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Pham MT, Yang FL, Liu IC, Liang PH, Lin HC. Non-Heme Iron Enzymes Catalyze Heterobicyclic and Spirocyclic Isoquinolone Core Formation in Piperazine Alkaloid Biosynthesis. Angew Chem Int Ed Engl 2024; 63:e202401324. [PMID: 38499463 DOI: 10.1002/anie.202401324] [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: 01/19/2024] [Revised: 03/16/2024] [Accepted: 03/18/2024] [Indexed: 03/20/2024]
Abstract
We report the discovery and biosynthesis of new piperazine alkaloids-arizonamides, and their derived compounds-arizolidines, featuring heterobicyclic and spirocyclic isoquinolone skeletons, respectively. Their biosynthetic pathway involves two crucial non-heme iron enzymes, ParF and ParG, for core skeleton construction. ParF has a dual function facilitating 2,3-alkene formation of helvamide, as a substrate for ParG, and oxidative cleavage of piperazine. Notably, ParG exhibits catalytic versatility in multiple oxidative reactions, including cyclization and ring reconstruction. A key amino acid residue Phe67 was characterized to control the formation of the constrained arizonamide B backbone by ParG.
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Affiliation(s)
- Mai-Truc Pham
- Institute of Biological Chemistry, Academia Sinica, Taipei, 115, Taiwan R.O.C
- Chemical Biology and Molecular Biophysics Program, Taiwan International Graduate Program, Academia Sinica, Taipei, 115, Taiwan R.O.C
- Department of Chemistry, National Tsing Hua University, Hsinchu, 300, Taiwan R.O.C
| | - Feng-Ling Yang
- Institute of Biological Chemistry, Academia Sinica, Taipei, 115, Taiwan R.O.C
- Chemical Biology and Molecular Biophysics Program, Taiwan International Graduate Program, Academia Sinica, Taipei, 115, Taiwan R.O.C
| | - I-Chen Liu
- Institute of Biological Chemistry, Academia Sinica, Taipei, 115, Taiwan R.O.C
- Chemical Biology and Molecular Biophysics Program, Taiwan International Graduate Program, Academia Sinica, Taipei, 115, Taiwan R.O.C
| | - Po-Huang Liang
- Institute of Biological Chemistry, Academia Sinica, Taipei, 115, Taiwan R.O.C
- Chemical Biology and Molecular Biophysics Program, Taiwan International Graduate Program, Academia Sinica, Taipei, 115, Taiwan R.O.C
| | - Hsiao-Ching Lin
- Institute of Biological Chemistry, Academia Sinica, Taipei, 115, Taiwan R.O.C
- Chemical Biology and Molecular Biophysics Program, Taiwan International Graduate Program, Academia Sinica, Taipei, 115, Taiwan R.O.C
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2
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Geris R, Teles de Jesus VE, Ferreira da Silva A, Malta M. Exploring Culture Media Diversity to Produce Fungal Secondary Metabolites and Cyborg Cells. Chem Biodivers 2024; 21:e202302066. [PMID: 38335028 DOI: 10.1002/cbdv.202302066] [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: 12/20/2023] [Revised: 02/07/2024] [Accepted: 02/08/2024] [Indexed: 02/12/2024]
Abstract
Fungi are microorganisms of significant biotechnological importance due to their ability to provide food and produce several value-added secondary metabolites and enzymes. Its products move billions of dollars in the pharmaceutical, cosmetics, and additives sectors. These microorganisms also play a notable role in bionanotechnology, leading to the production of hybrid biological-inorganic materials (such as cyborg cells) and the use of their enzyme complex in the biosynthesis of nanoparticles. In this sense, optimizing the fungal growth process is necessary, with selecting the cultivation medium as one of the essential factors for the microorganism to reach its maximum metabolic expression. The culture medium's composition can also impact the nanomaterial's stability and prevent the incorporation of nanoparticles into fungal cells. Therefore, our main objectives are the following: (1) compile and discuss the most commonly employed culture media for the production of fungal secondary metabolites and the formation of cyborg cells, accompanied by preparation methods; (2) provide a six-step guide to investigating the fungal metabolomic profile and (3) discuss the main procedures of microbial cultivation to produce fungal cyborg cells.
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Affiliation(s)
- Regina Geris
- Laboratório de Biotecnologia e Química de Microrganismos (LBQM), Departamento de Química Orgânica, Instituto de Química, Universidade Federal da Bahia, Rua Barão de Jeremoabo S/n, 40170-115, Salvador, Brasil
| | - Vitória Evelyn Teles de Jesus
- Laboratório de Biotecnologia e Química de Microrganismos (LBQM), Departamento de Química Orgânica, Instituto de Química, Universidade Federal da Bahia, Rua Barão de Jeremoabo S/n, 40170-115, Salvador, Brasil
| | - Antonio Ferreira da Silva
- Laboratório de Biotecnologia e Química de Microrganismos (LBQM), Departamento de Química Orgânica, Instituto de Química, Universidade Federal da Bahia, Rua Barão de Jeremoabo S/n, 40170-115, Salvador, Brasil
| | - Marcos Malta
- Laboratório de Biotecnologia e Química de Microrganismos (LBQM), Departamento de Química Orgânica, Instituto de Química, Universidade Federal da Bahia, Rua Barão de Jeremoabo S/n, 40170-115, Salvador, Brasil
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3
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Martín JF, Liras P. Targeting of Specialized Metabolites Biosynthetic Enzymes to Membranes and Vesicles by Posttranslational Palmitoylation: A Mechanism of Non-Conventional Traffic and Secretion of Fungal Metabolites. Int J Mol Sci 2024; 25:1224. [PMID: 38279221 PMCID: PMC10816013 DOI: 10.3390/ijms25021224] [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: 12/08/2023] [Revised: 12/30/2023] [Accepted: 01/09/2024] [Indexed: 01/28/2024] Open
Abstract
In nature, the formation of specialized (secondary) metabolites is associated with the late stages of fungal development. Enzymes involved in the biosynthesis of secondary metabolites in fungi are located in distinct subcellular compartments including the cytosol, peroxisomes, endosomes, endoplasmic reticulum, different types of vesicles, the plasma membrane and the cell wall space. The enzymes traffic between these subcellular compartments and the secretion through the plasma membrane are still unclear in the biosynthetic processes of most of these metabolites. Recent reports indicate that some of these enzymes initially located in the cytosol are later modified by posttranslational acylation and these modifications may target them to membrane vesicle systems. Many posttranslational modifications play key roles in the enzymatic function of different proteins in the cell. These modifications are very important in the modulation of regulatory proteins, in targeting of proteins, intracellular traffic and metabolites secretion. Particularly interesting are the protein modifications by palmitoylation, prenylation and miristoylation. Palmitoylation is a thiol group-acylation (S-acylation) of proteins by palmitic acid (C16) that is attached to the SH group of a conserved cysteine in proteins. Palmitoylation serves to target acylated proteins to the cytosolic surface of cell membranes, e.g., to the smooth endoplasmic reticulum, whereas the so-called toxisomes are formed in trichothecene biosynthesis. Palmitoylation of the initial enzymes involved in the biosynthesis of melanin serves to target them to endosomes and later to the conidia, whereas other non-palmitoylated laccases are secreted directly by the conventional secretory pathway to the cell wall space where they perform the last step(s) of melanin biosynthesis. Six other enzymes involved in the biosynthesis of endocrosin, gliotoxin and fumitremorgin believed to be cytosolic are also targeted to vesicles, although it is unclear if they are palmitoylated. Bioinformatic analysis suggests that palmitoylation may be frequent in the modification and targeting of polyketide synthetases and non-ribosomal peptide synthetases. The endosomes may integrate other small vesicles with different cargo proteins, forming multivesicular bodies that finally fuse with the plasma membrane during secretion. Another important effect of palmitoylation is that it regulates calcium metabolism by posttranslational modification of the phosphatase calcineurin. Mutants defective in the Akr1 palmitoyl transferase in several fungi are affected in calcium transport and homeostasis, thus impacting on the biosynthesis of calcium-regulated specialized metabolites. The palmitoylation of secondary metabolites biosynthetic enzymes and their temporal distribution respond to the conidiation signaling mechanism. In summary, this posttranslational modification drives the spatial traffic of the biosynthetic enzymes between the subcellular organelles and the plasma membrane. This article reviews the molecular mechanism of palmitoylation and the known fungal palmitoyl transferases. This novel information opens new ways to improve the biosynthesis of the bioactive metabolites and to increase its secretion in fungi.
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Affiliation(s)
- Juan F. Martín
- Departamento de Biología Molecular, Área de Microbiología, Universidad de León, 24071 León, Spain;
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4
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Bradshaw AJ, Ramírez-Cruz V, Awan AR, Furci G, Guzmán-Dávalos L, Dentinger BTM. Phylogenomics of the psychoactive mushroom genus Psilocybe and evolution of the psilocybin biosynthetic gene cluster. Proc Natl Acad Sci U S A 2024; 121:e2311245121. [PMID: 38194448 PMCID: PMC10801892 DOI: 10.1073/pnas.2311245121] [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: 07/20/2023] [Accepted: 11/28/2023] [Indexed: 01/11/2024] Open
Abstract
Psychoactive mushrooms in the genus Psilocybe have immense cultural value and have been used for centuries in Mesoamerica. Despite the recent surge of interest in these mushrooms due to the psychotherapeutic potential of their natural alkaloid psilocybin, their phylogeny and taxonomy remain substantially incomplete. Moreover, the recent elucidation of the psilocybin biosynthetic gene cluster is known for only five of ~165 species of Psilocybe, four of which belong to only one of two major clades. We set out to improve the phylogeny of Psilocybe using shotgun sequencing of fungarium specimens, from which we obtained 71 metagenomes including from 23 types, and conducting phylogenomic analysis of 2,983 single-copy gene families to generate a fully supported phylogeny. Molecular clock analysis suggests the stem lineage of Psilocybe arose ~67 mya and diversified ~56 mya. We also show that psilocybin biosynthesis first arose in Psilocybe, with 4 to 5 possible horizontal transfers to other mushrooms between 40 and 9 mya. Moreover, predicted orthologs of the psilocybin biosynthetic genes revealed two distinct gene orders within the biosynthetic gene cluster that corresponds to a deep split within the genus, possibly a signature of two independent acquisitions of the cluster within Psilocybe.
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Affiliation(s)
- Alexander J. Bradshaw
- School of Biological Sciences, University of Utah, Salt Lake City, UT84112
- Natural History Museum of Utah, Collections and Research, University of Utah, Salt Lake City, UT84108
| | - Virginia Ramírez-Cruz
- Consejo Nacional de Humanidades, Ciencias y Tecnologías (CONAHCYT), Departamento de Botánica y Zoología, Universidad de Guadalajara, Zapopan45147, Mexico
| | - Ali R. Awan
- Genomics Innovation Unit, Guy’s and St.Thomas’ NHS Foundation Trust, St Thomas’ Hospital, LondonSE1 7EH, United Kingdom
| | | | - Laura Guzmán-Dávalos
- Departamento de Botánica y Zoología, Universidad de Guadalajara, Zapopan45147, Mexico
| | - Bryn T. M. Dentinger
- School of Biological Sciences, University of Utah, Salt Lake City, UT84112
- Natural History Museum of Utah, Collections and Research, University of Utah, Salt Lake City, UT84108
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5
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Fu R, Sun W, Liu B, Sun J, Wu Q, Liu X, Xiang M. Genome and transcriptome reveal lithophilic adaptation of Cladophialophora brunneola, a new rock-inhabiting fungus. Mycology 2024; 14:326-343. [PMID: 38187882 PMCID: PMC10769131 DOI: 10.1080/21501203.2023.2256764] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2023] [Accepted: 09/04/2023] [Indexed: 01/09/2024] Open
Abstract
Rock-inhabiting fungi (RIF) are slow-growing microorganisms that inhabit rocks and exhibit exceptional stress tolerance owing to their thick melanised cell walls. This study reports the identification of a novel rock-inhabiting fungus, Cladophialophora brunneola sp. nov. which was isolated from a karst landform in Guizhou, China, using a combination of morphological and phylogenetic analyses. The genome of C. brunneola was sequenced and assembled, with a total size of approximately 33.8 Mb, encoding 14,168 proteins and yielding an N50 length of 1.88 Mb. C. brunneola possessed a larger proportion of species-specific genes, and phylogenomic analysis positioned it in an early diverged lineage within Chaetothyriales. In comparison to non-RIF, C. brunneola displayed reduction in carbohydrate-active enzyme families (CAZymes) and secondary metabolite biosynthetic gene clusters (BGCs). Transcriptome analysis conducted under PEG-induced drought stress revealed elevated expression levels of genes associated with melanin synthesis pathways, cell wall biosynthesis, and lipid metabolism. This study contributes to our understanding of the genomic evolution and polyextremotolerance exhibited by rock-inhabiting fungi.
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Affiliation(s)
- Rong Fu
- State Key Laboratory of Mycology, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing, China
| | - Wei Sun
- State Key Laboratory of Mycology, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China
| | - Bingjie Liu
- State Key Laboratory of Mycology, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing, China
| | - Jingzu Sun
- State Key Laboratory of Mycology, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China
| | - Qi Wu
- State Key Laboratory of Mycology, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China
| | - Xingzhong Liu
- Department of Microbiology, College of Life Science, Nankai University, Tianjin, China
| | - Meichun Xiang
- State Key Laboratory of Mycology, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing, China
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6
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Alves de Castro P, Figueiredo Pinzan C, Dos Reis TF, Valero C, Van Rhijn N, Menegatti C, de Freitas Migliorini IL, Bromley M, Fleming AB, Traynor AM, Sarikaya-Bayram Ö, Bayram Ö, Malavazi I, Ebel F, Barbosa JCJ, Fill T, Pupo MT, Goldman GH. Aspergillus fumigatus mitogen-activated protein kinase MpkA is involved in gliotoxin production and self-protection. Nat Commun 2024; 15:33. [PMID: 38167253 PMCID: PMC10762094 DOI: 10.1038/s41467-023-44329-1] [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: 05/22/2023] [Accepted: 12/08/2023] [Indexed: 01/05/2024] Open
Abstract
Aspergillus fumigatus is a saprophytic fungus that can cause a variety of human diseases known as aspergillosis. Mycotoxin gliotoxin (GT) production is important for its virulence and must be tightly regulated to avoid excess production and toxicity to the fungus. GT self-protection by GliT oxidoreductase and GtmA methyltransferase activities is related to the subcellular localization of these enzymes and how GT can be sequestered from the cytoplasm to avoid increased cell damage. Here, we show that GliT:GFP and GtmA:GFP are localized in the cytoplasm and in vacuoles during GT production. The Mitogen-Activated Protein kinase MpkA is essential for GT production and self-protection, interacts physically with GliT and GtmA and it is necessary for their regulation and subsequent presence in the vacuoles. The sensor histidine kinase SlnASln1 is important for modulation of MpkA phosphorylation. Our work emphasizes the importance of MpkA and compartmentalization of cellular events for GT production and self-defense.
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Affiliation(s)
- Patrícia Alves de Castro
- Faculdade de Ciências Farmacêuticas de Ribeirão Preto, Universidade de São Paulo, Ribeirão Preto, Brazil
| | - Camila Figueiredo Pinzan
- Faculdade de Ciências Farmacêuticas de Ribeirão Preto, Universidade de São Paulo, Ribeirão Preto, Brazil
| | - Thaila Fernanda Dos Reis
- Faculdade de Ciências Farmacêuticas de Ribeirão Preto, Universidade de São Paulo, Ribeirão Preto, Brazil
| | - Clara Valero
- Faculdade de Ciências Farmacêuticas de Ribeirão Preto, Universidade de São Paulo, Ribeirão Preto, Brazil
- Manchester Fungal Infection Group, Division of Evolution, Infection and Genomic Sciences, School of Biological Sciences, Faculty of Biology, Medicine and Health, University of Manchester, Manchester, United Kingdom
| | - Norman Van Rhijn
- Manchester Fungal Infection Group, Division of Evolution, Infection and Genomic Sciences, School of Biological Sciences, Faculty of Biology, Medicine and Health, University of Manchester, Manchester, United Kingdom
| | - Carla Menegatti
- Faculdade de Ciências Farmacêuticas de Ribeirão Preto, Universidade de São Paulo, Ribeirão Preto, Brazil
| | | | - Michael Bromley
- Manchester Fungal Infection Group, Division of Evolution, Infection and Genomic Sciences, School of Biological Sciences, Faculty of Biology, Medicine and Health, University of Manchester, Manchester, United Kingdom
| | - Alastair B Fleming
- Department of Microbiology, Moyne Institute of Preventive Medicine, Trinity College Dublin, Dublin, Ireland
| | - Aimee M Traynor
- Department of Biology, Maynooth University, Maynooth, Co. Kildare, Ireland
| | | | - Özgür Bayram
- Department of Biology, Maynooth University, Maynooth, Co. Kildare, Ireland.
| | - Iran Malavazi
- Departamento de Genética e Evolução, Centro de Ciências Biológicas e da Saúde, Universidade Federal de São Carlos, São Carlos, São Paulo, Brazil
| | - Frank Ebel
- Institut für Infektionsmedizin und Zoonosen, Medizinische Fakultät, LMU, 80539, München, Germany
| | | | - Taícia Fill
- Instituto de Química, Universidade Estadual de Campinas, Campinas, Brazil
| | - Monica Tallarico Pupo
- Faculdade de Ciências Farmacêuticas de Ribeirão Preto, Universidade de São Paulo, Ribeirão Preto, Brazil
| | - Gustavo H Goldman
- Faculdade de Ciências Farmacêuticas de Ribeirão Preto, Universidade de São Paulo, Ribeirão Preto, Brazil.
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7
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Xue M, Hou X, Gu G, Dong J, Yang Y, Pan X, Zhang X, Xu D, Lai D, Zhou L. Activation of Ustilaginoidin Biosynthesis Gene uvpks1 in Villosiclava virens Albino Strain LN02 Influences Development, Stress Responses, and Inhibition of Rice Seed Germination. J Fungi (Basel) 2023; 10:31. [PMID: 38248941 PMCID: PMC10817433 DOI: 10.3390/jof10010031] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2023] [Revised: 12/28/2023] [Accepted: 12/29/2023] [Indexed: 01/23/2024] Open
Abstract
Villosiclava virens (anamorph: Ustilaginoidea virens) is the pathogen of rice false smut (RFS), which is a destructive rice fungal disease. The albino strain LN02 is a natural white-phenotype mutant of V. virens due to its incapability to produce toxic ustilaginoidins. In this study, three strains including the normal strain P1, albino strain LN02, and complemented strain uvpks1C-1 of the LN02 strain were employed to investigate the activation of the ustilaginoidin biosynthesis gene uvpks1 in the albino strain LN02 to influence sporulation, conidia germination, pigment production, stress responses, and the inhibition of rice seed germination. The activation of the ustilaginoidin biosynthesis gene uvpks1 increased fungal tolerances to NaCl-induced osmotic stress, Congo-red-induced cell wall stress, SDS-induced cell membrane stress, and H2O2-induced oxidative stress. The activation of uvpks1 also increased sporulation, conidia germination, pigment production, and the inhibition of rice seed germination. In addition, the activation of uvpks1 was able to increase the mycelial growth of the V. virens albino strain LN02 at 23 °C and a pH from 5.5 to 7.5. The findings help in understanding the effects of the activation of uvpks1 in albino strain LN02 on development, pigment production, stress responses, and the inhibition of rice seed germination by controlling ustilaginoidin biosynthesis.
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Affiliation(s)
| | | | | | | | | | | | | | | | | | - Ligang Zhou
- Department of Plant Pathology, College of Plant Protection, China Agricultural University, Beijing 100193, China; (M.X.); (X.H.); (G.G.); (J.D.); (Y.Y.); (X.P.); (X.Z.); (D.X.); (D.L.)
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8
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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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9
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Nguyen TP, Fang M, Kim J, Wang B, Lin E, Khivansara V, Barrows N, Rivera-Cancel G, Goralski M, Cervantes CL, Xie S, Peterson JM, Povedano JM, Antczak MI, Posner BA, Harvey CJB, Naughton BT, McFadden DG, Ready JM, De Brabander JK, Nijhawan D. Inducible mismatch repair streamlines forward genetic approaches to target identification of cytotoxic small molecules. Cell Chem Biol 2023; 30:1453-1467.e8. [PMID: 37607550 PMCID: PMC10841267 DOI: 10.1016/j.chembiol.2023.07.017] [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: 02/16/2023] [Revised: 05/24/2023] [Accepted: 07/30/2023] [Indexed: 08/24/2023]
Abstract
Orphan cytotoxins are small molecules for which the mechanism of action (MoA) is either unknown or ambiguous. Unveiling the mechanism of these compounds may lead to useful tools for biological investigation and new therapeutic leads. In selected cases, the DNA mismatch repair-deficient colorectal cancer cell line, HCT116, has been used as a tool in forward genetic screens to identify compound-resistant mutations, which have ultimately led to target identification. To expand the utility of this approach, we engineered cancer cell lines with inducible mismatch repair deficits, thus providing temporal control over mutagenesis. By screening for compound resistance phenotypes in cells with low or high rates of mutagenesis, we increased both the specificity and sensitivity of identifying resistance mutations. Using this inducible mutagenesis system, we implicate targets for multiple orphan cytotoxins, including a natural product and compounds emerging from a high-throughput screen, thus providing a robust tool for future MoA studies.
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Affiliation(s)
- Thu P Nguyen
- Department of Biochemistry, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA; Department of Internal Medicine, Program in Molecular Medicine and Division of Hematology/Oncology, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
| | - Min Fang
- Department of Biochemistry, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
| | - Jiwoong Kim
- Quantitative Biomedical Research Center, Department of Clinical Sciences, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA; Simmons Cancer Center, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
| | - Baiyun Wang
- Department of Biochemistry, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA; Department of Internal Medicine, Program in Molecular Medicine and Division of Hematology/Oncology, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
| | - Elisa Lin
- Department of Biochemistry, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA; Department of Internal Medicine, Program in Molecular Medicine and Division of Hematology/Oncology, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
| | - Vishal Khivansara
- Department of Biochemistry, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA; Department of Internal Medicine, Program in Molecular Medicine and Division of Hematology/Oncology, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
| | - Neha Barrows
- Department of Biochemistry, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA; Department of Internal Medicine, Program in Molecular Medicine and Division of Hematology/Oncology, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
| | - Giomar Rivera-Cancel
- Department of Biochemistry, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA; Department of Internal Medicine, Program in Molecular Medicine and Division of Hematology/Oncology, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
| | - Maria Goralski
- Department of Biochemistry, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA; Department of Internal Medicine, Program in Molecular Medicine and Division of Hematology/Oncology, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
| | - Christopher L Cervantes
- Department of Biochemistry, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA; Department of Internal Medicine, Program in Molecular Medicine and Division of Hematology/Oncology, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
| | - Shanhai Xie
- Department of Biochemistry, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA; Department of Internal Medicine, Program in Molecular Medicine and Division of Hematology/Oncology, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
| | - Johann M Peterson
- Department of Biochemistry, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA; Department of Internal Medicine, Program in Molecular Medicine and Division of Hematology/Oncology, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
| | - Juan Manuel Povedano
- Department of Biochemistry, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA; Department of Internal Medicine, Program in Molecular Medicine and Division of Endocrinology, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
| | - Monika I Antczak
- Department of Biochemistry, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
| | - Bruce A Posner
- Department of Biochemistry, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA; Simmons Cancer Center, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
| | | | | | - David G McFadden
- Department of Biochemistry, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA; Department of Internal Medicine, Program in Molecular Medicine and Division of Endocrinology, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA; Simmons Cancer Center, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
| | - Joseph M Ready
- Department of Biochemistry, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA; Simmons Cancer Center, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
| | - Jef K De Brabander
- Department of Biochemistry, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA; Simmons Cancer Center, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA.
| | - Deepak Nijhawan
- Department of Biochemistry, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA; Department of Internal Medicine, Program in Molecular Medicine and Division of Hematology/Oncology, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA; Simmons Cancer Center, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA.
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10
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Zhang S, Yang W, Chen J, Zhang C, Zhang S, Gao L. Whole genome sequencing and annotation of Scleroderma yunnanense, the only edible Scleroderma species. Genomics 2023; 115:110727. [PMID: 37839651 DOI: 10.1016/j.ygeno.2023.110727] [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: 05/30/2023] [Revised: 09/18/2023] [Accepted: 10/12/2023] [Indexed: 10/17/2023]
Abstract
Scleroderma yunnanense, an ectomycorrhizal fungus, is a popular edible mushroom within the Yunnan Province of Southwest China that holds great ecological and economic implications. However, despite its significance, there remains limited information about this species. Therefore, we sequenced S. yunnanense genome to identify the functional genes of S. yunnanense involved in secondary metabolite and carbohydrate production pathways. First, we present the 40.43 Mb high-quality reference genome for S. yunnanense, distributed across 35 contigs; moreover, the N50 contig size was found to reach 3.31 Mb and contained 8877 functional genes. Finally, genome annotation was conducted to compare the functional genes of S. yunnanense with protein sequences from different publicly available databases. Taken together, we identified 12 biosynthetic gene clusters across 10 contigs; among these were 13 key mevalonate (MVA) pathway enzymes, a key tyrosinase enzyme in the 3,4-dihydroxyphenylalanine (DOPA) pathway that is responsible for producing DOPA melanins, and 16 enzymes involved in uridine diphosphate glucose biosynthesis. Overall, this study presents the first genome assembly and annotation of S. yunnanense; ultimately, this information will be important in the elucidation of the biological activities and artificial domestication of this fungus.
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Affiliation(s)
- Shanshan Zhang
- Key Laboratory of Rare and Endangered Forest Plants of State Forestry and Grassland Administration, Yunnan Academy of Forestry and Grassland, Kunming 650201, China.
| | - Wenzhong Yang
- Key Laboratory of Rare and Endangered Forest Plants of State Forestry and Grassland Administration, Yunnan Academy of Forestry and Grassland, Kunming 650201, China
| | - Jian Chen
- Key Laboratory of Rare and Endangered Forest Plants of State Forestry and Grassland Administration, Yunnan Academy of Forestry and Grassland, Kunming 650201, China.
| | - Chuanguang Zhang
- Key Laboratory of Rare and Endangered Forest Plants of State Forestry and Grassland Administration, Yunnan Academy of Forestry and Grassland, Kunming 650201, China.
| | - Siqi Zhang
- Wenshan Prefecture Central Blood Station, Yunnan 663099, China
| | - Lanjing Gao
- College of Forestry, Beijing Forestry University, Beijing 100083, China
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11
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Jesmin R, Cary JW, Lebar MD, Majumdar R, Gummadidala PM, Dias T, Chandler S, Basu P, Decho AW, Keller NP, Chanda A. Vibrio gazogenes-dependent disruption of aflatoxin biosynthesis in Aspergillus flavus: the connection with endosomal uptake and hyphal morphogenesis. Front Microbiol 2023; 14:1208961. [PMID: 37744918 PMCID: PMC10516221 DOI: 10.3389/fmicb.2023.1208961] [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: 04/20/2023] [Accepted: 08/07/2023] [Indexed: 09/26/2023] Open
Abstract
Aflatoxins, a family of fungal secondary metabolites, are toxic and carcinogenic compounds that pose an enormous threat to global food safety and agricultural sustainability. Specifically agricultural products in African, Southeast Asian and hot and humid regions of American countries suffer most damage from aflatoxin producing molds due to the ideal climate conditions promoting their growth. Our recent studies suggest that Vibrio gazogenes (Vg), an estuarine bacterium non-pathogenic to plants and humans, can significantly inhibit aflatoxin biosynthesis in the producers. In this study, we investigated the mechanism underlying Vg-dependent aflatoxin inhibition using the prominent aflatoxin producer, Aspergillus flavus. We show that aflatoxin inhibition upon Vg treatment was associated with fungal uptake of Vg-prodigiosin, a red pigment, which was consistently visible inside fungal hyphae during treatment. The association of prodigiosin with aflatoxin inhibition was further evident as Serratia marcescens, another prodigiosin producer, significantly inhibited aflatoxin, while non-producers like Escherichia coli, Staphylococcus aureus, Vibrio harveyi, and Vibrio fischeri did not. Also, pure prodigiosin significantly inhibited aflatoxin biosynthesis. Endocytosis inhibitors, filipin and natamycin, reduced the Vg-prodigiosin uptake by the fungus leading to a significant increase in aflatoxin production, suggesting that uptake is endocytosis-dependent. The Vg treatment also reduced hyphal fusion (>98% inhibition) and branching, which are both endosome-dependent processes. Our results, therefore, collectively support our theory that Vg-associated aflatoxin inhibition is mediated by an endocytosis-dependent uptake of Vg-prodigiosin, which possibly leads to a disruption of normal endosomal functions.
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Affiliation(s)
| | - Jeffrey W. Cary
- Food and Feed Safety Research Unit, USDA/ARS, Southern Regional Research Center, New Orleans, LA, United States
| | - Matthew D. Lebar
- Food and Feed Safety Research Unit, USDA/ARS, Southern Regional Research Center, New Orleans, LA, United States
| | - Rajtilak Majumdar
- Northwest Irrigation and Soils Research, United States Department of Agriculture, Kimberly, ID, United States
| | - Phani M. Gummadidala
- University of North Carolina School of Medicine, Chapell Hill, NC, United States
| | - Travis Dias
- University of South Carolina School of Medicine, Greenville, NC, United States
| | - Savannah Chandler
- Department of Environmental Health Sciences, University of South Carolina, Columbia, SC, United States
| | - Paramita Basu
- New York College of Podiatric Medicine, New York, NY, United States
| | - Alan W. Decho
- Department of Environmental Health Sciences, University of South Carolina, Columbia, SC, United States
| | - Nancy P. Keller
- Department of Medical Microbiology and Immunology, Department of Plant Pathology, University of Wisconsin-Madison, Madison, WI, United States
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12
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Boruta T. Computation-aided studies related to the induction of specialized metabolite biosynthesis in microbial co-cultures: An introductory overview. Comput Struct Biotechnol J 2023; 21:4021-4029. [PMID: 37649711 PMCID: PMC10462793 DOI: 10.1016/j.csbj.2023.08.011] [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: 05/14/2023] [Revised: 08/14/2023] [Accepted: 08/14/2023] [Indexed: 09/01/2023] Open
Abstract
Co-cultivation is an effective method of inducing the production of specialized metabolites (SMs) in microbial strains. By mimicking the ecological interactions that take place in natural environment, this approach enables to trigger the biosynthesis of molecules which are not formed under monoculture conditions. Importantly, microbial co-cultivation may lead to the discovery of novel chemical entities of pharmaceutical interest. The experimental efforts aimed at the induction of SMs are greatly facilitated by computational techniques. The aim of this overview is to highlight the relevance of computational methods for the investigation of SM induction via microbial co-cultivation. The concepts related to the induction of SMs in microbial co-cultures are briefly introduced by addressing four areas associated with the SM induction workflows, namely the detection of SMs formed exclusively under co-culture conditions, the annotation of induced SMs, the identification of SM producer strains, and the optimization of fermentation conditions. The computational infrastructure associated with these areas, including the tools of multivariate data analysis, molecular networking, genome mining and mathematical optimization, is discussed in relation to the experimental results described in recent literature. The perspective on the future developments in the field, mainly in relation to the microbiome-related research, is also provided.
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Affiliation(s)
- Tomasz Boruta
- Lodz University of Technology, Faculty of Process and Environmental Engineering, Department of Bioprocess Engineering, ul. Wólczańska 213, 93-005 Łódź, Poland
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13
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Zhuo R, Chen Y, Xing M, Zhang Z, Tian S, Li B. Ena Proteins Respond to PacC-Mediated pH Signaling Pathway and Play a Crucial Role in Patulin Biosynthesis. J Fungi (Basel) 2023; 9:806. [PMID: 37623577 PMCID: PMC10455529 DOI: 10.3390/jof9080806] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2023] [Revised: 07/28/2023] [Accepted: 07/28/2023] [Indexed: 08/26/2023] Open
Abstract
Penicillium expansum is a main producer of patulin that causes severe postharvest decay and food safety issues in the fruit industry. Development, pathogenicity, and patulin production of P. expansum are strongly influenced by the PacC-pH signaling pathway. Global transcription factor PacC regulates various fungal biological processes through a complicated molecular network. In the present study, three Ena family genes (PeEnas), PeEnaA, PeEnaB, and PeEnaC, as important downstream targets of PePacC, were identified in P. expansum. Deletion of PeEnaA, PeEnaB, and PeEnaC showed little effect on mycelial growth under alkaline or high salinity conditions, but double and triple deletion of these genes impaired the virulence of P. expansum on apple fruit. Notably, patulin biosynthesis of P. expansum was distinctly inhibited in the deletion mutants of PeEnas. PeEnas regulated expressions of the patulin gene cluster, AP1, CreA, Sge1, and Hog1 at the transcriptional level and played roles in maintaining membrane potential. Overexpression of PeEnaC in ΔPePacC restored the patulin production defect of ΔPePacC. Our results indicated that, as downstream targets of PePacC, the PeEna family proteins play a crucial role in patulin biosynthesis in P. expansum.
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Affiliation(s)
- Ruiling Zhuo
- Key Laboratory of Plant Resources, Institute of Botany, Chinese Academy of Sciences, Beijing 100093, China
- China National Botanical Garden, Beijing 100093, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Yong Chen
- Key Laboratory of Plant Resources, Institute of Botany, Chinese Academy of Sciences, Beijing 100093, China
- China National Botanical Garden, Beijing 100093, China
| | - Mengyang Xing
- Key Laboratory of Plant Resources, Institute of Botany, Chinese Academy of Sciences, Beijing 100093, China
- China National Botanical Garden, Beijing 100093, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Zhanquan Zhang
- Key Laboratory of Plant Resources, Institute of Botany, Chinese Academy of Sciences, Beijing 100093, China
- China National Botanical Garden, Beijing 100093, China
| | - Shiping Tian
- Key Laboratory of Plant Resources, Institute of Botany, Chinese Academy of Sciences, Beijing 100093, China
- China National Botanical Garden, Beijing 100093, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Boqiang Li
- Key Laboratory of Plant Resources, Institute of Botany, Chinese Academy of Sciences, Beijing 100093, China
- China National Botanical Garden, Beijing 100093, China
- Key Laboratory of Post-Harvest Handling of Fruits, Ministry of Agriculture, Beijing 100093, China
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14
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Zhgun AA. Fungal BGCs for Production of Secondary Metabolites: Main Types, Central Roles in Strain Improvement, and Regulation According to the Piano Principle. Int J Mol Sci 2023; 24:11184. [PMID: 37446362 PMCID: PMC10342363 DOI: 10.3390/ijms241311184] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2023] [Revised: 06/28/2023] [Accepted: 07/03/2023] [Indexed: 07/15/2023] Open
Abstract
Filamentous fungi are one of the most important producers of secondary metabolites. Some of them can have a toxic effect on the human body, leading to diseases. On the other hand, they are widely used as pharmaceutically significant drugs, such as antibiotics, statins, and immunosuppressants. A single fungus species in response to various signals can produce 100 or more secondary metabolites. Such signaling is possible due to the coordinated regulation of several dozen biosynthetic gene clusters (BGCs), which are mosaically localized in different regions of fungal chromosomes. Their regulation includes several levels, from pathway-specific regulators, whose genes are localized inside BGCs, to global regulators of the cell (taking into account changes in pH, carbon consumption, etc.) and global regulators of secondary metabolism (affecting epigenetic changes driven by velvet family proteins, LaeA, etc.). In addition, various low-molecular-weight substances can have a mediating effect on such regulatory processes. This review is devoted to a critical analysis of the available data on the "turning on" and "off" of the biosynthesis of secondary metabolites in response to signals in filamentous fungi. To describe the ongoing processes, the model of "piano regulation" is proposed, whereby pressing a certain key (signal) leads to the extraction of a certain sound from the "musical instrument of the fungus cell", which is expressed in the production of a specific secondary metabolite.
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Affiliation(s)
- Alexander A Zhgun
- Group of Fungal Genetic Engineering, Federal Research Center "Fundamentals of Biotechnology", Russian Academy of Sciences, Leninsky Prosp. 33-2, 119071 Moscow, Russia
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15
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Trentin G, Bitencourt TA, Guedes A, Pessoni AM, Brauer VS, Pereira AK, Costa JH, Fill TP, Almeida F. Mass Spectrometry Analysis Reveals Lipids Induced by Oxidative Stress in Candida albicans Extracellular Vesicles. Microorganisms 2023; 11:1669. [PMID: 37512842 PMCID: PMC10383470 DOI: 10.3390/microorganisms11071669] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2023] [Revised: 06/02/2023] [Accepted: 06/06/2023] [Indexed: 07/30/2023] Open
Abstract
Candida albicans is a commensal fungus in healthy humans that causes infection in immunocompromised individuals through the secretion of several virulence factors. The successful establishment of infection is owing to elaborate strategies to cope with defensive molecules secreted by the host, including responses toward oxidative stress. Extracellular vesicle (EV) release is considered an alternative to the biomolecule secretory mechanism that favors fungal interactions with the host cells. During candidiasis establishment, the host environment becomes oxidative, and it impacts EV release and cargo. To simulate the host oxidative environment, we added menadione (an oxidative stress inducer) to the culture medium, and we explored C. albicans EV metabolites by metabolomics analysis. This study characterized lipidic molecules transported to an extracellular milieu by C. albicans after menadione exposure. Through Liquid Chromatography coupled with Mass Spectrometry (LC-MS) analyses, we identified biomolecules transported by EVs and supernatant. The identified molecules are related to several biological processes, such as glycerophospholipid and sphingolipid pathways, which may act at different levels by tuning compound production in accordance with cell requirements that favor a myriad of adaptive responses. Taken together, our results provide new insights into the role of EVs in fungal biology and host-pathogen interactions.
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Affiliation(s)
- Gabriel Trentin
- Department of Biochemistry and Immunology, Ribeirão Preto Medical School, University of São Paulo, Ribeirão Preto 14049-900, Brazil
| | - Tamires A Bitencourt
- Department of Biochemistry and Immunology, Ribeirão Preto Medical School, University of São Paulo, Ribeirão Preto 14049-900, Brazil
| | - Arthur Guedes
- Department of Biochemistry and Immunology, Ribeirão Preto Medical School, University of São Paulo, Ribeirão Preto 14049-900, Brazil
| | - André M Pessoni
- Department of Biochemistry and Immunology, Ribeirão Preto Medical School, University of São Paulo, Ribeirão Preto 14049-900, Brazil
| | - Veronica S Brauer
- Department of Biochemistry and Immunology, Ribeirão Preto Medical School, University of São Paulo, Ribeirão Preto 14049-900, Brazil
| | - Alana Kelyene Pereira
- Department of Organic Chemistry, Institute of Chemistry, University of Campinas, Campinas 13083-970, Brazil
| | - Jonas Henrique Costa
- Department of Organic Chemistry, Institute of Chemistry, University of Campinas, Campinas 13083-970, Brazil
| | - Taicia Pacheco Fill
- Department of Organic Chemistry, Institute of Chemistry, University of Campinas, Campinas 13083-970, Brazil
| | - Fausto Almeida
- Department of Biochemistry and Immunology, Ribeirão Preto Medical School, University of São Paulo, Ribeirão Preto 14049-900, Brazil
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16
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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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17
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Bundela R, Cameron RC, Singh AJ, McLellan RM, Richardson AT, Berry D, Nicholson MJ, Parker EJ. Generation of Alternate Indole Diterpene Architectures in Two Species of Aspergilli. J Am Chem Soc 2023; 145:2754-2758. [PMID: 36710518 PMCID: PMC9913125 DOI: 10.1021/jacs.2c11170] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2022] [Indexed: 01/31/2023]
Abstract
The significant structural diversity and potent bioactivity of the fungal indole diterpenes (IDTs) has attracted considerable interest in their biosynthesis. Although substantial skeletal diversity is generated by the action of noncanonical terpene cyclases, comparatively little is known about these enzymes, particularly those involved in the generation of the subgroup containing emindole SA and DA, which show alternate terpenoid skeletons. Here, we describe the IDT biosynthetic machinery generating these unusual IDT architectures from Aspergillus striatus and Aspergillus desertorum. The function of four putative cyclases was interrogated via heterologous expression. Two specific cyclases were identified that catalyze the formation of epimers emindole SA and DA from A. striatus and A. desertorum, respectively. These cyclases are both clustered along with all the elements required for basic IDT biosynthesis yet catalyze an unusual Markovnikov-like cyclization cascade with alternate stereochemical control. Their identification reveals that these alternate architectures are not generated by mechanistically sloppy or promiscuous enzymes, but by cyclases capable of delivering precise regio- and stereospecificities.
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Affiliation(s)
- Rudranuj Bundela
- Ferrier
Research Institute, Victoria University
of Wellington, PO Box 600, Wellington 6140, New Zealand
- Maurice
Wilkins Centre for Molecular Biodiscovery, Victoria University of Wellington, PO Box 600, Wellington 6140, New Zealand
| | - Rosannah C. Cameron
- Ferrier
Research Institute, Victoria University
of Wellington, PO Box 600, Wellington 6140, New Zealand
- Maurice
Wilkins Centre for Molecular Biodiscovery, Victoria University of Wellington, PO Box 600, Wellington 6140, New Zealand
| | - A. Jonathan Singh
- Ferrier
Research Institute, Victoria University
of Wellington, PO Box 600, Wellington 6140, New Zealand
- Maurice
Wilkins Centre for Molecular Biodiscovery, Victoria University of Wellington, PO Box 600, Wellington 6140, New Zealand
| | - Rose M. McLellan
- Ferrier
Research Institute, Victoria University
of Wellington, PO Box 600, Wellington 6140, New Zealand
- Maurice
Wilkins Centre for Molecular Biodiscovery, Victoria University of Wellington, PO Box 600, Wellington 6140, New Zealand
| | - Alistair T. Richardson
- Ferrier
Research Institute, Victoria University
of Wellington, PO Box 600, Wellington 6140, New Zealand
- Maurice
Wilkins Centre for Molecular Biodiscovery, Victoria University of Wellington, PO Box 600, Wellington 6140, New Zealand
| | - Daniel Berry
- Ferrier
Research Institute, Victoria University
of Wellington, PO Box 600, Wellington 6140, New Zealand
- Maurice
Wilkins Centre for Molecular Biodiscovery, Victoria University of Wellington, PO Box 600, Wellington 6140, New Zealand
| | - Matthew J. Nicholson
- Ferrier
Research Institute, Victoria University
of Wellington, PO Box 600, Wellington 6140, New Zealand
| | - Emily J. Parker
- Ferrier
Research Institute, Victoria University
of Wellington, PO Box 600, Wellington 6140, New Zealand
- Maurice
Wilkins Centre for Molecular Biodiscovery, Victoria University of Wellington, PO Box 600, Wellington 6140, New Zealand
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18
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Yu L, Wen D, Yang Y, Qiu X, Xiong D, Tian C. Comparative Transcriptomic Analysis of MAPK-Mediated Regulation of Pathogenicity, Stress Responses, and Development in Cytospora chrysosperma. PHYTOPATHOLOGY 2023; 113:239-251. [PMID: 36191174 DOI: 10.1094/phyto-04-22-0126-r] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/16/2023]
Abstract
Mitogen-activated protein kinase (MAPK) cascades are highly conserved signal transduction pathways that mediate cellular responses to various biotic and abiotic signals in plant-pathogenic fungi. Generally, there are three MAPKs in filamentous pathogenic fungi: Pmk1/Fus3/Kss1, Hog1, and Stl2. Our previous studies have shown that CcPmk1 is a core regulator of fungal pathogenicity in Cytospora chrysosperma, the causal agent of canker disease in a wide range of woody plants. Here, we identified and functionally characterized the other two MAPK genes (CcHog1 and CcSlt2) and then compared the transcriptional differences among these three MAPKs in C. chrysosperma. We found that the MAPKs shared convergent and distinct roles in fungal development, stress responses, and virulence. For example, CcHog1, CcSlt2, and CcPmk1 were all involved in conidiation and response to stresses, including hyperosmotic pressure, cell wall inhibition agents, and H2O2, but only CcPmk1 and CcSlt2 were required for hyphal growth and fungal pathogenicity. Transcriptomic analysis showed that numerous hyperosmosis- and cell wall-related genes significantly reduced their expression levels in ΔCcHog1 and ΔCcSlt2, respectively. Interestingly, RNA- and ribosome-related processes were significantly enriched in the upregulated genes of ΔCcSlt2, whereas they were significantly enriched in the downregulated genes of ΔCcPmk1. Moreover, two secondary metabolite gene clusters were significantly downregulated in ΔCcPmk1, ΔCcSlt2, and/or ΔCcHog1. Importantly, some virulence-associated genes were significantly downregulated in ΔCcPmk1 and/or ΔCcSlt2, such as candidate effector genes. Collectively, these results suggest that the similar and distinct phenotypes of each MAPK deletion mutant may result from the transcriptional regulation of a series of common or specific downstream genes, which provides a better understanding of the regulation network of MAPKs in C. chrysosperma.
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Affiliation(s)
- Lu Yu
- The Key Laboratory for Silviculture and Conservation of Ministry of Education, College of Forestry, Beijing Forestry University, Beijing, 100083, China
| | - Dasen Wen
- The Key Laboratory for Silviculture and Conservation of Ministry of Education, College of Forestry, Beijing Forestry University, Beijing, 100083, China
| | - Yuchen Yang
- The Key Laboratory for Silviculture and Conservation of Ministry of Education, College of Forestry, Beijing Forestry University, Beijing, 100083, China
| | - Xiaolin Qiu
- The Key Laboratory for Silviculture and Conservation of Ministry of Education, College of Forestry, Beijing Forestry University, Beijing, 100083, China
| | - Dianguang Xiong
- The Key Laboratory for Silviculture and Conservation of Ministry of Education, College of Forestry, Beijing Forestry University, Beijing, 100083, China
| | - Chengming Tian
- The Key Laboratory for Silviculture and Conservation of Ministry of Education, College of Forestry, Beijing Forestry University, Beijing, 100083, China
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19
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Cao F, Ma LF, Hu LS, Xu CX, Chen X, Zhan ZJ, Zhao QW, Mao XM. Coordination of Polyketide Release and Multiple Detoxification Pathways for Tolerable Production of Fungal Mycotoxins. Angew Chem Int Ed Engl 2023; 62:e202214814. [PMID: 36461785 DOI: 10.1002/anie.202214814] [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: 10/08/2022] [Revised: 12/01/2022] [Accepted: 12/02/2022] [Indexed: 12/04/2022]
Abstract
Efficient biosynthesis of microbial bioactive natural products (NPs) is beneficial for the survival of producers, while self-protection is necessary to avoid self-harm resulting from over-accumulation of NPs. The underlying mechanisms for the effective but tolerable production of bioactive NPs are not well understood. Herein, in the biosynthesis of two fungal polyketide mycotoxins aurovertin E (1) and asteltoxin, we show that the cyclases in the gene clusters promote the release of the polyketide backbone, and reveal that a signal peptide is crucial for their subcellular localization and full activity. Meanwhile, the fungus adopts enzymatic acetylation as the major detoxification pathway of 1. If intermediates are over-produced, the non-enzymatic shunt pathways work as salvage pathways to avoid excessive accumulation of the toxic metabolites for self-protection. These findings provided new insight into the interplay of efficient backbone release and multiple detoxification strategies for the production of fungal bioactive NPs.
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Affiliation(s)
- Fei Cao
- Research Center for Clinical Pharmacy, The First Affiliated Hospital & Institute of Pharmaceutical Biotechnology, School of Medicine, Zhejiang University, Hangzhou, 310058, China.,Zhejiang Provincial Key Laboratory for Microbial Biochemistry and Metabolic Engineering, Zhejiang University, Hangzhou, 310058, China
| | - Lie-Feng Ma
- College of Pharmaceutical Science, Zhejiang University of Technology, Hangzhou, 310014, China
| | - Long-Shuang Hu
- Stomatology Hospital, School of Stomatology, Zhejiang University School of Medicine, Clinical Research Center for Oral Diseases of Zhejiang Province, Key Laboratory of Oral Biomedical Research of Zhejiang Province, Cancer Center of Zhejiang University, Hangzhou, 310006, China
| | - Chu-Xuan Xu
- Research Center for Clinical Pharmacy, The First Affiliated Hospital & Institute of Pharmaceutical Biotechnology, School of Medicine, Zhejiang University, Hangzhou, 310058, China.,Zhejiang Provincial Key Laboratory for Microbial Biochemistry and Metabolic Engineering, Zhejiang University, Hangzhou, 310058, China
| | - Xuepeng Chen
- Stomatology Hospital, School of Stomatology, Zhejiang University School of Medicine, Clinical Research Center for Oral Diseases of Zhejiang Province, Key Laboratory of Oral Biomedical Research of Zhejiang Province, Cancer Center of Zhejiang University, Hangzhou, 310006, China
| | - Zha-Jun Zhan
- College of Pharmaceutical Science, Zhejiang University of Technology, Hangzhou, 310014, China
| | - Qing-Wei Zhao
- Research Center for Clinical Pharmacy, The First Affiliated Hospital & Institute of Pharmaceutical Biotechnology, School of Medicine, Zhejiang University, Hangzhou, 310058, China.,Zhejiang Provincial Key Laboratory for Microbial Biochemistry and Metabolic Engineering, Zhejiang University, Hangzhou, 310058, China
| | - Xu-Ming Mao
- Research Center for Clinical Pharmacy, The First Affiliated Hospital & Institute of Pharmaceutical Biotechnology, School of Medicine, Zhejiang University, Hangzhou, 310058, China.,Zhejiang Provincial Key Laboratory for Microbial Biochemistry and Metabolic Engineering, Zhejiang University, Hangzhou, 310058, China
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20
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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: 9] [Impact Index Per Article: 9.0] [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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21
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Llewellyn T, Nowell RW, Aptroot A, Temina M, Prescott TAK, Barraclough TG, Gaya E. Metagenomics Shines Light on the Evolution of "Sunscreen" Pigment Metabolism in the Teloschistales (Lichen-Forming Ascomycota). Genome Biol Evol 2023; 15:6986375. [PMID: 36634008 PMCID: PMC9907504 DOI: 10.1093/gbe/evad002] [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: 09/26/2022] [Revised: 11/25/2022] [Accepted: 01/09/2023] [Indexed: 01/13/2023] Open
Abstract
Fungi produce a vast number of secondary metabolites that shape their interactions with other organisms and the environment. Characterizing the genes underpinning metabolite synthesis is therefore key to understanding fungal evolution and adaptation. Lichenized fungi represent almost one-third of Ascomycota diversity and boast impressive secondary metabolites repertoires. However, most lichen biosynthetic genes have not been linked to their metabolite products. Here we used metagenomic sequencing to survey gene families associated with production of anthraquinones, UV-protectant secondary metabolites present in various fungi, but especially abundant in a diverse order of lichens, the Teloschistales (class Lecanoromycetes, phylum Ascomycota). We successfully assembled 24 new, high-quality lichenized-fungal genomes de novo and combined them with publicly available Lecanoromycetes genomes from taxa with diverse secondary chemistry to produce a whole-genome tree. Secondary metabolite biosynthetic gene cluster (BGC) analysis showed that whilst lichen BGCs are numerous and highly dissimilar, core enzyme genes are generally conserved across taxa. This suggests metabolite diversification occurs via re-shuffling existing enzyme genes with novel accessory genes rather than BGC gains/losses or de novo gene evolution. We identified putative anthraquinone BGCs in our lichen dataset that appear homologous to anthraquinone clusters from non-lichenized fungi, suggesting these genes were present in the common ancestor of the subphylum Pezizomycotina. Finally, we identified unique transporter genes in Teloschistales anthraquinone BGCs that may explain why these metabolites are so abundant and ubiquitous in these lichens. Our results support the importance of metagenomics for understanding the secondary metabolism of non-model fungi such as lichens.
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Affiliation(s)
| | - Reuben W Nowell
- Department of Life Sciences, Imperial College London, Silwood Park Campus, Ascot, Berkshire, SL5 7PY, UK,Department of Biology, University of Oxford, 11a Mansfield Road, Oxford, OX1 3SZ, UK
| | - Andre Aptroot
- Instituto de Biociências, Universidade Federal de Mato Grosso do Sul, Avenida Costa e Silva s/n Bairro Universitário, Campo Grande, Mato Grosso do Sul CEP 79070-900, Brazil
| | - Marina Temina
- Institute of Evolution, University of Haifa, 199 Aba Khoushy Ave, Mount Carmel, Haifa, 3498838, Israel
| | - Thomas A K Prescott
- Comparative Fungal Biology, Royal Botanic Gardens, Kew, Jodrell Laboratory, Richmond, TW9 3DS, UK
| | - Timothy G Barraclough
- Department of Life Sciences, Imperial College London, Silwood Park Campus, Ascot, Berkshire, SL5 7PY, UK,Department of Biology, University of Oxford, 11a Mansfield Road, Oxford, OX1 3SZ, UK
| | - Ester Gaya
- Comparative Fungal Biology, Royal Botanic Gardens, Kew, Jodrell Laboratory, Richmond, TW9 3DS, UK
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22
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Loi M, Logrieco AF, Pusztahelyi T, Leiter É, Hornok L, Pócsi I. Advanced mycotoxin control and decontamination techniques in view of an increased aflatoxin risk in Europe due to climate change. Front Microbiol 2023; 13:1085891. [PMID: 36762096 PMCID: PMC9907446 DOI: 10.3389/fmicb.2022.1085891] [Citation(s) in RCA: 12] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2022] [Accepted: 12/15/2022] [Indexed: 01/11/2023] Open
Abstract
Aflatoxins are toxic secondary metabolites produced by Aspergillus spp. found in staple food and feed commodities worldwide. Aflatoxins are carcinogenic, teratogenic, and mutagenic, and pose a serious threat to the health of both humans and animals. The global economy and trade are significantly affected as well. Various models and datasets related to aflatoxins in maize have been developed and used but have not yet been linked. The prevention of crop loss due to aflatoxin contamination is complex and challenging. Hence, the set-up of advanced decontamination is crucial to cope with the challenge of climate change, growing population, unstable political scenarios, and food security problems also in European countries. After harvest, decontamination methods can be applied during transport, storage, or processing, but their application for aflatoxin reduction is still limited. Therefore, this review aims to investigate the effects of environmental factors on aflatoxin production because of climate change and to critically discuss the present-day and novel decontamination techniques to unravel gaps and limitations to propose them as a tool to tackle an increased aflatoxin risk in Europe.
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Affiliation(s)
- Martina Loi
- Institute of Sciences of Food Production, National Research Council, Bari, Italy,*Correspondence: Martina Loi, ✉
| | - Antonio F. Logrieco
- Institute of Sciences of Food Production, National Research Council, Bari, Italy
| | - Tünde Pusztahelyi
- Central Laboratory of Agricultural and Food Products, Faculty of Agricultural and Food Sciences and Environmental Management, University of Debrecen, Debrecen, Hungary
| | - Éva Leiter
- Department of Molecular Biotechnology and Microbiology, Faculty of Science and Technology, Institute of Biotechnology, University of Debrecen, Debrecen, Hungary,ELRN-UD Fungal Stress Biology Research Group, University of Debrecen, Debrecen, Hungary
| | - László Hornok
- Hungarian University of Agriculture and Life Sciences, Gödöllő, Hungary
| | - István Pócsi
- Department of Molecular Biotechnology and Microbiology, Faculty of Science and Technology, Institute of Biotechnology, University of Debrecen, Debrecen, Hungary,ELRN-UD Fungal Stress Biology Research Group, University of Debrecen, Debrecen, Hungary
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Depsipeptides Targeting Tumor Cells: Milestones from In Vitro to Clinical Trials. MOLECULES (BASEL, SWITZERLAND) 2023; 28:molecules28020670. [PMID: 36677728 PMCID: PMC9864405 DOI: 10.3390/molecules28020670] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/15/2022] [Revised: 12/15/2022] [Accepted: 12/16/2022] [Indexed: 01/11/2023]
Abstract
Cancer is currently considered one of the most threatening diseases worldwide. Diet could be one of the factors that can be enhanced to comprehensively address a cancer patient's condition. Unfortunately, most molecules capable of targeting cancer cells are found in uncommon food sources. Among them, depsipeptides have emerged as one of the most reliable choices for cancer treatment. These cyclic amino acid oligomers, with one or more subunits replaced by a hydroxylated carboxylic acid resulting in one lactone bond in a core ring, have broadly proven their cancer-targeting efficacy, some even reaching clinical trials and being commercialized as "anticancer" drugs. This review aimed to describe these depsipeptides, their reported amino acid sequences, determined structure, and the specific mechanism by which they target tumor cells including apoptosis, oncosis, and elastase inhibition, among others. Furthermore, we have delved into state-of-the-art in vivo and clinical trials, current methods for purification and synthesis, and the recognized disadvantages of these molecules. The information collated in this review can help researchers decide whether these molecules should be incorporated into functional foods in the near future.
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Deng H, Liang X, Liu J, Zheng X, Fan TP, Cai Y. Advances and perspectives on perylenequinone biosynthesis. Front Microbiol 2022; 13:1070110. [PMID: 36605511 PMCID: PMC9808054 DOI: 10.3389/fmicb.2022.1070110] [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: 10/14/2022] [Accepted: 11/21/2022] [Indexed: 12/24/2022] Open
Abstract
Under illumination, the fungal secondary metabolites, perylenequinones (PQs) react with molecular oxygen to generate reactive oxygen species (ROS), which, in excess can damage cellular macromolecules and trigger apoptosis. Based on this property, PQs have been widely used as photosensitizers and applied in pharmaceuticals, which has stimulated research into the discovery of new PQs and the elucidation of their biosynthetic pathways. The PQs-associated literature covering from April 1967 to September 2022 is reviewed in three sections: (1) the sources, structural diversity, and biological activities of microbial PQs; (2) elucidation of PQ biosynthetic pathways, associated genes, and mechanisms of regulation; and (3) advances in pathway engineering and future potential strategies to modify cellular metabolism and improve PQ production.
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Affiliation(s)
- Huaxiang Deng
- Center for Synthetic Biochemistry, Shenzhen Institute of Synthetic Biology, Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences, Shenzhen, China,The Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi, Jiangsu, China,*Correspondence: Huaxiang Deng,
| | - Xinxin Liang
- The Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi, Jiangsu, China
| | - Jinbin Liu
- School of Marine and Bioengineering, Yancheng Institute of Technology, Yancheng, Jiangsu, China
| | - Xiaohui Zheng
- College of Life Sciences, Northwest University, Xi’an, Shanxi, China
| | - Tai-Ping Fan
- Department of Pharmacology, University of Cambridge, Cambridge, United Kingdom
| | - Yujie Cai
- The Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi, Jiangsu, China,Yujie Cai,
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25
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Genomic diversification of the specialized parasite of the fungus-growing ant symbiosis. Proc Natl Acad Sci U S A 2022; 119:e2213096119. [PMID: 36508678 PMCID: PMC9907069 DOI: 10.1073/pnas.2213096119] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022] Open
Abstract
Fungi shape the diversity of life. Characterizing the evolution of fungi is critical to understanding symbiotic associations across kingdoms. In this study, we investigate the genomic and metabolomic diversity of the genus Escovopsis, a specialized parasite of fungus-growing ant gardens. Based on 25 high-quality draft genomes, we show that Escovopsis forms a monophyletic group arising from a mycoparasitic fungal ancestor 61.82 million years ago (Mya). Across the evolutionary history of fungus-growing ants, the dates of origin of most clades of Escovopsis correspond to the dates of origin of the fungus-growing ants whose gardens they parasitize. We reveal that genome reduction, determined by both genomic sequencing and flow cytometry, is a consistent feature across the genus Escovopsis, largely occurring in coding regions, specifically in the form of gene loss and reductions in copy numbers of genes. All functional gene categories have reduced copy numbers, but resistance and virulence genes maintain functional diversity. Biosynthetic gene clusters (BGCs) contribute to phylogenetic differences among Escovopsis spp., and sister taxa in the Hypocreaceae. The phylogenetic patterns of co-diversification among BGCs are similarly exhibited across mass spectrometry analyses of the metabolomes of Escovopsis and their sister taxa. Taken together, our results indicate that Escovopsis spp. evolved unique genomic repertoires to specialize on the fungus-growing ant-microbe symbiosis.
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The Multifaceted Gene 275 Embedded in the PKS-PTS Gene Cluster Was Involved in the Regulation of Arthrobotrisin Biosynthesis, TCA Cycle, and Septa Formation in Nematode-Trapping Fungus Arthrobotrys oligospora. J Fungi (Basel) 2022; 8:jof8121261. [PMID: 36547594 PMCID: PMC9780802 DOI: 10.3390/jof8121261] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2022] [Revised: 11/25/2022] [Accepted: 11/28/2022] [Indexed: 12/03/2022] Open
Abstract
The predominant nematode-trapping fungus Arthrobotrys oligospora harbors a unique polyketide synthase-prenyltransferase (PKS-PTS) gene cluster AOL_s00215g responsible for the biosynthesis of sesquiterpenyl epoxy-cyclohexenoids (SECs) that are involved in the regulation of fungal growth, adhesive trap formation, antibacterial activity, and soil colonization. However, the function of one rare gene (AOL_s00215g275 (275)) embedded in the cluster has remained cryptic. Here, we constructed two mutants with the disruption of 275 and the overexpression of 275, respectively, and compared their fungal growth, morphology, resistance to chemical stress, nematicidal activity, transcriptomic and metabolic profiles, and infrastructures, together with binding affinity analysis. Both mutants displayed distinct differences in their TCA cycles, SEC biosynthesis, and endocytosis, combined with abnormal mitochondria, vacuoles, septa formation, and decreased nematicidal activity. Our results suggest that gene 275 might function as a separator and as an integrated gene with multiple potential functions related to three distinct genes encoding the retinoic acid induced-1, cortactin, and vacuolar iron transporter 1 proteins in this nematode-trapping fungus. Our unexpected findings provide insight into the intriguing organization and functions of a rare non-biosynthetic gene in a biosynthetic gene cluster.
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Quantitative characterization of filamentous fungal promoters on a single-cell resolution to discover cryptic natural products. SCIENCE CHINA LIFE SCIENCES 2022; 66:848-860. [PMID: 36287342 DOI: 10.1007/s11427-022-2175-0] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/30/2022] [Accepted: 08/15/2022] [Indexed: 11/05/2022]
Abstract
Characterization of filamentous fungal regulatory elements remains challenging because of time-consuming transformation technologies and limited quantitative methods. Here we established a method for quantitative assessment of filamentous fungal promoters based on flow cytometry detection of the superfolder green fluorescent protein at single-cell resolution. Using this quantitative method, we acquired a library of 93 native promoter elements from Aspergillus nidulans in a high-throughput format. The strengths of identified promoters covered a 37-fold range by flow cytometry. PzipA and PsltA were identified as the strongest promoters, which were 2.9- and 1.5-fold higher than that of the commonly used constitutive promoter PgpdA. Thus, we applied PzipA and PsltA to activate the silent nonribosomal peptide synthetase gene Afpes1 from Aspergillus fumigatus in its native host and the heterologous host A. nidulans. The metabolic products of Afpes1 were identified as new cyclic tetrapeptide derivatives, namely, fumiganins A and B. Our method provides an innovative strategy for natural product discovery in fungi.
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Genome-wide association mapping reveals genes underlying population-level metabolome diversity in a fungal crop pathogen. BMC Biol 2022; 20:224. [PMID: 36209159 PMCID: PMC9548119 DOI: 10.1186/s12915-022-01422-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2022] [Accepted: 09/27/2022] [Indexed: 11/12/2022] Open
Abstract
Background Fungi produce a wide range of specialized metabolites (SMs) involved in biotic interactions. Pathways for the production of SMs are often encoded in clusters of tightly arranged genes identified as biosynthetic gene clusters. Such gene clusters can undergo horizontal gene transfers between species and rapid evolutionary change within species. The acquisition, rearrangement, and deletion of gene clusters can generate significant metabolome diversity. However, the genetic basis underlying variation in SM production remains poorly understood. Results Here, we analyzed the metabolite production of a large population of the fungal pathogen of wheat, Zymoseptoria tritici. The pathogen causes major yield losses and shows variation in gene clusters. We performed untargeted ultra-high performance liquid chromatography-high resolution mass spectrometry to profile the metabolite diversity among 102 isolates of the same species. We found substantial variation in the abundance of the detected metabolites among isolates. Integrating whole-genome sequencing data, we performed metabolite genome-wide association mapping to identify loci underlying variation in metabolite production (i.e., metabolite-GWAS). We found that significantly associated SNPs reside mostly in coding and gene regulatory regions. Associated genes encode mainly transport and catalytic activities. The metabolite-GWAS identified also a polymorphism in the 3′UTR region of a virulence gene related to metabolite production and showing expression variation. Conclusions Taken together, our study provides a significant resource to unravel polymorphism underlying metabolome diversity within a species. Integrating metabolome screens should be feasible for a range of different plant pathogens and help prioritize molecular studies. Supplementary Information The online version contains supplementary material available at 10.1186/s12915-022-01422-z.
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Zhang X, Xu D, Hou X, Wei P, Fu J, Zhao Z, Jing M, Lai D, Yin W, Zhou L. UvSorA and UvSorB Involved in Sorbicillinoid Biosynthesis Contribute to Fungal Development, Stress Response and Phytotoxicity in Ustilaginoidea virens. Int J Mol Sci 2022; 23:ijms231911056. [PMID: 36232357 PMCID: PMC9570055 DOI: 10.3390/ijms231911056] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2022] [Revised: 09/14/2022] [Accepted: 09/16/2022] [Indexed: 11/18/2022] Open
Abstract
Ustilaginoidea virens (teleomorph: Villosiclava virens) is an important fungal pathogen that causes a devastating rice disease. It can produce mycotoxins including sorbicillinoids. The biosynthesis and biological functions of sorbicillinoids have not been reported in U. virens. In this study, we identified a sorbicillinoid biosynthetic gene cluster in which two polyketide synthase genes UvSorA and UvSorB were responsible for sorbicillinoid biosynthesis in U. virens. In ∆UvSorA and ∆UvSorB mutants, the mycelial growth, sporulation and hyphal hydrophobicity were increased dramatically, while the resistances to osmotic pressure, metal cations, and fungicides were reduced. Both phytotoxic activity of rice germinated seeds and cell wall integrity were also reduced. Furthermore, mycelia and cell walls of ∆UvSorA and ∆UvSorB mutants showed alterations of microscopic and submicroscopic structures. In addition, feeding experiment showed that sorbicillinoids could restore mycelial growth, sporulation, and cell wall integrity in ∆UvSorA and ∆UvSorB mutants. The results demonstrated that both UvSorA and UvSorB were responsible for sorbicillinoid biosynthesis in U. virens, and contributed to development (mycelial growth, sporulation, and cell wall integrity), stress responses, and phytotoxicity through sorbicillinoid mediation. It provides an insight into further investigation of biological functions and biosynthesis of sorbicillinoids.
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Affiliation(s)
- Xuping Zhang
- State Key Laboratory of Agrobiotechnology, Department of Plant Pathology, College of Plant Protection, China Agricultural University, Beijing 100193, China
| | - Dan Xu
- State Key Laboratory of Agrobiotechnology, Department of Plant Pathology, College of Plant Protection, China Agricultural University, Beijing 100193, China
| | - Xuwen Hou
- State Key Laboratory of Agrobiotechnology, Department of Plant Pathology, College of Plant Protection, China Agricultural University, Beijing 100193, China
| | - Penglin Wei
- State Key Laboratory of Mycology, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China
| | - Jiajin Fu
- State Key Laboratory of Agrobiotechnology, Department of Plant Pathology, College of Plant Protection, China Agricultural University, Beijing 100193, China
| | - Zhitong Zhao
- State Key Laboratory of Agrobiotechnology, Department of Plant Pathology, College of Plant Protection, China Agricultural University, Beijing 100193, China
| | - Mingpeng Jing
- State Key Laboratory of Agrobiotechnology, Department of Plant Pathology, College of Plant Protection, China Agricultural University, Beijing 100193, China
| | - Daowan Lai
- State Key Laboratory of Agrobiotechnology, Department of Plant Pathology, College of Plant Protection, China Agricultural University, Beijing 100193, China
| | - Wenbing Yin
- State Key Laboratory of Mycology, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China
- Correspondence: (W.Y.); (L.Z.)
| | - Ligang Zhou
- State Key Laboratory of Agrobiotechnology, Department of Plant Pathology, College of Plant Protection, China Agricultural University, Beijing 100193, China
- Correspondence: (W.Y.); (L.Z.)
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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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Sayari M, Dolatabadian A, El-Shetehy M, Rehal PK, Daayf F. Genome-Based Analysis of Verticillium Polyketide Synthase Gene Clusters. BIOLOGY 2022; 11:biology11091252. [PMID: 36138731 PMCID: PMC9495618 DOI: 10.3390/biology11091252] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/06/2022] [Revised: 08/11/2022] [Accepted: 08/15/2022] [Indexed: 11/16/2022]
Abstract
Simple Summary Fungi can produce many types of secondary metabolites, including mycotoxins. Poisonous mushrooms and mycotoxins that cause food spoilage have been known for a very long time. For example, Aspergillus flavus, which can grow on grains and nuts, produces highly toxic substances called Aflatoxins. Despite their menace to other living organisms, mycotoxins can be used for medicinal purposes, i.e., as antibiotics, growth-promoting compounds, and other kinds of drugs. These and other secondary metabolites produced by plant-pathogenic fungi may cause host plants to display disease symptoms and may play a substantial role in disease progression. Therefore, the identification and characterization of the genes involved in their biosynthesis are essential for understanding the molecular mechanism involved in their biosynthetic pathways and further promoting sustainable knowledge-based crop production. Abstract Polyketides are structurally diverse and physiologically active secondary metabolites produced by many organisms, including fungi. The biosynthesis of polyketides from acyl-CoA thioesters is catalyzed by polyketide synthases, PKSs. Polyketides play roles including in cell protection against oxidative stress, non-constitutive (toxic) roles in cell membranes, and promoting the survival of the host organisms. The genus Verticillium comprises many species that affect a wide range of organisms including plants, insects, and other fungi. Many are known as causal agents of Verticillium wilt diseases in plants. In this study, a comparative genomics approach involving several Verticillium species led us to evaluate the potential of Verticillium species for producing polyketides and to identify putative polyketide biosynthesis gene clusters. The next step was to characterize them and predict the types of polyketide compounds they might produce. We used publicly available sequences from ten species of Verticillium including V. dahliae, V. longisporum, V. nonalfalfae, V. alfalfae, V. nubilum, V. zaregamsianum, V. klebahnii, V. tricorpus, V. isaacii, and V. albo-atrum to identify and characterize PKS gene clusters by utilizing a range of bioinformatic and phylogenetic approaches. We found 32 putative PKS genes and possible clusters in the genomes of Verticillium species. All the clusters appear to be complete and functional. In addition, at least five clusters including putative DHN-melanin-, cytochalasin-, fusarielien-, fujikurin-, and lijiquinone-like compounds may belong to the active PKS repertoire of Verticillium. These results will pave the way for further functional studies to understand the role of these clusters.
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Affiliation(s)
- Mohammad Sayari
- Department of Plant Science, Faculty of Agricultural and Food Sciences, University of Manitoba, 222 Agriculture Building, Winnipeg, MB R3T 2N2, Canada
| | - Aria Dolatabadian
- Department of Plant Science, Faculty of Agricultural and Food Sciences, University of Manitoba, 222 Agriculture Building, Winnipeg, MB R3T 2N2, Canada
| | - Mohamed El-Shetehy
- Department of Plant Science, Faculty of Agricultural and Food Sciences, University of Manitoba, 222 Agriculture Building, Winnipeg, MB R3T 2N2, Canada
- Department of Botany, Faculty of Science, Tanta University, Tanta 31527, Egypt
| | - Pawanpuneet Kaur Rehal
- Department of Plant Science, Faculty of Agricultural and Food Sciences, University of Manitoba, 222 Agriculture Building, Winnipeg, MB R3T 2N2, Canada
| | - Fouad Daayf
- Department of Plant Science, Faculty of Agricultural and Food Sciences, University of Manitoba, 222 Agriculture Building, Winnipeg, MB R3T 2N2, Canada
- Correspondence:
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Ren H, Li X, Li Y, Li M, Sun J, Wang F, Zeng J, Chen Y, Wang L, Yan X, Fan Y, Jin D, Pei Y. Loss of function of VdDrs2, a P4-ATPase, impairs the toxin secretion and microsclerotia formation, and decreases the pathogenicity of Verticillium dahliae. FRONTIERS IN PLANT SCIENCE 2022; 13:944364. [PMID: 36072318 PMCID: PMC9443849 DOI: 10.3389/fpls.2022.944364] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 05/26/2022] [Accepted: 07/25/2022] [Indexed: 06/15/2023]
Abstract
Four P4-ATPase flippase genes, VdDrs2, VdNeo1, VdP4-4, and VdDnf1 were identified in Verticillium dahliae, one of the most devastating phytopathogenic fungi in the world. Knock out of VdDrs2, VdNeo1, and VdP4-4, or knock down of VdDnf1 significantly decreased the pathogenicity of the mutants in cotton. Among the mutants, the greatest decrease in pathogenicity was observed in ΔVdDrs2. VdDrs2 was localized to plasma membrane, vacuoles, and trans-Golgi network (TGN). In vivo observation showed that the infection of the cotton by ΔVdDrs2 was significantly delayed. The amount of two known Verticillium toxins, sulfacetamide, and fumonisin B1 in the fermentation broth produced by the ΔVdDrs2 strain was significantly reduced, and the toxicity of the crude Verticillium wilt toxins to cotton cells was attenuated. In addition, the defect of VdDrs2 impaired the synthesis of melanin and the formation of microsclerotia, and decreased the sporulation of V. dahliae. Our data indicate a key role of P4 ATPases-associated vesicle transport in toxin secretion of disease fungi and support the importance of mycotoxins in the pathogenicity of V. dahliae.
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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: 38] [Impact Index Per Article: 19.0] [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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Toopaang W, Bunnak W, Srisuksam C, Wattananukit W, Tanticharoen M, Yang YL, Amnuaykanjanasin A. Microbial polyketides and their roles in insect virulence: from genomics to biological functions. Nat Prod Rep 2022; 39:2008-2029. [PMID: 35822627 DOI: 10.1039/d1np00058f] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Covering: May 1966 up to January 2022Entomopathogenic microorganisms have potential for biological control of insect pests. Their main secondary metabolites include polyketides, nonribosomal peptides, and polyketide-nonribosomal peptide (PK-NRP) hybrids. Among these secondary metabolites, polyketides have mainly been studied for structural identification, pathway engineering, and for their contributions to medicine. However, little is known about the function of polyketides in insect virulence. This review focuses on the role of bacterial and fungal polyketides, as well as PK-NRP hybrids in insect infection and killing. We also discuss gene distribution and evolutional relationships among different microbial species. Further, the role of microbial polyketides and the hybrids in modulating insect-microbial symbiosis is also explored. Understanding the mechanisms of polyketides in insect pathogenesis, how compounds moderate the host-fungus interaction, and the distribution of PKS genes across different fungi and bacteria will facilitate the discovery and development of novel polyketide-derived bio-insecticides.
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Affiliation(s)
- Wachiraporn Toopaang
- National Center for Genetic Engineering and Biotechnology, National Science and Technology Development Agency, 113 Thailand Science Park, Phahonyothin Rd., Khlong Nueng, Amphoe Khlong Luang, Pathum Thani 12120, Thailand. .,Molecular and Biological Agricultural Sciences, Taiwan International Graduate Program, Academia Sinica and National Chung Hsing University, Taiwan.,Agricultural Biotechnology Research Center, Academia Sinica, Taipei 11529, Taiwan.
| | - Warapon Bunnak
- National Center for Genetic Engineering and Biotechnology, National Science and Technology Development Agency, 113 Thailand Science Park, Phahonyothin Rd., Khlong Nueng, Amphoe Khlong Luang, Pathum Thani 12120, Thailand.
| | - Chettida Srisuksam
- National Center for Genetic Engineering and Biotechnology, National Science and Technology Development Agency, 113 Thailand Science Park, Phahonyothin Rd., Khlong Nueng, Amphoe Khlong Luang, Pathum Thani 12120, Thailand.
| | - Wilawan Wattananukit
- National Center for Genetic Engineering and Biotechnology, National Science and Technology Development Agency, 113 Thailand Science Park, Phahonyothin Rd., Khlong Nueng, Amphoe Khlong Luang, Pathum Thani 12120, Thailand.
| | - Morakot Tanticharoen
- School of Bioresources and Technology, King Mongkut's University of Technology Thonburi, Bangkok 10140, Thailand
| | - Yu-Liang Yang
- Agricultural Biotechnology Research Center, Academia Sinica, Taipei 11529, Taiwan. .,Biotechnology Center in Southern Taiwan, Academia Sinica, Tainan 711010, Taiwan
| | - Alongkorn Amnuaykanjanasin
- National Center for Genetic Engineering and Biotechnology, National Science and Technology Development Agency, 113 Thailand Science Park, Phahonyothin Rd., Khlong Nueng, Amphoe Khlong Luang, Pathum Thani 12120, Thailand.
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Almeida H, Tsang A, Diallo AB. Improving candidate Biosynthetic Gene Clusters in fungi through reinforcement learning. Bioinformatics 2022; 38:3984-3991. [PMID: 35762945 PMCID: PMC9364373 DOI: 10.1093/bioinformatics/btac420] [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: 09/02/2021] [Revised: 05/17/2022] [Accepted: 06/23/2022] [Indexed: 12/24/2022] Open
Abstract
MOTIVATION Precise identification of Biosynthetic Gene Clusters (BGCs) is a challenging task. Performance of BGC discovery tools is limited by their capacity to accurately predict components belonging to candidate BGCs, often overestimating cluster boundaries. To support optimizing the composition and boundaries of candidate BGCs, we propose reinforcement learning approach relying on protein domains and functional annotations from expert curated BGCs. RESULTS The proposed reinforcement learning method aims to improve candidate BGCs obtained with state-of-the-art tools. It was evaluated on candidate BGCs obtained for two fungal genomes, Aspergillus niger and Aspergillus nidulans. The results highlight an improvement of the gene precision by above 15% for TOUCAN, fungiSMASH and DeepBGC; and cluster precision by above 25% for fungiSMASH and DeepBCG, allowing these tools to obtain almost perfect precision in cluster prediction. This can pave the way of optimizing current prediction of candidate BGCs in fungi, while minimizing the curation effort required by domain experts. AVAILABILITY AND IMPLEMENTATION https://github.com/bioinfoUQAM/RL-bgc-components. SUPPLEMENTARY INFORMATION Supplementary data are available at Bioinformatics online.
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Affiliation(s)
- Hayda Almeida
- Departement d’Informatique, UQAM, Montréal, QC H2X 3Y7, Canada,Centre for Structural and Functional Genomics, Concordia University, Montréal, QC H4B 1R6, Canada,Laboratoire d’Algèbre, de Combinatoire, et d’Informatique Mathématique (LACIM), UQAM, Montréal, QC H2X 3Y, Canada
| | - Adrian Tsang
- Departement d’Informatique, UQAM, Montréal, QC H2X 3Y7, Canada,Centre for Structural and Functional Genomics, Concordia University, Montréal, QC H4B 1R6, Canada
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Dey P, Malik A, Singh DK, Haange SB, von Bergen M, Jehmlich N. Insight Into the Molecular Mechanisms Underpinning the Mycoremediation of Multiple Metals by Proteomic Technique. Front Microbiol 2022; 13:872576. [PMID: 35756008 PMCID: PMC9221998 DOI: 10.3389/fmicb.2022.872576] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2022] [Accepted: 04/07/2022] [Indexed: 11/13/2022] Open
Abstract
We investigated the fungus Aspergillus fumigatus PD-18 responses when subjected to the multimetal combination (Total Cr, Cd2+, Cu2+, Ni2+, Pb2+, and Zn2+) in synthetic composite media. To understand how multimetal stress impacts fungal cells at the molecular level, the cellular response of A. fumigatus PD-18 to 30 mg/L multimetal stress (5 mg/L of each heavy metal) was determined by proteomics. The comparative fungal proteomics displayed the remarkable inherent intracellular and extracellular mechanism of metal resistance and tolerance potential of A. fumigatus PD-18. This study reported 2,238 proteins of which 434 proteins were exclusively expressed in multimetal extracts. The most predominant functional class expressed was for cellular processing and signaling. The type of proteins and the number of proteins that were upregulated due to various stress tolerance mechanisms were post-translational modification, protein turnover, and chaperones (42); translation, ribosomal structure, and biogenesis (60); and intracellular trafficking, secretion, and vesicular transport (18). In addition, free radical scavenging antioxidant proteins, such as superoxide dismutase, were upregulated upto 3.45-fold and transporter systems, such as protein transport (SEC31), upto 3.31-fold to combat the oxidative stress caused by the multiple metals. Also, protein–protein interaction network analysis revealed that cytochrome c oxidase and 60S ribosomal protein played key roles to detoxify the multimetal. To the best of our knowledge, this study of A. fumigatus PD-18 provides valuable insights toward the growing research in comprehending the metal microbe interactions in the presence of multimetal. This will facilitate in development of novel molecular markers for contaminant bioremediation.
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Affiliation(s)
- Priyadarshini Dey
- Applied Microbiology Lab, Centre for Rural Development and Technology, Indian Institute of Technology Delhi, New Delhi, India
- Department of Molecular Systems Biology, Helmholtz Centre for Environmental Research, Helmholtz Association of German Research Centres (HZ), Leipzig, Germany
- Department of Biotechnology, MS Ramaiah Institute of Technology, Bengaluru, India
| | - Anushree Malik
- Applied Microbiology Lab, Centre for Rural Development and Technology, Indian Institute of Technology Delhi, New Delhi, India
| | - Dileep Kumar Singh
- Department of Zoology, Faculty of Science, University of Delhi, New Delhi, India
| | - Sven-Bastiaan Haange
- Department of Molecular Systems Biology, Helmholtz Centre for Environmental Research, Helmholtz Association of German Research Centres (HZ), Leipzig, Germany
| | - Martin von Bergen
- Department of Molecular Systems Biology, Helmholtz Centre for Environmental Research, Helmholtz Association of German Research Centres (HZ), Leipzig, Germany
- Institute of Biochemistry, Faculty of Biosciences, Pharmacy and Psychology, University of Leipzig, Leipzig, Germany
- German Centre for Integrative Biodiversity, Research (iDiv) Halle-Jena-Leipzig, Leipzig, Germany
| | - Nico Jehmlich
- Department of Molecular Systems Biology, Helmholtz Centre for Environmental Research, Helmholtz Association of German Research Centres (HZ), Leipzig, Germany
- *Correspondence: Nico Jehmlich,
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Skellam E. Subcellular localization of fungal specialized metabolites. Fungal Biol Biotechnol 2022; 9:11. [PMID: 35614515 PMCID: PMC9134587 DOI: 10.1186/s40694-022-00140-z] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2022] [Accepted: 05/10/2022] [Indexed: 01/07/2023] Open
Abstract
Fungal specialized metabolites play an important role in the environment and have impacted human health and survival significantly. These specialized metabolites are often the end product of a series of sequential and collaborating biosynthetic enzymes that reside within different subcellular compartments. A wide variety of methods have been developed to understand fungal specialized metabolite biosynthesis in terms of the chemical conversions and the biosynthetic enzymes required, however there are far fewer studies elucidating the compartmentalization of the same enzymes. This review illustrates the biosynthesis of specialized metabolites where the localization of all, or some, of the biosynthetic enzymes have been determined and describes the methods used to identify the sub-cellular localization.
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Affiliation(s)
- Elizabeth Skellam
- Department of Chemistry and BioDiscovery Institute, University of North Texas, 1155 Union Circle, Denton, TX, 76201, USA.
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Gaspar ML, Pawlowska TE. Innate immunity in fungi: Is regulated cell death involved? PLoS Pathog 2022; 18:e1010460. [PMID: 35587923 PMCID: PMC9119436 DOI: 10.1371/journal.ppat.1010460] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022] Open
Affiliation(s)
- Maria Laura Gaspar
- School of Integrative Plant Science, Cornell University, Ithaca, New York, United States of America
| | - Teresa E. Pawlowska
- School of Integrative Plant Science, Cornell University, Ithaca, New York, United States of America
- * E-mail:
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Akiyama DY, Rocha MC, Costa JH, Teles CB, da Silva Zuccoli G, Malavazi I, Fill TP. The Penicillium brasilianum Histone Deacetylase Clr3 Regulates Secondary Metabolite Production and Tolerance to Oxidative Stress. J Fungi (Basel) 2022; 8:jof8050514. [PMID: 35628769 PMCID: PMC9146837 DOI: 10.3390/jof8050514] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2022] [Revised: 05/10/2022] [Accepted: 05/13/2022] [Indexed: 02/01/2023] Open
Abstract
Most of the biosynthetic gene clusters (BGCs) found in microbes are silent under standard laboratory cultivation conditions due to the lack of expression triggering stimuli, representing a considerable drawback in drug discovery. To access the full biosynthetic potential, studies towards the activation of cryptic BGCs are essential. Histone acetylation status is an important regulator of chromatin structure, which impacts cell physiology and the expression of BGCs. In this study, clr3, a gene encoding a histone deacetylase in Penicillium brasilianum LaBioMMi 136, is deleted and associated phenotypic and metabolic changes are evaluated. The results indicate reduced growth under oxidative stress conditions in the ∆clr3 strain, higher intracellular reactive oxygen species (ROS) levels, and a different transcriptional profile of 13 ROS-related genes of both strains under basal and ROS-induced conditions. Moreover, the production of 14 secondary metabolites, including austin-related meroterpenoids, brasiliamides, verruculogen, penicillic acid, and cyclodepsipeptides was evaluated in the ∆clr3 strain, most of them being reduced. Accordingly, the addition of epigenetic modulators responsible for HDAC inhibition into P. brasilianum’s growth media also culminated in the reduction in secondary metabolite production. The results suggest that Clr3 plays an essential role in secondary metabolite biosynthesis in P. brasilianum, thus offering new strategies for the regulation of natural product synthesis by assessing chromatin modification.
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Affiliation(s)
- Daniel Yuri Akiyama
- Department of Organic Chemistry, Institute of Chemistry, State University of Campinas, Campinas 13083-970, SP, Brazil; (D.Y.A.); (J.H.C.)
| | - Marina Campos Rocha
- Department of Genetic and Evolution, Federal University of São Carlos, São Carlos 13565-905, SP, Brazil;
| | - Jonas Henrique Costa
- Department of Organic Chemistry, Institute of Chemistry, State University of Campinas, Campinas 13083-970, SP, Brazil; (D.Y.A.); (J.H.C.)
| | - Caroline Brandão Teles
- Department of Biochemistry and Tissue Biology, Institute of Biology, State University of Campinas, Campinas 13083-970, SP, Brazil; (C.B.T.); (G.d.S.Z.)
| | - Giuliana da Silva Zuccoli
- Department of Biochemistry and Tissue Biology, Institute of Biology, State University of Campinas, Campinas 13083-970, SP, Brazil; (C.B.T.); (G.d.S.Z.)
| | - Iran Malavazi
- Department of Genetic and Evolution, Federal University of São Carlos, São Carlos 13565-905, SP, Brazil;
- Correspondence: (I.M.); (T.P.F.)
| | - Taicia Pacheco Fill
- Department of Organic Chemistry, Institute of Chemistry, State University of Campinas, Campinas 13083-970, SP, Brazil; (D.Y.A.); (J.H.C.)
- Correspondence: (I.M.); (T.P.F.)
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Sun WW, Li CY, Chiang YM, Lin TS, Warren S, Chang FR, Wang CCC. Characterization of a silent azaphilone biosynthesis gene cluster in Aspergillus terreus NIH 2624. Fungal Genet Biol 2022; 160:103694. [PMID: 35398258 PMCID: PMC9701353 DOI: 10.1016/j.fgb.2022.103694] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2020] [Revised: 03/04/2022] [Accepted: 04/03/2022] [Indexed: 11/28/2022]
Abstract
Filamentous fungal secondary metabolites are an important source of bioactive components. Genome sequencing ofAspergillus terreusrevealed many silent secondary metabolite biosynthetic gene clusters presumed to be involved in producing secondary metabolites. Activation of silent gene clusters through overexpressing a pathway-specific regulator is an effective avenue for discovering novel fungal secondary metabolites. Replacement of the native promoter of the pathway-specific activator with the inducible Tet-on system to activate thetazpathway led to the discovery of a series of azaphilone secondary metabolites, among which azaterrilone A (1) was purified and identified for the first time. Genetic deletion of core PKS genes and transcriptional analysis further characterized thetazgene cluster to consist of 16 genes with the NR-PKS and the HR-PKS collaborating in a convergent mode. Based on the putative gene functions and the characterized compounds structural information, a biosynthetic pathway of azaterrilone A (1) was proposed.
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Affiliation(s)
- Wei-Wen Sun
- Department of Pharmacology and Pharmaceutical Sciences, University of Southern California, School of Pharmacy, 1985 Zonal Avenue, Los Angeles, CA 90089, USA
| | - Chi-Ying Li
- Department of Pharmacology and Pharmaceutical Sciences, University of Southern California, School of Pharmacy, 1985 Zonal Avenue, Los Angeles, CA 90089, USA
| | - Yi-Ming Chiang
- Department of Pharmacology and Pharmaceutical Sciences, University of Southern California, School of Pharmacy, 1985 Zonal Avenue, Los Angeles, CA 90089, USA; Graduate Institute of Pharmaceutical Science, Chia Nan University of Pharmacy and Science, Tainan 71710, Taiwan
| | - Tzu-Shyang Lin
- Department of Pharmacology and Pharmaceutical Sciences, University of Southern California, School of Pharmacy, 1985 Zonal Avenue, Los Angeles, CA 90089, USA
| | - Shauna Warren
- Department of Pharmacology and Pharmaceutical Sciences, University of Southern California, School of Pharmacy, 1985 Zonal Avenue, Los Angeles, CA 90089, USA
| | - Fang-Rong Chang
- Graduate Institute of Natural Products, College of Pharmacy, Kaohsiung Medical University, Kaohsiung 807, Taiwan.
| | - Clay C C Wang
- Department of Pharmacology and Pharmaceutical Sciences, University of Southern California, School of Pharmacy, 1985 Zonal Avenue, Los Angeles, CA 90089, USA; Department of Chemistry, University of Southern California, College of Letters, Arts, and Sciences, Los Angeles, CA 90089, USA.
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Abstract
Contamination of food and feed with toxin-producing fungi is a major threat in agriculture and for human health. The filamentous fungus Alternaria alternata is one of the most widespread postharvest contaminants and a weak plant pathogen. It produces a large variety of secondary metabolites with alternariol and its derivatives as characteristic mycotoxin. Other important phyto- and mycotoxins are perylene quinones (PQs), some of which have anticancer properties. Here, we discovered that the PQ altertoxin (ATX) biosynthesis shares most enzymes with the 1,8-dihydroxynaphthalene (1,8-DHN) melanin pathway. However, melanin was formed in aerial hyphae and spores, and ATXs were synthesized in substrate hyphae. This spatial separation is achieved through the promiscuity of a polyketide synthase, presumably producing a pentaketide (T4HN), a hexaketide (AT4HN), and a heptaketide (YWA1) as products. T4HN directly enters the altertoxin and DHN melanin pathway, whereas AT4HN and YWA1 can be converted only in aerial hyphae, which probably leads to a higher T4HN concentration, favoring 1,8-DHN melanin formation. Whereas the production of ATXs was strictly dependent on the CmrA transcription factor, melanin could still be produced in the absence of CmrA to some extent. This suggests that different cues regulate melanin and toxin formation. Since DHN melanin is produced by many fungi, PQs or related compounds may be produced in many more fungi than so far assumed.
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Turning the world’s DNA into new medicines. Trends Biotechnol 2022; 40:766-767. [DOI: 10.1016/j.tibtech.2022.01.014] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2022] [Accepted: 01/31/2022] [Indexed: 11/19/2022]
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Oppong-Danquah E, Blümel M, Scarpato S, Mangoni A, Tasdemir D. Induction of Isochromanones by Co-Cultivation of the Marine Fungus Cosmospora sp. and the Phytopathogen Magnaporthe oryzae. Int J Mol Sci 2022; 23:782. [PMID: 35054969 PMCID: PMC8775470 DOI: 10.3390/ijms23020782] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2021] [Revised: 01/07/2022] [Accepted: 01/09/2022] [Indexed: 02/04/2023] Open
Abstract
Microbial co-cultivation is a promising approach for the activation of biosynthetic gene clusters (BGCs) that remain transcriptionally silent under artificial culture conditions. As part of our project aiming at the discovery of marine-derived fungal agrochemicals, we previously used four phytopathogens as model competitors in the co-cultivation of 21 marine fungal strains. Based on comparative untargeted metabolomics analyses and anti-phytopathogenic activities of the co-cultures, we selected the co-culture of marine Cosmospora sp. with the phytopathogen Magnaporthe oryzae for in-depth chemical studies. UPLC-MS/MS-based molecular networking (MN) of the co-culture extract revealed an enhanced diversity of compounds in several molecular families, including isochromanones, specifically induced in the co-culture. Large scale co-cultivation of Cosmospora sp. and M. oryzae resulted in the isolation of five isochromanones from the whole co-culture extract, namely the known soudanones A, E, D (1-3) and their two new derivatives, soudanones H-I (4-5), the known isochromans, pseudoanguillosporins A and B (6, 7), naphtho-γ-pyrones, cephalochromin and ustilaginoidin G (8, 9), and ergosterol (10). Their structures were established by NMR, HR-ESIMS, FT-IR, electronic circular dichroism (ECD) spectroscopy, polarimetry ([α]D), and Mosher's ester reaction. Bioactivity assays revealed antimicrobial activity of compounds 2 and 3 against the phytopathogens M. oryzae and Phytophthora infestans, while pseudoanguillosporin A (6) showed the broadest and strongest anti-phytopathogenic activity against Pseudomonas syringae, Xanthomonas campestris, M. oryzae and P. infestans. This is the first study assessing the anti-phytopathogenic activities of soudanones.
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Affiliation(s)
- Ernest Oppong-Danquah
- GEOMAR Centre for Marine Biotechnology (GEOMAR-Biotech), Research Unit Marine Natural Product Chemistry, GEOMAR Helmholtz Centre for Ocean Research Kiel, Am Kiel-Kanal 44, 24106 Kiel, Germany; (E.O.-D.); (M.B.)
| | - Martina Blümel
- GEOMAR Centre for Marine Biotechnology (GEOMAR-Biotech), Research Unit Marine Natural Product Chemistry, GEOMAR Helmholtz Centre for Ocean Research Kiel, Am Kiel-Kanal 44, 24106 Kiel, Germany; (E.O.-D.); (M.B.)
| | - Silvia Scarpato
- Dipartimento di Farmacia, Università degli Studi di Napoli Federico II, via Domenico Montesano 49, 80131 Napoli, Italy; (S.S.); (A.M.)
| | - Alfonso Mangoni
- Dipartimento di Farmacia, Università degli Studi di Napoli Federico II, via Domenico Montesano 49, 80131 Napoli, Italy; (S.S.); (A.M.)
| | - Deniz Tasdemir
- GEOMAR Centre for Marine Biotechnology (GEOMAR-Biotech), Research Unit Marine Natural Product Chemistry, GEOMAR Helmholtz Centre for Ocean Research Kiel, Am Kiel-Kanal 44, 24106 Kiel, Germany; (E.O.-D.); (M.B.)
- Faculty of Mathematics and Natural Science, Kiel University, Christian-Albrechts-Platz 4, 24118 Kiel, Germany
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Reductive inactivation of the hemiaminal pharmacophore for resistance against tetrahydroisoquinoline antibiotics. Nat Commun 2021; 12:7085. [PMID: 34873166 PMCID: PMC8648761 DOI: 10.1038/s41467-021-27404-3] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2021] [Accepted: 11/11/2021] [Indexed: 12/24/2022] Open
Abstract
Antibiotic resistance is becoming one of the major crises, among which hydrolysis reaction is widely employed by bacteria to destroy the reactive pharmacophore. Correspondingly, antibiotic producer has canonically co-evolved this approach with the biosynthetic capability for self-resistance. Here we discover a self-defense strategy featuring with reductive inactivation of hemiaminal pharmacophore by short-chain dehydrogenases/reductases (SDRs) NapW and homW, which are integrated with the naphthyridinomycin biosynthetic pathway. We determine the crystal structure of NapW·NADPH complex and propose a catalytic mechanism by molecular dynamics simulation analysis. Additionally, a similar detoxification strategy is identified in the biosynthesis of saframycin A, another member of tetrahydroisoquinoline (THIQ) antibiotics. Remarkably, similar SDRs are widely spread in bacteria and able to inactive other THIQ members including the clinical anticancer drug, ET-743. These findings not only fill in the missing intracellular events of temporal-spatial shielding mode for cryptic self-resistance during THIQs biosynthesis, but also exhibit a sophisticated damage-control in secondary metabolism and general immunity toward this family of antibiotics. Antibiotic-producing organisms need to co-evolve self-protection mechanisms to avoid any damage to themselves caused by the antibiotic pharmacophore (the reactive part of the compound). In this study, the authors report a self-defense strategy in naphthyridinomycin (NDM)-producing Streptomyces lusitanus, that comprises reductive inactivation of the hemiaminal pharmacophore by short-chain dehydrogenases/reductases (SDRs) NapW and HomW.
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Membrane based separation and purification of fusarubins from Fusarium solani. Sep Purif Technol 2021. [DOI: 10.1016/j.seppur.2021.119576] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
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Meng X, Fang Y, Ding M, Zhang Y, Jia K, Li Z, Collemare J, Liu W. Developing fungal heterologous expression platforms to explore and improve the production of natural products from fungal biodiversity. Biotechnol Adv 2021; 54:107866. [PMID: 34780934 DOI: 10.1016/j.biotechadv.2021.107866] [Citation(s) in RCA: 24] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2021] [Revised: 10/04/2021] [Accepted: 11/05/2021] [Indexed: 12/14/2022]
Abstract
Natural products from fungi represent an important source of biologically active metabolites notably for therapeutic agent development. Genome sequencing revealed that the number of biosynthetic gene clusters (BGCs) in fungi is much larger than expected. Unfortunately, most of them are silent or barely expressed under laboratory culture conditions. Moreover, many fungi in nature are uncultivable or cannot be genetically manipulated, restricting the extraction and identification of bioactive metabolites from these species. Rapid exploration of the tremendous number of cryptic fungal BGCs necessitates the development of heterologous expression platforms, which will facilitate the efficient production of natural products in fungal cell factories. Host selection, BGC assembly methods, promoters used for heterologous gene expression, metabolic engineering strategies and compartmentalization of biosynthetic pathways are key aspects for consideration to develop such a microbial platform. In the present review, we summarize current progress on the above challenges to promote research effort in the relevant fields.
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Affiliation(s)
- Xiangfeng Meng
- State Key Laboratory of Microbial Technology, Microbial Technology Institute, Shandong University, No. 72 Binhai Road, Qingdao 266237, PR China
| | - Yu Fang
- State Key Laboratory of Microbial Technology, Microbial Technology Institute, Shandong University, No. 72 Binhai Road, Qingdao 266237, PR China
| | - Mingyang Ding
- State Key Laboratory of Microbial Technology, Microbial Technology Institute, Shandong University, No. 72 Binhai Road, Qingdao 266237, PR China
| | - Yanyu Zhang
- State Key Laboratory of Microbial Technology, Microbial Technology Institute, Shandong University, No. 72 Binhai Road, Qingdao 266237, PR China
| | - Kaili Jia
- State Key Laboratory of Microbial Technology, Microbial Technology Institute, Shandong University, No. 72 Binhai Road, Qingdao 266237, PR China
| | - Zhongye Li
- State Key Laboratory of Microbial Technology, Microbial Technology Institute, Shandong University, No. 72 Binhai Road, Qingdao 266237, PR China
| | - Jérôme Collemare
- Westerdijk Fungal Biodiversity Institute, Uppsalalaan 8, 3584 CT Utrecht, the Netherlands.
| | - Weifeng Liu
- State Key Laboratory of Microbial Technology, Microbial Technology Institute, Shandong University, No. 72 Binhai Road, Qingdao 266237, PR China.
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Gilchrist CLM, Chooi YH. Synthaser: a CD-Search enabled Python toolkit for analysing domain architecture of fungal secondary metabolite megasynth(et)ases. Fungal Biol Biotechnol 2021; 8:13. [PMID: 34763725 PMCID: PMC8582187 DOI: 10.1186/s40694-021-00120-9] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2021] [Accepted: 10/29/2021] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Fungi are prolific producers of secondary metabolites (SMs), which are bioactive small molecules with important applications in medicine, agriculture and other industries. The backbones of a large proportion of fungal SMs are generated through the action of large, multi-domain megasynth(et)ases such as polyketide synthases (PKSs) and nonribosomal peptide synthetases (NRPSs). The structure of these backbones is determined by the domain architecture of the corresponding megasynth(et)ase, and thus accurate annotation and classification of these architectures is an important step in linking SMs to their biosynthetic origins in the genome. RESULTS Here we report synthaser, a Python package leveraging the NCBI's conserved domain search tool for remote prediction and classification of fungal megasynth(et)ase domain architectures. Synthaser is capable of batch sequence analysis, and produces rich textual output and interactive visualisations which allow for quick assessment of the megasynth(et)ase diversity of a fungal genome. Synthaser uses a hierarchical rule-based classification system, which can be extensively customised by the user through a web application ( http://gamcil.github.io/synthaser ). We show that synthaser provides more accurate domain architecture predictions than comparable tools which rely on curated profile hidden Markov model (pHMM)-based approaches; the utilisation of the NCBI conserved domain database also allows for significantly greater flexibility compared to pHMM approaches. In addition, we demonstrate how synthaser can be applied to large scale genome mining pipelines through the construction of an Aspergillus PKS similarity network. CONCLUSIONS Synthaser is an easy to use tool that represents a significant upgrade to previous domain architecture analysis tools. It is freely available under a MIT license from PyPI ( https://pypi.org/project/synthaser ) and GitHub ( https://github.com/gamcil/synthaser ).
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Affiliation(s)
- Cameron L M Gilchrist
- School of Molecular Sciences, The University of Western Australia, 35 Stirling Hwy, Crawley, 6009, Australia.
| | - Yit-Heng Chooi
- School of Molecular Sciences, The University of Western Australia, 35 Stirling Hwy, Crawley, 6009, Australia.
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Du X, Li H, Qi J, Chen C, Lu Y, Wang Y. Genome mining of secondary metabolites from a marine-derived Aspergillus terreus B12. Arch Microbiol 2021; 203:5621-5633. [PMID: 34459930 DOI: 10.1007/s00203-021-02548-4] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2021] [Revised: 08/15/2021] [Accepted: 08/19/2021] [Indexed: 12/29/2022]
Abstract
Owing to the prominent capabilities of bioconversion and biosynthesis, A. terreus has become attractive in biotechnical and pharmaceutical industry. In this work, an Aspergillus strain with potential antibacterial activities, was isolated from sponge in South China Sea. Based on the morphological and phylogenetic analysis, the strain was identified as A. terreus B12. Via the Illumina MiSeq sequencing platform, the complete genome was obtained, showing a genetic richness of biosynthetic gene clusters (BGCs), which might underpin the metabolic plasticity and adaptive resilience for the strain. Genome mining identified 67 BGCs, among which, 6 gene clusters could allocate to known BGCs (100% identity), corresponding to diverse metabolites like clavaric acid, dihydroisoflavipucine/isoflavipucine, dimethylcoprogen, alternariol, aspterric acid, and pyranonigrin E. Moreover, a range of compounds was isolated from B12 fermentation, e.g., terrein, butyrolactone I, terretonin A&E, acoapetaline B, and epi-aszonalenins A. Of note, acoapetaline B and epi-aszonalenins A, which had been respectively reported in plants and A. novofumigatus but with scarce information, was unexpectedly obtained from this species for the first time. The genomic and metabolic heterogeneity observed in strain B12, should be at least partially attributed to the genetic variability and biochemical diversity of A. terreus, which could be an interesting issue open to future efforts.
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Affiliation(s)
- Xinyang Du
- School of Life Science and Technology, China Pharmaceutical University, Nanjing, 211198, China
| | - Huanhuan Li
- School of Life Science and Technology, China Pharmaceutical University, Nanjing, 211198, China
| | - Jiangfeng Qi
- School of Life Science and Technology, China Pharmaceutical University, Nanjing, 211198, China
| | - Chaoyi Chen
- School of Life Science and Technology, China Pharmaceutical University, Nanjing, 211198, China
| | - Yuanyuan Lu
- School of Life Science and Technology, China Pharmaceutical University, Nanjing, 211198, China
| | - Ying Wang
- School of Life Science and Technology, China Pharmaceutical University, Nanjing, 211198, China.
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Wu Z, Li Y, Zhang L, Ding Z, Shi G. Microbial production of small peptide: pathway engineering and synthetic biology. Microb Biotechnol 2021; 14:2257-2278. [PMID: 33459516 PMCID: PMC8601181 DOI: 10.1111/1751-7915.13743] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2020] [Revised: 12/12/2020] [Accepted: 12/13/2020] [Indexed: 01/14/2023] Open
Abstract
Small peptides are a group of natural products with low molecular weights and complex structures. The diverse structures of small peptides endow them with broad bioactivities and suggest their potential therapeutic use in the medical field. The remaining challenge is methods to address the main limitations, namely (i) the low amount of available small peptides from natural sources, and (ii) complex processes required for traditional chemical synthesis. Therefore, harnessing microbial cells as workhorse appears to be a promising approach to synthesize these bioactive peptides. As an emerging engineering technology, synthetic biology aims to create standard, well-characterized and controllable synthetic systems for the biosynthesis of natural products. In this review, we describe the recent developments in the microbial production of small peptides. More importantly, synthetic biology approaches are considered for the production of small peptides, with an emphasis on chassis cells, the evolution of biosynthetic pathways, strain improvements and fermentation.
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Affiliation(s)
- Zhiyong Wu
- Key Laboratory of Industrial BiotechnologyMinistry of EducationSchool of BiotechnologyJiangnan UniversityWuxiJiangsu Province214122China
- National Engineering Laboratory for Cereal Fermentation TechnologyJiangnan University1800 Lihu AvenueWuxiJiangsu Province214122China
- Jiangsu Provisional Research Center for Bioactive Product Processing TechnologyJiangnan University1800 Lihu AvenueWuxiJiangsu Province214122China
| | - Youran Li
- Key Laboratory of Industrial BiotechnologyMinistry of EducationSchool of BiotechnologyJiangnan UniversityWuxiJiangsu Province214122China
- National Engineering Laboratory for Cereal Fermentation TechnologyJiangnan University1800 Lihu AvenueWuxiJiangsu Province214122China
- Jiangsu Provisional Research Center for Bioactive Product Processing TechnologyJiangnan University1800 Lihu AvenueWuxiJiangsu Province214122China
| | - Liang Zhang
- Key Laboratory of Industrial BiotechnologyMinistry of EducationSchool of BiotechnologyJiangnan UniversityWuxiJiangsu Province214122China
- National Engineering Laboratory for Cereal Fermentation TechnologyJiangnan University1800 Lihu AvenueWuxiJiangsu Province214122China
- Jiangsu Provisional Research Center for Bioactive Product Processing TechnologyJiangnan University1800 Lihu AvenueWuxiJiangsu Province214122China
| | - Zhongyang Ding
- Key Laboratory of Industrial BiotechnologyMinistry of EducationSchool of BiotechnologyJiangnan UniversityWuxiJiangsu Province214122China
- National Engineering Laboratory for Cereal Fermentation TechnologyJiangnan University1800 Lihu AvenueWuxiJiangsu Province214122China
- Jiangsu Provisional Research Center for Bioactive Product Processing TechnologyJiangnan University1800 Lihu AvenueWuxiJiangsu Province214122China
| | - Guiyang Shi
- Key Laboratory of Industrial BiotechnologyMinistry of EducationSchool of BiotechnologyJiangnan UniversityWuxiJiangsu Province214122China
- National Engineering Laboratory for Cereal Fermentation TechnologyJiangnan University1800 Lihu AvenueWuxiJiangsu Province214122China
- Jiangsu Provisional Research Center for Bioactive Product Processing TechnologyJiangnan University1800 Lihu AvenueWuxiJiangsu Province214122China
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Liu Q, Xu Y, Zhang X, Li K, Li X, Wang F, Xu F, Dong C. Infection Process and Genome Assembly Provide Insights into the Pathogenic Mechanism of Destructive Mycoparasite Calcarisporium cordycipiticola with Host Specificity. J Fungi (Basel) 2021; 7:918. [PMID: 34829206 PMCID: PMC8620734 DOI: 10.3390/jof7110918] [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: 09/30/2021] [Revised: 10/23/2021] [Accepted: 10/25/2021] [Indexed: 11/21/2022] Open
Abstract
Calcarisporium cordycipiticola is the pathogen in the white mildew disease of Cordyceps militaris, one of the popular mushrooms. This disease frequently occurs and there is no effective method for disease prevention and control. In the present study, C. militaris is found to be the only host of C. cordycipiticola, indicating strict host specificity. The infection process was monitored by fluorescent labeling and scanning and transmission electron microscopes. C. cordycipiticola can invade into the gaps among hyphae of the fruiting bodies of the host and fill them gradually. It can degrade the hyphae of the host by both direct contact and noncontact. The parasitism is initially biotrophic, and then necrotrophic as mycoparasitic interaction progresses. The approximate chromosome-level genome assembly of C. cordycipiticola yielded an N50 length of 5.45 Mbp and a total size of 34.51 Mbp, encoding 10,443 proteins. Phylogenomic analysis revealed that C. cordycipiticola is phylogenetically close to its specific host, C. militaris. A comparative genomic analysis showed that the number of CAZymes of C. cordycipiticola was much less than in other mycoparasites, which might be attributed to its host specificity. Secondary metabolite cluster analysis disclosed the great biosynthetic capabilities and potential mycotoxin production capability. This study provides insights into the potential pathogenesis and interaction between mycoparasite and its host.
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Affiliation(s)
- Qing Liu
- State Key Laboratory of Mycology, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China; (Q.L.); (Y.X.); (X.Z.); (K.L.); (X.L.); (F.W.)
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Yanyan Xu
- State Key Laboratory of Mycology, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China; (Q.L.); (Y.X.); (X.Z.); (K.L.); (X.L.); (F.W.)
| | - Xiaoling Zhang
- State Key Laboratory of Mycology, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China; (Q.L.); (Y.X.); (X.Z.); (K.L.); (X.L.); (F.W.)
| | - Kuan Li
- State Key Laboratory of Mycology, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China; (Q.L.); (Y.X.); (X.Z.); (K.L.); (X.L.); (F.W.)
| | - Xiao Li
- State Key Laboratory of Mycology, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China; (Q.L.); (Y.X.); (X.Z.); (K.L.); (X.L.); (F.W.)
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Fen Wang
- State Key Laboratory of Mycology, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China; (Q.L.); (Y.X.); (X.Z.); (K.L.); (X.L.); (F.W.)
| | - Fangxu Xu
- Experimental Teaching Center, Shenyang Normal University, Shenyang 110034, China;
| | - Caihong Dong
- State Key Laboratory of Mycology, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China; (Q.L.); (Y.X.); (X.Z.); (K.L.); (X.L.); (F.W.)
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