93. https://doi.org/10.1074/jbc.M413210200 .
doi: 10.1074/jbc.M413210200
Lee J, Reiter W, Dohnal I, Gregori C, Beese-Sims S, Kuchler K, et al. MAPK Hog1 closes the S cerevisiae glycerol channel Fps1 by phosphorylating and displacing its positive regulators. Genes Dev. 2013;27(23):2590–601. https://doi.org/10.1101/gad.229310.113 .
doi: 10.1101/gad.229310.113
De Groot MJ, Van Den Dool C, Wösten HA, Levisson M, VanKuyk PA, Ruijter GJ, De Vries RP. Regulation of pentose catabolic pathway genes of Aspergillus niger. Food Technol Biotechnol. 2007;45(2):134–8.
Mert HH, Dizbay M. The effect of osmotic pressure and salinity of the medium on the growth and sporulation of Aspergillus niger and Paecilomyces lilacinum species. Mycopathologia. 1977;61(2):125–7. https://doi.org/10.1007/BF00443842 .
doi: 10.1007/BF00443842
Beever RE, Laracy EP. Osmotic adjustment in the filamentous fungus Aspergillus nidulans. J Bacteriol. 1986;168(3):1358–65. https://doi.org/10.1128/jb.168.3.1358-1365.1986 .
doi: 10.1128/jb.168.3.1358-1365.1986
Ianutsevich EA, Tereshina VM. Combinatorial impact of osmotic and heat shocks on the composition of membrane lipids and osmolytes in Aspergillus niger. Microbiology. 2019;165(5):554–62. https://doi.org/10.1099/mic.0.000796 .
doi: 10.1099/mic.0.000796
Poulsen RB, Nøhr J, Douthwaite S, Hansen LV, Iversen JJ, Visser J, Ruijter GJ. Increased NADPH concentration obtained by metabolic engineering of the pentose phosphate pathway in Aspergillus niger. Fed Eur Biochem Soc J. 2005;272(6):1313–25. https://doi.org/10.1111/j.1742-4658.2005.04554.x .
doi: 10.1111/j.1742-4658.2005.04554.x
Shroff RA, Lockington RA, Kelly JM. Analysis of mutations in the creA gene involved in carbon catabolite repression in Aspergillus nidulans. Can J Microbiol. 1996;42(9):950–9. https://doi.org/10.1139/m96-122 .
doi: 10.1139/m96-122
Saha BC, Kennedy GJ. Production of xylitol from mixed sugars of xylose and arabinose without co-producing arabitol. Biocatal Agricult Biotechnol. 2020;29:101786. https://doi.org/10.1016/j.bcab.2020.101786 .
doi: 10.1016/j.bcab.2020.101786
Sakakibara Y, Saha BC, Taylor P. Microbial production of xylitol from L-arabinose by metabolically engineered Escherichia coli. J Biosci Bioeng. 2009;107(5):506–11. https://doi.org/10.1016/j.jbiosc.2008.12.017 .
doi: 10.1016/j.jbiosc.2008.12.017
Yoon BH, Jeon WY, Shim WY, Kim JH. L-arabinose pathway engineering for arabitol-free xylitol production in Candida tropicalis. Biotechnol Lett. 2011;33(4):747–53. https://doi.org/10.1007/s10529-010-0487-2 .
doi: 10.1007/s10529-010-0487-2