1
|
Zhao P, Cao S, Wang J, Lin J, Zhang Y, Liu C, Liu H, Zhang Q, Wang M, Meng Y, Yin X, Qi J, Zhang L, Xia X. Activation of secondary metabolite gene clusters in Chaetomium olivaceum via the deletion of a histone deacetylase. Appl Microbiol Biotechnol 2024; 108:332. [PMID: 38734756 PMCID: PMC11088548 DOI: 10.1007/s00253-024-13173-8] [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: 01/09/2024] [Revised: 04/23/2024] [Accepted: 05/04/2024] [Indexed: 05/13/2024]
Abstract
Histone acetylation modifications in filamentous fungi play a crucial role in epigenetic gene regulation and are closely linked to the transcription of secondary metabolite (SM) biosynthetic gene clusters (BGCs). Histone deacetylases (HDACs) play a pivotal role in determining the extent of histone acetylation modifications and act as triggers for the expression activity of target BGCs. The genus Chaetomium is widely recognized as a rich source of novel and bioactive SMs. Deletion of a class I HDAC gene of Chaetomium olivaceum SD-80A, g7489, induces a substantial pleiotropic effect on the expression of SM BGCs. The C. olivaceum SD-80A ∆g7489 strain exhibited significant changes in morphology, sporulation ability, and secondary metabolic profile, resulting in the emergence of new compound peaks. Notably, three polyketides (A1-A3) and one asterriquinone (A4) were isolated from this mutant strain. Furthermore, our study explored the BGCs of A1-A4, confirming the function of two polyketide synthases (PKSs). Collectively, our findings highlight the promising potential of molecular epigenetic approaches for the elucidation of novel active compounds and their biosynthetic elements in Chaetomium species. This finding holds great significance for the exploration and utilization of Chaetomium resources. KEY POINTS: • Deletion of a class I histone deacetylase activated secondary metabolite gene clusters. • Three polyketides and one asterriquinone were isolated from HDAC deleted strain. • Two different PKSs were reported in C. olivaceum SD-80A.
Collapse
Affiliation(s)
- Peipei Zhao
- Biology Institute, Qilu University of Technology (Shandong Academy of Sciences), Jinan, 250103, Shandong, China
| | - Shengling Cao
- Biology Institute, Qilu University of Technology (Shandong Academy of Sciences), Jinan, 250103, Shandong, China
| | - Jiahui Wang
- Biology Institute, Qilu University of Technology (Shandong Academy of Sciences), Jinan, 250103, Shandong, China
| | - Jiaying Lin
- Biology Institute, Qilu University of Technology (Shandong Academy of Sciences), Jinan, 250103, Shandong, China
| | - Yunzeng Zhang
- Department of Thoracic Surgery, Shandong Public Health Clinical Center, Jinan, 250013, Shandong, China
| | - Chengwei Liu
- Key Laboratory for Enzyme and Enzyme-Like Material Engineering of Heilongjiang, College of Life Science, Northeast Forestry University, Harbin, 150040, Heilongjiang, China
| | - Hairong Liu
- Biology Institute, Qilu University of Technology (Shandong Academy of Sciences), Jinan, 250103, Shandong, China
| | - Qingqing Zhang
- Biology Institute, Qilu University of Technology (Shandong Academy of Sciences), Jinan, 250103, Shandong, China
| | - Mengmeng Wang
- Biology Institute, Qilu University of Technology (Shandong Academy of Sciences), Jinan, 250103, Shandong, China
| | - Yiwei Meng
- Biology Institute, Qilu University of Technology (Shandong Academy of Sciences), Jinan, 250103, Shandong, China
| | - Xin Yin
- Biology Institute, Qilu University of Technology (Shandong Academy of Sciences), Jinan, 250103, Shandong, China
| | - Jun Qi
- Biology Institute, Qilu University of Technology (Shandong Academy of Sciences), Jinan, 250103, Shandong, China
| | - Lixin Zhang
- Biology Institute, Qilu University of Technology (Shandong Academy of Sciences), Jinan, 250103, Shandong, China
- State Key Laboratory of Bioreactor Engineering, School of Biotechnology, East China University of Science and Technology (ECUST), Shanghai, 200237, China
| | - Xuekui Xia
- Biology Institute, Qilu University of Technology (Shandong Academy of Sciences), Jinan, 250103, Shandong, China.
| |
Collapse
|
2
|
Deng L, Zhong M, Li Y, Hu G, Zhang C, Peng Q, Zhang Z, Fang J, Yu X. High hydrostatic pressure harnesses the biosynthesis of secondary metabolites via the regulation of polyketide synthesis genes of hadal sediment-derived fungi. Front Microbiol 2023; 14:1207252. [PMID: 37383634 PMCID: PMC10293889 DOI: 10.3389/fmicb.2023.1207252] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2023] [Accepted: 05/24/2023] [Indexed: 06/30/2023] Open
Abstract
Deep-sea fungi have evolved extreme environmental adaptation and possess huge biosynthetic potential of bioactive compounds. However, not much is known about the biosynthesis and regulation of secondary metabolites of deep-sea fungi under extreme environments. Here, we presented the isolation of 15 individual fungal strains from the sediments of the Mariana Trench, which were identified by internal transcribed spacer (ITS) sequence analysis as belonging to 8 different fungal species. High hydrostatic pressure (HHP) assays were performed to identify the piezo-tolerance of the hadal fungi. Among these fungi, Aspergillus sydowii SYX6 was selected as the representative due to the excellent tolerance of HHP and biosynthetic potential of antimicrobial compounds. Vegetative growth and sporulation of A. sydowii SYX6 were affected by HHP. Natural product analysis with different pressure conditions was also performed. Based on bioactivity-guided fractionation, diorcinol was purified and characterized as the bioactive compound, showing significant antimicrobial and antitumor activity. The core functional gene associated with the biosynthetic gene cluster (BGC) of diorcinol was identified in A. sydowii SYX6, named as AspksD. The expression of AspksD was apparently regulated by the HHP treatment, correlated with the regulation of diorcinol production. Based on the effect of the HHP tested here, high pressure affected the fungal development and metabolite production, as well as the expression level of biosynthetic genes which revealed the adaptive relationship between the metabolic pathway and the high-pressure environment at the molecular level.
Collapse
Affiliation(s)
- Ludan Deng
- Shanghai Engineering Research Center of Hadal Science and Technology, College of Marine Sciences, Shanghai Ocean University, Shanghai, China
| | - Maosheng Zhong
- Shanghai Engineering Research Center of Hadal Science and Technology, College of Marine Sciences, Shanghai Ocean University, Shanghai, China
| | - Yongqi Li
- Shanghai Engineering Research Center of Hadal Science and Technology, College of Marine Sciences, Shanghai Ocean University, Shanghai, China
| | - Guangzhao Hu
- Shanghai Engineering Research Center of Hadal Science and Technology, College of Marine Sciences, Shanghai Ocean University, Shanghai, China
| | - Changhao Zhang
- Shanghai Engineering Research Center of Hadal Science and Technology, College of Marine Sciences, Shanghai Ocean University, Shanghai, China
| | - Qingqing Peng
- Shanghai Engineering Research Center of Hadal Science and Technology, College of Marine Sciences, Shanghai Ocean University, Shanghai, China
| | - Zhizhen Zhang
- Ocean College, Zhoushan Campus, Zhejiang University, Zhoushan, China
| | - Jiasong Fang
- Shanghai Engineering Research Center of Hadal Science and Technology, College of Marine Sciences, Shanghai Ocean University, Shanghai, China
| | - Xi Yu
- Shanghai Engineering Research Center of Hadal Science and Technology, College of Marine Sciences, Shanghai Ocean University, Shanghai, China
| |
Collapse
|
3
|
Hao YJ, Zou ZB, Xie MM, Zhang Y, Xu L, Yu HY, Ma HB, Yang XW. Ferroptosis Inhibitory Compounds from the Deep-Sea-Derived Fungus Penicillium sp. MCCC 3A00126. Mar Drugs 2023; 21:md21040234. [PMID: 37103373 PMCID: PMC10144380 DOI: 10.3390/md21040234] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2022] [Revised: 03/27/2023] [Accepted: 04/07/2023] [Indexed: 04/28/2023] Open
Abstract
Two new xanthones (1 and 2) were isolated from the deep-sea-derived fungus Penicillium sp. MCCC 3A00126 along with 34 known compounds (3-36). The structures of the new compounds were established by spectroscopic data. The absolute configuration of 1 was validated by comparison of experimental and calculated ECD spectra. All isolated compounds were evaluated for cytotoxicity and ferroptosis inhibitory activities. Compounds 14 and 15 exerted potent cytotoxicity against CCRF-CEM cells, with IC50 values of 5.5 and 3.5 μM, respectively, whereas 26, 28, 33, and 34 significantly inhibited RSL3-induced ferroptosis, with EC50 values of 11.6, 7.2, 11.8, and 2.2 μM, respectively.
Collapse
Affiliation(s)
- You-Jia Hao
- College of Marine Sciences, Shanghai Ocean University, 999 Hucheng Ring Road, Shanghai 201306, China
- Key Laboratory of Marine Genetic Resources, Third Institute of Oceanography, Ministry of Natural Resources, 184 Daxue Road, Xiamen 361005, China
| | - Zheng-Biao Zou
- Key Laboratory of Marine Genetic Resources, Third Institute of Oceanography, Ministry of Natural Resources, 184 Daxue Road, Xiamen 361005, China
| | - Ming-Min Xie
- Key Laboratory of Marine Genetic Resources, Third Institute of Oceanography, Ministry of Natural Resources, 184 Daxue Road, Xiamen 361005, China
| | - Yong Zhang
- Key Laboratory of Marine Genetic Resources, Third Institute of Oceanography, Ministry of Natural Resources, 184 Daxue Road, Xiamen 361005, China
| | - Lin Xu
- Key Laboratory of Marine Genetic Resources, Third Institute of Oceanography, Ministry of Natural Resources, 184 Daxue Road, Xiamen 361005, China
| | - Hao-Yu Yu
- Key Laboratory of Marine Genetic Resources, Third Institute of Oceanography, Ministry of Natural Resources, 184 Daxue Road, Xiamen 361005, China
| | - Hua-Bin Ma
- Institute of Drug Discovery Technology, Ningbo University, Ningbo 315211, China
| | - Xian-Wen Yang
- Key Laboratory of Marine Genetic Resources, Third Institute of Oceanography, Ministry of Natural Resources, 184 Daxue Road, Xiamen 361005, China
| |
Collapse
|
4
|
Han H, Yu C, Qi J, Wang P, Zhao P, Gong W, Xie C, Xia X, Liu C. High-efficient production of mushroom polyketide compounds in a platform host Aspergillus oryzae. Microb Cell Fact 2023; 22:60. [PMID: 36998045 PMCID: PMC10064546 DOI: 10.1186/s12934-023-02071-9] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2022] [Accepted: 03/24/2023] [Indexed: 04/01/2023] Open
Abstract
BACKGROUND Orsellinic acid (2,4-dihydroxy-6-methylbenzoic acid, OA) and its structural analog o-Orsellinaldehyde, have become widely used intermediates in clinical drugs synthesis. Although the research on the biosynthesis of such compounds has made significant progress, due to the lack of suitable hosts, there is still far from the industrial production of such compounds based on synthetic biology. RESULTS With the help of genome mining, we found a polyketide synthase (PKS, HerA) in the genome of the Hericium erinaceus, which shares 60% amino acid sequence homology with ArmB from Armillaria mellea, an identified PKS capable of synthesizing OA. To characterize the function of HerA, we cloned herA and heterologously expressed it in Aspergillus oryzae, and successfully detected the production of OA. Subsequently, the introduction of an incomplete PKS (Pks5) from Ustilago maydis containing only three domains (AMP-ACP-R), which was into herA-containing A. oryzae, the resulted in the production of o-Orsellinaldehyde. Considering the economic value of OA and o-Orsellinaldehyde, we then optimized the yield of these compounds in A. oryzae. The screening showed that when maltose was used as carbon source, the yields of OA and o-Orsellinaldehyde were 57.68 mg/L and 15.71 mg/L respectively, while the yields were 340.41 mg/Kg and 84.79 mg/Kg respectively in rice medium for 10 days. CONCLUSIONS Herein, we successfully expressed the genes of basidiomycetes using A. oryzae heterologous host. As a fungus of ascomycetes, which not only correctly splices genes of basidiomycetes containing multiple introns, but also efficiently produces their metabolites. This study highlights that A. oryzae is an excellent host for the heterologous production of fungal natural products, and has the potential to become an efficient chassis for the production of basidiomycete secondary metabolites in synthetic biology.
Collapse
Affiliation(s)
- Haiyan Han
- Key Laboratory for Enzyme and Enzyme-Like Material Engineering of Heilongjiang, College of Life Science, Northeast Forestry University, Harbin, 150040, Heilongjiang, China
| | - Chunyan Yu
- Key Laboratory for Enzyme and Enzyme-Like Material Engineering of Heilongjiang, College of Life Science, Northeast Forestry University, Harbin, 150040, Heilongjiang, China
| | - Jianzhao Qi
- Key Laboratory for Enzyme and Enzyme-Like Material Engineering of Heilongjiang, College of Life Science, Northeast Forestry University, Harbin, 150040, Heilongjiang, China
| | - Pengchao Wang
- Key Laboratory for Enzyme and Enzyme-Like Material Engineering of Heilongjiang, College of Life Science, Northeast Forestry University, Harbin, 150040, Heilongjiang, China
| | - Peipei Zhao
- Biology Institute, Qilu University of Technology (Shandong Academy of Sciences), Jinan, 250103, Shandong, China
| | - Wenbing Gong
- Institute of Bast Fiber Crops, Chinese Academy of Agricultural Sciences, Changsha, 410205, Hunan, China
| | - Chunliang Xie
- Institute of Bast Fiber Crops, Chinese Academy of Agricultural Sciences, Changsha, 410205, Hunan, China
| | - Xuekui Xia
- Biology Institute, Qilu University of Technology (Shandong Academy of Sciences), Jinan, 250103, Shandong, China.
| | - Chengwei Liu
- Key Laboratory for Enzyme and Enzyme-Like Material Engineering of Heilongjiang, College of Life Science, Northeast Forestry University, Harbin, 150040, Heilongjiang, China.
| |
Collapse
|
5
|
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.
Collapse
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
| |
Collapse
|
6
|
Zhao F, Sun C, Liu Z, Cabrera A, Escobar M, Huang S, Yuan Q, Nie Q, Luo KL, Lin A, Vanegas JA, Zhu T, Hilton IB, Gao X. Multiplex Base-Editing Enables Combinatorial Epigenetic Regulation for Genome Mining of Fungal Natural Products. J Am Chem Soc 2023; 145:413-421. [PMID: 36542862 PMCID: PMC10162584 DOI: 10.1021/jacs.2c10211] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
Genome mining of cryptic natural products (NPs) remains challenging, especially in filamentous fungi, owing to their complex genetic regulation. Increasing evidence indicates that several epigenetic modifications often act cooperatively to control fungal gene transcription, yet the ability to predictably manipulate multiple genes simultaneously is still largely limited. Here, we developed a multiplex base-editing (MBE) platform that significantly improves the capability and throughput of fungal genome manipulation, leading to the simultaneous inactivation of up to eight genes using a single transformation. We then employed MBE to inactivate three negative epigenetic regulators combinatorially in Aspergillus nidulans, enabling the activation of eight cryptic gene clusters compared to the wild-type strains. A group of novel NPs harboring unique cichorine and polyamine hybrid chemical scaffolds were identified, which were not reported previously. We envision that our scalable and efficient MBE platform can be readily applied in other filamentous fungi for the genome mining of novel NPs, providing a powerful approach for the exploitation of fungal chemical diversity.
Collapse
Affiliation(s)
- Fanglong Zhao
- Department of Chemical and Biomolecular Engineering, Rice University, Houston, Texas 77005, United States
| | - Chunxiao Sun
- Department of Chemical and Biomolecular Engineering, Rice University, Houston, Texas 77005, United States
| | - Zhiwen Liu
- Department of Chemical and Biomolecular Engineering, Rice University, Houston, Texas 77005, United States
| | - Alan Cabrera
- Department of Bioengineering, Rice University, Houston, Texas 77005, United States
| | - Mario Escobar
- Department of BioSciences, Rice University, Houston, Texas 77005, United States
| | - Shunyu Huang
- Department of Chemical and Biomolecular Engineering, Rice University, Houston, Texas 77005, United States
| | - Qichen Yuan
- Department of Chemical and Biomolecular Engineering, Rice University, Houston, Texas 77005, United States
| | - Qiuyue Nie
- Department of Chemical and Biomolecular Engineering, Rice University, Houston, Texas 77005, United States
| | - Kevin Lee Luo
- Department of Chemical and Biomolecular Engineering, Rice University, Houston, Texas 77005, United States
| | - Angela Lin
- Department of BioSciences, Rice University, Houston, Texas 77005, United States
| | - Jeffrey A Vanegas
- Department of Chemical and Biomolecular Engineering, Rice University, Houston, Texas 77005, United States
| | - Tong Zhu
- Shanghai Engineering Research Center of Molecular Therapeutics and New Drug Development, School of Chemistry and Molecular Engineering, East China Normal University, Shanghai 200062, China
| | - Isaac B Hilton
- Department of Bioengineering, Rice University, Houston, Texas 77005, United States
| | - Xue Gao
- Department of Chemical and Biomolecular Engineering, Rice University, Houston, Texas 77005, United States.,Department of Bioengineering, Rice University, Houston, Texas 77005, United States.,Department of Chemistry, Rice University, Houston, Texas 77005, United States
| |
Collapse
|
7
|
Zhang T, Cai G, Rong X, Wang Y, Gong K, Liu W, Wang L, Pang X, Yu L. A Combination of Genome Mining with an OSMAC Approach Facilitates the Discovery of and Contributions to the Biosynthesis of Melleolides from the Basidiomycete Armillaria tabescens. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2022; 70:12430-12441. [PMID: 36134616 DOI: 10.1021/acs.jafc.2c04079] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/16/2023]
Abstract
Genome mining revealed that the genomes of basidiomycetes may include a considerable number of biosynthetic gene clusters (BGCs), yet numerous clusters remain unidentified. Herein, we report a combination of genome mining with an OSMAC (one strain, many compounds) approach to characterize the spectrum of melleolides produced by Armillaria tabescens CPCC 401429. Using F1 fermentation medium, the metabolic pathway of the gene cluster mel was successfully upregulated. From the extracts of the wild-type strain, two new melleolides (1 and 2), along with five new orsellinic acid-derived lactams (10-14), were isolated, and their structures were elucidated by LC-HR-ESIMS/MS and 2D-NMR. Several melleolides exhibited moderate anti-carcinoma (A549, NCI-H520, and H1299) effects with IC50 values of 4.0-48.8 μM. RNA-sequencing based transcriptomic profiling broadened our knowledge of the genetic background, regulation, and mechanisms of melleolide biosynthesis. These results may promote downstream metabolic engineering studies of melleolides. Our study demonstrates the approach is effective for discovering new secondary metabolites from Armillaria sp. and will facilitate the mining of the unexploited biosynthetic potential in other basidiomycetes.
Collapse
Affiliation(s)
- Tao Zhang
- Institute of Medicinal Biotechnology, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing 100050, China
| | - Guowei Cai
- Institute of Medicinal Biotechnology, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing 100050, China
- Medical Research Center, Binzhou Medical University Hospital, Binzhou, Shandong 256603, China
| | - Xiaoting Rong
- Institute of Medicinal Biotechnology, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing 100050, China
- College of Biotechnology, Jiangsu University of Science and Technology, Zhenjiang, Jiangsu 212003, China
| | - Yuquan Wang
- Institute of Medicinal Biotechnology, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing 100050, China
| | - KaiKai Gong
- Medical Research Center, Binzhou Medical University Hospital, Binzhou, Shandong 256603, China
| | - Wancang Liu
- Institute of Medicinal Biotechnology, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing 100050, China
| | - Lu Wang
- Institute of Medicinal Biotechnology, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing 100050, China
| | - Xu Pang
- Institute of Medicinal Biotechnology, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing 100050, China
| | - Liyan Yu
- Institute of Medicinal Biotechnology, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing 100050, China
| |
Collapse
|
8
|
Berger H, Bacher M, Labuda R, Eppel IM, Bayer F, Sulyok M, Gasparotto E, Zehetbauer F, Doppler M, Gratzl H, Strauss J. Polaramycin B, and not physical interaction, is the signal that rewires fungal metabolism in the Streptomyces-Aspergillus interaction. Environ Microbiol 2022; 24:4899-4914. [PMID: 35848075 PMCID: PMC9796313 DOI: 10.1111/1462-2920.16118] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2022] [Accepted: 06/26/2022] [Indexed: 01/01/2023]
Abstract
Co-culturing the bacterium Streptomyces rapamycinicus and the ascomycete Aspergillus nidulans has previously been shown to trigger the production of orsellinic acid (ORS) and its derivates in the fungal cells. Based on these studies it was assumed that direct physical contact is a prerequisite for the metabolic reaction that involves a fungal amino acid starvation response and activating chromatin modifications at the biosynthetic gene cluster (BGC). Here we show that not physical contact, but a guanidine containing macrolide, named polaramycin B, triggers the response. The substance is produced constitutively by the bacterium and above a certain concentration, provokes the production of ORS. In addition, several other secondary metabolites were induced by polaramycin B. Our genome-wide transcriptome analysis showed that polaramycin B treatment causes downregulation of fungal genes necessary for membrane stability, general metabolism and growth. A compensatory genetic response can be observed in the fungus that included upregulation of BGCs and genes necessary for ribosome biogenesis, translation and membrane stability. Our work discovered a novel chemical communication, in which the antifungal bacterial metabolite polaramycin B leads to the production of antibacterial defence chemicals and to the upregulation of genes necessary to compensate for the cellular damage caused by polaramycin B.
Collapse
Affiliation(s)
- Harald Berger
- Department of Applied Genetics and Cell Biology, Institute of Microbial GeneticsUniversity of Natural Resources and Life Sciences, ViennaTulln/DonauAustria
| | - Markus Bacher
- Research Platform Bioactive Microbial Metabolites (BiMM)Tulln/DonauAustria
- Department of Chemistry, Institute of Chemistry of Renewable ResourcesUniversity of Natural Resources and Life Sciences, ViennaTulln/DonauAustria
| | - Roman Labuda
- Research Platform Bioactive Microbial Metabolites (BiMM)Tulln/DonauAustria
- Department for Farm Animals and Veterinary Public Health, Institute of Milk Hygiene, Milk Technology and Food ScienceUniversity of Veterinary Medicine, ViennaViennaAustria
| | - Isabel Maria Eppel
- Department of Applied Genetics and Cell Biology, Institute of Microbial GeneticsUniversity of Natural Resources and Life Sciences, ViennaTulln/DonauAustria
| | - Florentina Bayer
- Department of Applied Genetics and Cell Biology, Institute of Microbial GeneticsUniversity of Natural Resources and Life Sciences, ViennaTulln/DonauAustria
| | - Michael Sulyok
- Department of Agro‐BiotechnologyInstitute of Bioanalytics and Agro‐Metabolomics, University of Natural Resources and Life Sciences, ViennaTulln/DonauAustria
| | - Erika Gasparotto
- Department of Applied Genetics and Cell Biology, Institute of Microbial GeneticsUniversity of Natural Resources and Life Sciences, ViennaTulln/DonauAustria
- Research Platform Bioactive Microbial Metabolites (BiMM)Tulln/DonauAustria
| | - Franz Zehetbauer
- Department of Applied Genetics and Cell Biology, Institute of Microbial GeneticsUniversity of Natural Resources and Life Sciences, ViennaTulln/DonauAustria
| | - Maria Doppler
- Department of Agro‐BiotechnologyInstitute of Bioanalytics and Agro‐Metabolomics, University of Natural Resources and Life Sciences, ViennaTulln/DonauAustria
| | - Hannes Gratzl
- Research Platform Bioactive Microbial Metabolites (BiMM)Tulln/DonauAustria
- Department of Agro‐BiotechnologyInstitute of Bioanalytics and Agro‐Metabolomics, University of Natural Resources and Life Sciences, ViennaTulln/DonauAustria
| | - Joseph Strauss
- Department of Applied Genetics and Cell Biology, Institute of Microbial GeneticsUniversity of Natural Resources and Life Sciences, ViennaTulln/DonauAustria
- Research Platform Bioactive Microbial Metabolites (BiMM)Tulln/DonauAustria
| |
Collapse
|
9
|
Wei Q, Wang ZP, Zhang X, Zou Y. Diaryl Ether Formation by a Versatile Thioesterase Domain. J Am Chem Soc 2022; 144:9554-9558. [PMID: 35639490 DOI: 10.1021/jacs.2c02813] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Abstract
Oxidative coupling and oxidative rearrangement are two of the most common biosynthetic strategies to form diaryl ethers. In contrast, enzymatic diaryl ether generation that proceeds in a nonoxidative manner has not been characterized thus far. Here, we discovered a versatile thioesterase (TE) domain from the nonreducing polyketide synthase (nrPKS) AN7909, which catalyzes diaryl ether formation through a series of successive steps involving esterification, a Smiles rearrangement, and hydrolysis. Further mutations and biochemical analyses with synthetic mimic substrates provide insight into the proposed catalytic process of the TE domain.
Collapse
Affiliation(s)
- Qian Wei
- College of Pharmaceutical Sciences, Southwest University, Chongqing 400715, People's Republic of China
| | - Ze-Ping Wang
- College of Pharmaceutical Sciences, Southwest University, Chongqing 400715, People's Republic of China
| | - Xiao Zhang
- College of Pharmaceutical Sciences, Southwest University, Chongqing 400715, People's Republic of China
| | - Yi Zou
- College of Pharmaceutical Sciences, Southwest University, Chongqing 400715, People's Republic of China
| |
Collapse
|
10
|
Liu Q, Zhang D, Xu Y, Gao S, Gong Y, Cai X, Yao M, Yang X. Cloning and Functional Characterization of the Polyketide Synthases Based on Genome Mining of Preussia isomera XL-1326. Front Microbiol 2022; 13:819086. [PMID: 35602042 PMCID: PMC9116485 DOI: 10.3389/fmicb.2022.819086] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2021] [Accepted: 03/31/2022] [Indexed: 11/21/2022] Open
Abstract
Fungal polyketides (PKs) are one of the largest families of structurally diverse bioactive natural products biosynthesized by multidomain megasynthases, in which thioesterase (TE) domains act as nonequivalent decision gates determining both the shape and the yield of the polyketide intermediate. The endophytic fungus Preussia isomera XL-1326 was discovered to have an excellent capacity for secreting diverse bioactive PKs, i.e., the hot enantiomers (±)-preuisolactone A with antibacterial activity, the single-spiro minimoidione B with α-glucosidase inhibition activity, and the uncommon heptaketide setosol with antifungal activity, which drive us to illustrate how the unique PKs are biosynthesized. In this study, we first reported the genome sequence information of P. isomera. Based on genome mining, we discovered nine transcriptionally active genes encoding polyketide synthases (PKSs), Preu1–Preu9, of which those of Preu3, Preu4, and Preu6 were cloned and functionally characterized due to possessing complete sets of synthetic and release domains. Through heterologous expression in Saccharomyces cerevisiae, Preu3 and Preu6 could release high yields of orsellinic acid (OA) derivatives [3-methylorsellinic acid (3-MOA) and lecanoric acid, respectively]. Correspondingly, we found that Preu3 and Preu6 were clustered into OA derivative synthase groups by phylogenetic analysis. Next, with TE domain swapping, we constructed a novel “non-native” PKS, Preu6-TEPreu3, which shared a very low identity with OA synthase, OrsA, from Aspergillus nidulans but could produce a large amount of OA. In addition, with the use of Preu6-TEPreu3, we synthesized methyl 3-methylorsellinate (synthetic oak moss of great economic value) from 3-MOA as the substrate, and interestingly, 3-MOA exhibited remarkable antibacterial activities, while methyl 3-methylorsellinate displayed broad-spectrum antifungal activity. Taken together, we identified two novel PKSs to biosynthesize 3-MOA and lecanoric acid, respectively, with information on such kinds of PKSs rarely reported, and constructed one novel “non-native” PKS to largely biosynthesize OA. This work is our first step to explore the biosynthesis of the PKs in P. isomera, and it also provides a new platform for high-level environment-friendly production of OA derivatives and the development of new antimicrobial agents.
Collapse
Affiliation(s)
- Qingpei Liu
- The Modernization Engineering Technology Research Center of Ethnic Minority Medicine of Hubei Province, School of Pharmaceutical Sciences, South-Central Minzu University, Wuhan, China
| | - Dan Zhang
- The Modernization Engineering Technology Research Center of Ethnic Minority Medicine of Hubei Province, School of Pharmaceutical Sciences, South-Central Minzu University, Wuhan, China
| | - Yao Xu
- The Modernization Engineering Technology Research Center of Ethnic Minority Medicine of Hubei Province, School of Pharmaceutical Sciences, South-Central Minzu University, Wuhan, China
| | - Shuaibiao Gao
- The Modernization Engineering Technology Research Center of Ethnic Minority Medicine of Hubei Province, School of Pharmaceutical Sciences, South-Central Minzu University, Wuhan, China
| | - Yifu Gong
- The Modernization Engineering Technology Research Center of Ethnic Minority Medicine of Hubei Province, School of Pharmaceutical Sciences, South-Central Minzu University, Wuhan, China
| | - Xianhua Cai
- The Modernization Engineering Technology Research Center of Ethnic Minority Medicine of Hubei Province, School of Pharmaceutical Sciences, South-Central Minzu University, Wuhan, China
| | - Ming Yao
- The Modernization Engineering Technology Research Center of Ethnic Minority Medicine of Hubei Province, School of Pharmaceutical Sciences, South-Central Minzu University, Wuhan, China
| | - Xiaolong Yang
- The Modernization Engineering Technology Research Center of Ethnic Minority Medicine of Hubei Province, School of Pharmaceutical Sciences, South-Central Minzu University, Wuhan, China
| |
Collapse
|
11
|
Ninomiya A, Urayama SI, Hagiwara D. Antibacterial diphenyl ether production induced by co-culture of Aspergillus nidulans and Aspergillus fumigatus. Appl Microbiol Biotechnol 2022; 106:4169-4185. [PMID: 35595930 DOI: 10.1007/s00253-022-11964-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2022] [Revised: 05/04/2022] [Accepted: 05/07/2022] [Indexed: 11/30/2022]
Abstract
Fungi are a rich source of secondary metabolites with potent biological activities. Co-culturing a fungus with another microorganism has drawn much attention as a practical method for stimulating fungal secondary metabolism. However, in most cases, the molecular mechanisms underlying the activation of secondary metabolite production in co-culture are poorly understood. To elucidate such a mechanism, in this study, we established a model fungal-fungal co-culture system, composed of Aspergillus nidulans and Aspergillus fumigatus. In the co-culture of A. nidulans and A. fumigatus, production of antibacterial diphenyl ethers was enhanced. Transcriptome analysis by RNA-sequencing showed that the co-culture activated expression of siderophore biosynthesis genes in A. fumigatus and two polyketide biosynthetic gene clusters (the ors and cic clusters) in A. nidulans. Gene disruption experiments revealed that the ors cluster is responsible for diphenyl ether production in the co-culture. Interestingly, the ors cluster was previously reported to be upregulated by co-culture of A. nidulans with the bacterium Streptomyces rapamycinicus; orsellinic acid was the main product of the cluster in that co-culture. In other words, the main product of the ors cluster was different in fungal-fungal and bacterial-fungal co-culture. The genes responsible for biosynthesis of the bacterial- and fungal-induced polyketides were deduced using a heterologous expression system in Aspergillus oryzae. The molecular genetic mechanisms that trigger biosynthesis of two different types of compounds in A. nidulans in response to the fungus and the bacterium were demonstrated, which provides an insight into complex secondary metabolic response of fungi to microorganisms. KEY POINTS: • Co-culture of two fungal species triggered antibiotic diphenyl ether production. • The co-culture affected expression levels of several genes for secondary metabolism. • Gene cluster essential for induction of the antibiotics production was determined.
Collapse
Affiliation(s)
- Akihiro Ninomiya
- Faculty of Life and Environmental Sciences, University of Tsukuba, 1-1-1 Tennodai, Tsukuba, Ibaraki, 305-8577, Japan.,Graduate School of Agricultural and Life Sciences, The University of Tokyo, 1-1-1 Yayoi, Bunkyo, Tokyo, 113-8657, Japan
| | - Syun-Ichi Urayama
- Faculty of Life and Environmental Sciences, University of Tsukuba, 1-1-1 Tennodai, Tsukuba, Ibaraki, 305-8577, Japan.,Microbiology Research Center for Sustainability, University of Tsukuba, 1-1-1 Tennodai, Tsukuba, Ibaraki, 305-8577, Japan
| | - Daisuke Hagiwara
- Faculty of Life and Environmental Sciences, University of Tsukuba, 1-1-1 Tennodai, Tsukuba, Ibaraki, 305-8577, Japan. .,Microbiology Research Center for Sustainability, University of Tsukuba, 1-1-1 Tennodai, Tsukuba, Ibaraki, 305-8577, Japan.
| |
Collapse
|
12
|
Fajardo-Hernández C, Khan FST, Flores-Bocanegra L, Prieto-Davó A, Wan B, Ma R, Qader M, Villanueva-Silva R, Martínez-Cárdenas A, López-Lobato MA, Hematian S, Franzblau SG, Raja HA, García-Contreras R, Figueroa M. Insights into the Chemical Diversity of Selected Fungi from the Tza Itzá Cenote of the Yucatan Peninsula. ACS OMEGA 2022; 7:12171-12185. [PMID: 35449929 PMCID: PMC9016812 DOI: 10.1021/acsomega.2c00544] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/26/2022] [Accepted: 03/14/2022] [Indexed: 06/14/2023]
Abstract
Cenotes are habitats with unique physical, chemical, and biological features. Unexplored microorganisms from these sinkholes represent a potential source of bioactive molecules. Thus, a series of cultivable fungi (Aspergillus spp. NCA257, NCA264, and NCA276, Stachybotrys sp. NCA252, and Cladosporium sp. NCA273) isolated from the cenote Tza Itzá were subjected to chemical, coculture, and metabolomic analyses. Nineteen compounds were obtained and tested for their antimicrobial potential against ESKAPE pathogens, Mycobacterium tuberculosis, and nontuberculous mycobacteria. In particular, phenylspirodrimanes from Stachybotrys sp. NCA252 showed significant activity against MRSA, MSSA, and mycobacterial strains. On the other hand, the absolute configuration of the new compound 17-deoxy-aspergillin PZ (1) isolated from Aspergillus sp. NCA276 was established via single-crystal X-ray crystallography. Also, the chemical analysis of the cocultures between Aspergillus and Cladosporium strains revealed the production of metabolites that were not present or were barely detected in the monocultures. Finally, molecular networking analysis of the LC-MS-MS/MS data for each fungus was used as a tool for the annotation of additional compounds, increasing the chemical knowledge on the corresponding fungal strains. Overall, this is the first systematic chemical study on fungi isolated from a sinkhole in Mexico.
Collapse
Affiliation(s)
- Carlos
A. Fajardo-Hernández
- Departamento
de Farmacia, Facultad de Química, Universidad Nacional Autónoma de México, Ciudad de México 04510, Mexico
| | - Firoz Shah Tuglak Khan
- Department
of Chemistry and Biochemistry, University
of North Carolina Greensboro, Greensboro, North Carolina 27402, United States
| | - Laura Flores-Bocanegra
- Department
of Chemistry and Biochemistry, University
of North Carolina Greensboro, Greensboro, North Carolina 27402, United States
| | - Alejandra Prieto-Davó
- Unidad
de Química en Sisal, Facultad de Química, Universidad Nacional Autónoma de México, Sisal, Yucatán 97356, Mexico
| | - Baojie Wan
- Institute
for Tuberculosis Research, College of Pharmacy, University of Illinois at Chicago, Chicago, Illinois 60612, United States
| | - Rui Ma
- Institute
for Tuberculosis Research, College of Pharmacy, University of Illinois at Chicago, Chicago, Illinois 60612, United States
| | - Mallique Qader
- Institute
for Tuberculosis Research, College of Pharmacy, University of Illinois at Chicago, Chicago, Illinois 60612, United States
| | - Rodrigo Villanueva-Silva
- Departamento
de Farmacia, Facultad de Química, Universidad Nacional Autónoma de México, Ciudad de México 04510, Mexico
| | - Anahí Martínez-Cárdenas
- Departamento
de Farmacia, Facultad de Química, Universidad Nacional Autónoma de México, Ciudad de México 04510, Mexico
| | - Marian A. López-Lobato
- Departamento
de Farmacia, Facultad de Química, Universidad Nacional Autónoma de México, Ciudad de México 04510, Mexico
| | - Shabnam Hematian
- Department
of Chemistry and Biochemistry, University
of North Carolina Greensboro, Greensboro, North Carolina 27402, United States
| | - Scott G. Franzblau
- Institute
for Tuberculosis Research, College of Pharmacy, University of Illinois at Chicago, Chicago, Illinois 60612, United States
| | - Huzefa A. Raja
- Department
of Chemistry and Biochemistry, University
of North Carolina Greensboro, Greensboro, North Carolina 27402, United States
| | - Rodolfo García-Contreras
- Departamento
de Microbiología y Parasitología, Facultad de Medicina, Universidad Nacional Autónoma de México, Ciudad de México 04510, Mexico
| | - Mario Figueroa
- Departamento
de Farmacia, Facultad de Química, Universidad Nacional Autónoma de México, Ciudad de México 04510, Mexico
| |
Collapse
|
13
|
Hayasaka A, Hashimoto K, Konno K, Tanaka K, Hashimoto M. Isolation, Identification, and DFT-based Conformational Analysis of Sesquikarahanadienone and its Congeners from Freshwater Dothideomycetes Neohelicascus aquaticus KT4120. BULLETIN OF THE CHEMICAL SOCIETY OF JAPAN 2022. [DOI: 10.1246/bcsj.20220063] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
Affiliation(s)
- Ayane Hayasaka
- Faculty of Agriculture and Life Science, Hirosaki University, 3-Bunkyo-cho, Hirosaki, 036-8561, Japan
| | - Kazuki Hashimoto
- Faculty of Agriculture and Life Science, Hirosaki University, 3-Bunkyo-cho, Hirosaki, 036-8561, Japan
| | - Katsuhiro Konno
- Institute of Natural Medicine, University of Toyama, Toyama 930-0194, Japan
| | - Kazuaki Tanaka
- Faculty of Agriculture and Life Science, Hirosaki University, 3-Bunkyo-cho, Hirosaki, 036-8561, Japan
| | - Masaru Hashimoto
- Faculty of Agriculture and Life Science, Hirosaki University, 3-Bunkyo-cho, Hirosaki, 036-8561, Japan
| |
Collapse
|
14
|
Tang S, Men P, Zhang W, Li H, Li Z, Huang X, Lu X. Identification of a polyketide biosynthesis gene cluster by transcriptional regulator activation in Aspergillus terreus. Fungal Genet Biol 2022; 160:103690. [DOI: 10.1016/j.fgb.2022.103690] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2021] [Revised: 03/10/2022] [Accepted: 03/23/2022] [Indexed: 11/27/2022]
|
15
|
Xiang P, Li SM. Formation of 3-Orsellinoxypropanoic Acid in Penicillum crustosum is Catalyzed by a Bifunctional Nonreducing Polyketide Synthase. Org Lett 2022; 24:462-466. [PMID: 34962820 DOI: 10.1021/acs.orglett.1c04189] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
The heterologous expression of a nonreducing polyketide synthase gene oesA from Penicillium crustosum led to the identification of orsellinoylpropanoic acid (1). Domain deletion and recombination proved that OesA catalyzes not only the formation of orsellinic acid but also its transfer to 3-hydroxypropanoic acid. Both ACP domains contribute independently and complementarily to the product formation. Feeding experiments provided evidence that only the orsellinyl residue is derived from acetate.
Collapse
Affiliation(s)
- Pan Xiang
- Institut für Pharmazeutische Biologie und Biotechnologie, Fachbereich Pharmazie, Philipps-Universität Marburg, Robert-Koch-Straße 4, 35037 Marburg, Germany
| | - Shu-Ming Li
- Institut für Pharmazeutische Biologie und Biotechnologie, Fachbereich Pharmazie, Philipps-Universität Marburg, Robert-Koch-Straße 4, 35037 Marburg, Germany
| |
Collapse
|
16
|
Tippelt A, Nett M. Saccharomyces cerevisiae as host for the recombinant production of polyketides and nonribosomal peptides. Microb Cell Fact 2021; 20:161. [PMID: 34412657 PMCID: PMC8374128 DOI: 10.1186/s12934-021-01650-y] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2021] [Accepted: 08/05/2021] [Indexed: 01/30/2023] Open
Abstract
As a robust, fast growing and genetically tractable organism, the budding yeast Saccharomyces cerevisiae is one of the most widely used hosts in biotechnology. Its applications range from the manufacturing of vaccines and hormones to bulk chemicals and biofuels. In recent years, major efforts have been undertaken to expand this portfolio to include structurally complex natural products, such as polyketides and nonribosomally synthesized peptides. These compounds often have useful pharmacological properties, which make them valuable drugs for the treatment of infectious diseases, cancer, or autoimmune disorders. In nature, polyketides and nonribosomal peptides are generated by consecutive condensation reactions of short chain acyl-CoAs or amino acids, respectively, with the substrates and reaction intermediates being bound to large, multidomain enzymes. For the reconstitution of these multistep catalytic processes, the enzymatic assembly lines need to be functionally expressed and the required substrates must be supplied in reasonable quantities. Furthermore, the production hosts need to be protected from the toxicity of the biosynthetic products. In this review, we will summarize and evaluate the status quo regarding the heterologous production of polyketides and nonribosomal peptides in S. cerevisiae. Based on a comprehensive literature analysis, prerequisites for a successful pathway reconstitution could be deduced, as well as recurring bottlenecks in this microbial host.
Collapse
Affiliation(s)
- Anna Tippelt
- Department of Biochemical and Chemical Engineering, Laboratory of Technical Biology, TU Dortmund University, Emil-Figge-Strasse 66, 44227, Dortmund, Germany
| | - Markus Nett
- Department of Biochemical and Chemical Engineering, Laboratory of Technical Biology, TU Dortmund University, Emil-Figge-Strasse 66, 44227, Dortmund, Germany.
| |
Collapse
|
17
|
Wang W, Yu Y, Keller NP, Wang P. Presence, Mode of Action, and Application of Pathway Specific Transcription Factors in Aspergillus Biosynthetic Gene Clusters. Int J Mol Sci 2021; 22:ijms22168709. [PMID: 34445420 PMCID: PMC8395729 DOI: 10.3390/ijms22168709] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2021] [Revised: 08/10/2021] [Accepted: 08/10/2021] [Indexed: 01/21/2023] Open
Abstract
Fungal secondary metabolites are renowned toxins as well as valuable sources of antibiotics, cholesterol-lowering drugs, and immunosuppressants; hence, great efforts were levied to understand how these compounds are genetically regulated. The genes encoding for the enzymes required for synthesizing secondary metabolites are arranged in biosynthetic gene clusters (BGCs). Often, BGCs contain a pathway specific transcription factor (PSTF), a valuable tool in shutting down or turning up production of the BGC product. In this review, we present an in-depth view of PSTFs by examining over 40 characterized BGCs in the well-studied fungal species Aspergillus nidulans and Aspergillus fumigatus. Herein, we find BGC size is a predictor for presence of PSTFs, consider the number and the relative location of PSTF in regard to the cluster(s) regulated, discuss the function and the evolution of PSTFs, and present application strategies for pathway specific activation of cryptic BGCs.
Collapse
Affiliation(s)
- Wenjie Wang
- Ocean College, Zhejiang University, Zhoushan 316021, China; (W.W.); (Y.Y.)
- Department of Medical Microbiology and Immunology, University of Wisconsin-Madison, Madison, WI 53706, USA
| | - Yuchao Yu
- Ocean College, Zhejiang University, Zhoushan 316021, China; (W.W.); (Y.Y.)
| | - Nancy P. Keller
- Department of Medical Microbiology and Immunology, University of Wisconsin-Madison, Madison, WI 53706, USA
- Department of Bacteriology, University of Wisconsin-Madison, Madison, WI 53706, USA
- Correspondence: (N.P.K.); (P.W.)
| | - Pinmei Wang
- Ocean College, Zhejiang University, Zhoushan 316021, China; (W.W.); (Y.Y.)
- Correspondence: (N.P.K.); (P.W.)
| |
Collapse
|
18
|
Park SC, Lee JH, Hwang JY, Kwon OS, Liao L, Oh DC, Oh KB, Shin J. Ochraceopetalin, a Mixed-Biogenetic Salt of Polyketide and Amino Acid Origins from a Marine-Derived Aspergillus ochraceopetaliformis Fungus. Mar Drugs 2021; 19:md19080413. [PMID: 34436252 PMCID: PMC8401040 DOI: 10.3390/md19080413] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2021] [Revised: 07/24/2021] [Accepted: 07/24/2021] [Indexed: 11/25/2022] Open
Abstract
Ochraceopetalin (1), a mixed-biogenetic salt compound and its component 2 were isolated from the culture broths of a marine-derived fungus, Aspergillus ochraceopetaliformis. Based on combined spectroscopic and chemical analyses, the structure of 1 was determined to be a sulfonated diphenylether-aminol-amino acid ester guanidinium salt of an unprecedented structural class, while 2 was determined to be the corresponding sulfonated diphenylether. Ochraceopetaguanidine (3), the other guanidine-bearing aminol amino acid ester component, was also prepared and structurally elucidated. Compound 1 exhibited significant cytotoxicity against K562 and A549 cells.
Collapse
Affiliation(s)
- Sung Chul Park
- Natural Products Research Institute, College of Pharmacy, Seoul National University, San 56-1, Sillim, Gwanak, Seoul 151-742, Korea; (S.C.P.); (J.-H.L.); (J.-Y.H.); (O.-S.K.); (L.L.); (D.-C.O.)
| | - Jung-Ho Lee
- Natural Products Research Institute, College of Pharmacy, Seoul National University, San 56-1, Sillim, Gwanak, Seoul 151-742, Korea; (S.C.P.); (J.-H.L.); (J.-Y.H.); (O.-S.K.); (L.L.); (D.-C.O.)
| | - Ji-Yeon Hwang
- Natural Products Research Institute, College of Pharmacy, Seoul National University, San 56-1, Sillim, Gwanak, Seoul 151-742, Korea; (S.C.P.); (J.-H.L.); (J.-Y.H.); (O.-S.K.); (L.L.); (D.-C.O.)
| | - Oh-Seok Kwon
- Natural Products Research Institute, College of Pharmacy, Seoul National University, San 56-1, Sillim, Gwanak, Seoul 151-742, Korea; (S.C.P.); (J.-H.L.); (J.-Y.H.); (O.-S.K.); (L.L.); (D.-C.O.)
| | - Lijuan Liao
- Natural Products Research Institute, College of Pharmacy, Seoul National University, San 56-1, Sillim, Gwanak, Seoul 151-742, Korea; (S.C.P.); (J.-H.L.); (J.-Y.H.); (O.-S.K.); (L.L.); (D.-C.O.)
- College of Life Sciences, Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Dong-Chan Oh
- Natural Products Research Institute, College of Pharmacy, Seoul National University, San 56-1, Sillim, Gwanak, Seoul 151-742, Korea; (S.C.P.); (J.-H.L.); (J.-Y.H.); (O.-S.K.); (L.L.); (D.-C.O.)
| | - Ki-Bong Oh
- Department of Agricultural Biotechnology, College of Agriculture and Life Science, Seoul National University, San 56-1, Sillim, Gwanak, Seoul 151-921, Korea
- Correspondence: (K.-B.O.); (J.S.); Tel.: +82-2-880-4646 (K.-B.O.); +82-2-880-2484 (J.S.)
| | - Jongheon Shin
- Natural Products Research Institute, College of Pharmacy, Seoul National University, San 56-1, Sillim, Gwanak, Seoul 151-742, Korea; (S.C.P.); (J.-H.L.); (J.-Y.H.); (O.-S.K.); (L.L.); (D.-C.O.)
- Correspondence: (K.-B.O.); (J.S.); Tel.: +82-2-880-4646 (K.-B.O.); +82-2-880-2484 (J.S.)
| |
Collapse
|
19
|
Kim W, Liu R, Woo S, Kang KB, Park H, Yu YH, Ha HH, Oh SY, Yang JH, Kim H, Yun SH, Hur JS. Linking a Gene Cluster to Atranorin, a Major Cortical Substance of Lichens, through Genetic Dereplication and Heterologous Expression. mBio 2021; 12:e0111121. [PMID: 34154413 PMCID: PMC8262933 DOI: 10.1128/mbio.01111-21] [Citation(s) in RCA: 24] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2021] [Accepted: 05/27/2021] [Indexed: 02/07/2023] Open
Abstract
The depside and depsidone series compounds of polyketide origin accumulate in the cortical or medullary layers of lichen thalli. Despite the taxonomic and ecological significance of lichen chemistry and its pharmaceutical potentials, there has been no single piece of genetic evidence linking biosynthetic genes to lichen substances. Thus, we systematically analyzed lichen polyketide synthases (PKSs) for categorization and identification of the biosynthetic gene cluster (BGC) involved in depside/depsidone production. Our in-depth analysis of the interspecies PKS diversity in the genus Cladonia and a related Antarctic lichen, Stereocaulon alpinum, identified 45 BGC families, linking lichen PKSs to 15 previously characterized PKSs in nonlichenized fungi. Among these, we identified highly syntenic BGCs found exclusively in lichens producing atranorin (a depside). Heterologous expression of the putative atranorin PKS gene (coined atr1) yielded 4-O-demethylbarbatic acid, found in many lichens as a precursor compound, indicating an intermolecular cross-linking activity of Atr1 for depside formation. Subsequent introductions of tailoring enzymes into the heterologous host yielded atranorin, one of the most common cortical substances of macrolichens. Phylogenetic analysis of fungal PKS revealed that the Atr1 is in a novel PKS clade that included two conserved lichen-specific PKS families likely involved in biosynthesis of depsides and depsidones. Here, we provide a comprehensive catalog of PKS families of the genus Cladonia and functionally characterize a biosynthetic gene cluster from lichens, establishing a cornerstone for studying the genetics and chemical evolution of diverse lichen substances. IMPORTANCE Lichens play significant roles in ecosystem function and comprise about 20% of all known fungi. Polyketide-derived natural products accumulate in the cortical and medullary layers of lichen thalli, some of which play key roles in protection from biotic and abiotic stresses (e.g., herbivore attacks and UV irradiation). To date, however, no single lichen product has been linked to respective biosynthetic genes with genetic evidence. Here, we identified a gene cluster family responsible for biosynthesis of atranorin, a cortical substance found in diverse lichen species, by categorizing lichen polyketide synthase and reconstructing the atranorin biosynthetic pathway in a heterologous host. This study will help elucidate lichen secondary metabolism, harnessing the lichen's chemical diversity, hitherto obscured due to limited genetic information on lichens.
Collapse
Affiliation(s)
- Wonyong Kim
- Korean Lichen Research Institute, Sunchon National University, Suncheon, South Korea
| | - Rundong Liu
- Korean Lichen Research Institute, Sunchon National University, Suncheon, South Korea
| | - Sunmin Woo
- Research Institute of Pharmaceutical Sciences, College of Pharmacy, Sookmyung Women's University, Seoul, South Korea
| | - Kyo Bin Kang
- Research Institute of Pharmaceutical Sciences, College of Pharmacy, Sookmyung Women's University, Seoul, South Korea
| | - Hyun Park
- Division of Biotechnology, College of Life Sciences and Biotechnology, Korea University, Seoul, South Korea
| | - Young Hyun Yu
- College of Pharmacy, Sunchon National University, Suncheon, South Korea
- Research Institute of Life and Pharmaceutical Sciences, Sunchon National University, Suncheon, South Korea
| | - Hyung-Ho Ha
- College of Pharmacy, Sunchon National University, Suncheon, South Korea
- Research Institute of Life and Pharmaceutical Sciences, Sunchon National University, Suncheon, South Korea
| | - Seung-Yoon Oh
- Department of Biology and Chemistry, Changwon National University, Changwon, South Korea
| | - Ji Ho Yang
- Korean Lichen Research Institute, Sunchon National University, Suncheon, South Korea
| | - Hangun Kim
- College of Pharmacy, Sunchon National University, Suncheon, South Korea
- Research Institute of Life and Pharmaceutical Sciences, Sunchon National University, Suncheon, South Korea
| | - Sung-Hwan Yun
- Department of Medical Sciences, Soonchunhyang University, Asan, South Korea
| | - Jae-Seoun Hur
- Korean Lichen Research Institute, Sunchon National University, Suncheon, South Korea
| |
Collapse
|
20
|
Do TH, Nguyen TT, Dao TBN, Vo HC, Huynh BLC, Nguyen TAT, Mai DT, Vo TPG, Sichaem J, Nguyen NH, Duong TH. A new diphenyl ether from Parmotrema indicum Hale growing in Vietnam. Nat Prod Res 2021; 36:4879-4885. [PMID: 33823690 DOI: 10.1080/14786419.2021.1907748] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
Abstract
Chemical investigation of the lichen Parmotrema indicum Hale led to the isolation of one new diphenyl ether, parmetherine D (1), along with eight known compounds (2-9). The structures were determined by analysis of MS and NMR data and by comparison with the literature. Compounds 1, 2, and 7 were evaluated for α-glucosidase inhibition. Only compound 1 exhibited significant inhibition.
Collapse
Affiliation(s)
- Thanh-Hung Do
- NTT Hi-Tech Institute, Nguyen Tat Thanh University, Ho Chi Minh City, Vietnam
| | - Thanh-Trung Nguyen
- Institute of Research and Development, Duy Tan University, Da Nang, Vietnam.,Faculty of Pharmacy, Duy Tan University, Da Nang, Vietnam
| | - Thi-Bich-Ngoc Dao
- Department of Chemistry, University of Education, Ho Chi Minh City, Vietnam
| | - Huu-Canh Vo
- Department of Chemistry, University of Education, Ho Chi Minh City, Vietnam
| | | | | | - Dinh-Tri Mai
- Graduate University of Science and Technology, Vietnam Academy of Science and Technology, Ha Noi, Vietnam.,Institute of Chemical Technology, Vietnam Academy of Science and Technology, Ho Chi Minh City, Vietnam
| | - Thi-Phi-Giao Vo
- Faculty of Biology, Ho Chi Minh University of Science, National University, Ho Chi Minh City, Vietnam
| | - Jirapast Sichaem
- Research Unit in Natural Products Chemistry and Bioactivities, Faculty of Science and Technology, Thammasat University Lampang Campus, Lampang, Thailand
| | - Ngoc-Hong Nguyen
- CirTech Institute, Ho Chi Minh City University of Technology (HUTECH), Ho Chi Minh City, Vietnam
| | - Thuc-Huy Duong
- Department of Chemistry, University of Education, Ho Chi Minh City, Vietnam
| |
Collapse
|
21
|
Bhattarai K, Bhattarai K, Kabir ME, Bastola R, Baral B. Fungal natural products galaxy: Biochemistry and molecular genetics toward blockbuster drugs discovery. ADVANCES IN GENETICS 2021; 107:193-284. [PMID: 33641747 DOI: 10.1016/bs.adgen.2020.11.006] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/04/2022]
Abstract
Secondary metabolites synthesized by fungi have become a precious source of inspiration for the design of novel drugs. Indeed, fungi are prolific producers of fascinating, diverse, structurally complex, and low-molecular-mass natural products with high therapeutic leads, such as novel antimicrobial compounds, anticancer compounds, immunosuppressive agents, among others. Given that these microorganisms possess the extraordinary capacity to secrete diverse chemical scaffolds, they have been highly exploited by the giant pharma companies to generate small molecules. This has been made possible because the isolation of metabolites from fungal natural sources is feasible and surpasses the organic synthesis of compounds, which otherwise remains a significant bottleneck in the drug discovery process. Here in this comprehensive review, we have discussed recent studies on different fungi (pathogenic, non-pathogenic, commensal, and endophytic/symbiotic) from different habitats (terrestrial and marines), the specialized metabolites they biosynthesize, and the drugs derived from these specialized metabolites. Moreover, we have unveiled the logic behind the biosynthesis of vital chemical scaffolds, such as NRPS, PKS, PKS-NRPS hybrid, RiPPS, terpenoids, indole alkaloids, and their genetic mechanisms. Besides, we have provided a glimpse of the concept behind mycotoxins, virulence factor, and host immune response based on fungal infections.
Collapse
Affiliation(s)
- Keshab Bhattarai
- Pharmaceutical Institute, Department of Pharmaceutical Biology, University of Tübingen, Tübingen, Germany
| | - Keshab Bhattarai
- Central Department of Chemistry, Tribhuvan University, Kirtipur, Kathmandu, Nepal
| | - Md Ehsanul Kabir
- Animal Health Research Division, Bangladesh Livestock Research Institute, Savar, Dhaka, Bangladesh
| | - Rina Bastola
- Spinal Cord Injury Association-Nepal (SCIAN), Pokhara, Nepal
| | - Bikash Baral
- Department of Biochemistry, University of Turku, Turku, Finland.
| |
Collapse
|
22
|
Enzymology and biosynthesis of the orsellinic acid derived medicinal meroterpenoids. Curr Opin Biotechnol 2020; 69:52-59. [PMID: 33383296 DOI: 10.1016/j.copbio.2020.11.016] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2020] [Revised: 11/02/2020] [Accepted: 11/30/2020] [Indexed: 01/07/2023]
Abstract
The advent of synthetic biology has yielded fruitful studies on orsellinic acid-derived meroterpenoids, which reportedly possess important biological activities. Genomics and transcriptomics have significantly accelerated the discovery of the biosynthetic genes for orsellinic acid-derived fungal and plant meroterpenoids. Subsequently, a well-developed heterologous host provides a convenient platform to generate a supply of useful natural products. Furthermore, in vitro reconstitution and genome editing tools have been increasingly employed as efficient means to fully understand the enzyme reaction mechanisms. With the knowledge of the biosynthetic machinery, combinatorial and engineered biosyntheses have yielded novel molecules with improved bioactivities. These studies will lay the foundation for the production of meroterpenoids with novel medicinal properties.
Collapse
|
23
|
Khan I, Xie WL, Yu YC, Sheng H, Xu Y, Wang JQ, Debnath SC, Xu JZ, Zheng DQ, Ding WJ, Wang PM. Heteroexpression of Aspergillus nidulans laeA in Marine-Derived Fungi Triggers Upregulation of Secondary Metabolite Biosynthetic Genes. Mar Drugs 2020; 18:md18120652. [PMID: 33352941 PMCID: PMC7766385 DOI: 10.3390/md18120652] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2020] [Revised: 12/04/2020] [Accepted: 12/15/2020] [Indexed: 11/26/2022] Open
Abstract
Fungi are a prospective resource of bioactive compounds, but conventional methods of drug discovery are not effective enough to fully explore their metabolic potential. This study aimed to develop an easily attainable method to elicit the metabolic potential of fungi using Aspergillus nidulans laeA as a transcription regulation tool. In this study, functional analysis of Aspergillus nidulans laeA (AnLaeA) and Aspergillus sp. Z5 laeA (Az5LaeA) was done in the fungus Aspergillus sp. Z5. Heterologous AnLaeA-and native Az5LaeA-overexpression exhibited similar phenotypic effects and caused an increase in production of a bioactive compound diorcinol in Aspergillus sp. Z5, which proved the conserved function of this global regulator. In particular, heteroexpression of AnLaeA showed a significant impact on the expression of velvet complex genes, diorcinol synthesis-related genes, and different transcription factors (TFs). Moreover, heteroexpression of AnLaeA influenced the whole genome gene expression of Aspergillus sp. Z5 and triggered the upregulation of many genes. Overall, these findings suggest that heteroexpression of AnLaeA in fungi serves as a simple and easy method to explore their metabolic potential. In relation to this, AnLaeA was overexpressed in the fungus Penicillium sp. LC1-4, which resulted in increased production of quinolactacin A.
Collapse
|
24
|
Lünne F, Niehaus EM, Lipinski S, Kunigkeit J, Kalinina SA, Humpf HU. Identification of the polyketide synthase PKS7 responsible for the production of lecanoric acid and ethyl lecanorate in Claviceps purpurea. Fungal Genet Biol 2020; 145:103481. [DOI: 10.1016/j.fgb.2020.103481] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2020] [Revised: 10/14/2020] [Accepted: 10/23/2020] [Indexed: 12/25/2022]
|
25
|
El-Kashef DH, Youssef FS, Reimche I, Teusch N, Müller WEG, Lin W, Frank M, Liu Z, Proksch P. Polyketides from the marine-derived fungus Aspergillus falconensis: In silico and in vitro cytotoxicity studies. Bioorg Med Chem 2020; 29:115883. [PMID: 33248353 DOI: 10.1016/j.bmc.2020.115883] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2020] [Revised: 11/13/2020] [Accepted: 11/16/2020] [Indexed: 11/24/2022]
Abstract
Fermentation of the marine-derived fungus Aspergillus falconensis, isolated from sediment collected from the Red Sea, Egypt on solid rice medium containing 3.5% NaCl yielded a new dibenzoxepin derivative (1) and a new natural isocoumarin (2) along with six known compounds (3-8). Changes in the metabolic profile of the fungus were induced by replacing NaCl with 3.5% (NH4)2SO4 that resulted in the accumulation of three further known compounds (9-11), which were not detected when the fungus was cultivated in the presence of NaCl. The structures of the new compounds were elucidated by HRESIMS and 1D/2D NMR as well as by comparison with the literature. Molecular docking was conducted for all isolated compounds on crucial enzymes involved in the formation, progression and metastasis of cancer which included human cyclin-dependent kinase 2 (CDK-2), human DNA topoisomerase II (TOP-2) and matrix metalloproteinase 13 (MMP-13). Diorcinol (7), sulochrin (9) and monochlorosulochrin (10) displayed notable stability within the active pocket of CDK-2 with free binding energy (ΔG) equals to -25.72, -25.03 and -25.37 Kcal/mol, respectively whereas sulochrin (9) exerted the highest fitting score within MMP-13 active center (ΔG = -33.83 Kcal/mol). In vitro cytotoxic assessment using MTT assay showed that sulochrin (9) exhibited cytotoxic activity versus L5178Y mouse lymphoma cells with an IC50 value of 5.1 µM and inhibition of migration of MDA-MB 231 breast cancer cells at a concentration of 70 µM.
Collapse
Affiliation(s)
- Dina H El-Kashef
- Institute of Pharmaceutical Biology and Biotechnology, Faculty of Mathematics and Natural Sciences, Heinrich-Heine-University Düsseldorf, 40225 Düsseldorf, Germany; Department of Pharmacognosy, Faculty of Pharmacy, Minia University, 61519 Minia, Egypt
| | - Fadia S Youssef
- Institute of Pharmaceutical Biology and Biotechnology, Faculty of Mathematics and Natural Sciences, Heinrich-Heine-University Düsseldorf, 40225 Düsseldorf, Germany; Department of Pharmacognosy, Faculty of Pharmacy, Ain Shams University Abbassia, 11566 Cairo, Egypt
| | - Irene Reimche
- Department of Biomedical Sciences, Institute of Health Research and Education, University of Osnabrück, 49074 Osnabrück, Germany
| | - Nicole Teusch
- Department of Biomedical Sciences, Institute of Health Research and Education, University of Osnabrück, 49074 Osnabrück, Germany
| | - Werner E G Müller
- Institute of Physiological Chemistry, Johannes Gutenberg University Mainz, 55128 Mainz, Germany
| | - Wenhan Lin
- State Key Laboratory of Natural and Biomimetic Drugs, Peking University, Beijing 100191, China
| | - Marian Frank
- Institute of Pharmaceutical Biology and Biotechnology, Faculty of Mathematics and Natural Sciences, Heinrich-Heine-University Düsseldorf, 40225 Düsseldorf, Germany
| | - Zhen Liu
- Institute of Pharmaceutical Biology and Biotechnology, Faculty of Mathematics and Natural Sciences, Heinrich-Heine-University Düsseldorf, 40225 Düsseldorf, Germany
| | - Peter Proksch
- Institute of Pharmaceutical Biology and Biotechnology, Faculty of Mathematics and Natural Sciences, Heinrich-Heine-University Düsseldorf, 40225 Düsseldorf, Germany; Hubei Key Laboratory of Natural Products Research and Development, College of Biological and Pharmaceutical Sciences, China Three Gorges University, Yichang 443002, China
| |
Collapse
|
26
|
Wang Z, Doshi A, Chowdhury R, Wang Y, Maranas CD, Cirino PC. Engineering sensitivity and specificity of AraC-based biosensors responsive to triacetic acid lactone and orsellinic acid. Protein Eng Des Sel 2020; 33:5993570. [DOI: 10.1093/protein/gzaa027] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2020] [Revised: 10/01/2020] [Accepted: 10/09/2020] [Indexed: 11/14/2022] Open
Abstract
Abstract
We previously described the design of triacetic acid lactone (TAL) biosensor ‘AraC-TAL1’, based on the AraC regulatory protein. Although useful as a tool to screen for enhanced TAL biosynthesis, this variant shows elevated background (leaky) expression, poor sensitivity and relaxed inducer specificity, including responsiveness to orsellinic acid (OA). More sensitive biosensors specific to either TAL or OA can aid in the study and engineering of polyketide synthases that produce these and similar compounds. In this work, we employed a TetA-based dual-selection to isolate new TAL-responsive AraC variants showing reduced background expression and improved TAL sensitivity. To improve TAL specificity, OA was included as a ‘decoy’ ligand during negative selection, resulting in the isolation of a TAL biosensor that is inhibited by OA. Finally, to engineer OA-specific AraC variants, the iterative protein redesign and optimization computational framework was employed, followed by 2 rounds of directed evolution, resulting in a biosensor with 24-fold improved OA/TAL specificity, relative to AraC-TAL1.
Collapse
Affiliation(s)
- Zhiqing Wang
- Department of Chemical and Biomolecular Engineering, University of Houston, 4726 Calhoun Rd, Houston, TX 77204-4004 Houston, TX, USA
| | - Aarti Doshi
- Department of Biology and Biochemistry, University of Houston, 3507 Cullen Blvd, Houston, TX 77204-5008 Houston, TX, USA
| | - Ratul Chowdhury
- Department of Chemical and Biomedical Engineering, Penn State University, University Park, PA 16802-4400 PA, USA
| | - Yixi Wang
- Department of Chemical and Biomolecular Engineering, University of Houston, 4726 Calhoun Rd, Houston, TX 77204-4004 Houston, TX, USA
| | - Costas D Maranas
- Department of Chemical and Biomedical Engineering, Penn State University, University Park, PA 16802-4400 PA, USA
| | - Patrick C Cirino
- Department of Chemical and Biomolecular Engineering, University of Houston, 4726 Calhoun Rd, Houston, TX 77204-4004 Houston, TX, USA
- Department of Biology and Biochemistry, University of Houston, 3507 Cullen Blvd, Houston, TX 77204-5008 Houston, TX, USA
| |
Collapse
|
27
|
Schüller A, Wolansky L, Berger H, Studt L, Gacek-Matthews A, Sulyok M, Strauss J. A novel fungal gene regulation system based on inducible VPR-dCas9 and nucleosome map-guided sgRNA positioning. Appl Microbiol Biotechnol 2020; 104:9801-9822. [PMID: 33006690 PMCID: PMC7595996 DOI: 10.1007/s00253-020-10900-9] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2020] [Revised: 08/31/2020] [Accepted: 09/08/2020] [Indexed: 12/16/2022]
Abstract
Programmable transcriptional regulation is a powerful tool to study gene functions. Current methods to selectively regulate target genes are mainly based on promoter exchange or on overexpressing transcriptional activators. To expand the discovery toolbox, we designed a dCas9-based RNA-guided synthetic transcription activation system for Aspergillus nidulans that uses enzymatically disabled "dead" Cas9 fused to three consecutive activation domains (VPR-dCas9). The dCas9-encoding gene is under the control of an estrogen-responsive promoter to allow induction timing and to avoid possible negative effects by strong constitutive expression of the highly active VPR domains. Especially in silent genomic regions, facultative heterochromatin and strictly positioned nucleosomes can constitute a relevant obstacle to the transcriptional machinery. To avoid this negative impact and to facilitate optimal positioning of RNA-guided VPR-dCas9 to targeted promoters, we have created a genome-wide nucleosome map from actively growing cells and stationary cultures to identify the cognate nucleosome-free regions (NFRs). Based on these maps, different single-guide RNAs (sgRNAs) were designed and tested for their targeting and activation potential. Our results demonstrate that the system can be used to regulate several genes in parallel and, depending on the VPR-dCas9 positioning, expression can be pushed to very high levels. We have used the system to turn on individual genes within two different biosynthetic gene clusters (BGCs) which are silent under normal growth conditions. This method also opens opportunities to stepwise activate individual genes in a cluster to decipher the correlated biosynthetic pathway. Graphical abstract KEYPOINTS: • An inducible RNA-guided transcriptional regulator based on VPR-dCas9 was established in Aspergillus nidulans. • Genome-wide nucleosome positioning maps were created that facilitate sgRNA positioning. • The system was successfully applied to activate genes within two silent biosynthetic gene clusters.
Collapse
Affiliation(s)
- Andreas Schüller
- Fungal Genetics Lab, Institute of Microbial Genetics, Department of Applied Genetics and Cell Biology, BOKU-University of Natural Resources and Life Sciences Vienna, BOKU-Campus Tulln, Konrad Lorenz Strasse 24, A-3430, Tulln an der Donau, Austria
| | - Lisa Wolansky
- Institute Krems Bioanalytics , IMC FH Krems University of Applied Sciences , Krems, Austria
| | - Harald Berger
- Fungal Genetics Lab, Institute of Microbial Genetics, Department of Applied Genetics and Cell Biology, BOKU-University of Natural Resources and Life Sciences Vienna, BOKU-Campus Tulln, Konrad Lorenz Strasse 24, A-3430, Tulln an der Donau, Austria
| | - Lena Studt
- Fungal Genetics Lab, Institute of Microbial Genetics, Department of Applied Genetics and Cell Biology, BOKU-University of Natural Resources and Life Sciences Vienna, BOKU-Campus Tulln, Konrad Lorenz Strasse 24, A-3430, Tulln an der Donau, Austria
| | - Agnieszka Gacek-Matthews
- Fungal Genetics Lab, Institute of Microbial Genetics, Department of Applied Genetics and Cell Biology, BOKU-University of Natural Resources and Life Sciences Vienna, BOKU-Campus Tulln, Konrad Lorenz Strasse 24, A-3430, Tulln an der Donau, Austria
- Institute of Microbiology, Functional Microbiology Division, University of Veterinary Sciences Vienna, Wien, Austria
| | - Michael Sulyok
- Institute of Bioanalytics and Agrometabolomics, Department of Agrobiotechnology, BOKU-University of Natural Resources and Life Sciences Vienna, BOKU-Campus Tulln, Konrad-Lorenz-Straße 20, A-3430 Tulln an der Donau, Austria
| | - Joseph Strauss
- Fungal Genetics Lab, Institute of Microbial Genetics, Department of Applied Genetics and Cell Biology, BOKU-University of Natural Resources and Life Sciences Vienna, BOKU-Campus Tulln, Konrad Lorenz Strasse 24, A-3430, Tulln an der Donau, Austria.
| |
Collapse
|
28
|
Caesar LK, Kelleher NL, Keller NP. In the fungus where it happens: History and future propelling Aspergillus nidulans as the archetype of natural products research. Fungal Genet Biol 2020; 144:103477. [PMID: 33035657 DOI: 10.1016/j.fgb.2020.103477] [Citation(s) in RCA: 43] [Impact Index Per Article: 10.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2020] [Revised: 09/21/2020] [Accepted: 09/30/2020] [Indexed: 02/08/2023]
Abstract
In 1990 the first fungal secondary metabolite biosynthetic gene was cloned in Aspergillus nidulans. Thirty years later, >30 biosynthetic gene clusters (BGCs) have been linked to specific natural products in this one fungal species. While impressive, over half of the BGCs in A. nidulans remain uncharacterized and their compounds structurally and functionally unknown. Here, we provide a comprehensive review of past advances that have enabled A. nidulans to rise to its current status as a natural product powerhouse focusing on the discovery and annotation of secondary metabolite clusters. From genome sequencing, heterologous expression, and metabolomics to CRISPR and epigenetic manipulations, we present a guided tour through the evolution of technologies developed and utilized in the last 30 years. These insights provide perspective to future efforts to fully unlock the biosynthetic potential of A. nidulans and, by extension, the potential of other filamentous fungi.
Collapse
Affiliation(s)
- Lindsay K Caesar
- Department of Chemistry, Northwestern University, Evanston, IL, United States
| | - Neil L Kelleher
- Department of Chemistry, Northwestern University, Evanston, IL, United States; Department of Molecular Biosciences, Northwestern University, Evanston, IL, United States; Proteomics Center of Excellence, Northwestern University, Evanston, IL, United States
| | - Nancy P Keller
- Department of Medical Microbiology and Immunology, University of Wisconsin- Madison, Madison, WI, United States; Department of Bacteriology, University of Wisconsin-Madison, Madison, WI, United States.
| |
Collapse
|
29
|
Tuan NT, Dam NP, Van Hieu M, Trang DTX, Danh LT, Men TT, De TQ, Bach LT, Kanaori K. Chemical Constituents of the Lichen Parmotrema Tinctorum and their Antifungal Activity. Chem Nat Compd 2020. [DOI: 10.1007/s10600-020-03017-y] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
|
30
|
Malik A, Ardalani H, Anam S, McNair LM, Kromphardt KJ, Frandsen RJN, Franzyk H, Staerk D, Kongstad KT. Antidiabetic xanthones with α-glucosidase inhibitory activities from an endophytic Penicillium canescens. Fitoterapia 2020; 142:104522. [DOI: 10.1016/j.fitote.2020.104522] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2020] [Revised: 02/17/2020] [Accepted: 02/19/2020] [Indexed: 10/25/2022]
|
31
|
Mesnage R, Oestreicher N, Poirier F, Nicolas V, Boursier C, Vélot C. Transcriptome profiling of the fungus Aspergillus nidulans exposed to a commercial glyphosate-based herbicide under conditions of apparent herbicide tolerance. ENVIRONMENTAL RESEARCH 2020; 182:109116. [PMID: 32069763 DOI: 10.1016/j.envres.2020.109116] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/07/2019] [Revised: 12/18/2019] [Accepted: 01/02/2020] [Indexed: 05/20/2023]
Abstract
Glyphosate-based herbicides, such as Roundup®, are the most widely used non-selective, broad-spectrum herbicides. The release of these compounds in large amounts into the environment is susceptible to affect soil quality and health, especially because of the non-target effects on a large range of organisms including soil microorganisms. The soil filamentous fungus Aspergillus nidulans, a well-characterized experimental model organism that can be used as a bio-indicator for agricultural soil health, has been previously shown to be highly affected by Roundup GT Plus (R450: 450 g/L of glyphosate) at concentrations far below recommended agricultural application rate, including at a dose that does not cause any macroscopic effect. In this study, we determined alterations in the transcriptome of A. nidulans when exposed to R450 at a dose corresponding to the no-observed-adverse-effect level (NOAEL) for macroscopic parameters. A total of 1816 distinct genes had their expression altered. The most affected biological functions were protein synthesis, amino acids and secondary metabolisms, stress response, as well as detoxification pathways through cytochromes P450, glutathione-S-transferases, and ABC transporters. These results partly explain the molecular mechanisms underlying alterations in growth parameters detected at higher concentrations for this ascomycete fungus. In conclusion, our results highlight molecular disturbances in a soil fungus under conditions of apparent tolerance to the herbicide, and thus confirm the need to question the principle of "substantial equivalence" when applied to plants made tolerant to herbicides.
Collapse
Affiliation(s)
- Robin Mesnage
- Gene Expression and Therapy Group, King's College London, Faculty of Life Sciences & Medicine, Department of Medical and Molecular Genetics, 8th Floor, Tower Wing, Guy's Hospital, Great Maze Pond, London, SE1 9RT, United Kingdom; CRIIGEN, 42 Rue de Lisbonne, 75008, Paris, France.
| | - Nathalie Oestreicher
- Equipe VEAC, Université Paris-Sud, Faculté des Sciences, Bât. 350, Avenue Jean Perrin, 91405, Orsay, France; Pôle Risques MRSH-CNRS, EA2608, Université de Caen, Esplanade de la Paix, 14032, Caen, France.
| | - Florence Poirier
- Université Paris 13, UFR SMBH, Plateforme PPUP13, 1 Rue de Chablis, 93017, Bobigny Cedex, France.
| | - Valérie Nicolas
- UMS-IPSIT, US31 Inserm-UMS3679 CNRS, Plateformes Trans-Prot et d'Imagerie Cellulaire, Université Paris-Sud, Faculté de Pharmacie, Tour E1, 5 Rue Jean-Baptiste Clément, 92296, Châtenay-Malabry, France.
| | - Céline Boursier
- UMS-IPSIT, US31 Inserm-UMS3679 CNRS, Plateformes Trans-Prot et d'Imagerie Cellulaire, Université Paris-Sud, Faculté de Pharmacie, Tour E1, 5 Rue Jean-Baptiste Clément, 92296, Châtenay-Malabry, France.
| | - Christian Vélot
- CRIIGEN, 42 Rue de Lisbonne, 75008, Paris, France; Equipe VEAC, Université Paris-Sud, Faculté des Sciences, Bât. 350, Avenue Jean Perrin, 91405, Orsay, France; Pôle Risques MRSH-CNRS, EA2608, Université de Caen, Esplanade de la Paix, 14032, Caen, France.
| |
Collapse
|
32
|
Perlatti B, Lan N, Jiang Y, An Z, Bills G. Identification of Secondary Metabolites from Aspergillus pachycristatus by Untargeted UPLC-ESI-HRMS/MS and Genome Mining. Molecules 2020; 25:molecules25040913. [PMID: 32085602 PMCID: PMC7071103 DOI: 10.3390/molecules25040913] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2020] [Accepted: 02/14/2020] [Indexed: 11/16/2022] Open
Abstract
Aspergillus pachycristatus is an industrially important fungus for the production of the antifungal echinocandin B and is closely related to model organism A. nidulans. Its secondary metabolism is largely unknown except for the production of echinocandin B and sterigmatocystin. We constructed mutants for three genes that regulate secondary metabolism in A. pachycristatus NRRL 11440, and evaluated the secondary metabolites produced by wild type and mutants strains. The secondary metabolism was explored by metabolic networking of UPLC-HRMS/MS data. The genes and metabolites of A. pachycristatus were compared to those of A.nidulans FGSC A4 as a reference to identify compounds and link them to their encoding genes. Major differences in chromatographic profiles were observable among the mutants. At least 28 molecules were identified in crude extracts that corresponded to nine characterized gene clusters. Moreover, metabolic networking revealed the presence of a yet unexplored array of secondary metabolites, including several undescribed fellutamides derivatives. Comparative reference to its sister species, A. nidulans, was an efficient way to dereplicate known compounds, whereas metabolic networking provided information that allowed prioritization of unknown compounds for further metabolic exploration. The mutation of global regulator genes proved to be a useful tool for expanding the expression of metabolic diversity in A. pachycristatus.
Collapse
Affiliation(s)
- Bruno Perlatti
- Texas Therapeutic Institute, The Brown Foundation Institute of Molecular Medicine, University of Texas Health Science Center at Houston, Houston, TX 77054, USA; (N.L.); (Z.A.); (G.B.)
- Correspondence:
| | - Nan Lan
- Texas Therapeutic Institute, The Brown Foundation Institute of Molecular Medicine, University of Texas Health Science Center at Houston, Houston, TX 77054, USA; (N.L.); (Z.A.); (G.B.)
| | - Yongying Jiang
- Institute for Applied Cancer Science, M.D. Anderson Cancer Center, Houston, TX 77054, USA;
| | - Zhiqiang An
- Texas Therapeutic Institute, The Brown Foundation Institute of Molecular Medicine, University of Texas Health Science Center at Houston, Houston, TX 77054, USA; (N.L.); (Z.A.); (G.B.)
| | - Gerald Bills
- Texas Therapeutic Institute, The Brown Foundation Institute of Molecular Medicine, University of Texas Health Science Center at Houston, Houston, TX 77054, USA; (N.L.); (Z.A.); (G.B.)
| |
Collapse
|
33
|
Staples R, LaDuca RL, Roze LV, Laivenieks M, Linz JE, Beaudry R, Fryday A, Schilmiller AL, Koptina AV, Smith B, Trail F. Structure and Chemical Analysis of Major Specialized Metabolites Produced by the Lichen Evernia prunastri. Chem Biodivers 2020; 17:e1900465. [PMID: 31701649 DOI: 10.1002/cbdv.201900465] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2019] [Accepted: 10/21/2019] [Indexed: 01/06/2023]
Abstract
We performed comparative profiling of four specialized metabolites in the lichen Evernia prunastri, collected at three different geographic locations, California and Maine, USA, and Yoshkar Ola, Mari El, Russia. Among the compounds produced at high concentrations that were identified in all three specimens, evernic acid, usnic acid, lecanoric acid and chloroatranorin, evernic acid was the most abundant. Two depsidones, salazinic acid and physodic acid, were detected in the Yoshkar-Ola collection only. The crystalline structure of evernic acid (2-hydroxy-4-[(2-hydroxy-4-methoxy-6-methylbenzoyl)oxy]-6-methylbenzoate) (hmb) revealed two crystallographically and conformationally distinct hmb anions, along with two monovalent sodium atoms. One hmb moiety contained an exotetradentate binding mode to sodium, whereas the other exhibited an exohexadentate binding mode to sodium. Embedded edge-sharing {Na2 O8 }n sodium-oxygen chains connected the hmb anions into the full three-dimensional crystal structure of the title compound. The crystal used for single-crystal X-ray diffraction exhibited non-merohedral twinning. The data suggest the importance of the acetyl-polymalonyl pathway products to processes of maintaining integrity of the lichen holobiont community.
Collapse
Affiliation(s)
- Richard Staples
- Department of Chemistry, Michigan State University, East Lansing, MI 48824, USA
| | - Robert L LaDuca
- Department of Chemistry, Michigan State University, East Lansing, MI 48824, USA
| | - Ludmila V Roze
- Plant Biology Laboratories, Department of Plant Biology, Michigan State University, 612 Wilson Road, Room 342, East Lansing, MI 48824, USA
| | - Maris Laivenieks
- Plant Biology Laboratories, Department of Plant Biology, Michigan State University, 612 Wilson Road, Room 342, East Lansing, MI 48824, USA
| | - John E Linz
- Department of Food Science and Human Nutrition, Michigan State University, East Lansing, MI 48824, USA
| | - Randolph Beaudry
- Department of Horticulture, Michigan State University, East Lansing, MI 48824, USA
| | - Alan Fryday
- Plant Biology Laboratories, Department of Plant Biology, Michigan State University, 612 Wilson Road, Room 342, East Lansing, MI 48824, USA
| | - Anthony L Schilmiller
- RTSF Mass Spectrometry and Metabolomics Core, Michigan State University, East Lansing, MI 48824, USA
| | - Anna V Koptina
- Division of Pharmacognosy, Department of Medicinal Chemistry, Uppsala University, Uppsala, 75123, Sweden
| | - Benjamin Smith
- Plant Biology Laboratories, Department of Plant Biology, Michigan State University, 612 Wilson Road, Room 342, East Lansing, MI 48824, USA
| | - Frances Trail
- Plant Biology Laboratories, Department of Plant Biology, Michigan State University, 612 Wilson Road, Room 342, East Lansing, MI 48824, USA.,Department of Plant, Soil and Microbial Sciences, Michigan State University, East Lansing, MI 48824, USA
| |
Collapse
|
34
|
Chen Y, Yang W, Zou G, Chen S, Pang J, She Z. Bioactive polyketides from the mangrove endophytic fungi Phoma sp. SYSU-SK-7. Fitoterapia 2019; 139:104369. [PMID: 31626911 DOI: 10.1016/j.fitote.2019.104369] [Citation(s) in RCA: 22] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2019] [Revised: 10/04/2019] [Accepted: 10/04/2019] [Indexed: 10/25/2022]
Abstract
Five new polyketides, colletotric B (2), 3-hydroxy-5-methoxy-2,4,6-trimethylbenzoic acid (3), colletotric C (4), chaetochromone D (6) and 8-hydroxy-pregaliellalactone B (9), together with four known analogues (1, 5 and 7-8) were isolated from the mangrove endophytic fungus Phoma sp. SYSU-SK-7. Their structures were elucidated by analysis of extensive spectroscopic data and mass spectrometric data. Compounds 1-2 showed strong antimicrobial activity against the P. aeruginosa, MRSA and C. albicans with the MIC values in the range of 1.67-6.28 μg/ml. Furthermore, Compounds 1-5 also exhibited significant α-glucosidase inhibitory activity with the IC50 values in the range of 36.2-90.6 μM. Compound 7 was found to inhibited radical scavenging activity against DPPH with the EC50 value of 11.8 μM.
Collapse
Affiliation(s)
- Yan Chen
- School of Chemistry, Sun Yat-Sen University, Guangzhou 510275, PR China; School of Marin Sciences, Sun Yat-sen University, South China Sea Bio-Resource Exploitation and Utilization Collaborative Innovation Center, Guangzhou 510006, China
| | - Wencong Yang
- School of Chemistry, Sun Yat-Sen University, Guangzhou 510275, PR China
| | - Ge Zou
- School of Chemistry, Sun Yat-Sen University, Guangzhou 510275, PR China
| | - Shenyu Chen
- School of Chemistry, Sun Yat-Sen University, Guangzhou 510275, PR China
| | - Jiyan Pang
- School of Chemistry, Sun Yat-Sen University, Guangzhou 510275, PR China
| | - Zhigang She
- School of Chemistry, Sun Yat-Sen University, Guangzhou 510275, PR China; School of Marin Sciences, Sun Yat-sen University, South China Sea Bio-Resource Exploitation and Utilization Collaborative Innovation Center, Guangzhou 510006, China.
| |
Collapse
|
35
|
Bertrand RL, Sorensen JL. Lost in Translation: Challenges with Heterologous Expression of Lichen Polyketide Synthases. ChemistrySelect 2019. [DOI: 10.1002/slct.201901762] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
|
36
|
Romsdahl J, Wang CCC. Recent advances in the genome mining of Aspergillus secondary metabolites (covering 2012-2018). MEDCHEMCOMM 2019; 10:840-866. [PMID: 31303983 PMCID: PMC6590338 DOI: 10.1039/c9md00054b] [Citation(s) in RCA: 50] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/31/2019] [Accepted: 04/11/2019] [Indexed: 02/01/2023]
Abstract
Secondary metabolites (SMs) produced by filamentous fungi possess diverse bioactivities that make them excellent drug candidates. Whole genome sequencing has revealed that fungi have the capacity to produce a far greater number of SMs than have been isolated, since many of the genes involved in SM biosynthesis are either silent or expressed at very low levels in standard laboratory conditions. There has been significant effort to activate SM biosynthetic genes and link them to their downstream products, as the SMs produced by these "cryptic" pathways offer a promising source for new drug discovery. Further, an understanding of the genes involved in SM biosynthesis facilitates product yield optimization of first-generation molecules and genetic engineering of second-generation analogs. This review covers advances made in genome mining SMs produced by Aspergillus nidulans, Aspergillus fumigatus, Aspergillus niger, and Aspergillus terreus in the past six years (2012-2018). Genetic identification and molecular characterization of SM biosynthetic gene clusters, along with proposed biosynthetic pathways, will be discussed in depth.
Collapse
Affiliation(s)
- Jillian Romsdahl
- Department of Pharmacology and Pharmaceutical Sciences , School of Pharmacy , University of Southern California , 1985 Zonal Avenue , Los Angeles , CA 90089 , USA . ; Tel: (323) 442 1670
| | - Clay C C Wang
- Department of Pharmacology and Pharmaceutical Sciences , School of Pharmacy , University of Southern California , 1985 Zonal Avenue , Los Angeles , CA 90089 , USA . ; Tel: (323) 442 1670
- Department of Chemistry , Dornsife College of Letters, Arts, and Sciences , University of Southern California , 3551 Trousdale Pkwy , Los Angeles , CA 90089 , USA
| |
Collapse
|
37
|
Affiliation(s)
- Cheng Feng
- College of Pharmaceutical Sciences, Southwest University, Chongqing 400715, P. R. China
| | - Qian Wei
- College of Pharmaceutical Sciences, Southwest University, Chongqing 400715, P. R. China
| | - Changhua Hu
- College of Pharmaceutical Sciences, Southwest University, Chongqing 400715, P. R. China
| | - Yi Zou
- College of Pharmaceutical Sciences, Southwest University, Chongqing 400715, P. R. China
| |
Collapse
|
38
|
Uka V, Moore GG, Arroyo-Manzanares N, Nebija D, De Saeger S, Diana Di Mavungu J. Secondary Metabolite Dereplication and Phylogenetic Analysis Identify Various Emerging Mycotoxins and Reveal the High Intra-Species Diversity in Aspergillus flavus. Front Microbiol 2019; 10:667. [PMID: 31024476 PMCID: PMC6461017 DOI: 10.3389/fmicb.2019.00667] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2018] [Accepted: 03/18/2019] [Indexed: 12/18/2022] Open
Abstract
Aspergillus flavus is one of the most important mycotoxigenic species from the genus Aspergillus, due to its ability to synthesize the potent hepatocarcinogen, aflatoxin B1. Moreover, this fungus is capable of producing several other toxic metabolites from the class of indole-tetramates, non-ribosomal peptides, and indole-diterpenoids. Populations of A. flavus are characterized by considerable diversity in terms of morphological, functional and genetic features. Although for many years A. flavus was considered an asexual fungus, researchers have shown evidence that at best these fungi can exhibit a predominantly asexual existence. We now know that A. flavus contains functional genes for mating, uncovering sexuality as potential contributor for its diversification. Based on our results, we reconfirm that A. flavus is a predominant producer of B-type aflatoxins. Moreover, this fungus can decisively produce AFM1 and AFM2. We did not observe any clear relationship between mating-type genes and particular class of metabolites, probably other parameters such as sexual/asexual ratio should be investigated. A dynamic secondary metabolism was found also in strains intended to be used as biocontrol agents. In addition we succeeded to provide mass spectrometry fragmentation spectra for the most important classes of A. flavus metabolites, which will serve as identification cards for future studies. Both, metabolic and phylogenetic analysis proved a high intra-species diversity for A. flavus. These findings contribute to our understanding about the diversity of Aspergillus section Flavi species, raising the necessity for polyphasic approaches (morphological, metabolic, genetic, etc.) when dealing with this type of complex group of species.
Collapse
Affiliation(s)
- Valdet Uka
- Center of Excellence in Mycotoxicology and Public Health, Faculty of Pharmaceutical Sciences, Ghent University, Ghent, Belgium.,Department of Pharmacy, Faculty of Medicine, University of Prishtina, Prishtina, Kosovo†
| | - Geromy G Moore
- Southern Regional Research Center, Agricultural Research Service, United States Department of Agriculture, New Orleans, LA, United States
| | - Natalia Arroyo-Manzanares
- Department of Analytical Chemistry, Faculty of Chemistry, Regional Campus of International Excellence "Campus Mare-Nostrum", University of Murcia, Murcia, Spain
| | - Dashnor Nebija
- Department of Pharmacy, Faculty of Medicine, University of Prishtina, Prishtina, Kosovo†
| | - Sarah De Saeger
- Center of Excellence in Mycotoxicology and Public Health, Faculty of Pharmaceutical Sciences, Ghent University, Ghent, Belgium
| | - José Diana Di Mavungu
- Center of Excellence in Mycotoxicology and Public Health, Faculty of Pharmaceutical Sciences, Ghent University, Ghent, Belgium
| |
Collapse
|
39
|
Hitzenhammer E, Büschl C, Sulyok M, Schuhmacher R, Kluger B, Wischnitzki E, Schmoll M. YPR2 is a regulator of light modulated carbon and secondary metabolism in Trichoderma reesei. BMC Genomics 2019; 20:211. [PMID: 30866811 PMCID: PMC6417087 DOI: 10.1186/s12864-019-5574-8] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2018] [Accepted: 02/28/2019] [Indexed: 12/19/2022] Open
Abstract
BACKGROUND Filamentous fungi have evolved to succeed in nature by efficient growth and degradation of substrates, but also due to the production of secondary metabolites including mycotoxins. For Trichoderma reesei, as a biotechnological workhorse for homologous and heterologous protein production, secondary metabolite secretion is of particular importance for industrial application. Recent studies revealed an interconnected regulation of enzyme gene expression and carbon metabolism with secondary metabolism. RESULTS Here, we investigated gene regulation by YPR2, one out of two transcription factors located within the SOR cluster of T. reesei, which is involved in biosynthesis of sorbicillinoids. Transcriptome analysis showed that YPR2 exerts its major function in constant darkness upon growth on cellulose. Targets (direct and indirect) of YPR2 overlap with induction specific genes as well as with targets of the carbon catabolite repressor CRE1 and a considerable proportion is regulated by photoreceptors as well. Functional category analysis revealed both effects on carbon metabolism and secondary metabolism. Further, we found indications for an involvement of YPR2 in regulation of siderophores. In agreement with transcriptome data, mass spectrometric analyses revealed a broad alteration in metabolite patterns in ∆ypr2. Additionally, YPR2 positively influenced alamethicin levels along with transcript levels of the alamethicin synthase tex1 and is essential for production of orsellinic acid in darkness. CONCLUSIONS YPR2 is an important regulator balancing secondary metabolism with carbon metabolism in darkness and depending on the carbon source. The function of YPR2 reaches beyond the SOR cluster in which ypr2 is located and happens downstream of carbon catabolite repression mediated by CRE1.
Collapse
Affiliation(s)
- Eva Hitzenhammer
- AIT - Austrian Institute of Technology GmbH, Center for Health and Bioresources, Konrad-Lorenz-Strasse 24, 3430 Tulln, Austria
| | - Christoph Büschl
- Department of Agrobiotechnology (IFA-Tulln), Center for Analytical Chemistry, University of Natural Resources and Life Sciences Vienna, (BOKU), Konrad-Lorenz-Straße 20, 3430 Tulln, Austria
| | - Michael Sulyok
- Department of Agrobiotechnology (IFA-Tulln), Center for Analytical Chemistry, University of Natural Resources and Life Sciences Vienna, (BOKU), Konrad-Lorenz-Straße 20, 3430 Tulln, Austria
| | - Rainer Schuhmacher
- Department of Agrobiotechnology (IFA-Tulln), Center for Analytical Chemistry, University of Natural Resources and Life Sciences Vienna, (BOKU), Konrad-Lorenz-Straße 20, 3430 Tulln, Austria
| | - Bernhard Kluger
- Department of Agrobiotechnology (IFA-Tulln), Center for Analytical Chemistry, University of Natural Resources and Life Sciences Vienna, (BOKU), Konrad-Lorenz-Straße 20, 3430 Tulln, Austria
| | - Elisabeth Wischnitzki
- AIT - Austrian Institute of Technology GmbH, Center for Health and Bioresources, Konrad-Lorenz-Strasse 24, 3430 Tulln, Austria
| | - Monika Schmoll
- AIT - Austrian Institute of Technology GmbH, Center for Health and Bioresources, Konrad-Lorenz-Strasse 24, 3430 Tulln, Austria
| |
Collapse
|
40
|
Biosynthetic Gene Content of the 'Perfume Lichens' Evernia prunastri and Pseudevernia furfuracea. Molecules 2019; 24:molecules24010203. [PMID: 30626017 PMCID: PMC6337363 DOI: 10.3390/molecules24010203] [Citation(s) in RCA: 23] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2018] [Revised: 12/29/2018] [Accepted: 01/04/2019] [Indexed: 12/26/2022] Open
Abstract
Lichen-forming fungi produce a vast number of unique natural products with a wide variety of biological activities and human uses. Although lichens have remarkable potential in natural product research and industry, the molecular mechanisms underlying the biosynthesis of lichen metabolites are poorly understood. Here we use genome mining and comparative genomics to assess biosynthetic gene clusters and their putative regulators in the genomes of two lichen-forming fungi, which have substantial commercial value in the perfume industry, Evernia prunastri and Pseudevernia furfuracea. We report a total of 80 biosynthetic gene clusters (polyketide synthases (PKS), non-ribosomal peptide synthetases and terpene synthases) in E. prunastri and 51 in P. furfuracea. We present an in-depth comparison of 11 clusters, which show high homology between the two species. A ketosynthase (KS) phylogeny shows that biosynthetic gene clusters from E. prunastri and P. furfuracea are widespread across the Fungi. The phylogeny includes 15 genomes of lichenized fungi and all fungal PKSs with known functions from the MIBiG database. Phylogenetically closely related KS domains predict not only similar PKS architecture but also similar cluster architecture. Our study highlights the untapped biosynthetic richness of lichen-forming fungi, provides new insights into lichen biosynthetic pathways and facilitates heterologous expression of lichen biosynthetic gene clusters.
Collapse
|
41
|
Wang Y, Geng C, Yuan X, Hua M, Tian F, Li C. Identification of a putative polyketide synthase gene involved in usnic acid biosynthesis in the lichen Nephromopsis pallescens. PLoS One 2018; 13:e0199110. [PMID: 30020937 PMCID: PMC6051580 DOI: 10.1371/journal.pone.0199110] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2018] [Accepted: 05/31/2018] [Indexed: 11/30/2022] Open
Abstract
Usnic acid is a unique polyketide produced by lichens. To characterize usnic acid biosynthesis, the transcriptome of the usnic-acid-producing lichen-forming fungus Nephromopsis pallescens was sequenced using Illumina NextSeq technology. Seven complete non-reducing polyketide synthase genes and nine highly-reducing polyketide synthase genes were obtained through transcriptome analysis. Gene expression results obtained by qPCR and usnic acid detection with LCMS-IT-TOF showed that Nppks7 is probably involved in usnic acid biosynthesis in N. pallescens. Nppks7 is a non-reducing polyketide synthase with a MeT domain that also possesses beta-ketoacyl-ACP synthase, acyl transferase, product template, acyl carrier protein, C-methyltransferase, and Claisen cyclase domains. Phylogenetic analysis shows that Nppks7and other polyketide synthases from lichens form a unique monophyletic clade. Taken together, our data indicate that Nppks7 is a novel PKS in N. pallescens that is likely involved in usnic acid biosynthesis.
Collapse
Affiliation(s)
- Yi Wang
- Key Laboratory of Forest Plant Cultivation and Utilization, Yunnan Academy of Forestry, Kunming Yunnan, China
- Engineering Research Center of Chinese Ministry of Education for Edible and Medicinal Fungi, Jilin Agricultural University, Changchun, China
| | - Changan Geng
- State Key Laboratory of Phytochemistry and Plant Resources in West China, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, China
| | - Xiaolong Yuan
- Key Laboratory of Forest Plant Cultivation and Utilization, Yunnan Academy of Forestry, Kunming Yunnan, China
| | - Mei Hua
- Key Laboratory of Forest Plant Cultivation and Utilization, Yunnan Academy of Forestry, Kunming Yunnan, China
| | - Fenghua Tian
- Engineering Research Center of Chinese Ministry of Education for Edible and Medicinal Fungi, Jilin Agricultural University, Changchun, China
| | - Changtian Li
- Engineering Research Center of Chinese Ministry of Education for Edible and Medicinal Fungi, Jilin Agricultural University, Changchun, China
| |
Collapse
|
42
|
Calcott MJ, Ackerley DF, Knight A, Keyzers RA, Owen JG. Secondary metabolism in the lichen symbiosis. Chem Soc Rev 2018; 47:1730-1760. [PMID: 29094129 DOI: 10.1039/c7cs00431a] [Citation(s) in RCA: 116] [Impact Index Per Article: 19.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
Lichens, which are defined by a core symbiosis between a mycobiont (fungal partner) and a photobiont (photoautotrophic partner), are in fact complex assemblages of microorganisms that constitute a largely untapped source of bioactive secondary metabolites. Historically, compounds isolated from lichens have predominantly been those produced by the dominant fungal partner, and these continue to be of great interest for their unique chemistry and biotechnological potential. In recent years it has become apparent that many photobionts and lichen-associated bacteria also produce a range of potentially valuable molecules. There is evidence to suggest that the unique nature of the symbiosis has played a substantial role in shaping many aspects of lichen chemistry, for example driving bacteria to produce metabolites that do not bring them direct benefit but are useful to the lichen as a whole. This is most evident in studies of cyanobacterial photobionts, which produce compounds that differ from free living cyanobacteria and are unique to symbiotic organisms. The roles that these and other lichen-derived molecules may play in communication and maintaining the symbiosis are poorly understood at present. Nonetheless, advances in genomics, mass spectrometry and other analytical technologies are continuing to illuminate the wealth of biological and chemical diversity present within the lichen holobiome. Implementation of novel biodiscovery strategies such as metagenomic screening, coupled with synthetic biology approaches to reconstitute, re-engineer and heterologously express lichen-derived biosynthetic gene clusters in a cultivable host, offer a promising means for tapping into this hitherto inaccessible wealth of natural products.
Collapse
Affiliation(s)
- Mark J Calcott
- School of Biological Sciences, Victoria University of Wellington, New Zealand.
| | | | | | | | | |
Collapse
|
43
|
Qadri M, Nalli Y, Jain SK, Chaubey A, Ali A, Strobel GA, Vishwakarma RA, Riyaz-Ul-Hassan S. An Insight into the Secondary Metabolism of Muscodor yucatanensis: Small-Molecule Epigenetic Modifiers Induce Expression of Secondary Metabolism-Related Genes and Production of New Metabolites in the Endophyte. MICROBIAL ECOLOGY 2017; 73:954-965. [PMID: 27924400 DOI: 10.1007/s00248-016-0901-y] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/10/2016] [Accepted: 11/13/2016] [Indexed: 05/02/2023]
Abstract
Muscodor spp. are proficient producers of bioactive volatile organic compounds (VOCs) with many potential applications. However, all members of this genus produce varying amounts and types of VOCs which suggests the involvement of epigenetics as a possible explanation. The members of this genus are poorly explored for the production of soluble compounds (extrolites). In this study, the polyketide synthase (PKS) and non-ribosomal peptide synthetase (NRPS) genes from an endophyte, Muscodor yucatanensis Ni30, were cloned and sequenced. The PKS genes belonged to reduced, partially reduced, non-reduced, and highly reduced subtypes. Strains over-expressing PKS genes were developed through the use of small-molecule epigenetic modifiers (suberoylanilide hydroxamic acid (SAHA) and 5-azacytidine). The putative epigenetic variants of this organism differed considerably from the wild type in morphological features and cultural characteristics as well as metabolites that were produced. Each variant produced a different set of VOCs distinct from the wild type, and several VOCs including methyl 3-(3,5-di-tert-butyl-4-hydroxyphenyl)hexane-2,4-diol and 2-carboxymethyl-3-n-hexylmaleic appeared in the variant strains, the production of which could be attributed to the activity of otherwise silent PKS genes. The bioactive extrolite brefeldin A was isolated and characterized from the wild type. However, this metabolite was not detected in EV-1, but instead, two other products were isolated and characterized as ergosterol and xylaguaianol C. Hence, M. yucatanensis has the genetic potential to produce several previously undetectable VOCs and organic solvent soluble products. It is also the case that small-molecule epigenetic modifiers can be used to produce stable variant strains of fungi with the potential to produce new molecules. Finally, this work hints to the prospect that the epigenetics of an endophytic microorganism can be influenced by any number of environmental and chemical factors associated with its host plant which may help to explain the enormous chemical diversity of secondary metabolic products found in Muscodor spp.
Collapse
Affiliation(s)
- Masroor Qadri
- Microbial Biotechnology Division, CSIR-Indian Institute of Integrative Medicine, Canal Road, Jammu Tawi, 180001, India
| | - Yedukondalu Nalli
- Natural Product Chemistry Division, CSIR-Indian Institute of Integrative Medicine, Canal Road, Jammu Tawi, 180001, India
- Academy of Scientific and Innovative Research (AcSIR), CSIR-Indian Institute of Integrative Medicine, Canal Road, Jammu Tawi, 180001, India
| | - Shreyans K Jain
- Natural Product Chemistry Division, CSIR-Indian Institute of Integrative Medicine, Canal Road, Jammu Tawi, 180001, India
- Academy of Scientific and Innovative Research (AcSIR), CSIR-Indian Institute of Integrative Medicine, Canal Road, Jammu Tawi, 180001, India
| | - Asha Chaubey
- Academy of Scientific and Innovative Research (AcSIR), CSIR-Indian Institute of Integrative Medicine, Canal Road, Jammu Tawi, 180001, India
- Fermentation Division, CSIR-Indian Institute of Integrative Medicine, Canal Road, Jammu Tawi, 180001, India
| | - Asif Ali
- Natural Product Chemistry Division, CSIR-Indian Institute of Integrative Medicine, Canal Road, Jammu Tawi, 180001, India
- Academy of Scientific and Innovative Research (AcSIR), CSIR-Indian Institute of Integrative Medicine, Canal Road, Jammu Tawi, 180001, India
| | - Gary A Strobel
- Department of Plant Sciences, Montana State University, Bozeman, MT, 59717, USA
| | - Ram A Vishwakarma
- Natural Product Chemistry Division, CSIR-Indian Institute of Integrative Medicine, Canal Road, Jammu Tawi, 180001, India
- Academy of Scientific and Innovative Research (AcSIR), CSIR-Indian Institute of Integrative Medicine, Canal Road, Jammu Tawi, 180001, India
| | - Syed Riyaz-Ul-Hassan
- Microbial Biotechnology Division, CSIR-Indian Institute of Integrative Medicine, Canal Road, Jammu Tawi, 180001, India.
- Academy of Scientific and Innovative Research (AcSIR), CSIR-Indian Institute of Integrative Medicine, Canal Road, Jammu Tawi, 180001, India.
| |
Collapse
|
44
|
Serrano R, González-Menéndez V, Rodríguez L, Martín J, Tormo JR, Genilloud O. Co-culturing of Fungal Strains Against Botrytis cinerea as a Model for the Induction of Chemical Diversity and Therapeutic Agents. Front Microbiol 2017; 8:649. [PMID: 28469610 PMCID: PMC5396503 DOI: 10.3389/fmicb.2017.00649] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2016] [Accepted: 03/29/2017] [Indexed: 01/10/2023] Open
Abstract
New fungal SMs (SMs) have been successfully described to be produced by means of in vitro-simulated microbial community interactions. Co-culturing of fungi has proved to be an efficient way to induce cell–cell interactions that can promote the activation of cryptic pathways, frequently silent when the strains are grown in laboratory conditions. Filamentous fungi represent one of the most diverse microbial groups known to produce bioactive natural products. Triggering the production of novel antifungal compounds in fungi could respond to the current needs to fight health compromising pathogens and provide new therapeutic solutions. In this study, we have selected the fungus Botrytis cinerea as a model to establish microbial interactions with a large set of fungal strains related to ecosystems where they can coexist with this phytopathogen, and to generate a collection of extracts, obtained from their antagonic microbial interactions and potentially containing new bioactive compounds. The antifungal specificity of the extracts containing compounds induced after B. cinerea interaction was determined against two human fungal pathogens (Candida albicans and Aspergillus fumigatus) and three phytopathogens (Colletotrichum acutatum, Fusarium proliferatum, and Magnaporthe grisea). In addition, their cytotoxicity was also evaluated against the human hepatocellular carcinoma cell line (HepG2). We have identified by LC-MS the production of a wide variety of known compounds induced from these fungal interactions, as well as novel molecules that support the potential of this approach to generate new chemical diversity and possible new therapeutic agents.
Collapse
Affiliation(s)
- Rachel Serrano
- Fundación MEDINA, Centro de Excelencia en Investigación de Medicamentos Innovadores en AndalucíaGranada, Spain
| | - Víctor González-Menéndez
- Fundación MEDINA, Centro de Excelencia en Investigación de Medicamentos Innovadores en AndalucíaGranada, Spain
| | - Lorena Rodríguez
- Fundación MEDINA, Centro de Excelencia en Investigación de Medicamentos Innovadores en AndalucíaGranada, Spain
| | - Jesús Martín
- Fundación MEDINA, Centro de Excelencia en Investigación de Medicamentos Innovadores en AndalucíaGranada, Spain
| | - José R Tormo
- Fundación MEDINA, Centro de Excelencia en Investigación de Medicamentos Innovadores en AndalucíaGranada, Spain
| | - Olga Genilloud
- Fundación MEDINA, Centro de Excelencia en Investigación de Medicamentos Innovadores en AndalucíaGranada, Spain
| |
Collapse
|
45
|
Armaleo D, Sun X, Culberson C. Insights from the first putative biosynthetic gene cluster for a lichen depside and depsidone. Mycologia 2017; 103:741-54. [DOI: 10.3852/10-335] [Citation(s) in RCA: 74] [Impact Index Per Article: 10.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Affiliation(s)
- Daniele Armaleo
- Department of Biology, Duke University, North Carolina 27708
| | - Xiameng Sun
- Hematology Branch, NHLBI, NIH, Bethesda, Maryland 20892
| | | |
Collapse
|
46
|
Gu BB, Tang J, Wang SP, Sun F, Yang F, Li L, Xu Y, Lin HW. Structure, absolute configuration, and variable-temperature1H-NMR study of (±)-versiorcinols A–C, three racemates of diorcinol monoethers from the sponge-associated fungus Aspergillus versicolor 16F-11. RSC Adv 2017. [DOI: 10.1039/c7ra06106d] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
Structure, absolute configuration, and variable-temperature1H-NMR study of three racemates of diorcinol monoethers, (±)-versiorcinols A–C.
Collapse
Affiliation(s)
- Bin-Bin Gu
- Key Laboratory for Marine Drugs
- Department of Pharmacy
- State Key Laboratory of Oncogenes and Related Genes
- Renji Hospital School of Medicine
- Shanghai Jiao Tong University
| | - Jie Tang
- Key Laboratory for Marine Drugs
- Department of Pharmacy
- State Key Laboratory of Oncogenes and Related Genes
- Renji Hospital School of Medicine
- Shanghai Jiao Tong University
| | - Shu-Ping Wang
- Key Laboratory for Marine Drugs
- Department of Pharmacy
- State Key Laboratory of Oncogenes and Related Genes
- Renji Hospital School of Medicine
- Shanghai Jiao Tong University
| | - Fan Sun
- Key Laboratory for Marine Drugs
- Department of Pharmacy
- State Key Laboratory of Oncogenes and Related Genes
- Renji Hospital School of Medicine
- Shanghai Jiao Tong University
| | - Fan Yang
- Key Laboratory for Marine Drugs
- Department of Pharmacy
- State Key Laboratory of Oncogenes and Related Genes
- Renji Hospital School of Medicine
- Shanghai Jiao Tong University
| | - Lei Li
- Key Laboratory for Marine Drugs
- Department of Pharmacy
- State Key Laboratory of Oncogenes and Related Genes
- Renji Hospital School of Medicine
- Shanghai Jiao Tong University
| | - Ying Xu
- Key Laboratory for Marine Drugs
- Department of Pharmacy
- State Key Laboratory of Oncogenes and Related Genes
- Renji Hospital School of Medicine
- Shanghai Jiao Tong University
| | - Hou-Wen Lin
- Key Laboratory for Marine Drugs
- Department of Pharmacy
- State Key Laboratory of Oncogenes and Related Genes
- Renji Hospital School of Medicine
- Shanghai Jiao Tong University
| |
Collapse
|
47
|
Chen AJ, Frisvad JC, Sun BD, Varga J, Kocsubé S, Dijksterhuis J, Kim DH, Hong SB, Houbraken J, Samson RA. Aspergillus section Nidulantes (formerly Emericella): Polyphasic taxonomy, chemistry and biology. Stud Mycol 2016; 84:1-118. [PMID: 28050053 PMCID: PMC5198626 DOI: 10.1016/j.simyco.2016.10.001] [Citation(s) in RCA: 90] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/01/2022] Open
Abstract
Aspergillus section Nidulantes includes species with striking morphological characters, such as biseriate conidiophores with brown-pigmented stipes, and if present, the production of ascomata embedded in masses of Hülle cells with often reddish brown ascospores. The majority of species in this section have a sexual state, which were named Emericella in the dual name nomenclature system. In the present study, strains belonging to subgenus Nidulantes were subjected to multilocus molecular phylogenetic analyses using internal transcribed spacer region (ITS), partial β-tubulin (BenA), calmodulin (CaM) and RNA polymerase II second largest subunit (RPB2) sequences. Nine sections are accepted in subgenus Nidulantes including the new section Cavernicolus. A polyphasic approach using morphological characters, extrolites, physiological characters and phylogeny was applied to investigate the taxonomy of section Nidulantes. Based on this approach, section Nidulantes is subdivided in seven clades and 65 species, and 10 species are described here as new. Morphological characters including colour, shape, size, and ornamentation of ascospores, shape and size of conidia and vesicles, growth temperatures are important for identifying species. Many species of section Nidulantes produce the carcinogenic mycotoxin sterigmatocystin. The most important mycotoxins in Aspergillus section Nidulantes are aflatoxins, sterigmatocystin, emestrin, fumitremorgins, asteltoxins, and paxillin while other extrolites are useful drugs or drug lead candidates such as echinocandins, mulundocandins, calbistrins, varitriols, variecolins and terrain. Aflatoxin B1 is produced by four species: A. astellatus, A. miraensis, A. olivicola, and A. venezuelensis.
Collapse
Affiliation(s)
- A J Chen
- Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, 100193, PR China; CBS-KNAW Fungal Biodiversity Centre, Uppsalalaan 8, 3584 CT, Utrecht, The Netherlands
| | - J C Frisvad
- Department of Systems Biology, Søltofts Plads B. 221, Technical University of Denmark, 2800, Kongens Lyngby, Denmark
| | - B D Sun
- China General Microbiological Culture Collection Centre, Institute of Microbiology, Chinese Academy of Sciences, Beichen West Road, Chaoyang District, Beijing, 100101, PR China
| | - J Varga
- Department of Microbiology, Faculty of Science and Informatics, University of Szeged, H-6726, Szeged, Hungary
| | - S Kocsubé
- Department of Microbiology, Faculty of Science and Informatics, University of Szeged, H-6726, Szeged, Hungary
| | - J Dijksterhuis
- CBS-KNAW Fungal Biodiversity Centre, Uppsalalaan 8, 3584 CT, Utrecht, The Netherlands
| | - D H Kim
- Division of Forest Environment Protection, Kangwon National University, Chuncheon, 24341, Republic of Korea
| | - S-B Hong
- Korean Agricultural Culture Collection, National Institute of Agricultural Science, 166, Nongsaengmyeong-ro, Iseo-myeon, Wanju-gun, Jeollabuk-do, 55365, Republic of Korea
| | - J Houbraken
- CBS-KNAW Fungal Biodiversity Centre, Uppsalalaan 8, 3584 CT, Utrecht, The Netherlands
| | - R A Samson
- CBS-KNAW Fungal Biodiversity Centre, Uppsalalaan 8, 3584 CT, Utrecht, The Netherlands
| |
Collapse
|
48
|
Structural Elucidation and Free Radical Scavenging Activity of a new o-Orsellinic Acid Derivative Isolated from the Lichen Cladonia rappii. Nat Prod Commun 2016. [DOI: 10.1177/1934578x1601100932] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022] Open
Abstract
Rappiidic acid, a new o-orsellinic acid derivative, was isolated from the lichen Cladonia rappii. Its capability to scavenge reactive oxygen species (ROS) and reactive nitrogen species (RNS) was investigated and compared with resveratrol and (+)-usnic acid. Usnic acid at 100 μM was the most efficient ROS scavenger, exhibiting activity 3-fold higher than that of resveratrol. At the same concentration, rappidic acid scavenged 23.1% of ROS formed, demonstrating that this compound is twice as active as resveratrol. Both compounds were shown to be poor RNS scavengers.
Collapse
|
49
|
KdmB, a Jumonji Histone H3 Demethylase, Regulates Genome-Wide H3K4 Trimethylation and Is Required for Normal Induction of Secondary Metabolism in Aspergillus nidulans. PLoS Genet 2016; 12:e1006222. [PMID: 27548260 PMCID: PMC4993369 DOI: 10.1371/journal.pgen.1006222] [Citation(s) in RCA: 52] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2015] [Accepted: 07/06/2016] [Indexed: 12/12/2022] Open
Abstract
Histone posttranslational modifications (HPTMs) are involved in chromatin-based regulation of fungal secondary metabolite biosynthesis (SMB) in which the corresponding genes—usually physically linked in co-regulated clusters—are silenced under optimal physiological conditions (nutrient-rich) but are activated when nutrients are limiting. The exact molecular mechanisms by which HPTMs influence silencing and activation, however, are still to be better understood. Here we show by a combined approach of quantitative mass spectrometry (LC-MS/MS), genome-wide chromatin immunoprecipitation (ChIP-seq) and transcriptional network analysis (RNA-seq) that the core regions of silent A. nidulans SM clusters generally carry low levels of all tested chromatin modifications and that heterochromatic marks flank most of these SM clusters. During secondary metabolism, histone marks typically associated with transcriptional activity such as H3 trimethylated at lysine-4 (H3K4me3) are established in some, but not all gene clusters even upon full activation. KdmB, a Jarid1-family histone H3 lysine demethylase predicted to comprise a BRIGHT domain, a zinc-finger and two PHD domains in addition to the catalytic Jumonji domain, targets and demethylates H3K4me3 in vivo and mediates transcriptional downregulation. Deletion of kdmB leads to increased transcription of about ~1750 genes across nutrient-rich (primary metabolism) and nutrient-limiting (secondary metabolism) conditions. Unexpectedly, an equally high number of genes exhibited reduced expression in the kdmB deletion strain and notably, this group was significantly enriched for genes with known or predicted functions in secondary metabolite biosynthesis. Taken together, this study extends our general knowledge about multi-domain KDM5 histone demethylases and provides new details on the chromatin-level regulation of fungal secondary metabolite production. In this work we monitored by proteomic analysis and ChIP-seq the genome-wide distribution of several key modifications on histone H3 in the model fungus Aspergillus nidulans cultivated either under optimal physiological conditions (active growth) or less favourable conditions which are known to promote the production of secondary metabolites (SM). When we correlated the chromatin status to transcriptional activities in actively growing cells we found that the silenced SM gene clusters are flanked by heterochromatic domains presumably contributing to silencing but that the bodies of the clusters only carry background levels of any of the investigated marks. In nutrient-depleted conditions, activating marks were invading some, but by far not all transcribed clusters, leaving open the question how activation of these regions occurs at the chromatin level. Surprisingly, a large number of these gene clusters actually depend on KdmB for normal activation and it will be interesting to see in future how this protein thought to mainly act as repressor by removing positive H3K4m3 marks switches gears to activate transcription directly or indirectly.
Collapse
|
50
|
Alves PC, Hartmann DO, Núñez O, Martins I, Gomes TL, Garcia H, Galceran MT, Hampson R, Becker JD, Silva Pereira C. Transcriptomic and metabolomic profiling of ionic liquid stimuli unveils enhanced secondary metabolism in Aspergillus nidulans. BMC Genomics 2016; 17:284. [PMID: 27072538 PMCID: PMC4830055 DOI: 10.1186/s12864-016-2577-6] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2015] [Accepted: 03/08/2016] [Indexed: 12/13/2022] Open
Abstract
BACKGROUND The inherent potential of filamentous fungi, especially of Ascomycota, for producing diverse bioactive metabolites remains largely silent under standard laboratory culture conditions. Innumerable strategies have been described to trigger their production, one of the simplest being manipulation of the growth media composition. Supplementing media with ionic liquids surprisingly enhanced the diversity of extracellular metabolites generated by penicillia. This finding led us to evaluate the impact of ionic liquids' stimuli on the fungal metabolism in Aspergillus nidulans and how it reflects on the biosynthesis of secondary metabolites (SMs). RESULTS Whole transcriptional profiling showed that exposure to 0.7 M cholinium chloride or 1-ethyl-3-methylimidazolium chloride dramatically affected expression of genes encoding both primary and secondary metabolism. Both ionic liquids apparently induced stress responses and detoxification mechanisms but response profiles to each stimulus were unique. Primary metabolism was up-regulated by choline, but down-regulated by 1-ethyl-3-methylimidazolium chloride; both stimulated production of acetyl-CoA (key precursor to numerous SMs) and non proteinogenic amino acids (building blocks of bioactive classes of SMs). In total, twenty one of the sixty six described backbone genes underwent up-regulation. Accordingly, differential analysis of the fungal metabolome showed that supplementing growth media with ionic liquids resulted in ca. 40 differentially accumulated ion masses compared to control conditions. In particular, it stimulated production of monodictyphenone and orsellinic acid, otherwise cryptic. Expression levels of genes encoding corresponding polyketide biosynthetic enzymes (i.e. backbone genes) increased compared to control conditions. The corresponding metabolite extracts showed increased cell polarity modulation potential in an ex vivo whole tissue assay (The lial Live Targeted Epithelia; theLiTE™). CONCLUSIONS Ionic liquids, a diverse class of chemicals composed solely of ions, can provide an unexpected means to further resolve the diversity of natural compounds, guiding discovery of fungal metabolites with clinical potential.
Collapse
Affiliation(s)
- Paula C Alves
- Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa, Av. da República, 2780-157, Oeiras, Portugal
| | - Diego O Hartmann
- Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa, Av. da República, 2780-157, Oeiras, Portugal
| | - Oscar Núñez
- Department of Analytical Chemistry, University of Barcelona, Diagonal 645, E-08028, Barcelona, Spain.,Serra Hunter Fellow, Generalitat de Catalunya, Barcelona, Spain
| | - Isabel Martins
- Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa, Av. da República, 2780-157, Oeiras, Portugal
| | - Teresa L Gomes
- Thelial Technologies S.A., Parque Tecnológico de Cantanhede, Nucleo 04 Lote 3, 3060-197, Cantanhede, Portugal
| | - Helga Garcia
- Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa, Av. da República, 2780-157, Oeiras, Portugal
| | - Maria Teresa Galceran
- Department of Analytical Chemistry, University of Barcelona, Diagonal 645, E-08028, Barcelona, Spain
| | - Richard Hampson
- Thelial Technologies S.A., Parque Tecnológico de Cantanhede, Nucleo 04 Lote 3, 3060-197, Cantanhede, Portugal
| | - Jörg D Becker
- Instituto Gulbenkian de Ciência, Rua da Quinta Grande 6, 2780-156, Oeiras, Portugal
| | - Cristina Silva Pereira
- Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa, Av. da República, 2780-157, Oeiras, Portugal.
| |
Collapse
|