Fungi as chemical industries and genetic engineering for the production of biologically active secondary metabolites

Asian Pacific Journal of Tropical Biomedicine

Volumn 4, Issue 11, 2014, Pages 859-870

  Khan, Abid Ali ^a,b   Bacha, Nafees ^b   Ahmad, Bashir ^b   Lutfullah, Ghosia ^b   Farooq, Umar ^a   Cox, Russell John ^c  

^a COMSATS Institute of Information Technology ^*  (Pakistan)

^b UNIVERSITY OF PESHAWAR   (Pakistan)

^c UNIVERSITY OF BRISTOL   (United Kingdom)

Author keywords

Chemical biology; Fungi; Microbiology; Molecular genetics; Natural products

Indexed keywords

ALKALOID; CARBON 13; CARBON 14; ISOPRENOID; NATURAL PRODUCT; NONRIBOSOMAL PEPTIDE SYNTHETASE; POLYKETIDE;

A DOMAIN; BIOSYNTHESIS; BIOTECHNOLOGY; C DOMAIN; CHEMICAL INDUSTRY; FUNGUS; GENE INACTIVATION; GENE OVEREXPRESSION; GENE SILENCING; GENETIC ENGINEERING; HETEROLOGOUS OVEREXPRESSION; HOMOLOGOUS OVEREXPRESSION; KNOCKOUT GENE; NONHUMAN; PCP DOMAIN; PROTEIN DOMAIN; REVIEW; SECONDARY METABOLISM;

FUNGI;

EID: 84922713680     PISSN: 22211691     EISSN: None     Source Type: Journal    
DOI: 10.12980/APJTB.4.2014APJTB-2014-0230     Document Type: Review

References (95)

1. Moore D, Frazer LN. Essential fungal genetics. New York: Springer; 2002.
2. Cox RJ. Polyketides, proteins and genes in fungi: programmed nano-machines begin to reveal their secrets. Org Biomol Chem 2007; 5(13): 2010-2026.
3. Ou SH. Rice diseases. 2nd ed. Wallingford: CAB International; 1985, p. 109-201.
4. Griffin DH. Fungal physiology: Wiley-Liss. 1996.
5. Goffeau A, Barrell BG, Bussey H, Davis RW, Dujon B, Feldmann H, et al. Life with 6000 genes. Science 1996; 274(5287): 546, 563-567.
6. Mewes HW, Albermann K, Bähr M, Frishman D, Gleissner A, Hani J, et al. Overview of the yeast genome. Nature 1997; 387(6632 Suppl): 7-65.
7. Zerikly M, Challis GL. Strategies for the discovery of new natural products by genome mining. Chembiochem 2009; 10(4): 625-633.
8. Newman DJ, Cragg GM, Snader KM. Natural products as sources of new drugs over the period 1981-2002. J Nat Prod 2003; 66(7): 1022-1037.
9. Lopez SN, Ramallo IA, Sierra MG, Zacchino SA, Furlan RLE. Chemically engineered extracts as an alternative source of bioactive natural product-like compounds. Proc Natl Acad Sci U S A 2007; 104(2): 441-444.
10. Bills GF, Platas G, Fillola A, Jiménez MR, Collado J, Vicente F, et al. Enhancement of antibiotic and secondary metabolite detection from filamentous fungi by growth on nutritional arrays. J Appl Microbiol 2008; 104(6): 1644-1658.
11. Munchhof MJ, Meyers A. An asymmetric route to chiral, nonracemic 2-substituted piperidines. Synthesis of (-)-pipecoline,(+)-coniine, and (-)-coniceine. J Org Chem 1995; 60(22): 7084-7085.
12. Hanson AD, Traynor PL, Ditz KM, Reicosky DA. Gramine in barley forage-effects of genotype and environment1. Crop Sci 1981; doi: DOI: 10.2135/cropsci1981.0011183x002100050024x.
13. Virag R. Intracavernous injection of papaverine for erectile failure. Lancet 1982; 320(8304): 938.
14. Brodie BB, Udenfriend S. The estimation of quinine in human plasma with a note on the estimation of quinidine. J Pharmacol Exper Ther 1943; 78(2): 154-158.
15. Gershenzon J, Dudareva N. The function of terpene natural products in the natural world. Nat Chem Biol 2007; 3(7): 408-414.
16. Sacchettini JC, Poulter CD. Creating isoprenoid diversity. Science 1997; 277(5333): 1788-1789.
17. Barkovich R, Liao JC. Review: metabolic engineering of isoprenoids. Metab Eng 2001; 3(1): 27-39.
18. Banthorpe DV, Baxendale D. Terpene biosynthesis. Part III. Biosynthesis of (+)-and (-)-camphor in Artemisia, Salvia, and Chrysanthemum species. J Chem Soc Perkin 1 1970; 19: 2694-2696.
19. Bouwmeester HJ, Gershenzon J, Konings MCLM, Croteau R. Biosynthesis of the monoterpenes limonene and carvone in the fruit of caraway. Demonstration of enzyme activities and their changes with development. Plant Physiol 1998; 117(3): 901-912.
20. Hughes PR. Myrcene: a precursor of pheromones in Ips beetles. J Insect Physiol 1974; 20(7): 1274-1275.
21. Wolf G. A history of vitamin A and retinoids. FASEB J 1996; 10(9): 1102-1107.
22. Govindachari TR, Mohamed PA, Parthasarathy PC. Ishwarane and aristolochene, two new sesquiterpene hydrocarbons from Aristolochia indica. Tetrahedron 1970; 26(2): 615-619.
23. Kawaide H, Sassa T, Kamiya Y. Plant-like biosynthesis of gibberellin A1 in the fungus Phaeosphaeria sp. L487. Phytochemistry 1995; 39(2): 305-310.
24. Finking R, Marahiel MA. Biosynthesis of nonribosomal peptides. Annu Rev Microbiol 2004; 58: 453-488.
25. Sieber SA, Marahiel MA. Molecular mechanisms underlying nonribosomal peptide synthesis: approaches to new antibiotics. Chem Rev 2005; 105(2): 715-738.
26. Mootz HD, Schwarzer D, Marahiel MA. Ways of assembling complex natural products on modular nonribosomal peptide synthetases. Chembiochem 2002; 3(6): 490-504.
27. Umezawa H, Maeda K, Takeuchi T, Okami Y. New antibiotics, bleomycin A and B. J Antibiot (Tokyo) 1966; 19(5): 200-209.
28. Weber G, Schörgendorfer K, Schneider-Scherzer E, Leitner E. The peptide synthetase catalyzing cyclosporine production in Tolypocladium niveum is encoded by a giant 45.8-kilobase open reading frame. Curr Genet 1994; 26(2): 120-125.
29. Fleming A. On the antibacterial action of cultures of a pénicillium, with special reference to their use in the isolation of B. influenzae. Br J Exp Pathol 1929; 10: 226-236.
30. Stachelhaus T, Marahiel MA. Modular structure of peptide synthetases revealed by dissection of the multifunctional enzyme GrsA. J Biol Chem 1995; 270: 6163-6169.
31. Mootz HD, Marahiel MA. The tyrocidine biosynthesis operon of Bacillus brevis: complete nucleotide sequence and biochemical characterization of functional internal denylation domains. J Bacteriol 1997; 179: 6843-6850.
32. Conti E, Stachelhaus T, Marahiel MA, Brick P. Structural basis for the activation of phenylalanine in the nonribosomal biosynthesis of gramicidin S. EMBO J 1997; 16(14): 4174-4183.
33. Stachelhaus T, Mootz HD, Bergendahl V, Marahiel MA. Peptide bond formation in nonribosomal peptide biosynthesis. Catalytic role of the condensation domain. J Biol Chem 1998; 273: 22773-22781.
34. Stachelhaus T, Huser A, Marahiel MA. Biochemical characterization of peptidyl carrier protein (PCP), the thiolation domain of multifunctional peptide synthetases. Chem Biol 1996; 3: 913-921.
35. Tao KJ, Du L, Sun XQ, Cai MH, Zhu TJ, Zhou XS, et al. Biosynthesis of aspergiolide A, a novel antitumor compound by a marine-derived fungus Aspergillus glaucus via the polyketide pathway. Tetrahedron Lett 2009; 50(9): 1082-1085.
36. Staunton J, Weissman KJ. Polyketide biosynthesis: a millennium review. Nat Prod Rep 2001; 18(4): 380-416.
37. Chan YA, Podevels AM, Kevany BM, Thomas MG. Biosynthesis of polyketide synthase extender units. Nat Prod Rep 2009; 26(1): 90-114.
38. Hertweck C, Luzhetskyy A, Rebets Y, Bechthold A. Type II polyketide synthases: gaining a deeper insight into enzymatic teamwork. Nat Prod Rep 2007; 24(1): 162-190.
39. Shen B. Polyketide biosynthesis beyond the type I, II and III polyketide synthase paradigms. Curr Opin Chem Biol 2003; 7(2): 285-295.
40. Gibson DG, Glass JI, Lartigue C, Noskov VN, Chuang RY, Algire MA, et al. Creation of a bacterial cell controlled by a chemically synthesized genome. Science 2010; 329(5987): 52-56.
41. Muller HJ, Carlson E, Schalet A. Mutation by alteration of the already existing gene. Genetics 1961; 46(2): 213-226.
42. Hopwood DA. Genetic contributions to understanding polyketide synthases. Chem Rev 1997; 97(7): 2465-2498.
43. Birch A, Massy-Westropp R, Moye CJ. Studies in relation to biosynthesis. VII. 2-Hydroxy-6-methylbenzoic acid in Penicillium griseofulvum Dierckx. Aust J Chem 1955; doi: 10.1071/ch9550539.
44. Crump MP, Crosby J, Dempsey CE, Parkinson JA, Murray M, Hopwood DA, et al. Solution structure of the actinorhodin polyketide synthase acyl carrier protein from Streptomyces coelicolor A3(2). Biochemistry 1997; 36(20): 6000-6008.
45. Deacon H. Towards a sustainable theory of health-related stigma: lessons from the HIV/AIDS literature. J Community Appl Soc Psychol 2006; 16(6): 418-425.
46. Shoolingin-Jordan P, Campuzano I. Biosynthesis of 6-methylsalicylic acid. In: Sankawa U, editor. Comprehensive Natural Products Chemistry. Vol 1. Oxford: Elsevier; 1999, p. 345-365.
47. Simpson TJ. Application of isotopic methods to secondary metabolic pathways. In: Leeper FJ, Vederas JC, editors. Biosynthesis. New York: Springer; 1998, p. 1-48.
48. Simpson TJ. Applications of multinuclear NMR to structural and biosynthetic studies of polyketide microbial metabolites. Chem Soc Rev 1987; 16: 123-160.
49. Vaidya JG, Rabba AS. Fungi in folk medicine. Mycologist 1993; 7: 131-133.
50. Pachlatko JP. Natural products in crop protection. Chimia 1998; 52: 29-47.
51. Fox T, Fertleman M, Cahill P, Palmer RD. Medical slang in British hospitals. Ethics Behav 2003; 13: 173-189.
52. Amann RI, Ludwig W, Schleifer KH. Phylogenetic identification and in situ detection of individual microbial cells without cultivation. Microbiol Reviews 1995; 59: 143-169.
53. Kaeberlein T, Lewis K, Epstein SS. Isolating "uncultivable" microorganisms in pure culture in a simulated natural environment. Science 2002; 296: 1127-1129.
54. Handelsman J. Metagenomics: applications of genomics to uncultured microorganisms. Microbiol Mol Biol Rev 2004; 68: 669-685.
55. Daniel R. The soil metagenome-a rich resource for the discovery of novel natural products. Curr Opin Biotechnol 2004; 15: 199-204.
56. Bode HB, Müller R. The impact of bacterial genomics on natural product research. Angew Chem Int Ed Engl 2005; 44: 6828-6846.
57. Pelzer S, Vente A, Bechthold A. Novel natural compounds obtained by genome-based screening and genetic engineering. Curr Opin Drug Discov Devel 2005; 8: 228-238.
58. Knight V, Sanglier JJ, DiTullio D, Braccili S, Bonner P, Waters J, et al. Diversifying microbial natural products for drug discovery. Appl Microbiol Biotechnol 2003; 62: 446-458.
59. Bode HB, Bethe B, Hofs R, Zeeck A. Big effects from small changes: possible ways to explore nature's chemical diversity. Chembiochem 2002; 3: 619-627.
60. Strobel G, Daisy B. Bioprospecting for microbial endophytes and their natural products. Microbiol Mol Biol Rev 2003; 67(4): 491-502.
61. Demain AL. From natural products discovery to commercialization: a success story. J Ind Microbiol Biotechnol 2006; 33(7): 486-495.
62. Gullo VP, Mcalpine J, Lam KS, Baker D, Petersen F. Drug discovery from natural products. J Ind Microbiol Biotechnol 2006; 33(7): 523-531.
63. Demain AL. Microbial biotechnology. Trends Biotechnol 2000; 18(1): 26-31.
64. Li JW, Vederas JC. Drug discovery and natural products: end of an era or an endless frontier? Science 2009; 325: 161-165.
65. Demain AL. Pharmaceutically active secondary metabolites of microorganisms. Appl Microbiol Biotechnol 1999; 52(4): 455-463.
66. Ebel R. Natural product diversity from marine fungi. In: Mander L, Liu HW, editors. Comprehensive natural products II: chemistry and biology. Oxford: Elsevier; 2010, p. 223-262.
67. Kilbey BJ. Charlotte Auerbach (1899-1994). Genetics 1995; 141(1): 1-5.
68. Jackson DA, Symons RH, Berg P. Biochemical method for inserting new genetic information into DNA of Simian Virus 40: circular SV40 DNA molecules containing lambda phage genes and the galactose operon of Escherichia coli. Proc Natl Acad Sci U S A 1972; 69(10): 2904-2909.
69. Goeddel DV, Kleid DG, Bolivar F, Heyneker HL, Yansura DG, Crea R, et al. Expression in Escherichia coli of chemically synthesized genes for human insulin. Proc Natl Acad Sci U S A 1979; 76(1): 106-110.
70. Meyer V. Genetic engineering of filamentous fungi-progress, obstacles and future trends. Biotechnol Adv 2008; 26(2): 177-185.
71. Ruiz-Díez B. Strategies for the transformation of filamentous fungi. J Appl Microbiol 2002; 92(2): 189-195.
72. Fincham JR. Transformation in fungi. Microbiol Rev 1989; 53(1): 148-170.
73. Gouka RJ, Gerk C, Hooykaas PJ, Bundock P, Musters W, Verrips CT, et al. Transformation of Aspergillus awamori by Agrobacterium tumefaciens-mediated homologous recombination. Nat Biotechnol 1999; 17(6): 598-601.
74. Michielse CB, Hooykaas PJ, van den Hondel CA, Ram AF. Agrobacterium-mediated transformation as a tool for functional genomics in fungi. Curr Genet 2005; 48(1): 1-17.
75. Haber JE. DNA repair: gatekeepers of recombination. Nature 1999; 398(6729): 665, 667.
76. Timberlake WE, Marshall MA. Genetic engineering of filamentous fungi. Science 1989; 244(4910): 1313-1317.
77. Jacobs DI, Olsthoorn MM, Maillet I, Akeroyd M, Breestraat S, Donkers S, et al. Effective lead selection for improved protein production in Aspergillus niger based on integrated genomics. Fungal Genet Biol 2009; 46: S141-S152.
78. Meyer V, Mueller D, Strowig T, Stahl U. Comparison of different transformation methods for Aspergillus giganteus. Curr Genet 2003; 43(5): 371-377.
79. Chi JT, Chang HY, Wang NN, Chang DS, Dunphy N, Brown PO. Genomewide view of gene silencing by small interfering RNAs. Proc Natl Acad Sci U S A 2003; 100(11): 6343-6346.
80. Meister G, Tuschl T. Mechanisms of gene silencing by doublestranded RNA. Nature 2004; 431(7006): 343-349.
81. Agrawal N, Malhotra P, Bhatnagar RK. siRNA-directed silencing of transgene expressed in cultured insect cells. Biochem Biophys Res Commun 2004; 320(2): 428-434.
82. Heneghan MN, Costa AM, Challen MP, Mills PR, Bailey A, Foster GD. A comparison of methods for successful triggering of gene silencing in Coprinus cinereus. Mol Biotechnol 2007; 35(3): 283-296.
83. Zheng XF, Kobayashi Y, Takeuchi M. Construction of a low-serine-type-carboxypeptidase-producing mutant of Aspergillus oryzae by the expression of antisense RNA and its use as a host for heterologous protein secretion. Appl Microbiol Biotechnol 1998; 49(1): 39-44.
84. Nakayashiki H. RNA silencing in fungi: mechanisms and applications. FEBS Lett 2005; 579(26): 5950-5957.
85. Bergmann S, Schümann J, Scherlach K, Lange C, Brakhage AA, Hertweck C. Genomics-driven discovery of PKS-NRPS hybrid metabolites from Aspergillus nidulans. Nat Chem Biol 2007; 3(4): 213-217.
86. Berdy J. Bioactive microbial metabolites. J Antibiot (Tokyo) 2005; 58(1): 1-26.
87. Karlsson J, Saloheimo M, Siika-Aho M, Tenkanen M, Penttilä M, Tjerneld F. Homologous expression and characterization of Cel61A (EG IV) of Trichoderma reesei. Eur J Biochem 2001; 268(24): 6498-6507.
88. Sims JW, Schmidt EW. Thioesterase-like role for fungal PKSNRPS hybrid reductive domains. J Am Chem Soc 2008; 130(33): 11149-11155.
89. Collemare J, Billard A, Böhnert HU, Lebrun MH. Biosynthesis of secondary metabolites in the rice blast fungus Magnaporthe grisea: the role of hybrid PKS-NRPS in pathogenicity. Mycol Res 2008; 112: 207-215.
90. Weinacker A, Chen A, Agrez M, Cone RI, Nishimura S, Wayner E, et al. Role of the integrin alpha v beta 6 in cell attachment to fibronectin. Heterologous expression of intact and secreted forms of the receptor. J Biol Chem 1994; 269(9): 6940-6948.
91. Sweeney HL, Straceski AJ, Leinwand LA, Tikunov BA, Faust L. Heterologous expression of a cardiomyopathic myosin that is defective in its actin interaction. J Biol Chem 1994; 269(3): 1603-1605.
92. Pickens LB, Tang Y, Chooi YH. Metabolic engineering for the production of natural products. Annu Rev Chem Biomol Eng 2011; 2: 211-236.
93. Pfeifer BA, Khosla C. Biosynthesis of polyketides in heterologous hosts. Microbiol Mol Biol Rev 2001; 65(1): 106-118.
94. Tang L, Shah S, Chung L, Carney J, Katz L, Khosla C, et al. Cloning and heterologous expression of the epothilone gene cluster. Science 2000; 287(5453): 640-642.
95. Ahmed S, Riaz S, Jamil A. Molecular cloning of fungal xylanases: an overview. Appl Microbiol Biotechnol 2009; 84(1): 19-35.