Genome Mining the Black-yeast Aureobasidium Pullulans NRRL 62031 for Biotechnological Traits

Overview

Journal BMC Genomics

Publisher Biomed Central

Specialty Genetics

Date 2025 Mar 14

PMID 40082747

Authors

Difan Xiao

Marielle Driller

Karla Stein

Lars M Blank

Till Tiso

Affiliations

Soon will be listed here.

Abstract

Aureobasidium pullulans is a yeast-like fungus known for its commercial biomanufacturing of pullulan. This study explores the genome of A. pullulans NRRL 62031, highlighting its biosynthetic potential, metabolic pathways, and physiological traits. Additionally, it demonstrates actual product formation and links molecular features to biotechnological applications. Phylogenetic analysis suggested it might be closely related to Aureobasidium melanogenum. While the functional annotation revealed a wide carbohydrate catabolism, growth evaluation demonstrated that the microbe can utilize not only saccharides but also polyols and organic acids. The extracellular cellulolytic, xylanolytic, and pectinolytic activities were indicated by the formation of visible halos on agar plates. The antiSMASH pipeline, NCBI Blastp alignment, and product qualification confirmed that A. pullulans NRRL 62031 can produce melanin, pullulan, polymalate, and polyol lipids. Moreover, yanuthone D, burnettramic acid A, choline, fructooligosaccharides, gluconic acid, and β-glucan might be synthesized by A. pullulans NRRL 62031. The results clearly show the extraordinary potential of A. pullulans NRRL 62031 as a microbial chassis for valorizing biomass residues into value-added bioproducts. The strong catabolic and anabolic capacities indicate significant promise for biotechnological applications. The results are discussed in the context of metabolic engineering of Aureobasidium.

References

Chi Z, Wang F, Chi Z, Yue L, Liu G, Zhang T . Bioproducts from Aureobasidium pullulans, a biotechnologically important yeast. Appl Microbiol Biotechnol. 2009; 82(5):793-804. DOI: 10.1007/s00253-009-1882-2. View

Andrews J, Spear R, Nordheim E . Population biology of Aureobasidium pullulans on apple leaf surfaces. Can J Microbiol. 2002; 48(6):500-13. DOI: 10.1139/w02-044. View

Urzi C, De Leo F, Lo Passo C, Criseo G . Intra-specific diversity of Aureobasidium pullulans strains isolated from rocks and other habitats assessed by physiological methods and by random amplified polymorphic DNA (RAPD). J Microbiol Methods. 1999; 36(1-2):95-105. DOI: 10.1016/s0167-7012(99)00014-7. View

Zalar P, Gostincar C, de Hoog G, Ursic V, Sudhadham M, Gunde-Cimerman N . Redefinition of Aureobasidium pullulans and its varieties. Stud Mycol. 2009; 61:21-38. PMC: 2610310. DOI: 10.3114/sim.2008.61.02. View

Li Y, Chi Z, Wang G, Wang Z, Liu G, Lee C . Taxonomy of Aureobasidium spp. and biosynthesis and regulation of their extracellular polymers. Crit Rev Microbiol. 2014; 41(2):228-37. DOI: 10.3109/1040841X.2013.826176. View

Nasr S, Mohammadimehr M, Geranpayeh Vaghei M, Amoozegar M, Shahzadeh Fazeli S . Aureobasidium mangrovei sp. nov., an ascomycetous species recovered from Hara protected forests in the Persian Gulf, Iran. Antonie Van Leeuwenhoek. 2018; 111(9):1697-1705. DOI: 10.1007/s10482-018-1059-z. View

Peterson S, Manitchotpisit P, Leathers T . Aureobasidium thailandense sp. nov. isolated from leaves and wooden surfaces. Int J Syst Evol Microbiol. 2012; 63(Pt 2):790-795. DOI: 10.1099/ijs.0.047613-0. View

Onetto C, Schmidt S, Roach M, Borneman A . Comparative genome analysis proposes three new Aureobasidium species isolated from grape juice. FEMS Yeast Res. 2020; 20(6). DOI: 10.1093/femsyr/foaa052. View

Leathers T . Biotechnological production and applications of pullulan. Appl Microbiol Biotechnol. 2003; 62(5-6):468-73. DOI: 10.1007/s00253-003-1386-4. View

10.

Sutherland I . Novel and established applications of microbial polysaccharides. Trends Biotechnol. 1998; 16(1):41-6. DOI: 10.1016/S0167-7799(97)01139-6. View

11.

Zhang H, Cai J, Dong J, Zhang D, Huang L, Xu Z . High-level production of poly (β-L: -malic acid) with a new isolated Aureobasidium pullulans strain. Appl Microbiol Biotechnol. 2011; 92(2):295-303. DOI: 10.1007/s00253-011-3358-4. View

12.

Cao W, Chen X, Luo J, Yin J, Qiao C, Wan Y . High molecular weight β-poly(L-malic acid) produced by A. pullulans with Ca²⁺ added repeated batch culture. Int J Biol Macromol. 2016; 85:192-9. DOI: 10.1016/j.ijbiomac.2015.12.056. View

13.

Cao W, Luo J, Zhao J, Qiao C, Ding L, Qi B . Intensification of β-poly(L: -malic acid) production by Aureobasidium pullulans ipe-1 in the late exponential growth phase. J Ind Microbiol Biotechnol. 2012; 39(7):1073-80. DOI: 10.1007/s10295-012-1111-3. View

14.

Manitchotpisit P, Watanapokasin R, Watanapoksin R, Price N, Bischoff K, Tayeh M . Aureobasidium pullulans as a source of liamocins (heavy oils) with anticancer activity. World J Microbiol Biotechnol. 2014; 30(8):2199-204. DOI: 10.1007/s11274-014-1639-7. View

15.

Saur K, Brumhard O, Scholz K, Hayen H, Tiso T . A pH shift induces high-titer liamocin production in Aureobasidium pullulans. Appl Microbiol Biotechnol. 2019; 103(12):4741-4752. DOI: 10.1007/s00253-019-09677-3. View

16.

Haala F, Dielentheis-Frenken M, Brandt F, Karmainski T, Blank L, Tiso T . DoE-based medium optimization for improved biosurfactant production with . Front Bioeng Biotechnol. 2024; 12:1379707. PMC: 10953688. DOI: 10.3389/fbioe.2024.1379707. View

17.

Liu F, Zhang J, Zhang L, Diao M, Ling P, Wang F . Correlation between the synthesis of pullulan and melanin in Aureobasidium pullulans. Int J Biol Macromol. 2021; 177:252-260. DOI: 10.1016/j.ijbiomac.2021.02.108. View

18.

Chi Z, Liu G, Liu C, Chi Z . Poly(β-L-malic acid) (PMLA) from Aureobasidium spp. and its current proceedings. Appl Microbiol Biotechnol. 2016; 100(9):3841-51. DOI: 10.1007/s00253-016-7404-0. View

19.

Manitchotpisit P, Skory C, Peterson S, Price N, Vermillion K, Leathers T . Poly(β-L-malic acid) production by diverse phylogenetic clades of Aureobasidium pullulans. J Ind Microbiol Biotechnol. 2011; 39(1):125-32. DOI: 10.1007/s10295-011-1007-7. View

20.

Qi C, Chi Z, Liu G, Chi Z . A high molecular weight polymalate is synthesized by the whole genome duplicated strain Aureobasidium melanogenum OUC. Int J Biol Macromol. 2022; 202:608-619. DOI: 10.1016/j.ijbiomac.2022.01.125. View