Epigenetic manipulation for secondary metabolite activation in endophytic fungi: current progress and future directions

[1]  Duoduo Wang,et al.  Advances and Challenges in CRISPR/Cas-Based Fungal Genome Engineering for Secondary Metabolite Production: A Review , 2023, Journal of fungi.

[2]  D. Lai,et al.  Recent Advances in Search of Bioactive Secondary Metabolites from Fungi Triggered by Chemical Epigenetic Modifiers , 2023, Journal of fungi.

[3]  T. Feng,et al.  Epigenetic Manipulation Induced Production of Immunosuppressive Chromones and Cytochalasins from the Mangrove Endophytic Fungus Phomopsis asparagi DHS-48 , 2022, Marine drugs.

[4]  Kajal,et al.  Advancement in the molecular perspective of plant-endophytic interaction to mitigate drought stress in plants , 2022, Frontiers in Microbiology.

[5]  Arunandan Kumar,et al.  Fungal Endophytes: an Accessible Source of Bioactive Compounds with Potential Anticancer Activity , 2022, Applied Biochemistry and Biotechnology.

[6]  A. Syed,et al.  Plants and endophytes – a partnership for the coumarin production through the microbial systems , 2022, Mycology.

[7]  Hanhong Bae,et al.  Endophytic Fungi: Key Insights, Emerging Prospects, and Challenges in Natural Product Drug Discovery , 2022, Microorganisms.

[8]  J. Kumar,et al.  Phenolic and flavonoid contents and antioxidant activity of an endophytic fungus Nigrospora sphaerica (EHL2), inhabiting the medicinal plant Euphorbia hirta (dudhi) L. , 2022, Archives of Microbiology.

[9]  R. Kumar,et al.  Mass Spectrometry-Based Technology and Workflows for Studying the Chemistry of Fungal Endophyte Derived Bioactive Compounds. , 2021, ACS chemical biology.

[10]  W. Yin,et al.  An Optimized and Efficient CRISPR/Cas9 System for the Endophytic Fungus Pestalotiopsis fici , 2021, Journal of fungi.

[11]  E. Rigobelo,et al.  Endophytic fungi: a tool for plant growth promotion and sustainable agriculture , 2021, Mycology.

[12]  J. Kumar,et al.  Bioactive potential evaluation and purification of compounds from an endophytic fungus Diaporthe longicolla, a resident of Saraca asoca (Roxb.) Willd. , 2021, Archives of Microbiology.

[13]  Swapnil C. Kamble,et al.  Biological potential of bioactive metabolites derived from fungal endophytes associated with medicinal plants , 2021, Mycological Progress.

[14]  W. Quax,et al.  Current State and Future Directions of Genetics and Genomics of Endophytic Fungi for Bioprospecting Efforts , 2021, Frontiers in Bioengineering and Biotechnology.

[15]  R. Adeleke,et al.  Bioprospecting of endophytic microorganisms for bioactive compounds of therapeutic importance , 2021, Archives of Microbiology.

[16]  M. Prasad,et al.  Enhancing phytoremediation of hazardous metal(loid)s using genome engineering CRISPR-Cas9 technology. , 2021, Journal of hazardous materials.

[17]  C. Brakebusch CRISPR Genome Editing: How to Make a Fantastic Method Even Better , 2021, Cells.

[18]  Swapnil C. Kamble,et al.  Plant associated fungal endophytes as a source of natural bioactive compounds , 2021, Mycology.

[19]  R. N. Kharwar,et al.  Fungal Endophytes as Efficient Sources of Plant-Derived Bioactive Compounds and Their Prospective Applications in Natural Product Drug Discovery: Insights, Avenues, and Challenges , 2021, Microorganisms.

[20]  M. Sulyok,et al.  A novel fungal gene regulation system based on inducible VPR-dCas9 and nucleosome map-guided sgRNA positioning , 2020, Applied Microbiology and Biotechnology.

[21]  M. Poças-Fonseca,et al.  Epigenetic manipulation of filamentous fungi for biotechnological applications: a systematic review , 2020, Biotechnology Letters.

[22]  F. Boyom,et al.  Recent advances in inducing endophytic fungal specialized metabolites using small molecule elicitors including epigenetic modifiers. , 2020, Phytochemistry.

[23]  J. van Staden,et al.  A critical review on exploiting the pharmaceutical potential of plant endophytic fungi. , 2020, Biotechnology advances.

[24]  B. Wilkinson,et al.  Epigenetic modulation of secondary metabolite profiles in Aspergillus calidoustus and Aspergillus westerdijkiae through histone deacetylase (HDAC) inhibition by vorinostat , 2020, The Journal of Antibiotics.

[25]  Stan J. J. Brouns,et al.  Evolutionary classification of CRISPR–Cas systems: a burst of class 2 and derived variants , 2019, Nature Reviews Microbiology.

[26]  C. Dai,et al.  The construction of CRISPR-Cas9 system for endophytic Phomopsis liquidambaris and its PmkkA-deficient mutant revealing the effect on rice. , 2019, Fungal genetics and biology : FG & B.

[27]  Jesús Martín,et al.  Extending the Metabolite Diversity of the Endophyte Dimorphosporicola tragani , 2019, Metabolites.

[28]  Jing Xu,et al.  Chemical Investigation Of Secondary Metabolites Produced By Mangrove Endophytic Fungus Phyllosticta Capitalensis , 2019, Natural product research.

[29]  M. Seidl,et al.  Chromatin-dependent regulation of secondary metabolite biosynthesis in fungi: is the picture complete? , 2019, FEMS microbiology reviews.

[30]  A. Shaytan,et al.  Linking chromatin composition and structural dynamics at the nucleosome level. , 2019, Current opinion in structural biology.

[31]  S. Saxena,et al.  Isolation and enhancement of resveratrol production in Xylaria psidii by exploring the phenomenon of epigenetics: using DNA methyltransferases and histone deacetylase as epigenetic modifiers , 2019, Molecular Biology Reports.

[32]  T. Gulyamova,et al.  Effect of Epigenetic Modifiers on Fermentation Parameters of Endophytic Fungi from Plants Growing in Uzbekistan , 2019, International Journal of Current Microbiology and Applied Sciences.

[33]  Yucheng Gu,et al.  Three new ɑ-pyrone derivatives induced by chemical epigenetic manipulation of Penicillium herquei, an endophytic fungus isolated from Cordyceps sinensis , 2019, Natural product research.

[34]  Suresh Kumar,et al.  Epigenetics of Modified DNA Bases: 5-Methylcytosine and Beyond , 2018, Front. Genet..

[35]  N. Keller Fungal secondary metabolism: regulation, function and drug discovery , 2018, Nature Reviews Microbiology.

[36]  P. Proksch,et al.  Epigenetic modification, co-culture and genomic methods for natural product discovery , 2018, Physical Sciences Reviews.

[37]  N. Keller,et al.  The epigenetic reader SntB regulates secondary metabolism, development and global histone modifications in Aspergillus flavus. , 2018, Fungal genetics and biology : FG & B.

[38]  Jennifer A. Doudna,et al.  CRISPR-Cas guides the future of genetic engineering , 2018, Science.

[39]  P. Cobine,et al.  Efficient genome editing in Fusarium oxysporum based on CRISPR/Cas9 ribonucleoprotein complexes. , 2018, Fungal genetics and biology : FG & B.

[40]  V. Gupta,et al.  Endophytic Fungi—Alternative Sources of Cytotoxic Compounds: A Review , 2018, Front. Pharmacol..

[41]  A. Mishra,et al.  Induction of Cryptic and Bioactive Metabolites through Natural Dietary Components in an Endophytic Fungus Colletotrichum gloeosporioides (Penz.) Sacc. , 2017, Front. Microbiol..

[42]  Maximilian Wenderoth,et al.  Establishment of CRISPR/Cas9 in Alternaria alternata. , 2017, Fungal genetics and biology : FG & B.

[43]  M. Spiteller,et al.  Epigenetic Modulation of Endophytic Eupenicillium sp. LG41 by a Histone Deacetylase Inhibitor for Production of Decalin-Containing Compounds. , 2017, Journal of natural products.

[44]  A. Arnold,et al.  An epigenetic modifier induces production of (10'S)-verruculide B, an inhibitor of protein tyrosine phosphatases by Phoma sp. nov. LG0217, a fungal endophyte of Parkinsonia microphylla. , 2017, Bioorganic & medicinal chemistry.

[45]  A. Chaubey,et al.  Epigenetic modifier induced enhancement of fumiquinazoline C production in Aspergillus fumigatus (GA-L7): an endophytic fungus from Grewia asiatica L. , 2017, AMB Express.

[46]  P. Proksch,et al.  Inducing secondary metabolite production by the endophytic fungus Chaetomium sp. through fungal–bacterial co-culture and epigenetic modification , 2016 .

[47]  Z. Lewis,et al.  KdmB, a Jumonji Histone H3 Demethylase, Regulates Genome-Wide H3K4 Trimethylation and Is Required for Normal Induction of Secondary Metabolism in Aspergillus nidulans , 2016, PLoS genetics.

[48]  A. Driessen,et al.  CRISPR/Cas9 Based Genome Editing of Penicillium chrysogenum. , 2016, ACS synthetic biology.

[49]  Wei Li,et al.  Polyketide Production of Pestaloficiols and Macrodiolide Ficiolides Revealed by Manipulations of Epigenetic Regulators in an Endophytic Fungus. , 2016, Organic letters.

[50]  L. Aravind,et al.  Adenine methylation in eukaryotes: Apprehending the complex evolutionary history and functional potential of an epigenetic modification , 2015, BioEssays : news and reviews in molecular, cellular and developmental biology.

[51]  L. Matzkin,et al.  Connecting genotypes, phenotypes and fitness: harnessing the power of CRISPR/Cas9 genome editing , 2015, Molecular ecology.

[52]  C. Hong,et al.  Efficient gene editing in Neurospora crassa with CRISPR technology , 2015, Fungal Biology and Biotechnology.

[53]  Lukas Reiter,et al.  Quantification of SAHA-Dependent Changes in Histone Modifications Using Data-Independent Acquisition Mass Spectrometry. , 2015, Journal of proteome research.

[54]  G. Challis,et al.  Discovery of microbial natural products by activation of silent biosynthetic gene clusters , 2015, Nature Reviews Microbiology.

[55]  C. Kubicek,et al.  Epigenetics as an emerging tool for improvement of fungal strains used in biotechnology , 2015, Applied Microbiology and Biotechnology.

[56]  Wei Xu,et al.  Epigenetic genome mining of an endophytic fungus leads to the pleiotropic biosynthesis of natural products. , 2015, Angewandte Chemie.

[57]  G. Zou,et al.  Efficient genome editing in filamentous fungus Trichoderma reesei using the CRISPR/Cas9 system , 2015, Cell Discovery.

[58]  Kai Blin,et al.  antiSMASH 3.0—a comprehensive resource for the genome mining of biosynthetic gene clusters , 2015, Nucleic Acids Res..

[59]  M. Sulyok,et al.  KdmA, a histone H3 demethylase with bipartite function, differentially regulates primary and secondary metabolism in A spergillus nidulans , 2015, Molecular microbiology.

[60]  S. Brady,et al.  eSNaPD: a versatile, web-based bioinformatics platform for surveying and mining natural product biosynthetic diversity from metagenomes. , 2014, Chemistry & biology.

[61]  M. Seyedsayamdost High-throughput platform for the discovery of elicitors of silent bacterial gene clusters , 2014, Proceedings of the National Academy of Sciences.

[62]  B. Scott,et al.  Histone H3K9 and H3K27 methylation regulates fungal alkaloid biosynthesis in a fungal endophyte–plant symbiosis , 2014, Molecular microbiology.

[63]  E. Seto,et al.  Erasers of histone acetylation: the histone deacetylase enzymes. , 2014, Cold Spring Harbor perspectives in biology.

[64]  Xiao-Long Yang,et al.  Epigenetic modifiers alter the secondary metabolite composition of a plant endophytic fungus, Pestalotiopsis crassiuscula obtained from the leaves of Fragaria chiloensis , 2014, Journal of Asian natural products research.

[65]  P. Proksch,et al.  Co-Cultivation—A Powerful Emerging Tool for Enhancing the Chemical Diversity of Microorganisms , 2014, Marine drugs.

[66]  R. Aramayo,et al.  Neurospora crassa, a model system for epigenetics research. , 2013, Cold Spring Harbor perspectives in biology.

[67]  I. Abe,et al.  Induced biosyntheses of a novel butyrophenone and two aromatic polyketides in the plant pathogen Stagonospora nodorum , 2013, Natural Products and Bioprospecting.

[68]  Y. Oshima,et al.  Benzophenones from an endophytic fungus, Graphiopsis chlorocephala, from Paeonia lactiflora cultivated in the presence of an NAD+-dependent HDAC inhibitor. , 2013, Organic letters.

[69]  W. Mousa,et al.  The Diversity of Anti-Microbial Secondary Metabolites Produced by Fungal Endophytes: An Interdisciplinary Perspective , 2013, Front. Microbiol..

[70]  I. Abe,et al.  Epigenetic modifier-induced biosynthesis of novel fusaric acid derivatives in endophytic fungi from Datura stramonium L. , 2013, Natural Products and Bioprospecting.

[71]  Axel A. Brakhage,et al.  Regulation of fungal secondary metabolism , 2012, Nature Reviews Microbiology.

[72]  Kyle R. Conway,et al.  ClusterMine360: a database of microbial PKS/NRPS biosynthesis , 2012, Nucleic Acids Res..

[73]  Yadong Wang,et al.  PRISM: Pair-read informed split-read mapping for base-pair level detection of insertion, deletion and structural variants , 2012, Bioinform..

[74]  I. Abe,et al.  Induced production of mycotoxins in an endophytic fungus from the medicinal plant Datura stramonium L. , 2012, Bioorganic & medicinal chemistry letters.

[75]  N. Lopes,et al.  Epigenetic modulation changed the secondary metabolite profile in the endophyte Nigrospora sphaerica SS67 , 2012 .

[76]  R. Barrangou,et al.  Cas9–crRNA ribonucleoprotein complex mediates specific DNA cleavage for adaptive immunity in bacteria , 2012, Proceedings of the National Academy of Sciences.

[77]  J. Doudna,et al.  A Programmable Dual-RNA–Guided DNA Endonuclease in Adaptive Bacterial Immunity , 2012, Science.

[78]  D. Kyle,et al.  Epigenetic Tailoring for the Production of Anti-Infective Cytosporones from the Marine Fungus Leucostoma persoonii , 2012, Marine drugs.

[79]  Stephan Beck,et al.  Methylome analysis using MeDIP-seq with low DNA concentrations , 2012, Nature Protocols.

[80]  C. Floerchinger,et al.  Modulation of volatile organic compound formation in the Mycodiesel-producing endophyte Hypoxylon sp. CI-4. , 2012, Microbiology.

[81]  Xudong Qu,et al.  Transcriptome mining of active biosynthetic pathways and their associated products in Streptomyces flaveolus. , 2011, Angewandte Chemie.

[82]  Tabitha M. Hardy,et al.  Epigenetic diet: impact on the epigenome and cancer. , 2011, Epigenomics.

[83]  F. Schroeder,et al.  Identification of cryptic products of the gliotoxin gene cluster using NMR-based comparative metabolomics and a model for gliotoxin biosynthesis. , 2011, Journal of the American Chemical Society.

[84]  Berghe,et al.  Nature or nurture: let food be your epigenetic medicine in chronic inflammatory disorders. , 2010, Biochemical pharmacology.

[85]  Anne Osbourn,et al.  Secondary metabolic gene clusters: evolutionary toolkits for chemical innovation. , 2010, Trends in genetics : TIG.

[86]  T. Tollefsbol,et al.  Epigenetic targets of bioactive dietary components for cancer prevention and therapy , 2010, Clinical Epigenetics.

[87]  D. Romagnolo,et al.  Resveratrol prevents epigenetic silencing of BRCA-1 by the aromatic hydrocarbon receptor in human breast cancer cells. , 2010, The Journal of nutrition.

[88]  D. Haft,et al.  SMURF: Genomic mapping of fungal secondary metabolite clusters. , 2010, Fungal genetics and biology : FG & B.

[89]  Timothy L. Foley,et al.  An orthogonal active site identification system (OASIS) for proteomic profiling of natural product biosynthesis. , 2009, ACS chemical biology.

[90]  P. Park ChIP–seq: advantages and challenges of a maturing technology , 2009, Nature Reviews Genetics.

[91]  N. Kelleher,et al.  A Proteomics Approach to Discovery of Natural Products and Their Biosynthetic Pathways , 2009, Nature Biotechnology.

[92]  Wei Li,et al.  BSMAP: whole genome bisulfite sequence MAPping program , 2009, BMC Bioinformatics.

[93]  Y. Reyes-Domínguez,et al.  Chromatin-level regulation of biosynthetic gene clusters. , 2009, Nature chemical biology.

[94]  F. Najar,et al.  Chemical induction of silent biosynthetic pathway transcription in Aspergillus niger , 2009, Journal of Industrial Microbiology & Biotechnology.

[95]  F. Sasse,et al.  Fungal endophytes and bioprospecting , 2009 .

[96]  Clifford A. Meyer,et al.  Model-based Analysis of ChIP-Seq (MACS) , 2008, Genome Biology.

[97]  M. Tribus,et al.  Histone Deacetylase Activity Regulates Chemical Diversity in Aspergillus , 2007, Eukaryotic Cell.

[98]  R. Barrangou,et al.  CRISPR Provides Acquired Resistance Against Viruses in Prokaryotes , 2007, Science.

[99]  C. Huber,et al.  Proteome analysis of Myxococcus xanthus by off-line two-dimensional chromatographic separation using monolithic poly-(styrene-divinylbenzene) columns combined with ion-trap tandem mass spectrometry. , 2006, Journal of proteome research.

[100]  William H. Majoros,et al.  Genomic sequence of the pathogenic and allergenic filamentous fungus Aspergillus fumigatus , 2005, Nature.

[101]  J. Bennett,et al.  Fungal secondary metabolism — from biochemistry to genomics , 2005, Nature Reviews Microbiology.

[102]  A. Ehrenhofer-Murray,et al.  Chromatin dynamics at DNA replication, transcription and repair. , 2004, European journal of biochemistry.

[103]  Hyun-Ok Yang,et al.  Mechanism of taxol‐induced apoptosis in human SKOV3 ovarian carcinoma cells , 2004, Journal of cellular biochemistry.

[104]  G. Strobel,et al.  Rainforest Endophytes and Bioactive Products , 2002, Critical reviews in biotechnology.

[105]  D. Sterner,et al.  Acetylation of Histones and Transcription-Related Factors , 2000, Microbiology and Molecular Biology Reviews.

[106]  C. Allis,et al.  The language of covalent histone modifications , 2000, Nature.

[107]  J. Jameson,et al.  Resveratrol, a polyphenolic compound found in grapes and wine, is an agonist for the estrogen receptor. , 1997, Proceedings of the National Academy of Sciences of the United States of America.

[108]  A. Stierle,et al.  Taxol and taxane production by Taxomyces andreanae, an endophytic fungus of Pacific yew. , 1993, Science.

[109]  D. Santi,et al.  Covalent bond formation between a DNA-cytosine methyltransferase and DNA containing 5-azacytosine. , 1984, Proceedings of the National Academy of Sciences of the United States of America.

[110]  R. Reeves,et al.  Sodium butyrate inhibits histone deacetylation in cultured cells , 1978, Cell.

[111]  Krm Toghueo Stimulation of the production of new volatile and non-volatile metabolites by endophytic Aspergillus niger using small organic chemicals , 2016 .

[112]  Axel A Brakhage,et al.  Fungal secondary metabolites - strategies to activate silent gene clusters. , 2011, Fungal genetics and biology : FG & B.

[113]  Ronald Breslow,et al.  Dimethyl sulfoxide to vorinostat: development of this histone deacetylase inhibitor as an anticancer drug , 2007, Nature Biotechnology.