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Sang M, Feng P, Chi LP, Zhang W. The biosynthetic logic and enzymatic machinery of approved fungi-derived pharmaceuticals and agricultural biopesticides. Nat Prod Rep 2024; 41:565-603. [PMID: 37990930 DOI: 10.1039/d3np00040k] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2023]
Abstract
Covering: 2000 to 2023The kingdom Fungi has become a remarkably valuable source of structurally complex natural products (NPs) with diverse bioactivities. Since the revolutionary discovery and application of the antibiotic penicillin from Penicillium, a number of fungi-derived NPs have been developed and approved into pharmaceuticals and pesticide agents using traditional "activity-guided" approaches. Although emerging genome mining algorithms and surrogate expression hosts have brought revolutionary approaches to NP discovery, the time and costs involved in developing these into new drugs can still be prohibitively high. Therefore, it is essential to maximize the utility of existing drugs by rational design and systematic production of new chemical structures based on these drugs by synthetic biology. To this purpose, there have been great advances in characterizing the diversified biosynthetic gene clusters associated with the well-known drugs and in understanding the biosynthesis logic mechanisms and enzymatic transformation processes involved in their production. We describe advances made in the heterogeneous reconstruction of complex NP scaffolds using fungal polyketide synthases (PKSs), non-ribosomal peptide synthetases (NRPSs), PKS/NRPS hybrids, terpenoids, and indole alkaloids and also discuss mechanistic insights into metabolic engineering, pathway reprogramming, and cell factory development. Moreover, we suggest pathways for expanding access to the fungal chemical repertoire by biosynthesis of representative family members via common platform intermediates and through the rational manipulation of natural biosynthetic machineries for drug discovery.
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Affiliation(s)
- Moli Sang
- State Key Laboratory of Microbial Technology, Shandong University, Qingdao, Shandong 266237, China.
| | - Peiyuan Feng
- State Key Laboratory of Microbial Technology, Shandong University, Qingdao, Shandong 266237, China.
| | - Lu-Ping Chi
- State Key Laboratory of Microbial Technology, Shandong University, Qingdao, Shandong 266237, China.
| | - Wei Zhang
- State Key Laboratory of Microbial Technology, Shandong University, Qingdao, Shandong 266237, China.
- CAS and Shandong Province Key Laboratory of Experimental Marine Biology, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, Shandong 266071, China
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2
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Jiang K, Luo P, Wang X, Lu L. Insight into advances for the biosynthetic progress of fermented echinocandins of antifungals. Microb Biotechnol 2024; 17:e14359. [PMID: 37885073 PMCID: PMC10832530 DOI: 10.1111/1751-7915.14359] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2023] [Revised: 10/04/2023] [Accepted: 10/11/2023] [Indexed: 10/28/2023] Open
Abstract
Invasive fungal infections have increased remarkably, which have become unprecedented concern to human health. However, the effectiveness of current antifungal drugs is limited due to drug resistance and toxic side-effects. It is urgently required to establish the effective biosynthetic strategy for developing novel and safe antifungal molecules economically. Echinocandins become a promising option as a mainstay family of antifungals, due to specifically targeting the fungal specific cell wall. To date, three kinds of echinocandins for caspofungin, anidulafungin, and micafungin, which derived from pneumocandin B0 , echinocandin B, and FR901379, are commercially available in clinic and have shown potential in managing invasive fungal infections in a cost-effective manner. However, current echinocandins-derived precursors all are produced by environmental fungal isolates with long fermentation cycle and low yields, which challenge the production efficacy of these precursors in industry. Therefore, understanding their biosynthetic machinery is of great importance for improving antifungal titres and creating new echinocandins-derived products. With the development of genome-wide sequencing and establishment of gene-editing technology, there are a growing number of reports on echinocandins-derived products and their biosynthetic gene clusters. This review briefly summarizes the discovery and development history of echinocandins, compares their structural characteristics and biosynthetic processes, and sums up existed strategies for improving their production. Moreover, the genomic analysis of related biosynthetic gene clusters of echinocandins is discussed, highlighting the similarities and differences among the clusters. Last, the biosynthetic processes of echinocandins are compared, focusing on the activation and attachment of side-chains and the formation of the hexapeptide core. This review aims to provide insights into the development and production of new echinocandin drugs by modifying the structure of echinocandin-derived precursors and/or optimizing the fermentation processes; and achieve a new microbial chassis for efficient production of echinocandins in heterologous hosts.
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Affiliation(s)
- Kaili Jiang
- Jiangsu Key Laboratory for Microbes and Functional Genomics, Jiangsu, Engineering and Technology Research Center for Microbiology, College of Life SciencesNanjing Normal UniversityNanjingChina
| | - Pan Luo
- Jiangsu Key Laboratory for Microbes and Functional Genomics, Jiangsu, Engineering and Technology Research Center for Microbiology, College of Life SciencesNanjing Normal UniversityNanjingChina
| | - Xinxin Wang
- Jiangsu Key Laboratory for Microbes and Functional Genomics, Jiangsu, Engineering and Technology Research Center for Microbiology, College of Life SciencesNanjing Normal UniversityNanjingChina
| | - Ling Lu
- Jiangsu Key Laboratory for Microbes and Functional Genomics, Jiangsu, Engineering and Technology Research Center for Microbiology, College of Life SciencesNanjing Normal UniversityNanjingChina
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3
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Pilz M, Cavelius P, Qoura F, Awad D, Brück T. Lipopeptides development in cosmetics and pharmaceutical applications: A comprehensive review. Biotechnol Adv 2023; 67:108210. [PMID: 37460047 DOI: 10.1016/j.biotechadv.2023.108210] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2023] [Revised: 07/05/2023] [Accepted: 07/09/2023] [Indexed: 07/25/2023]
Abstract
Lipopeptides are surface active, natural products of bacteria, fungi and green-blue algae origin, having diverse structures and functionalities. In analogy, a number of chemical synthesis techniques generated new designer lipopeptides with desirable features and functions. Lipopetides are self-assembly guided, supramolecular compounds which have the capacity of high-density presentation of the functional epitopes at the surface of the nanostructures. This feature contributes to their successful application in several industry sectors, including food, feed, personal care, and pharmaceutics. In this comprehensive review, the novel class of ribosomally synthesized lipopeptides is introduced alongside the more commonly occuring non-ribosomal lipopeptides. We highlight key representatives of the most researched as well as recently described lipopeptide families, with emphasis on structural features, self-assembly and associated functions. The common biological, chemical and hybrid production routes of lipopeptides, including prominent analogues and derivatives are also discussed. Furthermore, genetic engineering strategies aimed at increasing lipopeptide yields, diversity and biological activity are summarized and exemplified. With respect to application, this work mainly details the potential of lipopeptides in personal care and cosmetics industry as cleansing agents, moisturizer, anti-aging/anti-wrinkling, skin whitening and preservative agents as well as the pharmaceutical industry as anitimicrobial agents, vaccines, immunotherapy, and cancer drugs. Given that this review addresses human applications, we conclude on the topic of safety of lipopeptide formulations and their sustainable production.
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Affiliation(s)
- Melania Pilz
- Werner Siemens-Chair of Synthetic Biotechnology, Department of Chemistry, Technical University of Munich (TUM), 85748 Garching, Germany
| | - Philipp Cavelius
- Werner Siemens-Chair of Synthetic Biotechnology, Department of Chemistry, Technical University of Munich (TUM), 85748 Garching, Germany
| | - Farah Qoura
- Werner Siemens-Chair of Synthetic Biotechnology, Department of Chemistry, Technical University of Munich (TUM), 85748 Garching, Germany
| | - Dania Awad
- Werner Siemens-Chair of Synthetic Biotechnology, Department of Chemistry, Technical University of Munich (TUM), 85748 Garching, Germany.
| | - Thomas Brück
- Werner Siemens-Chair of Synthetic Biotechnology, Department of Chemistry, Technical University of Munich (TUM), 85748 Garching, Germany.
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4
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Zhang L, Wang C, Chen K, Zhong W, Xu Y, Molnár I. Engineering the biosynthesis of fungal nonribosomal peptides. Nat Prod Rep 2023; 40:62-88. [PMID: 35796260 DOI: 10.1039/d2np00036a] [Citation(s) in RCA: 13] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]
Abstract
Covering: 2011 up to the end of 2021.Fungal nonribosomal peptides (NRPs) and the related polyketide-nonribosomal peptide hybrid products (PK-NRPs) are a prolific source of bioactive compounds, some of which have been developed into essential drugs. The synthesis of these complex natural products (NPs) utilizes nonribosomal peptide synthetases (NRPSs), multidomain megaenzymes that assemble specific peptide products by sequential condensation of amino acids and amino acid-like substances, independent of the ribosome. NRPSs, collaborating polyketide synthase modules, and their associated tailoring enzymes involved in product maturation represent promising targets for NP structure diversification and the generation of small molecule unnatural products (uNPs) with improved or novel bioactivities. Indeed, reprogramming of NRPSs and recruiting of novel tailoring enzymes is the strategy by which nature evolves NRP products. The recent years have witnessed a rapid development in the discovery and identification of novel NRPs and PK-NRPs, and significant advances have also been made towards the engineering of fungal NRP assembly lines to generate uNP peptides. However, the intrinsic complexities of fungal NRP and PK-NRP biosynthesis, and the large size of the NRPSs still present formidable conceptual and technical challenges for the rational and efficient reprogramming of these pathways. This review examines key examples for the successful (and for some less-successful) re-engineering of fungal NRPS assembly lines to inform future efforts towards generating novel, biologically active peptides and PK-NRPs.
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Affiliation(s)
- Liwen Zhang
- Biotechnology Research Institute, The Chinese Academy of Agricultural Sciences, 12 Zhongguancun South Street, Beijing 100081, P. R. China.
| | - Chen Wang
- Biotechnology Research Institute, The Chinese Academy of Agricultural Sciences, 12 Zhongguancun South Street, Beijing 100081, P. R. China.
| | - Kang Chen
- Biotechnology Research Institute, The Chinese Academy of Agricultural Sciences, 12 Zhongguancun South Street, Beijing 100081, P. R. China.
| | - Weimao Zhong
- Southwest Center for Natural Products Research, University of Arizona, 250 E. Valencia Rd., Tucson, AZ 85706, USA
| | - Yuquan Xu
- Biotechnology Research Institute, The Chinese Academy of Agricultural Sciences, 12 Zhongguancun South Street, Beijing 100081, P. R. China.
| | - István Molnár
- Southwest Center for Natural Products Research, University of Arizona, 250 E. Valencia Rd., Tucson, AZ 85706, USA.,VTT Technical Research Centre of Finland, P.O. Box 1000, FI-02044 VTT, Espoo, Finland.
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Wei TY, Zheng Y, Wan M, Yang S, Tang J, Wu Y, Li J, Chen SX. Analysis of FR901379 Biosynthetic Genes in Coleophoma empetri by Clustered Regularly Interspaced Short Palindromic Repeats/Cas9-Based Genomic Manipulation. ACS Chem Biol 2022; 17:2130-2141. [PMID: 35822391 DOI: 10.1021/acschembio.2c00250] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023]
Abstract
The compound FR901379, a sulfated echinocandin produced by the filamentous fungus Coleophoma empetri F-11899, is an important intermediate for the synthesis of the antifungal drug micafungin. In this study, we established an efficient clustered regularly interspaced short palindromic repeats/Cas9-based gene editing tool for the industrial production strain C. empetri SIPI1284. With this method, the efficiency of gene mutagenesis in the target locus is up to 84%, which enables the rapid gene disruption for the analysis of FR901379 biosynthetic genes. Next, we verified the putative functional genes of the FR901379 biosynthetic gene cluster via gene disruption and gene complementation in vivo. These core functional genes included the nonribosomal peptide synthetase gene (CEnrps), the fatty-acyl-AMP ligase gene (CEligase) responsible for the formation of the activated form of palmitic acid and its transfer to CEnrps, four nonheme mononuclear iron oxygenase genes (CEoxy1, CEoxy2, CEoxy3, and CEoxy4) responsible for the synthesis of nonproteinogenic amino acids, l-homotyrosine biosynthesis genes (CEhtyA-D), two cytochrome P450 enzyme genes (CEp450-1 and CEp450-2), and a transcription regulator gene (CEhyp). In addition, by screening the whole genome, we identified two unknown genes (CEp450-3 and CEsul) responsible for the sulfonyloxy group of FR901379, which were separated from the core FR901379 biosynthetic cluster. Furthermore, during gene disruptions in the research, we obtained a series of FR901379 analogues and elucidated the relationship between the groups and antifungal activities.
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Affiliation(s)
- Teng-Yun Wei
- State Key Laboratory of New Drug and Pharmaceutical Process, China State Institute of Pharmaceutical Industry, Shanghai Institute of Pharmaceutical Industry, Shanghai 201203, China
| | - Yan Zheng
- State Key Laboratory of New Drug and Pharmaceutical Process, China State Institute of Pharmaceutical Industry, Shanghai Institute of Pharmaceutical Industry, Shanghai 201203, China
| | - Miyang Wan
- Department of Biological Medicines & Shanghai Engineering Research Center of Immunotherapeutics, School of Pharmacy, Fudan University, Shanghai 201203, China
| | - Songbai Yang
- State Key Laboratory of New Drug and Pharmaceutical Process, China State Institute of Pharmaceutical Industry, Shanghai Institute of Pharmaceutical Industry, Shanghai 201203, China
| | - Jiawei Tang
- Department of Biological Medicines & Shanghai Engineering Research Center of Immunotherapeutics, School of Pharmacy, Fudan University, Shanghai 201203, China
| | - Yuanjie Wu
- State Key Laboratory of New Drug and Pharmaceutical Process, China State Institute of Pharmaceutical Industry, Shanghai Institute of Pharmaceutical Industry, Shanghai 201203, China
| | - Jiyang Li
- Department of Biological Medicines & Shanghai Engineering Research Center of Immunotherapeutics, School of Pharmacy, Fudan University, Shanghai 201203, China
| | - Shao-Xin Chen
- State Key Laboratory of New Drug and Pharmaceutical Process, China State Institute of Pharmaceutical Industry, Shanghai Institute of Pharmaceutical Industry, Shanghai 201203, China
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Wei X, Wang WG, Matsuda Y. Branching and converging pathways in fungal natural product biosynthesis. Fungal Biol Biotechnol 2022; 9:6. [PMID: 35255990 PMCID: PMC8902786 DOI: 10.1186/s40694-022-00135-w] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2021] [Accepted: 02/19/2022] [Indexed: 12/15/2022] Open
Abstract
AbstractIn nature, organic molecules with great structural diversity and complexity are synthesized by utilizing a relatively small number of starting materials. A synthetic strategy adopted by nature is pathway branching, in which a common biosynthetic intermediate is transformed into different end products. A natural product can also be synthesized by the fusion of two or more precursors generated from separate metabolic pathways. This review article summarizes several representative branching and converging pathways in fungal natural product biosynthesis to illuminate how fungi are capable of synthesizing a diverse array of natural products.
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Vignolle GA, Schaffer D, Zehetner L, Mach RL, Mach-Aigner AR, Derntl C. FunOrder: A robust and semi-automated method for the identification of essential biosynthetic genes through computational molecular co-evolution. PLoS Comput Biol 2021; 17:e1009372. [PMID: 34570757 PMCID: PMC8476034 DOI: 10.1371/journal.pcbi.1009372] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2021] [Accepted: 08/23/2021] [Indexed: 11/24/2022] Open
Abstract
Secondary metabolites (SMs) are a vast group of compounds with different structures and properties that have been utilized as drugs, food additives, dyes, and as monomers for novel plastics. In many cases, the biosynthesis of SMs is catalysed by enzymes whose corresponding genes are co-localized in the genome in biosynthetic gene clusters (BGCs). Notably, BGCs may contain so-called gap genes, that are not involved in the biosynthesis of the SM. Current genome mining tools can identify BGCs, but they have problems with distinguishing essential genes from gap genes. This can and must be done by expensive, laborious, and time-consuming comparative genomic approaches or transcriptome analyses. In this study, we developed a method that allows semi-automated identification of essential genes in a BGC based on co-evolution analysis. To this end, the protein sequences of a BGC are blasted against a suitable proteome database. For each protein, a phylogenetic tree is created. The trees are compared by treeKO to detect co-evolution. The results of this comparison are visualized in different output formats, which are compared visually. Our results suggest that co-evolution is commonly occurring within BGCs, albeit not all, and that especially those genes that encode for enzymes of the biosynthetic pathway are co-evolutionary linked and can be identified with FunOrder. In light of the growing number of genomic data available, this will contribute to the studies of BGCs in native hosts and facilitate heterologous expression in other organisms with the aim of the discovery of novel SMs. The discovery and description of novel fungal secondary metabolites promises novel antibiotics, pharmaceuticals, and other useful compounds. A way to identify novel secondary metabolites is to express the corresponding genes in a suitable expression host. Consequently, a detailed knowledge or an accurate prediction of these genes is necessary. In fungi, the genes are co-localized in so-called biosynthetic gene clusters. Notably, the clusters may also contain genes that are not necessary for the biosynthesis of the secondary metabolites, so-called gap genes. We developed a method to detect co-evolved genes within the clusters and demonstrated that essential genes are co-evolving and can thus be differentiated from the gap genes. This adds an additional layer of information, which can support researchers with their decisions on which genes to study and express for the discovery of novel secondary metabolites.
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Affiliation(s)
- Gabriel A. Vignolle
- Institute of Chemical, Environmental and Bioscience Engineering, TU Wien, Vienna, Austria
| | - Denise Schaffer
- Institute of Chemical, Environmental and Bioscience Engineering, TU Wien, Vienna, Austria
| | - Leopold Zehetner
- Institute of Chemical, Environmental and Bioscience Engineering, TU Wien, Vienna, Austria
| | - Robert L. Mach
- Institute of Chemical, Environmental and Bioscience Engineering, TU Wien, Vienna, Austria
| | - Astrid R. Mach-Aigner
- Institute of Chemical, Environmental and Bioscience Engineering, TU Wien, Vienna, Austria
| | - Christian Derntl
- Institute of Chemical, Environmental and Bioscience Engineering, TU Wien, Vienna, Austria
- * E-mail:
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8
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Zhong L, Diao X, Zhang N, Li F, Zhou H, Chen H, Bai X, Ren X, Zhang Y, Wu D, Bian X. Engineering and elucidation of the lipoinitiation process in nonribosomal peptide biosynthesis. Nat Commun 2021; 12:296. [PMID: 33436600 PMCID: PMC7804268 DOI: 10.1038/s41467-020-20548-8] [Citation(s) in RCA: 30] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2020] [Accepted: 12/02/2020] [Indexed: 12/18/2022] Open
Abstract
Nonribosomal peptide synthetases containing starter condensation domains direct the biosynthesis of nonribosomal lipopeptides, which generally exhibit wide bioactivities. The acyl chain has strong impacts on bioactivity and toxicity, but the lack of an in-depth understanding of starter condensation domain-mediated lipoinitiation limits the bioengineering of NRPSs to obtain novel derivatives with desired acyl chains. Here, we show that the acyl chains of the lipopeptides rhizomide, holrhizin, and glidobactin were modified by engineering the starter condensation domain, suggesting a workable approach to change the acyl chain. Based on the structure of the mutated starter condensation domain of rhizomide biosynthetic enzyme RzmA in complex with octanoyl-CoA and related point mutation experiments, we identify a set of residues responsible for the selectivity of substrate acyl chains and extend the acyl chains from acetyl to palmitoyl. Furthermore, we illustrate three possible conformational states of starter condensation domains during the reaction cycle of the lipoinitiation process. Our studies provide further insights into the mechanism of lipoinitiation and the engineering of nonribosomal peptide synthetases. Nonribosomal lipopeptides contain an acyl chain important for bioactivity, but its incorporation into the peptidyl backbone, mediated by the starter condensation (Cs) domain of nonribosomal peptide synthases, is not fully understood. Here, the authors show that acyl chains of different lengths can be obtained by engineering Cs domains and identify residues that determine the selectivity for acyl chains.
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Affiliation(s)
- Lin Zhong
- Helmholtz International Lab for Anti-Infectives, Shandong University-Helmholtz Institute of Biotechnology, State Key Laboratory of Microbial Technology, Shandong University, Qingdao, Shandong, 266237, China
| | - Xiaotong Diao
- Helmholtz International Lab for Anti-Infectives, Shandong University-Helmholtz Institute of Biotechnology, State Key Laboratory of Microbial Technology, Shandong University, Qingdao, Shandong, 266237, China
| | - Na Zhang
- Helmholtz International Lab for Anti-Infectives, Shandong University-Helmholtz Institute of Biotechnology, State Key Laboratory of Microbial Technology, Shandong University, Qingdao, Shandong, 266237, China
| | - Fengwei Li
- Helmholtz International Lab for Anti-Infectives, Shandong University-Helmholtz Institute of Biotechnology, State Key Laboratory of Microbial Technology, Shandong University, Qingdao, Shandong, 266237, China
| | - Haibo Zhou
- Helmholtz International Lab for Anti-Infectives, Shandong University-Helmholtz Institute of Biotechnology, State Key Laboratory of Microbial Technology, Shandong University, Qingdao, Shandong, 266237, China
| | - Hanna Chen
- Helmholtz International Lab for Anti-Infectives, Shandong University-Helmholtz Institute of Biotechnology, State Key Laboratory of Microbial Technology, Shandong University, Qingdao, Shandong, 266237, China
| | - Xianping Bai
- Helmholtz International Lab for Anti-Infectives, Shandong University-Helmholtz Institute of Biotechnology, State Key Laboratory of Microbial Technology, Shandong University, Qingdao, Shandong, 266237, China
| | - Xintong Ren
- Helmholtz International Lab for Anti-Infectives, Shandong University-Helmholtz Institute of Biotechnology, State Key Laboratory of Microbial Technology, Shandong University, Qingdao, Shandong, 266237, China
| | - Youming Zhang
- Helmholtz International Lab for Anti-Infectives, Shandong University-Helmholtz Institute of Biotechnology, State Key Laboratory of Microbial Technology, Shandong University, Qingdao, Shandong, 266237, China.
| | - Dalei Wu
- Helmholtz International Lab for Anti-Infectives, Shandong University-Helmholtz Institute of Biotechnology, State Key Laboratory of Microbial Technology, Shandong University, Qingdao, Shandong, 266237, China. .,Suzhou Research Institute, Shandong University, Suzhou, Jiangsu, 215123, China.
| | - Xiaoying Bian
- Helmholtz International Lab for Anti-Infectives, Shandong University-Helmholtz Institute of Biotechnology, State Key Laboratory of Microbial Technology, Shandong University, Qingdao, Shandong, 266237, China.
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Echinocandins: structural diversity, biosynthesis, and development of antimycotics. Appl Microbiol Biotechnol 2020; 105:55-66. [PMID: 33270153 PMCID: PMC7778625 DOI: 10.1007/s00253-020-11022-y] [Citation(s) in RCA: 39] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2020] [Revised: 11/06/2020] [Accepted: 11/12/2020] [Indexed: 02/04/2023]
Abstract
Abstract Echinocandins are a clinically important class of non-ribosomal antifungal lipopeptides produced by filamentous fungi. Due to their complex structure, which is characterized by numerous hydroxylated non-proteinogenic amino acids, echinocandin antifungal agents are manufactured semisynthetically. The development of optimized echinocandin structures is therefore closely connected to their biosynthesis. Enormous efforts in industrial research and development including fermentation, classical mutagenesis, isotope labeling, and chemical synthesis eventually led to the development of the active ingredients caspofungin, micafungin, and anidulafungin, which are now used as first-line treatments against invasive mycosis. In the last years, echinocandin biosynthetic gene clusters have been identified, which allowed for the elucidation but also engineering of echinocandin biosynthesis on the molecular level. After a short description of the history of echinocandin research, this review provides an overview of the current knowledge of echinocandin biosynthesis with a special focus of the diverse structural elements, their biosynthetic background, and structure−activity relationships. Key points • Complex and highly oxidized lipopeptides produced by fungi. • Crucial in the design of drugs: side chain, solubility, and hydrolytic stability. • Genetic methods for engineering biosynthesis have recently become available. Supplementary Information The online version contains supplementary material available at 10.1007/s00253-020-11022-y.
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Wei TY, Wu YJ, Xie QP, Tang JW, Yu ZT, Yang SB, Chen SX. CRISPR/Cas9-Based Genome Editing in the Filamentous Fungus Glarea lozoyensis and Its Application in Manipulating gloF. ACS Synth Biol 2020; 9:1968-1977. [PMID: 32786921 DOI: 10.1021/acssynbio.9b00491] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/23/2023]
Abstract
Glarea lozoyensis is an important industrial fungus that produces the pneumocandin B0, which is used for the synthesis of antifungal drug caspofungin. However, because of the limitations and complications of traditional genetic tools, G. lozoyensis strain engineering has been hindered. In this study, we established an efficient CRISPR/Cas9-based gene editing tool in G. lozoyensis SIPI1208. With this method, gene mutagenesis efficiency in the target locus can be up to 80%, which enables the rapid gene knockout. According to the reports, GloF and Ap-HtyE, proline hydroxylases involved in pneumocandin and Echinocandin B biosynthesis, respectively, can catalyze the proline to generate different ratios of trans-3-hydroxy-l-proline to trans-4-hydroxy-l-proline. Heterologous expression of Ap-HtyE in G. lozoyensis decreased the ratio of pneumocandin C0 to (pneumocandin B0 + pneumocandin C0) from 33.5% to 11% without the addition of proline to the fermentation medium. Furthermore, the gloF was replaced by ap-htyE to study the production of pneumocandin C0. However, the gene replacement has been hampered by traditional gene tools since gloF and gloG, two contiguous genes indispensable in the biosynthesis of pneumocandins, are cotranscribed into one mRNA. With the CRISPR/Cas9 strategy, ap-htyE was knocked in and successfully replaced gloF, and results showed that the knock-in strain retained the ability to produce pneumocandin B0, but the production of pneumocandin C0 was abolished. Thus, this strain displayed a competitive advantage in the industrial production of pneumocandin B0. In summary, this study showed that the CRISPR/Cas9-based gene editing tool is efficient for manipulating genes in G. lozoyensis.
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Affiliation(s)
- Teng-Yun Wei
- Shanghai Institute of Pharmaceutical Industry, China State Institute of Pharmaceutical Industry, 285 Gebaini Road, Pudong, Shanghai 201203, China
| | - Yuan-Jie Wu
- Shanghai Institute of Pharmaceutical Industry, China State Institute of Pharmaceutical Industry, 285 Gebaini Road, Pudong, Shanghai 201203, China
| | - Qiu-Ping Xie
- Shanghai Institute of Pharmaceutical Industry, China State Institute of Pharmaceutical Industry, 285 Gebaini Road, Pudong, Shanghai 201203, China
| | - Jia-Wei Tang
- Shanghai Institute of Pharmaceutical Industry, China State Institute of Pharmaceutical Industry, 285 Gebaini Road, Pudong, Shanghai 201203, China
| | - Zhi-Tuo Yu
- Shanghai Institute of Pharmaceutical Industry, China State Institute of Pharmaceutical Industry, 285 Gebaini Road, Pudong, Shanghai 201203, China
| | - Song-Bai Yang
- Shanghai Institute of Pharmaceutical Industry, China State Institute of Pharmaceutical Industry, 285 Gebaini Road, Pudong, Shanghai 201203, China
| | - Shao-Xin Chen
- Shanghai Institute of Pharmaceutical Industry, China State Institute of Pharmaceutical Industry, 285 Gebaini Road, Pudong, Shanghai 201203, China
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11
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Liu W, Yuan L, Wang S. Recent Progress in the Discovery of Antifungal Agents Targeting the Cell Wall. J Med Chem 2020; 63:12429-12459. [PMID: 32692166 DOI: 10.1021/acs.jmedchem.0c00748] [Citation(s) in RCA: 34] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
Due to the limit of available treatments and the emergence of drug resistance in the clinic, invasive fungal infections are an intractable problem with high morbidity and mortality. The cell wall, as a fungi-specific structure, is an appealing target for the discovery and development of novel and low-toxic antifungal agents. In an attempt to accelerate the discovery of novel cell wall targeted drugs, this Perspective will provide a comprehensive review of the progress made to date on the development of fungal cell wall inhibitors. Specifically, this review will focus on the targets, discovery process, chemical structures, antifungal activities, and structure-activity relationships. Although two types of cell wall antifungal agents are clinically available or in clinical trials, it is still a long way for the other cell wall targeted inhibitors to be translated into clinical applications. Future efforts should be focused on the identification of inhibitors against novel conserved cell wall targets.
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Affiliation(s)
- Wei Liu
- Faculty of Pharmacy, School of Food and Biological Engineering, Shaanxi University of Science and Technology, Xuefu Middle Road, Xi'an 710021, People's Republic of China
| | - Lin Yuan
- Faculty of Pharmacy, School of Food and Biological Engineering, Shaanxi University of Science and Technology, Xuefu Middle Road, Xi'an 710021, People's Republic of China
| | - Shengzheng Wang
- Department of Medicinal Chemistry and Pharmaceutical Analysis, School of Pharmacy, Fourth Military Medical University, 169 Changle West Road, Xi'an 710032, People's Republic of China
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12
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Lan N, Perlatti B, Kvitek DJ, Wiemann P, Harvey CJB, Frisvad J, An Z, Bills GF. Acrophiarin (antibiotic S31794/F-1) from Penicillium arenicola shares biosynthetic features with both Aspergillus- and Leotiomycete-type echinocandins. Environ Microbiol 2020; 22:2292-2311. [PMID: 32239586 DOI: 10.1111/1462-2920.15004] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2019] [Accepted: 03/28/2020] [Indexed: 11/30/2022]
Abstract
The antifungal echinocandin lipopeptide, acrophiarin, was circumscribed in a patent in 1979. We confirmed that the producing strain NRRL 8095 is Penicillium arenicola and other strains of P. arenicola produced acrophiarin and acrophiarin analogues. Genome sequencing of NRRL 8095 identified the acrophiarin gene cluster. Penicillium arenicola and echinocandin-producing Aspergillus species belong to the family Aspergillaceae of the Eurotiomycetes, but several features of acrophiarin and its gene cluster suggest a closer relationship with echinocandins from Leotiomycete fungi. These features include hydroxy-glutamine in the peptide core instead of a serine or threonine residue, the inclusion of a non-heme iron, α-ketoglutarate-dependent oxygenase for hydroxylation of the C3 of the glutamine, and a thioesterase. In addition, P. arenicola bears similarity to Leotiomycete echinocandin-producing species because it exhibits self-resistance to exogenous echinocandins. Phylogenetic analysis of the genes of the echinocandin biosynthetic family indicated that most of the predicted proteins of acrophiarin gene cluster exhibited higher similarity to the predicted proteins of the pneumocandin gene cluster of the Leotiomycete Glarea lozoyensis than to those of the echinocandin B gene cluster from A. pachycristatus. The fellutamide gene cluster and related gene clusters are recognized as relatives of the echinocandins. Inclusion of the acrophiarin gene cluster into a comprehensive phylogenetic analysis of echinocandin gene clusters indicated the divergent evolutionary lineages of echinocandin gene clusters are descendants from a common ancestral progenitor. The minimal 10-gene cluster may have undergone multiple gene acquisitions or losses and possibly horizontal gene transfer after the ancestral separation of the two lineages.
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Affiliation(s)
- Nan Lan
- Texas Therapeutics Institute, The Brown Foundation Institute of Molecular Medicine, The University of Texas Health Science Center at Houston, Houston, TX, 77054, USA
| | - Bruno Perlatti
- Texas Therapeutics Institute, The Brown Foundation Institute of Molecular Medicine, The University of Texas Health Science Center at Houston, Houston, TX, 77054, USA
| | | | | | | | - Jens Frisvad
- Center for Microbial Biotechnology, Department of Systems Biology, Technical University of Denmark, DK-2800, Lyngby, Denmark
| | - Zhiqiang An
- Texas Therapeutics Institute, The Brown Foundation Institute of Molecular Medicine, The University of Texas Health Science Center at Houston, Houston, TX, 77054, USA
| | - Gerald F Bills
- Texas Therapeutics Institute, The Brown Foundation Institute of Molecular Medicine, The University of Texas Health Science Center at Houston, Houston, TX, 77054, USA
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13
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Howard KC, Dennis EK, Watt DS, Garneau-Tsodikova S. A comprehensive overview of the medicinal chemistry of antifungal drugs: perspectives and promise. Chem Soc Rev 2020; 49:2426-2480. [PMID: 32140691 DOI: 10.1039/c9cs00556k] [Citation(s) in RCA: 59] [Impact Index Per Article: 14.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Abstract
The emergence of new fungal pathogens makes the development of new antifungal drugs a medical imperative that in recent years motivates the talents of numerous investigators across the world. Understanding not only the structural families of these drugs but also their biological targets provides a rational means for evaluating the merits and selectivity of new agents for fungal pathogens and normal cells. An equally important aspect of modern antifungal drug development takes a balanced look at the problems of drug potency and drug resistance. The future development of new antifungal agents will rest with those who employ synthetic and semisynthetic methodology as well as natural product isolation to tackle these problems and with those who possess a clear understanding of fungal cell architecture and drug resistance mechanisms. This review endeavors to provide an introduction to a growing and increasingly important literature, including coverage of the new developments in medicinal chemistry since 2015, and also endeavors to spark the curiosity of investigators who might enter this fascinatingly complex fungal landscape.
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Affiliation(s)
- Kaitlind C Howard
- Department of Pharmaceutical Sciences, College of Pharmacy, University of Kentucky, Lexington, KY 40536-0596, USA.
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14
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Yuan K, Huang B, Qin T, Song P, Zhang K, Ji X, Ren L, Zhang S, Huang H. Effect of SDS on release of intracellular pneumocandin B 0 in extractive batch fermentation of Glarea lozoyensis. Appl Microbiol Biotechnol 2019; 103:6061-6069. [PMID: 31161390 PMCID: PMC6616208 DOI: 10.1007/s00253-019-09920-x] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2019] [Revised: 05/08/2019] [Accepted: 05/15/2019] [Indexed: 11/17/2022]
Abstract
Pneumocandin B0 is a hydrophobic secondary metabolite that accumulates in the mycelia of Glarea lozoyensis and inhibits fungal 1,3-β-glucan synthase. Extractive batch fermentation can promote the release of intracellular secondary metabolites into the fermentation broth and is often used in industry. The addition of extractants has been proven as an effective method to attain higher accumulation of hydrophobic secondary metabolites and circumvent troublesome solvent extraction. Various extractants exerted significant but different influences on the biomass and pneumocandin B0 yields. The maximum pneumocandin B0 yield (2528.67 mg/L) and highest extracellular pneumocandin B0 yield (580.33 mg/L) were achieved when 1.0 g/L SDS was added on the 13th day of extractive batch fermentation, corresponding to significant increases of 37.63 and 154% compared with the conventional batch fermentation, respectively. The mechanism behind this phenomenon is partly attributed to the release of intracellular pneumocandin B0 into the fermentation broth and the enhanced biosynthesis of pneumocandin B0 in the mycelia.
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Affiliation(s)
- Kai Yuan
- College of Biotechnology and Pharmaceutical Engineering, Nanjing Tech University, 30 South Puzhu Road, Nanjing, 211816, China
| | - Baoqi Huang
- College of Biotechnology and Pharmaceutical Engineering, Nanjing Tech University, 30 South Puzhu Road, Nanjing, 211816, China
| | - Tingting Qin
- College of Biotechnology and Pharmaceutical Engineering, Nanjing Tech University, 30 South Puzhu Road, Nanjing, 211816, China
| | - Ping Song
- College of Biotechnology and Pharmaceutical Engineering, Nanjing Tech University, 30 South Puzhu Road, Nanjing, 211816, China. .,School of Food Science and Pharmaceutical Engineering, Nanjing Normal University, 1 Wenyuan Road, Nanjing, 210023, China.
| | - Ke Zhang
- College of Biotechnology and Pharmaceutical Engineering, Nanjing Tech University, 30 South Puzhu Road, Nanjing, 211816, China
| | - Xiaojun Ji
- College of Biotechnology and Pharmaceutical Engineering, Nanjing Tech University, 30 South Puzhu Road, Nanjing, 211816, China
| | - Lujing Ren
- College of Biotechnology and Pharmaceutical Engineering, Nanjing Tech University, 30 South Puzhu Road, Nanjing, 211816, China.,School of Food Science and Pharmaceutical Engineering, Nanjing Normal University, 1 Wenyuan Road, Nanjing, 210023, China
| | - Sen Zhang
- Jiangsu Collaboration Innovation Center of Chinese Medical Resources Industrialization, College of Pharmacy, Nanjing University of Chinese Medicine, 138 Xianlin Road, Nanjing, 210023, China
| | - He Huang
- College of Biotechnology and Pharmaceutical Engineering, Nanjing Tech University, 30 South Puzhu Road, Nanjing, 211816, China.,School of Food Science and Pharmaceutical Engineering, Nanjing Normal University, 1 Wenyuan Road, Nanjing, 210023, China
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15
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Song P, Huang B, Zhang S, Zhang K, Yuan K, Ji X, Ren L, Wen J, Huang H. Novel osmotic stress control strategy for improved pneumocandin B 0 production in Glarea lozoyensis combined with a mechanistic analysis at the transcriptome level. Appl Microbiol Biotechnol 2018; 102:10729-10742. [PMID: 30413850 DOI: 10.1007/s00253-018-9440-4] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2018] [Revised: 08/18/2018] [Accepted: 10/04/2018] [Indexed: 11/26/2022]
Abstract
Pneumocandin B0, the precursor of the antifungal drug caspofungin, is a secondary metabolite of the fungus Glarea lozoyensis. In this study, we investigated the effects of mannitol as the sole carbon source on pneumocandin B0 production by G. lozoyensis. The osmotic pressure is more important in enhancing pneumocandin B0 production than is the substrate concentration. Based on the kinetic analysis, an osmotic stress control fed-batch strategy was developed. This strategy led to a maximum pneumocandin B0 concentration of 2711 mg/L with a productivity of 9.05 mg/L/h, representing 34.67 and 6.47% improvements, respectively, over the best result achieved by the one-stage fermentation. Furthermore, G. lozoyensis accumulated glutamate and proline as compatible solutes to resist osmotic stress, and these amino acids also provided the precursors for the enhanced pneumocandin B0 production. Osmotic stress also activated ROS (reactive oxygen species)-dependent signal transduction by upregulating the levels of related genes and increasing intracellular ROS levels by 20%. We also provided a possible mechanism for pneumocandin B0 accumulation based on signal transduction. These findings will improve our understanding of the regulatory mechanisms of pneumocandin B0 biosynthesis and may be applied to improve secondary metabolite production.
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Affiliation(s)
- Ping Song
- SynBio Research Platform, Collaborative Innovation Center of Chemical Science and Engineering (Tianjin), School of Chemical Engineering and Technology, Tianjin University, 92 Weijin Road, Tianjin, 300072, China
- Jiangsu Synergetic Innovation Center for Advanced Bio-Manufacture, College of Biotechnology and Pharmaceutical Engineering, Nanjing Tech University, 30 South Puzhu Road, Nanjing, 211816, China
| | - Baoqi Huang
- Jiangsu Synergetic Innovation Center for Advanced Bio-Manufacture, College of Biotechnology and Pharmaceutical Engineering, Nanjing Tech University, 30 South Puzhu Road, Nanjing, 211816, China
| | - Sen Zhang
- Jiangsu Collaboration Innovation Center of Chinese Medical Resources Industrialization, College of Pharmacy, Nanjing University of Chinese Medicine, 138 Xianlin Road, Nanjing, 210023, China
| | - Ke Zhang
- Jiangsu Synergetic Innovation Center for Advanced Bio-Manufacture, College of Biotechnology and Pharmaceutical Engineering, Nanjing Tech University, 30 South Puzhu Road, Nanjing, 211816, China
| | - Kai Yuan
- Jiangsu Synergetic Innovation Center for Advanced Bio-Manufacture, College of Biotechnology and Pharmaceutical Engineering, Nanjing Tech University, 30 South Puzhu Road, Nanjing, 211816, China
| | - Xiaojun Ji
- Jiangsu Synergetic Innovation Center for Advanced Bio-Manufacture, College of Biotechnology and Pharmaceutical Engineering, Nanjing Tech University, 30 South Puzhu Road, Nanjing, 211816, China
| | - Lujing Ren
- Jiangsu Synergetic Innovation Center for Advanced Bio-Manufacture, College of Biotechnology and Pharmaceutical Engineering, Nanjing Tech University, 30 South Puzhu Road, Nanjing, 211816, China
| | - Jianping Wen
- SynBio Research Platform, Collaborative Innovation Center of Chemical Science and Engineering (Tianjin), School of Chemical Engineering and Technology, Tianjin University, 92 Weijin Road, Tianjin, 300072, China
| | - He Huang
- School of Pharmaceutical Sciences, Nanjing Tech University, Nanjing, 211816, China.
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16
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Song P, Yuan K, Ji XJ, Ren LJ, Zhang S, Wen JP, Huang H. Effects of Cotton Seed Powder as the Seed Medium Nitrogen Source on the Morphology and Pneumocandin B 0 Yield of Glarea lozoyensis. Front Microbiol 2018; 9:2352. [PMID: 30364147 PMCID: PMC6191469 DOI: 10.3389/fmicb.2018.02352] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2018] [Accepted: 09/13/2018] [Indexed: 12/22/2022] Open
Abstract
Pneumocandin B0 is an important antifungal drug precursor produced by filamentous fungus Glarea lozoyensis. The high broth viscosity of cultures of this organism results in lower oxygen solubility and higher energy consumption for agitation and aeration, which mostly caused by the morphologies of filamentous fungi in submerged culture. In this study, the effects of different seed medium nitrogen sources on morphology and fermentation behavior of G. lozoyensis were investigated, and cotton seed powder resulted in small, compact pellets. Moreover, pneumocandin B0 yield in Erlenmeyer flasks were increased by 22.9%. Furthermore, pneumocandin B0 yield in a 50-L fermenter reached 2,100 mg/L and the dissolved oxygen maintained above 30%. Additionally, activities of phosphofructokinase (PFK), isocitrate dehydrogenase (ICDH), glucose 6-phosphate dehydrogenase (G6PDH), and malic enzyme (ME) were increased by 87.5, 50, 41.6, and 10.7%, respectively. This study demonstrates the feasibility and advantages of using cotton seed powder for controlling the fungal morphology and improving the product yield in pneumocandin fermentations.
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Affiliation(s)
- Ping Song
- School of Chemical Engineering and Technology, Department of Biochemical Engineering, Tianjin University, Tianjin, China
| | - Kai Yuan
- College of Biotechnology and Pharmaceutical Engineering, Nanjing Tech University, Nanjing, China
| | - Xiao-Jun Ji
- College of Biotechnology and Pharmaceutical Engineering, Nanjing Tech University, Nanjing, China
| | - Lu-Jing Ren
- College of Biotechnology and Pharmaceutical Engineering, Nanjing Tech University, Nanjing, China
| | - Sen Zhang
- Jiangsu Collaboration Innovation Center of Chinese Medical Resources Industrialization, College of Pharmacy, Nanjing University of Chinese Medicine, Nanjing, China
| | - Jian-Ping Wen
- School of Chemical Engineering and Technology, Department of Biochemical Engineering, Tianjin University, Tianjin, China
| | - He Huang
- School of Pharmaceutical Sciences, Nanjing Tech University, Nanjing, China
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17
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Biosynthesis of pneumocandin lipopeptides and perspectives for its production and related echinocandins. Appl Microbiol Biotechnol 2018; 102:9881-9891. [PMID: 30255232 DOI: 10.1007/s00253-018-9382-x] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2018] [Revised: 09/03/2018] [Accepted: 09/06/2018] [Indexed: 10/28/2022]
Abstract
Fungal diseases are a global public health problem. Invasive fungal infections pose a serious threat to patients with compromised immune systems, such as those undergoing organ or bone marrow transplants, cancer, or HIV/AIDS. Pneumocandins are antifungal lipohexapeptides of the echinocandin family that noncompetitively inhibit of 1,3-β-glucan synthase of fungal cell wall and provide the precursor for the semisynthesis of caspofungin, which is widely used as first-line therapy for invasive fungal infections. Recently, the biosynthetic steps leading to formation of pneumocandin B0 and echinocandin B have been elucidated, and thus, provide a framework and attractive model for further design new antifungal therapeutics around natural variations in echinocandin structural diversities via genetic and chemical tools. In this article, we analyze the biosynthetic pathway of pneumocandins and other echinocandins, provide an update on the array of pneumocandin analogues generated by genetic manipulation, and summarize advances in the enhancement of pneumocandin B0 production by random mutagenesis and fermentation optimization. We also give offer advice on the development of improved pneumocandin drug candidates and more efficient production of pneumocandin B0.
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18
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Song P, Yuan K, Qin T, Zhang K, Ji XJ, Ren L, Guan R, Wen J, Huang H. Metabolomics profiling reveals the mechanism of increased pneumocandin B 0 production by comparing mutant and parent strains. J Ind Microbiol Biotechnol 2018; 45:767-780. [PMID: 29948195 DOI: 10.1007/s10295-018-2047-z] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2018] [Accepted: 05/18/2018] [Indexed: 11/26/2022]
Abstract
Metabolic profiling was used to discover mechanisms of increased pneumocandin B0 production in a high-yield strain by comparing it with its parent strain. Initially, 79 intracellular metabolites were identified, and the levels of 15 metabolites involved in six pathways were found to be directly correlated with pneumocandin B0 biosynthesis. Then by combining the analysis of key enzymes, acetyl-CoA and NADPH were identified as the main factors limiting pneumocandin B0 biosynthesis. Other metabolites, such as pyruvate, α-ketoglutaric acid, lactate, unsaturated fatty acids and previously unreported metabolite γ-aminobutyric acid were shown to play important roles in pneumocandin B0 biosynthesis and cell growth. Finally, the overall metabolic mechanism hypothesis was formulated and a rational feeding strategy was implemented that increased the pneumocandin B0 yield from 1821 to 2768 mg/L. These results provide practical and theoretical guidance for strain selection, medium optimization, and genetic engineering for pneumocandin B0 production.
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Affiliation(s)
- Ping Song
- Department Biochemical Engineering, School Chemical Engineering and Technology, Tianjin University, Tianjin, 300072, China
- College of Biotechnology and Pharmaceutical Engineering, Nanjing Tech University, Nanjing, 211816, China
| | - Kai Yuan
- College of Biotechnology and Pharmaceutical Engineering, Nanjing Tech University, Nanjing, 211816, China
| | - Tingting Qin
- College of Biotechnology and Pharmaceutical Engineering, Nanjing Tech University, Nanjing, 211816, China
| | - Ke Zhang
- College of Biotechnology and Pharmaceutical Engineering, Nanjing Tech University, Nanjing, 211816, China
| | - Xiao-Jun Ji
- College of Biotechnology and Pharmaceutical Engineering, Nanjing Tech University, Nanjing, 211816, China
| | - Lujing Ren
- College of Biotechnology and Pharmaceutical Engineering, Nanjing Tech University, Nanjing, 211816, China
| | - Rongfeng Guan
- Laboratory for Advanced Technology in Environmental Protection of Jiangsu Province, Yancheng Institute of Technology, Yancheng, 224051, China
| | - Jianping Wen
- Department Biochemical Engineering, School Chemical Engineering and Technology, Tianjin University, Tianjin, 300072, China.
| | - He Huang
- School of Pharmaceutical Sciences, Nanjing Tech University, Nanjing, 211816, China.
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19
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Yue Q, Li Y, Chen L, Zhang X, Liu X, An Z, Bills GF. Genomics-driven discovery of a novel self-resistance mechanism in the echinocandin-producing fungus Pezicula radicicola. Environ Microbiol 2018. [PMID: 29528534 DOI: 10.1111/1462-2920.14089] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The echinocandins are antifungal lipopeptides targeting fungi via noncompetitive inhibition of the β-1,3-d-glucan synthase FKS1 subunit. A novel echinocandin resistance mechanism involving an auxiliary copy of FKS1 in echinocandin-producing fungus Pezicula radicicola NRRL 12192 was discovered. We sequenced the genome of NRRL 12192 and predicted two FKS1-encoding genes (prfks1n and prfks1a), rather than a single FKS1 gene typical of filamentous ascomycetes. The prfks1a gene sits immediately adjacent to an echinocandin (sporiofungin) gene cluster, which was confirmed by disruption of prnrps4 and abolishment of sporiofungin production. Disruption of prfks1a dramatically increased the strain's sensitivity to exogenous echinocandins. In the absence of echinocandins, transcription levels of prfks1a relative to β-tubulin in the wild type and in Δprnrps4 stains were similar. Moreover, prfks1a is consistently transcribed at low levels and is upregulated in the presence of exogenous echinocandin, but not during growth conditions promoting endogenous production of sporiofungin. Therefore, we conclude that prfks1a is primarily responsible for protecting the fungus against extracellular echinocandin toxicity. The presence of unclustered auxiliary copies of FKS1 with high similarity to prfks1a in two other echinocandin-producing strains suggests that this previously unrecognized resistance mechanism may be common in echinocandin-producing fungi of the family Dermataceae of the class Leotiomycetes.
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Affiliation(s)
- Qun Yue
- Texas Therapeutics Institute, The Brown Foundation Institute of Molecular Medicine, University of Texas Health Science Center at Houston, Houston, TX, USA.,Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing, 100081, People's Republic of China
| | - Yan Li
- Texas Therapeutics Institute, The Brown Foundation Institute of Molecular Medicine, University of Texas Health Science Center at Houston, Houston, TX, USA.,Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing, 100081, People's Republic of China
| | - Li Chen
- Texas Therapeutics Institute, The Brown Foundation Institute of Molecular Medicine, University of Texas Health Science Center at Houston, Houston, TX, USA
| | - Xiaoling Zhang
- State Key Laboratory of Mycology, Institute of Microbiology, Chinese Academy of Sciences, Beijing, People's Republic of China
| | - Xingzhong Liu
- State Key Laboratory of Mycology, Institute of Microbiology, Chinese Academy of Sciences, Beijing, People's Republic of China
| | - Zhiqiang An
- Texas Therapeutics Institute, The Brown Foundation Institute of Molecular Medicine, University of Texas Health Science Center at Houston, Houston, TX, USA
| | - Gerald F Bills
- Texas Therapeutics Institute, The Brown Foundation Institute of Molecular Medicine, University of Texas Health Science Center at Houston, Houston, TX, USA
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20
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Cryptic Production of trans-3-Hydroxyproline in Echinocandin B Biosynthesis. Appl Environ Microbiol 2018; 84:AEM.02370-17. [PMID: 29352089 DOI: 10.1128/aem.02370-17] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2017] [Accepted: 01/11/2018] [Indexed: 01/20/2023] Open
Abstract
Echinocandins are antifungal nonribosomal hexapeptides produced by fungi. Two of the amino acids are hydroxy-l-prolines: trans-4-hydroxy-l-proline and, in most echinocandin structures, (trans-2,3)-3-hydroxy-(trans-2,4)-4-methyl-l-proline. In the case of echinocandin biosynthesis by Glarea lozoyensis, both amino acids are found in pneumocandin A0, while in pneumocandin B0 the latter residue is replaced by trans-3-hydroxy-l-proline (3-Hyp). We have recently reported that all three amino acids are generated by the 2-oxoglutarate-dependent proline hydroxylase GloF. In echinocandin B biosynthesis by Aspergillus species, 3-Hyp derivatives have not been reported. Here we describe the heterologous production and kinetic characterization of HtyE, the 2-oxoglutarate-dependent proline hydroxylase from the echinocandin B biosynthetic cluster in Aspergillus pachycristatus Surprisingly, l-proline hydroxylation with HtyE resulted in an even higher proportion (∼30%) of 3-Hyp than that with GloF. This suggests that the selectivity for methylated 3-Hyp in echinocandin B biosynthesis is due solely to a substrate-specific adenylation domain of the nonribosomal peptide synthetase. Moreover, we observed that one product of HtyE catalysis, 3-hydroxy-4-methyl-l-proline, is slowly further oxidized at the methyl group, giving 3-hydroxy-4-hydroxymethyl-l-proline, upon prolonged incubation with HtyE. This dihydroxylated amino acid has been reported as a building block of cryptocandin, an echinocandin produced by CryptosporiopsisIMPORTANCE Secondary metabolites from bacteria and fungi are often produced by sets of biosynthetic enzymes encoded in distinct gene clusters. Usually, each enzyme catalyzes one biosynthetic step, but multiple reactions are also possible. Pneumocandins A0 and B0 are produced by the fungus Glarea lozoyensis They belong to the echinocandin family, a group of nonribosomal cyclic lipopeptides that exhibit a strong antifungal activity. Chemical derivatives are important drugs for the treatment of systemic fungal infections. We have recently shown that in the biosynthesis of pneumocandins A0 and B0, three hydroxyproline building blocks are provided by one proline hydroxylase. Here we demonstrate that the proline hydroxylase from echinocandin B biosynthesis in Aspergillus pachycristatus produces the same hydroxyprolines, with an increased proportion of trans-3-hydroxyproline. However, echinocandin B biosynthesis does not require trans-3-hydroxyproline; its formation remains cryptic. While one can only speculate on the evolutionary background of this unexpected finding, proline hydroxylation in G. lozoyensis and A. pachycristatus provides an unusual insight into peptide antibiotic biosynthesis-namely, the complex interplay between the selectivity of a hydroxylase and the substrate specificity of a nonribosomal peptide synthetase.
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Abstract
A personal selection of 32 recent papers is presented covering various aspects of current developments in bioorganic chemistry and novel natural products such as hitorin A from Chloranthus japonicus.
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