Advances in the discovery and study of Trichoderma natural products for biological control applications

Sophie Jin and Fabrizio Alberti

Nat. Prod. Rep., 2025, 42, 1367
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Breaking into nature's secret medicine cabinet: lichens – a biochemical goldmine ready for discovery

Garima Singh, Francesco Dal Grande, Francis M. Martin and Marnix H. Medema

New Phytologist, 2025, 246, 437
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Large-scale transcriptome mining enables macrocyclic diversification and improved bioactivity of the stephanotic acid scaffold

Xiaofeng Wang, Khadija Shafiq, Derrick A. Ousley, Desnor N. Chigumba, Dulciana Davis, Kali M. McDonough, Lisa S. Mydy, Jonathan Z. Sexton and Roland D. Kersten

Nat Commun, 2025, 16
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Fungal Metabolomics: A Comprehensive Approach to Understanding Pathogenesis in Humans and Identifying Potential Therapeutics

Vinicius Alves, Daniel Zamith-Miranda, Susana Frases and Joshua D. Nosanchuk

JoF, 2025, 11, 93
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Cyclochlorotine Hydroxylase CctR Reveals DUF3328 as a Family of Copper‐Dependent Metalloenzymes

Wentao Huang, Jakob K. Reinhardt, Anru Tian, Xiao Zhang, Binghui Li, Noah Gould, Sashirekha Nallapati, Alexander R. Ivanov, Yi Wang, Jason J. Guo, David E. Budil and Jing‐Ke Weng

Angew Chem Int Ed, 2025
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Recent Advances in Discovery, Bioengineering, and Bioactivity-Evaluation of Ribosomally Synthesized and Post-translationally Modified Peptides

Guannan Zhong, Zong-Jie Wang, Fu Yan, Youming Zhang and Liujie Huo

ACS Bio Med Chem Au, 2023, 3, 1
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Transcriptomics-Driven Discovery of New Meroterpenoid Rhynchospenes Involved in the Virulence of the Barley Pathogen Rhynchosporium commune

Reynaldi Darma, Zhuo Shang, Joe Bracegirdle, Stephen Moggach, Megan C. McDonald, Andrew M. Piggott, Peter S. Solomon and Yit-Heng Chooi

ACS Chem. Biol., 2025, 20, 421
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De Novo Long-Read Whole-Genome Assemblies and the Comparative Pan-Genome Analysis of Ascochyta Blight Pathogens Affecting Field Pea

Yvonne O. Ogaji, Robert C. Lee, Tim I. Sawbridge, Benjamin G. Cocks, Hans D. Daetwyler and Sukhjiwan Kaur

JoF, 2022, 8, 884
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Genus-wide analysis of Trichoderma antagonism toward Pythium and Globisporangium plant pathogens and the contribution of cellulases to the antagonism

Siqiao Chen, Paul Daly, Wilfred Mabeche Anjago, Rong Wang, Yishen Zhao, Xian Wen, Dongmei Zhou, Sheng Deng, Xisha Lin, Josef Voglmeir, Feng Cai, Qirong Shen, Irina S. Druzhinina, Lihui Wei and Karyn N. Johnson

Appl Environ Microbiol, 2024, 90
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Copper-Dependent Hydroxylation Catalyzed by the DUF3328 Enzyme CctR

Kaushik Seshadri, Chen-Yu Chiang, Kyle K. Nagasawa and Yi Tang

Org. Lett., 2025, 27, 8178
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Discovery and Characterization of a Myxobacterial Lanthipeptide with Unique Biosynthetic Features and Anti-inflammatory Activity

Xiaotong Wang, Xiaoyu Chen, Zong-Jie Wang, Mengwei Zhuang, Lin Zhong, Chengzhang Fu, Ronald Garcia, Rolf Müller, Youming Zhang, Jie Yan, Dalei Wu and Liujie Huo

J. Am. Chem. Soc., 2023, 145, 16924
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Cyclochlorotine Hydroxylase CctR Reveals DUF3328 as a Family of Copper‐Dependent Metalloenzymes

Wentao Huang, Jakob K. Reinhardt, Anru Tian, Xiao Zhang, Binghui Li, Noah Gould, Sashirekha Nallapati, Alexander R. Ivanov, Yi Wang, Jason J. Guo, David E. Budil and Jing‐Ke Weng

Angewandte Chemie, 2025
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Structural and Functional Analysis of Peptides Derived from KEX2-Processed Repeat Proteins in Agaricomycetes Using Reverse Genetics and Peptidomics

Eva Vogt, Lukas Sonderegger, Ying-Yu Chen, Tina Segessemann, Markus Künzler and Rebecca S. Shapiro

Microbiol Spectr, 2022, 10
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Chemistry and Biology of Ustiloxin Analogs as Mycotoxins

Xuwen Hou, Dan Xu, Gan Gu, Daowan Lai and Ligang Zhou

J. Agric. Food Chem., 2025
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Discovery of fungal onoceroid triterpenoids through domainless enzyme-targeted global genome mining

Jia Tang and Yudai Matsuda

Nat Commun, 2024, 15
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Bioinformatic exploration of RiPP biosynthetic gene clusters in lichens

Anna Pasinato and Garima Singh

Fungal Biol Biotechnol, 2025, 12
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The Biosynthetic Landscape of Triceptides Reveals Radical SAM Enzymes That Catalyze Cyclophane Formation on Tyr- and His-Containing Motifs

Ryosuke Sugiyama, Angelica Faith L. Suarez, Yohei Morishita, Thi Quynh Ngoc Nguyen, Yi Wei Tooh, Muhammad Nur Hadi Bin Roslan, Justin Lo Choy, Qi Su, Wei Yang Goh, Gregory Adrian Gunawan, Fong Tian Wong and Brandon I. Morinaka

J. Am. Chem. Soc., 2022, 144, 11580
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Tryptophan-Centric Bioinformatics Identifies New Lasso Peptide Modifications

Lonnie A. Harris, Hamada Saad, Kyle E. Shelton, Lingyang Zhu, Xiaorui Guo and Douglas A. Mitchell

Biochemistry, 2024, 63, 865
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Disulfide bridge-targeted metabolome mining unravels an antiparkinsonian peptide

Zhiwu Tong, Xiahong Xie, Huiming Ge, Ruihua Jiao, Tingting Wang, Xincun Wang, Wenying Zhuang, Gang Hu and Renxiang Tan

Acta Pharmaceutica Sinica B, 2024, 14, 881
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Exploring Bioactive Fungal RiPPs: Advances, Challenges, and Future Prospects

Qiuyue Nie, Chunxiao Sun, Shuai Liu and Xue Gao

Biochemistry, 2024, 63, 2948
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Characterization of the Biosynthetic Gene Cluster for the Ribosomally Synthesized Cyclic Peptide Epichloëcyclins in Epichloë festucae

Wei Zhang, Natasha T. Forester, Pranav Chettri, Maurice Heilijgers, Wade J. Mace, Evelyne Maes, Yulia Morozova, Emma R. Applegate, Richard D. Johnson and Linda J. Johnson

J. Agric. Food Chem., 2023, 71, 13965
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Aromatic side-chain crosslinking in RiPP biosynthesis

Sanath K. Kandy, Michael A. Pasquale and Jonathan R. Chekan

Nat Chem Biol, 2025, 21, 168
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The Venturia inaequalis effector repertoire is dominated by expanded families with predicted structural similarity, but unrelated sequence, to avirulence proteins from other plant-pathogenic fungi

Mercedes Rocafort, Joanna K. Bowen, Berit Hassing, Murray P. Cox, Brogan McGreal, Silvia de la Rosa, Kim M. Plummer, Rosie E. Bradshaw and Carl H. Mesarich

BMC Biol, 2022, 20
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Genomic Localization Bias of Secondary Metabolite Gene Clusters and Association with Histone Modifications in Aspergillus

Xin Zhang, Iseult Leahy, Jérȏme Collemare, Michael F Seidl and Tatiana Giraud

Genome Biology and Evolution, 2024, 16
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Recent advances in the biosynthesis of ribosomally synthesized and posttranslationally modified peptides of fungal origin

Taro Ozaki, Atsushi Minami and Hideaki Oikawa

J Antibiot, 2023, 76, 3
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The Cytotoxic Properties of Extreme Fungi’s Bioactive Components—An Updated Metabolic and Omics Overview

Attila Kiss, Farhad Hariri Akbari, Andrey Marchev, Viktor Papp and Iman Mirmazloum

Life, 2023, 13, 1623
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A class of benzofuranoindoline-bearing heptacyclic fungal RiPPs with anticancer activities

Qiuyue Nie, Fanglong Zhao, Xuerong Yu, Mithun C. Madhusudhanan, Caleb Chang, Siting Li, Sandipan Roy Chowdhury, Bryce Kille, Andy Xu, Rory Sharkey, Chunxiao Sun, Hongzhi Zeng, Shuai Liu, Dishu Zhou, Xin Yu, Kevin Yang, Sandra A. C. Figueiredo, Maria Zotova, Zichen Hu, Alan Y. Du, Dongyin Guan, Rui Tang, Todd Treangen, Jin Wang, Pedro N. Leão, Yang Gao, Junjie Chen, Peng Liu, Hans Renata and Xue Gao

Nat Chem Biol, 2025
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Trichoderma – genomes and genomics as treasure troves for research towards biology, biotechnology and agriculture

Miriam Schalamun and Monika Schmoll

Front. Fungal Biol., 2022, 3
DOI: 10.3389/ffunb.2022.1002161

Fungal RiPPs Side Chain Macrocyclization Catalyzed by Copper-Dependent DUF3328 Enzyme

Chen-Yu Chiang, Masao Ohashi and Yi Tang

J. Am. Chem. Soc., 2025, 147, 8113
DOI: 10.1021/jacs.4c18770

Copper-dependent halogenase catalyses unactivated C−H bond functionalization

Chen-Yu Chiang, Masao Ohashi, Jessie Le, Pan-Pan Chen, Qingyang Zhou, Songrong Qu, Undramaa Bat-Erdene, Shabnam Hematian, Jose A. Rodriguez, K. N. Houk, Yisong Guo, Joseph A. Loo and Yi Tang

Nature, 2025, 638, 126
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Triumphs and Challenges of Natural Product Discovery in the Postgenomic Era

Carolina Cano-Prieto, Agustina Undabarrena, Ana Calheiros de Carvalho, Jay D. Keasling and Pablo Cruz-Morales

Annual Review of Biochemistry, 2024, 93, 411
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