1
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Tang J, Matsuda Y. Discovery of fungal onoceroid triterpenoids through domainless enzyme-targeted global genome mining. Nat Commun 2024; 15:4312. [PMID: 38773118 PMCID: PMC11109268 DOI: 10.1038/s41467-024-48771-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2023] [Accepted: 05/09/2024] [Indexed: 05/23/2024] Open
Abstract
Genomics-guided methodologies have revolutionized the discovery of natural products. However, a major challenge in the field of genome mining is determining how to selectively extract biosynthetic gene clusters (BGCs) for untapped natural products from numerous available genome sequences. In this study, we developed a fungal genome mining tool that extracts BGCs encoding enzymes that lack a detectable protein domain (i.e., domainless enzymes) and are not recognized as biosynthetic proteins by existing bioinformatic tools. We searched for BGCs encoding a homologue of Pyr4-family terpene cyclases, which are representative examples of apparently domainless enzymes, in approximately 2000 fungal genomes and discovered several BGCs with unique features. The subsequent characterization of selected BGCs led to the discovery of fungal onoceroid triterpenoids and unprecedented onoceroid synthases. Furthermore, in addition to the onoceroids, a previously unreported sesquiterpene hydroquinone, of which the biosynthesis involves a Pyr4-family terpene cyclase, was obtained. Our genome mining tool has broad applicability in fungal genome mining and can serve as a beneficial platform for accessing diverse, unexploited natural products.
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Affiliation(s)
- Jia Tang
- Department of Chemistry, City University of Hong Kong, Tat Chee Avenue, Kowloon, Hong Kong SAR, China
| | - Yudai Matsuda
- Department of Chemistry, City University of Hong Kong, Tat Chee Avenue, Kowloon, Hong Kong SAR, China.
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2
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Hagar M, Morgan KD, Stumpf SD, Tsingos M, Banuelos CA, Sadar MD, Blodgett JAV, Andersen RJ, Ryan KS. Piperazate-Guided Isolation of Caveamides A and B, Cyclohexenylalanine-Containing Nonribosomal Peptides from a Cave Actinomycete. Org Lett 2024; 26:4127-4131. [PMID: 38718303 DOI: 10.1021/acs.orglett.4c01218] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/18/2024]
Abstract
Hybrid genome-mining/15N-NMR was used to target compounds containing piperazate (Piz) residues, leading to the discovery of caveamides A (1) and B (2) from Streptomyces sp. strain BE230, isolated from New Rankin Cave (Missouri). Caveamides are highly dynamic molecules containing an unprecedented β-ketoamide polyketide fragment, two Piz residues, and a new N-methyl-cyclohexenylalanine residue. Caveamide B (2) exhibited nanomolar cytotoxicity against several cancer cell lines and nanomolar antimicrobial activity against MRSA and E. coli.
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Affiliation(s)
- Mostafa Hagar
- Department of Chemistry, The University of British Columbia, Vancouver, British Columbia Canada V6T 1Z4
| | - Kalindi D Morgan
- Department of Chemistry, The University of British Columbia, Vancouver, British Columbia Canada V6T 1Z4
| | - Spencer D Stumpf
- Department of Biology, Washington University in St Louis, St Louis Missouri 63122, United States
| | - Maya Tsingos
- Department of Biology, Washington University in St Louis, St Louis Missouri 63122, United States
| | - Carmen A Banuelos
- Department of Genome Sciences, BC Cancer, Vancouver, British Columbia Canada V5Z 1L3
| | - Marianne D Sadar
- Department of Genome Sciences, BC Cancer, Vancouver, British Columbia Canada V5Z 1L3
| | - Joshua A V Blodgett
- Department of Biology, Washington University in St Louis, St Louis Missouri 63122, United States
| | - Raymond J Andersen
- Department of Chemistry, The University of British Columbia, Vancouver, British Columbia Canada V6T 1Z4
- Department of Earth, Ocean, and Atmospheric Sciences, The University of British Columbia, Vancouver, British Columbia Canada V6T 1Z4
| | - Katherine S Ryan
- Department of Chemistry, The University of British Columbia, Vancouver, British Columbia Canada V6T 1Z4
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3
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Pelton JM, Hochuli JE, Sadecki PW, Katoh T, Suga H, Hicks LM, Muratov EN, Tropsha A, Bowers AA. Cheminformatics-Guided Cell-Free Exploration of Peptide Natural Products. J Am Chem Soc 2024; 146:8016-8030. [PMID: 38470819 DOI: 10.1021/jacs.3c11306] [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] [Indexed: 03/14/2024]
Abstract
There have been significant advances in the flexibility and power of in vitro cell-free translation systems. The increasing ability to incorporate noncanonical amino acids and complement translation with recombinant enzymes has enabled cell-free production of peptide-based natural products (NPs) and NP-like molecules. We anticipate that many more such compounds and analogs might be accessed in this way. To assess the peptide NP space that is directly accessible to current cell-free technologies, we developed a peptide parsing algorithm that breaks down peptide NPs into building blocks based on ribosomal translation logic. Using the resultant data set, we broadly analyze the biophysical properties of these privileged compounds and perform a retrobiosynthetic analysis to predict which peptide NPs could be directly synthesized in augmented cell-free translation reactions. We then tested these predictions by preparing a library of highly modified peptide NPs. Two macrocyclases, PatG and PCY1, were used to effect the head-to-tail macrocyclization of candidate NPs. This retrobiosynthetic analysis identified a collection of high-priority building blocks that are enriched throughout peptide NPs, yet they had not previously been tested in cell-free translation. To expand the cell-free toolbox into this space, we established, optimized, and characterized the flexizyme-enabled ribosomal incorporation of piperazic acids. Overall, these results demonstrate the feasibility of cell-free translation for peptide NP total synthesis while expanding the limits of the technology. This work provides a novel computational tool for exploration of peptide NP chemical space, that could be expanded in the future to allow design of ribosomal biosynthetic pathways for NPs and NP-like molecules.
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Affiliation(s)
- Jarrett M Pelton
- Division of Chemical Biology and Medicinal Chemistry, UNC Eshelman School of Pharmacy, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599, United States
| | - Joshua E Hochuli
- Curriculum in Bioinformatics and Computational Biology, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599, United States
| | - Patric W Sadecki
- Department of Chemistry, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599, United States
| | - Takayuki Katoh
- Department of Chemistry, Graduate School of Science, The University of Tokyo, Tokyo, 113-0033, Japan
| | - Hiroaki Suga
- Department of Chemistry, Graduate School of Science, The University of Tokyo, Tokyo, 113-0033, Japan
| | - Leslie M Hicks
- Department of Chemistry, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599, United States
- Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599, United States
| | - Eugene N Muratov
- Division of Chemical Biology and Medicinal Chemistry, UNC Eshelman School of Pharmacy, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599, United States
| | - Alexander Tropsha
- Division of Chemical Biology and Medicinal Chemistry, UNC Eshelman School of Pharmacy, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599, United States
| | - Albert A Bowers
- Division of Chemical Biology and Medicinal Chemistry, UNC Eshelman School of Pharmacy, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599, United States
- Department of Chemistry, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599, United States
- Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599, United States
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4
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Sun R, You R, Yu X, Zhao D, Li L. Discovery and Synthesis of a Gram-Negative-Active Cationic Lipopeptide Antibiotic Inspired by Primary Sequences from Underexplored Gram-Negative Bacteria. Org Lett 2024; 26:1348-1352. [PMID: 38341869 DOI: 10.1021/acs.orglett.3c04232] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/13/2024]
Abstract
The emergence of multidrug-resistant Gram-negative pathogens poses a serious threat to global health. Gram-negative bacteria have become increasingly recognized as underexplored sources of Gram-negative-active cationic lipopeptide (CLP) antibiotics. We systematically screened 8982 sequenced genomes from 42 underexplored Gram-negative bacterial genera and identified eight potential CLP biosynthetic gene clusters. Their predicted products were rapidly accessed by solid-phase total synthesis, which led to the novel antibiotic chospeptin with good activities against clinically isolated colistin-resistant Gram-negative pathogens.
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Affiliation(s)
- Runze Sun
- State Key Laboratory of Microbial Metabolism and School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, 800 Dongchuan Road, Shanghai 200240, China
| | - Ruixiang You
- State Key Laboratory of Microbial Metabolism and School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, 800 Dongchuan Road, Shanghai 200240, China
- College of Life Sciences, Shanghai Normal University, 100 Guilin Road, Shanghai 200234, China
| | - Xuchang Yu
- State Key Laboratory of Microbial Metabolism and School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, 800 Dongchuan Road, Shanghai 200240, China
- State Key Laboratory of Bioreactor Engineering and School of Biotechnology, East China University of Science and Technology, 130 Meilong Road, Shanghai 200237, China
| | - Di Zhao
- State Key Laboratory of Microbial Metabolism and School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, 800 Dongchuan Road, Shanghai 200240, China
| | - Lei Li
- State Key Laboratory of Microbial Metabolism and School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, 800 Dongchuan Road, Shanghai 200240, China
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5
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Li Q, Li S, Li S, Hao X, Wang A, Si S, Xu Y, Shu J, Gan M. Antimicrobial and Anti-inflammatory Cyclic Tetrapeptides from the Co-cultures of Two Marine-Derived Fungi. JOURNAL OF NATURAL PRODUCTS 2024; 87:365-370. [PMID: 38276888 DOI: 10.1021/acs.jnatprod.3c01115] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/27/2024]
Abstract
Violaceotides B-E (1-4), four new cyclic tetrapeptides, along with seven known compounds, were identified from the sponge-associated Aspergillus insulicola IMB18-072 co-cultivated with the marine-derived Alternaria angustiovoidea IMB20-805. Their structures were elucidated by extensive analysis of spectroscopic data, including HRESIMS, 1D and 2D NMR, and MS/MS data. The absolute configurations were determined by the advanced Marfey's method. Compounds 2, 3, and violaceotide A (5) displayed selective antimicrobial activities against the aquatic pathogenic bacteria Edwardsiella tarda and E. ictaluri. In addition, compounds 1-5 showed inhibitory activities against the LPS-induced expression of the inflammatory mediator IL-6 in RAW264.7 cells at a concentration of 10 μM.
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Affiliation(s)
- Qin Li
- Institute of Medicinal Biotechnology, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing 100050, People's Republic of China
- Key Laboratory of Modern Preparation of Traditional Chinese Medicines, Ministry of Education, Jiangxi University of Traditional Chinese Medicine, Nanchang 330004, People's Republic of China
| | - Shasha Li
- Institute of Medicinal Biotechnology, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing 100050, People's Republic of China
| | - Shunwang Li
- Institute of Medicinal Biotechnology, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing 100050, People's Republic of China
| | - Xiaomeng Hao
- Institute of Medicinal Biotechnology, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing 100050, People's Republic of China
| | - Anqi Wang
- Institute of Medicinal Biotechnology, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing 100050, People's Republic of China
| | - Shuyi Si
- Institute of Medicinal Biotechnology, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing 100050, People's Republic of China
| | - Yanni Xu
- Institute of Medicinal Biotechnology, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing 100050, People's Republic of China
| | - Jicheng Shu
- Key Laboratory of Modern Preparation of Traditional Chinese Medicines, Ministry of Education, Jiangxi University of Traditional Chinese Medicine, Nanchang 330004, People's Republic of China
| | - Maoluo Gan
- Institute of Medicinal Biotechnology, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing 100050, People's Republic of China
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6
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Yan D, Matsuda Y. Global genome mining-driven discovery of an unusual biosynthetic logic for fungal polyketide-terpenoid hybrids. Chem Sci 2024; 15:3011-3017. [PMID: 38404388 PMCID: PMC10882540 DOI: 10.1039/d3sc06001b] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2023] [Accepted: 01/16/2024] [Indexed: 02/27/2024] Open
Abstract
Genome mining has facilitated the efficient discovery of untapped natural products. We performed global genome mining in fungi and discovered a series of biosynthetic gene clusters (BGCs) that appeared to afford polyketide-terpenoid hybrids via a distinct biosynthetic mechanism from those adopted by known pathways. Characterization of one of the BGCs revealed that it yields the drimane-phthalide hybrid 1. During the biosynthesis of 1, the farnesyl group is unusually introduced by the dimethylallyltryptophan synthase-type prenyltransferase MfmD and is then cyclized by the Pyr4-family terpene cyclase MfmH. The replacement of MfmH with its homologue OcdTC gave another hybrid molecule with a monocyclic terpenoid moiety. Moreover, PsetPT, an MfmD homologue, was found to perform dimethylallylation and was then engineered to install a geranyl group. Our study unraveled an unusual biosynthetic mechanism for fungal phthalide-terpenoid hybrids and provided insights into how their structural diversification could be achieved.
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Affiliation(s)
- Dexiu Yan
- Department of Chemistry, City University of Hong Kong Tat Chee Avenue Kowloon Hong Kong SAR China
| | - Yudai Matsuda
- Department of Chemistry, City University of Hong Kong Tat Chee Avenue Kowloon Hong Kong SAR China
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7
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Liu W, Tian X, Huang X, Malit JJL, Wu C, Guo Z, Tang JW, Qian PY. Discovery of P450-Modified Sesquiterpenoids Levinoids A-D through Global Genome Mining. JOURNAL OF NATURAL PRODUCTS 2024. [PMID: 38377956 DOI: 10.1021/acs.jnatprod.3c01136] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/22/2024]
Abstract
Cytochrome P450-modified bacterial terpenoids remain in a vast chemical space to be explored. In the present study, we conducted global genome mining of 223,829 bacterial genomes and identified 2892 bacterial terpenoid biosynthetic gene clusters (BGCs) with cytochrome P450 genes. Among these, we selected 562 with multiple P450 enzymes, which were further clustered as 355 gene cluster families by sequence similarity analysis. We then chose lev, a BGC from Streptomyces levis MCCC1A01616, for heterologous expression and discovered four new α-amorphene-type sesquiterpenoids, levinoids A-D (1-4). The structures and absolute configurations of these four new compounds were determined by employing extensive NMR analysis, NMR chemical shift calculations with DP4+, and ECD calculations. Furthermore, levinoid C (3) exhibited a moderate level of neuroprotective activity (EC50 = 21 μM) in the glutamate-induced excitotoxicity cell model. Our findings highlight the untapped chemical diversity of P450-modified bacterial terpenoids, opening new avenues for further exploration and discovery.
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Affiliation(s)
- Wenchao Liu
- Department of Ocean Science and Hong Kong Branch of Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou), The Hong Kong University of Science and Technology, Kowloon, Hong Kong, China
- Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou), Guangzhou 511458, China
- Division of Emerging Interdisciplinary Areas, The Hong Kong University of Science and Technology, Kowloon, Hong Kong, China
| | - Xueying Tian
- Department of Ocean Science and Hong Kong Branch of Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou), The Hong Kong University of Science and Technology, Kowloon, Hong Kong, China
- Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou), Guangzhou 511458, China
| | - Xin Huang
- Department of Ocean Science and Hong Kong Branch of Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou), The Hong Kong University of Science and Technology, Kowloon, Hong Kong, China
- Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou), Guangzhou 511458, China
| | | | - Chuanhai Wu
- Department of Ocean Science and Hong Kong Branch of Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou), The Hong Kong University of Science and Technology, Kowloon, Hong Kong, China
- Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou), Guangzhou 511458, China
| | - Zhihong Guo
- Department of Chemistry, Department of Physics, and Bioengineering Program, The Hong Kong University of Science and Technology, Kowloon, Hong Kong, China
| | - Jian-Wei Tang
- Department of Ocean Science and Hong Kong Branch of Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou), The Hong Kong University of Science and Technology, Kowloon, Hong Kong, China
- Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou), Guangzhou 511458, China
| | - Pei-Yuan Qian
- Department of Ocean Science and Hong Kong Branch of Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou), The Hong Kong University of Science and Technology, Kowloon, Hong Kong, China
- Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou), Guangzhou 511458, China
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8
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Li H, Ding W, Zhang Q. Discovery and engineering of ribosomally synthesized and post-translationally modified peptide (RiPP) natural products. RSC Chem Biol 2024; 5:90-108. [PMID: 38333193 PMCID: PMC10849128 DOI: 10.1039/d3cb00172e] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2023] [Accepted: 11/17/2023] [Indexed: 02/10/2024] Open
Abstract
Ribosomally synthesized and post-translationally modified peptides (RiPPs) represent a diverse superfamily of natural products with immense potential for drug development. This review provides a concise overview of the recent advances in the discovery of RiPP natural products, focusing on rational strategies such as bioactivity guided screening, enzyme or precursor-based genome mining, and biosynthetic engineering. The challenges associated with activating silent biosynthetic gene clusters and the development of elaborate catalytic systems are also discussed. The logical frameworks emerging from these research studies offer valuable insights into RiPP biosynthesis and engineering, paving the way for broader pharmaceutic applications of these peptide natural products.
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Affiliation(s)
- He Li
- Department of Chemistry, Fudan University Shanghai 200433 China
| | - Wei Ding
- State Key Laboratory of Microbial Metabolism, School of Life Sciences & Biotechnology, Shanghai Jiao Tong University Shanghai 200240 China
| | - Qi Zhang
- Department of Chemistry, Fudan University Shanghai 200433 China
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9
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Hussain H. How can we unlock the full potential of marine biological resources for novel drug discovery in an effective and ethical way? Expert Opin Drug Discov 2024; 19:125-130. [PMID: 37994413 DOI: 10.1080/17460441.2023.2285402] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2023] [Accepted: 11/15/2023] [Indexed: 11/24/2023]
Affiliation(s)
- Hidayat Hussain
- Department of Bioorganic Chemistry, Leibniz Institute of Plant Biochemistry, Halle (Saale), Germany
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10
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Messenger SR, McGuinniety EMR, Stevenson LJ, Owen JG, Challis GL, Ackerley DF, Calcott MJ. Metagenomic domain substitution for the high-throughput modification of nonribosomal peptides. Nat Chem Biol 2024; 20:251-260. [PMID: 37996631 DOI: 10.1038/s41589-023-01485-1] [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: 06/01/2023] [Accepted: 10/12/2023] [Indexed: 11/25/2023]
Abstract
The modular nature of nonribosomal peptide biosynthesis has driven efforts to generate peptide analogs by substituting amino acid-specifying domains within nonribosomal peptide synthetase (NRPS) enzymes. Rational NRPS engineering has increasingly focused on finding evolutionarily favored recombination sites for domain substitution. Here we present an alternative evolution-inspired approach that involves large-scale diversification and screening. By amplifying amino acid-specifying domains en masse from soil metagenomic DNA, we substitute more than 1,000 unique domains into a pyoverdine NRPS. Initial fluorescence and mass spectrometry screens followed by sequencing reveal more than 100 functional domain substitutions, collectively yielding 16 distinct pyoverdines as major products. This metagenomic approach does not require the high success rates demanded by rational NRPS engineering but instead enables the exploration of large numbers of substitutions in parallel. This opens possibilities for the discovery and production of nonribosomal peptides with diverse biological activities.
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Affiliation(s)
- Sarah R Messenger
- School of Biological Sciences, Victoria University of Wellington, Wellington, New Zealand
- Maurice Wilkins Centre for Molecular Biodiscovery, Victoria University of Wellington, Wellington, New Zealand
| | - Edward M R McGuinniety
- School of Biological Sciences, Victoria University of Wellington, Wellington, New Zealand
- Maurice Wilkins Centre for Molecular Biodiscovery, Victoria University of Wellington, Wellington, New Zealand
| | - Luke J Stevenson
- School of Biological Sciences, Victoria University of Wellington, Wellington, New Zealand
- Maurice Wilkins Centre for Molecular Biodiscovery, Victoria University of Wellington, Wellington, New Zealand
- Ferrier Research Institute, Victoria University of Wellington, Wellington, New Zealand
| | - Jeremy G Owen
- School of Biological Sciences, Victoria University of Wellington, Wellington, New Zealand
- Maurice Wilkins Centre for Molecular Biodiscovery, Victoria University of Wellington, Wellington, New Zealand
| | - Gregory L Challis
- Department of Chemistry, University of Warwick, Coventry, UK
- Warwick Integrative Synthetic Biology Centre, University of Warwick, Coventry, UK
- Biomedicine Discovery Institute, Department of Biochemistry and Molecular Biology, Monash University, Clayton, Victoria, Australia
- ARC Centre of Excellence for Innovations in Peptide and Protein Science, Monash University, Clayton, Victoria, Australia
| | - David F Ackerley
- School of Biological Sciences, Victoria University of Wellington, Wellington, New Zealand.
- Maurice Wilkins Centre for Molecular Biodiscovery, Victoria University of Wellington, Wellington, New Zealand.
| | - Mark J Calcott
- School of Biological Sciences, Victoria University of Wellington, Wellington, New Zealand.
- Maurice Wilkins Centre for Molecular Biodiscovery, Victoria University of Wellington, Wellington, New Zealand.
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11
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Cao J, Yang B, Zhang M, Yu F. Regulation of T16H subcellular localization for promoting its catalytic efficiency in yeast cells. Biotechnol Lett 2024; 46:29-35. [PMID: 37971563 DOI: 10.1007/s10529-023-03442-3] [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: 06/23/2023] [Revised: 09/03/2023] [Accepted: 10/16/2023] [Indexed: 11/19/2023]
Abstract
To investigate the effect of subcellular localization on the transformation efficiency of heterologous expressed functional P450s in yeast. Microbial biotransformation offers a promising substitute for the direct extraction of natural products, but its viability in industrial applications depends on achieving high transformation efficiencies. To investigate the influence of subcellular microenvironments on the activity of heterologously expressed P450s, Catharanthus roseus tabersonine 16-hydroxylase (T16H) was chosen, and its subcellular localization was regulated by fusing organelle-localization signals. Interestingly, this manipulation had no effect on the gene expression levels of T16H, but resulted in varying conversion rates from tabersonine to 16-hydroxy tabersonine. Notably, the highest transformation efficiency was observed in yeast cells expressing peroxisome-localized T16H. Given the alkaline pH optimum for P450s, the alkaline peroxisomal lumen could be a suitable compartment for P450s reactions to achieve high transformation efficiency using yeast cells. Different organelle-localization of T16H in yeast cells resulted in varying conversion rates, suggesting that compartmentalizing the expression of target enzymes could be a viable approach to increase transformation efficiency in yeast.
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Affiliation(s)
- Jiancong Cao
- School of Biological Engineering, Dalian Polytechnic University, Dalian, 116034, China
| | - Bingrun Yang
- School of Biological Engineering, Dalian Polytechnic University, Dalian, 116034, China
| | - Mengxia Zhang
- School of Biological Engineering, Dalian Polytechnic University, Dalian, 116034, China
| | - Fang Yu
- School of Biological Engineering, Dalian Polytechnic University, Dalian, 116034, China.
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12
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Baranova MN, Pilipenko EA, Gabibov AG, Terekhov SS, Smirnov IV. Animal Microbiomes as a Source of Novel Antibiotic-Producing Strains. Int J Mol Sci 2023; 25:537. [PMID: 38203702 PMCID: PMC10779147 DOI: 10.3390/ijms25010537] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2023] [Revised: 12/25/2023] [Accepted: 12/27/2023] [Indexed: 01/12/2024] Open
Abstract
Natural compounds continue to serve as the most fruitful source of new antimicrobials. Analysis of bacterial genomes have revealed that the biosynthetic potential of antibiotic producers by far exceeds the number of already discovered structures. However, due to the repeated discovery of known substances, it has become necessary to change both approaches to the search for antibiotics and the sources of producer strains. The pressure of natural selection and the diversity of interactions in symbiotic communities make animal microbiomes promising sources of novel substances. Here, microorganisms associated with various animals were examined in terms of their antimicrobial agents. The application of alternative cultivation techniques, ultrahigh-throughput screening, and genomic analysis facilitated the investigation of compounds produced by unique representatives of the animal microbiota. We believe that new strategies of antipathogen defense will be discovered by precisely studying cell-cell and host-microbe interactions in microbiomes in the wild.
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Affiliation(s)
- Margarita N. Baranova
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry of the Russian Academy of Sciences, 117997 Moscow, Russia; (M.N.B.); (A.G.G.)
| | - Ekaterina A. Pilipenko
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry of the Russian Academy of Sciences, 117997 Moscow, Russia; (M.N.B.); (A.G.G.)
| | - Alexander G. Gabibov
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry of the Russian Academy of Sciences, 117997 Moscow, Russia; (M.N.B.); (A.G.G.)
- Department of Chemistry, Lomonosov Moscow State University, 119991 Moscow, Russia
| | - Stanislav S. Terekhov
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry of the Russian Academy of Sciences, 117997 Moscow, Russia; (M.N.B.); (A.G.G.)
- Department of Chemistry, Lomonosov Moscow State University, 119991 Moscow, Russia
| | - Ivan V. Smirnov
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry of the Russian Academy of Sciences, 117997 Moscow, Russia; (M.N.B.); (A.G.G.)
- Department of Chemistry, Lomonosov Moscow State University, 119991 Moscow, Russia
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13
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Li X, Gadar-Lopez AE, Chen L, Jayachandran S, Cruz-Morales P, Keasling JD. Mining natural products for advanced biofuels and sustainable bioproducts. Curr Opin Biotechnol 2023; 84:103003. [PMID: 37769513 DOI: 10.1016/j.copbio.2023.103003] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2023] [Revised: 09/03/2023] [Accepted: 09/03/2023] [Indexed: 10/03/2023]
Abstract
Recently, there has been growing interest in the sustainable production of biofuels and bioproducts derived from renewable sources. Natural products, the largest and more structurally diverse group of metabolites, hold significant promise as sources for such bio-based products. However, there are two primary challenges in harnessing natural products' potential: precise mining of biosynthetic gene clusters (BGCs) that can be used as scaffolds or bioparts and their functional expression for biofuel and bioproduct manufacture. In this review, we explore recent advances in the development of bioinformatic tools for BGC mining and the manipulation of various hosts for natural product-based biofuels and bioproducts manufacture. Moreover, we discuss potential strategies for expanding the chemical diversity of biofuels and bioproducts and enhancing their overall yield.
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Affiliation(s)
- Xiaowei Li
- Novo Nordisk Foundation Center for Biosustainability, Danmarks Tekniske Universitet, Kongens Lyngby, Denmark
| | - Adrian E Gadar-Lopez
- Novo Nordisk Foundation Center for Biosustainability, Danmarks Tekniske Universitet, Kongens Lyngby, Denmark
| | - Ling Chen
- Novo Nordisk Foundation Center for Biosustainability, Danmarks Tekniske Universitet, Kongens Lyngby, Denmark
| | - Sidharth Jayachandran
- Novo Nordisk Foundation Center for Biosustainability, Danmarks Tekniske Universitet, Kongens Lyngby, Denmark
| | - Pablo Cruz-Morales
- Novo Nordisk Foundation Center for Biosustainability, Danmarks Tekniske Universitet, Kongens Lyngby, Denmark.
| | - Jay D Keasling
- Novo Nordisk Foundation Center for Biosustainability, Danmarks Tekniske Universitet, Kongens Lyngby, Denmark; Lawrence Berkeley National Laboratory, Biological Systems and Engineering Division, Berkeley, CA, USA; Joint BioEnergy Institute, Emeryville, CA, USA; Departments of Chemical & Biomolecular Engineering and of Bioengineering, University of California, Berkeley, CA 94720, USA; Center for Synthetic Biochemistry, Shenzhen Institutes for Advanced Technologies, Shenzhen, China.
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14
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King AM, Zhang Z, Glassey E, Siuti P, Clardy J, Voigt CA. Systematic mining of the human microbiome identifies antimicrobial peptides with diverse activity spectra. Nat Microbiol 2023; 8:2420-2434. [PMID: 37973865 DOI: 10.1038/s41564-023-01524-6] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2022] [Accepted: 10/12/2023] [Indexed: 11/19/2023]
Abstract
Human-associated bacteria secrete modified peptides to control host physiology and remodel the microbiota species composition. Here we scanned 2,229 Human Microbiome Project genomes of species colonizing skin, gastrointestinal tract, urogenital tract, mouth and trachea for gene clusters encoding RiPPs (ribosomally synthesized and post-translationally modified peptides). We found 218 lanthipeptides and 25 lasso peptides, 70 of which were synthesized and expressed in E. coli and 23 could be purified and functionally characterized. They were tested for activity against bacteria associated with healthy human flora and pathogens. New antibiotics were identified against strains implicated in skin, nasal and vaginal dysbiosis as well as from oral strains selectively targeting those in the gut. Extended- and narrow-spectrum antibiotics were found against methicillin-resistant Staphylococcus aureus and vancomycin-resistant Enterococci. Mining natural products produced by human-associated microbes will enable the elucidation of ecological relationships and may be a rich resource for antimicrobial discovery.
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Affiliation(s)
- Andrew M King
- Synthetic Biology Center, Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Zhengan Zhang
- Synthetic Biology Center, Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Emerson Glassey
- Synthetic Biology Center, Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Piro Siuti
- Synthetic Biology Group, Global Discovery Chemistry, Novartis Institutes for BioMedical Research, Cambridge, MA, USA
| | - Jon Clardy
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA, USA
| | - Christopher A Voigt
- Synthetic Biology Center, Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA, USA.
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15
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Chen JW, Chen S, Chen GQ. Recent advances in natural compounds inducing non-apoptotic cell death for anticancer drug resistance. CANCER DRUG RESISTANCE (ALHAMBRA, CALIF.) 2023; 6:729-747. [PMID: 38239395 PMCID: PMC10792489 DOI: 10.20517/cdr.2023.78] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/08/2023] [Revised: 09/22/2023] [Accepted: 10/10/2023] [Indexed: 01/22/2024]
Abstract
The induction of cell death is recognized as a potent strategy for cancer treatment. Apoptosis is an extensively studied form of cell death, and multiple anticancer drugs exert their therapeutic effects by inducing it. Nonetheless, apoptosis evasion is a hallmark of cancer, rendering cancer cells resistant to chemotherapy drugs. Consequently, there is a growing interest in exploring novel non-apoptotic forms of cell death, such as ferroptosis, necroptosis, pyroptosis, and paraptosis. Natural compounds with anticancer properties have garnered significant attention due to their advantages, including a reduced risk of drug resistance. Over the past two decades, numerous natural compounds have been discovered to exert anticancer and anti-resistance effects by triggering these four non-apoptotic cell death mechanisms. This review primarily focuses on these four non-apoptotic cell death mechanisms and their recent advancements in overcoming drug resistance in cancer treatment. Meanwhile, it highlights the role of natural compounds in effectively addressing cancer drug resistance through the induction of these forms of non-apoptotic cell death.
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Affiliation(s)
- Jia-Wen Chen
- Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing 100193, China
- State Key Laboratory of Chinese Medicine and Molecular Pharmacology (Incubation), The Hong Kong Polytechnic University Shenzhen Research Institute, Shenzhen 518057, Guangdong, China
| | - Sibao Chen
- Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing 100193, China
- State Key Laboratory of Chinese Medicine and Molecular Pharmacology (Incubation), The Hong Kong Polytechnic University Shenzhen Research Institute, Shenzhen 518057, Guangdong, China
- Department of Food Science and Nutrition, The Hong Kong Polytechnic University, Hung Hom, Hong Kong 999077, China
- Research Centre for Chinese Medicine Innovation, The Hong Kong Polytechnic University, Hung Hom, Hong Kong 999077, China
| | - Guo-Qing Chen
- State Key Laboratory of Chinese Medicine and Molecular Pharmacology (Incubation), The Hong Kong Polytechnic University Shenzhen Research Institute, Shenzhen 518057, Guangdong, China
- Department of Food Science and Nutrition, The Hong Kong Polytechnic University, Hung Hom, Hong Kong 999077, China
- Research Centre for Chinese Medicine Innovation, The Hong Kong Polytechnic University, Hung Hom, Hong Kong 999077, China
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16
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Bautista-Crescencio C, Casimiro-Ramos A, Fragoso-Vázquez MJ, Correa-Basurto J, Olano C, Hernández-Rodríguez C, Villa-Tanaca L. Streptomyces albidoflavus Q antifungal metabolites inhibit the ergosterol biosynthesis pathway and yeast growth in fluconazole-resistant Candida glabrata: phylogenomic and metabolomic analyses. Microbiol Spectr 2023; 11:e0127123. [PMID: 37754674 PMCID: PMC10581079 DOI: 10.1128/spectrum.01271-23] [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: 03/23/2023] [Accepted: 08/08/2023] [Indexed: 09/28/2023] Open
Abstract
There is an urgent need to develop new antifungals due to the increasing prevalence of multidrug-resistant fungal infections and the recent emergence of COVID-19-associated candidiasis. A good study model for evaluating new antifungal compounds is Candida glabrata, an opportunistic fungal pathogen with intrinsic resistance to azoles (the most common clinical drugs for treating fungal infections). The aim of the current contribution was to conduct in vitro tests of antifungal metabolites produced by the bacteria Streptomyces albidoflavus Q, identify their molecular structures, and utilize several techniques to provide evidence of their therapeutic target. S. albidoflavus was isolated from maize rhizospheric soil in Mexico and identified by phylogenomic analysis using a 92-gene core. Of the 66 metabolites identified in S. albidoflavus Q by a liquid chromatography-high resolution mass spectrometry (LC-HRMS) metabolomic analysis of the lyophilized supernatant, six were selected by the Way2drug server based on their in silico binding to the likely target, 3-hydroxy-3-methyl-glutaryl-CoA reductase (HMGR, the key enzyme in the ergosterol biosynthesis pathway). Molecular modeling studies show a relatively high binding affinity for the CgHMGR enzyme by two secondary metabolites: isogingerenone B (diaryl heptanoid) and notoginsenoside J (polycyclic triterpene). These secondary metabolites were able to inhibit ergosterol synthesis and affect yeast viability in vitro. They also caused alterations in the ultrastructure of the yeast cytoplasmic membrane, as evidenced by transmission electron microscopy. The putative target of isogingerenone B and notoginsenoside J is distinct from that of azole drugs (the most common clinical antifungals). The target for the latter is the lanosterol 14 alpha-demethylase enzyme (Erg11). IMPORTANCE Multidrug resistance has emerged among yeasts of the genus Candida, posing a severe threat to global health. The problem has been exacerbated by the pandemic associated with COVID-19, during which resistant strains of Candida auris and Candida glabrata have been isolated from patients infected with the SARS-CoV-2 virus. To confront this challenge, the World Health Organization has invoked scientists to search for new antifungals with alternative molecular targets. This study identified 66 metabolites produced by the bacteria Streptomyces albidoflavus Q, 6 of which had promising properties for potential antifungal activity. The metabolites were tested in vitro as inhibitors of ergosterol synthesis and C. glabrata growth, with positive results. They were also found to damage the cytoplasmic membrane of the fungus. The corresponding molecular structures and their probable therapeutic target were established. The target is apparently distinct from that of azole drugs.
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Affiliation(s)
- Celia Bautista-Crescencio
- Departamento de Microbiología, Laboratorio de Biología Molecular de Bacterias y Levaduras, Escuela Nacional de Ciencias Biológicas, Instituto Politécnico Nacional. Prolongación de Carpio y Plan de Ayala, Casco de Santo Tomás, Ciudad de México, Ciudad de México, México
| | - Arturo Casimiro-Ramos
- Departamento de Microbiología, Laboratorio de Biología Molecular de Bacterias y Levaduras, Escuela Nacional de Ciencias Biológicas, Instituto Politécnico Nacional. Prolongación de Carpio y Plan de Ayala, Casco de Santo Tomás, Ciudad de México, Ciudad de México, México
| | - M. Jonathan Fragoso-Vázquez
- Departamento de Química Orgánica, Escuela Nacional de Ciencias, Biológicas, Instituto Politécnico Nacional, Prolongación de Carpio y Plan de Ayala, Col. Casco de Santo Tomás, Ciudad de México, México
| | - José Correa-Basurto
- Laboratorio de Diseño y Desarrollo de Nuevos Fármacos e Innovación Biotecnológica (Laboratory for the Design and Development of New Drugs and Biotechnological Innovation), SEPI-Escuela Superior de Medicina del Instituto Politécnico Nacional, Plan de San Luis y Salvador Díaz Mirón, Casco de Santo Tomás, Ciudad de México, México
| | - Carlos Olano
- Departamento de Biología Funcional, Universidad de Oviedo, Oviedo, Spain
| | - César Hernández-Rodríguez
- Departamento de Microbiología, Laboratorio de Biología Molecular de Bacterias y Levaduras, Escuela Nacional de Ciencias Biológicas, Instituto Politécnico Nacional. Prolongación de Carpio y Plan de Ayala, Casco de Santo Tomás, Ciudad de México, Ciudad de México, México
| | - Lourdes Villa-Tanaca
- Departamento de Microbiología, Laboratorio de Biología Molecular de Bacterias y Levaduras, Escuela Nacional de Ciencias Biológicas, Instituto Politécnico Nacional. Prolongación de Carpio y Plan de Ayala, Casco de Santo Tomás, Ciudad de México, Ciudad de México, México
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17
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Goel N, Zaidi S, Khare SK. Whole genome sequencing and functional analysis of a novel biofilm-eradicating strain Nocardiopsis lucentensis EMB25. World J Microbiol Biotechnol 2023; 39:292. [PMID: 37653174 DOI: 10.1007/s11274-023-03738-6] [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: 07/07/2023] [Accepted: 08/24/2023] [Indexed: 09/02/2023]
Abstract
The process of biofilm formation is intricate and multifaceted, requiring the individual cells to secrete extracellular polymeric substances (EPS) that subsequently aggregate and adhere to various surfaces. The issue of biofilms is a significant concern for public health due to the increased resistance of microorganisms associated with biofilms to antimicrobial agents. The current study describes the whole genome and corresponding functions of a biofilm inhibiting and eradicating actinobacteria isolate identified as Nocardiopsis lucentensis EMB25. The N. lucentensis EMB25 has 6.5 Mbp genome with 71.62% GC content. The genome analysis by BLAST Ring Image Generator (BRIG) revealed it to be closely related to Nocardiopsis dassonvillei NOCA502F. Interestingly, based on orthologous functional groups reflected by average nucleotide identity (ANI) analysis, it was 81.48% similar to N. arvandica DSM4527. Also, it produces lanthipeptides and linear azole(in)e-containing peptides (LAPs) akin to N. arvandica. The secondary metabolite search revealed the presence of major gene clusters involved in terpene, ectoine, siderophores, Lanthipeptides, RiPP-like, and T1PKS biosynthesis. After 24 h of treatment, the cell-free extract effectively eradicates the pre-existing biofilm of P. aeruginosa PseA. Also, the isolated bacteria exhibited antibacterial activity against MRSA, Staphylococcus aureus and Bacillus subtilis bacteria. Overall, this finding offers valuable insights into the identification of BGCs, which contain enzymes that play a role in the biosynthesis of natural products. Specifically, it sheds light on the functional aspects of these BGCs in relation to N. lucentensis.
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Affiliation(s)
- Nikky Goel
- Enzyme and Microbial Biochemistry Laboratory, Department of Chemistry, Indian Institute of Technology, Hauz Khas, New Delhi, 110016, India
| | - Saniya Zaidi
- Enzyme and Microbial Biochemistry Laboratory, Department of Chemistry, Indian Institute of Technology, Hauz Khas, New Delhi, 110016, India
| | - Sunil Kumar Khare
- Enzyme and Microbial Biochemistry Laboratory, Department of Chemistry, Indian Institute of Technology, Hauz Khas, New Delhi, 110016, India.
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18
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Choksket S, Kaur M, Pinnaka AK, Korpole S. An antimicrobial thiopeptide producing novel actinomycetes Streptomyces terrae sp. nov., isolated from subsurface soil of arable land. FEMS MICROBES 2023; 4:xtad014. [PMID: 37701422 PMCID: PMC10495126 DOI: 10.1093/femsmc/xtad014] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2023] [Revised: 06/22/2023] [Accepted: 08/09/2023] [Indexed: 09/14/2023] Open
Abstract
An antimicrobial producing Gram-positive, aerobic, nonmotile, and filamentous actinobacterial strain SKN60T was isolated from soil The isolate exhibited 99.3% and 99.0% identity with Streptomyces laurentii ATCC 31255T and S. roseicoloratus TRM 44457T, respectively, in 16S rRNA gene sequence analysis. However, the genome sequence displayed maximum ANI (88.45%) and AAI (85.61%) with S. roseicoloratus TRM 44457T. Similarly, the dDDH showed 33.7% identity with S. roseicoloratus TRM 44457T. It formed a cluster with S. roseicoloratus TRM 44457T and S. laurentii ATCC 31255T in phylogenomic tree. Cell wall analysis revealed the presence of diphosphatidylglycerol, phosphatidylethanolamine, and phosphatidylcholine as major polar lipids and diaminopimelic acid as diagnostic diamino acid. Major fatty acids were iso-C15:0, anteiso-C15:0, and iso-C16:0. The G+C content was found to be 72.3 mol%. Genome sequence analysis using antiSMASH database showed occurrence of a thiopeptide biosynthesis gene cluster with 94% similarity to berninamycin from S. bernensis UC5144. The mass of 1146 Da is identical with berninamycin. But subtle differences observed in leader peptide sequence of thiopeptide and berninamycin. Notably, S. bernensis is not validly reported and thus SKN60T is the only strain containing berninamycin BGC as no other phylogenetic relative had it. Additionally, strain SKN60T differed in phenotypic and genetic characteristics with all phylogenetic relatives of the genus Streptomyces. Therefore, it is proposed as a novel species with the name Streptomyces terrae sp. nov. strain SKN60T (=MTCC 13163T; = JCM 35768T).
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Affiliation(s)
- Stanzin Choksket
- CSIR-Institute of Microbial Technology, Sector 39A, Chandigarh-160036, India
| | - Mahaldeep Kaur
- CSIR-Institute of Microbial Technology, Sector 39A, Chandigarh-160036, India
| | - Anil Kumar Pinnaka
- CSIR-Institute of Microbial Technology, Sector 39A, Chandigarh-160036, India
| | - Suresh Korpole
- CSIR-Institute of Microbial Technology, Sector 39A, Chandigarh-160036, India
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19
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Li L. Accessing hidden microbial biosynthetic potential from underexplored sources for novel drug discovery. Biotechnol Adv 2023:108176. [PMID: 37211187 DOI: 10.1016/j.biotechadv.2023.108176] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2022] [Revised: 05/15/2023] [Accepted: 05/16/2023] [Indexed: 05/23/2023]
Abstract
Microbial natural products and their structural analogues have widely used as pharmaceutical agents, especially for infectious diseases and cancer. Despite this success, new structural classes with innovative chemistry and modes of action are urgently needed to be developed to combat the growing antimicrobial resistance and other public health problems. The advances in next-generation sequencing technologies and powerful computational tools open up new opportunities to explore microbial biosynthetic potential from underexplored sources, with millions of secondary metabolites awaiting discovery. The review highlights challenges associated with discovery of new chemical entities, rich reservoirs provided by untapped taxa, ecological niches or host microbiomes, emerging synthetic biotechnologies to unearth the hidden microbial biosynthetic potential for novel drug discovery at scale and speed.
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Affiliation(s)
- Lei Li
- State Key Laboratory of Microbial Metabolism and School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, 800 Dongchuan Rd., Shanghai 200240, China.
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20
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Yılmaz TM, Mungan MD, Berasategui A, Ziemert N. FunARTS, the Fungal bioActive compound Resistant Target Seeker, an exploration engine for target-directed genome mining in fungi. Nucleic Acids Res 2023:7173779. [PMID: 37207330 DOI: 10.1093/nar/gkad386] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2023] [Revised: 04/21/2023] [Accepted: 05/02/2023] [Indexed: 05/21/2023] Open
Abstract
There is an urgent need to diversify the pipeline for discovering novel natural products due to the increase in multi-drug resistant infections. Like bacteria, fungi also produce secondary metabolites that have potent bioactivity and rich chemical diversity. To avoid self-toxicity, fungi encode resistance genes which are often present within the biosynthetic gene clusters (BGCs) of the corresponding bioactive compounds. Recent advances in genome mining tools have enabled the detection and prediction of BGCs responsible for the biosynthesis of secondary metabolites. The main challenge now is to prioritize the most promising BGCs that produce bioactive compounds with novel modes of action. With target-directed genome mining methods, it is possible to predict the mode of action of a compound encoded in an uncharacterized BGC based on the presence of resistant target genes. Here, we introduce the 'fungal bioactive compound resistant target seeker' (FunARTS) available at https://funarts.ziemertlab.com. This is a specific and efficient mining tool for the identification of fungal bioactive compounds with interesting and novel targets. FunARTS rapidly links housekeeping and known resistance genes to BGC proximity and duplication events, allowing for automated, target-directed mining of fungal genomes. Additionally, FunARTS generates gene cluster networking by comparing the similarity of BGCs from multi-genomes.
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Affiliation(s)
- Turgut Mesut Yılmaz
- Translational Genome Mining for Natural Products, Interfaculty Institute of Microbiology and Infection Medicine Tübingen (IMIT), Interfaculty Institute for Biomedical Informatics (IBMI), University of Tübingen, Auf der Morgenstelle 28, 72076, Tübingen, Germany
| | - Mehmet Direnç Mungan
- Translational Genome Mining for Natural Products, Interfaculty Institute of Microbiology and Infection Medicine Tübingen (IMIT), Interfaculty Institute for Biomedical Informatics (IBMI), University of Tübingen, Auf der Morgenstelle 28, 72076, Tübingen, Germany
| | - Aileen Berasategui
- University of Tübingen, Cluster of Excellence 'Controlling Microbes to Fight Infections', Auf der Morgenstelle 28, Tübingen 72076, Germany
| | - Nadine Ziemert
- Translational Genome Mining for Natural Products, Interfaculty Institute of Microbiology and Infection Medicine Tübingen (IMIT), Interfaculty Institute for Biomedical Informatics (IBMI), University of Tübingen, Auf der Morgenstelle 28, 72076, Tübingen, Germany
- German Center for Infection Research (DZIF), Partner Site Tübingen, Tübingen, Germany
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21
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Zill NA, Du Y, Marinkovich S, Gu D, Seidel J, Zhang W. Bioactive Natural Product Discovery via Deuterium Adduct Bioactivity Screening. ACS Chem Biol 2023; 18:1192-1199. [PMID: 37125845 DOI: 10.1021/acschembio.3c00083] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/02/2023]
Abstract
The discovery of bioactive natural products lies at the forefront of human medicine. The continued discovery of these molecules is imperative in the fight against infection and disease. While natural products have historically dominated the drug market, discovery in recent years has slowed significantly, partly due to limitations in current discovery methodologies. This work demonstrates a new workflow, deuterium adduct bioactivity screening (DABS), which pairs untargeted isotope labeling with whole cell binding assays for bioactive natural product discovery. DABS was validated and led to the discovery of a new isoprenyl guanidine alkaloid, zillamycin, which showed anti-cancer and anti-microbial activities. DABS thus represents a new workflow to accelerate discovery of natural products with a wide range of bioactive potentials.
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Affiliation(s)
- Nicholas A Zill
- Department of Chemical and Biomolecular Engineering, University of California Berkeley, Berkeley, California 94720, United States
| | - Yongle Du
- California Institute for Quantitative Biosciences, University of California Berkeley, Berkeley, California 94720, United States
| | - Samantha Marinkovich
- Department of Chemical and Biomolecular Engineering, University of California Berkeley, Berkeley, California 94720, United States
| | - Di Gu
- Department of Chemistry, University of California Berkeley, Berkeley, California 94720, United States
| | - Jeremy Seidel
- Department of Chemical and Biomolecular Engineering, University of California Berkeley, Berkeley, California 94720, United States
| | - Wenjun Zhang
- Department of Chemical and Biomolecular Engineering, University of California Berkeley, Berkeley, California 94720, United States
- California Institute for Quantitative Biosciences, University of California Berkeley, Berkeley, California 94720, United States
- Hong Kong Branch of the Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou), The Hong Kong University of Science and Technology, Hong Kong 999077, China
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22
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Wang Z, Li Z, Niu C, Yang L, Zhai Y, Li D, Wu G, Zhang Z, He X. Aniline-induced production of aniline-containing polyketides and related bicyclic polyketides by the Yellow River wetland-derived fungus Talaromyces funiculosus. Front Microbiol 2023; 14:1200680. [PMID: 37266016 PMCID: PMC10230029 DOI: 10.3389/fmicb.2023.1200680] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2023] [Accepted: 04/24/2023] [Indexed: 06/03/2023] Open
Abstract
Introduction and Methods Silencing gene activation can effectively enrich the diversity of fungal secondary metabolites. Results and Discussion Cultivation of the Yellow River wetland-derived fungus Talaromyces funiculosus HPU-Y01 with aniline led to the isolation of one new aniline-containing polyketide tanicutone A (1), two new bicyclic polyketides tanicutones B-C (2-3), a new related trienoic acid 8-methyldeca-2,4,6-trienoic acid (5), and a known compound 4. The planar structures and configurations of 1-5 were determined by NMR, MS, and ECD calculations. Compound 2 featured a key aldehyde group and showed promising inhibitory activity against Vibrio parahaemolyticus with a minimum inhibitory concentration (MIC) value of 0.17 μg/mL. This is a rare report of aniline-induced fungal production of tetrahydronaphthone polyketides.
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Affiliation(s)
- Zhenhui Wang
- School of Medicine, Henan Polytechnic University, Jiaozuo, China
| | - Zhanlin Li
- School of Medicine, Henan Polytechnic University, Jiaozuo, China
| | - Chao Niu
- School of Medicine, Henan Polytechnic University, Jiaozuo, China
| | - Lanping Yang
- School of Medicine, Henan Polytechnic University, Jiaozuo, China
| | - Yangyang Zhai
- School of Medicine, Henan Polytechnic University, Jiaozuo, China
| | - Dehai Li
- Key Laboratory of Marine Drugs, Chinese Ministry of Education, School of Medicine and Pharmacy, Ocean University of China, Qingdao, China
| | - Guangwei Wu
- College of Chemical Engineering, Nanjing Forestry University, Nanjing, China
| | - Zhenzhen Zhang
- School of Medicine, Henan Polytechnic University, Jiaozuo, China
| | - Xueqian He
- School of Medicine, Henan Polytechnic University, Jiaozuo, China
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23
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Baranova AA, Alferova VA, Korshun VA, Tyurin AP. Modern Trends in Natural Antibiotic Discovery. Life (Basel) 2023; 13:life13051073. [PMID: 37240718 DOI: 10.3390/life13051073] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2023] [Revised: 04/10/2023] [Accepted: 04/21/2023] [Indexed: 05/28/2023] Open
Abstract
Natural scaffolds remain an important basis for drug development. Therefore, approaches to natural bioactive compound discovery attract significant attention. In this account, we summarize modern and emerging trends in the screening and identification of natural antibiotics. The methods are divided into three large groups: approaches based on microbiology, chemistry, and molecular biology. The scientific potential of the methods is illustrated with the most prominent and recent results.
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Affiliation(s)
- Anna A Baranova
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Miklukho-Maklaya 16/10, 117997 Moscow, Russia
- Gause Institute of New Antibiotics, Bolshaya Pirogovskaya 11, 119021 Moscow, Russia
| | - Vera A Alferova
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Miklukho-Maklaya 16/10, 117997 Moscow, Russia
- Gause Institute of New Antibiotics, Bolshaya Pirogovskaya 11, 119021 Moscow, Russia
| | - Vladimir A Korshun
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Miklukho-Maklaya 16/10, 117997 Moscow, Russia
| | - Anton P Tyurin
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Miklukho-Maklaya 16/10, 117997 Moscow, Russia
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24
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Brinkhaus HO, Rajan K, Schaub J, Zielesny A, Steinbeck C. Open data and algorithms for open science in AI-driven molecular informatics. Curr Opin Struct Biol 2023; 79:102542. [PMID: 36805192 DOI: 10.1016/j.sbi.2023.102542] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2022] [Revised: 01/10/2023] [Accepted: 01/13/2023] [Indexed: 02/19/2023]
Abstract
Recent years have seen a sharp increase in the development of deep learning and artificial intelligence-based molecular informatics. There has been a growing interest in applying deep learning to several subfields, including the digital transformation of synthetic chemistry, extraction of chemical information from the scientific literature, and AI in natural product-based drug discovery. The application of AI to molecular informatics is still constrained by the fact that most of the data used for training and testing deep learning models are not available as FAIR and open data. As open science practices continue to grow in popularity, initiatives which support FAIR and open data as well as open-source software have emerged. It is becoming increasingly important for researchers in the field of molecular informatics to embrace open science and to submit data and software in open repositories. With the advent of open-source deep learning frameworks and cloud computing platforms, academic researchers are now able to deploy and test their own deep learning models with ease. With the development of new and faster hardware for deep learning and the increasing number of initiatives towards digital research data management infrastructures, as well as a culture promoting open data, open source, and open science, AI-driven molecular informatics will continue to grow. This review examines the current state of open data and open algorithms in molecular informatics, as well as ways in which they could be improved in future.
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Affiliation(s)
- Henning Otto Brinkhaus
- Institute for Inorganic and Analytical Chemistry, Friedrich Schiller University Jena, Lessingstr. 8, 07743 Jena, Germany
| | - Kohulan Rajan
- Institute for Inorganic and Analytical Chemistry, Friedrich Schiller University Jena, Lessingstr. 8, 07743 Jena, Germany
| | - Jonas Schaub
- Institute for Inorganic and Analytical Chemistry, Friedrich Schiller University Jena, Lessingstr. 8, 07743 Jena, Germany
| | - Achim Zielesny
- Institute for Bioinformatics and Chemoinformatics, Westphalian University of Applied Sciences, August-Schmidt-Ring 10, 45665 Recklinghausen, Germany
| | - Christoph Steinbeck
- Institute for Inorganic and Analytical Chemistry, Friedrich Schiller University Jena, Lessingstr. 8, 07743 Jena, Germany.
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25
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Liu J, Li SM. Genomics-Guided Efficient Identification of 2,5-Diketopiperazine Derivatives from Actinobacteria. Chembiochem 2023; 24:e202200502. [PMID: 36098493 PMCID: PMC10092475 DOI: 10.1002/cbic.202200502] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2022] [Revised: 09/12/2022] [Indexed: 02/04/2023]
Abstract
Secondary metabolites derived from microorganism constitute an important part of natural products. Mining of the microbial genomes revealed a large number of uncharacterized biosynthetic gene clusters, indicating their greater potential to synthetize specialized or secondary metabolites (SMs) than identified by classic fermentation and isolation approaches. Various bioinformatics tools have been developed to analyze and identify such gene clusters, thus accelerating significantly the mining process. Heterologous expression of an individual biosynthetic gene cluster has been proven as an efficient way to activate the genes and identify the encoded metabolites that cannot be detected under normal laboratory cultivation conditions. Herein, we describe a concept of genomics-guided approach by performing genome mining and heterologous expression to uncover novel CDPS-derived DKPs and functionally characterize novel tailoring enzymes embedded in the biosynthetic pathways. Recent works focused on the identification of the nucleobase-related and dimeric DKPs are also presented.
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Affiliation(s)
- Jing Liu
- Institut für Pharmazeutische Biologie und Biotechnologie, Fachbereich Pharmazie, Philipps-Universität Marburg, Robert-Koch-Straße 4, 35037, Marburg, Germany.,Current address: Department of Natural Products in Organismic Interactions, Max Planck Institute for Terrestrial Microbiology, Karl-von-Frisch-Straße 10, 35043, Marburg, Germany
| | - Shu-Ming Li
- Institut für Pharmazeutische Biologie und Biotechnologie, Fachbereich Pharmazie, Philipps-Universität Marburg, Robert-Koch-Straße 4, 35037, Marburg, Germany
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26
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Götze S, Vij R, Burow K, Thome N, Urbat L, Schlosser N, Pflanze S, Müller R, Hänsch VG, Schlabach K, Fazlikhani L, Walther G, Dahse HM, Regestein L, Brunke S, Hube B, Hertweck C, Franken P, Stallforth P. Ecological Niche-Inspired Genome Mining Leads to the Discovery of Crop-Protecting Nonribosomal Lipopeptides Featuring a Transient Amino Acid Building Block. J Am Chem Soc 2023; 145:2342-2353. [PMID: 36669196 PMCID: PMC9897216 DOI: 10.1021/jacs.2c11107] [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: 10/19/2022] [Indexed: 01/22/2023]
Abstract
Investigating the ecological context of microbial predator-prey interactions enables the identification of microorganisms, which produce multiple secondary metabolites to evade predation or to kill the predator. In addition, genome mining combined with molecular biology methods can be used to identify further biosynthetic gene clusters that yield new antimicrobials to fight the antimicrobial crisis. In contrast, classical screening-based approaches have limitations since they do not aim to unlock the entire biosynthetic potential of a given organism. Here, we describe the genomics-based identification of keanumycins A-C. These nonribosomal peptides enable bacteria of the genus Pseudomonas to evade amoebal predation. While being amoebicidal at a nanomolar level, these compounds also exhibit a strong antimycotic activity in particular against the devastating plant pathogen Botrytis cinerea and they drastically inhibit the infection of Hydrangea macrophylla leaves using only supernatants of Pseudomonas cultures. The structures of the keanumycins were fully elucidated through a combination of nuclear magnetic resonance, tandem mass spectrometry, and degradation experiments revealing an unprecedented terminal imine motif in keanumycin C extending the family of nonribosomal amino acids by a highly reactive building block. In addition, chemical synthesis unveiled the absolute configuration of the unusual dihydroxylated fatty acid of keanumycin A, which has not yet been reported for this lipodepsipeptide class. Finally, a detailed genome-wide microarray analysis of Candida albicans exposed to keanumycin A shed light on the mode-of-action of this potential natural product lead, which will aid the development of new pharmaceutical and agrochemical antifungals.
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Affiliation(s)
- Sebastian Götze
- Department
of Paleobiotechnology, Leibniz Institute for Natural Product Research
and Infection Biology, Hans Knöll
Institute, Beutenbergstraße 11a, 07745 Jena, Germany
| | - Raghav Vij
- Department
of Microbial Pathogenicity Mechanisms, Leibniz Institute for Natural
Product Research and Infection Biology, Hans Knöll Institute, Beutenbergstraße 11a, 07745 Jena, Germany
| | - Katja Burow
- Research
Centre for Horticultural Crops (FGK), Fachhochschule
Erfurt, Kühnhäuser
Straße 101, 99090 Erfurt, Germany
| | - Nicola Thome
- Department
of Paleobiotechnology, Leibniz Institute for Natural Product Research
and Infection Biology, Hans Knöll
Institute, Beutenbergstraße 11a, 07745 Jena, Germany
| | - Lennart Urbat
- Department
of Paleobiotechnology, Leibniz Institute for Natural Product Research
and Infection Biology, Hans Knöll
Institute, Beutenbergstraße 11a, 07745 Jena, Germany
| | - Nicolas Schlosser
- Bio
Pilot Plant, Leibniz Institute for Natural Product Research and Infection
Biology, Hans Knöll Institute, Beutenbergstraße 11a, 07745 Jena, Germany
| | - Sebastian Pflanze
- Department
of Paleobiotechnology, Leibniz Institute for Natural Product Research
and Infection Biology, Hans Knöll
Institute, Beutenbergstraße 11a, 07745 Jena, Germany
| | - Rita Müller
- Department
of Microbial Pathogenicity Mechanisms, Leibniz Institute for Natural
Product Research and Infection Biology, Hans Knöll Institute, Beutenbergstraße 11a, 07745 Jena, Germany
| | - Veit G. Hänsch
- Department
of Biomolecular Chemistry, Leibniz Institute for Natural Product Research
and Infection Biology, Hans Knöll
Institute, Beutenbergstraße 11a, 07745 Jena, Germany
| | - Kevin Schlabach
- Department
of Paleobiotechnology, Leibniz Institute for Natural Product Research
and Infection Biology, Hans Knöll
Institute, Beutenbergstraße 11a, 07745 Jena, Germany
| | - Leila Fazlikhani
- Research
Centre for Horticultural Crops (FGK), Fachhochschule
Erfurt, Kühnhäuser
Straße 101, 99090 Erfurt, Germany
| | - Grit Walther
- National
Reference Center for Invasive Fungal Infections, Hans Knöll Institute, Beutenbergstraße 11a, 07745 Jena, Germany
| | - Hans-Martin Dahse
- Department
of Infection Biology, Leibniz Institute for Natural Product Research
and Infection Biology, Hans Knöll
Institute, Beutenbergstraße 11a, 07745 Jena, Germany
| | - Lars Regestein
- Bio
Pilot Plant, Leibniz Institute for Natural Product Research and Infection
Biology, Hans Knöll Institute, Beutenbergstraße 11a, 07745 Jena, Germany
| | - Sascha Brunke
- Department
of Microbial Pathogenicity Mechanisms, Leibniz Institute for Natural
Product Research and Infection Biology, Hans Knöll Institute, Beutenbergstraße 11a, 07745 Jena, Germany
| | - Bernhard Hube
- Department
of Microbial Pathogenicity Mechanisms, Leibniz Institute for Natural
Product Research and Infection Biology, Hans Knöll Institute, Beutenbergstraße 11a, 07745 Jena, Germany
| | - Christian Hertweck
- Department
of Biomolecular Chemistry, Leibniz Institute for Natural Product Research
and Infection Biology, Hans Knöll
Institute, Beutenbergstraße 11a, 07745 Jena, Germany
| | - Philipp Franken
- Research
Centre for Horticultural Crops (FGK), Fachhochschule
Erfurt, Kühnhäuser
Straße 101, 99090 Erfurt, Germany
- Molecular
Phytopathology, Friedrich Schiller University, 07745 Jena, Germany
| | - Pierre Stallforth
- Department
of Paleobiotechnology, Leibniz Institute for Natural Product Research
and Infection Biology, Hans Knöll
Institute, Beutenbergstraße 11a, 07745 Jena, Germany
- Faculty
of Chemistry and Earth Sciences, Institute of Organic Chemistry and
Macromolecular Chemistry, Friedrich Schiller
University Jena, Humboldtstraße 10, 07743 Jena, Germany
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27
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Zhang B, Zheng K, Hong R. Biomimetic Synthesis of Chejuenolides A-C by a Cryptic Lactone-Based Macrocyclization: Stereochemical Implications in Biosynthesis. ACS CENTRAL SCIENCE 2023; 9:84-92. [PMID: 36712486 PMCID: PMC9881209 DOI: 10.1021/acscentsci.2c01096] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/16/2022] [Indexed: 06/18/2023]
Abstract
A hypothetical Mannich macrocyclization in the biosynthesis of chejuenolides A-C served as the basis for the synthetic design herein. Using a lactone-based linear precursor constructed via a tactic sequence of aldol-Julia-aldol reactions on a gram scale, the biomimetic total synthesis and structural validation of chejuenolides A-C were successfully achieved for the first time. The β-oxo-δ-lactone unit in the macrocyclized adducts was fragile and readily converted to a series of C2/C18-diastereoisomers via a decarboxylation and protonation pathway. Stereochemical identification of the biosynthetic precursor (O3P2) confirmed structural adherence to the given macrocycles and previously clarified lankacidins. Moreover, the stereovariants of the linear precursor designed for the macrocyclization event highlighted the unparalleled impact of using this biomimetic approach to determine the stereoselectivity in the proposed enzymatic reaction by reviving the lost or unstable intermediate.
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Affiliation(s)
- Bingbing Zhang
- CAS
Key Laboratory of Synthetic Chemistry of Natural Substances, Center
for Excellence in Molecular Synthesis, Shanghai
Institute of Organic Chemistry, Chinese Academy of Sciences, Shanghai 200032, PR China
- University
of Chinese Academy of Sciences, Beijing 100049, PR China
| | - Kuan Zheng
- CAS
Key Laboratory of Synthetic Chemistry of Natural Substances, Center
for Excellence in Molecular Synthesis, Shanghai
Institute of Organic Chemistry, Chinese Academy of Sciences, Shanghai 200032, PR China
| | - Ran Hong
- CAS
Key Laboratory of Synthetic Chemistry of Natural Substances, Center
for Excellence in Molecular Synthesis, Shanghai
Institute of Organic Chemistry, Chinese Academy of Sciences, Shanghai 200032, PR China
- University
of Chinese Academy of Sciences, Beijing 100049, PR China
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28
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Genome insights into the plant growth-promoting bacterium Saccharibacillus brassicae ATSA2 T. AMB Express 2023; 13:9. [PMID: 36680648 PMCID: PMC9867790 DOI: 10.1186/s13568-023-01514-1] [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: 07/21/2022] [Accepted: 01/09/2023] [Indexed: 01/22/2023] Open
Abstract
Endophytes can facilitate the improvement of plant growth and health in agriculturally important crops, yet their genomes and secondary metabolites remain largely unexplored. We previously isolated Saccharibacillus brassicae strain ATSA2T from surface-sterilized seeds of kimchi cabbage and represented a novel species of the genus Saccharibacillus. In this study, we evaluated the plant growth-promoting (PGP) effect of strain ATSA2T in kimchi cabbage, bok choy, and pepper plants grown in soils. We found a significant effect on the shoot and root biomass, and chlorophyll contents following strain ATSA2T treatment. Strain ATSA2T displayed PGP traits such as indole acetic acid (IAA, 62.9 μg/mL) and siderophore production, and phosphate solubilization activity. Furthermore, genome analysis of this strain suggested the presence of gene clusters involved in iron acquisition (fhuABD, afuABC, fbpABC, and fepCDG) and phosphate solubilization (pstABCHS, phoABHLU, and phnCDEP) and other phytohormone biosynthesis genes, including indole-3-acetic acid (trpABCDEFG), in the genome. Interestingly, the secondary metabolites cerecidin, carotenoid, siderophore (staphylobactin), and bacillaene underlying plant growth promotion were found in the whole genome via antiSMASH analysis. Overall, physiological testing and genome analysis data provide comprehensive insights into plant growth-promoting mechanisms, suggesting the relevance of strain ATSA2T in agricultural biotechnology.
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29
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Sánchez-Hidalgo M, García MJ, González I, Oves-Costales D, Genilloud O. Complete Genome Sequence Analysis of Kribbella sp. CA-293567 and Identification of the Kribbellichelins A & B and Sandramycin Biosynthetic Gene Clusters. Microorganisms 2023; 11:microorganisms11020265. [PMID: 36838228 PMCID: PMC9962454 DOI: 10.3390/microorganisms11020265] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2022] [Revised: 01/13/2023] [Accepted: 01/17/2023] [Indexed: 01/20/2023] Open
Abstract
Minor genera actinomycetes are considered a promising source of new secondary metabolites. The strain Kribbella sp. CA-293567 produces sandramycin and kribbellichelins A & B In this work, we describe the complete genome sequencing of this strain and the in silico identification of biosynthetic gene clusters (BGCs), focusing on the pathways encoding sandramycin and kribbellichelins A-B. We also present a comparative analysis of the biosynthetic potential of 38 publicly available genomes from Kribbella strains.
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30
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Yang W, Chen T, Chen Y, Tan Q, Ou Y, Li G, Wang B, Hu D, Yao H, She Z. Antiplasmodial Asperterpenoids from Two Aspergillus oryzae Transformants with Heterologous Expression of Sesterterpene Genes. J Org Chem 2022; 87:16807-16819. [PMID: 36469695 DOI: 10.1021/acs.joc.2c02501] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
The synthetic biology approach enables efficient and directional mining of target compounds during drug discovery. Ten new asperterpenoids (6-15) and five known analogues (1-5), possessing a rare 5/7/3/6/5 skeleton, were obtained from two Aspergillus oryzae transformants with heterologous expression of a terpene cyclase gene AstC with one or two P450 genes AstB/A under the guidance of molecular networking. Their planar structures were determined by 1D and 2D NMR and HR-ESI-MS. The absolute configurations of compounds 6 and 9-13 were determined by single crystal X-ray diffraction, and those of compounds 7-8 and 14-15 were compared with the ECD of known compounds. Seven of all the compounds are the first asperterpenoid oxidation products at C-17 or at C-25. In bioassay, compounds 1-2, 4-5, and 6-8 displayed moderate to strong eliminating activities against chloroquine-sensitive strain (P.f.3D7) with EC50 values ranging from 2.1 to 19.3 μM. The structure-activity relationship (SAR) was discussed, which showed that substituents at C-3, C-11, C-17, C-18, and C-23 of asperterpenoids significantly affected anti-plasma parasite activity.
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Affiliation(s)
- Wencong Yang
- School of Chemistry, Sun Yat-Sen University, Guangzhou 510275, P.R. China
| | - Tao Chen
- School of Chemistry, Sun Yat-Sen University, Guangzhou 510275, P.R. China
| | - Yan Chen
- School of Chemistry, Sun Yat-Sen University, Guangzhou 510275, P.R. China.,School of Pharmacy, Anhui Medical University, Hefei 230032, P.R. China
| | - Qi Tan
- School of Chemistry, Sun Yat-Sen University, Guangzhou 510275, P.R. China
| | - Yanghui Ou
- Guangdong Key Laboratory of Animal Conservation and Resource Utilization, Guangdong Public Laboratory of Wild Animal Conservation and Utilization, Institute of Zoology, Guangdong Academy of Sciences, Guangzhou 510260, P.R. China
| | - Gang Li
- Guangdong Key Laboratory of Animal Conservation and Resource Utilization, Guangdong Public Laboratory of Wild Animal Conservation and Utilization, Institute of Zoology, Guangdong Academy of Sciences, Guangzhou 510260, P.R. China
| | - Bo Wang
- School of Chemistry, Sun Yat-Sen University, Guangzhou 510275, P.R. China
| | - Dan Hu
- College of Pharmacy, Jinan University, Guangzhou 510632, P.R. China
| | - Hongliang Yao
- Guangdong Key Laboratory of Animal Conservation and Resource Utilization, Guangdong Public Laboratory of Wild Animal Conservation and Utilization, Institute of Zoology, Guangdong Academy of Sciences, Guangzhou 510260, P.R. China
| | - Zhigang She
- School of Chemistry, Sun Yat-Sen University, Guangzhou 510275, P.R. China
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31
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Zhang T, Cai G, Rong X, Xu J, Jiang B, Wang H, Li X, Wang L, Zhang R, He W, Yu L. Mining and characterization of the PKS-NRPS hybrid for epicoccamide A: a mannosylated tetramate derivative from Epicoccum sp. CPCC 400996. Microb Cell Fact 2022; 21:249. [PMID: 36419162 PMCID: PMC9685919 DOI: 10.1186/s12934-022-01975-2] [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: 10/10/2022] [Accepted: 11/16/2022] [Indexed: 11/27/2022] Open
Abstract
BACKGROUND Genomic analysis indicated that the genomes of ascomycetes might carry dozens of biosynthetic gene clusters (BGCs), yet many clusters have remained enigmatic. The ascomycete genus Epicoccum, belonging to the family Didymellaceae, is ubiquitous that colonizes different types of substrates and is associated with phyllosphere or decaying vegetation. Species of this genus are prolific producers of bioactive substances. The epicoccamides, as biosynthetically distinct mannosylated tetramate, were first isolated in 2003 from Epicoccum sp. In this study, using a combination of genome mining, chemical identification, genetic deletion, and bioinformatic analysis, we identified the required BGC epi responsible for epicoccamide A biosynthesis in Epicoccum sp. CPCC 400996. RESULTS The unconventional biosynthetic gene cluster epi was obtained from an endophyte Epicoccum sp. CPCC 400996 through AntiSMASH-based genome mining. The cluster epi includes six putative open reading frames (epiA-epiF) altogether, in which the epiA encodes a tetramate-forming polyketide synthase and nonribosomal peptide synthetases (PKS-NRPS hybrid). Sequence alignments and bioinformatic analysis to other metabolic pathways of fungal tetramates, we proposed that the gene cluster epi could be involved in generating epicoccamides. Genetic knockout of epiA completely abolished the biosynthesis of epicoccamide A (1), thereby establishing the correlation between the BGC epi and biosynthesis of epicoccamide A. Bioinformatic adenylation domain signature analysis of EpiA and other fungal PKS-NRPSs (NRPs) indicated that the EpiA is L-alanine incorporating tetramates megasynthase. Furthermore, based on the molecular structures of epicoccamide A and deduced gene functions of the cluster epi, a hypothetic metabolic pathway for biosynthesizing compound 1 was proposed. The corresponding tetramates releasing during epicoccamide A biosynthesis was catalyzed through Dieckmann-type cyclization, in which the reductive (R) domain residing in terminal module of EpiA accomplished the conversion. These results unveiled the underlying mechanism of epicoccamides biosynthesis and these findings might provide opportunities for derivatization of epicoccamides or generation of new chemical entities. CONCLUSION Genome mining and genetic inactivation experiments unveiled a previously uncharacterized PKS - NRPS hybrid-based BGC epi responsible for the generation of epicoccamide A (1) in endophyte Epicoccum sp. CPCC 400996. In addition, based on the gene cluster data, a hypothetical biosynthetic pathway of epicoccamide A was proposed.
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Affiliation(s)
- Tao Zhang
- grid.506261.60000 0001 0706 7839Institute of Medicinal Biotechnology, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, 100050 China
| | - Guowei Cai
- grid.506261.60000 0001 0706 7839Institute of Medicinal Biotechnology, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, 100050 China ,grid.452240.50000 0004 8342 6962Medical Research Center, Binzhou Medical University Hospital, Binzhou, 256603 Shandong China
| | - Xiaoting Rong
- grid.506261.60000 0001 0706 7839Institute of Medicinal Biotechnology, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, 100050 China ,grid.510447.30000 0000 9970 6820College of Biotechnology, Jiangsu University of Science and Technology, Zhenjiang, 212003 Jiangsu China
| | - Jingwen Xu
- grid.506261.60000 0001 0706 7839Institute of Medicinal Biotechnology, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, 100050 China
| | - Bingya Jiang
- grid.506261.60000 0001 0706 7839Institute of Medicinal Biotechnology, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, 100050 China
| | - Hao Wang
- grid.506261.60000 0001 0706 7839Institute of Medicinal Biotechnology, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, 100050 China
| | - Xinxin Li
- grid.506261.60000 0001 0706 7839Institute of Medicinal Biotechnology, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, 100050 China
| | - Lu Wang
- grid.506261.60000 0001 0706 7839Institute of Medicinal Biotechnology, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, 100050 China
| | - Ran Zhang
- grid.506261.60000 0001 0706 7839Institute of Medicinal Biotechnology, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, 100050 China
| | - Wenni He
- grid.506261.60000 0001 0706 7839Institute of Medicinal Biotechnology, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, 100050 China
| | - Liyan Yu
- grid.506261.60000 0001 0706 7839Institute of Medicinal Biotechnology, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, 100050 China
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32
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Yu C, Chen L, Gao YL, Liu J, Li PL, Zhang ML, Li Q, Zhang HD, Tang MC, Li L. Discovery and biosynthesis of macrophasetins from the plant pathogen fungus Macrophomina phaseolina. Front Microbiol 2022; 13:1056392. [PMID: 36452919 PMCID: PMC9701702 DOI: 10.3389/fmicb.2022.1056392] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2022] [Accepted: 10/17/2022] [Indexed: 09/16/2023] Open
Abstract
3-Decalinoyltetramic acids (DTAs) are a class of natural products with chemical diversity and potent bioactivities. In fungal species there is a general biosynthetic route to synthesize this type of compounds, which usually features a polyketide synthase-nonribosomal peptide synthetase (PKS-NRPS) and a lipocalin-like Diels-Alderase (LLDAse). Using a synthetic biology approach, combining the bioinformatics analysis prediction and heterologous expression, we mined a PKS-NRPS and LLDAse encoding gene cluster from the plant pathogenic fungus Macrophomina phaseolina and characterized the cluster to be responsible for the biosynthesis of novel DTAs, macrophasetins. In addition, we investigated the biosynthesis of these compounds and validated the accuracy of the phylogeny-guided bioinformatics analysis prediction. Our results provided a proof of concept example to this approach, which may facilitate the discovery of novel DTAs from the fungal kingdom.
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Affiliation(s)
- Cui Yu
- Engineering Research Center of Industrial Microbiology (Ministry of Education) and College of Life Sciences, Fujian Normal University, Fuzhou, China
| | - Lin Chen
- State Key Laboratory of Microbial Metabolism, Joint International Research Laboratory of Metabolic and Developmental Sciences, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, China
- Zhangjiang Institute for Advanced Study, Shanghai Jiao Tong University, Shanghai, China
| | - Yang Le Gao
- Engineering Research Center of Industrial Microbiology (Ministry of Education) and College of Life Sciences, Fujian Normal University, Fuzhou, China
| | - Jia Liu
- Engineering Research Center of Industrial Microbiology (Ministry of Education) and College of Life Sciences, Fujian Normal University, Fuzhou, China
| | - Pei Lin Li
- Engineering Research Center of Industrial Microbiology (Ministry of Education) and College of Life Sciences, Fujian Normal University, Fuzhou, China
| | - Ming Liang Zhang
- Engineering Research Center of Industrial Microbiology (Ministry of Education) and College of Life Sciences, Fujian Normal University, Fuzhou, China
| | - Qin Li
- Engineering Research Center of Industrial Microbiology (Ministry of Education) and College of Life Sciences, Fujian Normal University, Fuzhou, China
| | - Huai Dong Zhang
- Engineering Research Center of Industrial Microbiology (Ministry of Education) and College of Life Sciences, Fujian Normal University, Fuzhou, China
| | - Man Cheng Tang
- State Key Laboratory of Microbial Metabolism, Joint International Research Laboratory of Metabolic and Developmental Sciences, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, China
- Zhangjiang Institute for Advanced Study, Shanghai Jiao Tong University, Shanghai, China
| | - Li Li
- Engineering Research Center of Industrial Microbiology (Ministry of Education) and College of Life Sciences, Fujian Normal University, Fuzhou, China
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33
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Hooper AR, Oštrek A, Milian‐Lopez A, Sarlah D. Bioinspired Total Synthesis of Pyritide A2 through Pyridine Ring Synthesis. Angew Chem Int Ed Engl 2022; 61:e202212299. [PMID: 36123301 PMCID: PMC9827874 DOI: 10.1002/anie.202212299] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2022] [Indexed: 01/12/2023]
Abstract
Pyritides belong to the ribosomally synthesized and post-translationally modified peptide class of natural products that were recently genome-predicted and are structurally defined by unique pyridine-containing macrocycles. Inspired by their biosynthesis, proceeding through peptide modification and cycloaddition to form the heterocyclic core, we report the chemical synthesis of pyritide A2 involving pyridine ring synthesis from an amino acid precursor through aza-Diels-Alder reaction. This strategy permitted the preparation of the decorated pyridine core with an appended amino acid residue in two steps from a commercially available arginine derivative and secured pyritide A2 in ten steps. Moreover, the synthetic logic enables efficient preparation of different pyridine subunits associated with pyritides, allowing rapid and convergent access to this new class of natural products and analogues thereof.
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Affiliation(s)
- Annie R. Hooper
- Department of Chemistry and Carl R. Woese Institute for Genomic BiologyUniversity of Illinois at Urbana-ChampaignUrbanaIL 61801USA
| | - Andraž Oštrek
- Department of Chemistry and Carl R. Woese Institute for Genomic BiologyUniversity of Illinois at Urbana-ChampaignUrbanaIL 61801USA,Department of ChemistryUniversity of PaviaViale Taramelli 1227100PaviaItaly
| | - Ana Milian‐Lopez
- Department of Chemistry and Carl R. Woese Institute for Genomic BiologyUniversity of Illinois at Urbana-ChampaignUrbanaIL 61801USA
| | - David Sarlah
- Department of Chemistry and Carl R. Woese Institute for Genomic BiologyUniversity of Illinois at Urbana-ChampaignUrbanaIL 61801USA,Department of ChemistryUniversity of PaviaViale Taramelli 1227100PaviaItaly
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34
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Huang JH, Lv JM, Xiao LY, Xu Q, Lin FL, Wang GQ, Chen GD, Qin SY, Hu D, Gao H. Characterization of a new fusicoccane-type diterpene synthase and an associated P450 enzyme. Beilstein J Org Chem 2022; 18:1396-1402. [PMID: 36262672 PMCID: PMC9551204 DOI: 10.3762/bjoc.18.144] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2022] [Accepted: 09/19/2022] [Indexed: 01/05/2023] Open
Abstract
Fusicoccane-type terpenoids are a subgroup of diterpenoids featured with a unique 5-8-5 ring system. They are widely distributed in nature and possess a variety of biological activities. Up to date, only five fusicoccane-type diterpene synthases have been identified. Here, we identify a two-gene biosynthetic gene cluster containing a new fusicoccane-type diterpene synthase gene tadA and an associated cytochrome P450 gene tadB from Talaromyces wortmannii ATCC 26942. Heterologous expression reveals that TadA catalyzes the formation of a new fusicoccane-type diterpene talaro-7,13-diene. D2O isotope labeling combined with site-directed mutagenesis indicates that TadA might employ a different C2,6 cyclization strategy from the known fusicoccane-type diterpene synthases, in which a neutral intermediate is firstly formed and then protonated by an environmental proton. In addition, we demonstrate that the associated cytochrome P450 enzyme TadB is able to catalyze multiple oxidation of talaro-7,13-diene to yield talaro-6,13-dien-5,8-dione.
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Affiliation(s)
- Jia-Hua Huang
- Institute of Traditional Chinese Medicine & Natural Products, College of Pharmacy / Guangdong Province Key Laboratory of Pharmacodynamic Constituents of TCM and New Drugs Research / International Cooperative Laboratory of Traditional Chinese Medicine Modernization and Innovative Drug Development of Ministry of Education (MOE) of China, Jinan University, Guangzhou 510632, China
| | - Jian-Ming Lv
- Institute of Traditional Chinese Medicine & Natural Products, College of Pharmacy / Guangdong Province Key Laboratory of Pharmacodynamic Constituents of TCM and New Drugs Research / International Cooperative Laboratory of Traditional Chinese Medicine Modernization and Innovative Drug Development of Ministry of Education (MOE) of China, Jinan University, Guangzhou 510632, China
| | - Liang-Yan Xiao
- Institute of Traditional Chinese Medicine & Natural Products, College of Pharmacy / Guangdong Province Key Laboratory of Pharmacodynamic Constituents of TCM and New Drugs Research / International Cooperative Laboratory of Traditional Chinese Medicine Modernization and Innovative Drug Development of Ministry of Education (MOE) of China, Jinan University, Guangzhou 510632, China
| | - Qian Xu
- Institute of Traditional Chinese Medicine & Natural Products, College of Pharmacy / Guangdong Province Key Laboratory of Pharmacodynamic Constituents of TCM and New Drugs Research / International Cooperative Laboratory of Traditional Chinese Medicine Modernization and Innovative Drug Development of Ministry of Education (MOE) of China, Jinan University, Guangzhou 510632, China
| | - Fu-Long Lin
- Institute of Traditional Chinese Medicine & Natural Products, College of Pharmacy / Guangdong Province Key Laboratory of Pharmacodynamic Constituents of TCM and New Drugs Research / International Cooperative Laboratory of Traditional Chinese Medicine Modernization and Innovative Drug Development of Ministry of Education (MOE) of China, Jinan University, Guangzhou 510632, China
| | - Gao-Qian Wang
- Institute of Traditional Chinese Medicine & Natural Products, College of Pharmacy / Guangdong Province Key Laboratory of Pharmacodynamic Constituents of TCM and New Drugs Research / International Cooperative Laboratory of Traditional Chinese Medicine Modernization and Innovative Drug Development of Ministry of Education (MOE) of China, Jinan University, Guangzhou 510632, China
| | - Guo-Dong Chen
- Institute of Traditional Chinese Medicine & Natural Products, College of Pharmacy / Guangdong Province Key Laboratory of Pharmacodynamic Constituents of TCM and New Drugs Research / International Cooperative Laboratory of Traditional Chinese Medicine Modernization and Innovative Drug Development of Ministry of Education (MOE) of China, Jinan University, Guangzhou 510632, China
| | - Sheng-Ying Qin
- Clinical Experimental Center, First Affiliated Hospital of Jinan University, Guangzhou 510630, China,
| | - Dan Hu
- Institute of Traditional Chinese Medicine & Natural Products, College of Pharmacy / Guangdong Province Key Laboratory of Pharmacodynamic Constituents of TCM and New Drugs Research / International Cooperative Laboratory of Traditional Chinese Medicine Modernization and Innovative Drug Development of Ministry of Education (MOE) of China, Jinan University, Guangzhou 510632, China
- Shenzhen Institute of Synthetic Biology, Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences, Shenzhen 518055, China
| | - Hao Gao
- Institute of Traditional Chinese Medicine & Natural Products, College of Pharmacy / Guangdong Province Key Laboratory of Pharmacodynamic Constituents of TCM and New Drugs Research / International Cooperative Laboratory of Traditional Chinese Medicine Modernization and Innovative Drug Development of Ministry of Education (MOE) of China, Jinan University, Guangzhou 510632, China
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Striving for sustainable biosynthesis: discovery, diversification, and production of antimicrobial drugs in Escherichia coli. Biochem Soc Trans 2022; 50:1315-1328. [PMID: 36196987 DOI: 10.1042/bst20220218] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2022] [Revised: 09/07/2022] [Accepted: 09/12/2022] [Indexed: 11/17/2022]
Abstract
New antimicrobials need to be discovered to fight the advance of multidrug-resistant pathogens. A promising approach is the screening for antimicrobial agents naturally produced by living organisms. As an alternative to studying the native producer, it is possible to use genetically tractable microbes as heterologous hosts to aid the discovery process, facilitate product diversification through genetic engineering, and ultimately enable environmentally friendly production. In this mini-review, we summarize the literature from 2017 to 2022 on the application of Escherichia coli and E. coli-based platforms as versatile and powerful systems for the discovery, characterization, and sustainable production of antimicrobials. We highlight recent developments in high-throughput screening methods and genetic engineering approaches that build on the strengths of E. coli as an expression host and that led to the production of antimicrobial compounds. In the last section, we briefly discuss new techniques that have not been applied to discover or engineer antimicrobials yet, but that may be useful for this application in the future.
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36
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Pentostatin Biosynthesis Pathway Elucidation and Its Application. FERMENTATION 2022. [DOI: 10.3390/fermentation8090459] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022] Open
Abstract
Pentostatin (PNT), a nucleoside antibiotic with a 1,3-diazo ring structure, is distributed in several actinomycetes and fungi species. Its special structure makes PNT possess a wide spectrum of biological and pharmacological properties, such as antibacterial, antitrypanosomal, anticancer, antiviral, herbicidal, insecticidal, and immunomodulatory effects. Because of the promising adenosine deaminase inhibitory activity of PNT, its extensive application in the clinical treatment of malignant tumors has been extensively studied. However, the fermentation level of microbial-derived PNT is low and cannot meet medical needs. Because the biosynthesis pathway of PNT is obscure, only high-yield mutant screening and optimization of medium components and fermentation processes have been conducted for enhancing its production. Recently, the biosynthesis pathways of PNT in actinomycetes and fungi hosts have been revealed successively, and the large-scale production of PNT by systematic metabolic engineering will become an inevitable trend. Therefore, this review covers all aspects of PNT research, in which major advances in understanding the resource microorganisms, mechanism of action, and biosynthesis pathway of PNT were achieved and diverse clinical applications of PNT were emphasized, and it will lay the foundation for commercial transformation and industrial technology of PNT based on systematic metabolic engineering.
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Zhai X, Yao L, Zhou YJ. Construction of microbial chassis for terpenoid discovery. Synth Syst Biotechnol 2022; 7:1181-1182. [PMID: 36262714 PMCID: PMC9554750 DOI: 10.1016/j.synbio.2022.09.002] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2022] [Revised: 09/05/2022] [Accepted: 09/14/2022] [Indexed: 11/17/2022] Open
Affiliation(s)
- Xiaoxin Zhai
- Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian, 116023, China
- CAS Key Laboratory of Separation Science for Analytical Chemistry, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian, 116023, China
- Dalian Key Laboratory of Energy Biotechnology, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian, 116023, China
| | - Lun Yao
- Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian, 116023, China
- CAS Key Laboratory of Separation Science for Analytical Chemistry, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian, 116023, China
- Dalian Key Laboratory of Energy Biotechnology, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian, 116023, China
| | - Yongjin J. Zhou
- Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian, 116023, China
- CAS Key Laboratory of Separation Science for Analytical Chemistry, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian, 116023, China
- Dalian Key Laboratory of Energy Biotechnology, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian, 116023, China
- Corresponding author. Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian, 116023, China.
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38
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Xu W, Yang Q, Yang F, Xie X, Goodwin PH, Deng X, Tian B, Yang L. Evaluation and Genome Analysis of Bacillus subtilis YB-04 as a Potential Biocontrol Agent Against Fusarium Wilt and Growth Promotion Agent of Cucumber. Front Microbiol 2022; 13:885430. [PMID: 35756052 PMCID: PMC9218633 DOI: 10.3389/fmicb.2022.885430] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2022] [Accepted: 05/06/2022] [Indexed: 12/13/2022] Open
Abstract
Cucumber wilt caused by Fusarium oxysporum f.sp. cucumerinum (Foc) is a highly destructive disease that leads to reduced yield in cucumbers. In this study, strain YB-04 was isolated from wheat straw and identified as Bacillus subtilis. It displayed strong antagonistic activity against F. oxysporum f.sp. cucumerinum in dual culture and exhibited significant biocontrol of cucumber Fusarium wilt with a higher control effect than those of previously reported Bacillus strains and displayed pronounced growth promotion of cucumber seedlings. B. subtilis YB-04 could secrete extracellular protease, amylase, cellulose, and β-1,3-glucanase and be able to produce siderophores and indole acetic acid. Inoculation with B. subtilis YB-04 or Foc increased cucumber defense-related enzyme activities for PPO, SOD, CAT, PAL, and LOX. However, the greatest increase was with the combination of B. subtilis YB-04 and Foc. Sequencing the genome of B. subtilis YB-04 showed that it had genes for the biosynthesis of various secondary metabolites, carbohydrate-active enzymes, and assimilation of nitrogen, phosphorous, and potassium. B. subtilis YB-04 appears to be a promising biological control agent against the Fusarium wilt of cucumber and promotes cucumber growth by genomic, physiological, and phenotypic analysis.
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Affiliation(s)
- Wen Xu
- Henan International Joint Laboratory of Crop Protection, Henan Biopesticide Engineering Research Center, Institute of Plant Protection Research, Graduate T&R Base of Zhengzhou University, Henan Academy of Agricultural Sciences, Zhengzhou, China
| | - Qian Yang
- Henan International Joint Laboratory of Crop Protection, Henan Biopesticide Engineering Research Center, Institute of Plant Protection Research, Graduate T&R Base of Zhengzhou University, Henan Academy of Agricultural Sciences, Zhengzhou, China.,School of Agricultural Sciences, Zhengzhou University, Zhengzhou, China
| | - Fan Yang
- Institute of Horticulture, Henan Academy of Agricultural Sciences, Zhengzhou, China
| | - Xia Xie
- Henan International Joint Laboratory of Crop Protection, Henan Biopesticide Engineering Research Center, Institute of Plant Protection Research, Graduate T&R Base of Zhengzhou University, Henan Academy of Agricultural Sciences, Zhengzhou, China
| | - Paul H Goodwin
- School of Environmental Sciences, University of Guelph, Guelph, ON, Canada
| | - Xiaoxu Deng
- Henan International Joint Laboratory of Crop Protection, Henan Biopesticide Engineering Research Center, Institute of Plant Protection Research, Graduate T&R Base of Zhengzhou University, Henan Academy of Agricultural Sciences, Zhengzhou, China
| | - Baoming Tian
- School of Agricultural Sciences, Zhengzhou University, Zhengzhou, China
| | - Lirong Yang
- Henan International Joint Laboratory of Crop Protection, Henan Biopesticide Engineering Research Center, Institute of Plant Protection Research, Graduate T&R Base of Zhengzhou University, Henan Academy of Agricultural Sciences, Zhengzhou, China
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Ziko L, AbdelRaheem O, Nabil M, Aziz RK, Siam R. Bioprospecting the microbiome of Red Sea Atlantis II brine pool for peptidases and biosynthetic genes with promising antibacterial activity. Microb Cell Fact 2022; 21:109. [PMID: 35655185 PMCID: PMC9161539 DOI: 10.1186/s12934-022-01835-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: 03/28/2022] [Accepted: 05/05/2022] [Indexed: 11/23/2022] Open
Abstract
Background The search for novel antimicrobial agents is crucial as antibiotic-resistant pathogens continue to emerge, rendering the available antibiotics no longer effective. Likewise, new anti-cancer drugs are needed to combat the emergence of multi-drug resistant tumors. Marine environments are wealthy sources for natural products. Additionally, extreme marine environments are interesting niches to search for bioactive natural compounds. In the current study, a fosmid library of metagenomic DNA isolated from Atlantis II Deep Lower Convective Layer (ATII LCL), was functionally screened for antibacterial activity as well as anticancer effects. Results Two clones exhibited antibacterial effects against the marine Bacillus Cc6 strain, namely clones 102-5A and 88-1G and they were further tested against eleven other challenging strains, including six safe relatives of ESKAPE pathogens (Enterococcus faecium, Staphylococcus aureus, Klebsiella pneumoniae, Acinetobacter baumannii, Pseudomonas aeruginosa, and Enterobacter spp.), a safe relative to Mycobacterium tuberculosis and four resistant clinical isolates. Clone 88-1G resulted in clear zones of inhibition against eight bacterial strains, while clone 102-5A resulted in zones of inhibition against five bacterial strains. The whole cell lysates of clone 88-1G showed 15% inhibition of Mtb ClpP protease -Mycobacterium tuberculosis drug target-, while whole cell lysates of clone 102-5A showed 19% inhibition of Mtb ClpP protease. Whole cell lysates from the selected clones exhibited anticancer effects against MCF-7 breast cancer cells (cell viability at 50% v/v was 46.2% ± 9.9 for 88-1G clone and 38% ± 7 for 102-5A clone), U2OS osteosarcoma cells (cell viability at 50% v/v was 64.6% ± 12.3 for 88-1G clone and 28.3% ± 1.7 for 102-5A clone) and 1BR hTERT human fibroblast cells (cell viability at 50% v/v was 74.4% ± 5.6 for 88-1G clone and 57.6% ± 8.9 for 102-5A clone). Sequencing of 102-5A and 88-1G clones, and further annotation detected putative proteases and putative biosynthetic genes in clones 102-5A and 88-1G, respectively. Conclusions The ATII LCL metagenome hosts putative peptidases and biosynthetic genes that confer antibiotic and anti-cancer effects. The tested clones exhibited promising antibacterial activities against safe relative strains to ESKAPE pathogens and Mycobacterium tuberculosis. Thus, searching the microbial dark matter of extreme environments is a promising approach to identify new molecules with pharmaceutical potential use. Supplementary Information The online version contains supplementary material available at 10.1186/s12934-022-01835-z.
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Affiliation(s)
- Laila Ziko
- School of Life and Medical Sciences, University of Hertfordshire, Hosted by Global Academic Foundation, 11865, New Administrative Capital, Egypt.,Department of Biology, School of Sciences and Engineering, The American University in Cairo, 11835, New Cairo, Egypt
| | - Omnia AbdelRaheem
- Graduate Program of Biotechnology, School of Sciences and Engineering, The American University in Cairo, 11835, New Cairo, Egypt
| | - Marina Nabil
- Graduate Program of Biotechnology, School of Sciences and Engineering, The American University in Cairo, 11835, New Cairo, Egypt
| | - Ramy K Aziz
- Department of Microbiology and Immunology, Faculty of Pharmacy, Cairo University, 11562, Cairo, Egypt.,Microbiology and Immunology Research Program, Children's Cancer Hospital Egypt 57357, 11617, Cairo, Egypt
| | - Rania Siam
- Department of Biology, School of Sciences and Engineering, The American University in Cairo, 11835, New Cairo, Egypt. .,University of Medicine and Health Sciences, Basseterre, West Indies, Saint Kitts and Nevis.
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Fobofou SA, Savidge T. Microbial metabolites: cause or consequence in gastrointestinal disease? Am J Physiol Gastrointest Liver Physiol 2022; 322:G535-G552. [PMID: 35271353 PMCID: PMC9054261 DOI: 10.1152/ajpgi.00008.2022] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/10/2022] [Revised: 03/07/2022] [Accepted: 03/07/2022] [Indexed: 01/31/2023]
Abstract
Systems biology studies have established that changes in gastrointestinal microbiome composition and function can adversely impact host physiology. Notable diseases synonymously associated with dysbiosis include inflammatory bowel diseases, cancer, metabolic disorders, and opportunistic and recurrent pathogen infections. However, there is a scarcity of mechanistic data that advances our understanding of taxonomic correlations with pathophysiological host-microbiome interactions. Generally, to survive a hostile gut environment, microbes are highly metabolically active and produce trans-kingdom signaling molecules to interact with competing microorganisms and the host. These specialized metabolites likely play important homeostatic roles, and identifying disease-specific taxa and their effector pathways can provide better strategies for diagnosis, treatment, and prevention, as well as the discovery of innovative therapeutics. The signaling role of microbial biotransformation products such as bile acids, short-chain fatty acids, polysaccharides, and dietary tryptophan is increasingly recognized, but little is known about the identity and function of metabolites that are synthesized by microbial biosynthetic gene clusters, including ribosomally synthesized and posttranslationally modified peptides (RiPPs), nonribosomal peptides (NRPs), polyketides (PKs), PK-NRP hybrids, and terpenes. Here we consider how bioactive natural products directly encoded by the human microbiome can contribute to the pathophysiology of gastrointestinal disease, cancer, autoimmune, antimicrobial-resistant bacterial and viral infections (including COVID-19). We also present strategies used to discover these compounds and the biological activities they exhibit, with consideration of therapeutic interventions that could emerge from understanding molecular causation in gut microbiome research.
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Affiliation(s)
- Serge Alain Fobofou
- Department of Pathology and Immunology, Baylor College of Medicine, Houston, Texas
- Department of Pathology, Texas Children's Microbiome Center, Texas Children's Hospital, Houston, Texas
| | - Tor Savidge
- Department of Pathology and Immunology, Baylor College of Medicine, Houston, Texas
- Department of Pathology, Texas Children's Microbiome Center, Texas Children's Hospital, Houston, Texas
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41
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Lin LP, Wu M, Jiang N, Wang W, Tan RX. Carbon-nitrogen bond formation to construct novel polyketide-indole hybrids from the indole-3-carbinol exposed culture of Daldinia eschscholzii. Synth Syst Biotechnol 2022; 7:750-755. [PMID: 35387230 PMCID: PMC8943216 DOI: 10.1016/j.synbio.2022.02.004] [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: 01/15/2022] [Revised: 01/29/2022] [Accepted: 02/07/2022] [Indexed: 11/26/2022] Open
Abstract
A plenty of cytochrome P450s have been annotated in the Daldinia eschosholzii genome. Inspired by the fact that some P450s have been reported to catalyze the carbon-nitrogen (C–N) bond formation, we were curious about whether hybrids through C–N bond formation could be generated in the indole-3-carbinol (I3C) exposed culture of D. eschscholzii. As expected, two skeletally undescribed polyketide-indole hybrids, designated as indolpolyketone A and B (1 and 2), were isolated and assigned to be constructed through C–N bond formation. Their structures were elucidated by 1D and 2D NMR spectra. The absolute configurations of 1 and 2 were determined by comparing the recorded and calculated electronic circular dichroism (ECD) spectra. Furthermore, the plausible biosynthetic pathways for 1 and 2 were proposed. Compounds 1 and 2 exhibited significant antiviral activity against H1N1 with IC50 values of 45.2 and 31.4 μM, respectively. In brief, compounds 1 and 2 were reported here for the first time and were the first example of polyketide-indole hybrids pieced together through C–N bond formation in the I3C-exposed culture of D. eschscholzii. Therefore, this study expands the knowledge about the chemical production of D. eschscholzii through precursor-directed biosynthesis (PDB).
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42
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Jiang YQ, Lin JP. Recent progress in strategies for steroid production in yeasts. World J Microbiol Biotechnol 2022; 38:93. [PMID: 35441962 DOI: 10.1007/s11274-022-03276-7] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2022] [Accepted: 03/24/2022] [Indexed: 10/18/2022]
Abstract
As essential structural molecules of fungal cell membrane, ergosterol is not only an important component of fungal growth and stress-resistance but also a key precursor for manufacturing steroid drugs of pharmaceutical or agricultural significance. So far, ergosterol biosynthesis in yeast has been elucidated elaborately, and efforts have been made to increase ergosterol production through regulation of ergosterol metabolism and storage. Furthermore, the same intermediates shared by yeasts and animals or plants make the construction of heterologous sterol pathways in yeast a promising approach to synthesize valuable steroids, such as phytosteroids and animal steroid hormones. During these challenging processes, several obstacles have arisen and been combated with great endeavors. This paper reviews recent research progress of yeast metabolic engineering for improving the production of ergosterol and heterologous steroids. The remaining tactics are also discussed.
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Affiliation(s)
- Yi-Qi Jiang
- Key Laboratory of Biomass Chemical Engineering of Ministry of Education, College of Chemical and Biological Engineering, Zhejiang University, Hangzhou, 310027, China
| | - Jian-Ping Lin
- Key Laboratory of Biomass Chemical Engineering of Ministry of Education, College of Chemical and Biological Engineering, Zhejiang University, Hangzhou, 310027, China.
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43
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Clark CM, Nguyen L, Pham VC, Sanchez LM, Murphy BT. Automated Microbial Library Generation Using the Bioinformatics Platform IDBac. Molecules 2022; 27:2038. [PMID: 35408437 PMCID: PMC9000433 DOI: 10.3390/molecules27072038] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2022] [Revised: 03/15/2022] [Accepted: 03/16/2022] [Indexed: 11/21/2022] Open
Abstract
Libraries of microorganisms have served as a cornerstone of therapeutic drug discovery, though the continued re-isolation of known natural product chemical entities has remained a significant obstacle to discovery efforts. A major contributing factor to this redundancy is the duplication of bacterial taxa in a library, which can be mitigated through the use of a variety of DNA sequencing strategies and/or mass spectrometry-informed bioinformatics platforms so that the library is created with minimal phylogenetic, and thus minimal natural product overlap. IDBac is a MALDI-TOF mass spectrometry-based bioinformatics platform used to assess overlap within collections of environmental bacterial isolates. It allows environmental isolate redundancy to be reduced while considering both phylogeny and natural product production. However, manually selecting isolates for addition to a library during this process was time intensive and left to the researcher's discretion. Here, we developed an algorithm that automates the prioritization of hundreds to thousands of environmental microorganisms in IDBac. The algorithm performs iterative reduction of natural product mass feature overlap within groups of isolates that share high homology of protein mass features. Employing this automation serves to minimize human bias and greatly increase efficiency in the microbial strain prioritization process.
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Affiliation(s)
- Chase M. Clark
- Department of Pharmaceutical Sciences, Center for Biomolecular Sciences, College of Pharmacy, University of Illinois at Chicago, 833 S. Wood St., Chicago, IL 60612, USA;
| | - Linh Nguyen
- Institute of Marine Biochemistry, Vietnam Academy of Science and Technology, Nghiado, Caugiay, Hanoi 10000, Vietnam; (L.N.); (V.C.P.)
| | - Van Cuong Pham
- Institute of Marine Biochemistry, Vietnam Academy of Science and Technology, Nghiado, Caugiay, Hanoi 10000, Vietnam; (L.N.); (V.C.P.)
| | - Laura M. Sanchez
- Department of Chemistry and Biochemistry, University of California Santa Cruz, 1156 High Street, Santa Cruz, CA 95064, USA;
| | - Brian T. Murphy
- Department of Pharmaceutical Sciences, Center for Biomolecular Sciences, College of Pharmacy, University of Illinois at Chicago, 833 S. Wood St., Chicago, IL 60612, USA;
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Romano G, Almeida M, Varela Coelho A, Cutignano A, Gonçalves LG, Hansen E, Khnykin D, Mass T, Ramšak A, Rocha MS, Silva TH, Sugni M, Ballarin L, Genevière AM. Biomaterials and Bioactive Natural Products from Marine Invertebrates: From Basic Research to Innovative Applications. Mar Drugs 2022; 20:md20040219. [PMID: 35447892 PMCID: PMC9027906 DOI: 10.3390/md20040219] [Citation(s) in RCA: 19] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2022] [Revised: 03/16/2022] [Accepted: 03/16/2022] [Indexed: 12/22/2022] Open
Abstract
Aquatic invertebrates are a major source of biomaterials and bioactive natural products that can find applications as pharmaceutics, nutraceutics, cosmetics, antibiotics, antifouling products and biomaterials. Symbiotic microorganisms are often the real producers of many secondary metabolites initially isolated from marine invertebrates; however, a certain number of them are actually synthesized by the macro-organisms. In this review, we analysed the literature of the years 2010–2019 on natural products (bioactive molecules and biomaterials) from the main phyla of marine invertebrates explored so far, including sponges, cnidarians, molluscs, echinoderms and ascidians, and present relevant examples of natural products of interest to public and private stakeholders. We also describe omics tools that have been more relevant in identifying and understanding mechanisms and processes underlying the biosynthesis of secondary metabolites in marine invertebrates. Since there is increasing attention on finding new solutions for a sustainable large-scale supply of bioactive compounds, we propose that a possible improvement in the biodiscovery pipeline might also come from the study and utilization of aquatic invertebrate stem cells.
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Affiliation(s)
- Giovanna Romano
- Marine Biotechnology Department, Stazione Zoologica Anton Dohrn, Villa Comunale, 80121 Naples, Italy;
- Correspondence: (G.R.); (L.B.)
| | - Mariana Almeida
- 3B’s Research Group, I3B’s—Research Institute on Biomaterials, Biodegradables and Biomimetics of University of Minho, Headquarters of the European Institute of Excellence on Tissue Engineering and Regenerative Medicine, AvePark—Parque de Ciência e Tecnologia, Barco, 4805-017 Guimarães, Portugal; (M.A.); (M.S.R.); (T.H.S.)
- ICVS/3B´s—PT Government Associate Laboratory, 4710-057 Braga, Portugal
| | - Ana Varela Coelho
- ITQB NOVA, Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa, Av. da República, 2780-157 Oeiras, Portugal; (A.V.C.); (L.G.G.)
| | - Adele Cutignano
- Marine Biotechnology Department, Stazione Zoologica Anton Dohrn, Villa Comunale, 80121 Naples, Italy;
- CNR-Institute of Biomolecular Chemistry, Via Campi Flegrei 34, 80078 Pozzuoli, Italy
| | - Luis G Gonçalves
- ITQB NOVA, Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa, Av. da República, 2780-157 Oeiras, Portugal; (A.V.C.); (L.G.G.)
| | - Espen Hansen
- Marbio, UiT-The Arctic University of Norway, 9037 Tromso, Norway;
| | - Denis Khnykin
- Laboratory for Immunohistochemistry and Immunopathology (LIIPAT), Department of Pathology, Oslo University Hospital-Rikshospitalet, 0450 Oslo, Norway;
| | - Tali Mass
- Faculty of Natural Science, Department of Marine Biology, Charney School of Marine Sciences, University of Haifa, Haifa 3498838, Israel;
| | - Andreja Ramšak
- National Institute of Biology, Marine Biology Station, Fornače 41, SI-6330 Piran, Slovenia;
| | - Miguel S. Rocha
- 3B’s Research Group, I3B’s—Research Institute on Biomaterials, Biodegradables and Biomimetics of University of Minho, Headquarters of the European Institute of Excellence on Tissue Engineering and Regenerative Medicine, AvePark—Parque de Ciência e Tecnologia, Barco, 4805-017 Guimarães, Portugal; (M.A.); (M.S.R.); (T.H.S.)
- ICVS/3B´s—PT Government Associate Laboratory, 4710-057 Braga, Portugal
| | - Tiago H. Silva
- 3B’s Research Group, I3B’s—Research Institute on Biomaterials, Biodegradables and Biomimetics of University of Minho, Headquarters of the European Institute of Excellence on Tissue Engineering and Regenerative Medicine, AvePark—Parque de Ciência e Tecnologia, Barco, 4805-017 Guimarães, Portugal; (M.A.); (M.S.R.); (T.H.S.)
- ICVS/3B´s—PT Government Associate Laboratory, 4710-057 Braga, Portugal
| | - Michela Sugni
- Department of Environmental Science and Policy, University of Milan, Via Celoria, 2, 20133 Milan, Italy;
| | - Loriano Ballarin
- Department of Biology, University of Padova, Via U. Bassi 58/B, 35100 Padova, Italy
- Correspondence: (G.R.); (L.B.)
| | - Anne-Marie Genevière
- Biologie Intégrative des Organismes Marins (BIOM), Observatoire Océanologique de Banyuls-sur-Mer, Sorbonne Université, CNRS, 1 Avenue Pierre Fabre, 66650 Banyuls-sur-Mer, France;
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Fierro F, Vaca I, Castillo NI, García-Rico RO, Chávez R. Penicillium chrysogenum, a Vintage Model with a Cutting-Edge Profile in Biotechnology. Microorganisms 2022; 10:microorganisms10030573. [PMID: 35336148 PMCID: PMC8954384 DOI: 10.3390/microorganisms10030573] [Citation(s) in RCA: 17] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2021] [Revised: 02/15/2022] [Accepted: 02/17/2022] [Indexed: 12/20/2022] Open
Abstract
The discovery of penicillin entailed a decisive breakthrough in medicine. No other medical advance has ever had the same impact in the clinical practise. The fungus Penicillium chrysogenum (reclassified as P. rubens) has been used for industrial production of penicillin ever since the forties of the past century; industrial biotechnology developed hand in hand with it, and currently P. chrysogenum is a thoroughly studied model for secondary metabolite production and regulation. In addition to its role as penicillin producer, recent synthetic biology advances have put P. chrysogenum on the path to become a cell factory for the production of metabolites with biotechnological interest. In this review, we tell the history of P. chrysogenum, from the discovery of penicillin and the first isolation of strains with high production capacity to the most recent research advances with the fungus. We will describe how classical strain improvement programs achieved the goal of increasing production and how the development of different molecular tools allowed further improvements. The discovery of the penicillin gene cluster, the origin of the penicillin genes, the regulation of penicillin production, and a compilation of other P. chrysogenum secondary metabolites will also be covered and updated in this work.
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Affiliation(s)
- Francisco Fierro
- Departamento de Biotecnología, Universidad Autónoma Metropolitana-Unidad Iztapalapa, Ciudad de México 09340, Mexico
- Correspondence:
| | - Inmaculada Vaca
- Departamento de Química, Facultad de Ciencias, Universidad de Chile, Santiago 7800003, Chile;
| | - Nancy I. Castillo
- Grupo de Investigación en Ciencias Biológicas y Químicas, Facultad de Ciencias, Universidad Antonio Nariño, Bogotá 110231, Colombia;
| | - Ramón Ovidio García-Rico
- Grupo de Investigación GIMBIO, Departamento De Microbiología, Facultad de Ciencias Básicas, Universidad de Pamplona, Pamplona 543050, Colombia;
| | - Renato Chávez
- Departamento de Biología, Facultad de Química y Biología, Universidad de Santiago de Chile, Santiago 9170020, Chile;
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