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Bogdanov A, Salib MN, Chase AB, Hammerlindl H, Muskat MN, Luedtke S, Barbosa da Silva E, O’Donoghue AJ, Wu LF, Altschuler SJ, Molinski TF, Jensen PR. Small Molecule in situ Resin Capture - A Compound First Approach to Natural Product Discovery. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.03.02.530684. [PMID: 37398257 PMCID: PMC10312467 DOI: 10.1101/2023.03.02.530684] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/04/2023]
Abstract
Microbial natural products remain an important resource for drug discovery. Yet, commonly employed discovery techniques are plagued by the rediscovery of known compounds, the relatively few microbes that can be cultured, and laboratory growth conditions that do not elicit biosynthetic gene expression among myriad other challenges. Here we introduce a culture independent approach to natural product discovery that we call the Small Molecule In situ Resin Capture (SMIRC) technique. SMIRC exploits in situ environmental conditions to elicit compound production and represents a new approach to access poorly explored chemical space by capturing natural products directly from the environments in which they are produced. In contrast to traditional methods, this compound-first approach can capture structurally complex small molecules across all domains of life in a single deployment while relying on Nature to provide the complex and poorly understood environmental cues needed to elicit biosynthetic gene expression. We illustrate the effectiveness of SMIRC in marine habitats with the discovery of numerous new compounds and demonstrate that sufficient compound yields can be obtained for NMR-based structure assignment. Two new compound classes are reported including one novel carbon skeleton that possesses a functional group not previously observed among natural products and a second that possesses potent biological activity. We introduce expanded deployments, in situ cultivation, and metagenomics as methods to facilitate compound discovery, enhance yields, and link compounds to producing organisms. This compound first approach can provide unprecedented access to new natural product chemotypes with broad implications for drug discovery.
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Affiliation(s)
- Alexander Bogdanov
- Scripps Institution of Oceanography, University of California, San Diego, La Jolla, CA 92093, USA
| | - Mariam N. Salib
- Department of Chemistry and Biochemistry, University of California, San Diego, La Jolla, CA 92093, USA
| | - Alexander B. Chase
- Scripps Institution of Oceanography, University of California, San Diego, La Jolla, CA 92093, USA
- Department of Earth Sciences, Southern Methodist University, Dallas, TX 75275, USA
| | - Heinz Hammerlindl
- Department of Pharmaceutical Chemistry, University of California, San Francisco, San Francisco, CA 94158, USA
| | - Mitchell N. Muskat
- Scripps Institution of Oceanography, University of California, San Diego, La Jolla, CA 92093, USA
| | - Stephanie Luedtke
- Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California, San Diego, La Jolla, CA 92093
| | - Elany Barbosa da Silva
- Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California, San Diego, La Jolla, CA 92093
| | - Anthony J. O’Donoghue
- Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California, San Diego, La Jolla, CA 92093
| | - Lani F. Wu
- Department of Pharmaceutical Chemistry, University of California, San Francisco, San Francisco, CA 94158, USA
| | - Steven J. Altschuler
- Department of Pharmaceutical Chemistry, University of California, San Francisco, San Francisco, CA 94158, USA
| | - Tadeusz F. Molinski
- Department of Chemistry and Biochemistry, University of California, San Diego, La Jolla, CA 92093, USA
| | - Paul R. Jensen
- Scripps Institution of Oceanography, University of California, San Diego, La Jolla, CA 92093, USA
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52
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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: 2] [Impact Index Per Article: 2.0] [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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53
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Kou X, Shi P, Gao C, Ma P, Xing H, Ke Q, Zhang D. Data-Driven Elucidation of Flavor Chemistry. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2023; 71:6789-6802. [PMID: 37102791 PMCID: PMC10176570 DOI: 10.1021/acs.jafc.3c00909] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/11/2023]
Abstract
Flavor molecules are commonly used in the food industry to enhance product quality and consumer experiences but are associated with potential human health risks, highlighting the need for safer alternatives. To address these health-associated challenges and promote reasonable application, several databases for flavor molecules have been constructed. However, no existing studies have comprehensively summarized these data resources according to quality, focused fields, and potential gaps. Here, we systematically summarized 25 flavor molecule databases published within the last 20 years and revealed that data inaccessibility, untimely updates, and nonstandard flavor descriptions are the main limitations of current studies. We examined the development of computational approaches (e.g., machine learning and molecular simulation) for the identification of novel flavor molecules and discussed their major challenges regarding throughput, model interpretability, and the lack of gold-standard data sets for equitable model evaluation. Additionally, we discussed future strategies for the mining and designing of novel flavor molecules based on multi-omics and artificial intelligence to provide a new foundation for flavor science research.
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Affiliation(s)
- Xingran Kou
- Collaborative Innovation Center of Fragrance Flavour and Cosmetics, School of Perfume and Aroma Technology, Shanghai Institute of Technology, Shanghai 201418, China
| | - Peiqin Shi
- Collaborative Innovation Center of Fragrance Flavour and Cosmetics, School of Perfume and Aroma Technology, Shanghai Institute of Technology, Shanghai 201418, China
| | - Chukun Gao
- Laboratory for Physical Chemistry, ETH Zürich, 8093 Zürich, Switzerland
| | - Peihua Ma
- Department of Nutrition and Food Science, University of Maryland, College Park, Maryland 20742, United States
| | - Huadong Xing
- CAS Key Laboratory of Computational Biology, Shanghai Institute of Nutrition and Health, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai 200031, China
| | - Qinfei Ke
- Collaborative Innovation Center of Fragrance Flavour and Cosmetics, School of Perfume and Aroma Technology, Shanghai Institute of Technology, Shanghai 201418, China
| | - Dachuan Zhang
- National Centre of Competence in Research (NCCR) Catalysis, Institute of Environmental Engineering, ETH Zürich, 8093 Zürich, Switzerland
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54
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Ye S, Molloy B, Pérez-Victoria I, Montero I, Braña AF, Olano C, Arca S, Martín J, Reyes F, Salas JA, Méndez C. Uncovering the Cryptic Gene Cluster ahb for 3-amino-4-hydroxybenzoate Derived Ahbamycins, by Searching SARP Regulator Encoding Genes in the Streptomyces argillaceus Genome. Int J Mol Sci 2023; 24:ijms24098197. [PMID: 37175904 PMCID: PMC10179220 DOI: 10.3390/ijms24098197] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2023] [Revised: 04/29/2023] [Accepted: 04/30/2023] [Indexed: 05/15/2023] Open
Abstract
Genome mining using standard bioinformatics tools has allowed for the uncovering of hidden biosynthesis gene clusters for specialized metabolites in Streptomyces genomes. In this work, we have used an alternative approach consisting in seeking "Streptomyces Antibiotic Regulatory Proteins" (SARP) encoding genes and analyzing their surrounding DNA region to unearth cryptic gene clusters that cannot be identified using standard bioinformatics tools. This strategy has allowed the unveiling of the new ahb cluster in Streptomyces argillaceus, which had not been retrieved before using antiSMASH. The ahb cluster is highly preserved in other Streptomyces strains, which suggests a role for their encoding compounds in specific environmental conditions. By combining overexpression of three regulatory genes and generation of different mutants, we were able to activate the ahb cluster, and to identify and chemically characterize the encoded compounds that we have named ahbamycins (AHBs). These constitute a new family of metabolites derived from 3-amino-4-hydroxybenzoate (3,4-AHBA) known for having antibiotic and antitumor activity. Additionally, by overexpressing three genes of the cluster (ahbH, ahbI, and ahbL2) for the synthesis and activation of 3,4-AHBA, a new hybrid compound, AHB18, was identified which had been produced from a metabolic crosstalk between the AHB and the argimycin P pathways. The identification of this new BGC opens the possibility to generate new compounds by combinatorial biosynthesis.
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Affiliation(s)
- Suhui Ye
- Departamento de Biología Funcional e Instituto Universitario de Oncología del Principado de Asturias (I.U.O.P.A), Universidad de Oviedo, 33006 Oviedo, Spain
- Instituto de Investigación Sanitaria de Asturias (ISPA), 33011 Oviedo, Spain
| | - Brian Molloy
- Departamento de Biología Funcional e Instituto Universitario de Oncología del Principado de Asturias (I.U.O.P.A), Universidad de Oviedo, 33006 Oviedo, Spain
| | - Ignacio Pérez-Victoria
- Fundación MEDINA, Centro de Excelencia en Investigación de Medicamentos Innovadores en Andalucía, Armilla, 18016 Granada, Spain
| | - Ignacio Montero
- Departamento de Biología Funcional e Instituto Universitario de Oncología del Principado de Asturias (I.U.O.P.A), Universidad de Oviedo, 33006 Oviedo, Spain
- Instituto de Investigación Sanitaria de Asturias (ISPA), 33011 Oviedo, Spain
| | - Alfredo F Braña
- Departamento de Biología Funcional e Instituto Universitario de Oncología del Principado de Asturias (I.U.O.P.A), Universidad de Oviedo, 33006 Oviedo, Spain
| | - Carlos Olano
- Departamento de Biología Funcional e Instituto Universitario de Oncología del Principado de Asturias (I.U.O.P.A), Universidad de Oviedo, 33006 Oviedo, Spain
- Instituto de Investigación Sanitaria de Asturias (ISPA), 33011 Oviedo, Spain
| | - Sonia Arca
- Departamento de Biología Funcional e Instituto Universitario de Oncología del Principado de Asturias (I.U.O.P.A), Universidad de Oviedo, 33006 Oviedo, Spain
| | - Jesús Martín
- Fundación MEDINA, Centro de Excelencia en Investigación de Medicamentos Innovadores en Andalucía, Armilla, 18016 Granada, Spain
| | - Fernando Reyes
- Fundación MEDINA, Centro de Excelencia en Investigación de Medicamentos Innovadores en Andalucía, Armilla, 18016 Granada, Spain
| | - José A Salas
- Departamento de Biología Funcional e Instituto Universitario de Oncología del Principado de Asturias (I.U.O.P.A), Universidad de Oviedo, 33006 Oviedo, Spain
- Instituto de Investigación Sanitaria de Asturias (ISPA), 33011 Oviedo, Spain
| | - Carmen Méndez
- Departamento de Biología Funcional e Instituto Universitario de Oncología del Principado de Asturias (I.U.O.P.A), Universidad de Oviedo, 33006 Oviedo, Spain
- Instituto de Investigación Sanitaria de Asturias (ISPA), 33011 Oviedo, Spain
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55
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Hagen EH, Blackwell AD, Lightner AD, Sullivan RJ. Homo medicus: The transition to meat eating increased pathogen pressure and the use of pharmacological plants in Homo. AMERICAN JOURNAL OF BIOLOGICAL ANTHROPOLOGY 2023; 180:589-617. [PMID: 36815505 DOI: 10.1002/ajpa.24718] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/27/2022] [Revised: 01/31/2023] [Accepted: 02/08/2023] [Indexed: 02/24/2023]
Abstract
The human lineage transitioned to a more carnivorous niche 2.6 mya and evolved a large body size and slower life history, which likely increased zoonotic pathogen pressure. Evidence for this increase includes increased zoonotic infections in modern hunter-gatherers and bushmeat hunters, exceptionally low stomach pH compared to other primates, and divergence in immune-related genes. These all point to change, and probably intensification, in the infectious disease environment of Homo compared to earlier hominins and other apes. At the same time, the brain, an organ in which immune responses are constrained, began to triple in size. We propose that the combination of increased zoonotic pathogen pressure and the challenges of defending a large brain and body from pathogens in a long-lived mammal, selected for intensification of the plant-based self-medication strategies already in place in apes and other primates. In support, there is evidence of medicinal plant use by hominins in the middle Paleolithic, and all cultures today have sophisticated, plant-based medical systems, add spices to food, and regularly consume psychoactive plant substances that are harmful to helminths and other pathogens. We propose that the computational challenges of discovering effective plant-based treatments, the consequent ability to consume more energy-rich animal foods, and the reduced reliance on energetically-costly immune responses helped select for increased cognitive abilities and unique exchange relationships in Homo. In the story of human evolution, which has long emphasized hunting skills, medical skills had an equal role to play.
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Affiliation(s)
- Edward H Hagen
- Department of Anthropology, Washington State University, Pullman, Washington, USA
| | - Aaron D Blackwell
- Department of Anthropology, Washington State University, Pullman, Washington, USA
| | - Aaron D Lightner
- Department of Anthropology, Washington State University, Pullman, Washington, USA
- Department of the Study of Religion, Aarhus University, Aarhus, Denmark
| | - Roger J Sullivan
- Department of Anthropology, California State University, Sacramento, California, USA
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56
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Huang YQ, Sun P, Chen Y, Liu HX, Hao GF, Song BA. Bioinformatics toolbox for exploring target mutation-induced drug resistance. Brief Bioinform 2023; 24:7026012. [PMID: 36738254 DOI: 10.1093/bib/bbad033] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2022] [Revised: 12/25/2022] [Accepted: 01/14/2023] [Indexed: 02/05/2023] Open
Abstract
Drug resistance is increasingly among the main issues affecting human health and threatening agriculture and food security. In particular, developing approaches to overcome target mutation-induced drug resistance has long been an essential part of biological research. During the past decade, many bioinformatics tools have been developed to explore this type of drug resistance, and they have become popular for elucidating drug resistance mechanisms in a low cost, fast and effective way. However, these resources are scattered and underutilized, and their strengths and limitations have not been systematically analyzed and compared. Here, we systematically surveyed 59 freely available bioinformatics tools for exploring target mutation-induced drug resistance. We analyzed and summarized these resources based on their functionality, data volume, data source, operating principle, performance, etc. And we concisely discussed the strengths, limitations and application examples of these tools. Specifically, we tested some predictive tools and offered some thoughts from the clinician's perspective. Hopefully, this work will provide a useful toolbox for researchers working in the biomedical, pesticide, bioinformatics and pharmaceutical engineering fields, and a good platform for non-specialists to quickly understand drug resistance prediction.
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Affiliation(s)
- Yuan-Qin Huang
- National Key Laboratory of Green Pesticide, Key Laboratory of Green Pesticide and Agricultural Bioengineering, Ministry of Education, Guizhou University, Guiyang 550025, P. R. China
| | - Ping Sun
- National Key Laboratory of Green Pesticide, Key Laboratory of Green Pesticide and Agricultural Bioengineering, Ministry of Education, Guizhou University, Guiyang 550025, P. R. China
| | - Yi Chen
- National Key Laboratory of Green Pesticide, Key Laboratory of Green Pesticide and Agricultural Bioengineering, Ministry of Education, Guizhou University, Guiyang 550025, P. R. China
| | - Huan-Xiang Liu
- Faculty of Applied Science, Macao Polytechnic University, Macao 999078, SAR, China
| | - Ge-Fei Hao
- National Key Laboratory of Green Pesticide, Key Laboratory of Green Pesticide and Agricultural Bioengineering, Ministry of Education, Guizhou University, Guiyang 550025, P. R. China
| | - Bao-An Song
- National Key Laboratory of Green Pesticide, Key Laboratory of Green Pesticide and Agricultural Bioengineering, Ministry of Education, Guizhou University, Guiyang 550025, P. R. China
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57
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Wilson K, de Rond T, Burkhardt I, Steele TS, Schäfer RJB, Podell S, Allen EE, Moore BS. Terpene biosynthesis in marine sponge animals. Proc Natl Acad Sci U S A 2023; 120:e2220934120. [PMID: 36802428 PMCID: PMC9992776 DOI: 10.1073/pnas.2220934120] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2022] [Accepted: 01/25/2023] [Indexed: 02/23/2023] Open
Abstract
Sea sponges are the largest marine source of small-molecule natural products described to date. Sponge-derived molecules, such as the chemotherapeutic eribulin, the calcium-channel blocker manoalide, and antimalarial compound kalihinol A, are renowned for their impressive medicinal, chemical, and biological properties. Sponges contain microbiomes that control the production of many natural products isolated from these marine invertebrates. In fact, all genomic studies to date investigating the metabolic origins of sponge-derived small molecules concluded that microbes-not the sponge animal host-are the biosynthetic producers. However, early cell-sorting studies suggested the sponge animal host may play a role particularly in the production of terpenoid molecules. To investigate the genetic underpinnings of sponge terpenoid biosynthesis, we sequenced the metagenome and transcriptome of an isonitrile sesquiterpenoid-containing sponge of the order Bubarida. Using bioinformatic searches and biochemical validation, we identified a group of type I terpene synthases (TSs) from this sponge and multiple other species, the first of this enzyme class characterized from the sponge holobiome. The Bubarida TS-associated contigs consist of intron-containing genes homologous to sponge genes and feature GC percentage and coverage consistent with other eukaryotic sequences. We identified and characterized TS homologs from five different sponge species isolated from geographically distant locations, thereby suggesting a broad distribution amongst sponges. This work sheds light on the role of sponges in secondary metabolite production and speaks to the possibility that other sponge-specific molecules originate from the animal host.
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Affiliation(s)
- Kayla Wilson
- Scripps Institution of Oceanography, University of California, San Diego, La Jolla, CA92093
| | - Tristan de Rond
- Scripps Institution of Oceanography, University of California, San Diego, La Jolla, CA92093
- School of Chemical Sciences, University of Auckland, Auckland1142, New Zealand
| | - Immo Burkhardt
- Scripps Institution of Oceanography, University of California, San Diego, La Jolla, CA92093
| | - Taylor S. Steele
- Scripps Institution of Oceanography, University of California, San Diego, La Jolla, CA92093
- Department of Chemistry & Biochemistry, University of California, San Diego, La Jolla, CA92093
| | - Rebecca J. B. Schäfer
- Scripps Institution of Oceanography, University of California, San Diego, La Jolla, CA92093
| | - Sheila Podell
- Scripps Institution of Oceanography, University of California, San Diego, La Jolla, CA92093
| | - Eric E. Allen
- Scripps Institution of Oceanography, University of California, San Diego, La Jolla, CA92093
| | - Bradley S. Moore
- Scripps Institution of Oceanography, University of California, San Diego, La Jolla, CA92093
- Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California, San Diego, La Jolla, CA92093
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58
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Wang X, Jarmusch SA, Frisvad JC, Larsen TO. Current status of secondary metabolite pathways linked to their related biosynthetic gene clusters in Aspergillus section Nigri. Nat Prod Rep 2023; 40:237-274. [PMID: 35587705 DOI: 10.1039/d1np00074h] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
Abstract
Covering: up to the end of 2021Aspergilli are biosynthetically 'talented' micro-organisms and therefore the natural products community has continually been interested in the wealth of biosynthetic gene clusters (BGCs) encoding numerous secondary metabolites related to these fungi. With the rapid increase in sequenced fungal genomes combined with the continuous development of bioinformatics tools such as antiSMASH, linking new structures to unknown BGCs has become much easier when taking retro-biosynthetic considerations into account. On the other hand, in most cases it is not as straightforward to prove proposed biosynthetic pathways due to the lack of implemented genetic tools in a given fungal species. As a result, very few secondary metabolite biosynthetic pathways have been characterized even amongst some of the most well studied Aspergillus spp., section Nigri (black aspergilli). This review will cover all known biosynthetic compound families and their structural diversity known from black aspergilli. We have logically divided this into sub-sections describing major biosynthetic classes (polyketides, non-ribosomal peptides, terpenoids, meroterpenoids and hybrid biosynthesis). Importantly, we will focus the review on metabolites which have been firmly linked to their corresponding BGCs.
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Affiliation(s)
- Xinhui Wang
- DTU Bioengineering, Technical University of Denmark, DK-2800, Kgs. Lyngby, Denmark.
| | - Scott A Jarmusch
- DTU Bioengineering, Technical University of Denmark, DK-2800, Kgs. Lyngby, Denmark.
| | - Jens C Frisvad
- DTU Bioengineering, Technical University of Denmark, DK-2800, Kgs. Lyngby, Denmark.
| | - Thomas O Larsen
- DTU Bioengineering, Technical University of Denmark, DK-2800, Kgs. Lyngby, Denmark.
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Li Y, Xu Z, Chen P, Zuo C, Chen L, Yan W, Jiao R, Ye Y. Genome Mining and Heterologous Expression Guided the Discovery of Antimicrobial Naphthocyclinones from Streptomyces eurocidicus CGMCC 4.1086. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2023; 71:2914-2923. [PMID: 36731876 DOI: 10.1021/acs.jafc.2c06928] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/18/2023]
Abstract
A type II polyketide synthase biosynthetic gene cluster (nap) was identified in Streptomyces eurocidicus CGMCC 4.1086 via genome mining. The heterologous expression of the cryptic nap gene cluster in Streptomyces albus J1074 generated dimerized aromatic polyketide naphthocyclinones (1-3), whose structures were determined via extensive analysis using nuclear magnetic resonance and high-resolution electrospray ionization mass spectroscopy. The biological pathway of naphthocyclinone synthesis was revealed via in vivo gene deletion, in vitro biochemical reactions, and comparative genomics. Remarkably, 3 played a crucial role in inhibiting Phytophthora capsici and Phytophthora sojae, with EC50 values of 6.1 and 20.2 μg/mL, respectively. Furthermore, 3 exhibited a potent protective effect against P. capsici and P. sojae in greenhouse tests.
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Affiliation(s)
- Yu Li
- College of Plant Protection, State & Local Joint Engineering Research Center of Green Pesticide Invention and Application, Nanjing Agricultural University, Nanjing 210095, P. R. China
- Key Laboratory of Integrated Management of Crop Diseases and Pests, Ministry of Education, Nanjing 210095, P. R. China
| | - Zifei Xu
- State Key Laboratory of Pharmaceutical Biotechnology, Institute of Functional Biomolecules, School of Life Sciences, Nanjing University, Nanjing 210023, China
| | - Ping Chen
- College of Plant Protection, State & Local Joint Engineering Research Center of Green Pesticide Invention and Application, Nanjing Agricultural University, Nanjing 210095, P. R. China
- Key Laboratory of Integrated Management of Crop Diseases and Pests, Ministry of Education, Nanjing 210095, P. R. China
| | - Chen Zuo
- College of Plant Protection, State & Local Joint Engineering Research Center of Green Pesticide Invention and Application, Nanjing Agricultural University, Nanjing 210095, P. R. China
- Key Laboratory of Integrated Management of Crop Diseases and Pests, Ministry of Education, Nanjing 210095, P. R. China
| | - Liyifan Chen
- College of Plant Protection, State & Local Joint Engineering Research Center of Green Pesticide Invention and Application, Nanjing Agricultural University, Nanjing 210095, P. R. China
- Key Laboratory of Integrated Management of Crop Diseases and Pests, Ministry of Education, Nanjing 210095, P. R. China
| | - Wei Yan
- College of Plant Protection, State & Local Joint Engineering Research Center of Green Pesticide Invention and Application, Nanjing Agricultural University, Nanjing 210095, P. R. China
- Key Laboratory of Integrated Management of Crop Diseases and Pests, Ministry of Education, Nanjing 210095, P. R. China
| | - Ruihua Jiao
- State Key Laboratory of Pharmaceutical Biotechnology, Institute of Functional Biomolecules, School of Life Sciences, Nanjing University, Nanjing 210023, China
| | - Yonghao Ye
- College of Plant Protection, State & Local Joint Engineering Research Center of Green Pesticide Invention and Application, Nanjing Agricultural University, Nanjing 210095, P. R. China
- Key Laboratory of Integrated Management of Crop Diseases and Pests, Ministry of Education, Nanjing 210095, P. R. China
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Dhakal D, Kokkaliari S, Rubin GM, Paul VJ, Ding Y, Luesch H. Biosynthesis of Lyngbyastatins 1 and 3, Cytotoxic Depsipeptides from an Okeania sp. Marine Cyanobacterium. JOURNAL OF NATURAL PRODUCTS 2023; 86:85-93. [PMID: 36546857 PMCID: PMC10197921 DOI: 10.1021/acs.jnatprod.2c00782] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/21/2023]
Abstract
Lyngbyastatins (Lbns) 1 (1) and 3 (2) belong to a group of cyclic depsipeptides that inhibit cancer cell proliferation. These compounds have been isolated from different marine cyanobacterial collections, while further development of these compounds relies on their lengthy total synthesis. Biosynthetic studies of these compounds can provide viable strategies to access these compounds and develop new analogs. In this study, we report the identification and characterization of one Lbn biosynthetic gene cluster (BGC) from the marine cyanobacterium Okeania sp. VPG18-21. We initially identified 1 and 2 in the organic extract by mass spectrometry and performed the targeted isolation of these compounds, which feature a (2S,3R)-3-amino-2-methylpentanoic acid (MAP) and a (2S,3R)-3-amino-2-methylhexanoic acid (Amha) moiety, respectively. Parallel metagenomic sequencing of VPG18-21 led to the identification of a putative Lbn BGC that encodes six megaenzymes (LbnA-F), including one polyketide synthase (PKS, LbnE), four nonribosomal peptide synthetases (NRPSs, LbnB-D and -F), and one PKS-NRPS hybrid (LbnA). Bioinformatic analysis of these enzymes suggested that the BGC produces 1 and 2. Furthermore, our biochemical studies of three recombinant adenylation domains uncovered their substrate specificities, supporting the identity of the BGC. Finally, we identified near-complete Lbn-like BGCs in the genomes of two other marine cyanobacteria.
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Affiliation(s)
- Dipesh Dhakal
- Department of Medicinal Chemistry and Center for Natural Products, Drug Discovery and Development (CNPD3), University of Florida, 1345 Center Drive, Gainesville, Florida 32610, United States
| | - Sofia Kokkaliari
- Department of Medicinal Chemistry and Center for Natural Products, Drug Discovery and Development (CNPD3), University of Florida, 1345 Center Drive, Gainesville, Florida 32610, United States
| | - Garret M. Rubin
- Department of Medicinal Chemistry and Center for Natural Products, Drug Discovery and Development (CNPD3), University of Florida, 1345 Center Drive, Gainesville, Florida 32610, United States
| | - Valerie J. Paul
- Smithsonian Marine Station at Ft. Pierce, 701 Seaway Drive, Ft. Pierce, Florida 34949, United States
| | - Yousong Ding
- Department of Medicinal Chemistry and Center for Natural Products, Drug Discovery and Development (CNPD3), University of Florida, 1345 Center Drive, Gainesville, Florida 32610, United States
| | - Hendrik Luesch
- Department of Medicinal Chemistry and Center for Natural Products, Drug Discovery and Development (CNPD3), University of Florida, 1345 Center Drive, Gainesville, Florida 32610, United States
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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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Zhao H, Yang Y, Wang S, Yang X, Zhou K, Xu C, Zhang X, Fan J, Hou D, Li X, Lin H, Tan Y, Wang S, Chu XY, Zhuoma D, Zhang F, Ju D, Zeng X, Chen YZ. NPASS database update 2023: quantitative natural product activity and species source database for biomedical research. Nucleic Acids Res 2023; 51:D621-D628. [PMID: 36624664 PMCID: PMC9825494 DOI: 10.1093/nar/gkac1069] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2022] [Revised: 10/16/2022] [Accepted: 10/26/2022] [Indexed: 11/30/2022] Open
Abstract
Quantitative activity and species source data of natural products (NPs) are important for drug discovery, medicinal plant research, and microbial investigations. Activity values of NPs against specific targets are useful for discovering targeted therapeutic agents and investigating the mechanism of medicinal plants. Composition/concentration values of NPs in individual species facilitate the assessments and investigations of the therapeutic quality of herbs and phenotypes of microbes. Here, we describe an update of the NPASS natural product activity and species source database previously featured in NAR. This update includes: (i) new data of ∼95 000 records of the composition/concentration values of ∼1 490 NPs/NP clusters in ∼390 species, (ii) extended data of activity values of ∼43 200 NPs against ∼7 700 targets (∼40% and ∼32% increase, respectively), (iii) extended data of ∼31 600 species sources of ∼94 400 NPs (∼26% and ∼32% increase, respectively), (iv) new species types of ∼440 co-cultured microbes and ∼420 engineered microbes, (v) new data of ∼66 600 NPs without experimental activity values but with estimated activity profiles from the established chemical similarity tool Chemical Checker, (vi) new data of the computed drug-likeness properties and the absorption, distribution, metabolism, excretion and toxicity (ADMET) properties for all NPs. NPASS update version is freely accessible at http://bidd.group/NPASS.
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Affiliation(s)
- Hui Zhao
- Department of Biological Medicines & Shanghai Engineering Research Center of Immunotherapeutics, Fudan University School of Pharmacy, Shanghai 201203, China
| | - Yuan Yang
- Department of Biological Medicines & Shanghai Engineering Research Center of Immunotherapeutics, Fudan University School of Pharmacy, Shanghai 201203, China
| | - Shuaiqi Wang
- Department of Biological Medicines & Shanghai Engineering Research Center of Immunotherapeutics, Fudan University School of Pharmacy, Shanghai 201203, China
| | - Xue Yang
- Department of Biological Medicines & Shanghai Engineering Research Center of Immunotherapeutics, Fudan University School of Pharmacy, Shanghai 201203, China
| | - Kaicheng Zhou
- Department of Biological Medicines & Shanghai Engineering Research Center of Immunotherapeutics, Fudan University School of Pharmacy, Shanghai 201203, China
| | - Caili Xu
- Department of Biological Medicines & Shanghai Engineering Research Center of Immunotherapeutics, Fudan University School of Pharmacy, Shanghai 201203, China
| | - Xuyao Zhang
- Department of Biological Medicines & Shanghai Engineering Research Center of Immunotherapeutics, Fudan University School of Pharmacy, Shanghai 201203, China
| | - Jiajun Fan
- Department of Biological Medicines & Shanghai Engineering Research Center of Immunotherapeutics, Fudan University School of Pharmacy, Shanghai 201203, China
| | - Dongyue Hou
- Department of Biological Medicines & Shanghai Engineering Research Center of Immunotherapeutics, Fudan University School of Pharmacy, Shanghai 201203, China
| | - Xingxiu Li
- Department of Biological Medicines & Shanghai Engineering Research Center of Immunotherapeutics, Fudan University School of Pharmacy, Shanghai 201203, China
| | - Hanbo Lin
- Department of Biological Medicines & Shanghai Engineering Research Center of Immunotherapeutics, Fudan University School of Pharmacy, Shanghai 201203, China
| | - Ying Tan
- The State Key Laboratory of Chemical Oncogenomics & Key Laboratory of Chemical Biology, Tsinghua University Shenzhen Graduate School, Shenzhen Kivita Innovative Drug Discovery Institute, China
| | - Shanshan Wang
- Qian Xuesen Collaborative Research Center of Astrochemistry and Space Life Sciences, Institute of Drug Discovery Technology, Ningbo University, Ningbo 315211, China
| | - Xin-Yi Chu
- Qian Xuesen Collaborative Research Center of Astrochemistry and Space Life Sciences, Institute of Drug Discovery Technology, Ningbo University, Ningbo 315211, China
| | | | - Fengying Zhang
- Key Lab of Agricultural Products Processing and Quality Control of Nanchang City, Jiangxi Agricultural University, Nanchang 330045, China
| | - Dianwen Ju
- Department of Biological Medicines & Shanghai Engineering Research Center of Immunotherapeutics, Fudan University School of Pharmacy, Shanghai 201203, China
| | - Xian Zeng
- Department of Biological Medicines & Shanghai Engineering Research Center of Immunotherapeutics, Fudan University School of Pharmacy, Shanghai 201203, China
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Matilla MA, Monson RE, Murphy A, Schicketanz M, Rawlinson A, Duncan C, Mata J, Leeper F, Salmond GPC. Solanimycin: Biosynthesis and Distribution of a New Antifungal Antibiotic Regulated by Two Quorum-Sensing Systems. mBio 2022; 13:e0247222. [PMID: 36214559 PMCID: PMC9765074 DOI: 10.1128/mbio.02472-22] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2022] [Accepted: 09/02/2022] [Indexed: 11/20/2022] Open
Abstract
The increasing emergence of drug-resistant fungal infections has necessitated a search for new compounds capable of combating fungal pathogens of plants, animals, and humans. Microorganisms represent the main source of antibiotics with applicability in agriculture and in the clinic, but many aspects of their metabolic potential remain to be explored. This report describes the discovery and characterization of a new antifungal compound, solanimycin, produced by a hybrid polyketide/nonribosomal peptide (PKS/NRPS) system in Dickeya solani, the enterobacterial pathogen of potato. Solanimycin was active against a broad range of plant-pathogenic fungi of global economic concern and the human pathogen Candida albicans. The genomic cluster responsible for solanimycin production was defined and analyzed to identify the corresponding biosynthetic proteins, which include four multimodular PKS/NRPS proteins and several tailoring enzymes. Antifungal production in D. solani was enhanced in response to experimental conditions found in infected potato tubers and high-density fungal cultures. Solanimycin biosynthesis was cell density dependent in D. solani and was controlled by both the ExpIR acyl-homoserine lactone and Vfm quorum-sensing systems of the bacterial phytopathogen. The expression of the solanimycin cluster was also regulated at the post-transcriptional level, with the regulator RsmA playing a major role. The solanimycin biosynthetic cluster was conserved across phylogenetically distant bacterial genera, and multiple pieces of evidence support that the corresponding gene clusters were acquired by horizontal gene transfer. Given its potent broad-range antifungal properties, this study suggests that solanimycin and related molecules may have potential utility for agricultural and clinical exploitation. IMPORTANCE Fungal infections represent a major clinical, agricultural, and food security threat worldwide, which is accentuated due to the difficult treatment of these infections. Microorganisms represent a prolific source of antibiotics, and current data support that this enormous biosynthetic potential has been scarcely explored. To improve the performance in the discovery of novel antimicrobials, there is a need to diversify the isolation niches for new antibiotic-producing microorganisms as well as to scrutinize novel phylogenetic positions. With the identification of the antifungal antibiotic solanimycin in a broad diversity of phytopathogenic Dickeya spp., we provide further support for the potential of plant-associated bacteria for the biosynthesis of novel antimicrobials. The complex regulatory networks involved in solanimycin production reflect the high metabolic cost of bacterial secondary metabolism. This metabolic regulatory control makes many antibiotics cryptic under standard laboratory conditions, and mimicking environmental conditions, as shown here, is a strategy to activate cryptic antibiotic clusters.
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Affiliation(s)
- Miguel A. Matilla
- Department of Biochemistry, University of Cambridge, Cambridge, United Kingdom
- Department of Environmental Protection, Estación Experimental del Zaidín, Consejo Superior de Investigaciones Científicas, Granada, Spain
| | - Rita E. Monson
- Department of Biochemistry, University of Cambridge, Cambridge, United Kingdom
| | - Annabel Murphy
- Yusuf Hamied Department of Chemistry, University of Cambridge, Cambridge, United Kingdom
| | - Muriel Schicketanz
- Department of Biochemistry, University of Cambridge, Cambridge, United Kingdom
| | - Alison Rawlinson
- Department of Biochemistry, University of Cambridge, Cambridge, United Kingdom
| | - Caia Duncan
- Department of Biochemistry, University of Cambridge, Cambridge, United Kingdom
| | - Juan Mata
- Department of Biochemistry, University of Cambridge, Cambridge, United Kingdom
| | - Finian Leeper
- Yusuf Hamied Department of Chemistry, University of Cambridge, Cambridge, United Kingdom
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Biermann F, Wenski SL, Helfrich EJN. Navigating and expanding the roadmap of natural product genome mining tools. Beilstein J Org Chem 2022; 18:1656-1671. [PMID: 36570563 PMCID: PMC9749553 DOI: 10.3762/bjoc.18.178] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2022] [Accepted: 11/02/2022] [Indexed: 12/12/2022] Open
Abstract
Natural products are structurally highly diverse and exhibit a wide array of biological activities. As a result, they serve as an important source of new drug leads. Traditionally, natural products have been discovered by bioactivity-guided fractionation. The advent of genome sequencing technology has resulted in the introduction of an alternative approach towards novel natural product scaffolds: Genome mining. Genome mining is an in-silico natural product discovery strategy in which sequenced genomes are analyzed for the potential of the associated organism to produce natural products. Seemingly universal biosynthetic principles have been deciphered for most natural product classes that are used to detect natural product biosynthetic gene clusters using pathway-encoded conserved key enzymes, domains, or motifs as bait. Several generations of highly sophisticated tools have been developed for the biosynthetic rule-based identification of natural product gene clusters. Apart from these hard-coded algorithms, multiple tools that use machine learning-based approaches have been designed to complement the existing genome mining tool set and focus on natural product gene clusters that lack genes with conserved signature sequences. In this perspective, we take a closer look at state-of-the-art genome mining tools that are based on either hard-coded rules or machine learning algorithms, with an emphasis on the confidence of their predictions and potential to identify non-canonical natural product biosynthetic gene clusters. We highlight the genome mining pipelines' current strengths and limitations by contrasting their advantages and disadvantages. Moreover, we introduce two indirect biosynthetic gene cluster identification strategies that complement current workflows. The combination of all genome mining approaches will pave the way towards a more comprehensive understanding of the full biosynthetic repertoire encoded in microbial genome sequences.
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Affiliation(s)
- Friederike Biermann
- Institute for Molecular Bio Science, Goethe University Frankfurt, Max-von-Laue Str. 9, 60438 Frankfurt am Main, Germany
- LOEWE Center for Translational Biodiversity Genomics (TBG), Senckenberganlage 25, 60325 Frankfurt am Main, Germany
| | - Sebastian L Wenski
- Institute for Molecular Bio Science, Goethe University Frankfurt, Max-von-Laue Str. 9, 60438 Frankfurt am Main, Germany
- LOEWE Center for Translational Biodiversity Genomics (TBG), Senckenberganlage 25, 60325 Frankfurt am Main, Germany
| | - Eric J N Helfrich
- Institute for Molecular Bio Science, Goethe University Frankfurt, Max-von-Laue Str. 9, 60438 Frankfurt am Main, Germany
- LOEWE Center for Translational Biodiversity Genomics (TBG), Senckenberganlage 25, 60325 Frankfurt am Main, Germany
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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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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] [MESH Headings] [Grants] [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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Quiros-Guerrero LM, Nothias LF, Gaudry A, Marcourt L, Allard PM, Rutz A, David B, Queiroz EF, Wolfender JL. Inventa: A computational tool to discover structural novelty in natural extracts libraries. Front Mol Biosci 2022; 9:1028334. [PMID: 36438653 PMCID: PMC9692083 DOI: 10.3389/fmolb.2022.1028334] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2022] [Accepted: 10/18/2022] [Indexed: 09/05/2023] Open
Abstract
Collections of natural extracts hold potential for the discovery of novel natural products with original modes of action. The prioritization of extracts from collections remains challenging due to the lack of a workflow that combines multiple-source information to facilitate the data interpretation. Results from different analytical techniques and literature reports need to be organized, processed, and interpreted to enable optimal decision-making for extracts prioritization. Here, we introduce Inventa, a computational tool that highlights the structural novelty potential within extracts, considering untargeted mass spectrometry data, spectral annotation, and literature reports. Based on this information, Inventa calculates multiple scores that inform their structural potential. Thus, Inventa has the potential to accelerate new natural products discovery. Inventa was applied to a set of plants from the Celastraceae family as a proof of concept. The Pristimera indica (Willd.) A.C.Sm roots extract was highlighted as a promising source of potentially novel compounds. Its phytochemical investigation resulted in the isolation and de novo characterization of thirteen new dihydro-β-agarofuran sesquiterpenes, five of them presenting a new 9-oxodihydro-β-agarofuran base scaffold.
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Affiliation(s)
- Luis-Manuel Quiros-Guerrero
- Institute of Pharmaceutical Sciences of Western Switzerland, University of Geneva, Geneva, Switzerland
- School of Pharmaceutical Sciences, University of Geneva, Geneva, Switzerland
| | - Louis-Félix Nothias
- Institute of Pharmaceutical Sciences of Western Switzerland, University of Geneva, Geneva, Switzerland
- School of Pharmaceutical Sciences, University of Geneva, Geneva, Switzerland
| | - Arnaud Gaudry
- Institute of Pharmaceutical Sciences of Western Switzerland, University of Geneva, Geneva, Switzerland
- School of Pharmaceutical Sciences, University of Geneva, Geneva, Switzerland
| | - Laurence Marcourt
- Institute of Pharmaceutical Sciences of Western Switzerland, University of Geneva, Geneva, Switzerland
- School of Pharmaceutical Sciences, University of Geneva, Geneva, Switzerland
| | - Pierre-Marie Allard
- Institute of Pharmaceutical Sciences of Western Switzerland, University of Geneva, Geneva, Switzerland
- School of Pharmaceutical Sciences, University of Geneva, Geneva, Switzerland
- Department of Biology, University of Fribourg, Fribourg, Switzerland
| | - Adriano Rutz
- Institute of Pharmaceutical Sciences of Western Switzerland, University of Geneva, Geneva, Switzerland
- School of Pharmaceutical Sciences, University of Geneva, Geneva, Switzerland
| | - Bruno David
- Green Mission Pierre Fabre, Institut de Recherche Pierre Fabre, Toulouse, France
| | - Emerson Ferreira Queiroz
- Institute of Pharmaceutical Sciences of Western Switzerland, University of Geneva, Geneva, Switzerland
- School of Pharmaceutical Sciences, University of Geneva, Geneva, Switzerland
| | - Jean-Luc Wolfender
- Institute of Pharmaceutical Sciences of Western Switzerland, University of Geneva, Geneva, Switzerland
- School of Pharmaceutical Sciences, University of Geneva, Geneva, Switzerland
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Roik A, Reverter M, Pogoreutz C. A roadmap to understanding diversity and function of coral reef-associated fungi. FEMS Microbiol Rev 2022; 46:fuac028. [PMID: 35746877 PMCID: PMC9629503 DOI: 10.1093/femsre/fuac028] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2022] [Revised: 06/01/2022] [Accepted: 06/14/2022] [Indexed: 01/09/2023] Open
Abstract
Tropical coral reefs are hotspots of marine productivity, owing to the association of reef-building corals with endosymbiotic algae and metabolically diverse bacterial communities. However, the functional importance of fungi, well-known for their contribution to shaping terrestrial ecosystems and global nutrient cycles, remains underexplored on coral reefs. We here conceptualize how fungal functional traits may have facilitated the spread, diversification, and ecological adaptation of marine fungi on coral reefs. We propose that functions of reef-associated fungi may be diverse and go beyond their hitherto described roles of pathogens and bioeroders, including but not limited to reef-scale biogeochemical cycles and the structuring of coral-associated and environmental microbiomes via chemical mediation. Recent technological and conceptual advances will allow the elucidation of the physiological, ecological, and chemical contributions of understudied marine fungi to coral holobiont and reef ecosystem functioning and health and may help provide an outlook for reef management actions.
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Affiliation(s)
- Anna Roik
- Helmholtz Institute for Functional Marine Biodiversity, University of Oldenburg, Ammerländer Heerstraße 231, 26129 Oldenburg, Germany
- Institute for Chemistry and Biology of the Marine Environment, Carl von Ossietzky University of Oldenburg, Wilhelmshaven, 26046, Germany
- Alfred Wegener Institute, Helmholtz Centre for Polar and Marine Research (AWI), Am Handelshafen 12, 27570 Bremerhaven, Germany
| | - Miriam Reverter
- Institute for Chemistry and Biology of the Marine Environment, Carl von Ossietzky University of Oldenburg, Wilhelmshaven, 26046, Germany
- School of Biological and Marine Sciences, University of Plymouth, Plymouth PL4 8AA, United Kingdom
| | - Claudia Pogoreutz
- Laboratory for Biological Geochemistry, School of Architecture, Civil and Environmental Engineering, École Polytechnique Fédérale de Lausanne (EPFL), 1015 Lausanne, Switzerland
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Hwang GJ, Jang M, Son S, Kim GS, Lee B, Heo KT, Kim GJ, Choi H, Hur JS, Jang JP, Ko SK, Hong YS, Ahn JS, Jang JH. Ulleungdolin, a Polyketide-Peptide Hybrid Bearing a 2,4-Di- O-methyl-β-d-antiarose from Streptomyces sp. 13F051 Co-cultured with Leohumicola minima 15S071. JOURNAL OF NATURAL PRODUCTS 2022; 85:2445-2453. [PMID: 36197044 DOI: 10.1021/acs.jnatprod.2c00682] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/16/2023]
Abstract
A new secondary metabolite, ulleungdolin (1), was isolated from the co-culture of an actinomycete, Streptomyces sp. 13F051, and a fungus, Leohumicola minima 15S071. Based on the NMR, UV, and MS data, it was deduced that the planar structure of 1 comprised an isoindolinone (IsoID) with an octanoic acid, a tripeptide, and a sugar. The tripeptide has the unprecedented amino acids norcoronamic acid, 3-hydroxy-glutamine, and 4-hydroxy-phenylglycine and is linked by a C-N bond with IsoID. The absolute configurations were determined by chemical derivatization, extensive spectroscopic methods, and electronic circular dichroism calculations and supported by bioinformatic analyses. Bioactivity evaluation studies indicated that 1 had an antimigration effect on MDA-MB-231 breast cancer cells.
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Affiliation(s)
- Gwi Ja Hwang
- Chemical Biology Research Center, Korea Research Institute of Bioscience and Biotechnology, Cheongju 28116, South Korea
- Department of Biomolecular Science, KRIBB School of Bioscience, University of Science and Technology, Daejeon 34141, South Korea
| | - Mina Jang
- Chemical Biology Research Center, Korea Research Institute of Bioscience and Biotechnology, Cheongju 28116, South Korea
- New Drug Development Center, Daegu-Gyeongbuk Medical Innovation Foundation, Daegu 41061, South Korea
| | - Sangkeun Son
- Chemical Biology Research Center, Korea Research Institute of Bioscience and Biotechnology, Cheongju 28116, South Korea
- Antimicrobial Discovery Center, Department of Biology, Northeastern University, Boston, Massachusetts 02115, United States
| | - Gil Soo Kim
- Chemical Biology Research Center, Korea Research Institute of Bioscience and Biotechnology, Cheongju 28116, South Korea
- Department of Biomolecular Science, KRIBB School of Bioscience, University of Science and Technology, Daejeon 34141, South Korea
| | - Byeongsan Lee
- Chemical Biology Research Center, Korea Research Institute of Bioscience and Biotechnology, Cheongju 28116, South Korea
| | - Kyung Taek Heo
- Chemical Biology Research Center, Korea Research Institute of Bioscience and Biotechnology, Cheongju 28116, South Korea
- Department of Biomolecular Science, KRIBB School of Bioscience, University of Science and Technology, Daejeon 34141, South Korea
| | - Geum Jin Kim
- College of Pharmacy and Institute of Cell Culture, Yeungnam University, Gyeongsan 38541, South Korea
| | - Hyukjae Choi
- College of Pharmacy and Institute of Cell Culture, Yeungnam University, Gyeongsan 38541, South Korea
| | - Jae-Seoun Hur
- Korean Lichen Research Institute, Sunchon National University, Suncheon 57922, South Korea
| | - Jun-Pil Jang
- Chemical Biology Research Center, Korea Research Institute of Bioscience and Biotechnology, Cheongju 28116, South Korea
| | - Sung-Kyun Ko
- Chemical Biology Research Center, Korea Research Institute of Bioscience and Biotechnology, Cheongju 28116, South Korea
- Department of Biomolecular Science, KRIBB School of Bioscience, University of Science and Technology, Daejeon 34141, South Korea
| | - Young-Soo Hong
- Chemical Biology Research Center, Korea Research Institute of Bioscience and Biotechnology, Cheongju 28116, South Korea
- Department of Biomolecular Science, KRIBB School of Bioscience, University of Science and Technology, Daejeon 34141, South Korea
| | - Jong Seog Ahn
- Chemical Biology Research Center, Korea Research Institute of Bioscience and Biotechnology, Cheongju 28116, South Korea
- Department of Biomolecular Science, KRIBB School of Bioscience, University of Science and Technology, Daejeon 34141, South Korea
| | - Jae-Hyuk Jang
- Chemical Biology Research Center, Korea Research Institute of Bioscience and Biotechnology, Cheongju 28116, South Korea
- Department of Biomolecular Science, KRIBB School of Bioscience, University of Science and Technology, Daejeon 34141, South Korea
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Yadav K, Dwivedi S, Gupta S, Dubey AK, Singh VK, Tanveer A, Yadav S, Yadav D. Genome mining of Fusarium reveals structural and functional diversity of pectin lyases: a bioinformatics approach. 3 Biotech 2022; 12:261. [PMID: 36082361 PMCID: PMC9445148 DOI: 10.1007/s13205-022-03333-w] [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: 03/09/2022] [Accepted: 08/25/2022] [Indexed: 11/26/2022] Open
Abstract
Pectin lyase (PNL) is an important enzyme of the pectinases group which degrades pectin polymer to 4,5-unsaturated oligogalacturonides by a unique β-elimination mechanism and is used in several industries. The existence of multigene families of pectin lyases has been investigated by mining microbial genomes. In the present study, 52 pectin lyase genes were predicted from sequenced six species of Fusarium, namely F. fujikuroi, F. graminearum, F. proliferatum, F. oxysporum, F. verticillioides and F. virguliforme. These sequences were in silico characterized for several physico-chemical, structural and functional attributes. The translated PNL proteins showed variability with 344-1142 amino acid residues, 35.44-127.41 kDa molecular weight, and pI ranging from 4.63 to 9.28. The aliphatic index ranged from 75.33 to 84.75. Multiple sequence alignment analysis showed several conserved amino acid residues and five distinct groups marked as I, II, III, IV, and V were observed in the phylogenetic tree. The Three-dimensional Structure of five of these PNLs, each representing a distinct group of phylogenetic trees was predicted using I-TASSER Server and validated. The pectin lyase proteins of Fusarium species revealed close similarity with pectin lyase of Aspergillus niger PelA(1IDJ) and PelB(1QCX). Diversity in the structural motifs was observed among Fusarium species with 2 β-sheets, 1 β-hairpin, 7-12 β bulges, 18-25 strands, 6 -11 helices, 1 helix-helix interaction, 32-49 β turns, 2-6 γ turns and 2- 3 disulfide bonds. The unique Pec_lyase domain was uniformly observed among all PNL proteins confirming its identity. The genome-wide mining of Fusarium species was attempted to provide the diversity of PNL genes, which could be explored for diverse applications after performing cloning and expression studies. Supplementary Information The online version contains supplementary material available at 10.1007/s13205-022-03333-w.
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Affiliation(s)
- Kanchan Yadav
- Department of Biotechnology, Deen Dayal Upadhyaya Gorakhpur University, Gorakhpur, Uttar Pradesh 273009 India
| | - Shruti Dwivedi
- Department of Biotechnology, Deen Dayal Upadhyaya Gorakhpur University, Gorakhpur, Uttar Pradesh 273009 India
| | - Supriya Gupta
- Department of Biotechnology, Deen Dayal Upadhyaya Gorakhpur University, Gorakhpur, Uttar Pradesh 273009 India
| | - Amit K. Dubey
- Department of Biotechnology, Deen Dayal Upadhyaya Gorakhpur University, Gorakhpur, Uttar Pradesh 273009 India
| | - Vinay K. Singh
- Centre for Bioinformatics, School of Biotechnology, Banaras Hindu University, Varanasi, Uttar Pradesh 221005 India
| | - Aiman Tanveer
- Department of Biotechnology, Deen Dayal Upadhyaya Gorakhpur University, Gorakhpur, Uttar Pradesh 273009 India
| | - Sangeeta Yadav
- Department of Biotechnology, Deen Dayal Upadhyaya Gorakhpur University, Gorakhpur, Uttar Pradesh 273009 India
| | - Dinesh Yadav
- Department of Biotechnology, Deen Dayal Upadhyaya Gorakhpur University, Gorakhpur, Uttar Pradesh 273009 India
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71
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Sukmarini L. Marine Bacterial Ribosomal Peptides: Recent Genomics- and Synthetic Biology-Based Discoveries and Biosynthetic Studies. Mar Drugs 2022; 20:md20090544. [PMID: 36135733 PMCID: PMC9505594 DOI: 10.3390/md20090544] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2022] [Revised: 08/18/2022] [Accepted: 08/21/2022] [Indexed: 11/27/2022] Open
Abstract
Marine biodiversity is represented by an exceptional and ample array of intriguing natural product chemistries. Due to their extensive post-translational modifications, ribosomal peptides—also known as ribosomally synthesized and post-translationally modified peptides (RiPPs)—exemplify a widely diverse class of natural products, endowing a broad range of pharmaceutically and biotechnologically relevant properties for therapeutic or industrial applications. Most RiPPs are of bacterial origin, yet their marine derivatives have been quite rarely investigated. Given the rapid advancement engaged in a more powerful genomics approach, more biosynthetic gene clusters and pathways for these ribosomal peptides continue to be increasingly characterized. Moreover, the genome-mining approach in integration with synthetic biology techniques has markedly led to a revolution of RiPP natural product discovery. Therefore, this present short review article focuses on the recent discovery of RiPPs from marine bacteria based on genome mining and synthetic biology approaches during the past decade. Their biosynthetic studies are discussed herein, particularly the organization of targeted biosynthetic gene clusters linked to the encoded RiPPs with potential bioactivities.
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Affiliation(s)
- Linda Sukmarini
- Research Center for Applied Microbiology, National Research and Innovation Agency (BRIN), Jl. Raya Bogor, Km. 46, Cibinong 16911, West Java, Indonesia
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72
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Reher R, Aron AT, Fajtová P, Stincone P, Wagner B, Pérez-Lorente AI, Liu C, Shalom IYB, Bittremieux W, Wang M, Jeong K, Matos-Hernandez ML, Alexander KL, Caro-Diaz EJ, Naman CB, Scanlan JHW, Hochban PMM, Diederich WE, Molina-Santiago C, Romero D, Selim KA, Sass P, Brötz-Oesterhelt H, Hughes CC, Dorrestein PC, O'Donoghue AJ, Gerwick WH, Petras D. Native metabolomics identifies the rivulariapeptolide family of protease inhibitors. Nat Commun 2022; 13:4619. [PMID: 35941113 PMCID: PMC9358669 DOI: 10.1038/s41467-022-32016-6] [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: 01/15/2022] [Accepted: 07/12/2022] [Indexed: 11/15/2022] Open
Abstract
The identity and biological activity of most metabolites still remain unknown. A bottleneck in the exploration of metabolite structures and pharmaceutical activities is the compound purification needed for bioactivity assignments and downstream structure elucidation. To enable bioactivity-focused compound identification from complex mixtures, we develop a scalable native metabolomics approach that integrates non-targeted liquid chromatography tandem mass spectrometry and detection of protein binding via native mass spectrometry. A native metabolomics screen for protease inhibitors from an environmental cyanobacteria community reveals 30 chymotrypsin-binding cyclodepsipeptides. Guided by the native metabolomics results, we select and purify five of these compounds for full structure elucidation via tandem mass spectrometry, chemical derivatization, and nuclear magnetic resonance spectroscopy as well as evaluation of their biological activities. These results identify rivulariapeptolides as a family of serine protease inhibitors with nanomolar potency, highlighting native metabolomics as a promising approach for drug discovery, chemical ecology, and chemical biology studies. Bioactivity-guided isolation of specialized metabolites is an iterative process. Here, the authors demonstrate a native metabolomics approach that allows for fast screening of complex metabolite extracts against a protein of interest and simultaneous structure annotation.
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Affiliation(s)
- Raphael Reher
- Scripps Institution of Oceanography, University of California San Diego, La Jolla, CA, USA.,Institute of Pharmacy, Martin-Luther-University Halle-Wittenberg, Halle, Germany.,Institute of Pharmaceutical Biology and Biotechnology, University of Marburg, Marburg, Germany
| | - Allegra T Aron
- Skaggs School of Pharmacy and Pharmaceutical Science, University of California San Diego, La Jolla, CA, USA
| | - Pavla Fajtová
- Skaggs School of Pharmacy and Pharmaceutical Science, University of California San Diego, La Jolla, CA, USA
| | - Paolo Stincone
- Cluster of Excellence "Controlling Microbes to Fight Infections" (CMFI), University of Tuebingen, Tuebingen, Germany
| | - Berenike Wagner
- Cluster of Excellence "Controlling Microbes to Fight Infections" (CMFI), University of Tuebingen, Tuebingen, Germany.,Interfaculty Institute of Microbiology and Infection Medicine, University of Tuebingen, Tuebingen, Germany
| | - Alicia I Pérez-Lorente
- Instituto de Hortofruticultura Subtropical y Mediterránea "La Mayora," Consejo Superior de Investigaciones Científicas, Departamento de Microbiología, Universidad de Málaga, Málaga, Spain
| | - Chenxi Liu
- Skaggs School of Pharmacy and Pharmaceutical Science, University of California San Diego, La Jolla, CA, USA
| | - Ido Y Ben Shalom
- Skaggs School of Pharmacy and Pharmaceutical Science, University of California San Diego, La Jolla, CA, USA
| | - Wout Bittremieux
- Skaggs School of Pharmacy and Pharmaceutical Science, University of California San Diego, La Jolla, CA, USA
| | - Mingxun Wang
- Skaggs School of Pharmacy and Pharmaceutical Science, University of California San Diego, La Jolla, CA, USA
| | - Kyowon Jeong
- Applied Bioinformatics, Computer Science Department, University of Tuebingen, Tuebingen, Germany
| | - Marie L Matos-Hernandez
- Department of Pharmaceutical Sciences, School of Pharmacy, University of Puerto Rico - Medical Sciences Campus, San Juan, Puerto Rico
| | - Kelsey L Alexander
- Scripps Institution of Oceanography, University of California San Diego, La Jolla, CA, USA.,Department of Chemistry and Biochemistry, University of California San Diego, La Jolla, CA, USA
| | - Eduardo J Caro-Diaz
- Department of Pharmaceutical Sciences, School of Pharmacy, University of Puerto Rico - Medical Sciences Campus, San Juan, Puerto Rico
| | - C Benjamin Naman
- Li Dak Sum Yip Yio Chin Kenneth Li Marine Biopharmaceutical Research Center, Department of Marine Pharmacy, College of Food and Pharmaceutical Sciences, Ningbo University, Ningbo, China
| | - J H William Scanlan
- Department of Pharmaceutical Chemistry and Center for Tumor Biology and Immunology (ZTI), University of Marburg, Marburg, Germany
| | - Phil M M Hochban
- Department of Pharmaceutical Chemistry and Center for Tumor Biology and Immunology (ZTI), University of Marburg, Marburg, Germany
| | - Wibke E Diederich
- Department of Pharmaceutical Chemistry and Center for Tumor Biology and Immunology (ZTI), University of Marburg, Marburg, Germany
| | - Carlos Molina-Santiago
- Instituto de Hortofruticultura Subtropical y Mediterránea "La Mayora," Consejo Superior de Investigaciones Científicas, Departamento de Microbiología, Universidad de Málaga, Málaga, Spain
| | - Diego Romero
- Instituto de Hortofruticultura Subtropical y Mediterránea "La Mayora," Consejo Superior de Investigaciones Científicas, Departamento de Microbiología, Universidad de Málaga, Málaga, Spain
| | - Khaled A Selim
- Cluster of Excellence "Controlling Microbes to Fight Infections" (CMFI), University of Tuebingen, Tuebingen, Germany.,Interfaculty Institute of Microbiology and Infection Medicine, University of Tuebingen, Tuebingen, Germany
| | - Peter Sass
- Cluster of Excellence "Controlling Microbes to Fight Infections" (CMFI), University of Tuebingen, Tuebingen, Germany.,Interfaculty Institute of Microbiology and Infection Medicine, University of Tuebingen, Tuebingen, Germany
| | - Heike Brötz-Oesterhelt
- Cluster of Excellence "Controlling Microbes to Fight Infections" (CMFI), University of Tuebingen, Tuebingen, Germany.,Interfaculty Institute of Microbiology and Infection Medicine, University of Tuebingen, Tuebingen, Germany.,German Center for Infection Research, Partner Site Tuebingen, Tuebingen, Germany
| | - Chambers C Hughes
- Cluster of Excellence "Controlling Microbes to Fight Infections" (CMFI), University of Tuebingen, Tuebingen, Germany.,Interfaculty Institute of Microbiology and Infection Medicine, University of Tuebingen, Tuebingen, Germany.,German Center for Infection Research, Partner Site Tuebingen, Tuebingen, Germany
| | - Pieter C Dorrestein
- Skaggs School of Pharmacy and Pharmaceutical Science, University of California San Diego, La Jolla, CA, USA
| | - Anthony J O'Donoghue
- Skaggs School of Pharmacy and Pharmaceutical Science, University of California San Diego, La Jolla, CA, USA
| | - William H Gerwick
- Scripps Institution of Oceanography, University of California San Diego, La Jolla, CA, USA. .,Skaggs School of Pharmacy and Pharmaceutical Science, University of California San Diego, La Jolla, CA, USA.
| | - Daniel Petras
- Scripps Institution of Oceanography, University of California San Diego, La Jolla, CA, USA. .,Skaggs School of Pharmacy and Pharmaceutical Science, University of California San Diego, La Jolla, CA, USA. .,Cluster of Excellence "Controlling Microbes to Fight Infections" (CMFI), University of Tuebingen, Tuebingen, Germany. .,Interfaculty Institute of Microbiology and Infection Medicine, University of Tuebingen, Tuebingen, Germany.
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73
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Koch L. Charting the world's microbiomes. Nat Rev Genet 2022; 23:523. [PMID: 35821096 DOI: 10.1038/s41576-022-00520-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
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74
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Single cell mutant selection for metabolic engineering of actinomycetes. Metab Eng 2022; 73:124-133. [PMID: 35809806 DOI: 10.1016/j.ymben.2022.07.002] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2022] [Revised: 05/31/2022] [Accepted: 07/01/2022] [Indexed: 11/23/2022]
Abstract
Actinomycetes are important producers of pharmaceuticals and industrial enzymes. However, wild type strains require laborious development prior to industrial usage. Here we present a generally applicable reporter-guided metabolic engineering tool based on random mutagenesis, selective pressure, and single-cell sorting. We developed fluorescence-activated cell sorting (FACS) methodology capable of reproducibly identifying high-performing individual cells from a mutant population directly from liquid cultures. Actinomycetes are an important source of catabolic enzymes, where product yields determine industrial viability. We demonstrate 5-fold yield improvement with an industrial cholesterol oxidase ChoD producer Streptomyces lavendulae to 20.4 U g-1 in three rounds. Strain development is traditionally followed by production medium optimization, which is a time-consuming multi-parameter problem that may require hard to source ingredients. Ultra-high throughput screening allowed us to circumvent medium optimization and we identified high ChoD yield production strains directly from mutant libraries grown under preset culture conditions. Genome-mining based drug discovery is a promising source of bioactive compounds, which is complicated by the observation that target metabolic pathways may be silent under laboratory conditions. We demonstrate our technology for drug discovery by activating a silent mutaxanthene metabolic pathway in Amycolatopsis. We apply the method for industrial strain development and increase mutaxanthene yields 9-fold to 99 mg l-1 in a second round of mutant selection. In summary, the ability to screen tens of millions of mutants in a single cell format offers broad applicability for metabolic engineering of actinomycetes for activation of silent metabolic pathways and to increase yields of proteins and natural products.
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75
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A wealth of new biosynthetic pathways from the global ocean microbiome. Nature 2022:10.1038/d41586-022-01545-x. [PMID: 35732716 DOI: 10.1038/d41586-022-01545-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
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76
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Abstract
Natural microbial communities are phylogenetically and metabolically diverse. In addition to underexplored organismal groups1, this diversity encompasses a rich discovery potential for ecologically and biotechnologically relevant enzymes and biochemical compounds2,3. However, studying this diversity to identify genomic pathways for the synthesis of such compounds4 and assigning them to their respective hosts remains challenging. The biosynthetic potential of microorganisms in the open ocean remains largely uncharted owing to limitations in the analysis of genome-resolved data at the global scale. Here we investigated the diversity and novelty of biosynthetic gene clusters in the ocean by integrating around 10,000 microbial genomes from cultivated and single cells with more than 25,000 newly reconstructed draft genomes from more than 1,000 seawater samples. These efforts revealed approximately 40,000 putative mostly new biosynthetic gene clusters, several of which were found in previously unsuspected phylogenetic groups. Among these groups, we identified a lineage rich in biosynthetic gene clusters (‘Candidatus Eudoremicrobiaceae’) that belongs to an uncultivated bacterial phylum and includes some of the most biosynthetically diverse microorganisms in this environment. From these, we characterized the phospeptin and pythonamide pathways, revealing cases of unusual bioactive compound structure and enzymology, respectively. Together, this research demonstrates how microbiomics-driven strategies can enable the investigation of previously undescribed enzymes and natural products in underexplored microbial groups and environments. Global ocean microbiome survey reveals the bacterial family ‘Candidatus Eudoremicrobiaceae’, which includes some of the most biosynthetically diverse microorganisms in the ocean environment.
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77
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Brassart PL, Thomas OP, Courdavault V, Papon N. Towards a Better Understanding of Toxin Biosynthesis in Seaweeds. Chembiochem 2022; 23:e202200223. [PMID: 35666802 DOI: 10.1002/cbic.202200223] [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: 04/19/2022] [Revised: 06/02/2022] [Indexed: 11/06/2022]
Abstract
Harmful algal blooms (HABs) represent both ecological and public health hazards in the marine environment. Indeed, some algae can produce metabolites that have negative effects on marine ecosystems and mammals. Kainoid derivatives such as kainic acid (KA) and domoic acid (DA) are considered some of the most toxic metabolites of marine origin biosynthesized by a limited number of micro- and macroalgae. While recent works have provided the first insights into the biosynthetic route of KA in red algae and DA in diatoms, the DA biosynthetic pathway has remained uncharacterized for red algae. In a recent work, the research groups of Chekan and Moore have not only elucidated the biosynthetic pathway of DA in the red alga Chondria armata but also shed light on its complex evolution among marine species. We discuss here the importance of pursuing active research in this area to gain insights into secondary biosynthetic pathways in marine organisms for diagnostic and metabolic engineering perspectives.
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Affiliation(s)
| | - Olivier P Thomas
- School of the Biological and Chemical Sciences, Ryan Institute, National University of Ireland Galway, H91TK33, Galway, Republic of Ireland
| | - Vincent Courdavault
- Biomolécules et Biotechnologies Végétales, BBV, EA2106, Université de Tours, Tours, France
| | - Nicolas Papon
- Univ Angers, Univ Brest, IRF, SFR ICAT, 49000, Angers, France
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78
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Iorio M, Gentile A, Brunati C, Tocchetti A, Landini P, Maffioli SI, Donadio S, Sosio M. Allopeptimicins: unique antibacterial metabolites generated by hybrid PKS-NRPS, with original self-defense mechanism in Actinoallomurus. RSC Adv 2022; 12:16640-16655. [PMID: 35754877 PMCID: PMC9169493 DOI: 10.1039/d2ra02094g] [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: 03/31/2022] [Accepted: 05/25/2022] [Indexed: 11/21/2022] Open
Abstract
In the search for structurally novel metabolites with antibacterial activity, innovative approaches must be implemented to increase the probability of discovering novel chemistry from microbial sources. Here we report on the application of metabolomic tools to the genus Actinoallomurus, a poorly explored member of the Actinobacteria. From examining extracts derived from 88 isolates belonging to this genus, we identified a family of cyclodepsipeptides acylated with a C20 polyketide chain, which we named allopeptimicins. These molecules possess unusual structural features, including several double bonds in the amino-polyketide chain and four non-proteinogenic amino acids in the octapeptide. Remarkably, allopeptimicins are produced as a complex of active and inactive congeners, the latter carrying a sulfate group on the polyketide amine. This modification is also a mechanism of self-protection in the producer strain. The structural uniqueness of allopeptimicins is reflected in a biosynthetic gene cluster showing a mosaic structure, with dedicated gene cassettes devoted to formation of specialized precursors and modular assembly lines related to those from different pathways.
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79
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A Putative Effector LtCSEP1 from Lasiodiplodia theobromae Inhibits BAX-Triggered Cell Death and Suppresses Immunity Responses in Nicotiana benthamiana. PLANTS 2022; 11:plants11111462. [PMID: 35684232 PMCID: PMC9182993 DOI: 10.3390/plants11111462] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/27/2022] [Revised: 05/24/2022] [Accepted: 05/25/2022] [Indexed: 11/17/2022]
Abstract
Lasiodiplodia theobromae is a causal agent of grapevine trunk disease, and it poses a significant threat to the grape industry worldwide. Fungal effectors play an essential role in the interaction between plants and pathogens. However, few studies have been conducted to understand the functions of individual effectors in L. theobromae. In this study, we identified and characterized a candidate secreted effector protein, LtCSEP1, in L. theobromae. Gene expression analysis suggested that transcription of LtCSEP1 in L. theobromae was induced at the early infection stages in the grapevine. Yeast secretion assay revealed that LtCSEP1 contains a functional signal peptide. Transient expression of LtCSEP1 in Nicotiana benthamiana suppresses BAX-trigged cell death and significantly inhibits the flg22-induced PTI-associated gene expression. Furthermore, the ectopic expression of LtCSEP1 in N. benthamiana enhanced disease susceptibility to L. theobromae by downregulating the defense-related genes. These results demonstrated that LtCSEP1 is a potential effector of L. theobromae, which contributes to suppressing the plant’s defenses.
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80
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Ancient plant-like terpene biosynthesis in corals. Nat Chem Biol 2022; 18:664-669. [PMID: 35606558 PMCID: PMC9179088 DOI: 10.1038/s41589-022-01026-2] [Citation(s) in RCA: 32] [Impact Index Per Article: 16.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2021] [Accepted: 03/30/2022] [Indexed: 01/16/2023]
Abstract
Octocorals are major contributors of terpenoid chemical diversity in the ocean. Natural products from other sessile marine animals are primarily biosynthesized by symbiotic microbes rather than by the host. Here, we challenge this long-standing paradigm by describing a monophyletic lineage of animal-encoded terpene cyclases (TCs) ubiquitous in octocorals. We characterized 15 TC enzymes from nine genera, several of which produce precursors of iconic coral-specific terpenoids, such as pseudopterosin, lophotoxin and eleutherobin. X-ray crystallography revealed that coral TCs share conserved active site residues and structural features with bacterial TCs. The identification of coral TCs enabled the targeted identification of the enzyme that constructs the coral-exclusive capnellane scaffold. Several TC genes are colocalized with genes that encode enzymes known to modify terpenes. This work presents an example of biosynthetic capacity in the kingdom Animalia that rivals the chemical complexity generated by plants, unlocking the biotechnological potential of octocorals for biomedical applications.
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81
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Mungan MD, Harbig TA, Perez NH, Edenhart S, Stegmann E, Nieselt K, Ziemert N. Secondary Metabolite Transcriptomic Pipeline (SeMa-Trap), an expression-based exploration tool for increased secondary metabolite production in bacteria. Nucleic Acids Res 2022; 50:W682-W689. [PMID: 35580059 PMCID: PMC9252823 DOI: 10.1093/nar/gkac371] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2022] [Revised: 04/20/2022] [Accepted: 04/29/2022] [Indexed: 11/14/2022] Open
Abstract
For decades, natural products have been used as a primary resource in drug discovery pipelines to find new antibiotics, which are mainly produced as secondary metabolites by bacteria. The biosynthesis of these compounds is encoded in co-localized genes termed biosynthetic gene clusters (BGCs). However, BGCs are often not expressed under laboratory conditions. Several genetic manipulation strategies have been developed in order to activate or overexpress silent BGCs. Significant increases in production levels of secondary metabolites were indeed achieved by modifying the expression of genes encoding regulators and transporters, as well as genes involved in resistance or precursor biosynthesis. However, the abundance of genes encoding such functions within bacterial genomes requires prioritization of the most promising ones for genetic manipulation strategies. Here, we introduce the ‘Secondary Metabolite Transcriptomic Pipeline’ (SeMa-Trap), a user-friendly web-server, available at https://sema-trap.ziemertlab.com. SeMa-Trap facilitates RNA-Seq based transcriptome analyses, finds co-expression patterns between certain genes and BGCs of interest, and helps optimize the design of comparative transcriptomic analyses. Finally, SeMa-Trap provides interactive result pages for each BGC, allowing the easy exploration and comparison of expression patterns. In summary, SeMa-Trap allows a straightforward prioritization of genes that could be targeted via genetic engineering approaches to (over)express BGCs of interest.
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Affiliation(s)
- Mehmet Direnç Mungan
- Interfaculty Institute of Microbiology and Infection Medicine Tübingen (IMIT), University of Tübingen, Auf der Morgenstelle 28, 72076 Tübingen, Germany.,Interfaculty Institute for Bioinformatics and Medical Informatics (IBMI), University of Tübingen, 72076 Tübingen, Germany.,German Center for Infection Research (DZIF), Partnersite Tübingen, 72076 Tübingen, Germany
| | - Theresa Anisja Harbig
- Interfaculty Institute for Bioinformatics and Medical Informatics (IBMI), University of Tübingen, 72076 Tübingen, Germany
| | - Naybel Hernandez Perez
- Interfaculty Institute of Microbiology and Infection Medicine Tübingen (IMIT), University of Tübingen, Auf der Morgenstelle 28, 72076 Tübingen, Germany
| | - Simone Edenhart
- Interfaculty Institute of Microbiology and Infection Medicine Tübingen (IMIT), University of Tübingen, Auf der Morgenstelle 28, 72076 Tübingen, Germany
| | - Evi Stegmann
- Interfaculty Institute of Microbiology and Infection Medicine Tübingen (IMIT), University of Tübingen, Auf der Morgenstelle 28, 72076 Tübingen, Germany.,German Center for Infection Research (DZIF), Partnersite Tübingen, 72076 Tübingen, Germany
| | - Kay Nieselt
- Interfaculty Institute for Bioinformatics and Medical Informatics (IBMI), University of Tübingen, 72076 Tübingen, Germany
| | - Nadine Ziemert
- Interfaculty Institute of Microbiology and Infection Medicine Tübingen (IMIT), University of Tübingen, Auf der Morgenstelle 28, 72076 Tübingen, Germany.,Interfaculty Institute for Bioinformatics and Medical Informatics (IBMI), University of Tübingen, 72076 Tübingen, Germany.,German Center for Infection Research (DZIF), Partnersite Tübingen, 72076 Tübingen, Germany
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82
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Liu J, Harken L, Yang Y, Xie X, Li SM. Widely Distributed Bifunctional Bacterial Cytochrome P450 Enzymes Catalyze both Intramolecular C-C Bond Formation in cyclo-l-Tyr-l-Tyr and Its Coupling with Nucleobases. Angew Chem Int Ed Engl 2022; 61:e202200377. [PMID: 35201649 PMCID: PMC9401060 DOI: 10.1002/anie.202200377] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2022] [Indexed: 12/30/2022]
Abstract
Tailoring enzymes are important modification biocatalysts in natural product biosynthesis. We report herein six orthologous two‐gene clusters for mycocyclosin and guatyromycine biosynthesis. Expression of the cyclodipeptide synthase genes gymA1–gymA6 in Escherichia coli resulted in the formation of cyclo‐l‐Tyr‐l‐Tyr as the major product. Reconstruction of the biosynthetic pathways in Streptomyces albus and biochemical investigation proved that the cytochrome P450 enzymes GymB1–GymB6 act as both intramolecular oxidases and intermolecular nucleobase transferases. They catalyze not only the oxidative C−C coupling within cyclo‐l‐Tyr‐l‐Tyr, leading to mycocyclosin, but also its connection with guanine and hypoxanthine, and are thus responsible for the formation of tyrosine‐containing guatyromycines, instead of the reported tryptophan‐nucleobase adducts. Phylogenetic data suggest the presence of at least 47 GymB orthologues, indicating the occurrence of a widely distributed enzyme class.
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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
| | - Lauritz Harken
- Institut für Pharmazeutische Biologie und Biotechnologie, Fachbereich Pharmazie, Philipps-Universität Marburg, Robert-Koch-Straße 4, 35037, Marburg, Germany
| | - Yiling Yang
- Institut für Pharmazeutische Biologie und Biotechnologie, Fachbereich Pharmazie, Philipps-Universität Marburg, Robert-Koch-Straße 4, 35037, Marburg, Germany
| | - Xiulan Xie
- Fachbereich Chemie, Philipps-Universität Marburg, Hans-Meerwein-Straße 4, 35032, 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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83
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Stierle SA, Li SM. Biosynthesis of Xylariolide D in Penicillium crustosum Implies a Chain Branching Reaction Catalyzed by a Highly Reducing Polyketide Synthase. J Fungi (Basel) 2022; 8:jof8050493. [PMID: 35628749 PMCID: PMC9147667 DOI: 10.3390/jof8050493] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2022] [Revised: 05/03/2022] [Accepted: 05/06/2022] [Indexed: 11/25/2022] Open
Abstract
Fungi are important sources for the discovery of natural products. During the last decades, technological progress and the increasing number of sequenced genomes facilitated the exploration of new secondary metabolites. Among those, polyketides represent a structurally diverse group with manifold biological activities. In this study, we successfully used genome mining and genetic manipulation for functional proof of a polyketide biosynthetic gene cluster from the filamentous fungus Penicillium crustosum. Gene activation in the native host and heterologous expression in Aspergillus nidulans led to the identification of the xil cluster, being responsible for the formation of the 6-methyl-2-pyrone derivative xylariolide D. Feeding with 13C-labeled precursors supported the hypothesis of chain branching during the backbone formation catalyzed by a highly reducing fungal polyketide synthase. A cytochrome P450-catalyzed hydroxylation converts the PKS product to the final metabolite. This proved that just two enzymes are required for the biosynthesis of xylariolide D.
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84
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Gavriilidou A, Kautsar SA, Zaburannyi N, Krug D, Müller R, Medema MH, Ziemert N. Compendium of specialized metabolite biosynthetic diversity encoded in bacterial genomes. Nat Microbiol 2022; 7:726-735. [PMID: 35505244 DOI: 10.1038/s41564-022-01110-2] [Citation(s) in RCA: 100] [Impact Index Per Article: 50.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2021] [Accepted: 03/24/2022] [Indexed: 12/27/2022]
Abstract
Bacterial specialized metabolites are a proven source of antibiotics and cancer therapies, but whether we have sampled all the secondary metabolite chemical diversity of cultivated bacteria is not known. We analysed ~170,000 bacterial genomes and ~47,000 metagenome assembled genomes (MAGs) using a modified BiG-SLiCE and the new clust-o-matic algorithm. We estimate that only 3% of the natural products potentially encoded in bacterial genomes have been experimentally characterized. We show that the variation in secondary metabolite biosynthetic diversity drops significantly at the genus level, identifying it as an appropriate taxonomic rank for comparison. Equal comparison of genera based on relative evolutionary distance revealed that Streptomyces bacteria encode the largest biosynthetic diversity by far, with Amycolatopsis, Kutzneria and Micromonospora also encoding substantial diversity. Finally, we find that several less-well-studied taxa, such as Weeksellaceae (Bacteroidota), Myxococcaceae (Myxococcota), Pleurocapsa and Nostocaceae (Cyanobacteria), have potential to produce highly diverse sets of secondary metabolites that warrant further investigation.
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Affiliation(s)
- Athina Gavriilidou
- Translational Genome Mining for Natural Products, Interfaculty Institute of Microbiology and Infection Medicine Tübingen (IMIT), Interfaculty Institute for Biomedical Informatics (IBMI), University of Tübingen, Tübingen, Germany
| | - Satria A Kautsar
- Bioinformatics Group, Wageningen University, Wageningen, the Netherlands.,Chemistry Department, Scripps Research Florida, Jupiter, FL, USA
| | - Nestor Zaburannyi
- Helmholtz Institute for Pharmaceutical Research Saarland (HIPS)-Helmholtz Centre for Infection Research (HZI), Saarbrücken, Germany.,German Center for Infection Research (DZIF), Partner site Hannover-Braunschweig, Braunschweig, Germany
| | - Daniel Krug
- Helmholtz Institute for Pharmaceutical Research Saarland (HIPS)-Helmholtz Centre for Infection Research (HZI), Saarbrücken, Germany.,German Center for Infection Research (DZIF), Partner site Hannover-Braunschweig, Braunschweig, Germany
| | - Rolf Müller
- Helmholtz Institute for Pharmaceutical Research Saarland (HIPS)-Helmholtz Centre for Infection Research (HZI), Saarbrücken, Germany.,German Center for Infection Research (DZIF), Partner site Hannover-Braunschweig, Braunschweig, Germany
| | - Marnix H Medema
- Bioinformatics Group, Wageningen University, Wageningen, the Netherlands.
| | - 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, Tübingen, Germany. .,Cluster of Excellence 'Controlling Microbes to Fight Infections' (CMFI), University of Tübingen, Tübingen, Germany. .,German Centre for Infection Research (DZIF), Partnersite Tübingen, Tübingen, Germany.
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85
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Yang F, Zhang S, Pan W, Yao R, Zhang W, Zhang Y, Wang G, Zhang Q, Cheng Y, Dong J, Ruan C, Cui L, Wu H, Xue F. Signaling repurposable drug combinations against COVID-19 by developing the heterogeneous deep herb-graph method. Brief Bioinform 2022; 23:6580251. [PMID: 35514205 DOI: 10.1093/bib/bbac124] [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: 08/13/2021] [Revised: 02/07/2022] [Accepted: 03/15/2022] [Indexed: 11/14/2022] Open
Abstract
BACKGROUND Coronavirus disease 2019 (COVID-19) has spurred a boom in uncovering repurposable existing drugs. Drug repurposing is a strategy for identifying new uses for approved or investigational drugs that are outside the scope of the original medical indication. MOTIVATION Current works of drug repurposing for severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) are mostly limited to only focusing on chemical medicines, analysis of single drug targeting single SARS-CoV-2 protein, one-size-fits-all strategy using the same treatment (same drug) for different infected stages of SARS-CoV-2. To dilute these issues, we initially set the research focusing on herbal medicines. We then proposed a heterogeneous graph embedding method to signaled candidate repurposing herbs for each SARS-CoV-2 protein, and employed the variational graph convolutional network approach to recommend the precision herb combinations as the potential candidate treatments against the specific infected stage. METHOD We initially employed the virtual screening method to construct the 'Herb-Compound' and 'Compound-Protein' docking graph based on 480 herbal medicines, 12,735 associated chemical compounds and 24 SARS-CoV-2 proteins. Sequentially, the 'Herb-Compound-Protein' heterogeneous network was constructed by means of the metapath-based embedding approach. We then proposed the heterogeneous-information-network-based graph embedding method to generate the candidate ranking lists of herbs that target structural, nonstructural and accessory SARS-CoV-2 proteins, individually. To obtain precision synthetic effective treatments forvarious COVID-19 infected stages, we employed the variational graph convolutional network method to generate candidate herb combinations as the recommended therapeutic therapies. RESULTS There were 24 ranking lists, each containing top-10 herbs, targeting 24 SARS-CoV-2 proteins correspondingly, and 20 herb combinations were generated as the candidate-specific treatment to target the four infected stages. The code and supplementary materials are freely available at https://github.com/fanyang-AI/TCM-COVID19.
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Affiliation(s)
- Fan Yang
- The Department of Epidemiology and Biostatistics, School of Public Health, Cheeloo College of Medicine, Shandong University, China
| | - Shuaijie Zhang
- The Department of Epidemiology and Biostatistics, School of Public Health, Cheeloo College of Medicine, Shandong University, China
| | - Wei Pan
- The Department of Epidemiology and Biostatistics, School of Public Health, Cheeloo College of Medicine, Shandong University, China
| | - Ruiyuan Yao
- Shandong University of Traditional Chinese Medicine, Jinan, China
| | - Weiguo Zhang
- Shandong University of Traditional Chinese Medicine, Jinan, China
| | - Yanchun Zhang
- Institute for Sustainable Industries & Liveable Cities, Victoria University, Australia; The Department of New Networks, Peng Cheng Laboratory, Shenzhen, China
| | - Guoyin Wang
- Chongqing Key Laboratory of Computational Intelligence, Chongqing University of Posts and Telecommunications, Chongqing, China
| | - Qianghua Zhang
- Chongqing Key Laboratory of Computational Intelligence, Chongqing University of Posts and Telecommunications, Chongqing, China
| | - Yunlong Cheng
- Chongqing Key Laboratory of Computational Intelligence, Chongqing University of Posts and Telecommunications, Chongqing, China
| | - Jihua Dong
- The School of Foreign Languages and Literature, Shandong University
| | - Chunyang Ruan
- Department of Data Science and Big Data Technology, Shanghai International Studies University, Shanghai, 200083, China
| | - Lizhen Cui
- School of Software, Shandong University, Jinan, China
| | - Hao Wu
- School of Software, Shandong University, Jinan, China
| | - Fuzhong Xue
- The Department of Epidemiology and Biostatistics, School of Public Health, Cheeloo College of Medicine, Shandong University, China
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86
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Hu X, Tang Y, Liu Y, Pei X, Huang Z, Song F, Zhang H. Comprehensive Genomic Analysis of Marine Strain Streptomyces sp. 891, an Excellent Producer of Chrysomycin A with Therapeutic Potential. Mar Drugs 2022; 20:287. [PMID: 35621938 PMCID: PMC9144908 DOI: 10.3390/md20050287] [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: 03/27/2022] [Revised: 04/20/2022] [Accepted: 04/22/2022] [Indexed: 11/29/2022] Open
Abstract
Chrysomycin A is one of the most promising therapeutic candidates for treating infections caused by multidrug-resistant Gram-positive bacteria. By hybridizing next-step generation (Illumina) and third-generation (PacBio) sequencing technologies, a high-quality chromosome-level genome together with a plasmid was firstly assembled for chrysomycin A-producing marine strain 891. Phylogenetic analysis of the 16S rRNA gene and genome sequences revealed that this strain unambiguously belonged to the genus Streptomyces, and its genomic features and functional genes were comprehensively analyzed and annotated. AntiSMASH analysis of this strain unveiled one key biosynthetic gene cluster, T2PKS, responsible for the biosynthesis of chrysomycin, the biosynthesis pathway of which was putatively proposed. These findings definitely shed light on further investigation for construction of a robust industrial strain with high-yield chrysomycin A production using genetic engineering techniques and combinatorial biology approaches.
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Affiliation(s)
- Xu Hu
- School of Pharmaceutical Sciences, Zhejiang University of Technology, Hangzhou 310014, China; (X.H.); (Y.T.); (Y.L.); (X.P.); (Z.H.)
- College of Life and Environmental Sciences, Hangzhou Normal University, Hangzhou 311121, China
| | - Yuqi Tang
- School of Pharmaceutical Sciences, Zhejiang University of Technology, Hangzhou 310014, China; (X.H.); (Y.T.); (Y.L.); (X.P.); (Z.H.)
| | - Yuanyuan Liu
- School of Pharmaceutical Sciences, Zhejiang University of Technology, Hangzhou 310014, China; (X.H.); (Y.T.); (Y.L.); (X.P.); (Z.H.)
| | - Xinwei Pei
- School of Pharmaceutical Sciences, Zhejiang University of Technology, Hangzhou 310014, China; (X.H.); (Y.T.); (Y.L.); (X.P.); (Z.H.)
| | - Ziwei Huang
- School of Pharmaceutical Sciences, Zhejiang University of Technology, Hangzhou 310014, China; (X.H.); (Y.T.); (Y.L.); (X.P.); (Z.H.)
| | - Fuhang Song
- School of Light Industry, Beijing Technology and Business University, Beijing 100048, China;
| | - Huawei Zhang
- School of Pharmaceutical Sciences, Zhejiang University of Technology, Hangzhou 310014, China; (X.H.); (Y.T.); (Y.L.); (X.P.); (Z.H.)
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87
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Esposito R, Federico S, Bertolino M, Zupo V, Costantini M. Marine Demospongiae: A Challenging Treasure of Bioactive Compounds. Mar Drugs 2022; 20:244. [PMID: 35447918 PMCID: PMC9032870 DOI: 10.3390/md20040244] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2022] [Revised: 03/29/2022] [Accepted: 03/29/2022] [Indexed: 02/06/2023] Open
Abstract
In the last decades, it has been demonstrated that marine organisms are a substantial source of bioactive compounds with possible biotechnological applications. Marine sponges, in particular those belonging to the class of Demospongiae, have been considered among the most interesting invertebrates for their biotechnological potential. In this review, particular attention is devoted to natural compounds/extracts isolated from Demospongiae and their associated microorganisms with important biological activities for pharmacological applications such as antiviral, anticancer, antifouling, antimicrobial, antiplasmodial, antifungal and antioxidant. The data here presented show that this class of sponges is an exciting source of compounds, which are worth developing into new drugs, such as avarol, a hydroquinone isolated from the marine sponge Disidea avara, which is used as an antitumor, antimicrobial and antiviral drug.
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Affiliation(s)
- Roberta Esposito
- Department of Ecosustainable Marine Biotechnology, Stazione Zoologica Anton Dohrn, Villa Comunale, 80121 Napoli, Italy; (R.E.); (S.F.)
- Department of Biology, University of Naples Federico II, Complesso Universitario di Monte Sant’Angelo, Via Cin-thia 21, 80126 Naples, Italy
| | - Serena Federico
- Department of Ecosustainable Marine Biotechnology, Stazione Zoologica Anton Dohrn, Villa Comunale, 80121 Napoli, Italy; (R.E.); (S.F.)
| | - Marco Bertolino
- Department of Earth, Environment and Life Sciences (DISTAV), Università degli Studi di Genova, Corso Europa 26, 16132 Genova, Italy;
| | - Valerio Zupo
- Department of Ecosustainable Marine Biotechnology, Stazione Zoologica Anton Dohrn, Villa Comunale, 80121 Napoli, Italy; (R.E.); (S.F.)
| | - Maria Costantini
- Department of Ecosustainable Marine Biotechnology, Stazione Zoologica Anton Dohrn, Villa Comunale, 80121 Napoli, Italy; (R.E.); (S.F.)
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88
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Purdy TN, Moore BS, Lukowski AL. Harnessing ortho-Quinone Methides in Natural Product Biosynthesis and Biocatalysis. JOURNAL OF NATURAL PRODUCTS 2022; 85:688-701. [PMID: 35108487 PMCID: PMC9006567 DOI: 10.1021/acs.jnatprod.1c01026] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/26/2023]
Abstract
The implementation of ortho-quinone methide (o-QM) intermediates in complex molecule assembly represents a remarkably efficient strategy designed by Nature and utilized by synthetic chemists. o-QMs have been taken advantage of in biomimetic syntheses for decades, yet relatively few examples of o-QM-generating enzymes in natural product biosynthetic pathways have been reported. The biosynthetic enzymes that have been discovered thus far exhibit tremendous potential for biocatalytic applications, enabling the selective production of desirable compounds that are otherwise intractable or inherently difficult to achieve by traditional synthetic methods. Characterization of this biosynthetic machinery has the potential to shine a light on new enzymes capable of similar chemistry on diverse substrates, thus expanding our knowledge of Nature's catalytic repertoire. The presently known o-QM-generating enzymes include flavin-dependent oxidases, hetero-Diels-Alderases, S-adenosyl-l-methionine-dependent pericyclases, and α-ketoglutarate-dependent nonheme iron enzymes. In this review, we discuss their diverse enzymatic mechanisms and potential as biocatalysts in constructing natural product molecules such as cannabinoids.
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Affiliation(s)
- Trevor N Purdy
- Center for Marine Biotechnology and Biomedicine, Scripps Institution of Oceanography, La Jolla, California 92093, United States
| | - Bradley S Moore
- Center for Marine Biotechnology and Biomedicine, Scripps Institution of Oceanography, La Jolla, California 92093, United States
- Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California at San Diego, La Jolla, California 92093, United States
| | - April L Lukowski
- Center for Marine Biotechnology and Biomedicine, Scripps Institution of Oceanography, La Jolla, California 92093, United States
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89
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Liu M, Sun ZL, Zeng Z, Lam KM. MGF6mARice: prediction of DNA N6-methyladenine sites in rice by exploiting molecular graph feature and residual block. Brief Bioinform 2022; 23:6553606. [PMID: 35325050 DOI: 10.1093/bib/bbac082] [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: 11/22/2021] [Revised: 02/13/2022] [Accepted: 02/16/2022] [Indexed: 11/12/2022] Open
Abstract
DNA N6-methyladenine (6mA) is produced by the N6 position of the adenine being methylated, which occurs at the molecular level, and is involved in numerous vital biological processes in the rice genome. Given the shortcomings of biological experiments, researchers have developed many computational methods to predict 6mA sites and achieved good performance. However, the existing methods do not consider the occurrence mechanism of 6mA to extract features from the molecular structure. In this paper, a novel deep learning method is proposed by devising DNA molecular graph feature and residual block structure for 6mA sites prediction in rice, named MGF6mARice. Firstly, the DNA sequence is changed into a simplified molecular input line entry system (SMILES) format, which reflects chemical molecular structure. Secondly, for the molecular structure data, we construct the DNA molecular graph feature based on the principle of graph convolutional network. Then, the residual block is designed to extract higher level, distinguishable features from molecular graph features. Finally, the prediction module is used to obtain the result of whether it is a 6mA site. By means of 10-fold cross-validation, MGF6mARice outperforms the state-of-the-art approaches. Multiple experiments have shown that the molecular graph feature and residual block can promote the performance of MGF6mARice in 6mA prediction. To the best of our knowledge, it is the first time to derive a feature of DNA sequence by considering the chemical molecular structure. We hope that MGF6mARice will be helpful for researchers to analyze 6mA sites in rice.
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Affiliation(s)
- Mengya Liu
- School of Computer Science and Technology, Anhui University, Hefei, 230601, China
| | - Zhan-Li Sun
- School of Artificial Intelligence, Anhui University, Hefei, 230601, China
| | - Zhigang Zeng
- School of Artificial Intelligence and Automation, Huazhong University of Science and Technology, Wuhan, 430074, China
| | - Kin-Man Lam
- Department of Electronic and Information Engineering, The Hong Kong Polytechnic University, Hong Kong, China
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90
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Zhou X, Liu Z. Unlocking plant metabolic diversity: A (pan)-genomic view. PLANT COMMUNICATIONS 2022; 3:100300. [PMID: 35529944 PMCID: PMC9073316 DOI: 10.1016/j.xplc.2022.100300] [Citation(s) in RCA: 17] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/13/2021] [Revised: 12/12/2021] [Accepted: 01/13/2022] [Indexed: 05/28/2023]
Abstract
Plants produce a remarkable diversity of structurally and functionally diverse natural chemicals that serve as adaptive compounds throughout their life cycles. However, unlocking this metabolic diversity is significantly impeded by the size, complexity, and abundant repetitive elements of typical plant genomes. As genome sequencing becomes routine, we anticipate that links between metabolic diversity and genetic variation will be strengthened. In addition, an ever-increasing number of plant genomes have revealed that biosynthetic gene clusters are not only a hallmark of microbes and fungi; gene clusters for various classes of compounds have also been found in plants, and many are associated with important agronomic traits. We present recent examples of plant metabolic diversification that have been discovered through the exploration and exploitation of various genomic and pan-genomic data. We also draw attention to the fundamental genomic and pan-genomic basis of plant chemodiversity and discuss challenges and future perspectives for investigating metabolic diversity in the coming pan-genomics era.
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Affiliation(s)
- Xuan Zhou
- Joint Center for Single Cell Biology, School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai 200240, China
- Shanghai Collaborative Innovation Center of Agri-Seeds, School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Zhenhua Liu
- Joint Center for Single Cell Biology, School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai 200240, China
- Shanghai Collaborative Innovation Center of Agri-Seeds, School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai 200240, China
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91
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Liu J, Harken L, Yang Y, Xie X, Li SM. Widely Distributed Bifunctional Bacterial Cytochrome P450 Enzymes Catalyze both Intramolecular C‐C Bond Formation in cyclo‐l‐Tyr‐l‐Tyr and Its Coupling with Nucleobases. Angew Chem Int Ed Engl 2022. [DOI: 10.1002/ange.202200377] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Affiliation(s)
- Jing Liu
- Philipps-Universitat Marburg Universitatsbibliothek: Philipps-Universitat Marburg Pharmazie GERMANY
| | - Lauritz Harken
- Philipps-Universität Marburg: Philipps-Universitat Marburg Pharmazie GERMANY
| | - Yiling Yang
- Philipps-Universitat Marburg Institut Pharm.Biol.Biotechnol. GERMANY
| | - Xiulan Xie
- Philipps-Universität Marburg: Philipps-Universitat Marburg Chemie GERMANY
| | - Shu-Ming Li
- Philipps-Universität Marburg Institut für Pharmazeutische Biologie Robert-Koch-Str. 4 35037 Marburg GERMANY
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92
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Saldívar-González FI, Aldas-Bulos VD, Medina-Franco JL, Plisson F. Natural product drug discovery in the artificial intelligence era. Chem Sci 2022; 13:1526-1546. [PMID: 35282622 PMCID: PMC8827052 DOI: 10.1039/d1sc04471k] [Citation(s) in RCA: 50] [Impact Index Per Article: 25.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2021] [Accepted: 12/10/2021] [Indexed: 12/19/2022] Open
Abstract
Natural products (NPs) are primarily recognized as privileged structures to interact with protein drug targets. Their unique characteristics and structural diversity continue to marvel scientists for developing NP-inspired medicines, even though the pharmaceutical industry has largely given up. High-performance computer hardware, extensive storage, accessible software and affordable online education have democratized the use of artificial intelligence (AI) in many sectors and research areas. The last decades have introduced natural language processing and machine learning algorithms, two subfields of AI, to tackle NP drug discovery challenges and open up opportunities. In this article, we review and discuss the rational applications of AI approaches developed to assist in discovering bioactive NPs and capturing the molecular "patterns" of these privileged structures for combinatorial design or target selectivity.
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Affiliation(s)
- F I Saldívar-González
- DIFACQUIM Research Group, School of Chemistry, Department of Pharmacy, Universidad Nacional Autónoma de México Avenida Universidad 3000 04510 Mexico Mexico
| | - V D Aldas-Bulos
- Unidad de Genómica Avanzada, Laboratorio Nacional de Genómica para la Biodiversidad (Langebio), Centro de Investigación y de Estudios Avanzados del IPN Irapuato Guanajuato Mexico
| | - J L Medina-Franco
- DIFACQUIM Research Group, School of Chemistry, Department of Pharmacy, Universidad Nacional Autónoma de México Avenida Universidad 3000 04510 Mexico Mexico
| | - F Plisson
- CONACYT - Unidad de Genómica Avanzada, Laboratorio Nacional de Genómica para la Biodiversidad (Langebio), Centro de Investigación y de Estudios Avanzados del IPN Irapuato Guanajuato Mexico
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93
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Turning the world’s DNA into new medicines. Trends Biotechnol 2022; 40:766-767. [DOI: 10.1016/j.tibtech.2022.01.014] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2022] [Accepted: 01/31/2022] [Indexed: 11/19/2022]
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94
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Zhang Y, Guo X, Yang H, Shi S. The Studies in Constructing Yeast Cell Factories for the Production of Fatty Acid Alkyl Esters. Front Bioeng Biotechnol 2022; 9:799032. [PMID: 35087801 PMCID: PMC8787340 DOI: 10.3389/fbioe.2021.799032] [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: 10/21/2021] [Accepted: 11/19/2021] [Indexed: 12/25/2022] Open
Abstract
Fatty acid alkyl esters have broad applications in biofuels, lubricant formulas, paints, coatings, and cosmetics. Traditionally, these esters are mostly produced through unsustainable and energy-intensive processes. In contrast, microbial production of esters from renewable and sustainable feedstocks may provide a promising alternative and has attracted widespread attention in recent years. At present, yeasts are used as ideal hosts for producing such esters, due to their availability for high-density fermentation, resistance to phage infection, and tolerance against toxic inhibitors. Here, we summarize recent development on the biosynthesis of alkyl esters, including fatty acid ethyl esters (FAEEs), fatty acid short-branched chain alkyl esters (FASBEs), and wax esters (WEs) by various yeast cell factories. We focus mainly on the enzyme engineering strategies of critical wax ester synthases, and the pathway engineering strategies employed for the biosynthesis of various ester products. The bottlenecks that limit productivity and their potential solutions are also discussed in this review.
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Affiliation(s)
- Yang Zhang
- Beijing Advanced Innovation Center for Soft Matter Science and Engineering, College of Life Science and Technology, Beijing University of Chemical Technology, Beijing, China.,CAS Key Laboratory of Microbial Physiological and Metabolic Engineering, State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China
| | - Xiao Guo
- Beijing Advanced Innovation Center for Soft Matter Science and Engineering, College of Life Science and Technology, Beijing University of Chemical Technology, Beijing, China
| | - Huaiyi Yang
- CAS Key Laboratory of Microbial Physiological and Metabolic Engineering, State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China
| | - Shuobo Shi
- Beijing Advanced Innovation Center for Soft Matter Science and Engineering, College of Life Science and Technology, Beijing University of Chemical Technology, Beijing, China
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95
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Miller CA, Ho JML, Bennett MR. Strategies for Improving Small-Molecule Biosensors in Bacteria. BIOSENSORS 2022; 12:bios12020064. [PMID: 35200325 PMCID: PMC8869690 DOI: 10.3390/bios12020064] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/16/2021] [Revised: 01/14/2022] [Accepted: 01/18/2022] [Indexed: 05/03/2023]
Abstract
In recent years, small-molecule biosensors have become increasingly important in synthetic biology and biochemistry, with numerous new applications continuing to be developed throughout the field. For many biosensors, however, their utility is hindered by poor functionality. Here, we review the known types of mechanisms of biosensors within bacterial cells, and the types of approaches for optimizing different biosensor functional parameters. Discussed approaches for improving biosensor functionality include methods of directly engineering biosensor genes, considerations for choosing genetic reporters, approaches for tuning gene expression, and strategies for incorporating additional genetic modules.
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Affiliation(s)
- Corwin A. Miller
- Department of Biosciences, Rice University MS-140, 6100 Main St., Houston, TX 77005, USA; (C.A.M.); (J.M.L.H.)
| | - Joanne M. L. Ho
- Department of Biosciences, Rice University MS-140, 6100 Main St., Houston, TX 77005, USA; (C.A.M.); (J.M.L.H.)
| | - Matthew R. Bennett
- Department of Biosciences, Rice University MS-140, 6100 Main St., Houston, TX 77005, USA; (C.A.M.); (J.M.L.H.)
- Department of Bioengineering, Rice University MS-140, 6100 Main St., Houston, TX 77005, USA
- Correspondence:
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96
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Mackay AS, Payne RJ, Malins LR. Electrochemistry for the Chemoselective Modification of Peptides and Proteins. J Am Chem Soc 2022; 144:23-41. [PMID: 34968405 DOI: 10.1021/jacs.1c11185] [Citation(s) in RCA: 36] [Impact Index Per Article: 18.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
Although electrochemical strategies for small-molecule synthesis are flourishing, this technology has yet to be fully exploited for the mild and chemoselective modification of peptides and proteins. With the growing number of diverse peptide natural products being identified and the emergence of modified proteins as therapeutic and diagnostic agents, methods for electrochemical modification stand as alluring prospects for harnessing the reactivity of polypeptides to build molecular complexity. As a mild and inherently tunable reaction platform, electrochemistry is arguably well-suited to overcome the chemo- and regioselectivity issues which limit existing bioconjugation strategies. This Perspective will showcase recently developed electrochemical approaches to peptide and protein modification. The article also highlights the wealth of untapped opportunities for the production of homogeneously modified biomolecules, with an eye toward realizing the enormous potential of electrochemistry for chemoselective bioconjugation chemistry.
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Affiliation(s)
- Angus S Mackay
- School of Chemistry, The University of Sydney, Sydney, NSW 2006, Australia
- Australian Research Council Centre of Excellence for Innovations in Peptide and Protein Science, The University of Sydney, Sydney, NSW 2006, Australia
| | - Richard J Payne
- School of Chemistry, The University of Sydney, Sydney, NSW 2006, Australia
- Australian Research Council Centre of Excellence for Innovations in Peptide and Protein Science, The University of Sydney, Sydney, NSW 2006, Australia
| | - Lara R Malins
- Research School of Chemistry, Australian National University, Canberra, ACT 2601, Australia
- Australian Research Council Centre of Excellence for Innovations in Peptide and Protein Science, Australian National University, Canberra, ACT 2601, Australia
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97
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Krell T, Matilla MA. Antimicrobial resistance: progress and challenges in antibiotic discovery and anti-infective therapy. Microb Biotechnol 2022; 15:70-78. [PMID: 34610194 PMCID: PMC8719825 DOI: 10.1111/1751-7915.13945] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2021] [Accepted: 09/25/2021] [Indexed: 02/06/2023] Open
Abstract
The alarming rise in the emergence of antimicrobial resistance in human, animal and plant pathogens is challenging global health and food production. Traditional strategies used for antibiotic discovery persistently result in the re-isolation of known compounds, calling for the need to develop more rational strategies to identify new antibiotics. Additionally, anti-infective therapy approaches targeting bacterial signalling pathways related to virulence is emerging as an alternative to the use of antibiotics. In this perspective article, we critically analyse approaches aimed at revitalizing the identification of new antibiotics and to advance antivirulence therapies. The development of high-throughput in vivo, in vitro and in silico platforms, together with the progress in chemical synthesis, analytical chemistry and structural biology, are reviving a research area that is of tremendous relevance for global health.
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Affiliation(s)
- Tino Krell
- Department of Environmental ProtectionEstación Experimental del ZaidínConsejo Superior de Investigaciones CientíficasProf. Albareda 1Granada18008Spain
| | - Miguel A. Matilla
- Department of Environmental ProtectionEstación Experimental del ZaidínConsejo Superior de Investigaciones CientíficasProf. Albareda 1Granada18008Spain
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98
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Danchin A. In vivo, in vitro and in silico: an open space for the development of microbe-based applications of synthetic biology. Microb Biotechnol 2022; 15:42-64. [PMID: 34570957 PMCID: PMC8719824 DOI: 10.1111/1751-7915.13937] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2021] [Accepted: 09/14/2021] [Indexed: 12/24/2022] Open
Abstract
Living systems are studied using three complementary approaches: living cells, cell-free systems and computer-mediated modelling. Progresses in understanding, allowing researchers to create novel chassis and industrial processes rest on a cycle that combines in vivo, in vitro and in silico studies. This design-build-test-learn iteration loop cycle between experiments and analyses combines together physiology, genetics, biochemistry and bioinformatics in a way that keeps going forward. Because computer-aided approaches are not directly constrained by the material nature of the entities of interest, we illustrate here how this virtuous cycle allows researchers to explore chemistry which is foreign to that present in extant life, from whole chassis to novel metabolic cycles. Particular emphasis is placed on the importance of evolution.
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Affiliation(s)
- Antoine Danchin
- Kodikos LabsInstitut Cochin24 rue du Faubourg Saint‐JacquesParis75014France
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99
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Liu J, Yang Y, Harken L, Li SM. Elucidation of the Streptoazine Biosynthetic Pathway in Streptomyces aurantiacus Reveals the Presence of a Promiscuous Prenyltransferase/Cyclase. JOURNAL OF NATURAL PRODUCTS 2021; 84:3100-3109. [PMID: 34846144 DOI: 10.1021/acs.jnatprod.1c00844] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/13/2023]
Abstract
Heterologous expression of a three-gene cluster from Streptomyces aurantiacus coding for a cyclodipeptide synthase, a prenyltransferase, and a methyltransferase led to the elucidation of the biosynthetic steps of streptoazine C (2). In vivo biotransformation experiments proved the high flexibility of the prenyltransferase SasB toward tryptophan-containing cyclodipeptides for regular C-3-prenylation. Furthermore, their corresponding dehydrogenated derivatives prepared by using cyclodipeptide oxidases were also used for prenylation. This study provides an enzyme with high substrate promiscuity from a less explored group of prenyltransferases for potential use to generate prenylated derivatives.
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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
| | - Yiling Yang
- Institut für Pharmazeutische Biologie und Biotechnologie, Fachbereich Pharmazie, Philipps-Universität Marburg, Robert-Koch Straße 4, 35037 Marburg, Germany
| | - Lauritz Harken
- Institut für Pharmazeutische Biologie und Biotechnologie, Fachbereich Pharmazie, Philipps-Universität Marburg, Robert-Koch Straße 4, 35037 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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100
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Harken L, Liu J, Kreuz O, Berger R, Li SM. Biosynthesis of Guatrypmethine C Implies Two Different Oxidases for exo Double Bond Installation at the Diketopiperazine Ring. ACS Catal 2021. [DOI: 10.1021/acscatal.1c04609] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Affiliation(s)
- Lauritz Harken
- Institut für Pharmazeutische Biologie und Biotechnologie, Fachbereich Pharmazie, Philipps-Universität Marburg, Robert-Koch-Straße 4, 35037 Marburg, Germany
| | - Jing Liu
- Institut für Pharmazeutische Biologie und Biotechnologie, Fachbereich Pharmazie, Philipps-Universität Marburg, Robert-Koch-Straße 4, 35037 Marburg, Germany
| | - Oliver Kreuz
- Fachbereich Chemie, Philipps-Universität Marburg, Hans-Meerwein-Straße 4, 35032 Marburg, Germany
| | - Robert Berger
- Fachbereich Chemie, Philipps-Universität Marburg, Hans-Meerwein-Straße 4, 35032 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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