Review
Biochemistry & Molecular Biology
Brett C. Covington, Fei Xu, Mohammad R. Seyedsayamdost
Summary: Microbial natural products are important for therapeutic leads and research innovation. Silent biosynthetic gene clusters in bacteria contain hidden reservoirs of potential natural products. Various methods have been developed to interrogate these silent clusters, with different strategies and approaches for each category.
ANNUAL REVIEW OF BIOCHEMISTRY, VOL 90, 2021
(2021)
Article
Microbiology
Peng Hou, Vincent V. Nowak, Chanel J. Taylor, Mark J. Calcott, Allison Knight, Jeremy G. Owen
Summary: In this study, 322 actinomycetes were isolated and their genome sequences were obtained from New Zealand lichens. By enumerating biosynthetic gene clusters (BGCs) and comparing to reference collections, it was found that actinomycetes from New Zealand lichens have the genetic capacity to produce large numbers of natural products, which are expected to be different from those identified in previous soil-based studies. This study sheds light on the actinomycete assemblage in New Zealand lichens and highlights the potential of lichen-sourced actinobacteria for discovering new secondary metabolites.
Article
Multidisciplinary Sciences
Vincent Libis, Logan W. MacIntyre, Rabia Mehmood, Liliana Guerrero, Melinda A. Ternei, Niv Antonovsky, Jan Burian, Zongqiang Wang, Sean F. Brady
Summary: The study presents a parallelized method for identifying, mobilizing, and heterologously expressing bacterial gene clusters (BGCs), leading to the discovery of therapeutically relevant bioactive molecules. The approach efficiently localizes clones carrying intact BGCs, resulting in the identification of several natural products.
NATURE COMMUNICATIONS
(2022)
Article
Biology
Satria A. Kautsar, Justin J. J. van der Hooft, Dick de Ridder, Marnix H. Medema
Summary: BiG-SLiCE is a tool designed to cluster massive numbers of BGCs by representing them in Euclidean space to group BGCs into GCFs in a non-pairwise, near-linear fashion. It was used to analyze over 1.2 million BGCs collected from microbial genomes and metagenome-assembled genomes within 10 days. The tool offers a query mode to efficiently place newly sequenced BGCs into previously computed GCFs, along with a powerful output visualization engine for user-friendly data exploration.
Article
Microbiology
Darwin Linardi, Weiyi She, Qian Zhang, Yi Yu, Pei-Yuan Qian, Henry Lam
Summary: The study developed a high throughput proteomics-based method to complement genome mining methods for the identification of biosynthetic pathways in Streptomyces species.
FRONTIERS IN MICROBIOLOGY
(2022)
Review
Biotechnology & Applied Microbiology
Wenfang Wang, Guosong Zheng, Yinhua Lu
Summary: Recent advances in cloning strategies of microbial natural product biosynthetic gene clusters focus on efficiently capturing BGCs, selecting and optimizing vectors for carrying large-size DNA, and methods for assembling targeted DNA fragments with appropriate vectors. The future direction aims to develop novel, universal, and high-efficiency methods for cloning NP BGCs.
FRONTIERS IN BIOENGINEERING AND BIOTECHNOLOGY
(2021)
Article
Agriculture, Multidisciplinary
Jin-Tao Cheng, Han-Min Wang, Jia-Hui Yu, Chen-Fan Sun, Fei Cao, Xin-Hang Jiang, Xin-Ai Chen, Qing-Wei Zhao, Li-She Gan, Rong-Rong Xie, Shi-Lei Wang, Jia Li, Yi Zang, Xu-Ming Mao
Summary: A novel compound identified from an engineered fungus showed promising bioactivity in suppressing liver fibrosis, suggesting potential for pharmaceutical development or dietary therapy.
JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY
(2021)
Article
Biotechnology & Applied Microbiology
Guang-Lei Ma, Lingyi Xin, Yanghui Liao, Zhi-Soon Chong, Hartono Candra, Li Mei Pang, Sean Qiu En Lee, Martin Muthee Gakuubi, Siew Bee Ng, Zhao-Xun Liang
Summary: Angucyclines are structurally diverse, aromatic polyketides with potent bioactivity. The biosynthetic origin of their structural complexity and diversity has attracted considerable attention. In this study, a Streptomyces strain that produces balmoralmycin and related compounds was identified. The biosynthetic gene cluster for balmoralmycin was characterized, and a proposed biosynthetic pathway was established. The elucidation of the biosynthesis of balmoralmycin provides insights into the origin of structural diversity in angucyclines.
APPLIED AND ENVIRONMENTAL MICROBIOLOGY
(2022)
Article
Microbiology
Vinod K. Gupta, Utpal Bakshi, Daniel Chang, Aileen R. Lee, John M. M. Davis III, Sriram Chandrasekaran, Yong-Su Jin, Michael F. Freeman, Jaeyun Sung
Summary: Researchers present an automated computational pipeline called TaxiBGC, which can predict experimentally characterized BGCs and infer their known secondary metabolites (SMs) in shotgun metagenomes by considering the microbial species source. TaxiBGC shows significant advantages over existing methods based on rigorous benchmarking on simulated metagenomes. By applying TaxiBGC on thousands of human microbiome samples, they associate BGCs encoding bacteriocins with different human body sites and diseases, revealing a possible novel role of this antibiotic class in maintaining the stability of microbial ecosystems throughout the human body. Additionally, they report for the first time gut microbial BGC associations shared among multiple pathologies. Ultimately, TaxiBGC is expected to facilitate future investigations into the chemical ecology of microbial communities across diverse niches and pathologies.
Review
Chemistry, Multidisciplinary
Hai-Yan He, Haruka Niikura, Yi-Ling Du, Katherine S. Ryan
Summary: This review summarizes synthetic and biosynthetic approaches to diverse nitrogen-nitrogen-bond-containing functional groups, with a focus on biosynthetic pathways and enzymes.
CHEMICAL SOCIETY REVIEWS
(2022)
Article
Multidisciplinary Sciences
Samar M. Abdelrahman, Nastassia Patin, Amro Hanora, Akram Aboseidah, Shimaa Desoky, Salha G. Desoky, Frank J. Stewart, Nicole B. Lopanik
Summary: Bacteria associated with marine nudibranchs show potential as a rich source of bioactive compounds and natural product biosynthetic genes. Some of these bacteria exhibit antimicrobial and antitumor activities, and they contain gene clusters for natural product biosynthesis.
Article
Microbiology
Alberto C. Rodriguez-Sanchez, Luz A. Gonzalez-Salazar, Lorena Rodriguez-Orduna, Andres Cumsille, Agustina Undabarrena, Beatriz Camara, Nelly Selem-Mojica, Cuauhtemoc Licona-Cassani
Summary: In this study, a phylogenetic analysis was proposed to classify biosynthetic gene clusters (BGCs) into regulatory mechanisms based on protein domain information. The study focused on actinobacterial strains from different environments and found that despite environmental variations, the isolated microorganisms shared similar regulatory mechanisms, suggesting the potential to activate new BGCs using known activators.
FRONTIERS IN MICROBIOLOGY
(2023)
Article
Chemistry, Multidisciplinary
Eduard Ebberink, Simon Fernandes, Georgios Hatzopoulos, Ninad Agashe, Po-Han Chang, Nora Guidotti, Timothy M. Reichart, Luc Reymond, Marie-Claire Velluz, Fabian Schneider, Cedric Pourroy, Carsten Janke, Pierre Gonczy, Beat Fierz, Charlotte Aumeier
Summary: Microtubules, an essential component of the cytoskeleton, carry post-translational modifications (PTMs) that are crucial for cellular regulation. The study demonstrates that polyglutamylation of a-tubulin promotes its detyrosination, and the length of polyglutamyl chains affects this process. Manipulating polyglutamylation levels in cells also leads to changes in detyrosination, confirming the connection between these two modifications.
Article
Environmental Sciences
Ao-Qi Du, Ti-Ti Ying, Zhen-Yi Zhou, Wen-Chao Yu, Gang-Ao Hu, Xian Luo, Man-Jing Ma, Yan-Lei Yu, Hong Wang, Bin Wei
Summary: Photorhabdus strains have a rich potential for non-ribosomal peptide biosynthesis, particularly in terms of their NRPS BGCs. These NRPS BGCs are diverse and novel, with many encoding known bioactive peptides. Molecular similarity network analysis revealed that the non-ribosomal peptide biosynthetic potential of Photorhabdus is largely untapped, highlighting the core peptides that deserve further study.
ENVIRONMENTAL MICROBIOLOGY REPORTS
(2022)
Article
Biotechnology & Applied Microbiology
Wenli Guo, Zhihong Xiao, Tingting Huang, Kai Zhang, Hai-Xue Pan, Gong-Li Tang, Zixin Deng, Rubing Liang, Shuangjun Lin
Summary: A strong constitutive promoter, stnYp, was identified in Streptomyces flocculus CGMCC4.1223, which effectively activated silent biosynthetic genes and improved heterologous gene expression in various Streptomyces hosts.
MICROBIAL CELL FACTORIES
(2023)