151
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Walsh CT, Wencewicz TA. Prospects for new antibiotics: a molecule-centered perspective. J Antibiot (Tokyo) 2013; 67:7-22. [DOI: 10.1038/ja.2013.49] [Citation(s) in RCA: 272] [Impact Index Per Article: 24.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2013] [Revised: 04/22/2013] [Accepted: 05/01/2013] [Indexed: 12/12/2022]
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152
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Chiang YM, Oakley CE, Ahuja M, Entwistle R, Schultz A, Chang SL, Sung CT, Wang CCC, Oakley BR. An efficient system for heterologous expression of secondary metabolite genes in Aspergillus nidulans. J Am Chem Soc 2013; 135:7720-31. [PMID: 23621425 PMCID: PMC3697937 DOI: 10.1021/ja401945a] [Citation(s) in RCA: 154] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
Abstract
Fungal secondary metabolites (SMs) are an important source of medically valuable compounds. Genome projects have revealed that fungi have many SM biosynthetic gene clusters that are not normally expressed. To access these potentially valuable, cryptic clusters, we have developed a heterologous expression system in Aspergillus nidulans . We have developed an efficient system for amplifying genes from a target fungus, placing them under control of a regulatable promoter, transferring them into A. nidulans , and expressing them. We have validated this system by expressing nonreducing polyketide synthases of Aspergillus terreus and additional genes required for compound production and release. We have obtained compound production and release from six of these nonreducing polyketide synthases and have identified the products. To demonstrate that the procedure allows transfer and expression of entire secondary metabolite biosynthetic pathways, we have expressed all the genes of a silent A. terreus cluster and demonstrate that it produces asperfuranone. Further, by expressing the genes of this pathway in various combinations, we have clarified the asperfuranone biosynthetic pathway. We have also developed procedures for deleting entire A. nidulans SM clusters. This allows us to remove clusters that might interfere with analyses of heterologously expressed genes and to eliminate unwanted toxins.
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Affiliation(s)
- Yi-Ming Chiang
- Department of Pharmacology and Pharmaceutical Sciences, School of Pharmacy, University of Southern California, 1985 Zonal Avenue, Los Angeles, California 90089, United States
- Graduate Institute of Pharmaceutical Science, Chia Nan University of Pharmacy and Science, Tainan 71710, Taiwan, Republic of China
| | - C. Elizabeth Oakley
- Department of Molecular Biosciences, University of Kansas, 1200 Sunnyside Avenue, Lawrence, Kansas 66045, United States
| | - Manmeet Ahuja
- Department of Molecular Biosciences, University of Kansas, 1200 Sunnyside Avenue, Lawrence, Kansas 66045, United States
| | - Ruth Entwistle
- Department of Molecular Biosciences, University of Kansas, 1200 Sunnyside Avenue, Lawrence, Kansas 66045, United States
| | - Aric Schultz
- Department of Molecular Biosciences, University of Kansas, 1200 Sunnyside Avenue, Lawrence, Kansas 66045, United States
- Current address: Department of Microbiology and Immunology, University of Michigan Medical School, Ann Arbor, MI 48109, United States
| | - Shu-Lin Chang
- Department of Pharmacology and Pharmaceutical Sciences, School of Pharmacy, University of Southern California, 1985 Zonal Avenue, Los Angeles, California 90089, United States
- Department of Biotechnology, Chia Nan University of Pharmacy and Science, Tainan 71710, Taiwan, Republic of China
| | - Calvin T. Sung
- Department of Pharmacology and Pharmaceutical Sciences, School of Pharmacy, University of Southern California, 1985 Zonal Avenue, Los Angeles, California 90089, United States
| | - Clay C. C. Wang
- Department of Pharmacology and Pharmaceutical Sciences, School of Pharmacy, University of Southern California, 1985 Zonal Avenue, Los Angeles, California 90089, United States
- Department of Chemistry, College of Letters, Arts, and Sciences, University of Southern California, Los Angeles, California 90089, United States
| | - Berl R. Oakley
- Department of Molecular Biosciences, University of Kansas, 1200 Sunnyside Avenue, Lawrence, Kansas 66045, United States
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153
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Kozyrovska NO. Crosstalk between endophytes and a plant host within information-processing networks. ACTA ACUST UNITED AC 2013. [DOI: 10.7124/bc.00081d] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
Affiliation(s)
- N. O. Kozyrovska
- Institute of Molecular Biology and Genetics, National Academy of Sciences of Ukraine
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154
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König CC, Scherlach K, Schroeckh V, Horn F, Nietzsche S, Brakhage AA, Hertweck C. Bacterium induces cryptic meroterpenoid pathway in the pathogenic fungus Aspergillus fumigatus. Chembiochem 2013; 14:938-42. [PMID: 23649940 DOI: 10.1002/cbic.201300070] [Citation(s) in RCA: 105] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2013] [Indexed: 12/16/2022]
Abstract
Stimulating encounter: The intimate, physical interaction between the soil-derived bacterium Streptomyces rapamycinicus and the human pathogenic fungus Aspergillus fumigatus led to the activation of an otherwise silent polyketide synthase (PKS) gene cluster coding for an unusual prenylated polyphenol (fumicycline A). The meroterpenoid pathway is regulated by a pathway-specific activator gene as well as by epigenetic factors.
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Affiliation(s)
- Claudia C König
- Department of Molecular and Applied Microbiology, Leibniz Institute for Natural Product Research and Infection Biology, Beutenbergstrasse 11a, 07745 Jena, Germany
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155
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Affiliation(s)
- Jin-Ming Gao
- Shaanxi Engineering Center of Bioresource Chemistry & Sustainable Utilization, Department of Chemistry and Chemical Engineering, College of Science, Northwest A&F University, 3 Taicheng Road, Yangling 712100, Shaanxi, China.
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156
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Asai T, Otsuki S, Sakurai H, Yamashita K, Ozeki T, Oshima Y. Benzophenones from an endophytic fungus, Graphiopsis chlorocephala, from Paeonia lactiflora cultivated in the presence of an NAD+-dependent HDAC inhibitor. Org Lett 2013; 15:2058-61. [PMID: 23578108 DOI: 10.1021/ol400781b] [Citation(s) in RCA: 40] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023]
Abstract
Graphiopsis chlorocephala was separated from the surface-sterilized healthy leaves of Paeonia lactiflora (Paeoniaceae) and cultivated with nicotinamide (an NAD(+)-dependent HDAC inhibitor). The culture conditions significantly enhanced secondary metabolite production in the fungus and led to the isolation of a structurally diverse set of new benzophenones, cephalanones A-F (1-6), and a known 2-(2,6-dihydroxy-4-methylbenzoyl)-6-hydroxybenzoic acid (7). The structures of 1-6 were determined from NMR data, single crystal X-ray diffraction, and chemical transformations.
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Affiliation(s)
- Teigo Asai
- Graduate School of Pharmaceutical Sciences, Tohoku University, Aoba-yama, Aoba-ku, Sendai 980-8578, Japan.
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157
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Palmer JM, Bok JW, Lee S, Dagenais TRT, Andes DR, Kontoyiannis DP, Keller NP. Loss of CclA, required for histone 3 lysine 4 methylation, decreases growth but increases secondary metabolite production in Aspergillus fumigatus. PeerJ 2013; 1:e4. [PMID: 23638376 PMCID: PMC3629006 DOI: 10.7717/peerj.4] [Citation(s) in RCA: 55] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2012] [Accepted: 12/04/2012] [Indexed: 12/13/2022] Open
Abstract
Secondary metabolite (SM) production in filamentous fungi is mechanistically associated with chromatin remodeling of specific SM clusters. One locus recently shown to be involved in SM suppression in Aspergillus nidulans was CclA, a member of the histone 3 lysine 4 methylating COMPASS complex. Here we examine loss of CclA and a putative H3K4 demethylase, HdmA, in the human pathogen Aspergillus fumigatus. Although deletion of hdmA showed no phenotype under the conditions tested, the cclA deletant was deficient in tri- and di-methylation of H3K4 and yielded a slowly growing strain that was rich in the production of several SMs, including gliotoxin. Similar to deletion of other chromatin modifying enzymes, ΔcclA was sensitive to 6-azauracil indicating a defect in transcriptional elongation. Despite the poor growth, the ΔcclA mutant had wild-type pathogenicity in a murine model and the Toll-deficient Drosophila model of invasive aspergillosis. These data indicate that tri- and di-methylation of H3K4 is involved in the regulation of several secondary metabolites in A. fumigatus, however does not contribute to pathogenicity under the conditions tested.
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Affiliation(s)
- Jonathan M Palmer
- Department of Medical Microbiology and Immunology, University of Wisconsin-Madison, Madison, WI, USA
| | - Jin Woo Bok
- Department of Medical Microbiology and Immunology, University of Wisconsin-Madison, Madison, WI, USA
| | - Seul Lee
- Department of Medical Microbiology and Immunology, University of Wisconsin-Madison, Madison, WI, USA
| | - Taylor R T Dagenais
- Department of Medical Microbiology and Immunology, University of Wisconsin-Madison, Madison, WI, USA
| | - David R Andes
- Department of Medical Microbiology and Immunology, University of Wisconsin-Madison, Madison, WI, USA
| | - Dimitrios P Kontoyiannis
- Department of Infectious Disease, University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Nancy P Keller
- Department of Medical Microbiology and Immunology, University of Wisconsin-Madison, Madison, WI, USA.,Department of Bacteriology, University of Wisconsin-Madison, Madison, WI, USA
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158
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Hamed RB, Gomez-Castellanos JR, Henry L, Ducho C, McDonough MA, Schofield CJ. The enzymes of β-lactam biosynthesis. Nat Prod Rep 2013; 30:21-107. [DOI: 10.1039/c2np20065a] [Citation(s) in RCA: 146] [Impact Index Per Article: 13.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
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159
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de la Cruz M, Martín J, González-Menéndez V, Pérez-Victoria I, Moreno C, Tormo JR, El Aouad N, Guarro J, Vicente F, Reyes F, Bills GF. Chemical and physical modulation of antibiotic activity in emericella species. Chem Biodivers 2012; 9:1095-113. [PMID: 22700228 DOI: 10.1002/cbdv.201100362] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Abstract
The addition of epigenetic modifying agents and ion-exchange resins to culture media and solid-state fermentations have been promoted as ways to stimulate expression of latent biosynthetic gene clusters and to modulate secondary metabolite biosynthesis. We asked how combination of these treatments would affect a population of screening isolates and their patterns of antibiosis relative to fermentation controls. A set of 43 Emericella strains, representing 25 species and varieties, were grown on a nutrient-rich medium comprising glucose, casein hydrolysate, urea, and mineral salts. Each strain was grown in untreated agitated liquid medium, a medium treated with suberoylanilide hydroxamic acid, a histone deacetylase inhibitor, 5-azacytidine, a DNA methylation inhibitor, an Amberlite non-ionic polyacrylate resin, and the same medium incorporated into an inert static vermiculite matrix. Species-inherent metabolic differences more strongly influenced patterns of antibiosis than medium treatments. The antibacterial siderophore, desferritriacetylfusigen, was detected in most species in liquid media, but not in the vermiculite medium. The predominant antifungal component detected was echinocandin B. Some species produced this antifungal regardless of treatment, although higher quantities were often produced in vermiculite. Several species are reported for the first time to produce echinocandin B. A new echinocandin analog, echinocandin E, was identified from E. quadrilineata.
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Affiliation(s)
- Mercedes de la Cruz
- Fundación MEDINA, Centro de Excelencia en Investigación de Medicamentos Innovadores en Andalucía, Avda. del Conocimiento 3, Parque Tecnológico de Ciencias de la Salud, ES-18100 Armilla, Granada
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160
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Soukup AA, Chiang YM, Bok JW, Reyes-Dominguez Y, Oakley BR, Wang CCC, Strauss J, Keller NP. Overexpression of the Aspergillus nidulans histone 4 acetyltransferase EsaA increases activation of secondary metabolite production. Mol Microbiol 2012; 86:314-30. [PMID: 22882998 PMCID: PMC3514908 DOI: 10.1111/j.1365-2958.2012.08195.x] [Citation(s) in RCA: 86] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 07/31/2012] [Indexed: 01/07/2023]
Abstract
Regulation of secondary metabolite (SM) gene clusters in Aspergillus nidulans has been shown to occur through cluster-specific transcription factors or through global regulators of chromatin structure such as histone methyltransferases, histone deacetylases, or the putative methyltransferase LaeA. A multicopy suppressor screen for genes capable of returning SM production to the SM deficient ΔlaeA mutant resulted in identification of the essential histone acetyltransferase EsaA, able to complement an esa1 deletion in Saccharomyces cereviseae. Here we report that EsaA plays a novel role in SM cluster activation through histone 4 lysine 12 (H4K12) acetylation in four examined SM gene clusters (sterigmatocystin, penicillin, terrequinone and orsellinic acid), in contrast to no increase in H4K12 acetylation of the housekeeping tubA promoter. This augmented SM cluster acetylation requires LaeA for full effect and correlates with both increased transcript levels and metabolite production relative to wild type. H4K12 levels may thus represent a unique indicator of relative production potential, notably of SMs.
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Affiliation(s)
- Alexandra A. Soukup
- Department of Genetics, University of Wisconsin-Madison, 1550 Linden Drive, Madison, WI, USA 53706
| | - Yi-Ming Chiang
- Graduate Institute of Pharmaceutical Science, Chia Nan University of Pharmacy and Science, Tainan, Taiwan, ROC 71710,Department of Pharmacology and Pharmaceutical Sciences, University of Southern California, 1985 Zonal Avenue, Los Angeles, CA, USA 90033
| | - Jin Woo Bok
- Department of Bacteriology, University of Wisconsin-Madison, 1550 Linden Drive, Madison, WI, USA 53706
| | - Yazmid Reyes-Dominguez
- Fungal Genetics and Genomics Unit, University of Natural Resources and Life Sciences Vienna, and Austrian Institute of Technology GmbH, University and Research Center Campus Tulln, Konrad Lorenz Strasse 24, Tulln/Donau, Austria A-3430
| | - Berl R. Oakley
- Department of Molecular Biosciences, University of Kansas, 1200 Sunnyside Avenue, Lawrence, KS, USA 66045
| | - Clay C. C. Wang
- Department of Pharmacology and Pharmaceutical Sciences, University of Southern California, 1985 Zonal Avenue, Los Angeles, CA, USA 90033,Department of Chemistry, University of Southern California, 1985 Zonal Avenue, Los Angeles, CA, USA 90033
| | - Joseph Strauss
- Fungal Genetics and Genomics Unit, University of Natural Resources and Life Sciences Vienna, and Austrian Institute of Technology GmbH, University and Research Center Campus Tulln, Konrad Lorenz Strasse 24, Tulln/Donau, Austria A-3430
| | - Nancy P. Keller
- Department of Bacteriology, University of Wisconsin-Madison, 1550 Linden Drive, Madison, WI, USA 53706,Department of Medical Microbiology and Immunology, University of Wisconsin-Madison, 1550 Linden Drive, Madison, WI, USA 53706,Corresponding author: 3476 Microbial Sciences, 1550 Linden Drive, Madison, WI, USA 53706 Phone: (608) 262-9795 Fax: (608)262-8418
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161
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162
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Sasso S, Pohnert G, Lohr M, Mittag M, Hertweck C. Microalgae in the postgenomic era: a blooming reservoir for new natural products. FEMS Microbiol Rev 2012; 36:761-85. [DOI: 10.1111/j.1574-6976.2011.00304.x] [Citation(s) in RCA: 115] [Impact Index Per Article: 9.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2011] [Accepted: 08/29/2011] [Indexed: 01/20/2023] Open
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163
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Purpurogemutantin and purpurogemutantidin, new drimenyl cyclohexenone derivatives produced by a mutant obtained by diethyl sulfate mutagenesis of a marine-derived Penicillium purpurogenum G59. Mar Drugs 2012; 10:1266-1287. [PMID: 22822371 PMCID: PMC3397438 DOI: 10.3390/md10061266] [Citation(s) in RCA: 52] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2012] [Revised: 05/24/2012] [Accepted: 05/24/2012] [Indexed: 11/16/2022] Open
Abstract
Two new drimenyl cyclohexenone derivatives, named purpurogemutantin (1) and purpurogemutantidin (2), and the known macrophorin A (3) were isolated from a bioactive mutant BD-1-6 obtained by random diethyl sulfate (DES) mutagenesis of a marine-derived Penicillium purpurogenum G59. Structures and absolute configurations of 1 and 2 were determined by extensive spectroscopic methods, especially 2D NMR and electronic circular dichroism (ECD) analysis. Possible biosynthetic pathways for 1-3 were also proposed and discussed. Compounds 1 and 2 significantly inhibited human cancer K562, HL-60, HeLa, BGC-823 and MCF-7 cells, and compound 3 also inhibited the K562 and HL-60 cells. Both bioassay and chemical analysis (HPLC, LC-ESIMS) demonstrated that the parent strain G59 did not produce 1-3, and that DES-induced mutation(s) in the mutant BD-1-6 activated some silent biosynthetic pathways in the parent strain G59, including one set for 1-3 production.
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164
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Wang X, You J, King JB, Powell DR, Cichewicz RH. Waikialoid A suppresses hyphal morphogenesis and inhibits biofilm development in pathogenic Candida albicans. JOURNAL OF NATURAL PRODUCTS 2012; 75:707-715. [PMID: 22400916 PMCID: PMC3338887 DOI: 10.1021/np2009994] [Citation(s) in RCA: 47] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/26/2023]
Abstract
A chemically prolific strain of Aspergillus was isolated from a soil sample collected near Waikiki Beach, Honolulu, Hawaii. The fungus produced several secondary metabolites, which were purified and placed in our natural products library and were later screened for substances capable of inhibiting biofilm formation by Candida albicans. It was determined that one of the secondary metabolites from the Hawaiian fungal isolate, a new complex prenylated indole alkaloid named waikialoid A (1), inhibited biofilm formation with an IC(50) value of 1.4 μM. Another structurally unrelated, presumably polyketide metabolite, waikialide A (15), also inhibited C. albicans biofilm formation, but was much less potent (IC(50) value of 32.4 μM). Microscopy studies revealed that compound 1 also inhibited C. albicans hyphal morphogenesis. While metabolite 1 appears ineffective at disrupting preformed biofilms, the accumulated data indicate that the new compound may exert its activity against C. albicans during the early stages of surface colonization involving cell adherence, hyphal development, and/or biofilm assembly. Unlike some other stephacidin/notoamide compounds, metabolite 1 was not cytotoxic to fungi or human cells (up to 200 μM), which makes this an intriguing model compound for studying the adjunctive use of biofilm inhibitors in combination with standard antifungal antibiotics.
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165
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Activation of the dormant secondary metabolite production by introducing gentamicin-resistance in a marine-derived Penicillium purpurogenum G59. Mar Drugs 2012; 10:559-582. [PMID: 22611354 PMCID: PMC3347015 DOI: 10.3390/md10030559] [Citation(s) in RCA: 48] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2011] [Revised: 02/13/2012] [Accepted: 02/21/2012] [Indexed: 11/16/2022] Open
Abstract
A new approach to activate silent gene clusters for dormant secondary metabolite production has been developed by introducing gentamicin-resistance to an originally inactive, marine-derived fungal strain Penicillium purpurogenum G59. Upon treatment of the G59 spores with a high concentration of gentamicin in aqueous DMSO, a total of 181 mutants were obtained by single colony isolation. In contrast to the strain G59, the EtOAc extracts of nine mutant cultures showed inhibitory effects on K562 cells, indicating that the nine mutants had acquired capability to produce antitumor metabolites. This was evidenced by TLC and HPLC analysis of EtOAc extracts of G59 and the nine mutants. Further isolation and characterization demonstrated that four antitumor secondary metabolites, janthinone (1), fructigenine A (2), aspterric acid methyl ester (3) and citrinin (4), were newly produced by mutant 5-1-4 compared to the parent strain G59, and which were also not found in the secondary metabolites of other Penicillium purpurogenum strains. However, Compounds 1–4 inhibited the proliferation of K562 cells with inhibition rates of 34.6% (1), 60.8% (2), 31.7% (3) and 67.1% (4) at 100 μg/mL, respectively. The present study demonstrated the effectiveness of a simple, yet practical approach to activate the production of dormant fungal secondary metabolites by introducing acquired resistance to aminoglycoside antibiotics, which could be applied to the studies for eliciting dormant metabolic potential of fungi to obtain cryptic secondary metabolites.
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166
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Ul-Hassan SR, Strobel GA, Booth E, Knighton B, Floerchinger C, Sears J. Modulation of volatile organic compound formation in the Mycodiesel-producing endophyte Hypoxylon sp. CI-4. Microbiology (Reading) 2012; 158:465-473. [DOI: 10.1099/mic.0.054643-0] [Citation(s) in RCA: 59] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023] Open
Affiliation(s)
| | - Gary A. Strobel
- Department of Plant Sciences, Montana State University, Bozeman, MT 59717, USA
| | - Eric Booth
- Department of Plant Sciences, Montana State University, Bozeman, MT 59717, USA
| | - Berk Knighton
- Department of Chemistry, Montana State University, Bozeman, MT 59717, USA
| | - Cody Floerchinger
- Department of Chemistry, Montana State University, Bozeman, MT 59717, USA
| | - Joe Sears
- Center for Lab Services/RJ Lee Group, 2710 North 20th Ave, Pasco, WA 99301, USA
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167
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Liu SY, Lin JQ, Wu HL, Wang CC, Huang SJ, Luo YF, Sun JH, Zhou JX, Yan SJ, He JG, Wang J, He ZM. Bisulfite sequencing reveals that Aspergillus flavus holds a hollow in DNA methylation. PLoS One 2012; 7:e30349. [PMID: 22276181 PMCID: PMC3262820 DOI: 10.1371/journal.pone.0030349] [Citation(s) in RCA: 50] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2011] [Accepted: 12/14/2011] [Indexed: 12/12/2022] Open
Abstract
Aspergillus flavus first gained scientific attention for its production of aflatoxin. The underlying regulation of aflatoxin biosynthesis has been serving as a theoretical model for biosynthesis of other microbial secondary metabolites. Nevertheless, for several decades, the DNA methylation status, one of the important epigenomic modifications involved in gene regulation, in A. flavus remains to be controversial. Here, we applied bisulfite sequencing in conjunction with a biological replicate strategy to investigate the DNA methylation profiling of A. flavus genome. Both the bisulfite sequencing data and the methylome comparisons with other fungi confirm that the DNA methylation level of this fungus is negligible. Further investigation into the DNA methyltransferase of Aspergillus uncovers its close relationship with RID-like enzymes as well as its divergence with the methyltransferase of species with validated DNA methylation. The lack of repeat contents of the A. flavus' genome and the high RIP-index of the small amount of remanent repeat potentially support our speculation that DNA methylation may be absent in A. flavus or that it may possess de novo DNA methylation which occurs very transiently during the obscure sexual stage of this fungal species. This work contributes to our understanding on the DNA methylation status of A. flavus, as well as reinforces our views on the DNA methylation in fungal species. In addition, our strategy of applying bisulfite sequencing to DNA methylation detection in species with low DNA methylation may serve as a reference for later scientific investigations in other hypomethylated species.
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Affiliation(s)
- Si-Yang Liu
- MOE Key Laboratory of Aquatic Product Safety, Key Laboratory of Gene Engineering of the Ministry of Education, School of Life Sciences, Sun Yat-sen University, Guangzhou, China
- BGI-Shenzhen, Shenzhen, China
| | - Jian-Qing Lin
- MOE Key Laboratory of Aquatic Product Safety, Key Laboratory of Gene Engineering of the Ministry of Education, School of Life Sciences, Sun Yat-sen University, Guangzhou, China
| | | | - Cheng-Cheng Wang
- MOE Key Laboratory of Aquatic Product Safety, Key Laboratory of Gene Engineering of the Ministry of Education, School of Life Sciences, Sun Yat-sen University, Guangzhou, China
| | | | - Yan-Feng Luo
- MOE Key Laboratory of Aquatic Product Safety, Key Laboratory of Gene Engineering of the Ministry of Education, School of Life Sciences, Sun Yat-sen University, Guangzhou, China
| | | | - Jian-Xiang Zhou
- MOE Key Laboratory of Aquatic Product Safety, Key Laboratory of Gene Engineering of the Ministry of Education, School of Life Sciences, Sun Yat-sen University, Guangzhou, China
| | | | - Jian-Guo He
- MOE Key Laboratory of Aquatic Product Safety, Key Laboratory of Gene Engineering of the Ministry of Education, School of Life Sciences, Sun Yat-sen University, Guangzhou, China
- * E-mail: (J-GH); (JW); (Z-MH)
| | - Jun Wang
- BGI-Shenzhen, Shenzhen, China
- * E-mail: (J-GH); (JW); (Z-MH)
| | - Zhu-Mei He
- MOE Key Laboratory of Aquatic Product Safety, Key Laboratory of Gene Engineering of the Ministry of Education, School of Life Sciences, Sun Yat-sen University, Guangzhou, China
- * E-mail: (J-GH); (JW); (Z-MH)
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168
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Frisvad JC. Media and growth conditions for induction of secondary metabolite production. Methods Mol Biol 2012; 944:47-58. [PMID: 23065607 DOI: 10.1007/978-1-62703-122-6_3] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
Growth media and incubation conditions have a very strong influence of secondary metabolite production. There is no consensus on which media are the optimal for metabolite production, but a series of useful and effective media and incubation conditions have been listed here. Chemically well-defined media are suited for biochemical studies, but in order to get chemical diversity expressed in filamentous fungi, sources rich in amino acids, vitamins, and trace metals have to be added, such as yeast extract and oatmeal. A battery of solid agar media is recommended for exploration of chemical diversity as agar plug samples are easily analyzed to get an optimal representation of the qualitative secondary metabolome. Standard incubation for a week at 25°C in darkness is recommended, but optimal conditions have to be modified depending on the ecology and physiology of different filamentous fungi.
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Affiliation(s)
- Jens C Frisvad
- Department of Systems Biology, Center for Microbial Biotechnology, Technical University of Denmark, Kongens Lyngby, Denmark.
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169
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Lim FY, Sanchez JF, Wang CC, Keller NP. Toward awakening cryptic secondary metabolite gene clusters in filamentous fungi. Methods Enzymol 2012; 517:303-24. [PMID: 23084945 PMCID: PMC3703436 DOI: 10.1016/b978-0-12-404634-4.00015-2] [Citation(s) in RCA: 93] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
Abstract
Mining for novel natural compounds is of eminent importance owing to the continuous need for new pharmaceuticals. Filamentous fungi are historically known to harbor the genetic capacity for an arsenal of natural compounds, both beneficial and detrimental to humans. The majority of these metabolites are still cryptic or silent under standard laboratory culture conditions. Mining for these cryptic natural products can be an excellent source for identifying new compound classes. Capitalizing on the current knowledge on how secondary metabolite gene clusters are regulated has allowed the research community to unlock many hidden fungal treasures, as described in this chapter.
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Affiliation(s)
- Fang Yun Lim
- Department of Medical Microbiology and Immunology, University of Wisconsin, Madison, Wisconsin, USA
| | - James F. Sanchez
- Department of Pharmacology and Pharmaceutical Sciences, University of Southern California, School of Pharmacy, Los Angeles, California, USA
| | - Clay C.C. Wang
- Department of Pharmacology and Pharmaceutical Sciences, University of Southern California, School of Pharmacy, Los Angeles, California, USA,Department of Chemistry, University of Southern California, College of Letters, Arts, and Sciences, Los Angeles, California, USA
| | - Nancy P. Keller
- Department of Medical Microbiology and Immunology, University of Wisconsin, Madison, Wisconsin, USA,Corresponding author:
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170
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Mukherjee PK, Horwitz BA, Kenerley CM. Secondary metabolism in Trichoderma – a genomic perspective. Microbiology (Reading) 2012; 158:35-45. [DOI: 10.1099/mic.0.053629-0] [Citation(s) in RCA: 226] [Impact Index Per Article: 18.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023] Open
Affiliation(s)
- Prasun K. Mukherjee
- Nuclear Agriculture and Biotechnology Division, Bhabha Atomic Research Centre, Trombay, Mumbai 400085, India
| | - Benjamin A. Horwitz
- Department of Biology, Technion – Israel Institute of Technology, Haifa 32000, Israel
| | - Charles M. Kenerley
- Department of Plant Pathology and Microbiology, Texas A&M University, College Station, TX, USA
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171
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Gacek A, Strauss J. The chromatin code of fungal secondary metabolite gene clusters. Appl Microbiol Biotechnol 2012; 95:1389-404. [PMID: 22814413 PMCID: PMC3427479 DOI: 10.1007/s00253-012-4208-8] [Citation(s) in RCA: 111] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2012] [Revised: 05/24/2012] [Accepted: 05/24/2012] [Indexed: 01/07/2023]
Abstract
Secondary metabolite biosynthesis genes in fungi are usually physically linked and organized in large gene clusters. The physical linkage of genes involved in the same biosynthetic pathway minimizes the amount of regulatory steps necessary to regulate the biosynthetic machinery and thereby contributes to physiological economization. Regulation by chromatin accessibility is a proficient molecular mechanism to synchronize transcriptional activity of large genomic regions. Chromatin regulation largely depends on DNA and histone modifications and the histone code hypothesis proposes that a certain combination of modifications, such as acetylation, methylation or phosphorylation, is needed to perform a specific task. A number of reports from several laboratories recently demonstrated that fungal secondary metabolite (SM) biosynthesis clusters are controlled by chromatin-based mechanisms and histone acetyltransferases, deacetylases, methyltransferases, and proteins involved in heterochromatin formation were found to be involved. This led to the proposal that establishment of repressive chromatin domains over fungal SM clusters under primary metabolic conditions is a conserved mechanism that prevents SM production during the active growth phase. Consequently, transcriptional activation of SM clusters requires reprogramming of the chromatin landscape and replacement of repressive histone marks by activating marks. This review summarizes recent advances in our understanding of chromatin-based SM cluster regulation and highlights some of the open questions that remain to be answered before we can draw a more comprehensive picture.
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Affiliation(s)
- Agnieszka Gacek
- Fungal Genetics and Genomics Unit, Department of Applied Genetics and Cell Biology, University of Natural Resources and Life Science, University and Research Center—Campus Tulln, 3430 Tulln/Donau, Austria
| | - Joseph Strauss
- Fungal Genetics and Genomics Unit, Department of Applied Genetics and Cell Biology, University of Natural Resources and Life Science, University and Research Center—Campus Tulln, 3430 Tulln/Donau, Austria ,Health and Environment Department, Austrian Institute of Technology, University and Research Center—Campus Tulln, 3430 Tulln/Donau, Austria
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172
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Imhoff JF, Labes A, Wiese J. Bio-mining the microbial treasures of the ocean: New natural products. Biotechnol Adv 2011; 29:468-82. [DOI: 10.1016/j.biotechadv.2011.03.001] [Citation(s) in RCA: 152] [Impact Index Per Article: 11.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2011] [Revised: 02/25/2011] [Accepted: 03/09/2011] [Indexed: 01/10/2023]
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173
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Schmitt EK, Moore CM, Krastel P, Petersen F. Natural products as catalysts for innovation: a pharmaceutical industry perspective. Curr Opin Chem Biol 2011; 15:497-504. [DOI: 10.1016/j.cbpa.2011.05.018] [Citation(s) in RCA: 43] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2011] [Revised: 05/11/2011] [Accepted: 05/23/2011] [Indexed: 12/21/2022]
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174
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Yin W, Keller NP. Transcriptional regulatory elements in fungal secondary metabolism. J Microbiol 2011; 49:329-39. [PMID: 21717315 DOI: 10.1007/s12275-011-1009-1] [Citation(s) in RCA: 114] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2011] [Accepted: 03/15/2011] [Indexed: 01/19/2023]
Abstract
Filamentous fungi produce a variety of secondary metabolites of diverse beneficial and detrimental activities to humankind. The genes required for a given secondary metabolite are typically arranged in a gene cluster. There is considerable evidence that secondary metabolite gene regulation is, in part, by transcriptional control through hierarchical levels of transcriptional regulatory elements involved in secondary metabolite cluster regulation. Identification of elements regulating secondary metabolism could potentially provide a means of increasing production of beneficial metabolites, decreasing production of detrimental metabolites, aid in the identification of 'silent' natural products and also contribute to a broader understanding of molecular mechanisms by which secondary metabolites are produced. This review summarizes regulation of secondary metabolism associated with transcriptional regulatory elements from a broad view as well as the tremendous advances in discovery of cryptic or novel secondary metabolites by genomic mining.
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Affiliation(s)
- Wenbing Yin
- Department of Medical Microbiology and Immunology, University of Wisconsin-Madison, Madison, WI 53706, USA
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175
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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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176
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Giles SS, Soukup AA, Lauer C, Shaaban M, Lin A, Oakley BR, Wang CCC, Keller NP. Cryptic Aspergillus nidulans antimicrobials. Appl Environ Microbiol 2011; 77:3669-75. [PMID: 21478304 PMCID: PMC3127626 DOI: 10.1128/aem.02000-10] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2010] [Accepted: 03/16/2011] [Indexed: 01/15/2023] Open
Abstract
Secondary metabolite (SM) production by fungi is hypothesized to provide some fitness attribute for the producing organisms. However, most SM clusters are "silent" when fungi are grown in traditional laboratory settings, and it is difficult to ascertain any function or activity of these SM cluster products. Recently, the creation of a chromatin remodeling mutant in Aspergillus nidulans induced activation of several cryptic SM gene clusters. Systematic testing of nine purified metabolites from this mutant identified an emodin derivate with efficacy against both human fungal pathogens (inhibiting both spore germination and hyphal growth) and several bacteria. The ability of catalase to diminish this antimicrobial activity implicates reactive oxygen species generation, specifically, the generation of hydrogen peroxide, as the mechanism of emodin hydroxyl activity.
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Affiliation(s)
- Steve S. Giles
- Department of Medical Microbiology and Immunology, University of Wisconsin—Madison, Madison, Wisconsin
| | | | - Carrie Lauer
- Department of Medical Microbiology and Immunology, University of Wisconsin—Madison, Madison, Wisconsin
| | - Mona Shaaban
- Department of Medical Microbiology and Immunology, University of Wisconsin—Madison, Madison, Wisconsin
- Microbiology and Immunology, Faculty of Pharmacy, Mansoura University, Mansoura, Egypt
| | - Alexander Lin
- Department of Pharmacology and Pharmaceutical Sciences
| | - Berl R. Oakley
- Department of Molecular Biosciences, University of Kansas, Lawrence, Kansas
| | - Clay C. C. Wang
- Department of Pharmacology and Pharmaceutical Sciences
- Department of Chemistry, University of Southern California, 1985 Zonal Avenue, Los Angeles, California 90033
| | - Nancy P. Keller
- Department of Medical Microbiology and Immunology, University of Wisconsin—Madison, Madison, Wisconsin
- Department of Bacteriology, University of Wisconsin—Madison, Madison, Wisconsin
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177
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Chu HY, Wegel E, Osbourn A. From hormones to secondary metabolism: the emergence of metabolic gene clusters in plants. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2011; 66:66-79. [PMID: 21443624 DOI: 10.1111/j.1365-313x.2011.04503.x] [Citation(s) in RCA: 62] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/20/2023]
Abstract
Gene clusters for the synthesis of secondary metabolites are a common feature of microbial genomes. Well-known examples include clusters for the synthesis of antibiotics in actinomycetes, and also for the synthesis of antibiotics and toxins in filamentous fungi. Until recently it was thought that genes for plant metabolic pathways were not clustered, and this is certainly true in many cases; however, five plant secondary metabolic gene clusters have now been discovered, all of them implicated in synthesis of defence compounds. An obvious assumption might be that these eukaryotic gene clusters have arisen by horizontal gene transfer from microbes, but there is compelling evidence to indicate that this is not the case. This raises intriguing questions about how widespread such clusters are, what the significance of clustering is, why genes for some metabolic pathways are clustered and those for others are not, and how these clusters form. In answering these questions we may hope to learn more about mechanisms of genome plasticity and adaptive evolution in plants. It is noteworthy that for the five plant secondary metabolic gene clusters reported so far, the enzymes for the first committed steps all appear to have been recruited directly or indirectly from primary metabolic pathways involved in hormone synthesis. This may or may not turn out to be a common feature of plant secondary metabolic gene clusters as new clusters emerge.
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Affiliation(s)
- Hoi Yee Chu
- Department of Metabolic Biology, John Innes Centre, Colney Lane, Norwich NR4 7UH, UK
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178
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179
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Multifactorial induction of an orphan PKS-NRPS gene cluster in Aspergillus terreus. ACTA ACUST UNITED AC 2011; 18:198-209. [PMID: 21236704 DOI: 10.1016/j.chembiol.2010.12.011] [Citation(s) in RCA: 77] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2010] [Revised: 11/16/2010] [Accepted: 12/13/2010] [Indexed: 12/26/2022]
Abstract
Mining the genome of the pathogenic fungus Aspergillus terreus revealed the presence of an orphan polyketide-nonribosomal-peptide synthetase (PKS-NRPS) gene cluster. Induced expression of the transcriptional activator gene adjacent to the PKS-NRPS gene was not sufficient for the activation of the silent pathway. Monitoring gene expression, metabolic profiling, and using a lacZ reporter strain allowed for the systematic investigation of physiological conditions that eventually led to the discovery of isoflavipucine and dihydroisoflavipucine. Phytotoxin formation is only activated in the presence of certain amino acids, stimulated at alkaline pH, but strictly repressed in the presence of glucose. Global carbon catabolite repression by CreA cannot be abolished by positive-acting factors such as PacC and overrides the pathway activator. Gene inactivation and stable isotope labeling experiments unveiled the molecular basis for flavipucine/fruit rot toxin biosynthesis.
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180
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Strauss J, Reyes-Dominguez Y. Regulation of secondary metabolism by chromatin structure and epigenetic codes. Fungal Genet Biol 2011; 48:62-9. [PMID: 20659575 PMCID: PMC3935439 DOI: 10.1016/j.fgb.2010.07.009] [Citation(s) in RCA: 140] [Impact Index Per Article: 10.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2010] [Revised: 07/02/2010] [Accepted: 07/19/2010] [Indexed: 01/07/2023]
Abstract
Chromatin, composed of DNA wrapped around an octamer of histones, is the relevant substrate for all genetic processes in eukaryotic nuclei. Changes in chromatin structure are associated with the activation and silencing of gene transcription and reversible post-translational modifications of histones are now known to direct chromatin structure transitions. Recent studies in several fungal species have identified a chromatin-based regulation of secondary metabolism (SM) gene clusters representing an upper-hierarchical level for the coordinated control of large chromosomal elements. Regulation by chromatin transition processes provides a mechanistic model to explain how different SM clusters located at dispersed genomic regions can be simultaneously silenced during primary metabolism. Activation of SM clusters has been shown to be associated with increased acetylation of histones H3 and H4 and, consequently, inhibition of histone de-acetylase activities also leads to increased production of secondary metabolites. New findings suggest that SM clusters are silenced by heterochromatic histone marks and that the "closed" heterochromatic structures are reversed during SM activation. This process is mediated by the conserved activator of SM, LaeA. Despite the increase in knowledge about these processes, much remains to be learned from chromatin-level regulation of SM. For example, which proteins "position" the chromatin restructuring signal onto SM clusters or how exactly LaeA works to mediate the low level of heterochromatic marks inside different clusters remain open questions. Answers to these and other chromatin-related questions would certainly complete our understanding of SM gene regulation and signaling and, because for many predicted SM clusters corresponding products have not been identified so far, anti-silencing strategies would open new ways for the identification of novel bioactive substances.
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Affiliation(s)
- Joseph Strauss
- Corresponding author. Fax: +43 1 36006 6392. (J. Strauss)
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181
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Abstract
Aspergillus flavus is saprophytic soil fungus that infects and contaminates preharvest and postharvest seed crops with the carcinogenic secondary metabolite aflatoxin. The fungus is also an opportunistic animal and human pathogen causing aspergillosis diseases with incidence increasing in the immunocompromised population. Whole genome sequences of A. flavus have been released and reveal 55 secondary metabolite clusters that are regulated by different environmental regimes and the global secondary metabolite regulators LaeA and VeA. Characteristics of A. flavus associated with pathogenicity and niche specialization include secondary metabolite production, enzyme elaboration, and a sophisticated oxylipin host crosstalk associated with a quorum-like development program. One of the more promising strategies in field control involves the use of atoxic strains of A. flavus in competitive exclusion studies. In this review, we discuss A. flavus as an agricultural and medical threat and summarize recent research advances in genomics, elucidation of parameters of pathogenicity, and control measures.
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Affiliation(s)
- Saori Amaike
- Department of Plant Pathology, University of Wisconsin, Madison, Wisconsin 53706, USA
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182
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Pollier J, Moses T, Goossens A. Combinatorial biosynthesis in plants: A (p)review on its potential and future exploitation. Nat Prod Rep 2011; 28:1897-916. [DOI: 10.1039/c1np00049g] [Citation(s) in RCA: 50] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
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183
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Vervoort HC, Drašković M, Crews P. Histone deacetylase inhibitors as a tool to up-regulate new fungal biosynthetic products: isolation of EGM-556, a cyclodepsipeptide, from Microascus sp. Org Lett 2010; 13:410-3. [PMID: 21174394 DOI: 10.1021/ol1027199] [Citation(s) in RCA: 48] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
Abstract
The histone deacetylase (HDAC) inhibitor suberoylanilide hydroxamic acid (SAHA) was used to turn on the biosynthesis of EGM-556, a new cyclodepsipeptide of hybrid biosynthetic origin, isolated from the Floridian marine sediment-derived fungus Microascus sp. The absolute configurations of three chiral centers were determined by Marfey's derivatization. EGM-556 represents one of the few examples in which silent biosynthetic genes, encoding a new secondary metabolite, were activated by means of epigenetic manipulation of the fungal metabolome.
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Affiliation(s)
- Hélène C Vervoort
- Department of Chemistry and Biochemistry, University of California, Santa Cruz, California 95064, USA
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184
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Chiang YM, Meyer KM, Praseuth M, Baker SE, Bruno KS, Wang CCC. Characterization of a polyketide synthase in Aspergillus niger whose product is a precursor for both dihydroxynaphthalene (DHN) melanin and naphtho-γ-pyrone. Fungal Genet Biol 2010; 48:430-7. [PMID: 21176790 DOI: 10.1016/j.fgb.2010.12.001] [Citation(s) in RCA: 63] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2010] [Revised: 12/03/2010] [Accepted: 12/06/2010] [Indexed: 10/18/2022]
Abstract
The genome sequencing of the fungus Aspergillus niger uncovered a large cache of genes encoding enzymes thought to be involved in the production of secondary metabolites yet to be identified. Identification and structural characterization of many of these predicted secondary metabolites are hampered by their low concentration relative to the known A. niger metabolites such as the naphtho-γ-pyrone family of polyketides. We deleted a non-reducing PKS gene in A. niger strain ATCC 11414, a daughter strain of A. niger ATCC strain 1015 whose genome was sequenced by the DOE Joint Genome Institute. This PKS encoding gene we name albA is a predicted ortholog of alb1 from Aspergillus fumigatus which is responsible for production of the naphtho-γ-pyrone precursor for the 1,8-dihydroxynaphthalene (DHN) melanin/spore pigment. Our results show that the A. nigeralbA PKS is responsible for both the production of the spore pigment precursor and a family of naphtho-γ-pyrones commonly found in significant quantity in A. niger culture extracts. The generation of an A. niger strain devoid of naphtho-γ-pyrones will greatly facilitate the elucidation of cryptic biosynthetic pathways in this organism.
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Affiliation(s)
- Yi-Ming Chiang
- Graduate Institute of Pharmaceutical Science, Chia Nan University of Pharmacy and Science, Tainan 71710, Taiwan, ROC
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185
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Wu QX, Crews MS, Draskovic M, Sohn J, Johnson TA, Tenney K, Valeriote FA, Yao XJ, Bjeldanes LF, Crews P. Azonazine, a novel dipeptide from a Hawaiian marine sediment-derived fungus, Aspergillus insulicola. Org Lett 2010; 12:4458-61. [PMID: 20866076 PMCID: PMC2953366 DOI: 10.1021/ol101396n] [Citation(s) in RCA: 97] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Azonazine, a unique hexacyclic dipeptide, was isolated from a Hawaiian marine sediment-derived fungus eventually identified as Aspergillus insulicola. Its absolute configuration, 2R,10R,11S,19R, was established using NMR, HRESIMS, and CD data plus insights derived from molecular models. A possible route for its biogenesis is proposed, and biological properties were explored against cancer cell lines and in an NFκB inhibition assay.
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Affiliation(s)
- Quan-Xiang Wu
- State Key Laboratory of Applied Organic Chemistry, College of Chemistry and Chemical Engineering, Lanzhou University, Lanzhou 730000, China
- Department of Chemistry and Biochemistry, University of California Santa Cruz, CA 95064
| | - Mitchell S. Crews
- Department of Chemistry and Biochemistry, University of California Santa Cruz, CA 95064
| | - Marija Draskovic
- Department of Chemistry and Biochemistry, University of California Santa Cruz, CA 95064
| | - Johann Sohn
- Department of Nutritional Sciences and Toxicology, University of California Berkeley, CA 94720
| | - Tyler A. Johnson
- Department of Chemistry and Biochemistry, University of California Santa Cruz, CA 95064
- Department of Nutritional Sciences and Toxicology, University of California Berkeley, CA 94720
| | - Karen Tenney
- Department of Chemistry and Biochemistry, University of California Santa Cruz, CA 95064
| | | | - Xiao-Jun Yao
- State Key Laboratory of Applied Organic Chemistry, College of Chemistry and Chemical Engineering, Lanzhou University, Lanzhou 730000, China
| | - Leonard F. Bjeldanes
- Department of Nutritional Sciences and Toxicology, University of California Berkeley, CA 94720
| | - Phillip Crews
- Department of Chemistry and Biochemistry, University of California Santa Cruz, CA 95064
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186
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Osbourn A. Gene clusters for secondary metabolic pathways: an emerging theme in plant biology. PLANT PHYSIOLOGY 2010; 154:531-5. [PMID: 20921179 PMCID: PMC2949040 DOI: 10.1104/pp.110.161315] [Citation(s) in RCA: 72] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/16/2010] [Accepted: 07/02/2010] [Indexed: 05/18/2023]
Affiliation(s)
- Anne Osbourn
- Department of Metabolic Biology, John Innes Centre, Norwich, United Kingdom.
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187
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Osbourn A. Secondary metabolic gene clusters: evolutionary toolkits for chemical innovation. Trends Genet 2010; 26:449-57. [DOI: 10.1016/j.tig.2010.07.001] [Citation(s) in RCA: 219] [Impact Index Per Article: 15.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2010] [Revised: 07/03/2010] [Accepted: 07/13/2010] [Indexed: 11/30/2022]
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188
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Llarrull LI, Testero SA, Fisher JF, Mobashery S. The future of the β-lactams. Curr Opin Microbiol 2010; 13:551-7. [PMID: 20888287 DOI: 10.1016/j.mib.2010.09.008] [Citation(s) in RCA: 135] [Impact Index Per Article: 9.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2010] [Revised: 09/08/2010] [Accepted: 09/09/2010] [Indexed: 11/15/2022]
Abstract
In the 80 years since their discovery the β-lactam antibiotics have progressed through structural generations, each in response to the progressive evolution of bacterial resistance mechanisms. The generational progression was driven by the ingenious, but largely empirical, manipulation of structure by medicinal chemists. Nonetheless, the true creative force in these efforts was Nature, and as the discovery of new β-lactams from Nature has atrophied while at the same time multi-resistant and opportunistic bacterial pathogens have burgeoned, the time for empirical drug discovery has passed. We concisely summarize recent developments with respect to bacterial resistance, the identity of the new β-lactams, and the emerging non-empirical strategies that will ensure that this incredible class of antibiotics has a future.
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Affiliation(s)
- Leticia I Llarrull
- Department of Chemistry and Biochemistry, University of Notre Dame, Notre Dame, IN 46556, USA
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189
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Garvey GS, Keller NP. Fungal Secondary Metabolites and Their Fundamental Roles in Human Mycoses. CURRENT FUNGAL INFECTION REPORTS 2010. [DOI: 10.1007/s12281-010-0032-8] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2023]
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190
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Heneghan MN, Yakasai AA, Halo LM, Song Z, Bailey AM, Simpson TJ, Cox RJ, Lazarus CM. First Heterologous Reconstruction of a Complete Functional Fungal Biosynthetic Multigene Cluster. Chembiochem 2010; 11:1508-12. [DOI: 10.1002/cbic.201000259] [Citation(s) in RCA: 85] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
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191
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Palmer JM, Keller NP. Secondary metabolism in fungi: does chromosomal location matter? Curr Opin Microbiol 2010; 13:431-6. [PMID: 20627806 DOI: 10.1016/j.mib.2010.04.008] [Citation(s) in RCA: 152] [Impact Index Per Article: 10.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2010] [Revised: 04/22/2010] [Accepted: 04/27/2010] [Indexed: 10/19/2022]
Abstract
Filamentous fungi produce a vast array of small molecules called secondary metabolites, which include toxins as well as antibiotics. Coregulated gene clusters are the hallmark of fungal secondary metabolism, and there is a growing body of evidence that suggests regulation is at least, in part, epigenetic. Chromatin-level control is involved in several silencing phenomena observed in fungi including mating type switching, telomere position effect (TPE), silencing of ribosomal DNA, regulation of genes involved in nutrient acquisition, and as presented here, secondary metabolite cluster expression. These phenomena are tied together by the underlying theme of chromosomal location, often near centromeres and telomeres, where facultative heterochromatin plays a role in transcription. Secondary metabolite gene clusters are often located subtelomerically and recently it has been shown that proteins involved in chromatin remodeling, such as LaeA, ClrD, CclA, and HepA mediate cluster regulation.
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Affiliation(s)
- Jonathan M Palmer
- Plant Pathology Department, University of Wisconsin, Madison, WI 53706, USA
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192
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Wang X, Filho JGS, Hoover AR, King JB, Ellis TK, Powell DR, Cichewicz RH. Chemical epigenetics alters the secondary metabolite composition of guttate excreted by an atlantic-forest-soil-derived Penicillium citreonigrum. JOURNAL OF NATURAL PRODUCTS 2010; 73:942-948. [PMID: 20450206 PMCID: PMC2878378 DOI: 10.1021/np100142h] [Citation(s) in RCA: 123] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/26/2023]
Abstract
Chemical epigenetic manipulation of Penicillium citreonigrum led to profound changes in the secondary metabolite profile of its guttate. While guttate from control cultures exhibited a relatively simple assemblage of secondary metabolites, the guttate collected from cultures treated with 50 muM 5-azacytidine (a DNA methyltransferase inhibitor) was highly enriched in compounds representing at least three distinct biosynthetic families. The metabolites obtained from the fungus included six azaphilones (sclerotiorin (1), sclerotioramine (6), ochrephilone (2), dechloroisochromophilone III (3), dechloroisochromophilone IV (4), and 6-((3E,5E)-5,7-dimethyl-2-methylenenona-3,5-dienyl)-2,4-dihydroxy-3-methylbenzaldehyde (5)), pencolide (7), and two new meroterpenes (atlantinones A and B (9 and 10, respectively)). While pencolide was detected in the exudates of both control and 5-azacytidine-treated cultures, all of the other natural products were found exclusively in the guttates of the epigenetically modified fungus. All of the metabolites from the P. citreonigrum guttate were tested for antimicrobial activity in a disk diffusion assay. Both sclerotiorin and sclerotioramine caused modest inhibition of Staphylococcus epidermidis growth; however, only sclerotioramine was active against a panel of Candida strains.
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193
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Harvey AL, Clark RL, Mackay SP, Johnston BF. Current strategies for drug discovery through natural products. Expert Opin Drug Discov 2010; 5:559-68. [PMID: 22823167 DOI: 10.1517/17460441.2010.488263] [Citation(s) in RCA: 61] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
Abstract
IMPORTANCE TO THE FIELD Natural products are the most consistently successful source of drug leads, both historically and currently. Despite this, the use of natural products in industrial drug discovery has fallen out of favour. Natural products are likely to continue to be sources of new commercially viable drug leads because the chemical novelty associated with natural products is higher than that of any other source: this is particularly important when searching for lead molecules against newly discovered targets for which there are no known small molecule leads. Areas to be covered: Current drug discovery strategies involving natural products are described in three sections: developments from traditionally used medicines, random testing of natural compounds on biological assays and use of virtual screening techniques with structures of natural products. WHAT THE READER WILL GAIN The reader will gain an insight into the potential for natural products in current drug discovery paradigms, particularly in the value of using natural products in virtual screening approaches. TAKE HOME MESSAGE Drug discovery would be enriched if fuller use was made of the chemistry of natural products.
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Affiliation(s)
- Alan L Harvey
- University of Strathclyde, Strathclyde Institute of Pharmacy and Biomedical Sciences, 27 Taylor Street, Glasgow G4 0NR, UK +44 141 553 4155 ; +44 141 552 8376 ;
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Chiang YM, Oakley BR, Keller NP, Wang CCC. Unraveling polyketide synthesis in members of the genus Aspergillus. Appl Microbiol Biotechnol 2010; 86:1719-36. [PMID: 20361326 DOI: 10.1007/s00253-010-2525-3] [Citation(s) in RCA: 67] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2010] [Revised: 02/22/2010] [Accepted: 02/24/2010] [Indexed: 12/16/2022]
Abstract
Aspergillus species have the ability to produce a wide range of secondary metabolites including polyketides that are generated by multi-domain polyketide synthases (PKSs). Recent biochemical studies using dissected single or multiple domains from PKSs have provided deep insight into how these PKSs control the structural outcome. Moreover, the recent genome sequencing of several species has greatly facilitated the understanding of the biosynthetic pathways for these secondary metabolites. In this review, we will highlight the current knowledge regarding polyketide biosynthesis in Aspergillus based on the domain architecture of non-reducing, highly reducing, and partially reducing PKSs, and PKS-non-ribosomal peptide synthetases.
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Affiliation(s)
- Yi-Ming Chiang
- Graduate Institute of Pharmaceutical Science, Chia Nan University of Pharmacy and Science, Tainan, 71710, Taiwan, Republic of China
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Archer T, Beninger RJ, Palomo T, Kostrzewa RM. Epigenetics and biomarkers in the staging of neuropsychiatric disorders. Neurotox Res 2010; 18:347-66. [PMID: 20237880 DOI: 10.1007/s12640-010-9163-5] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2010] [Revised: 01/29/2010] [Accepted: 02/18/2010] [Indexed: 01/05/2023]
Abstract
Epigenetics, or alterations in the phenotype or gene expression due to mechanisms other than changes in the underlying DNA sequence, reflects the sensitivity and responsiveness of human and animal brains in constantly varying circumstances regulating gene expression profiles that define the biomarkers and present the ultimate phenotypical outcomes, such as cognition and emotion. Epigenetics is associated with functionally relevant alterations to the genome in such a fashion that under the particular conditions of early, adolescent, and adult life, environmental signals may activate intracellular pathways that remodel the "epigenome," triggering changes in gene expression and neural function. Thus, genetic influences in neuropsychiatric disorders that are subject to clinical staging, epigenetics in schizophrenia, epigenetic considerations in the expression of sensorimotor gating resulting from disease conditions, biomarkers of drug use and addiction, current notions on the role of dopamine in schizophrenia spectrum disorders, and the discrete interactions of biomarkers in persistent memory were to greater or lesser extents reflected upon. The relative contributions of endophenotypes and epistasis for mediating epigenetic phenomena and the outcomes as observed in the analysis of biomarkers appear to offer a multitude of interactive combinations to further complicate the labyrinthine machinations of diagnosis, intervention, and prognosis.
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Affiliation(s)
- Trevor Archer
- Department of Psychology, University of Gothenburg, Box 500, 405 30, Gothenburg, Sweden.
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Molnár I, Gibson DM, Krasnoff SB. Secondary metabolites from entomopathogenic Hypocrealean fungi. Nat Prod Rep 2010; 27:1241-75. [DOI: 10.1039/c001459c] [Citation(s) in RCA: 166] [Impact Index Per Article: 11.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023]
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