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Jenkinson CB, Podgorny AR, Zhong C, Oakley BR. Computer-aided, resistance gene-guided genome mining for proteasome and HMG-CoA reductase inhibitors. J Ind Microbiol Biotechnol 2023; 50:kuad045. [PMID: 38061800 PMCID: PMC10734572 DOI: 10.1093/jimb/kuad045] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2023] [Accepted: 12/06/2023] [Indexed: 12/22/2023]
Abstract
Secondary metabolites (SMs) are biologically active small molecules, many of which are medically valuable. Fungal genomes contain vast numbers of SM biosynthetic gene clusters (BGCs) with unknown products, suggesting that huge numbers of valuable SMs remain to be discovered. It is challenging, however, to identify SM BGCs, among the millions present in fungi, that produce useful compounds. One solution is resistance gene-guided genome mining, which takes advantage of the fact that some BGCs contain a gene encoding a resistant version of the protein targeted by the compound produced by the BGC. The bioinformatic signature of such BGCs is that they contain an allele of an essential gene with no SM biosynthetic function, and there is a second allele elsewhere in the genome. We have developed a computer-assisted approach to resistance gene-guided genome mining that allows users to query large databases for BGCs that putatively make compounds that have targets of therapeutic interest. Working with the MycoCosm genome database, we have applied this approach to look for SM BGCs that target the proteasome β6 subunit, the target of the proteasome inhibitor fellutamide B, or HMG-CoA reductase, the target of cholesterol reducing therapeutics such as lovastatin. Our approach proved effective, finding known fellutamide and lovastatin BGCs as well as fellutamide- and lovastatin-related BGCs with variations in the SM genes that suggest they may produce structural variants of fellutamides and lovastatin. Gratifyingly, we also found BGCs that are not closely related to lovastatin BGCs but putatively produce novel HMG-CoA reductase inhibitors. ONE-SENTENCE SUMMARY A new computer-assisted approach to resistance gene-directed genome mining is reported along with its use to identify fungal biosynthetic gene clusters that putatively produce proteasome and HMG-CoA reductase inhibitors.
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Affiliation(s)
- Cory B Jenkinson
- Department of Molecular Biosciences, University of Kansas, Lawrence, KS 66045,USA
| | - Adam R Podgorny
- Department of Electrical Engineering and Computer Science, University of Kansas, Lawrence, KS 66045,USA
| | - Cuncong Zhong
- Department of Electrical Engineering and Computer Science, University of Kansas, Lawrence, KS 66045,USA
| | - Berl R Oakley
- Department of Molecular Biosciences, University of Kansas, Lawrence, KS 66045,USA
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Fan X, Han J, Zhang F, Chen W. Red yeast rice: a functional food used to reduce hyperlipidemia. FOOD REVIEWS INTERNATIONAL 2022. [DOI: 10.1080/87559129.2022.2043894] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/04/2022]
Affiliation(s)
- Xiangcheng Fan
- Department of Pharmacy, Changzheng Hospital, Naval Medical University (Second Military Medical University), Shanghai, China
- Shanghai Key Laboratory for Pharmaceutical Metabolite Research, Shanghai, China
| | - Jun Han
- Institute of Chinese Materia Madica, Shanghai University of Traditional Chinese Medicine, Shanghai, China
| | - Feng Zhang
- Department of Pharmacy, Changzheng Hospital, Naval Medical University (Second Military Medical University), Shanghai, China
- Shanghai Key Laboratory for Pharmaceutical Metabolite Research, Shanghai, China
| | - Wansheng Chen
- Department of Pharmacy, Changzheng Hospital, Naval Medical University (Second Military Medical University), Shanghai, China
- Department of Gastroenterology, Changzheng Hospital, Naval Medical University (Second Military Medical University), Shanghai, China
- Shanghai Key Laboratory for Pharmaceutical Metabolite Research, Shanghai, China
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Vederas JC. Explorations of fungal biosynthesis of reduced polyketides – a personal viewpoint. Nat Prod Rep 2014; 31:1253-9. [DOI: 10.1039/c4np00091a] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023]
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Shao Y, Lei M, Mao Z, Zhou Y, Chen F. Insights into Monascus biology at the genetic level. Appl Microbiol Biotechnol 2014; 98:3911-22. [PMID: 24633442 DOI: 10.1007/s00253-014-5608-8] [Citation(s) in RCA: 59] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2013] [Revised: 02/10/2014] [Accepted: 02/10/2014] [Indexed: 12/24/2022]
Abstract
The genus of Monascus was nominated by van Tieghem in 1884, but its fermented product-red mold rice (RMR), namely red yeast rice, has been used as folk medicines, food colorants, and fermentation starters for more than thousands of years in oriental countries. Nowadays, RMR is widely developed as food supplements around the world due to its functional compounds such as monacolin K (MK, also called lovastatin) and γ-aminobutyric acid. But the usage of RMR also incurs controversy resulting from contamination of citrinin (a kind of mycotoxin) produced by some Monascus strains. In the past decade, it has made great progress to Monascus spp. at the genetic level with the application of molecular biology techniques to restrain the citrinin production and increase the yields of MK and pigment in RMR, as well as aid Monascus classification and phylogenesis. Up to now, hundreds of papers about Monascus molecular biology (MMB) have been published in the international primary journals. However, to our knowledge, there is no MMB review issued until now. In this review, current understanding of Monascus spp. from the view of molecular biology will be covered and insights into research areas that need to be further investigated will also be discussed.
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Affiliation(s)
- Yanchun Shao
- State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan, 430070, People's Republic of China
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Abstract
The iterative type I polyketide synthases (IPKSs) are central to the biosynthesis of an enormously diverse array of natural products in fungi. These natural products, known as polyketides, exhibit a wide range of biological activities and include clinically important drugs as well as undesirable toxins. The PKSs synthesize these structurally diverse polyketides via a series of decarboxylative condensations of malonyl-CoA extender units and β-keto modifications in a highly programmed manner. Significant progress has been made over the past few years in understanding the biosynthetic mechanism and programming of fungal PKSs. The continuously expanding fungal genome sequence data have sparked genome-directed discoveries of new fungal PKSs and associated products. The increasing number of fungal PKSs that have been linked to their products along with in-depth biochemical and structural characterizations of these large enzymes have remarkably improved our knowledge on the molecular basis for polyketide structural diversity in fungi. This Perspective highlights the recent advances and examines how the newly expanded paradigm has contributed to our ability to link fungal PKS genes to chemical structures and vice versa. The knowledge will help us navigate through the logarithmically expanding seas of genomic information for polyketide compound discovery and provided opportunities to reprogram these megasynthases to generate new chemical entities.
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Affiliation(s)
- Yit-Heng Chooi
- Department of Chemical and Biomolecular Engineering, University of California, Los Angeles, California 90095
| | - Yi Tang
- Department of Chemical and Biomolecular Engineering, University of California, Los Angeles, California 90095
- Department of Chemistry and Biochemistry, University of California, Los Angeles, California 90095
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Yakasai AA, Davison J, Wasil Z, Halo LM, Butts CP, Lazarus CM, Bailey AM, Simpson TJ, Cox RJ. Nongenetic Reprogramming of a Fungal Highly Reducing Polyketide Synthase. J Am Chem Soc 2011; 133:10990-8. [DOI: 10.1021/ja204200x] [Citation(s) in RCA: 45] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/16/2023]
Affiliation(s)
- Ahmed A. Yakasai
- School of Chemistry, University of Bristol, Cantock’s Close, Bristol BS8 1TS, U.K
| | - Jack Davison
- School of Chemistry, University of Bristol, Cantock’s Close, Bristol BS8 1TS, U.K
| | - Zahida Wasil
- School of Chemistry, University of Bristol, Cantock’s Close, Bristol BS8 1TS, U.K
| | - Laura M. Halo
- School of Chemistry, University of Bristol, Cantock’s Close, Bristol BS8 1TS, U.K
| | - Craig P. Butts
- School of Chemistry, University of Bristol, Cantock’s Close, Bristol BS8 1TS, U.K
| | - Colin M. Lazarus
- School of Biological Sciences, University of Bristol, Woodland Road, Bristol BS8 1UG, U.K
| | - Andrew M. Bailey
- School of Biological Sciences, University of Bristol, Woodland Road, Bristol BS8 1UG, U.K
| | - Thomas J. Simpson
- School of Chemistry, University of Bristol, Cantock’s Close, Bristol BS8 1TS, U.K
| | - Russell J. Cox
- School of Chemistry, University of Bristol, Cantock’s Close, Bristol BS8 1TS, U.K
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Chen YP, Tseng CP, Liaw LL, Wang CL, Chen IC, Wu WJ, Wu MD, Yuan GF. Cloning and characterization of monacolin K biosynthetic gene cluster from Monascus pilosus. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2008; 56:5639-46. [PMID: 18578535 DOI: 10.1021/jf800595k] [Citation(s) in RCA: 63] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/02/2023]
Abstract
Monacolin K is a secondary metabolite synthesized by polyketide synthases (PKS) from Monascus, and it has the same structure as lovastatin, which is mainly produced by Aspergillus terreus. In the present study, a bacterial artificial chromosome (BAC) clone, mps01, was screened from the BAC library constructed from Monascus pilosus BCRC38072 genomic DNA. The putative monacolin K biosynthetic gene cluster was found within a 42 kb region in the mps01 clone. The deduced amino acid sequences encoded by the nine genes designated as mokA- mokI, which share over 54% similarity with the lovastatin biosynthetic gene cluster in A. terreus, were assumed to be involved in monacolin K biosynthesis. A gene disruption construct designed to replace the central part of mokA, a polyketide synthase gene, in wild-type M. pilosus BCRC38072 with a hygromycin B resistance gene through homologous recombination, resulted in a mokA-disrupted strain. The disruptant did not produce monacolin K, indicating that mokA encoded the PKS responsible for monacolin K biosynthesis in M. pilosus BCRC38072.
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Affiliation(s)
- Yi-Pei Chen
- Bioresource Collection and Research Center, Food Industry Research and Development Institute, National Chiao Tung University, HsinChu, Taiwan
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Schneider P, Misiek M, Hoffmeister D. In Vivo and In Vitro Production Options for Fungal Secondary Metabolites. Mol Pharm 2008; 5:234-42. [DOI: 10.1021/mp7001544] [Citation(s) in RCA: 53] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023]
Affiliation(s)
- Patrick Schneider
- Pharmaceutical Biology and Biotechnology, Albert-Ludwigs-Universität, Stefan-Meier-Strasse 19, 79104 Freiburg, Germany, and Department of Plant Pathology, University of Minnesota—Twin Cities Campus, 1991 Upper Buford Circle, St. Paul, Minnesota 55108
| | - Mathias Misiek
- Pharmaceutical Biology and Biotechnology, Albert-Ludwigs-Universität, Stefan-Meier-Strasse 19, 79104 Freiburg, Germany, and Department of Plant Pathology, University of Minnesota—Twin Cities Campus, 1991 Upper Buford Circle, St. Paul, Minnesota 55108
| | - Dirk Hoffmeister
- Pharmaceutical Biology and Biotechnology, Albert-Ludwigs-Universität, Stefan-Meier-Strasse 19, 79104 Freiburg, Germany, and Department of Plant Pathology, University of Minnesota—Twin Cities Campus, 1991 Upper Buford Circle, St. Paul, Minnesota 55108
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Hill AM. The biosynthesis, molecular genetics and enzymology of the polyketide-derived metabolites. Nat Prod Rep 2005; 23:256-320. [PMID: 16572230 DOI: 10.1039/b301028g] [Citation(s) in RCA: 121] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/03/2023]
Abstract
This review covers the biosynthesis of aliphatic and aromatic polyketides as well as mixed polyketide/NRPS metabolites, and discusses the molecular genetics and enzymology of the proteins responsible for their formation.
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