2019

1

Li, H; Booth, T; Chooi, Y-H* Fungal Polyketide-Nonribosomal Peptide Synthetases and their Associated Natural Products. In Comprehensive Natural Products III: Chemistry and Biology, Vol. 1; Abe, I; Tang, Y; Townsend, C, Ed.; Elsevier, 2019 (in press)

2021

66

Gilchrist, C.L.M., Chooi, Y. H. clinker & clustermap.js: automatic generation of gene cluster comparison figures, Bioinformatics, 2021; btab007, DOI:10.1093/bioinformatics/btab007

2020

65

Li H, Lacey AE, Shu S, Kalaitzis JA, Vuong D, Crombie A, Hu J, Gilchrist CLM, Lacey E, Piggott AM, Chooi YH. Hancockiamides: phenylpropanoid piperazines from Aspergillus hancockii are biosynthesised by a versatile dual single-module NRPS pathway. Org. Biomol. Chem. 2020, DOI:10.1039/D0OB02243H (Advanced Article)

64

Kessler SC, Zhang X, McDonald MC, Gilchrist CLM, Lin Z, Rightmyer A, Solomon PS, Turgeon BG*, Chooi YH.* Victorin, the host-selective cyclic peptide toxin from the oat pathogen Cochliobolus victoriae, is ribosomally encoded, Proc Natl Acad Sci U S A. 2020, 202010573. DOI:10.1073/pnas.2010573117 (Online ahead of print)

63

Gilchrist, C.; Lacey, H. J.; Vuong, D.; Pitt, J. I.; Lange, L.; Lacey, E.; Pilgaard, B.; Chooi, Y. H.*; & Piggott, A. M.*. Comprehensive chemotaxonomic and genomic profiling of a biosynthetically talented Australian fungus, Aspergillus burnettii sp. nov. Fungal Genet Biol 2020, 143, 103435. DOI:10.1016/j.fgb.2020.103435  

62

Kong, L; Wang, Q; Yang, W; Shen, J; Li, Y; Zheng, X; Wang, L; Chu, Y; Deng, Z; Chooi, Y-H*; You, D*. Three recently diverging duplicated methyltransferases exhibit substrate-dependent regioselectivity essential for xantholipin biosynthesis. ACS Chem. Biol. 2020,DOI:10.1021/acschembio.0c00296 

61

Crous, PW; Wingfield, MJ; Chooi, Y-H; Gilchrist, CLM; Lacey, E; Pitt, JI., et al. Fungal Planet description sheets: 1042–1111, Persoonia 2020, 44, 301– 459 DOI: 10.3767/persoonia.2020.44.11

60

Roux, I.; Woodcraft, C.; Hu, J.; Wolters, R.; Gilchrist, C. L. M.; Chooi, Y-H*, CRISPR-mediated activation of biosynthetic gene clusters for bioactive molecule discovery in filamentous fungi. ACS Synth Biol 2020, DOI:10.1021/acssynbio.0c00197

59

Lacey, HJ; Booth, TJ; Vuong, D; Rutledge, PJ; Lacey, E.; Chooi, Y-H*; Piggott, AM* Conglobatins B-E: cytotoxic analogues of the C2-symmetric macrodiolide conglobatin. J Antibiot, 2020, DOI:10.1038/s41429-020-0332-3

58

Muria-Gonzalez, MJ; Yap, H-YY; Breen, S; Mead, O; Wang, C; Chooi, YH; Barrow, RA; Solomon, PS. Volatile Molecules Secreted by the Wheat Pathogen Parastagonospora nodorum Are Involved in Development and Phytotoxicity. Front. Microbiol. 2020, DOI:10.3389/fmicb.2020.00466

57

Li, H; Gilchrist, CLM; Phan, CS; Lacey, HJ; Vuong, D; Moggach, SA; Lacey, E; Piggott, AM*; Chooi, YH*.  Biosynthesis of a New Benzazepine Alkaloid Nanangelenin A from Aspergillus nanangensis Involves an Unusual l-Kynurenine-Incorporating NRPS Catalyzing Regioselective Lactamization. J. Am. Chem. Soc. 2020, DOI:10.1021/jacs.0c01605

56

Li, H; Wei, H; Hu, J; Lacey, E; Sobolev, AN; Stubbs, KA; Solomon; PS*, Chooi, Y-H* Genomics-driven Discovery of Phytotoxic Cytochalasans involved in the Virulence of the Wheat Pathogen Parastagonospora nodorum. ACS Chem Biol. 2020,15(1),226-233  DOI:10.1021/acschembio.9b00791

2019

55

Rawlinson, C; See, PT; Moolhuijzen, P; Li, H; Moffat, CS; Chooi, Y-H*; Oliver, RP*. The identification and deletion of the PKS-NRPS gene responsible for production of the phytotoxic Triticone A/B in wheat fungal pathogen Pyrenophora tritici-repentis. Environ Microbiol 2019, DOI:10.1111/1462-2920.14854

54

Lacey, HJ; Gilchrist, CLM; Crombie, A; Kalaitzis, JA; Vuong, D; Rutledge, P; Turner, P; Pitt, JI; Lacey, E; Chooi, Y-H* and Piggott, AM* Nanangenines: drimane sesquiterpenoids as the dominant metabolite cohort of a novel Australian fungus, Aspergillus nanangensis. Beilstein J. Org. Chem. 2019, 15, 2631–2643. DOI:10.3762/bjoc.15.256

53

Li, H; Hu, J; Wei, H; Solomon, P; Stubbs, K; Chooi, Y-H* Biosynthesis of a Tricyclo[6.2.2.0^2,7]dodecane System by a Berberine Bridge Enzyme-like Aldolase. Chem. Eur. J. 2019 (Accepted Articles), DOI:10.1002/chem.201904360

52

Phan, CS; Li, H; Kessler, S; Solomon, PS; Piggott, AP; Chooi, Y-H* Bipolenins K–N: New sesquiterpenoids from the fungal plant pathogen Bipolaris sorokiniana. Beilstein J. Org. Chem. 2019, DOI:10.3762/bjoc.15.198  (invited contribution for the thematic issue "Terpenes")

51

Urquhart, AS; Hu, J; Chooi, Y-H*; Idnurm, A* The fungal gene cluster for biosynthesis of the antibacterial agent viriditoxin. Fungal Biol. Biotechnol. 2019, 6:9 DOI: 10.1186/s40694-019-0072-y

50

Hu, J; Li, H; Chooi, Y-H* Fungal Dirigent Protein Controls the Stereoselectivity of Multicopper Oxidase-Catalyzed Phenol Coupling in Viriditoxin Biosynthesis. J. Am. Chem. Soc. 2019, 141 (20), 8068-8072, DOI: 10.1021/jacs.9b03354

49

Thynne, E.; Mead, O. L.; Chooi, Y-H.; McDonald, M. C.; Solomon, P. S. Acquisition and loss of secondary metabolites shaped the evolutionary path of three emerging phytopathogens of wheat. Genome Biol Evol 2019, 21 (5), 1287-1291, DOI:10.1093/gbe/evz037

48

Lin, H. C.; Hewage, R. T.; Lu, Y. C.; Chooi, Y-H* Biosynthesis of bioactive natural products from Basidiomycota. Org Biomol Chem 2019, 17 (5), 1027.

47

Li, H.; Gilchrist, C. L. M.; Lacey, H. J.; Crombie, A.; Vuong, D.; Pitt, J. I.; Lacey, E.; Chooi, Y-H.*; Piggott, A. M.*  Discovery and Heterologous   Biosynthesis of the Burnettramic Acids: Rare PKS-NRPS-Derived Bolaamphiphilic Pyrrolizidinediones from an Australian Fungus, Aspergillus burnettii. Org. Lett. 2019, DOI:10.1021/acs.orglett.8b04042

46

Hu, J; Sarrami, F; Li, H; Zhang, G; Stubbs, KA; Lacey, E; Stewart, SG; Karton, A; Piggott, A; Chooi Y-H*  Heterologous biosynthesis of elsinochrome A sheds light on the formation of the photosensitive perylenequinone system. Chem. Sci. 2019, 10, 1457-1465  DOI: 10.1039/C8SC02870B

2018

45

Li, H; Hu, J; Wei, H; Solomon, PS; Vuong, D; Lacey, E; Stubbs, KA; Piggott, AM; Chooi, Y-H* (2018) Chemical Ecogenomics-Guided Discovery of Phytotoxic α-Pyrones from the Fungal Wheat Pathogen Parastagonospora nodorum. Organic Letters. DOI: 10.1021/acs.orglett.8b02617

44

Lin, SY; Chooi, Y-H* & Solomon PS* (2018) The global regulator of pathogenesis PnCon7 positively regulates Tox3 effector gene expression through direct interaction in the wheat pathogen Parastagonospora nodorum. Molecular Microbiology, DOI: 10.1111/mmi.13968

43

Gilchrist, CLM; Li, H; Chooi, Y-H.* (2018) Panning for gold in mould: can we increase the odds for fungal genome mining? Organic and Biomolecular Chemistry; DOI: 10.1039/C7OB03127K

2017

42

Liu N, Hung Y-S, Gao S-S, Hang L, Zou Y, Chooi Y-H*, Tang Y* (2017) Identification and Heterologous Production of a Benzoyl-Primed Tricarboxylic Acid Polyketide Intermediate from the Zaragozic Acid A Biosynthetic Pathway. Organic Letters.; Article ASAP DOI: 10.1021/acs.orglett.7b01534         

41

Yap H-YY, Muria-Gonzalez MJ, Kong B-H, Stubbs KA, Tan C-S, Ng S-T, Tan N-H, Solomon PS, Fung S-Y, Chooi Y-H* (2017) Heterologous expression of cytotoxic sesquiterpenoids from the medicinal mushroom Lignosus rhinocerotis in yeast. Microbial Cell Factories.; 16(1):103. DOI: 10.1186/s12934-017-0713-x

40

Pitt JI, Lange L , Lacey AE, Vuong D, Midgley DJ, Greenfield P, Bradbury M, Lacey E, Busk PK, Pilgaard B, Chooi YH* and Piggott AM* (2017) Aspergillus hancockii sp. nov., a Biosynthetically Talented Fungus Endemic to Southeastern Australian Soils, PLoS ONE,  DOI: 10.1371/journal.pone.0170254 

39

Zheng X, Cheng Q, Yao F, Wang C, Kong L, Cao B, Min X, Lin S, Deng Z, Chooi YH*, You D* (2017) Biosynthesis of the pyrrolidine protein synthesis inhibitor anisomycin involves novel gene ensemble and cryptic biosynthetic steps Proceedings of the National Academy of Sciences U.S.A., DOI: 10.1073/pnas.1701361114

38

Chooi YH*, Zhang G, Hu J, Muria-Gonzalez MJ, Tran PN, Pettitt A, Maier AG, Barrow RA & Solomon PS (2017) Functional genomics-guided discovery of a light-activated phytotoxin in the wheat pathogen Parastagonospora nodorum via pathway activation. Environmental Microbiology, DOI: 10.1111/1462-2920.13711

2016

37

Kong L, Zhang W, Chooi YH, Wang L, Cao B, Deng Z, Chu Y, You D. A Multifunctional Monooxygenase XanO4 Catalyzes Xanthone Formation in Xantholipin Biosynthesis via a Cryptic Demethoxylation. Cell Chemical Biology, 2016; 23(4): 508–16; DOI: 10.1016/j.chembiol.2016.03.013

2015

36

Yap HYY, Chooi YH, Fung SY, Ng ST, Tan CS, Tan NH. Transcriptome Analysis Revealed Highly Expressed Genes Encoding Secondary Metabolite Pathways and Small Cysteine-Rich Proteins in the Sclerotium of Lignosus rhinocerotis. PLoS ONE, 2015; 10(11):       e0143549. DOI:     10.1371/journal.pone.0143549

35

Sato M, Yagishita F, Mino T, Uchiyama N, Patel A, Chooi YH, Goda Y, Xu W, Noguchi H, Yamamoto T, Hotta K, Houk KN, Tang Y, Watanabe K. Involvement of Lipocalin-like CghA in Decalin-Forming Stereoselective Intramolecular [4 + 2] Cycloaddition. ChemBioChem. 2015; DOI: 10.1002/cbic.201500386

34

Mao XM, Zhan ZJ, Grayson MN, Tang MC, Xu W, Li YQ, Yin WB, Lin HC, Chooi YH, Houk KN, Tang Y.Efficient Biosynthesis of Fungal Polyketides Containing the Dioxabicyclo-octane Ring System. J Am Chem Soc. 2015; DOI: 10.1021/jacs.5b07816

33

Medema MH, Kottmann R, Yilmaz P, Cummings M, Biggins JB, Blin K, de Bruijn I, Chooi YH, Claesen J, Coates RC, Cruz-Morales P, Duddela S, Düsterhus S, Edwards DJ, Fewer DP, Garg N, Geiger C, Gomez-Escribano JP, Greule A, Hadjithomas M, Haines AS, Helfrich EJ, Hillwig ML, Ishida K, Jones AC, Jones CS, Jungmann K, Kegler C, Kim HU, Kötter P, Krug D, Masschelein J, Melnik AV, Mantovani SM, Monroe EA, Moore M, Moss N, Nützmann HW, Pan G, Pati A, Petras D, Reen FJ, Rosconi F, Rui Z, Tian Z, Tobias NJ, Tsunematsu Y, Wiemann P, Wyckoff E, Yan X, Yim G, Yu F, Xie Y, Aigle B, Apel AK, Balibar CJ, Balskus EP, Barona-Gómez F, Bechthold A, Bode HB, Borriss R, Brady SF, Brakhage AA, Caffrey P, Cheng YQ, Clardy J, Cox RJ, De Mot R, Donadio S, Donia MS, van der Donk WA, Dorrestein PC, Doyle S, Driessen AJ, Ehling-Schulz M, Entian KD, Fischbach MA, Gerwick L, Gerwick WH, Gross H, Gust B, Hertweck C, Höfte M, Jensen SE, Ju J, Katz L, Kaysser L, Klassen JL, Keller NP, Kormanec J, Kuipers OP, Kuzuyama T, Kyrpides NC, Kwon HJ, Lautru S, Lavigne R, Lee CY, Linquan B, Liu X, Liu W, Luzhetskyy A, Mahmud T, Mast Y, Méndez C, Metsä-Ketelä M, Micklefield J, Mitchell DA, Moore BS, Moreira LM, Müller R, Neilan BA, Nett M, Nielsen J, O'Gara F, Oikawa H, Osbourn A, Osburne MS, Ostash B, Payne SM, Pernodet JL, Petricek M, Piel J, Ploux O, Raaijmakers JM, Salas JA, Schmitt EK, Scott B, Seipke RF, Shen B, Sherman DH, Sivonen K, Smanski MJ, Sosio M, Stegmann E, Süssmuth RD, Tahlan K, Thomas CM, Tang Y, Truman AW, Viaud M, Walton JD, Walsh CT, Weber T, van Wezel GP, Wilkinson B, Willey JM, Wohlleben W, Wright GD, Ziemert N, Zhang C, Zotchev SB, Breitling R, Takano E, Glöckner FO. Minimum information about a biosynthetic gene cluster. Nat Chem Biol. 2015; DOI: 10.1038/nchembio.1890

32

Tan KC, Phan HTT, Rybak K, John E, Chooi YH, Solomon PS, Oliver RP. Functional redundancy of necrotrophic effectors - consequences for exploitation for breeding. Front Plant Sci. 2015; DOI: 10.3389/fpls.2015.00501

31

Chooi YH*, Muria-Gonzalez MJ, Mead OL, Solomon PS. SnPKS19 encodes the polyketide synthase for alternariol mycotoxin biosynthesis in     the wheat pathogen Parastagonospora nodorum. Appl Environ Microb. 2015; DOI: 10.1128/AEM.00278-15

30

Mao XM, Xu W, Li D, Yin WB, Chooi YH, Li YQ, Tang Y, Hu YC. Epigenetic Genome Mining of an Endophytic Fungus Leads to the Pleiotropic Biosynthesis of Natural Products. Angew Chem Int Edit. 2015; DOI: 10.1002/ange.201502452

29

Muria-Gonzalez MJ, Chooi YH, Breen S, Solomon PS. The past, present and future of secondary metabolite research in the Dothideomycetes. Mol Plant Pathol. 2015; 16(1):92-107, DOI: 10.1111/mpp.12162

28

Lin HC, Chiou G, Chooi YH, McMahon TC, Xu W, Garg NK, Tang Y. Elucidation of the Concise Biosynthetic Pathway of the Communesin Indole Alkaloids. Angew Chem Int Edit. 2015; 54(10):3004-3007, DOI: 10.1002/anie.201411297

27

Chooi YH*, Krill C, Barrow RA, Chen SS, Trengove R, Oliver RP, Solomon PS. An In Planta-Expressed Polyketide Synthase Produces (R)-Mellein in the Wheat Pathogen Parastagonospora nodorum. Appl Environ Microb. 2015; 81(1):177-186, DOI: 10.1128/AEM.02745-14

26

Cacho RA, Tang Y, Chooi YH*. Next-generation sequencing approach for connecting secondary metabolites to biosynthetic gene clusters in fungi. Front Microbiol. 2015; 5, DOI: 10.3389/fmicb.2014.00774

2014

25

Zabala AO, Chooi YH, Choi MS, Lin HC, Tang Y. Fungal Polyketide Synthase Product Chain-Length Control by Partnering Thiohydrolase. ACS Chem Biol. 2014; 9(7):1576-1586, DOI: 10.1021/cb500284t

24

Yap HYY, Chooi YH, Firdaus-Raih M, Fung SY, Ng ST, Tan CS, Tan NH. The genome of the Tiger Milk mushroom, Lignosus rhinocerotis, provides insights into the genetic basis of its medicinal properties. BMC Genomics. 2014; 15, DOI: 10.1186/1471-2164-15-635

23

Lin HC, Tsunematsu Y, Dhingra S, Xu W, Fukutomi M, Chooi YH, Cane DE, Calvo AM, Watanabe K, Tang Y. Generation of Complexity in Fungal Terpene      Biosynthesis: Discovery of a Multifunctional Cytochrome P450 in the Fumagillin Pathway. J Am Chem Soc. 2014; 136(11):4426-4436, DOI: 10.1021/ja500881e

22

Chooi YH*, Solomon PS. A chemical ecogenomics approach to understand the roles of secondary metabolites in fungal cereal pathogens. Front Microbiol. 2014; 5, DOI: 10.3389/fmicb.2014.00640

21

Chooi YH*, Muria-Gonzalez MJ, Solomon PS. A genome-wide survey of the secondary metabolite biosynthesis genes in the wheat pathogen. Mycology.2014; 5(3):192-206, DOI: 10.1080/21501203.2014.928386

2013

20

Yin WB, Chooi YH, Smith AR, Cacho RA, Hu YC, White TC, Tang Y. Discovery of Cryptic Polyketide Metabolites from Dermatophytes Using Heterologous Expression in Aspergillus nidulans. ACS Synth Biol. 2013; 2(11):629-634.

19

Xu W, Chooi YH, Choi JW, Li S, Vederas JC, Da Silva NA, Tang Y. LovG: The Thioesterase Required for DihydromonacolinL Release and Lovastatin Nonaketide Synthase Turnover in Lovastatin Biosynthesis. Angew Chem Int Edit. 2013; 52(25):6472-6475.

18

Lin HC, Chooi YH, Dhingra S, Xu W, Calvo AM, Tang Y. The Fumagillin Biosynthetic Gene Cluster in Aspergillus fumigatus Encodes a Cryptic Terpene Cyclase Involved in the Formation of beta-trans-Bergamotene. J Am Chem Soc. 2013; 135(12):4616-4619.

17

Chooi YH, Hong YJ, Cacho RA, Tantillo DJ, Tang Y. A Cytochrome P450 Serves as an Unexpected Terpene Cyclase during Fungal Meroterpenoid Biosynthesis. J Am Chem Soc. 2013; 135(45):16805-16808.

16

Chooi YH, Fang JX, Liu H, Filler SG, Wang P, Tang Y. Genome Mining of a Prenylated and Immunosuppressive Polyketide from Pathogenic Fungi. Org Lett. 2013; 15(4):780-783.

15

Cacho RA, Chooi YH, Zhou H, Tang Y. Complexity Generation in Fungal Polyketide Biosynthesis: A Spirocycle-Forming P450 in the Concise   Pathway to the Antifungal Drug Griseofulvin. ACS Chem Biol. 2013; 8(10):2322-2330.

2012

14

Zabala AO, Xu W, Chooi YH*, Tang Y*. Characterization of a Silent Azaphilone Gene Cluster from Aspergillus niger ATCC 1015 Reveals a Hydroxylation-Mediated Pyran-Ring Formation. Chem Biol. 2012; 19(8):1049-1059.

13

Wackler B, Lackner G, Chooi YH, Hoffmeister D. Characterization of the Suillus grevillei Quinone Synthetase GreA Supports a Nonribosomal Code for Aromatic alpha-Keto Acids. Chembiochem. 2012; 13(12):1798-1804.

12

Liu Q, Yao F, Chooi YH, Kang QJ, Xu W, Li YR, Shao YC, Shi YF, Deng ZX, Tang Y, You DL. Elucidation of Piericidin A1 Biosynthetic Locus Revealed a Thioesterase-Dependent Mechanism of alpha-Pyridone Ring Formation. Chem Biol. 2012; 19(2):243-253.

11

Chooi YH, Wang P, Fang JX, Li Y, Wu K, Wang P, Tang Y. Discovery and Characterization of a Group of Fungal Polycyclic Polyketide Prenyltransferases. J Am Chem Soc. 2012; 134(22):9428-9437.

10

Chooi YH, Tang Y. Navigating the Fungal Polyketide Chemical Space: From Genes to Molecules. J Org Chem. 2012; 77(22):9933-9953.

9

Cacho RA, Jiang W, Chooi YH, Walsh CT, Tang Y. Identification and Characterization of the Echinocandin B Biosynthetic Gene Cluster from Emericella rugulosa NRRL 11440. J Am Chem Soc. 2012; 134(40):16781-16790.

2011

8

Wang P, Gao X, Chooi YH, Deng ZX, Tang Y. Genetic characterization of enzymes involved in the priming steps of oxytetracycline biosynthesis in Streptomyces rimosus. Microbiol-Sgm. 2011; 157:2401-2409.

7

Qiao KJ, Chooi YH*, Tang Y* Identification and engineering of the cytochalasin gene cluster from Aspergillus clavatus NRRL 1. Metab Eng. 2011;   13(6):723-732.

6

Pickens LB, Tang Y, Chooi YH. Metabolic Engineering for the Production of Natural Products. Annu Rev Chem Biomol. 2011; 2:211-236.

5

Li YR, Chooi YH, Sheng YW, Valentine JS, Tang Y. Comparative Characterization of Fungal Anthracenone and Naphthacenedione Biosynthetic Pathways Reveals an alpha-Hydroxylation-Dependent Claisen-like Cyclization Catalyzed by a Dimanganese Thioesterase. J Am Chem Soc. 2011; 133(39):15773-15785.

4

Gao X, Chooi YH, Ames BD, Wang P, Walsh CT, Tang Y. Fungal Indole Alkaloid Biosynthesis: Genetic and Biochemical Investigation of the Tryptoquialanine Pathway in Penicillium aethiopicum. J Am Chem Soc. 2011; 133(8):2729-2741.

2010

3

Chooi YH, Tang Y. Adding the Lipo to Lipopeptides: Do More with Less. Chem Biol. 2010; 17(8):791-793.

2

Chooi YH, Cacho R, Tang Y. Identification of the Viridicatumtoxin and Griseofulvin Gene Clusters from Penicillium aethiopicum. Chem Biol. 2010;   17(5):483-494.

2008

1

Chooi YH, Stalker DM, Davis MA, Fujii I, Elix JA, Louwhoff SHJJ, Lawrie AC. Cloning and sequence characterization of a non-reducing polyketide synthase gene from the lichen Xanthoparmelia semiviridis. Mycol Res. 2008; 112:147-161.