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Zhang H, Guo L, Su Y, Wang R, Yang W, Mu W, Xuan L, Huang L, Wang J, Gao W. Hosts engineering and in vitro enzymatic synthesis for the discovery of novel natural products and their derivatives. Crit Rev Biotechnol 2024; 44:1121-1139. [PMID: 37574211 DOI: 10.1080/07388551.2023.2236787] [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: 11/03/2022] [Revised: 05/23/2023] [Accepted: 06/17/2023] [Indexed: 08/15/2023]
Abstract
Novel natural products (NPs) and their derivatives are important sources for drug discovery, which have been broadly applied in the fields of agriculture, livestock, and medicine, making the synthesis of NPs and their derivatives necessarily important. In recent years, biosynthesis technology has received increasing attention due to its high efficiency in the synthesis of high value-added novel products and its advantages of green, environmental protection, and controllability. In this review, the technological advances of biosynthesis strategies in the discovery of novel NPs and their derivatives are outlined, with an emphasis on two areas of host engineering and in vitro enzymatic synthesis. In terms of hosts engineering, multiple microorganisms, including Streptomyces, Aspergillus, and Penicillium, have been used as the biosynthetic gene clusters (BGCs) provider and host strain for the expression of BGCs to discover new compounds over the past years. In addition, the use of in vitro enzymatic synthesis strategy to generate novel compounds such as triterpenoid saponins and flavonoids is also hereby described.
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Affiliation(s)
- Huanyu Zhang
- School of Pharmaceutical Science and Technology, Tianjin University, Tianjin, P.R. China
- Key Laboratory of Systems Bioengineering, Ministry of Education, Tianjin University, Tianjin, P.R. China
| | - Lanping Guo
- National Resource Center for Chinese Meteria Medica, China Academy of Chinese Medical Sciences, Beijing, P.R. China
| | - Yaowu Su
- School of Pharmaceutical Science and Technology, Tianjin University, Tianjin, P.R. China
- Key Laboratory of Systems Bioengineering, Ministry of Education, Tianjin University, Tianjin, P.R. China
| | - Rubing Wang
- School of Pharmaceutical Science and Technology, Tianjin University, Tianjin, P.R. China
- Key Laboratory of Systems Bioengineering, Ministry of Education, Tianjin University, Tianjin, P.R. China
| | - Wenqi Yang
- School of Pharmaceutical Science and Technology, Tianjin University, Tianjin, P.R. China
- Key Laboratory of Systems Bioengineering, Ministry of Education, Tianjin University, Tianjin, P.R. China
| | - Wenrong Mu
- College of Pharmacy, Henan University of Chinese Medicine, Zhengzhou, P.R. China
| | - Liangshuang Xuan
- College of Pharmacy, Henan University of Chinese Medicine, Zhengzhou, P.R. China
| | - Luqi Huang
- National Resource Center for Chinese Meteria Medica, China Academy of Chinese Medical Sciences, Beijing, P.R. China
| | - Juan Wang
- School of Pharmaceutical Science and Technology, Tianjin University, Tianjin, P.R. China
- Key Laboratory of Systems Bioengineering, Ministry of Education, Tianjin University, Tianjin, P.R. China
| | - Wenyuan Gao
- School of Pharmaceutical Science and Technology, Tianjin University, Tianjin, P.R. China
- Key Laboratory of Systems Bioengineering, Ministry of Education, Tianjin University, Tianjin, P.R. China
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Löhr NA, Platz L, Hoffmeister D, Müller M. From the forest floor to the lab: Insights into the diversity and complexity of mushroom polyketide synthases. Curr Opin Chem Biol 2024; 82:102510. [PMID: 39128325 DOI: 10.1016/j.cbpa.2024.102510] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2024] [Revised: 07/12/2024] [Accepted: 07/15/2024] [Indexed: 08/13/2024]
Abstract
Mushroom-forming fungi exhibit a distinctive ecology, which is unsurprisingly also reflected in unique and divergent biosynthetic pathways. We review this phenomenon through the lens of the polyketide metabolism, where mushrooms often deviate from established principles and challenge conventional paradigms. This is evident not only by non-canonical enzyme architectures and functions but also by their propensity for multi-product synthases rather than single-product pathways. Nevertheless, mushrooms also feature many polyketides familiar from plants, bacteria, and fungi of their sister division Ascomycota, which, however, are the result of an independent evolution. In this regard, the captivating biosynthetic pathways of mushrooms might even help us understand the biological pressures that led to the simultaneous production of the same natural products (via convergent evolution, co-evolution, and/or metaevolution) and thus address the question of their raison d'être.
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Affiliation(s)
- Nikolai A Löhr
- Institute of Pharmacy, Department of Pharmaceutical Microbiology, Friedrich Schiller University Jena, Winzerlaer Strasse 2, 07745 Jena, Germany; Department of Pharmaceutical Microbiology, Leibniz Institute for Natural Product Research and Infection Biology - Hans Knöll Institute, Winzerlaer Strasse 2, 07745 Jena, Germany
| | - Lukas Platz
- Institute of Pharmaceutical Sciences, Albert-Ludwigs-Universität Freiburg, Albertstrasse 25, 79104 Freiburg, Germany
| | - Dirk Hoffmeister
- Institute of Pharmacy, Department of Pharmaceutical Microbiology, Friedrich Schiller University Jena, Winzerlaer Strasse 2, 07745 Jena, Germany; Department of Pharmaceutical Microbiology, Leibniz Institute for Natural Product Research and Infection Biology - Hans Knöll Institute, Winzerlaer Strasse 2, 07745 Jena, Germany
| | - Michael Müller
- Institute of Pharmaceutical Sciences, Albert-Ludwigs-Universität Freiburg, Albertstrasse 25, 79104 Freiburg, Germany.
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3
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Brown GW. The cytidine deaminase APOBEC3C has unique sequence and genome feature preferences. Genetics 2024; 227:iyae092. [PMID: 38946641 DOI: 10.1093/genetics/iyae092] [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: 01/17/2024] [Accepted: 05/22/2024] [Indexed: 07/02/2024] Open
Abstract
APOBEC proteins are cytidine deaminases that restrict the replication of viruses and transposable elements. Several members of the APOBEC3 family, APOBEC3A, APOBEC3B, and APOBEC3H-I, can access the nucleus and cause what is thought to be indiscriminate deamination of the genome, resulting in mutagenesis and genome instability. Although APOBEC3C is also present in the nucleus, the full scope of its deamination target preferences is unknown. By expressing human APOBEC3C in a yeast model system, I have defined the APOBEC3C mutation signature, as well as the preferred genome features of APOBEC3C targets. The APOBEC3C mutation signature is distinct from those of the known cancer genome mutators APOBEC3A and APOBEC3B. APOBEC3C produces DNA strand-coordinated mutation clusters, and APOBEC3C mutations are enriched near the transcription start sites of active genes. Surprisingly, APOBEC3C lacks the bias for the lagging strand of DNA replication that is seen for APOBEC3A and APOBEC3B. The unique preferences of APOBEC3C constitute a mutation profile that will be useful in defining sites of APOBEC3C mutagenesis in human genomes.
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Affiliation(s)
- Grant W Brown
- Department of Biochemistry, University of Toronto, 1 King's College Circle, Toronto, ON, Canada M5S 1A8
- Donnelly Centre for Cellular and Biomolecular Research, University of Toronto, 160 College Street, Toronto, ON, Canada M5S 3E1
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Nielsen MR, Sørensen T, Pedersen TB, Westphal KR, Díaz Fernández De Quincoces L, Sondergaard TE, Wimmer R, Brown DW, Sørensen JL. Final piece to the Fusarium pigmentation puzzle - Unraveling of the phenalenone biosynthetic pathway responsible for perithecial pigmentation in the Fusarium solani species complex. Fungal Genet Biol 2024; 174:103912. [PMID: 39004163 DOI: 10.1016/j.fgb.2024.103912] [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: 04/18/2024] [Revised: 06/29/2024] [Accepted: 07/04/2024] [Indexed: 07/16/2024]
Abstract
The Fusarium solani species complex (FSSC) is comprised of important pathogens of plants and humans. A distinctive feature of FSSC species is perithecial pigmentation. While the dark perithecial pigments of other Fusarium species are derived from fusarubins synthesized by polyketide synthase 3 (PKS3), the perithecial pigments of FSSC are derived from an unknown metabolite synthesized by PKS35. Here, we confirm in FSSC species Fusarium vanettenii that PKS35 (fsnI) is required for perithecial pigment synthesis by deletion analysis and that fsnI is closely related to phnA from Penicillium herquei, as well as duxI from Talaromyces stipentatus, which produce prephenalenone as an early intermediate in herqueinone and duclauxin synthesis respectively. The production of prephenalenone by expression of fsnI in Saccharomyces cerevisiae indicates that it is also an early intermediate in perithecial pigment synthesis. We next identified a conserved cluster of 10 genes flanking fsnI in F. vanettenii that when expressed in F. graminearum led to the production of a novel corymbiferan lactone F as a likely end product of the phenalenone biosynthetic pathway in FSSC.
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Affiliation(s)
- Mikkel Rank Nielsen
- Department of Chemistry and Bioscience, Aalborg University, Niels Bohrs Vej 8A, 6700 Esbjerg, Denmark
| | - Trine Sørensen
- Department of Chemistry and Bioscience, Aalborg University, Fredrik Bajers Vej 7H, 9220 Aalborg, Denmark
| | - Tobias Bruun Pedersen
- Department of Chemistry and Bioscience, Aalborg University, Niels Bohrs Vej 8A, 6700 Esbjerg, Denmark
| | - Klaus Ringsborg Westphal
- Department of Chemistry and Bioscience, Aalborg University, Fredrik Bajers Vej 7H, 9220 Aalborg, Denmark
| | | | - Teis Esben Sondergaard
- Department of Chemistry and Bioscience, Aalborg University, Fredrik Bajers Vej 7H, 9220 Aalborg, Denmark
| | - Reinhard Wimmer
- Department of Chemistry and Bioscience, Aalborg University, Fredrik Bajers Vej 7H, 9220 Aalborg, Denmark
| | - Daren W Brown
- National Center for Agricultural Utilization Research, U.S. Department of Agriculture, 1815 N University St. Peoria IL 61604, United States of America
| | - Jens Laurids Sørensen
- Department of Chemistry and Bioscience, Aalborg University, Niels Bohrs Vej 8A, 6700 Esbjerg, Denmark.
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Owens SL, Ahmed SR, Lang Harman RM, Stewart LE, Mori S. Natural Products That Contain Higher Homologated Amino Acids. Chembiochem 2024; 25:e202300822. [PMID: 38487927 DOI: 10.1002/cbic.202300822] [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: 12/04/2023] [Revised: 03/13/2024] [Indexed: 04/11/2024]
Abstract
This review focuses on discussing natural products (NPs) that contain higher homologated amino acids (homoAAs) in the structure as well as the proposed and characterized biosynthesis of these non-proteinogenic amino acids. Homologation of amino acids includes the insertion of a methylene group into its side chain. It is not a very common modification found in NP biosynthesis as approximately 450 homoAA-containing NPs have been isolated from four bacterial phyla (Cyanobacteria, Actinomycetota, Myxococcota, and Pseudomonadota), two fungal phyla (Ascomycota and Basidiomycota), and one animal phylum (Porifera), except for a few examples. Amino acids that are found to be homologated and incorporated in the NP structures include the following ten amino acids: alanine, arginine, cysteine, isoleucine, glutamic acid, leucine, phenylalanine, proline, serine, and tyrosine, where isoleucine, leucine, phenylalanine, and tyrosine share the comparable enzymatic pathway. Other amino acids have their individual homologation pathway (arginine, proline, and glutamic acid for bacteria), likely utilize the primary metabolic pathway (alanine and glutamic acid for fungi), or have not been reported (cysteine and serine). Despite its possible high potential in the drug discovery field, the biosynthesis of homologated amino acids has a large room to explore for future combinatorial biosynthesis and metabolic engineering purpose.
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Affiliation(s)
- Skyler L Owens
- Department of Chemistry and Biochemistry, Augusta University, 1120 15th Street, Augusta, GA 30912
| | - Shopno R Ahmed
- Department of Chemistry and Biochemistry, Augusta University, 1120 15th Street, Augusta, GA 30912
| | - Rebecca M Lang Harman
- Department of Chemistry and Biochemistry, Augusta University, 1120 15th Street, Augusta, GA 30912
| | - Laura E Stewart
- Department of Chemistry and Biochemistry, Augusta University, 1120 15th Street, Augusta, GA 30912
| | - Shogo Mori
- Department of Chemistry and Biochemistry, Augusta University, 1120 15th Street, Augusta, GA 30912
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Klomchit A, Calabon MS, Worabandit S, Weaver JA, Karima EM, Alberti F, Greco C, Mahanil S. Unveiling novel Neocosmospora species from Thai mangroves as potent biocontrol agents against Colletotrichum species. J Appl Microbiol 2024; 135:lxae114. [PMID: 38724454 DOI: 10.1093/jambio/lxae114] [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: 12/22/2023] [Revised: 02/29/2024] [Accepted: 05/08/2024] [Indexed: 05/18/2024]
Abstract
AIMS Neocosmospora species are saprobes, endophytes, and pathogens belonging to the family Nectriaceae. This study aims to investigate the taxonomy, biosynthetic potential, and application of three newly isolated Neocosmospora species from mangrove habitats in the southern part of Thailand using phylogeny, bioactivity screening, genome sequencing, and bioinformatics analysis. METHODS AND RESULTS Detailed descriptions, illustrations, and a multi-locus phylogenetic tree with large subunit ribosomal DNA (LSU), internal transcribed spacer (ITS), translation elongation factor 1-alpha (ef1-α), and RNA polymerase II second largest subunit (RPB2) regions showing the placement of three fungal strains, MFLUCC 17-0253, MFLUCC 17-0257, and MFLUCC 17-0259 clustered within the Neocosmospora clade with strong statistical support. Fungal crude extracts of the new species N. mangrovei MFLUCC 17-0253 exhibited strong antifungal activity to control Colletotrichum truncatum CG-0064, while N. ferruginea MFLUCC 17-0259 exhibited only moderate antifungal activity toward C. acutatum CC-0036. Thus, N. mangrovei MFLUCC 17-0253 was sequenced by Oxford nanopore technology. The bioinformatics analysis revealed that 49.17 Mb genome of this fungus harbors 41 potential biosynthetic gene clusters. CONCLUSION Two fungal isolates of Neocosmospora and a new species of N. mangrovei were reported in this study. These fungal strains showed activity against pathogenic fungi causing anthracnose in chili. In addition, full genome sequencing and bioinformatics analysis of N. mangrovei MFLUCC 17-0253 were obtained.
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Affiliation(s)
- Anthikan Klomchit
- School of Science, Mae Fah Luang University, Chiang Rai 57100, Thailand
| | - Mark S Calabon
- Division of Biological Sciences, College of Arts and Sciences, University of the Philippines Visayas, Miagao, Iloilo 5024, Philippines
| | | | - Jack A Weaver
- School of Life Sciences, University of Warwick, Gibbet Hill Road, Coventry CV4 7AL, United Kingdom
| | - Elfina M Karima
- Department of Biosciences, Swansea University, Swansea SA2 8PP, United Kingdom
| | - Fabrizio Alberti
- School of Life Sciences, University of Warwick, Gibbet Hill Road, Coventry CV4 7AL, United Kingdom
| | - Claudio Greco
- Department of Biosciences, Swansea University, Swansea SA2 8PP, United Kingdom
| | - Siraprapa Mahanil
- School of Science, Mae Fah Luang University, Chiang Rai 57100, Thailand
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7
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Tan LL, Heng E, Leong CY, Ng V, Yang LK, Seow DCS, Koduru L, Kanagasundaram Y, Ng SB, Peh G, Lim YH, Wong FT. Application of Cas12j for Streptomyces Editing. Biomolecules 2024; 14:486. [PMID: 38672502 PMCID: PMC11048056 DOI: 10.3390/biom14040486] [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: 02/26/2024] [Revised: 04/09/2024] [Accepted: 04/14/2024] [Indexed: 04/28/2024] Open
Abstract
In recent years, CRISPR-Cas toolboxes for Streptomyces editing have rapidly accelerated natural product discovery and engineering. However, Cas efficiencies are oftentimes strain-dependent, and the commonly used Streptococcus pyogenes Cas9 (SpCas9) is notorious for having high levels of off-target toxicity effects. Thus, a variety of Cas proteins is required for greater flexibility of genetic manipulation within a wider range of Streptomyces strains. This study explored the first use of Acidaminococcus sp. Cas12j, a hypercompact Cas12 subfamily, for genome editing in Streptomyces and its potential in activating silent biosynthetic gene clusters (BGCs) to enhance natural product synthesis. While the editing efficiencies of Cas12j were not as high as previously reported efficiencies of Cas12a and Cas9, Cas12j exhibited higher transformation efficiencies compared to SpCas9. Furthermore, Cas12j demonstrated significantly improved editing efficiencies compared to Cas12a in activating BGCs in Streptomyces sp. A34053, a strain wherein both SpCas9 and Cas12a faced limitations in accessing the genome. Overall, this study expanded the repertoire of Cas proteins for genome editing in actinomycetes and highlighted not only the potential of recently characterized Cas12j in Streptomyces but also the importance of having an extensive genetic toolbox for improving the editing success of these beneficial microbes.
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Affiliation(s)
- Lee Ling Tan
- Institute of Molecular and Cell Biology (IMCB), Agency for Science, Technology and Research (A*STAR), 61 Biopolis Drive, Proteos #07-06, Singapore 138673, Singapore; (L.L.T.); (E.H.)
| | - Elena Heng
- Institute of Molecular and Cell Biology (IMCB), Agency for Science, Technology and Research (A*STAR), 61 Biopolis Drive, Proteos #07-06, Singapore 138673, Singapore; (L.L.T.); (E.H.)
| | - Chung Yan Leong
- Singapore Institute of Food and Biotechnology Innovation (SIFBI), Agency for Science, Technology and Research (A*STAR), 31 Biopolis Way, Nanos #02-01, Singapore 138669, Singapore; (C.Y.L.); (V.N.); (L.K.Y.); (D.C.S.S.); (Y.K.); (S.B.N.)
| | - Veronica Ng
- Singapore Institute of Food and Biotechnology Innovation (SIFBI), Agency for Science, Technology and Research (A*STAR), 31 Biopolis Way, Nanos #02-01, Singapore 138669, Singapore; (C.Y.L.); (V.N.); (L.K.Y.); (D.C.S.S.); (Y.K.); (S.B.N.)
| | - Lay Kien Yang
- Singapore Institute of Food and Biotechnology Innovation (SIFBI), Agency for Science, Technology and Research (A*STAR), 31 Biopolis Way, Nanos #02-01, Singapore 138669, Singapore; (C.Y.L.); (V.N.); (L.K.Y.); (D.C.S.S.); (Y.K.); (S.B.N.)
| | - Deborah Chwee San Seow
- Singapore Institute of Food and Biotechnology Innovation (SIFBI), Agency for Science, Technology and Research (A*STAR), 31 Biopolis Way, Nanos #02-01, Singapore 138669, Singapore; (C.Y.L.); (V.N.); (L.K.Y.); (D.C.S.S.); (Y.K.); (S.B.N.)
| | - Lokanand Koduru
- Institute of Molecular and Cell Biology (IMCB), Agency for Science, Technology and Research (A*STAR), 61 Biopolis Drive, Proteos #07-06, Singapore 138673, Singapore; (L.L.T.); (E.H.)
| | - Yoganathan Kanagasundaram
- Singapore Institute of Food and Biotechnology Innovation (SIFBI), Agency for Science, Technology and Research (A*STAR), 31 Biopolis Way, Nanos #02-01, Singapore 138669, Singapore; (C.Y.L.); (V.N.); (L.K.Y.); (D.C.S.S.); (Y.K.); (S.B.N.)
| | - Siew Bee Ng
- Singapore Institute of Food and Biotechnology Innovation (SIFBI), Agency for Science, Technology and Research (A*STAR), 31 Biopolis Way, Nanos #02-01, Singapore 138669, Singapore; (C.Y.L.); (V.N.); (L.K.Y.); (D.C.S.S.); (Y.K.); (S.B.N.)
| | - Guangrong Peh
- Institute of Sustainability for Chemicals, Energy and Environment (ISCE2), Agency for Science, Technology and Research (A*STAR), 8 Biomedical Grove, Neuros #07-01, Singapore 138665, Singapore; (G.P.); (Y.H.L.)
| | - Yee Hwee Lim
- Institute of Sustainability for Chemicals, Energy and Environment (ISCE2), Agency for Science, Technology and Research (A*STAR), 8 Biomedical Grove, Neuros #07-01, Singapore 138665, Singapore; (G.P.); (Y.H.L.)
| | - Fong Tian Wong
- Institute of Molecular and Cell Biology (IMCB), Agency for Science, Technology and Research (A*STAR), 61 Biopolis Drive, Proteos #07-06, Singapore 138673, Singapore; (L.L.T.); (E.H.)
- Institute of Sustainability for Chemicals, Energy and Environment (ISCE2), Agency for Science, Technology and Research (A*STAR), 8 Biomedical Grove, Neuros #07-01, Singapore 138665, Singapore; (G.P.); (Y.H.L.)
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8
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Cook GD, Stasulli NM. Employing synthetic biology to expand antibiotic discovery. SLAS Technol 2024; 29:100120. [PMID: 38340893 DOI: 10.1016/j.slast.2024.100120] [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: 06/16/2023] [Revised: 01/04/2024] [Accepted: 02/07/2024] [Indexed: 02/12/2024]
Abstract
Antimicrobial-resistant (AMR) bacterial pathogens are a continually growing threat as our methods for combating these infections continue to be overcome by the evolution of resistance mechanisms. Recent therapeutic methods have not staved off the concern of AMR infections, so continued research focuses on new ways of identifying small molecules to treat AMR pathogens. While chemical modification of existing antibiotics is possible, there has been rapid development of resistance by pathogens that were initially susceptible to these compounds. Synthetic biology is becoming a key strategy in trying to predict and induce novel, natural antibiotics. Advances in cloning and mutagenesis techniques applied through a synthetic biology lens can help characterize the native regulation of antibiotic biosynthetic gene clusters (BGCs) to identify potential modifications leading to more potent antibiotic activity. Additionally, many cryptic antibiotic BGCs are derived from non-ribosomal peptide synthase (NRPS) and polyketide synthase (PKS) biosynthetic pathways; complex, clustered genetic sequences that give rise to amino acid-derived natural products. Synthetic biology can be applied to modify and metabolically engineer these enzyme-based systems to promote rapid and sustainable production of natural products and their variants. This review will focus on recent advances related to synthetic biology as applied to genetic pathway characterization and identification of antibiotics from naturally occurring BGCs. Specifically, we will summarize recent efforts to characterize BGCs via general genomic mutagenesis, endogenous gene expression, and heterologous gene expression.
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Affiliation(s)
- Greta D Cook
- Department of Biology and Environmental Science, University of New Haven, 300 Boston Post Rd, Dodds Hall 316, West Haven 06516 USA
| | - Nikolas M Stasulli
- Department of Biology and Environmental Science, University of New Haven, 300 Boston Post Rd, Dodds Hall 316, West Haven 06516 USA.
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9
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Bejenari M, Spedtsberg EML, Mathiesen J, Jeppesen AC, Cernat L, Toussaint A, Apostol C, Stoianov V, Pedersen TB, Nielsen MR, Sørensen JL. First-class - biosynthesis of 6-MSA and bostrycoidin type I polyketides in Yarrowia lipolytica. FRONTIERS IN FUNGAL BIOLOGY 2024; 5:1327777. [PMID: 38586602 PMCID: PMC10995274 DOI: 10.3389/ffunb.2024.1327777] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/13/2023] [Accepted: 02/09/2024] [Indexed: 04/09/2024]
Abstract
Fungal polyketides are a large group of secondary metabolites, valuable due to their diverse spectrum of pharmacological activities. Polyketide biosynthesis in filamentous fungi presents some challenges: small yield and low-purity titers. To tackle these issues, we switched to the yeast Yarrowia lipolytica, an easily cultivable heterologous host. As an oleaginous yeast, Y. lipolytica displays a high flux of acetyl- and malonyl-CoA precursors used in lipid synthesis. Likewise, acetyl- and malonyl-CoA are the building blocks of many natural polyketides, and we explored the possibility of redirecting this flux toward polyketide production. Despite its promising prospect, Y. lipolytica has so far only been used for heterologous expression of simple type III polyketide synthases (PKSs) from plants. Therefore, we decided to evaluate the potential of Y. lipolytica by targeting the more complex fungal polyketides synthesized by type I PKSs. We employed a CRISPR-Cas9-mediated genome editing method to achieve markerless gene integration of the genes responsible for bostrycoidin biosynthesis in Fusarium solani (fsr1, fsr2, and fsr3) and 6-methylsalicylic acid (6-MSA) biosynthesis in Aspergillus hancockii (6MSAS). Moreover, we attempted titer optimization through metabolic engineering by overexpressing two enzymes, TGL4 and AOX2, involved in lipid β-oxidation, but we did not observe an effect on polyketide production. With maximum titers of 403 mg/L 6-MSA and 35 mg/L bostrycoidin, the latter being substantially higher than our previous results in Saccharomyces cerevisiae (2.2 mg/L), this work demonstrates the potential of Y. lipolytica as a platform for heterologous production of complex fungal polyketides.
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Affiliation(s)
- Mihaela Bejenari
- Department of Chemistry and Bioscience, Aalborg University, Esbjerg, Denmark
| | - Eva Mie Lang Spedtsberg
- Department of Chemistry and Bioscience, Aalborg University, Esbjerg, Denmark
- Department of Energy, Aalborg University, Esbjerg, Denmark
| | - Julie Mathiesen
- Department of Chemistry and Bioscience, Aalborg University, Esbjerg, Denmark
| | | | - Lucia Cernat
- Department of Chemistry and Bioscience, Aalborg University, Esbjerg, Denmark
| | - Aouregane Toussaint
- Université Grenoble Alpes, Laboratoire de Physiologie Cellulaire Végétale, CEA, CNRS, INRA, IRIG-LPCV, Grenoble, France
| | - Cristina Apostol
- Department of Chemistry and Bioscience, Aalborg University, Esbjerg, Denmark
| | - Victor Stoianov
- Department of Chemistry and Bioscience, Aalborg University, Esbjerg, Denmark
| | | | - Mikkel Rank Nielsen
- Department of Chemistry and Bioscience, Aalborg University, Esbjerg, Denmark
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10
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Dror MJ, Misa J, Yee DA, Chu AM, Yu RK, Chan BB, Aoyama LS, Chaparala AP, O'Connor SE, Tang Y. Engineered biosynthesis of plant heteroyohimbine and corynantheine alkaloids in Saccharomyces cerevisiae. J Ind Microbiol Biotechnol 2024; 51:kuad047. [PMID: 38140980 PMCID: PMC10995622 DOI: 10.1093/jimb/kuad047] [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: 11/09/2023] [Accepted: 12/21/2023] [Indexed: 12/24/2023]
Abstract
Monoterpene indole alkaloids (MIAs) are a class of natural products comprised of thousands of structurally unique bioactive compounds with significant therapeutic values. Due to difficulties associated with isolation from native plant species and organic synthesis of these structurally complex molecules, microbial production of MIAs using engineered hosts are highly desired. In this work, we report the engineering of fully integrated Saccharomyces cerevisiae strains that allow de novo access to strictosidine, the universal precursor to thousands of MIAs at 30-40 mg/L. The optimization efforts were based on a previously reported yeast strain that is engineered to produce high titers of the monoterpene precursor geraniol through compartmentalization of mevalonate pathway in the mitochondria. Our approaches here included the use of CRISPR-dCas9 interference to identify mitochondria diphosphate transporters that negatively impact the titer of the monoterpene, followed by genetic inactivation; the overexpression of transcriptional regulators that increase cellular respiration and mitochondria biogenesis. Strain construction included the strategic integration of genes encoding both MIA biosynthetic and accessory enzymes into the genome under a variety of constitutive and inducible promoters. Following successful de novo production of strictosidine, complex alkaloids belonging to heteroyohimbine and corynantheine families were reconstituted in the host with introduction of additional downstream enzymes. We demonstrate that the serpentine/alstonine pair can be produced at ∼5 mg/L titer, while corynantheidine, the precursor to mitragynine can be produced at ∼1 mg/L titer. Feeding of halogenated tryptamine led to the biosynthesis of analogs of alkaloids in both families. Collectively, our yeast strain represents an excellent starting point to further engineer biosynthetic bottlenecks in this pathway and to access additional MIAs and analogs through microbial fermentation. ONE SENTENCE SUMMARY An Saccharomyces cerevisiae-based microbial platform was developed for the biosynthesis of monoterpene indole alkaloids, including the universal precursor strictosidine and further modified heteroyohimbine and corynantheidine alkaloids.
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Affiliation(s)
- Moriel J Dror
- Department of Chemical and Biomolecular Engineering, University of California, Los Angeles, Los Angeles, CA 90095, USA
- Department of Bioengineering, University of California, Los Angeles, Los Angeles, CA 90095, USA
| | - Joshua Misa
- Department of Chemical and Biomolecular Engineering, University of California, Los Angeles, Los Angeles, CA 90095, USA
| | - Danielle A Yee
- Department of Chemical and Biomolecular Engineering, University of California, Los Angeles, Los Angeles, CA 90095, USA
| | - Angela M Chu
- Stanford Genome Technology Center, Stanford University, Stanford, CA 94305, USA
| | - Rachel K Yu
- Department of Chemical and Biomolecular Engineering, University of California, Los Angeles, Los Angeles, CA 90095, USA
- Department of Molecular Cell and Developmental Biology, University of California, Los Angeles, Los Angeles, CA 90095, USA
| | - Bradley B Chan
- Department of Chemical and Biomolecular Engineering, University of California, Los Angeles, Los Angeles, CA 90095, USA
- Department of Bioengineering, University of California, Los Angeles, Los Angeles, CA 90095, USA
| | - Lauren S Aoyama
- Department of Chemical and Biomolecular Engineering, University of California, Los Angeles, Los Angeles, CA 90095, USA
| | - Anjali P Chaparala
- Department of Chemical and Biomolecular Engineering, University of California, Los Angeles, Los Angeles, CA 90095, USA
| | - Sarah E O'Connor
- Department of Natural Product Biosynthesis, Max Planck Institute for Chemical Ecology, Jena 07745, Germany
| | - Yi Tang
- Department of Chemical and Biomolecular Engineering, University of California, Los Angeles, Los Angeles, CA 90095, USA
- Department of Chemistry and Biochemistry, University of California, Los Angeles, Los Angeles, CA 90095, USA
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11
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Tay DWP, Tan LL, Heng E, Zulkarnain N, Ching KC, Wibowo M, Chin EJ, Tan ZYQ, Leong CY, Ng VWP, Yang LK, Seow DCS, Lim YW, Koh W, Koduru L, Kanagasundaram Y, Ng SB, Lim YH, Wong FT. Exploring a general multi-pronged activation strategy for natural product discovery in Actinomycetes. Commun Biol 2024; 7:50. [PMID: 38184720 PMCID: PMC10771470 DOI: 10.1038/s42003-023-05648-7] [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: 08/16/2023] [Accepted: 11/29/2023] [Indexed: 01/08/2024] Open
Abstract
Natural products possess significant therapeutic potential but remain underutilized despite advances in genomics and bioinformatics. While there are approaches to activate and upregulate natural product biosynthesis in both native and heterologous microbial strains, a comprehensive strategy to elicit production of natural products as well as a generalizable and efficient method to interrogate diverse native strains collection, remains lacking. Here, we explore a flexible and robust integrase-mediated multi-pronged activation approach to reliably perturb and globally trigger antibiotics production in actinobacteria. Across 54 actinobacterial strains, our approach yielded 124 distinct activator-strain combinations which consistently outperform wild type. Our approach expands accessible metabolite space by nearly two-fold and increases selected metabolite yields by up to >200-fold, enabling discovery of Gram-negative bioactivity in tetramic acid analogs. We envision these findings as a gateway towards a more streamlined, accelerated, and scalable strategy to unlock the full potential of Nature's chemical repertoire.
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Grants
- NRF-CRP19-2017-05-00 National Research Foundation Singapore (National Research Foundation-Prime Minister's office, Republic of Singapore)
- NRF-CRP19-2017-05-00 National Research Foundation Singapore (National Research Foundation-Prime Minister's office, Republic of Singapore)
- NRF-CRP19-2017-05-00 National Research Foundation Singapore (National Research Foundation-Prime Minister's office, Republic of Singapore)
- NRF-CRP19-2017-05-00 National Research Foundation Singapore (National Research Foundation-Prime Minister's office, Republic of Singapore)
- NRF-CRP19-2017-05-00 National Research Foundation Singapore (National Research Foundation-Prime Minister's office, Republic of Singapore)
- NRF-CRP19-2017-05-00 National Research Foundation Singapore (National Research Foundation-Prime Minister's office, Republic of Singapore)
- NRF-CRP19-2017-05-00 National Research Foundation Singapore (National Research Foundation-Prime Minister's office, Republic of Singapore)
- NRF-CRP19-2017-05-00 National Research Foundation Singapore (National Research Foundation-Prime Minister's office, Republic of Singapore)
- C211917006 Agency for Science, Technology and Research (A*STAR)
- C233017006 Agency for Science, Technology and Research (A*STAR)
- C211917003 Agency for Science, Technology and Research (A*STAR)
- C211917006 Agency for Science, Technology and Research (A*STAR)
- C233017006 Agency for Science, Technology and Research (A*STAR)
- C211917006 Agency for Science, Technology and Research (A*STAR)
- National Research Foundation Singapore (National Research Foundation-Prime Minister’s office, Republic of Singapore)
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Affiliation(s)
- Dillon W P Tay
- Institute of Sustainability for Chemicals, Energy and Environment (ISCE2), Agency for Science, Technology and Research (A*STAR), 8 Biomedical Grove, #07-01 Neuros Building, Singapore, 138665, Republic of Singapore
| | - Lee Ling Tan
- Molecular Engineering Lab, Institute of Molecular and Cell Biology (IMCB), Agency for Science, Technology and Research (A*STAR), 61 Biopolis Drive, #07-06, Proteos, Singapore, 138673, Republic of Singapore
| | - Elena Heng
- Molecular Engineering Lab, Institute of Molecular and Cell Biology (IMCB), Agency for Science, Technology and Research (A*STAR), 61 Biopolis Drive, #07-06, Proteos, Singapore, 138673, Republic of Singapore
| | - Nadiah Zulkarnain
- Molecular Engineering Lab, Institute of Molecular and Cell Biology (IMCB), Agency for Science, Technology and Research (A*STAR), 61 Biopolis Drive, #07-06, Proteos, Singapore, 138673, Republic of Singapore
| | - Kuan Chieh Ching
- Singapore Institute of Food and Biotechnology Innovation (SIFBI), Agency for Science, Technology and Research (A*STAR), 31 Biopolis Way, #01-02, Nanos, Singapore, 138669, Republic of Singapore
| | - Mario Wibowo
- Singapore Institute of Food and Biotechnology Innovation (SIFBI), Agency for Science, Technology and Research (A*STAR), 31 Biopolis Way, #01-02, Nanos, Singapore, 138669, Republic of Singapore
| | - Elaine Jinfeng Chin
- Singapore Institute of Food and Biotechnology Innovation (SIFBI), Agency for Science, Technology and Research (A*STAR), 31 Biopolis Way, #01-02, Nanos, Singapore, 138669, Republic of Singapore
| | - Zann Yi Qi Tan
- Singapore Institute of Food and Biotechnology Innovation (SIFBI), Agency for Science, Technology and Research (A*STAR), 31 Biopolis Way, #01-02, Nanos, Singapore, 138669, Republic of Singapore
| | - Chung Yan Leong
- Singapore Institute of Food and Biotechnology Innovation (SIFBI), Agency for Science, Technology and Research (A*STAR), 31 Biopolis Way, #01-02, Nanos, Singapore, 138669, Republic of Singapore
| | - Veronica Wee Pin Ng
- Singapore Institute of Food and Biotechnology Innovation (SIFBI), Agency for Science, Technology and Research (A*STAR), 31 Biopolis Way, #01-02, Nanos, Singapore, 138669, Republic of Singapore
| | - Lay Kien Yang
- Singapore Institute of Food and Biotechnology Innovation (SIFBI), Agency for Science, Technology and Research (A*STAR), 31 Biopolis Way, #01-02, Nanos, Singapore, 138669, Republic of Singapore
| | - Deborah C S Seow
- Singapore Institute of Food and Biotechnology Innovation (SIFBI), Agency for Science, Technology and Research (A*STAR), 31 Biopolis Way, #01-02, Nanos, Singapore, 138669, Republic of Singapore
| | - Yi Wee Lim
- Institute of Sustainability for Chemicals, Energy and Environment (ISCE2), Agency for Science, Technology and Research (A*STAR), 8 Biomedical Grove, #07-01 Neuros Building, Singapore, 138665, Republic of Singapore
| | - Winston Koh
- Bioinformatics Institute (BII), Agency of Science, Technology and Research (A*STAR), 30 Biopolis Street, #07-01, Matrix, Singapore, 138671, Republic of Singapore
| | - Lokanand Koduru
- Molecular Engineering Lab, Institute of Molecular and Cell Biology (IMCB), Agency for Science, Technology and Research (A*STAR), 61 Biopolis Drive, #07-06, Proteos, Singapore, 138673, Republic of Singapore
| | - Yoganathan Kanagasundaram
- Singapore Institute of Food and Biotechnology Innovation (SIFBI), Agency for Science, Technology and Research (A*STAR), 31 Biopolis Way, #01-02, Nanos, Singapore, 138669, Republic of Singapore
| | - Siew Bee Ng
- Singapore Institute of Food and Biotechnology Innovation (SIFBI), Agency for Science, Technology and Research (A*STAR), 31 Biopolis Way, #01-02, Nanos, Singapore, 138669, Republic of Singapore
| | - Yee Hwee Lim
- Institute of Sustainability for Chemicals, Energy and Environment (ISCE2), Agency for Science, Technology and Research (A*STAR), 8 Biomedical Grove, #07-01 Neuros Building, Singapore, 138665, Republic of Singapore.
- Synthetic Biology Translational Research Program, Yong Loo Lin School of Medicine, National University of Singapore, 10 Medical Drive, Singapore, 117597, Republic of Singapore.
| | - Fong Tian Wong
- Institute of Sustainability for Chemicals, Energy and Environment (ISCE2), Agency for Science, Technology and Research (A*STAR), 8 Biomedical Grove, #07-01 Neuros Building, Singapore, 138665, Republic of Singapore.
- Molecular Engineering Lab, Institute of Molecular and Cell Biology (IMCB), Agency for Science, Technology and Research (A*STAR), 61 Biopolis Drive, #07-06, Proteos, Singapore, 138673, Republic of Singapore.
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12
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Li X, Gadar-Lopez AE, Chen L, Jayachandran S, Cruz-Morales P, Keasling JD. Mining natural products for advanced biofuels and sustainable bioproducts. Curr Opin Biotechnol 2023; 84:103003. [PMID: 37769513 DOI: 10.1016/j.copbio.2023.103003] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2023] [Revised: 09/03/2023] [Accepted: 09/03/2023] [Indexed: 10/03/2023]
Abstract
Recently, there has been growing interest in the sustainable production of biofuels and bioproducts derived from renewable sources. Natural products, the largest and more structurally diverse group of metabolites, hold significant promise as sources for such bio-based products. However, there are two primary challenges in harnessing natural products' potential: precise mining of biosynthetic gene clusters (BGCs) that can be used as scaffolds or bioparts and their functional expression for biofuel and bioproduct manufacture. In this review, we explore recent advances in the development of bioinformatic tools for BGC mining and the manipulation of various hosts for natural product-based biofuels and bioproducts manufacture. Moreover, we discuss potential strategies for expanding the chemical diversity of biofuels and bioproducts and enhancing their overall yield.
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Affiliation(s)
- Xiaowei Li
- Novo Nordisk Foundation Center for Biosustainability, Danmarks Tekniske Universitet, Kongens Lyngby, Denmark
| | - Adrian E Gadar-Lopez
- Novo Nordisk Foundation Center for Biosustainability, Danmarks Tekniske Universitet, Kongens Lyngby, Denmark
| | - Ling Chen
- Novo Nordisk Foundation Center for Biosustainability, Danmarks Tekniske Universitet, Kongens Lyngby, Denmark
| | - Sidharth Jayachandran
- Novo Nordisk Foundation Center for Biosustainability, Danmarks Tekniske Universitet, Kongens Lyngby, Denmark
| | - Pablo Cruz-Morales
- Novo Nordisk Foundation Center for Biosustainability, Danmarks Tekniske Universitet, Kongens Lyngby, Denmark.
| | - Jay D Keasling
- Novo Nordisk Foundation Center for Biosustainability, Danmarks Tekniske Universitet, Kongens Lyngby, Denmark; Lawrence Berkeley National Laboratory, Biological Systems and Engineering Division, Berkeley, CA, USA; Joint BioEnergy Institute, Emeryville, CA, USA; Departments of Chemical & Biomolecular Engineering and of Bioengineering, University of California, Berkeley, CA 94720, USA; Center for Synthetic Biochemistry, Shenzhen Institutes for Advanced Technologies, Shenzhen, China.
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13
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Dunbar KL, Perlatti B, Liu N, Cornelius A, Mummau D, Chiang YM, Hon L, Nimavat M, Pallas J, Kordes S, Ng HL, Harvey CJB. Resistance gene-guided genome mining reveals the roseopurpurins as inhibitors of cyclin-dependent kinases. Proc Natl Acad Sci U S A 2023; 120:e2310522120. [PMID: 37983497 PMCID: PMC10691236 DOI: 10.1073/pnas.2310522120] [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: 06/23/2023] [Accepted: 09/09/2023] [Indexed: 11/22/2023] Open
Abstract
With the significant increase in the availability of microbial genome sequences in recent years, resistance gene-guided genome mining has emerged as a powerful approach for identifying natural products with specific bioactivities. Here, we present the use of this approach to reveal the roseopurpurins as potent inhibitors of cyclin-dependent kinases (CDKs), a class of cell cycle regulators implicated in multiple cancers. We identified a biosynthetic gene cluster (BGC) with a putative resistance gene with homology to human CDK2. Using targeted gene disruption and transcription factor overexpression in Aspergillus uvarum, and heterologous expression of the BGC in Aspergillus nidulans, we demonstrated that roseopurpurin C (1) is produced by this cluster and characterized its biosynthesis. We determined the potency, specificity, and mechanism of action of 1 as well as multiple intermediates and shunt products produced from the BGC. We show that 1 inhibits human CDK2 with a Kiapp of 44 nM, demonstrates selectivity for clinically relevant members of the CDK family, and induces G1 cell cycle arrest in HCT116 cells. Structural analysis of 1 complexed with CDK2 revealed the molecular basis of ATP-competitive inhibition.
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Affiliation(s)
| | | | | | | | | | | | | | | | | | - Sina Kordes
- Proteros Biostructures GmbH, PlaneggD-82152, Germany
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14
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Song Z, Zhou S, Zhang H, Keller NP, Oakley BR, Liu X, Yin WB. Fungal secondary metabolism is governed by an RNA-binding protein CsdA/RsdA complex. Nat Commun 2023; 14:7351. [PMID: 37963872 PMCID: PMC10645843 DOI: 10.1038/s41467-023-43205-2] [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: 01/23/2023] [Accepted: 11/03/2023] [Indexed: 11/16/2023] Open
Abstract
Production of secondary metabolites is controlled by a complicated regulatory network in eukaryotic cells. Several layers of regulators are involved in this process, ranging from pathway-specific regulation, to epigenetic control, to global regulation. Here, we discover that interaction of an RNA-binding protein CsdA with a regulator RsdA coordinates fungal secondary metabolism. Employing a genetic deletion approach and transcriptome analysis as well as metabolomics analysis, we reveal that CsdA and RsdA synergistically regulate fungal secondary metabolism comprehensively. Mechanistically, comprehensive genetic and biochemical studies prove that RsdA and CsdA co-localize in the nucleus and physically interact to achieve their functions. In particular, we demonstrate that CsdA mediates rsdA expression by binding specific motif "GUCGGUAU" of its pre-mRNA at a post-transcriptional level. We thus uncover a mechanism in which RNA-binding protein physically interacts with, and controls the expression level of, the RsdA to coordinate fungal secondary metabolism.
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Affiliation(s)
- Zili Song
- State Key Laboratory of Mycology, Institute of Microbiology, Chinese Academy of Sciences, 100101, Beijing, PR China
- Savaid Medical School, University of Chinese Academy of Sciences, 100049, Beijing, PR China
| | - Shuang Zhou
- State Key Laboratory of Mycology, Institute of Microbiology, Chinese Academy of Sciences, 100101, Beijing, PR China
| | - Hongjiao Zhang
- State Key Laboratory of Mycology, Institute of Microbiology, Chinese Academy of Sciences, 100101, Beijing, PR China
- Savaid Medical School, University of Chinese Academy of Sciences, 100049, Beijing, PR China
| | - Nancy P Keller
- Department of Medical Microbiology and Immunology, University of Wisconsin-Madison, Madison, WI, 53706, USA
| | - Berl R Oakley
- Department of Molecular Biosciences, University of Kansas, Lawrence, KS, 66045, USA
| | - Xiao Liu
- State Key Laboratory of Mycology, Institute of Microbiology, Chinese Academy of Sciences, 100101, Beijing, PR China
| | - Wen-Bing Yin
- State Key Laboratory of Mycology, Institute of Microbiology, Chinese Academy of Sciences, 100101, Beijing, PR China.
- Savaid Medical School, University of Chinese Academy of Sciences, 100049, Beijing, PR China.
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15
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Geistodt-Kiener A, Totozafy JC, Le Goff G, Vergne J, Sakai K, Ouazzani J, Mouille G, Viaud M, O'Connell RJ, Dallery JF. Yeast-based heterologous production of the Colletochlorin family of fungal secondary metabolites. Metab Eng 2023; 80:216-231. [PMID: 37863177 DOI: 10.1016/j.ymben.2023.10.002] [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: 07/05/2023] [Revised: 09/15/2023] [Accepted: 10/12/2023] [Indexed: 10/22/2023]
Abstract
Transcriptomic studies have revealed that fungal pathogens of plants activate the expression of numerous biosynthetic gene clusters (BGC) exclusively when in presence of a living host plant. The identification and structural elucidation of the corresponding secondary metabolites remain challenging. The aim was to develop a polycistronic system for heterologous expression of fungal BGCs in Saccharomyces cerevisiae. Here we adapted a polycistronic vector for efficient, seamless and cost-effective cloning of biosynthetic genes using in vivo assembly (also called transformation-assisted recombination) directly in Escherichia coli followed by heterologous expression in S. cerevisiae. Two vectors were generated with different auto-inducible yeast promoters and selection markers. The effectiveness of these vectors was validated with fluorescent proteins. As a proof-of-principle, we applied our approach to the Colletochlorin family of molecules. These polyketide secondary metabolites were known from the phytopathogenic fungus Colletotrichum higginsianum but had never been linked to their biosynthetic genes. Considering the requirement for a halogenase, and by applying comparative genomics, we identified a BGC putatively involved in the biosynthesis of Colletochlorins in C. higginsianum. Following the expression of those genes in S. cerevisiae, we could identify the presence of the precursor Orsellinic acid, Colletochlorins and their non-chlorinated counterparts, the Colletorins. In conclusion, the polycistronic vectors described herein were adapted for the host S. cerevisiae and allowed to link the Colletochlorin compound family to their corresponding biosynthetic genes. This system will now enable the production and purification of infection-specific secondary metabolites of fungal phytopathogens. More widely, this system could be applied to any fungal BGC of interest.
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Affiliation(s)
| | - Jean Chrisologue Totozafy
- Université Paris-Saclay, INRAE, AgroParisTech, Institut Jean-Pierre Bourgin, 78000, Versailles, France
| | - Géraldine Le Goff
- Centre National de La Recherche Scientifique, Institut de Chimie des Substances Naturelles ICSN, 91190, Gif-sur-Yvette, France
| | - Justine Vergne
- Université Paris-Saclay, INRAE, UR BIOGER, 91120, Palaiseau, France
| | - Kaori Sakai
- Université Paris-Saclay, INRAE, UR BIOGER, 91120, Palaiseau, France
| | - Jamal Ouazzani
- Centre National de La Recherche Scientifique, Institut de Chimie des Substances Naturelles ICSN, 91190, Gif-sur-Yvette, France
| | - Grégory Mouille
- Université Paris-Saclay, INRAE, AgroParisTech, Institut Jean-Pierre Bourgin, 78000, Versailles, France
| | - Muriel Viaud
- Université Paris-Saclay, INRAE, UR BIOGER, 91120, Palaiseau, France
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16
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Yuan Y, Huang C, Singh N, Xun G, Zhao H. Automated, self-resistance gene-guided, and high-throughput genome mining of bioactive natural products from Streptomyces. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.10.26.564101. [PMID: 37961497 PMCID: PMC10634842 DOI: 10.1101/2023.10.26.564101] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/15/2023]
Abstract
Natural products (NPs) produced by bacteria, fungi and plants are a major source of drug leads. Streptomyces species are particularly important in this regard as they produce numerous natural products with prominent bioactivities. Here we report a fully a utomated, s calable and high-throughput platform for discovery of bioactive n atural p roducts in S treptomyces (FAST-NPS). This platform comprises computational prediction and prioritization of target biosynthetic gene clusters (BGCs) guided by self-resistance genes, highly efficient and automated direct cloning and heterologous expression of BGCs, followed by high-throughput fermentation and product extraction from Streptomyces strains. As a proof of concept, we applied this platform to clone 105 BGCs ranging from 10 to 100 kb that contain potential self-resistance genes from 11 Streptomyces strains with a success rate of 95%. Heterologous expression of all successfully cloned BGCs in Streptomyces lividans TK24 led to the discovery of 23 natural products from 12 BGCs. We selected 5 of these 12 BGCs for further characterization and found each of them could produce at least one natural product with antibacterial and/or anti-tumor activity, which resulted in a total of 8 bioactive natural products. Overall, this work would greatly accelerate the discovery of bioactive natural products for biomedical and biotechnological applications. Graphic Abstracts
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17
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Okreglak V, Ling R, Ingaramo M, Thayer NH, Millett-Sikking A, Gottschling DE. Cell cycle-linked vacuolar pH dynamics regulate amino acid homeostasis and cell growth. Nat Metab 2023; 5:1803-1819. [PMID: 37640943 PMCID: PMC10590757 DOI: 10.1038/s42255-023-00872-1] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/03/2022] [Accepted: 07/21/2023] [Indexed: 08/31/2023]
Abstract
Amino acid homeostasis is critical for many cellular processes. It is well established that amino acids are compartmentalized using pH gradients generated between organelles and the cytoplasm; however, the dynamics of this partitioning has not been explored. Here we develop a highly sensitive pH reporter and find that the major amino acid storage compartment in Saccharomyces cerevisiae, the lysosome-like vacuole, alkalinizes before cell division and re-acidifies as cells divide. The vacuolar pH dynamics require the uptake of extracellular amino acids and activity of TORC1, the v-ATPase and the cycling of the vacuolar specific lipid phosphatidylinositol 3,5-bisphosphate, which is regulated by the cyclin-dependent kinase Pho85 (CDK5 in mammals). Vacuolar pH regulation enables amino acid sequestration and mobilization from the organelle, which is important for mitochondrial function, ribosome homeostasis and cell size control. Collectively, our data provide a new paradigm for the use of dynamic pH-dependent amino acid compartmentalization during cell growth/division.
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Affiliation(s)
- Voytek Okreglak
- Calico Life Sciences, LLC, South San Francisco, CA, USA.
- Altos Labs, Redwood City, CA, USA.
| | - Rachel Ling
- Calico Life Sciences, LLC, South San Francisco, CA, USA
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18
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Ozaki T. Structural diversification of fungal natural products by oxidative enzymes. Biosci Biotechnol Biochem 2023; 87:809-818. [PMID: 37197900 DOI: 10.1093/bbb/zbad062] [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: 03/14/2023] [Accepted: 05/10/2023] [Indexed: 05/19/2023]
Abstract
Ascomycota and basidiomycota fungi are prolific producers of biologically active natural products. Fungal natural products exhibit remarkable structural diversity and complexity, which are generated by the enzymes involved in their biosynthesis. After the formation of core skeletons, oxidative enzymes play a critical role in converting them into mature natural products. Besides simple oxidations, more complex transformations, such as multiple oxidations by single enzymes, oxidative cyclization, and skeletal rearrangement, are often observed. Those oxidative enzymes are of significant interest for the identification of new enzyme chemistry and have the potential to be biocatalysts for the synthesis of complex molecules. This review presents selected examples of unique oxidative transformations that have been found in the biosynthesis of fungal natural products. The development of strategies for refactoring the fungal biosynthetic pathways with an efficient genome-editing method is also introduced.
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Affiliation(s)
- Taro Ozaki
- Graduate School of Pharmaceutical Sciences, Tohoku University, Aoba-ku, Sendai, Japan
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19
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Prescott TAK, Hill R, Mas-Claret E, Gaya E, Burns E. Fungal Drug Discovery for Chronic Disease: History, New Discoveries and New Approaches. Biomolecules 2023; 13:986. [PMID: 37371566 DOI: 10.3390/biom13060986] [Citation(s) in RCA: 11] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2023] [Revised: 06/08/2023] [Accepted: 06/10/2023] [Indexed: 06/29/2023] Open
Abstract
Fungal-derived drugs include some of the most important medicines ever discovered, and have proved pivotal in treating chronic diseases. Not only have they saved millions of lives, but they have in some cases changed perceptions of what is medically possible. However, now the low-hanging fruit have been discovered it has become much harder to make the kind of discoveries that have characterised past eras of fungal drug discovery. This may be about to change with new commercial players entering the market aiming to apply novel genomic tools to streamline the discovery process. This review examines the discovery history of approved fungal-derived drugs, and those currently in clinical trials for chronic diseases. For key molecules, we discuss their possible ecological functions in nature and how this relates to their use in human medicine. We show how the conservation of drug receptors between fungi and humans means that metabolites intended to inhibit competitor fungi often interact with human drug receptors, sometimes with unintended benefits. We also plot the distribution of drugs, antimicrobial compounds and psychoactive mushrooms onto a fungal tree and compare their distribution to those of all fungal metabolites. Finally, we examine the phenomenon of self-resistance and how this can be used to help predict metabolite mechanism of action and aid the drug discovery process.
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Affiliation(s)
| | - Rowena Hill
- Earlham Institute, Norwich NR4 7UZ, Norfolk, UK
| | | | - Ester Gaya
- Royal Botanic Gardens, Kew, Richmond TW9 3AB, Surrey, UK
| | - Edie Burns
- Royal Botanic Gardens, Kew, Richmond TW9 3AB, Surrey, UK
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20
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Li L. Accessing hidden microbial biosynthetic potential from underexplored sources for novel drug discovery. Biotechnol Adv 2023:108176. [PMID: 37211187 DOI: 10.1016/j.biotechadv.2023.108176] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2022] [Revised: 05/15/2023] [Accepted: 05/16/2023] [Indexed: 05/23/2023]
Abstract
Microbial natural products and their structural analogues have widely used as pharmaceutical agents, especially for infectious diseases and cancer. Despite this success, new structural classes with innovative chemistry and modes of action are urgently needed to be developed to combat the growing antimicrobial resistance and other public health problems. The advances in next-generation sequencing technologies and powerful computational tools open up new opportunities to explore microbial biosynthetic potential from underexplored sources, with millions of secondary metabolites awaiting discovery. The review highlights challenges associated with discovery of new chemical entities, rich reservoirs provided by untapped taxa, ecological niches or host microbiomes, emerging synthetic biotechnologies to unearth the hidden microbial biosynthetic potential for novel drug discovery at scale and speed.
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Affiliation(s)
- Lei Li
- State Key Laboratory of Microbial Metabolism and School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, 800 Dongchuan Rd., Shanghai 200240, China.
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Gasparek M, Steel H, Papachristodoulou A. Deciphering mechanisms of production of natural compounds using inducer-producer microbial consortia. Biotechnol Adv 2023; 64:108117. [PMID: 36813010 DOI: 10.1016/j.biotechadv.2023.108117] [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: 07/21/2022] [Revised: 02/03/2023] [Accepted: 02/06/2023] [Indexed: 02/22/2023]
Abstract
Living organisms produce a wide range of metabolites. Because of their potential antibacterial, antifungal, antiviral, or cytostatic properties, such natural molecules are of high interest to the pharmaceutical industry. In nature, these metabolites are often synthesized via secondary metabolic biosynthetic gene clusters that are silent under the typical culturing conditions. Among different techniques used to activate these silent gene clusters, co-culturing of "producer" species with specific "inducer" microbes is a particularly appealing approach due to its simplicity. Although several "inducer-producer" microbial consortia have been reported in the literature and hundreds of different secondary metabolites with attractive biopharmaceutical properties have been described as a result of co-cultivating inducer-producer consortia, less attention has been devoted to the understanding of the mechanisms and possible means of induction for production of secondary metabolites in co-cultures. This lack of understanding of fundamental biological functions and inter-species interactions significantly limits the diversity and yield of valuable compounds using biological engineering tools. In this review, we summarize and categorize the known physiological mechanisms of production of secondary metabolites in inducer-producer consortia, and then discuss approaches that could be exploited to optimize the discovery and production of secondary metabolites.
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Affiliation(s)
- Miroslav Gasparek
- Department of Engineering Science, University of Oxford, Parks Road, Oxford OX1 3PJ, United Kingdom.
| | - Harrison Steel
- Department of Engineering Science, University of Oxford, Parks Road, Oxford OX1 3PJ, United Kingdom
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22
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Ren M, Jiang S, Wang Y, Pan X, Pan F, Wei X. Discovery and excavation of lichen bioactive natural products. Front Microbiol 2023; 14:1177123. [PMID: 37138611 PMCID: PMC10149937 DOI: 10.3389/fmicb.2023.1177123] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2023] [Accepted: 03/24/2023] [Indexed: 05/05/2023] Open
Abstract
Lichen natural products are a tremendous source of new bioactive chemical entities for drug discovery. The ability to survive in harsh conditions can be directly correlated with the production of some unique lichen metabolites. Despite the potential applications, these unique metabolites have been underutilized by pharmaceutical and agrochemical industries due to their slow growth, low biomass availability, and technical challenges involved in their artificial cultivation. At the same time, DNA sequence data have revealed that the number of encoded biosynthetic gene clusters in a lichen is much higher than in natural products, and the majority of them are silent or poorly expressed. To meet these challenges, the one strain many compounds (OSMAC) strategy, as a comprehensive and powerful tool, has been developed to stimulate the activation of silent or cryptic biosynthetic gene clusters and exploit interesting lichen compounds for industrial applications. Furthermore, the development of molecular network techniques, modern bioinformatics, and genetic tools is opening up a new opportunity for the mining, modification, and production of lichen metabolites, rather than merely using traditional separation and purification techniques to obtain small amounts of chemical compounds. Heterologous expressed lichen-derived biosynthetic gene clusters in a cultivatable host offer a promising means for a sustainable supply of specialized metabolites. In this review, we summarized the known lichen bioactive metabolites and highlighted the application of OSMAC, molecular network, and genome mining-based strategies in lichen-forming fungi for the discovery of new cryptic lichen compounds.
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Affiliation(s)
- Meirong Ren
- Key Laboratory of Biodiversity Conservation in Southwest China, State Forestry Administration, Southwest Forestry University, Kunming, China
| | - Shuhua Jiang
- State Key Laboratory of Mycology, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China
| | - Yanyan Wang
- State Key Laboratory of Mycology, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China
| | - Xinhua Pan
- Jiangxi Xiankelai Biotechnology Co., Ltd., Jiujiang, China
| | - Feng Pan
- Jiangxi Xiankelai Biotechnology Co., Ltd., Jiujiang, China
| | - Xinli Wei
- State Key Laboratory of Mycology, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China
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23
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Hewage RT, Tseng CC, Liang SY, Lai CY, Lin HC. Genome mining of cryptic bisabolenes that were biosynthesized by intramembrane terpene synthases from Antrodia cinnamomea. Philos Trans R Soc Lond B Biol Sci 2023; 378:20220033. [PMID: 36633275 PMCID: PMC9835599 DOI: 10.1098/rstb.2022.0033] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023] Open
Abstract
Terpenoids represent the largest structural family of natural products (NPs) and have various applications in the pharmaceutical, food and fragrance industries. Their diverse scaffolds are generated via a multi-step cyclization cascade of linear isoprene substrates catalysed by terpene synthases (TPSs). Bisabolene NPs, which are sesquiterpenes (C15), have wide applications in medicines and biofuels and serve as bioactive substances in ecology. Despite the discovery of some canonical class I TPSs that synthesize bisabolenes from plants, bacteria and insects, it remained unknown whether any bisabolene synthases from fungi could produce bisabolenes as a main product. Antrodia cinnamomea, a Basidiomycota fungus, is a medicinal mushroom indigenous to Taiwan and a known prolific producer of bioactive terpenoids, but little is known regarding the enzymes involved in the biosynthetic pathways. Here, we applied a genome mining approach against A. cinnamomea and discovered two non-canonical UbiA-type TPSs that both synthesize (+)-(S,Z)-α-bisabolene (1). It was determined that two tailoring enzymes, a P450 monooxygenase and a methyltransferase, install a C14-methyl ester on the bisabolene scaffold. In addition, four new bisabolene derivatives, 2 and 4-6, were characterized from heterologous reconstitution in Saccharomyces cerevisiae. Our study uncovered enzymatic tools to generate structurally diverse bisabolene NPs. This article is part of the theme issue 'Reactivity and mechanism in chemical and synthetic biology'.
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Affiliation(s)
- Ranuka T. Hewage
- Institute of Biological Chemistry, Academia Sinica, Taipei 115, Taiwan,Chemical Biology and Molecular Biophysics Program, Taiwan International Graduate Program, Academia Sinica, Taipei 11529, Taiwan,Department of Chemistry, National Taiwan University, Taipei 106, Taiwan,Department of Indigenous Medical Resources, Gampaha Wickramarachchi University of Indigenous Medicine, Yakkala 11870, Sri Lanka
| | - Cheng-Chung Tseng
- Institute of Biological Chemistry, Academia Sinica, Taipei 115, Taiwan,School of Pharmacy, College of Medicine, National Taiwan University, Taipei 100, Taiwan
| | - Suh-Yuen Liang
- Institute of Biological Chemistry, Academia Sinica, Taipei 115, Taiwan
| | - Chen-Yu Lai
- Institute of Biological Chemistry, Academia Sinica, Taipei 115, Taiwan
| | - Hsiao-Ching Lin
- Institute of Biological Chemistry, Academia Sinica, Taipei 115, Taiwan,Chemical Biology and Molecular Biophysics Program, Taiwan International Graduate Program, Academia Sinica, Taipei 11529, Taiwan,School of Pharmacy, College of Medicine, National Taiwan University, Taipei 100, Taiwan
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Tseng CC, Chen L, Lee C, Tu Z, Lin CH, Lin HC. Characterization and catalytic investigation of fungal single-module nonribosomal peptide synthetase in terpene-amino acid meroterpenoid biosynthesis. J Ind Microbiol Biotechnol 2023; 50:kuad043. [PMID: 38049376 PMCID: PMC10720950 DOI: 10.1093/jimb/kuad043] [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: 10/18/2023] [Accepted: 12/01/2023] [Indexed: 12/06/2023]
Abstract
Hybrid natural products are compounds that originate from diverse biosynthetic pathways and undergo a conjugation process, which enables them to expand their chemical diversity and biological functionality. Terpene-amino acid meroterpenoids have garnered increasing attention in recent years, driven by the discovery of noteworthy examples such as the anthelmintic CJ-12662, the insecticidal paeciloxazine, and aculene A (1). In the biosynthesis of terpene-amino acid natural products, single-module nonribosomal peptide synthetases (NRPSs) have been identified to be involved in the esterification step, catalyzing the fusion of modified terpene and amino acid components. Despite prior investigations into these NRPSs through gene deletion or in vivo experiments, the enzymatic basis and mechanistic insights underlying this family of single-module NRPSs remain unclear. In this study, we performed biochemical characterization of AneB by in vitro characterization, molecular docking, and site-directed mutagenesis. The enzyme reaction analyses, performed with L-proline and daucane/nordaucane sesquiterpene substrates, revealed that AneB specifically esterifies the C10-OH of aculenes with L-proline. Notably, in contrast to ThmA in CJ-12662 biosynthesis, which exclusively recognizes oxygenated amorpha-4,11-diene sesquiterpenes for L-tryptophan transfer, AneB demonstrates broad substrate selectivity, including oxygenated amorpha-4,11-diene and 2-phenylethanol, resulting in the production of diverse unnatural prolyl compounds. Furthermore, site-directed mutagenesis experiments indicated the involvement of H794 and D798 in the esterification catalyzed by AneB. Lastly, domain swapping between AneB and ThmA unveiled that the A‒T domains of ThmA can be effectively harnessed by the C domain of AneB for L-tryptophan transfer, thus highlighting the potential of the C domain of AneB for generating various terpene-amino acid meroterpenoid derivatives. ONE-SENTENCE SUMMARY The enzymatic basis and mechanistic insights into AneB, a single-module NRPS, highlight its capacity to generate various terpene-amino acid meroterpenoid derivatives.
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Affiliation(s)
- Cheng-Chung Tseng
- Institute of Biological Chemistry, Academia Sinica, Taipei 115, Taiwan R.O.C
- School of Pharmacy, National Taiwan University, Taipei 100, Taiwan R.O.C
| | - Li‐Xun Chen
- Institute of Biological Chemistry, Academia Sinica, Taipei 115, Taiwan R.O.C
- Institute of Biochemical Sciences, National Taiwan University, Taipei 106, Taiwan R.O.C
| | - Chi‐Fang Lee
- Institute of Biological Chemistry, Academia Sinica, Taipei 115, Taiwan R.O.C
- Institute of Biochemical Sciences, National Taiwan University, Taipei 106, Taiwan R.O.C
| | - Zhijay Tu
- Institute of Biological Chemistry, Academia Sinica, Taipei 115, Taiwan R.O.C
| | - Chun-Hung Lin
- Institute of Biological Chemistry, Academia Sinica, Taipei 115, Taiwan R.O.C
- Institute of Biochemical Sciences, National Taiwan University, Taipei 106, Taiwan R.O.C
| | - Hsiao-Ching Lin
- Institute of Biological Chemistry, Academia Sinica, Taipei 115, Taiwan R.O.C
- School of Pharmacy, National Taiwan University, Taipei 100, Taiwan R.O.C
- Institute of Biochemical Sciences, National Taiwan University, Taipei 106, Taiwan R.O.C
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Jenkinson CB, Podgorny AR, Zhong C, Oakley BR. Computer-aided, resistance gene-guided genome mining for proteasome and HMG-CoA reductase inhibitors. J Ind Microbiol Biotechnol 2023; 50:kuad045. [PMID: 38061800 PMCID: PMC10734572 DOI: 10.1093/jimb/kuad045] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2023] [Accepted: 12/06/2023] [Indexed: 12/22/2023]
Abstract
Secondary metabolites (SMs) are biologically active small molecules, many of which are medically valuable. Fungal genomes contain vast numbers of SM biosynthetic gene clusters (BGCs) with unknown products, suggesting that huge numbers of valuable SMs remain to be discovered. It is challenging, however, to identify SM BGCs, among the millions present in fungi, that produce useful compounds. One solution is resistance gene-guided genome mining, which takes advantage of the fact that some BGCs contain a gene encoding a resistant version of the protein targeted by the compound produced by the BGC. The bioinformatic signature of such BGCs is that they contain an allele of an essential gene with no SM biosynthetic function, and there is a second allele elsewhere in the genome. We have developed a computer-assisted approach to resistance gene-guided genome mining that allows users to query large databases for BGCs that putatively make compounds that have targets of therapeutic interest. Working with the MycoCosm genome database, we have applied this approach to look for SM BGCs that target the proteasome β6 subunit, the target of the proteasome inhibitor fellutamide B, or HMG-CoA reductase, the target of cholesterol reducing therapeutics such as lovastatin. Our approach proved effective, finding known fellutamide and lovastatin BGCs as well as fellutamide- and lovastatin-related BGCs with variations in the SM genes that suggest they may produce structural variants of fellutamides and lovastatin. Gratifyingly, we also found BGCs that are not closely related to lovastatin BGCs but putatively produce novel HMG-CoA reductase inhibitors. ONE-SENTENCE SUMMARY A new computer-assisted approach to resistance gene-directed genome mining is reported along with its use to identify fungal biosynthetic gene clusters that putatively produce proteasome and HMG-CoA reductase inhibitors.
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Affiliation(s)
- Cory B Jenkinson
- Department of Molecular Biosciences, University of Kansas, Lawrence, KS 66045,USA
| | - Adam R Podgorny
- Department of Electrical Engineering and Computer Science, University of Kansas, Lawrence, KS 66045,USA
| | - Cuncong Zhong
- Department of Electrical Engineering and Computer Science, University of Kansas, Lawrence, KS 66045,USA
| | - Berl R Oakley
- Department of Molecular Biosciences, University of Kansas, Lawrence, KS 66045,USA
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Kirchgaessner L, Wurlitzer JM, Seibold PS, Rakhmanov M, Gressler M. A genetic tool to express long fungal biosynthetic genes. Fungal Biol Biotechnol 2023; 10:4. [PMID: 36726159 PMCID: PMC9893682 DOI: 10.1186/s40694-023-00152-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2022] [Accepted: 01/22/2023] [Indexed: 02/03/2023] Open
Abstract
BACKGROUND Secondary metabolites (SMs) from mushroom-forming fungi (Basidiomycota) and early diverging fungi (EDF) such as Mucoromycota are scarcely investigated. In many cases, production of SMs is induced by unknown stress factors or is accompanied by seasonable developmental changes on fungal morphology. Moreover, many of these fungi are considered as non-culturable under laboratory conditions which impedes investigation into SM. In the post-genomic era, numerous novel SM genes have been identified especially from EDF. As most of them encode multi-module enzymes, these genes are usually long which limits cloning and heterologous expression in traditional hosts. RESULTS An expression system in Aspergillus niger is presented that is suitable for the production of SMs from both Basidiomycota and EDF. The akuB gene was deleted in the expression host A. niger ATNT∆pyrG, resulting in a deficient nonhomologous end-joining repair mechanism which in turn facilitates the targeted gene deletion via homologous recombination. The ∆akuB mutant tLK01 served as a platform to integrate overlapping DNA fragments of long SM genes into the fwnA locus required for the black pigmentation of conidia. This enables an easy discrimination of correct transformants by screening the transformation plates for fawn-colored colonies. Expression of the gene of interest (GOI) is induced dose-dependently by addition of doxycycline and is enhanced by the dual TetON/terrein synthase promoter system (ATNT) from Aspergillus terreus. We show that the 8 kb polyketide synthase gene lpaA from the basidiomycete Laetiporus sulphureus is correctly assembled from five overlapping DNA fragments and laetiporic acids are produced. In a second approach, we expressed the yet uncharacterized > 20 kb nonribosomal peptide synthetase gene calA from the EDF Mortierella alpina. Gene expression and subsequent LC-MS/MS analysis of mycelial extracts revealed the production of the antimycobacterial compound calpinactam. This is the first report on the heterologous production of a full-length SM multidomain enzyme from EDF. CONCLUSIONS The system allows the assembly, targeted integration and expression of genes of > 20 kb size in A. niger in one single step. The system is suitable for evolutionary distantly related SM genes from both Basidiomycota and EDF. This uncovers new SM resources including genetically intractable or non-culturable fungi.
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Affiliation(s)
- Leo Kirchgaessner
- grid.9613.d0000 0001 1939 2794Institute of Pharmacy, Department Pharmaceutical Microbiology, Friedrich Schiller University Jena, Winzerlaer Strasse 2, 07745 Jena, Germany ,grid.418398.f0000 0001 0143 807XDepartment Pharmaceutical Microbiology, Leibniz Institute for Natural Product Research and Infection Biology - Hans Knöll Institute, Winzerlaer Strasse 2, 07745 Jena, Germany ,grid.413047.50000 0001 0658 7859Faculty Medical Technology and Biotechnology, Ernst Abbe University of Applied Sciences Jena, Carl-Zeiss-Promenade 2, 07745 Jena, Germany
| | - Jacob M. Wurlitzer
- grid.9613.d0000 0001 1939 2794Institute of Pharmacy, Department Pharmaceutical Microbiology, Friedrich Schiller University Jena, Winzerlaer Strasse 2, 07745 Jena, Germany ,grid.418398.f0000 0001 0143 807XDepartment Pharmaceutical Microbiology, Leibniz Institute for Natural Product Research and Infection Biology - Hans Knöll Institute, Winzerlaer Strasse 2, 07745 Jena, Germany
| | - Paula S. Seibold
- grid.9613.d0000 0001 1939 2794Institute of Pharmacy, Department Pharmaceutical Microbiology, Friedrich Schiller University Jena, Winzerlaer Strasse 2, 07745 Jena, Germany ,grid.418398.f0000 0001 0143 807XDepartment Pharmaceutical Microbiology, Leibniz Institute for Natural Product Research and Infection Biology - Hans Knöll Institute, Winzerlaer Strasse 2, 07745 Jena, Germany
| | - Malik Rakhmanov
- grid.9613.d0000 0001 1939 2794Institute of Pharmacy, Department Pharmaceutical Microbiology, Friedrich Schiller University Jena, Winzerlaer Strasse 2, 07745 Jena, Germany ,grid.418398.f0000 0001 0143 807XDepartment Pharmaceutical Microbiology, Leibniz Institute for Natural Product Research and Infection Biology - Hans Knöll Institute, Winzerlaer Strasse 2, 07745 Jena, Germany
| | - Markus Gressler
- grid.9613.d0000 0001 1939 2794Institute of Pharmacy, Department Pharmaceutical Microbiology, Friedrich Schiller University Jena, Winzerlaer Strasse 2, 07745 Jena, Germany ,grid.418398.f0000 0001 0143 807XDepartment Pharmaceutical Microbiology, Leibniz Institute for Natural Product Research and Infection Biology - Hans Knöll Institute, Winzerlaer Strasse 2, 07745 Jena, Germany
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Kwan BD, Seligmann B, Nguyen TD, Franke J, Dang TTT. Leveraging synthetic biology and metabolic engineering to overcome obstacles in plant pathway elucidation. CURRENT OPINION IN PLANT BIOLOGY 2023; 71:102330. [PMID: 36599248 DOI: 10.1016/j.pbi.2022.102330] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/25/2022] [Revised: 11/22/2022] [Accepted: 12/01/2022] [Indexed: 06/17/2023]
Abstract
Major hurdles in plant biosynthetic pathway elucidation and engineering include the need for rapid testing of enzyme candidates and the lack of complex substrates that are often not accumulated in the plant, amenable to synthesis, or commercially available. Linking metabolic engineering with gene discovery in both yeast and plant holds great promise to expedite the elucidation process and, at the same time, provide a platform for the sustainable production of plant metabolites. In this review, we highlight how synthetic biology and metabolic engineering alleviated longstanding obstacles in plant pathway elucidation. Recent advances in developing these chassis that showcase established and emerging strategies in accelerating biosynthetic gene discovery will also be discussed.
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Affiliation(s)
- Brooke D Kwan
- Department of Chemistry, Irving K. Barber Faculty of Science, University of British Columbia, 3427 University Way, Kelowna, BC, Canada
| | - Benedikt Seligmann
- Leibniz University Hannover, Institute of Botany, Herrenhäuser Str. 2, 30419 Hannover, Germany
| | - Trinh-Don Nguyen
- Department of Chemistry, Irving K. Barber Faculty of Science, University of British Columbia, 3427 University Way, Kelowna, BC, Canada
| | - Jakob Franke
- Leibniz University Hannover, Institute of Botany, Herrenhäuser Str. 2, 30419 Hannover, Germany.
| | - Thu-Thuy T Dang
- Department of Chemistry, Irving K. Barber Faculty of Science, University of British Columbia, 3427 University Way, Kelowna, BC, Canada.
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Chiang CY, Ohashi M, Tang Y. Deciphering chemical logic of fungal natural product biosynthesis through heterologous expression and genome mining. Nat Prod Rep 2023; 40:89-127. [PMID: 36125308 PMCID: PMC9906657 DOI: 10.1039/d2np00050d] [Citation(s) in RCA: 10] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]
Abstract
Covering: 2010 to 2022Heterologous expression of natural product biosynthetic gene clusters (BGCs) has become a widely used tool for genome mining of cryptic pathways, bottom-up investigation of biosynthetic enzymes, and engineered biosynthesis of new natural product variants. In the field of fungal natural products, heterologous expression of a complete pathway was first demonstrated in the biosynthesis of tenellin in Aspergillus oryzae in 2010. Since then, advances in genome sequencing, DNA synthesis, synthetic biology, etc. have led to mining, assignment, and characterization of many fungal BGCs using various heterologous hosts. In this review, we will highlight key examples in the last decade in integrating heterologous expression into genome mining and biosynthetic investigations. The review will cover the choice of heterologous hosts, prioritization of BGCs for structural novelty, and how shunt products from heterologous expression can reveal important insights into the chemical logic of biosynthesis. The review is not meant to be exhaustive but is rather a collection of examples from researchers in the field, including ours, that demonstrates the usefulness and pitfalls of heterologous biosynthesis in fungal natural product discovery.
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Affiliation(s)
- Chen-Yu Chiang
- Dept. of Chemical and Biomolecular Engineering, 5531 Boelter Hall, 420 Westwood Plaza, Los Angeles, CA 90095, USA.
| | - Masao Ohashi
- Dept. of Chemical and Biomolecular Engineering, 5531 Boelter Hall, 420 Westwood Plaza, Los Angeles, CA 90095, USA.
| | - Yi Tang
- Dept. of Chemical and Biomolecular Engineering, 5531 Boelter Hall, 420 Westwood Plaza, Los Angeles, CA 90095, USA.
- Dept. of Chemistry and Biochemistry, 5531 Boelter Hall, 420 Westwood Plaza, Los Angeles, CA 90095, USA
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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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Unlocking the magic in mycelium: Using synthetic biology to optimize filamentous fungi for biomanufacturing and sustainability. Mater Today Bio 2023; 19:100560. [PMID: 36756210 PMCID: PMC9900623 DOI: 10.1016/j.mtbio.2023.100560] [Citation(s) in RCA: 11] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2022] [Revised: 01/19/2023] [Accepted: 01/20/2023] [Indexed: 01/22/2023] Open
Abstract
Filamentous fungi drive carbon and nutrient cycling across our global ecosystems, through its interactions with growing and decaying flora and their constituent microbiomes. The remarkable metabolic diversity, secretion ability, and fiber-like mycelial structure that have evolved in filamentous fungi have been increasingly exploited in commercial operations. The industrial potential of mycelial fermentation ranges from the discovery and bioproduction of enzymes and bioactive compounds, the decarbonization of food and material production, to environmental remediation and enhanced agricultural production. Despite its fundamental impact in ecology and biotechnology, molds and mushrooms have not, to-date, significantly intersected with synthetic biology in ways comparable to other industrial cell factories (e.g. Escherichia coli,Saccharomyces cerevisiae, and Komagataella phaffii). In this review, we summarize a suite of synthetic biology and computational tools for the mining, engineering and optimization of filamentous fungi as a bioproduction chassis. A combination of methods across genetic engineering, mutagenesis, experimental evolution, and computational modeling can be used to address strain development bottlenecks in established and emerging industries. These include slow mycelium growth rate, low production yields, non-optimal growth in alternative feedstocks, and difficulties in downstream purification. In the scope of biomanufacturing, we then detail previous efforts in improving key bottlenecks by targeting protein processing and secretion pathways, hyphae morphogenesis, and transcriptional control. Bringing synthetic biology practices into the hidden world of molds and mushrooms will serve to expand the limited panel of host organisms that allow for commercially-feasible and environmentally-sustainable bioproduction of enzymes, chemicals, therapeutics, foods, and materials of the future.
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Development of a yeast whole-cell biocatalyst for MHET conversion into terephthalic acid and ethylene glycol. Microb Cell Fact 2022; 21:280. [PMID: 36587193 PMCID: PMC9805092 DOI: 10.1186/s12934-022-02007-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2022] [Accepted: 12/20/2022] [Indexed: 01/02/2023] Open
Abstract
BACKGROUND Over the 70 years since the introduction of plastic into everyday items, plastic waste has become an increasing problem. With over 360 million tonnes of plastics produced every year, solutions for plastic recycling and plastic waste reduction are sorely needed. Recently, multiple enzymes capable of degrading PET (polyethylene terephthalate) plastic have been identified and engineered. In particular, the enzymes PETase and MHETase from Ideonella sakaiensis depolymerize PET into the two building blocks used for its synthesis, ethylene glycol (EG) and terephthalic acid (TPA). Importantly, EG and TPA can be re-used for PET synthesis allowing complete and sustainable PET recycling. RESULTS In this study we used Saccharomyces cerevisiae, a species utilized widely in bioindustrial fermentation processes, as a platform to develop a whole-cell catalyst expressing the MHETase enzyme, which converts monohydroxyethyl terephthalate (MHET) into TPA and EG. We assessed six expression architectures and identified those resulting in efficient MHETase expression on the yeast cell surface. We show that the MHETase whole-cell catalyst has activity comparable to recombinant MHETase purified from Escherichia coli. Finally, we demonstrate that surface displayed MHETase is active across a range of pHs, temperatures, and for at least 12 days at room temperature. CONCLUSIONS We demonstrate the feasibility of using S. cerevisiae as a platform for the expression and surface display of PET degrading enzymes and predict that the whole-cell catalyst will be a viable alternative to protein purification-based approaches for plastic degradation.
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Complementary Strategies to Unlock Biosynthesis Gene Clusters Encoding Secondary Metabolites in the Filamentous Fungus Podospora anserina. J Fungi (Basel) 2022; 9:jof9010009. [PMID: 36675830 PMCID: PMC9864250 DOI: 10.3390/jof9010009] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2022] [Revised: 12/09/2022] [Accepted: 12/19/2022] [Indexed: 12/24/2022] Open
Abstract
The coprophilous ascomycete Podospora anserina is known to have a high potential to synthesize a wide array of secondary metabolites (SMs). However, to date, the characterization of SMs in this species, as in other filamentous fungal species, is far less than expected by the functional prediction through genome mining, likely due to the inactivity of most SMs biosynthesis gene clusters (BGCs) under standard conditions. In this work, our main objective was to compare the global strategies usually used to deregulate SM gene clusters in P. anserina, including the variation of culture conditions and the modification of the chromatin state either by genetic manipulation or by chemical treatment, and to show the complementarity of the approaches between them. In this way, we showed that the metabolomics-driven comparative analysis unveils the unexpected diversity of metabolic changes in P. anserina and that the integrated strategies have a mutual complementary effect on the expression of the fungal metabolome. Then, our results demonstrate that metabolite production is significantly influenced by varied cultivation states and epigenetic modifications. We believe that the strategy described in this study will facilitate the discovery of fungal metabolites of interest and will improve the ability to prioritize the production of specific fungal SMs with an optimized treatment.
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A fungal NRPS-PKS enzyme catalyses the formation of the flavonoid naringenin. Nat Commun 2022; 13:6361. [PMID: 36289208 PMCID: PMC9606254 DOI: 10.1038/s41467-022-34150-7] [Citation(s) in RCA: 16] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2022] [Accepted: 10/14/2022] [Indexed: 12/25/2022] Open
Abstract
Biosynthesis of the flavonoid naringenin in plants and bacteria is commonly catalysed by a type III polyketide synthase (PKS) using one p-coumaroyl-CoA and three malonyl-CoA molecules as substrates. Here, we report a fungal non-ribosomal peptide synthetase -polyketide synthase (NRPS-PKS) hybrid FnsA for the naringenin formation. Feeding experiments with isotope-labelled precursors demonstrate that FnsA accepts not only p-coumaric acid (p-CA), but also p-hydroxybenzoic acid (p-HBA) as starter units, with three or four malonyl-CoA molecules for elongation, respectively. In vitro assays and MS/MS analysis prove that both p-CA and p-HBA are firstly activated by the adenylation domain of FnsA. Phylogenetic analysis reveals that the PKS portion of FnsA shares high sequence homology with type I PKSs. Refactoring the biosynthetic pathway in yeast with the involvement of fnsA provides an alternative approach for the production of flavonoids such as isorhamnetin and acacetin.
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Multiplexed mobilization and expression of biosynthetic gene clusters. Nat Commun 2022; 13:5256. [PMID: 36068239 PMCID: PMC9448795 DOI: 10.1038/s41467-022-32858-0] [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: 06/28/2022] [Accepted: 08/17/2022] [Indexed: 01/25/2023] Open
Abstract
Bacterial genomes contain large reservoirs of biosynthetic gene clusters (BGCs) that are predicted to encode unexplored natural products. Heterologous expression of previously unstudied BGCs should facilitate the discovery of additional therapeutically relevant bioactive molecules from bacterial culture collections, but the large-scale manipulation of BGCs remains cumbersome. Here, we describe a method to parallelize the identification, mobilization and heterologous expression of BGCs. Our solution simultaneously captures large numbers of BGCs by cloning the genomes of a strain collection in a large-insert library and uses the CONKAT-seq (co-occurrence network analysis of targeted sequences) sequencing pipeline to efficiently localize clones carrying intact BGCs which represent candidates for heterologous expression. Our discovery of several natural products, including an antibiotic that is active against multi-drug resistant Staphylococcus aureus, demonstrates the potential of leveraging economies of scale with this approach to systematically interrogate cryptic BGCs contained in strain collections. Efficient mobilization and expression of biosynthetic gene clusters (BGCs) into heterologous hosts is needed for microbial natural products discovery. Here, the authors improve the CONKAT-seq strategy by simultaneously capturing the BCGs into a single large insert library and demonstrate its ability to discover natural products with new structures and potent antibacterial activity.
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Schüller A, Studt-Reinhold L, Strauss J. How to Completely Squeeze a Fungus-Advanced Genome Mining Tools for Novel Bioactive Substances. Pharmaceutics 2022; 14:1837. [PMID: 36145585 PMCID: PMC9505985 DOI: 10.3390/pharmaceutics14091837] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2022] [Revised: 08/23/2022] [Accepted: 08/29/2022] [Indexed: 11/17/2022] Open
Abstract
Fungal species have the capability of producing an overwhelming diversity of bioactive substances that can have beneficial but also detrimental effects on human health. These so-called secondary metabolites naturally serve as antimicrobial "weapon systems", signaling molecules or developmental effectors for fungi and hence are produced only under very specific environmental conditions or stages in their life cycle. However, as these complex conditions are difficult or even impossible to mimic in laboratory settings, only a small fraction of the true chemical diversity of fungi is known so far. This also implies that a large space for potentially new pharmaceuticals remains unexplored. We here present an overview on current developments in advanced methods that can be used to explore this chemical space. We focus on genetic and genomic methods, how to detect genes that harbor the blueprints for the production of these compounds (i.e., biosynthetic gene clusters, BGCs), and ways to activate these silent chromosomal regions. We provide an in-depth view of the chromatin-level regulation of BGCs and of the potential to use the CRISPR/Cas technology as an activation tool.
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Affiliation(s)
| | | | - Joseph Strauss
- Institute of Microbial Genetics, Department of Applied Genetics and Cell Biology, University of Natural Resources and Life Sciences Vienna, A-3430 Tulln/Donau, Austria
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Wu J, Yang X, Duan Y, Wang P, Qi J, Gao JM, Liu C. Biosynthesis of Sesquiterpenes in Basidiomycetes: A Review. J Fungi (Basel) 2022; 8:913. [PMID: 36135638 PMCID: PMC9501842 DOI: 10.3390/jof8090913] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2022] [Revised: 08/10/2022] [Accepted: 08/26/2022] [Indexed: 11/19/2022] Open
Abstract
Sesquiterpenes are common small-molecule natural products with a wide range of promising applications and are biosynthesized by sesquiterpene synthase (STS). Basidiomycetes are valuable and important biological resources. To date, hundreds of related sesquiterpenoids have been discovered in basidiomycetes, and the biosynthetic pathways of some of these compounds have been elucidated. This review summarizes 122 STSs and 2 fusion enzymes STSs identified from 26 species of basidiomycetes over the past 20 years. The biological functions of enzymes and compound structures are described, and related research is discussed.
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Affiliation(s)
- Jiajun Wu
- Key Laboratory for Enzyme and Enzyme-like Material Engineering of Heilongjiang, College of Life Science, Northeast Forestry University, Harbin 150040, China
| | - Xiaoran Yang
- Key Laboratory for Enzyme and Enzyme-like Material Engineering of Heilongjiang, College of Life Science, Northeast Forestry University, Harbin 150040, China
| | - Yingce Duan
- Key Laboratory for Enzyme and Enzyme-like Material Engineering of Heilongjiang, College of Life Science, Northeast Forestry University, Harbin 150040, China
| | - Pengchao Wang
- Key Laboratory for Enzyme and Enzyme-like Material Engineering of Heilongjiang, College of Life Science, Northeast Forestry University, Harbin 150040, China
| | - Jianzhao Qi
- Key Laboratory for Enzyme and Enzyme-like Material Engineering of Heilongjiang, College of Life Science, Northeast Forestry University, Harbin 150040, China
- Shaanxi Key Laboratory of Natural Products & Chemical Biology, College of Chemistry & Pharmacy, Northwest A&F University, Yangling 712100, China
| | - Jin-Ming Gao
- Shaanxi Key Laboratory of Natural Products & Chemical Biology, College of Chemistry & Pharmacy, Northwest A&F University, Yangling 712100, China
| | - Chengwei Liu
- Key Laboratory for Enzyme and Enzyme-like Material Engineering of Heilongjiang, College of Life Science, Northeast Forestry University, Harbin 150040, China
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Knowles SL, Raja HA, Roberts CD, Oberlies NH. Fungal-fungal co-culture: a primer for generating chemical diversity. Nat Prod Rep 2022; 39:1557-1573. [PMID: 35137758 PMCID: PMC9384855 DOI: 10.1039/d1np00070e] [Citation(s) in RCA: 44] [Impact Index Per Article: 22.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2021] [Indexed: 01/25/2023]
Abstract
Covering: 2002 to 2020In their natural environment, fungi must compete for resources. It has been hypothesized that this competition likely induces the biosynthesis of secondary metabolites for defence. In a quest to discover new chemical diversity from fungal cultures, a growing trend has been to recapitulate this competitive environment in the laboratory, essentially growing fungi in co-culture. This review covers fungal-fungal co-culture studies beginning with the first literature report in 2002. Since then, there has been a growing number of new secondary metabolites reported as a result of fungal co-culture studies. Specifically, this review discusses and provides insights into (1) rationale for pairing fungal strains, (2) ways to grow fungi for co-culture, (3) different approaches to screening fungal co-cultures for chemical diversity, (4) determining the secondary metabolite-producing strain, and (5) final thoughts regarding the fungal-fungal co-culture approach. Our goal is to provide a set of practical strategies for fungal co-culture studies to generate unique chemical diversity that the natural products research community can utilize.
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Affiliation(s)
- Sonja L Knowles
- Department of Chemistry and Biochemistry, University of North Carolina at Greensboro, Greensboro, NC, USA.
| | - Huzefa A Raja
- Department of Chemistry and Biochemistry, University of North Carolina at Greensboro, Greensboro, NC, USA.
| | - Christopher D Roberts
- Department of Chemistry and Biochemistry, University of North Carolina at Greensboro, Greensboro, NC, USA.
| | - Nicholas H Oberlies
- Department of Chemistry and Biochemistry, University of North Carolina at Greensboro, Greensboro, NC, USA.
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Schafhauser T, Wibberg D, Binder A, Rückert C, Busche T, Wohlleben W, Kalinowski J. Genome Assembly and Genetic Traits of the Pleuromutilin-Producer Clitopilus passeckerianus DSM1602. J Fungi (Basel) 2022; 8:jof8080862. [PMID: 36012850 PMCID: PMC9410065 DOI: 10.3390/jof8080862] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2022] [Revised: 08/09/2022] [Accepted: 08/11/2022] [Indexed: 11/16/2022] Open
Abstract
The gilled mushroom Clitopilus passeckerianus (Entolomataceae, Agaricales, Basidiomycota) is well known to produce the terpenoid pleuromutilin, which is the biotechnological basis for medically important antibiotics such as lefamulin and retapamulin. Their unique mode of action and good tolerance entails an increasing demand of pleuromutilin-derived antibiotics in veterinary and human health care. Surprisingly, despite their pharmaceutical importance, no genome sequence is available of any pleuromutilin-producing fungus. Here, we present the high-quality draft genome sequence of the pleuromutilin-producer C. passeckerianus DSM1602 including functional genome annotation. More precisely, we employed a hybrid assembly strategy combining Illumina sequencing and Nanopore sequencing to assemble the mitochondrial genome as well as the nuclear genome. In accordance with the dikaryotic state of the fungus, the nuclear genome has a diploid character. Interestingly, the mitochondrial genome appears duplicated. Bioinformatic analysis revealed a versatile secondary metabolism with an emphasis on terpenoid biosynthetic enzymes in C. passeckerianus and also in related strains. Two alleles of biosynthetic gene clusters for pleuromutilin were found in the genome of C. passeckerianus. The pleuromutilin genes were reassembled with yeast-specific elements for heterologous expression in Saccharomyces cerevisiae. Our work lays the foundation for metabolic strain engineering towards higher yields of the valuable compound pleuromutilin.
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Affiliation(s)
- Thomas Schafhauser
- Mikrobiologie und Biotechnologie, Interfakultäres Institut für Mikrobiologie und Infektionsmedizin, Eberhard Karls Universität Tübingen, Auf der Morgenstelle 28, 72076 Tuebingen, Germany
- Correspondence: (T.S.); (J.K.)
| | - Daniel Wibberg
- Centrum für Biotechnologie, CeBiTec, Universität Bielefeld, Universitätsstr. 27, 33615 Bielefeld, Germany
- Institute of Bio- and Geosciences IBG-5, Computational Metagenomics, Forschungszentrum Jülich GmbH, 52425 Juelich, Germany
| | - Antonia Binder
- Mikrobiologie und Biotechnologie, Interfakultäres Institut für Mikrobiologie und Infektionsmedizin, Eberhard Karls Universität Tübingen, Auf der Morgenstelle 28, 72076 Tuebingen, Germany
- Institut für Mikrobiologie, Technische Universität Dresden, Zellescher Weg 20b, 01062 Dresden, Germany
| | - Christian Rückert
- Centrum für Biotechnologie, CeBiTec, Universität Bielefeld, Universitätsstr. 27, 33615 Bielefeld, Germany
| | - Tobias Busche
- Centrum für Biotechnologie, CeBiTec, Universität Bielefeld, Universitätsstr. 27, 33615 Bielefeld, Germany
| | - Wolfgang Wohlleben
- Mikrobiologie und Biotechnologie, Interfakultäres Institut für Mikrobiologie und Infektionsmedizin, Eberhard Karls Universität Tübingen, Auf der Morgenstelle 28, 72076 Tuebingen, Germany
- Cluster of Excellence EXC 2124—Controlling Microbes to Fight Infections, 72076 Tuebingen, Germany
- German Center for Infection Research (DZIF), Partner Site Tübingen, 72076 Tuebingen, Germany
| | - Jörn Kalinowski
- Centrum für Biotechnologie, CeBiTec, Universität Bielefeld, Universitätsstr. 27, 33615 Bielefeld, Germany
- Correspondence: (T.S.); (J.K.)
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Lee SR, Seyedsayamdost MR. Induction of Diverse Cryptic Fungal Metabolites by Steroids and Channel Blockers. Angew Chem Int Ed Engl 2022; 61:e202204519. [PMID: 35509119 PMCID: PMC9276648 DOI: 10.1002/anie.202204519] [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: 03/28/2022] [Indexed: 07/20/2023]
Abstract
Fungi offer a deep source of natural products but remain underutilized. Most biosynthetic gene clusters (BGCs) that can be detected are silent or "cryptic" in standard lab cultures and their products are thus not interrogated in routine screens. As genetic alterations are difficult and some strains can only be grown on agar, we have herein applied an agar-based high-throughput chemical genetic screen to identify inducers of fungal BGCs. Using R. solani and S. sclerotiorum as test cases, we report 13 cryptic metabolites in four compound groups, including sclerocyclane, a natural product with a novel scaffold. Steroids were the best elicitors and follow-up studies showed that plant-steroids trigger sclerocyclane synthesis, which shows antibiotic activity against B. plantarii, an ecological competitor of S. sclerotiorum. Our results open new paths to exploring the chemical ecology of fungal-plant interactions and provide a genetics-free approach for uncovering cryptic fungal metabolites.
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Affiliation(s)
- Seoung Rak Lee
- Department of Chemistry, Princeton University, Princeton, NJ 08544 (USA)
| | - Mohammad R. Seyedsayamdost
- Department of Chemistry, Princeton University, Princeton, NJ 08544 (USA)
- Department of Molecular Biology, Princeton University, Princeton, NJ 08544 (USA)
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40
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Tang MC, Shen C, Deng Z, Ohashi M, Tang Y. Combinatorial Biosynthesis of Terpenoids through Mixing-and-Matching Sesquiterpene Cyclase and Cytochrome P450 Pairs. Org Lett 2022; 24:4783-4787. [PMID: 35737509 PMCID: PMC9899527 DOI: 10.1021/acs.orglett.2c01785] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
Terpenoids are an important class of natural products with diverse structures and bioactivities. Their hydrocarbon scaffolds are mainly derived from the terpenes produced by terpene cyclases (TCs). Otherwise, new hydrocarbon scaffolds can be achieved through oxidative rearrangement catalyzed by oxygenases such as P450s. Herein, we report the functional characterization of α/β-trans-bergamotene-producing TCs and their multifunctional P450 partners mined from different fungal species. In addition, novel sesquiterpenoids with hydrocarbon scaffolds different from bergamotenes were generated by combinatorial biosynthesis through mixing-and-matching these TC and P450 pairs. Our results provide a successful example of expanding the chemical diversity of terpenoids by combining genome mining and synthetic biology.
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Affiliation(s)
- Man-Cheng Tang
- State Key Laboratory of Microbial Metabolism, School of Life Sciences & Biotechnology, Shanghai Jiao Tong University, Shanghai, 200240, China,Department of Chemical and Biomolecular Engineering, University of California, Los Angeles, California 90095, United States
| | - Cheng Shen
- State Key Laboratory of Microbial Metabolism, School of Life Sciences & Biotechnology, Shanghai Jiao Tong University, Shanghai, 200240, China
| | - Zixin Deng
- State Key Laboratory of Microbial Metabolism, School of Life Sciences & Biotechnology, Shanghai Jiao Tong University, Shanghai, 200240, China
| | - Masao Ohashi
- Department of Chemical and Biomolecular Engineering, University of California, Los Angeles, California 90095, United States
| | - Yi Tang
- Department of Chemical and Biomolecular Engineering, University of California, Los Angeles, California 90095, United States,Department of Chemistry and Biochemistry, University of California, Los Angeles, California 90095, United States,Corresponding Author:
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Mosunova OV, Navarro-Muñoz JC, Haksar D, van Neer J, Hoeksma J, den Hertog J, Collemare J. Evolution-Informed Discovery of the Naphthalenone Biosynthetic Pathway in Fungi. mBio 2022; 13:e0022322. [PMID: 35616333 PMCID: PMC9239057 DOI: 10.1128/mbio.00223-22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2022] [Accepted: 05/04/2022] [Indexed: 11/21/2022] Open
Abstract
Fungi produce a wide diversity of secondary metabolites with interesting biological activities for the health, industrial, and agricultural sectors. While fungal genomes have revealed an unexpectedly high number of biosynthetic pathways that far exceeds the number of known molecules, accessing and characterizing this hidden diversity remain highly challenging. Here, we applied a combined phylogenetic dereplication and comparative genomics strategy to explore eight lichenizing fungi. The determination of the evolutionary relationships of aromatic polyketide pathways resulted in the identification of an uncharacterized biosynthetic pathway that is conserved in distant fungal lineages. The heterologous expression of the homologue from Aspergillus parvulus linked this pathway to naphthalenone compounds, which were detected in cultures when the pathway was expressed. Our unbiased and rational strategy generated evolutionary knowledge that ultimately linked biosynthetic genes to naphthalenone polyketides. Applied to many more genomes, this approach can unlock the full exploitation of the fungal kingdom for molecule discovery. IMPORTANCE Fungi have provided us with life-changing small bioactive molecules, with the best-known examples being the first broad-spectrum antibiotic penicillin, immunosuppressive cyclosporine, and cholesterol-lowering statins. Since the 1980s, exploration of chemical diversity in nature has been highly reduced. However, the genomic era has revealed that fungal genomes are concealing an unexpected and largely unexplored chemical diversity. So far, fungal genomes have been exploited to predict the production potential of bioactive compounds or to find genes that control the production of known molecules of interest. But accessing and characterizing the full fungal chemical diversity require rational and, thus, efficient strategies. Our approach is to first determine the evolutionary relationships of fungal biosynthetic pathways in order to identify those that are already characterized and those that show a different evolutionary origin. This knowledge allows prioritizing the choice of the pathway to functionally characterize in a second stage using synthetic-biology tools like heterologous expression. A particular strength of this strategy is that it is always successful: it generates knowledge about the evolution of bioactive-molecule biosynthesis in fungi, it either yields novel molecules or links the studied pathway to already known molecules, and it reveals the chemical diversity within a given pathway, all at once. The strategy is very powerful to avoid studying the same pathway again and can be used with any fungal genome. Functional characterization using heterologous expression is particularly suitable for fungi that are difficult to grow or not genetically tractable. Thanks to the decreasing cost of gene synthesis, ultimately, only the genome sequence is needed to identify novel pathways and characterize the molecules that they produce. Such an evolution-informed strategy allows the efficient exploitation of the chemical diversity hidden in fungal genomes and is very promising for molecule discovery.
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Affiliation(s)
- Olga V. Mosunova
- Westerdijk Fungal Biodiversity Institute, Utrecht, The Netherlands
| | | | - Diksha Haksar
- Westerdijk Fungal Biodiversity Institute, Utrecht, The Netherlands
| | - Jacq van Neer
- Westerdijk Fungal Biodiversity Institute, Utrecht, The Netherlands
| | - Jelmer Hoeksma
- Hubrecht Institute-KNAW, Utrecht, The Netherlands
- University Medical Center Utrecht, Utrecht, The Netherlands
| | - Jeroen den Hertog
- University Medical Center Utrecht, Utrecht, The Netherlands
- Institute Biology Leiden, Leiden University, Leiden, The Netherlands
| | - Jérôme Collemare
- Westerdijk Fungal Biodiversity Institute, Utrecht, The Netherlands
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Song N, Cui K, Zhang K, Yang J, Liu J, Miao Z, Zhao F, Meng H, Chen L, Chen C, Li Y, Shao M, Zhang J, Wang H. The Role of m6A RNA Methylation in Cancer: Implication for Nature Products Anti-Cancer Research. Front Pharmacol 2022; 13:933332. [PMID: 35784761 PMCID: PMC9243580 DOI: 10.3389/fphar.2022.933332] [Citation(s) in RCA: 17] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2022] [Accepted: 05/27/2022] [Indexed: 12/20/2022] Open
Abstract
N6-methyladenosine (m6A) RNA methylation is identified as the most common, abundant and reversible RNA epigenetic modification in messenger RNA (mRNA) and non-coding RNA, especially within eukaryotic messenger RNAs (mRNAs), which post-transcriptionally directs many important processes of RNA. It has also been demonstrated that m6A modification plays a pivotal role in the occurrence and development of tumors by regulating RNA splicing, localization, translation, stabilization and decay. Growing number of studies have indicated that natural products have outstanding anti-cancer effects of their unique advantages of high efficiency and minimal side effects. However, at present, there are very few research articles to study and explore the relationship between natural products and m6A RNA modification in tumorigenesis. m6A is dynamically deposited, removed, and recognized by m6A methyltransferases (METTL3/14, METTL16, WTAP, RBM15/15B, VIRMA, CBLL1, and ZC3H13, called as “writers”), demethylases (FTO and ALKBH5, called as “erasers”), and m6A-specific binding proteins (YTHDF1/2/3, YTHDC1/2, IGH2BP1/2/3, hnRNPs, eIF3, and FMR1, called as “readers”), respectively. In this review, we summarize the biological function of m6A modification, the role of m6A and the related signaling pathway in cancer, such as AKT, NF-kB, MAPK, ERK, Wnt/β-catenin, STAT, p53, Notch signaling pathway, and so on. Furthermore, we reviewed the current research on nature products in anti-tumor, and further to get a better understanding of the anti-tumor mechanism, thus provide an implication for nature products with anti-cancer research by regulating m6A modification in the future.
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Affiliation(s)
- Na Song
- Department of Pathology, Key Laboratory of Clinical Molecular Pathology, The First Affiliated Hospital of Xinxiang Medical University, Xinxiang, China
- Department of Pathology, Xinxiang Medical University, Xinxiang, China
| | - Kai Cui
- Department of Pathology, Xinxiang Medical University, Xinxiang, China
| | - Ke Zhang
- Department of Pathology, Xinxiang Medical University, Xinxiang, China
| | - Jie Yang
- Department of Pathology, Xinxiang Medical University, Xinxiang, China
| | - Jia Liu
- Department of Pathology, Xinxiang Medical University, Xinxiang, China
| | - Zhuang Miao
- Department of Pathology, Xinxiang Medical University, Xinxiang, China
| | - Feiyue Zhao
- Department of Pathology, Xinxiang Medical University, Xinxiang, China
| | - Hongjing Meng
- Department of Pathology, Xinxiang Medical University, Xinxiang, China
| | - Lu Chen
- Department of Pathology, Xinxiang Medical University, Xinxiang, China
| | - Chong Chen
- Department of Pathology, Xinxiang Medical University, Xinxiang, China
| | - Yushan Li
- School of Public Health, Xinxiang Medical University, Xinxiang, China
| | - Minglong Shao
- The Second Affiliated Hospital of Xinxiang Medical University, Xinxiang, China
| | - Jinghang Zhang
- Department of Pathology, Key Laboratory of Clinical Molecular Pathology, The First Affiliated Hospital of Xinxiang Medical University, Xinxiang, China
- *Correspondence: Jinghang Zhang, ; Haijun Wang,
| | - Haijun Wang
- Department of Pathology, Key Laboratory of Clinical Molecular Pathology, The First Affiliated Hospital of Xinxiang Medical University, Xinxiang, China
- Department of Pathology, Xinxiang Medical University, Xinxiang, China
- *Correspondence: Jinghang Zhang, ; Haijun Wang,
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Fan Y, Ma Z, Zhang Y, Wang Y, Ding Y, Wang C, Cao S. Sulfur-Containing Compounds from Endophytic Fungi: Sources, Structures and Bioactivities. J Fungi (Basel) 2022; 8:jof8060628. [PMID: 35736111 PMCID: PMC9224594 DOI: 10.3390/jof8060628] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2022] [Revised: 06/10/2022] [Accepted: 06/10/2022] [Indexed: 12/01/2022] Open
Abstract
Endophytic fungi have attracted increasing attention as an under-explored source for the discovery and development of structurally and functionally diverse secondary metabolites. These microorganisms colonize their hosts, primarily plants, and demonstrate diverse ecological distribution. Among endophytic fungal natural products, sulfur-containing compounds feature one or more sulfur atoms and possess a range of bioactivities, e.g., cytotoxicity and antimicrobial activities. These natural products mainly belong to the classes of polyketides, nonribosomal peptides, terpenoids, and hybrids. Here, we reviewed the fungal producers, plant sources, chemical structures, and bioactivities of 143 new sulfur-containing compounds that were reported from 1985 to March 2022.
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Affiliation(s)
- Yaqin Fan
- Shandong Provincial Key Laboratory of Applied Mycology, School of Life Sciences, Qingdao Agricultural University, Qingdao 266109, China; (Y.F.); (Z.M.); (Y.Z.)
| | - Zhiheng Ma
- Shandong Provincial Key Laboratory of Applied Mycology, School of Life Sciences, Qingdao Agricultural University, Qingdao 266109, China; (Y.F.); (Z.M.); (Y.Z.)
| | - Yan Zhang
- Shandong Provincial Key Laboratory of Applied Mycology, School of Life Sciences, Qingdao Agricultural University, Qingdao 266109, China; (Y.F.); (Z.M.); (Y.Z.)
| | - Yufei Wang
- Key Laboratory of Chemistry and Engineering of Forest Products, State Ethnic Affairs Commission, Guangxi Collaborative Innovation Center for Chemistry and Engineering of Forest Products, School of Chemistry and Chemical Engineering, Guangxi Minzu University, Nanning 530006, China;
| | - Yousong Ding
- Department of Medicinal Chemistry, Center for Natural Products, Drug Discovery and Development, College of Pharmacy, University of Florida, Gainesville, FL 32610, USA;
| | - Cong Wang
- Key Laboratory of Chemistry and Engineering of Forest Products, State Ethnic Affairs Commission, Guangxi Collaborative Innovation Center for Chemistry and Engineering of Forest Products, School of Chemistry and Chemical Engineering, Guangxi Minzu University, Nanning 530006, China;
- Correspondence: (C.W.); (S.C.)
| | - Shugeng Cao
- Department of Pharmaceutical Sciences, Daniel K. Inouye College of Pharmacy, University of Hawai’i at Hilo, 200 W. Kawili St., Hilo, HI 96720, USA
- Correspondence: (C.W.); (S.C.)
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Lee SR, Seyedsayamdost MR. Induction of Diverse Cryptic Fungal Metabolites by Steroids and Channel Blockers. Angew Chem Int Ed Engl 2022. [DOI: 10.1002/ange.202204519] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
Affiliation(s)
- Seoung Rak Lee
- Department of Chemistry Princeton University Princeton NJ 08544 USA
| | - Mohammad R. Seyedsayamdost
- Department of Chemistry Princeton University Princeton NJ 08544 USA
- Department of Molecular Biology Princeton University Princeton NJ 08544 USA
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45
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Homma Y, Sugawara A, Morishita Y, Tsukada K, Ozaki T, Asai T. Discovery of a Cyclic Depsipeptide from Chaetomium mollipilium by the Genome Mining Approach. Org Lett 2022; 24:3504-3509. [PMID: 35543719 DOI: 10.1021/acs.orglett.2c01172] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Genome mining and bioinformatics analyses allowed us to rationally find a candidate biosynthetic gene cluster for a new cyclic depsipeptide of Chaetomium mollipilium. A heterologous reconstitution of the identified biosynthetic pathway predictably afforded a new cyclic depsipeptide composed of l-leucine, l-tryptophan, and a polyketide moiety. Interestingly, the 10-membered macrocycle structure generated equilibrium to an unprecedented cyclol structure. This study demonstrates the advantage of a synthetic biology method in achieving rational access to new natural products.
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Affiliation(s)
- Yuto Homma
- Graduate School of Pharmaceutical Sciences, Tohoku University, 6-3 Aza-Aoba, Aramaki, Aoba-ku, Sendai 980-8578, Japan
| | - Akihiro Sugawara
- Graduate School of Pharmaceutical Sciences, Tohoku University, 6-3 Aza-Aoba, Aramaki, Aoba-ku, Sendai 980-8578, Japan
| | - Yohei Morishita
- Graduate School of Pharmaceutical Sciences, Tohoku University, 6-3 Aza-Aoba, Aramaki, Aoba-ku, Sendai 980-8578, Japan
| | - Kento Tsukada
- Graduate School of Pharmaceutical Sciences, Tohoku University, 6-3 Aza-Aoba, Aramaki, Aoba-ku, Sendai 980-8578, Japan
| | - Taro Ozaki
- Graduate School of Pharmaceutical Sciences, Tohoku University, 6-3 Aza-Aoba, Aramaki, Aoba-ku, Sendai 980-8578, Japan
| | - Teigo Asai
- Graduate School of Pharmaceutical Sciences, Tohoku University, 6-3 Aza-Aoba, Aramaki, Aoba-ku, Sendai 980-8578, Japan
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46
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Augustijn HE, Medema MH. Freedom of expression: A synthetic route to metabolites. Cell 2022; 185:1449-1451. [PMID: 35487188 DOI: 10.1016/j.cell.2022.04.007] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2022] [Revised: 04/04/2022] [Accepted: 04/04/2022] [Indexed: 11/24/2022]
Abstract
Microbial specialized metabolites play key roles in microbiome interactions, but their biosynthetic pathways are difficult to characterize. In this issue, Patel et al. (2022) describe new technologies for the computer-aided redesign of gene clusters to facilitate heterologous expression across diverse hosts and showcase their utility by identifying a new class of microbiome-derived nucleotide metabolites.
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Affiliation(s)
- Hannah E Augustijn
- Bioinformatics Group, Wageningen University, Wageningen, The Netherlands; Institute of Biology, Leiden University, Leiden, The Netherlands
| | - Marnix H Medema
- Bioinformatics Group, Wageningen University, Wageningen, The Netherlands; Institute of Biology, Leiden University, Leiden, The Netherlands.
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47
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Liu J, Wang X, Dai G, Zhang Y, Bian X. Microbial chassis engineering drives heterologous production of complex secondary metabolites. Biotechnol Adv 2022; 59:107966. [PMID: 35487394 DOI: 10.1016/j.biotechadv.2022.107966] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2022] [Revised: 04/20/2022] [Accepted: 04/21/2022] [Indexed: 12/27/2022]
Abstract
The cryptic secondary metabolite biosynthetic gene clusters (BGCs) far outnumber currently known secondary metabolites. Heterologous production of secondary metabolite BGCs in suitable chassis facilitates yield improvement and discovery of new-to-nature compounds. The two juxtaposed conventional model microorganisms, Escherichia coli, Saccharomyces cerevisiae, have been harnessed as microbial chassis to produce a bounty of secondary metabolites with the help of certain host engineering. In last decade, engineering non-model microbes to efficiently biosynthesize secondary metabolites has received increasing attention due to their peculiar advantages in metabolic networks and/or biosynthesis. The state-of-the-art synthetic biology tools lead the way in operating genetic manipulation in non-model microorganisms for phenotypic optimization or yields improvement of desired secondary metabolites. In this review, we firstly discuss the pros and cons of several model and non-model microbial chassis, as well as the importance of developing broader non-model microorganisms as alternative programmable heterologous hosts to satisfy the desperate needs of biosynthesis study and industrial production. Then we highlight the lately advances in the synthetic biology tools and engineering strategies for optimization of non-model microbial chassis, in particular, the successful applications for efficient heterologous production of multifarious complex secondary metabolites, e.g., polyketides, nonribosomal peptides, as well as ribosomally synthesized and post-translationally modified peptides. Lastly, emphasis is on the perspectives of chassis cells development to access the ideal cell factory in the artificial intelligence-driven genome era.
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Affiliation(s)
- Jiaqi Liu
- Helmholtz International Lab for Anti-Infectives, Shandong University-Helmholtz Institute of Biotechnology, State Key Laboratory of Microbial Technology, Shandong University, Qingdao, Shandong 266237, PR China; Present address: Helmholtz-Institute for Pharmaceutical Research Saarland (HIPS), Helmholtz Centre for Infection Research (HZI), Saarland University, Campus E8 1, 66123 Saarbrücken, Germany
| | - Xue Wang
- Helmholtz International Lab for Anti-Infectives, Shandong University-Helmholtz Institute of Biotechnology, State Key Laboratory of Microbial Technology, Shandong University, Qingdao, Shandong 266237, PR China
| | - Guangzhi Dai
- Helmholtz International Lab for Anti-Infectives, Shandong University-Helmholtz Institute of Biotechnology, State Key Laboratory of Microbial Technology, Shandong University, Qingdao, Shandong 266237, PR 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, PR 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, PR China.
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49
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Misa J, Billingsley JM, Niwa K, Yu RK, Tang Y. Engineered Production of Strictosidine and Analogues in Yeast. ACS Synth Biol 2022; 11:1639-1649. [PMID: 35294193 PMCID: PMC9171786 DOI: 10.1021/acssynbio.2c00037] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023]
Abstract
Monoterpene indole alkaloids (MIAs) are an expansive class of plant natural products, many of which have been named on the World Health Organization's List of Essential Medicines. Low production from native plant hosts necessitates a more reliable source of these drugs to meet global demand. Here, we report the development of a yeast-based platform for high-titer production of the universal MIA precursor, strictosidine. Our fed-batch platform produces ∼50 mg/L strictosidine, starting from the commodity chemicals geraniol and tryptamine. The microbially produced strictosidine was purified to homogeneity and characterized by NMR. Additionally, our approach enables the production of halogenated strictosidine analogues through the feeding of modified tryptamines. The MIA platform strain enables rapid access to strictosidine for reconstitution and production of downstream MIA natural products.
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Affiliation(s)
- Joshua Misa
- Department of Chemical and Biomolecular Engineering, University of California, Los Angeles, Los Angeles, CA, 90095, USA
| | - John M. Billingsley
- Department of Chemical and Biomolecular Engineering, University of California, Los Angeles, Los Angeles, CA, 90095, USA
| | - Kanji Niwa
- Department of Chemical and Biomolecular Engineering, University of California, Los Angeles, Los Angeles, CA, 90095, USA
| | - Rachel K. Yu
- Department of Chemical and Biomolecular Engineering, University of California, Los Angeles, Los Angeles, CA, 90095, USA
| | - Yi Tang
- Department of Chemical and Biomolecular Engineering, University of California, Los Angeles, Los Angeles, CA, 90095, USA
- Department of Chemistry and Biochemistry, University of California, Los Angeles, Los Angeles, CA, 90095, USA
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Heterologous Expression of Secondary Metabolite Genes in Trichoderma reesei for Waste Valorization. J Fungi (Basel) 2022; 8:jof8040355. [PMID: 35448586 PMCID: PMC9032437 DOI: 10.3390/jof8040355] [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: 03/09/2022] [Revised: 03/27/2022] [Accepted: 03/28/2022] [Indexed: 01/07/2023] Open
Abstract
Trichoderma reesei (Hypocrea jecorina) was developed as a microbial cell factory for the heterologous expression of fungal secondary metabolites. This was achieved by inactivation of sorbicillinoid biosynthesis and construction of vectors for the rapid cloning and expression of heterologous fungal biosynthetic genes. Two types of megasynth(et)ases were used to test the strain and vectors, namely a non-reducing polyketide synthase (nr-PKS, aspks1) from Acremonium strictum and a hybrid highly-reducing PKS non-ribosomal peptide synthetase (hr-PKS-NRPS, tenS + tenC) from Beauveria bassiana. The resulting engineered T. reesei strains were able to produce the expected natural products 3-methylorcinaldehyde and pretenellin A on waste materials including potato, orange, banana and kiwi peels and barley straw. Developing T. reesei as a heterologous host for secondary metabolite production represents a new method for waste valorization by the direct conversion of waste biomass into secondary metabolites.
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