1
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Surwase AJ, Thakur NL. Production of marine-derived bioactive peptide molecules for industrial applications: A reverse engineering approach. Biotechnol Adv 2024; 77:108449. [PMID: 39260778 DOI: 10.1016/j.biotechadv.2024.108449] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2023] [Revised: 06/28/2024] [Accepted: 09/07/2024] [Indexed: 09/13/2024]
Abstract
This review examines a wide range of marine microbial-derived bioactive peptide molecules, emphasizing the significance of reverse engineering in their production. The discussion encompasses the advancements in Marine Natural Products (MNPs) bio-manufacturing through the integration of omics-driven microbial engineering and bioinformatics. The distinctive features of non-ribosomally synthesised peptides (NRPs), and ribosomally synthesised precursor peptides (RiPP) biosynthesis is elucidated and presented. Additionally, the article delves into the origins of common peptide modifications. It highlights various genome mining approaches for the targeted identification of Biosynthetic Gene Clusters (BGCs) and novel RiPP and NRPs-derived peptides. The review aims to demonstrate the advancements, prospects, and obstacles in engineering both RiPP and NRP biosynthetic pathways.
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Affiliation(s)
- Akash J Surwase
- CSIR-National Institute of Oceanography, Dona Paula 403004, Goa, India; Academy of Scientific and Innovative Research (AcSIR), Ghaziabad 201002, India.
| | - Narsinh L Thakur
- CSIR-National Institute of Oceanography, Dona Paula 403004, Goa, India; Academy of Scientific and Innovative Research (AcSIR), Ghaziabad 201002, India.
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2
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Li XL, Zhang JQ, Shen XJ, Zhang Y, Guo DA. Overview and limitations of database in global traditional medicines: A narrative review. Acta Pharmacol Sin 2024:10.1038/s41401-024-01353-1. [PMID: 39095509 DOI: 10.1038/s41401-024-01353-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2023] [Accepted: 07/02/2024] [Indexed: 08/04/2024] Open
Abstract
The study of traditional medicine has garnered significant interest, resulting in various research areas including chemical composition analysis, pharmacological research, clinical application, and quality control. The abundance of available data has made databases increasingly essential for researchers to manage the vast amount of information and explore new drugs. In this article we provide a comprehensive overview and summary of 182 databases that are relevant to traditional medicine research, including 73 databases for chemical component analysis, 70 for pharmacology research, and 39 for clinical application and quality control from published literature (2000-2023). The review categorizes the databases by functionality, offering detailed information on websites and capacities to facilitate easier access. Moreover, this article outlines the primary function of each database, supplemented by case studies to aid in database selection. A practical test was conducted on 68 frequently used databases using keywords and functionalities, resulting in the identification of highlighted databases. This review serves as a reference for traditional medicine researchers to choose appropriate databases and also provides insights and considerations for the function and content design of future databases.
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Affiliation(s)
- Xiao-Lan Li
- Shanghai Research Center for Modernization of Traditional Chinese Medicine, National Engineering Research Center of TCM Standardization Technology, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, 201203, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Jian-Qing Zhang
- Shanghai Research Center for Modernization of Traditional Chinese Medicine, National Engineering Research Center of TCM Standardization Technology, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, 201203, China
| | - Xuan-Jing Shen
- Shanghai Research Center for Modernization of Traditional Chinese Medicine, National Engineering Research Center of TCM Standardization Technology, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, 201203, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Yu Zhang
- Shanghai Research Center for Modernization of Traditional Chinese Medicine, National Engineering Research Center of TCM Standardization Technology, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, 201203, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - De-An Guo
- Shanghai Research Center for Modernization of Traditional Chinese Medicine, National Engineering Research Center of TCM Standardization Technology, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, 201203, China.
- University of Chinese Academy of Sciences, Beijing, 100049, China.
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3
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Yu YL, Chen S, Fang JB, Chen XM, Tang XY, Wang JH. Two new di-tert-butyl-type compounds from a saline-lake derived Streptomyces sp. XZB42. Nat Prod Res 2024; 38:2373-2379. [PMID: 36744675 DOI: 10.1080/14786419.2023.2175356] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2022] [Revised: 01/20/2023] [Accepted: 01/23/2023] [Indexed: 02/07/2023]
Abstract
Two novel di-tert-butyl-type structures (1-2), and five known compounds (3-7) were isolated from the chemical investigations of a saline lake actinomycete, Streptomyces sp. XZB42. The structures of the new compounds were elucidated by extensive NMR spectroscopic analysis, HRESIMS data, GIAO (gauge-including atomic orbitals) NMR and specific optical rotation (SOR).
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Affiliation(s)
- Ya-Lin Yu
- Institute of Marine Biology and Pharmacology, Ocean College, Zhejiang University, Zhoushan, People's Republic of China
| | - Shuang Chen
- Institute of Marine Biology and Pharmacology, Ocean College, Zhejiang University, Zhoushan, People's Republic of China
| | - Jie-Bin Fang
- Institute of Marine Biology and Pharmacology, Ocean College, Zhejiang University, Zhoushan, People's Republic of China
| | - Xiao-Ming Chen
- Institute of Marine Biology and Pharmacology, Ocean College, Zhejiang University, Zhoushan, People's Republic of China
| | - Xin-Yi Tang
- Institute of Marine Biology and Pharmacology, Ocean College, Zhejiang University, Zhoushan, People's Republic of China
| | - Jin-Hui Wang
- Institute of Marine Biology and Pharmacology, Ocean College, Zhejiang University, Zhoushan, People's Republic of China
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4
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Mayer AMS, Mayer VA, Swanson-Mungerson M, Pierce ML, Rodríguez AD, Nakamura F, Taglialatela-Scafati O. Marine Pharmacology in 2019-2021: Marine Compounds with Antibacterial, Antidiabetic, Antifungal, Anti-Inflammatory, Antiprotozoal, Antituberculosis and Antiviral Activities; Affecting the Immune and Nervous Systems, and Other Miscellaneous Mechanisms of Action. Mar Drugs 2024; 22:309. [PMID: 39057418 PMCID: PMC11278370 DOI: 10.3390/md22070309] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2024] [Revised: 06/22/2024] [Accepted: 06/27/2024] [Indexed: 07/28/2024] Open
Abstract
The current 2019-2021 marine pharmacology literature review provides a continuation of previous reviews covering the period 1998 to 2018. Preclinical marine pharmacology research during 2019-2021 was published by researchers in 42 countries and contributed novel mechanism-of-action pharmacology for 171 structurally characterized marine compounds. The peer-reviewed marine natural product pharmacology literature reported antibacterial, antifungal, antiprotozoal, antituberculosis, and antiviral mechanism-of-action studies for 49 compounds, 87 compounds with antidiabetic and anti-inflammatory activities that also affected the immune and nervous system, while another group of 51 compounds demonstrated novel miscellaneous mechanisms of action, which upon further investigation, may contribute to several pharmacological classes. Thus, in 2019-2021, a very active preclinical marine natural product pharmacology pipeline provided novel mechanisms of action as well as new lead chemistry for the clinical marine pharmaceutical pipeline targeting the therapy of several disease categories.
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Affiliation(s)
- Alejandro M. S. Mayer
- Department of Pharmacology, College of Graduate Studies, Midwestern University, 555 31st Street, Downers Grove, IL 60515, USA;
| | - Veronica A. Mayer
- Department of Nursing Education, School of Nursing, Aurora University, 347 S. Gladstone Ave., Aurora, IL 60506, USA;
| | - Michelle Swanson-Mungerson
- Department of Microbiology and Immunology, College of Graduate Studies, Midwestern University, 555 31st Street, Downers Grove, IL 60515, USA;
| | - Marsha L. Pierce
- Department of Pharmacology, College of Graduate Studies, Midwestern University, 555 31st Street, Downers Grove, IL 60515, USA;
| | - Abimael D. Rodríguez
- Molecular Sciences Research Center, University of Puerto Rico, 1390 Ponce de León Avenue, San Juan, PR 00926, USA;
| | - Fumiaki Nakamura
- Research Institute for Science and Engineering, Waseda University, 3-4-1 Okubo, Shinjuku-ku 169-8555, Tokyo, Japan;
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5
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Schniete JK, Fernández-Martínez LT. Natural product discovery in soil actinomycetes: unlocking their potential within an ecological context. Curr Opin Microbiol 2024; 79:102487. [PMID: 38733791 DOI: 10.1016/j.mib.2024.102487] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2023] [Revised: 02/23/2024] [Accepted: 04/25/2024] [Indexed: 05/13/2024]
Abstract
Natural products (NPs) produced by bacteria, particularly soil actinomycetes, often possess diverse bioactivities and play a crucial role in human health, agriculture, and biotechnology. Soil actinomycete genomes contain a vast number of predicted biosynthetic gene clusters (BGCs) yet to be exploited. Understanding the factors governing NP production in an ecological context and activating cryptic and silent BGCs in soil actinomycetes will provide researchers with a wealth of molecules with potential novel applications. Here, we highlight recent advances in NP discovery strategies employing ecology-inspired approaches and discuss the importance of understanding the environmental signals responsible for activation of NP production, particularly in a soil microbial community context, as well as the challenges that remain.
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Affiliation(s)
- Jana K Schniete
- Institute of Microbiology, Leibniz Universität Hannover, 30419 Hannover, Germany.
| | - Lorena T Fernández-Martínez
- School of Infection and Immunity, College of Medical, Veterinary and Life Sciences, University of Glasgow, Glasgow G12 8TA, UK.
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6
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Baunach M, Guljamow A, Miguel-Gordo M, Dittmann E. Harnessing the potential: advances in cyanobacterial natural product research and biotechnology. Nat Prod Rep 2024; 41:347-369. [PMID: 38088806 DOI: 10.1039/d3np00045a] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/21/2024]
Abstract
Covering: 2000 to 2023Cyanobacteria produce a variety of bioactive natural products that can pose a threat to humans and animals as environmental toxins, but also have potential for or inspire pharmaceutical use. As oxygenic phototrophs, cyanobacteria furthermore hold great promise for sustainable biotechnology. Yet, the necessary tools for exploiting their biotechnological potential have so far been established only for a few model strains of cyanobacteria, while large untapped biosynthetic resources are hidden in slow-growing cyanobacterial genera that are difficult to access by genetic techniques. In recent years, several approaches have been developed to circumvent the bottlenecks in cyanobacterial natural product research. Here, we summarize current progress that has been made in unlocking or characterizing cryptic metabolic pathways using integrated omics techniques, orphan gene cluster activation, use of genetic approaches in original producers, heterologous expression and chemo-enzymatic techniques. We are mainly highlighting genomic mining concepts and strategies towards high-titer production of cyanobacterial natural products from the last 10 years and discuss the need for further research developments in this field.
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Affiliation(s)
- Martin Baunach
- University of Potsdam, Institute of Biochemistry and Biology, Karl-Liebknecht-Str. 24/25, 14476 Potsdam, Germany.
- University of Bonn, Institute of Pharmaceutical Biology, Nußallee 6, 53115 Bonn, Germany
| | - Arthur Guljamow
- University of Potsdam, Institute of Biochemistry and Biology, Karl-Liebknecht-Str. 24/25, 14476 Potsdam, Germany.
| | - María Miguel-Gordo
- University of Potsdam, Institute of Biochemistry and Biology, Karl-Liebknecht-Str. 24/25, 14476 Potsdam, Germany.
| | - Elke Dittmann
- University of Potsdam, Institute of Biochemistry and Biology, Karl-Liebknecht-Str. 24/25, 14476 Potsdam, Germany.
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7
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Alwali AY, Santos D, Aguilar C, Birch A, Rodriguez-Orduña L, Roberts CB, Modi R, Licona-Cassani C, Parkinson EI. Discovery of Streptomyces species CS-62, a novel producer of the Acinetobacter baumannii selective antibiotic factumycin. J Ind Microbiol Biotechnol 2024; 51:kuae014. [PMID: 38632045 PMCID: PMC11066910 DOI: 10.1093/jimb/kuae014] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2024] [Accepted: 04/16/2024] [Indexed: 04/19/2024]
Abstract
Narrow-spectrum antibiotics are of great interest given their ability to spare the microbiome and decrease widespread antibiotic resistance compared to broad-spectrum antibiotics. Herein, we screened an in-house library of Actinobacteria strains for selective activity against Acinetobacter baumannii and successfully identified Streptomyces sp. CS-62 as a producer of a natural product with this valuable activity. Analysis of the cultures via high-resolution mass spectrometry and tandem mass spectrometry, followed by comparison with molecules in the Natural Product Atlas and the Global Natural Products Social Molecular Networking platform, suggested a novel natural product. Genome mining analysis initially supported the production of a novel kirromycin derivative. Isolation and structure elucidation via mass spectrometry and Nuclear Magnetic Resonance (NMR) analyses revealed that the active natural product was the known natural product factumycin, exposing omissions and errors in the consulted databases. While public databases are generally very useful for avoiding rediscovery of known molecules, rediscovery remains a problem due to public databases either being incomplete or having errors that result in failed dereplication. Overall, the work describes the ongoing problem of dereplication and the continued need for public database curation.
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Affiliation(s)
- Amir Y Alwali
- Department of Chemistry, Purdue University, West Lafayette, IN 47907, USA
| | - Diane Santos
- Department of Chemistry, Purdue University, West Lafayette, IN 47907, USA
| | - César Aguilar
- Department of Chemistry, Purdue University, West Lafayette, IN 47907, USA
| | - Audrey Birch
- Department of Chemistry, Purdue University, West Lafayette, IN 47907, USA
| | - Lorena Rodriguez-Orduña
- Centro de Biotecnología FEMSA, Tecnológico de Monterrey, Escuela de Ingeniería y Ciencias, 64849 Monterrey, México
| | - Carson B Roberts
- Department of Chemistry, Purdue University, West Lafayette, IN 47907, USA
| | - Ramya Modi
- Department of Chemistry, Purdue University, West Lafayette, IN 47907, USA
| | - Cuauhtemoc Licona-Cassani
- Centro de Biotecnología FEMSA, Tecnológico de Monterrey, Escuela de Ingeniería y Ciencias, 64849 Monterrey, México
| | - Elizabeth I Parkinson
- Department of Chemistry, Purdue University, West Lafayette, IN 47907, USA
- Department of Medicinal Chemistry and Molecular Pharmacology, Purdue University, West Lafayette, IN 47907, USA
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8
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Silva SG, Nabhan Homsi M, Keller-Costa T, Rocha U, Costa R. Natural product biosynthetic potential reflects macroevolutionary diversification within a widely distributed bacterial taxon. mSystems 2023; 8:e0064323. [PMID: 38018967 PMCID: PMC10734526 DOI: 10.1128/msystems.00643-23] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2023] [Accepted: 10/18/2023] [Indexed: 11/30/2023] Open
Abstract
IMPORTANCE This is the most comprehensive study performed thus far on the biosynthetic potential within the Flavobacteriaceae family. Our findings reveal intertwined taxonomic and natural product biosynthesis diversification within the family. We posit that the carbohydrate, peptide, and secondary metabolism triad synergistically shaped the evolution of this keystone bacterial taxon, acting as major forces underpinning the broad host range and opportunistic-to-pathogenic behavior encompassed by species in the family. This study further breaks new ground for future research on select Flavobacteriaceae spp. as reservoirs of novel drug leads.
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Affiliation(s)
- Sandra Godinho Silva
- Department of Bioengineering, Instituto Superior Técnico, University of Lisbon, Lisbon, Portugal
- iBB–Institute for Bioengineering and Biosciences and i4HB–Institute for Health and Bioeconomy, Instituto Superior Técnico, University of Lisbon, Lisbon, Portugal
| | - Masun Nabhan Homsi
- Department of Molecular Systems Biology, Helmholtz Centre for Environmental Research–UFZ, Leipzig, Germany
| | - Tina Keller-Costa
- Department of Bioengineering, Instituto Superior Técnico, University of Lisbon, Lisbon, Portugal
- iBB–Institute for Bioengineering and Biosciences and i4HB–Institute for Health and Bioeconomy, Instituto Superior Técnico, University of Lisbon, Lisbon, Portugal
| | - Ulisses Rocha
- Department of Environmental Microbiology, Helmholtz Centre for Environmental Research–UFZ, Leipzig, Germany
| | - Rodrigo Costa
- Department of Bioengineering, Instituto Superior Técnico, University of Lisbon, Lisbon, Portugal
- iBB–Institute for Bioengineering and Biosciences and i4HB–Institute for Health and Bioeconomy, Instituto Superior Técnico, University of Lisbon, Lisbon, Portugal
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9
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Cho MH, Cho KH, No KT. PhyloSophos: a high-throughput scientific name mapping algorithm augmented with explicit consideration of taxonomic science, and its application on natural product (NP) occurrence database processing. BMC Bioinformatics 2023; 24:475. [PMID: 38097955 PMCID: PMC10722791 DOI: 10.1186/s12859-023-05588-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2023] [Accepted: 11/29/2023] [Indexed: 12/17/2023] Open
Abstract
BACKGROUND The standardization of biological data using unique identifiers is vital for seamless data integration, comprehensive interpretation, and reproducibility of research findings, contributing to advancements in bioinformatics and systems biology. Despite being widely accepted as a universal identifier, scientific names for biological species have inherent limitations, including lack of stability, uniqueness, and convertibility, hindering their effective use as identifiers in databases, particularly in natural product (NP) occurrence databases, posing a substantial obstacle to utilizing this valuable data for large-scale research applications. RESULT To address these challenges and facilitate high-throughput analysis of biological data involving scientific names, we developed PhyloSophos, a Python package that considers the properties of scientific names and taxonomic systems to accurately map name inputs to entries within a chosen reference database. We illustrate the importance of assessing multiple taxonomic databases and considering taxonomic syntax-based pre-processing using NP occurrence databases as an example, with the ultimate goal of integrating heterogeneous information into a single, unified dataset. CONCLUSIONS We anticipate PhyloSophos to significantly aid in the systematic processing of poorly digitized and curated biological data, such as biodiversity information and ethnopharmacological resources, enabling full-scale bioinformatics analysis using these valuable data resources.
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Affiliation(s)
- Min Hyung Cho
- Bioinformatics and Molecular Design Research Center (BMDRC), 209, Veritas A Hall, Yonsei University, 85 Songdogwahak-ro, Yeonsu-gu, Incheon, 21983, Republic of Korea.
| | - Kwang-Hwi Cho
- School of Systems Biomedical Science, Soongsil University, Seoul, 06978, South Korea
| | - Kyoung Tai No
- Bioinformatics and Molecular Design Research Center (BMDRC), 209, Veritas A Hall, Yonsei University, 85 Songdogwahak-ro, Yeonsu-gu, Incheon, 21983, Republic of Korea
- Department of Integrative Biotechnology and Translational Medicine, 214, Veritas A Hall, Yonsei University, 85 Songdogwahak-ro, Yeonsu-gu, Incheon, 21983, Republic of Korea
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Xu HQ, Xiao H, Bu JH, Hong YF, Liu YH, Tao ZY, Ding SF, Xia YT, Wu E, Yan Z, Zhang W, Chen GX, Zhu F, Tao L. EMNPD: a comprehensive endophytic microorganism natural products database for prompt the discovery of new bioactive substances. J Cheminform 2023; 15:115. [PMID: 38017550 PMCID: PMC10683116 DOI: 10.1186/s13321-023-00779-9] [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: 07/11/2023] [Accepted: 11/05/2023] [Indexed: 11/30/2023] Open
Abstract
The discovery and utilization of natural products derived from endophytic microorganisms have garnered significant attention in pharmaceutical research. While remarkable progress has been made in this field each year, the absence of dedicated open-access databases for endophytic microorganism natural products research is evident. To address the increasing demand for mining and sharing of data resources related to endophytic microorganism natural products, this study introduces EMNPD, a comprehensive endophytic microorganism natural products database comprising manually curated data. Currently, EMNPD offers 6632 natural products from 1017 endophytic microorganisms, targeting 1286 entities (including 94 proteins, 282 cell lines, and 910 species) with 91 diverse bioactivities. It encompasses the physico-chemical properties of natural products, ADMET information, quantitative activity data with their potency, natural products contents with diverse fermentation conditions, systematic taxonomy, and links to various well-established databases. EMNPD aims to function as an open-access knowledge repository for the study of endophytic microorganisms and their natural products, thereby facilitating drug discovery research and exploration of bioactive substances. The database can be accessed at http://emnpd.idrblab.cn/ without the need for registration, enabling researchers to freely download the data. EMNPD is expected to become a valuable resource in the field of endophytic microorganism natural products and contribute to future drug development endeavors.
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Affiliation(s)
- Hong-Quan Xu
- Key Laboratory of Elemene Class Anti-cancer Chinese Medicines, School of Pharmacy, Hangzhou Normal University, Hangzhou, 311121, China
| | - Huan Xiao
- Key Laboratory of Elemene Class Anti-cancer Chinese Medicines, School of Pharmacy, Hangzhou Normal University, Hangzhou, 311121, China
| | - Jin-Hui Bu
- Key Laboratory of Elemene Class Anti-cancer Chinese Medicines, School of Pharmacy, Hangzhou Normal University, Hangzhou, 311121, China
| | - Yan-Feng Hong
- Key Laboratory of Elemene Class Anti-cancer Chinese Medicines, School of Pharmacy, Hangzhou Normal University, Hangzhou, 311121, China
| | - Yu-Hong Liu
- Key Laboratory of Elemene Class Anti-cancer Chinese Medicines, School of Pharmacy, Hangzhou Normal University, Hangzhou, 311121, China
| | - Zi-Yue Tao
- Key Laboratory of Elemene Class Anti-cancer Chinese Medicines, School of Pharmacy, Hangzhou Normal University, Hangzhou, 311121, China
| | - Shu-Fan Ding
- Key Laboratory of Elemene Class Anti-cancer Chinese Medicines, School of Pharmacy, Hangzhou Normal University, Hangzhou, 311121, China
| | - Yi-Tong Xia
- Key Laboratory of Elemene Class Anti-cancer Chinese Medicines, School of Pharmacy, Hangzhou Normal University, Hangzhou, 311121, China
| | - E Wu
- Rehabilitation and Nursing School, Hangzhou Vocational & Technical College, Hangzhou, 310018, Zhejiang, China
| | - Zhen Yan
- The Affiliated Hospital of Hangzhou Normal University, Hangzhou, 310000, China
- First Clinical Medical Institute, Nanjing University of Chinese Medicine, Nanjing, 210023, Jiangsu, China
| | - Wei Zhang
- College of Pharmaceutical Sciences, The Second Affiliated Hospital, Zhejiang University School of Medicine, Zhejiang University, Hangzhou, 310058, China
- Innovation Institute for Affiliated Intelligence in Medicine of Zhejiang University, Alibaba-Zhejiang University Joint Research Center of Future Digital Healthcare, Hangzhou, 330110, China
| | - Gong-Xing Chen
- Key Laboratory of Elemene Class Anti-cancer Chinese Medicines, School of Pharmacy, Hangzhou Normal University, Hangzhou, 311121, China
| | - Feng Zhu
- College of Pharmaceutical Sciences, The Second Affiliated Hospital, Zhejiang University School of Medicine, Zhejiang University, Hangzhou, 310058, China.
- Innovation Institute for Affiliated Intelligence in Medicine of Zhejiang University, Alibaba-Zhejiang University Joint Research Center of Future Digital Healthcare, Hangzhou, 330110, China.
| | - Lin Tao
- Key Laboratory of Elemene Class Anti-cancer Chinese Medicines, School of Pharmacy, Hangzhou Normal University, Hangzhou, 311121, China.
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11
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Pin M, Poynton EF, Jordan T, Kim J, Ledingham B, van Santen JA, Yang V, Maras A, Tavangar P, Gautam V, Peters H, Sajed T, Lee BL, Shreffler HA, Koller JT, Tretter ZM, Cort JR, Sumner LW, Wishart DS, Linington RG. A Data Deposition Platform for Sharing Nuclear Magnetic Resonance Data. JOURNAL OF NATURAL PRODUCTS 2023; 86:2554-2561. [PMID: 37935005 PMCID: PMC11119957 DOI: 10.1021/acs.jnatprod.3c00795] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/09/2023]
Abstract
Nuclear magnetic resonance (NMR) data are rarely deposited in open databases, leading to loss of critical scientific knowledge. Existing data reporting methods (images, tables, lists of values) contain less information than raw data and are poorly standardized. Together, these issues limit FAIR (findable, accessible, interoperable, reusable) access to these data, which in turn creates barriers for compound dereplication and the development of new data-driven discovery tools. Existing NMR databases either are not designed for natural products data or employ complex deposition interfaces that disincentivize deposition. Journals, including the Journal of Natural Products (JNP), are now requiring data submission as part of the publication process, creating the need for a streamlined, user-friendly mechanism to deposit and distribute NMR data.
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Affiliation(s)
- Matthew Pin
- Department of Chemistry, Simon Fraser University, 8888 University Drive, Burnaby, BC, V5A 1S6, Canada
| | - Ella F. Poynton
- Department of Chemistry, Simon Fraser University, 8888 University Drive, Burnaby, BC, V5A 1S6, Canada
| | - Tamara Jordan
- Department of Chemistry, Simon Fraser University, 8888 University Drive, Burnaby, BC, V5A 1S6, Canada
| | - Jonghyeok Kim
- Department of Chemistry, Simon Fraser University, 8888 University Drive, Burnaby, BC, V5A 1S6, Canada
| | - Benjamin Ledingham
- Department of Chemistry, Simon Fraser University, 8888 University Drive, Burnaby, BC, V5A 1S6, Canada
| | - Jeffrey A. van Santen
- Department of Chemistry, Simon Fraser University, 8888 University Drive, Burnaby, BC, V5A 1S6, Canada
- Unnatural Products, 2161 Delaware Ave. Suite A, Santa Cruz, CA 95060, USA
| | - Vera Yang
- Department of Chemistry, Simon Fraser University, 8888 University Drive, Burnaby, BC, V5A 1S6, Canada
| | - Andrew Maras
- Department of Chemistry, Simon Fraser University, 8888 University Drive, Burnaby, BC, V5A 1S6, Canada
| | - Pegah Tavangar
- Department of Chemistry, Simon Fraser University, 8888 University Drive, Burnaby, BC, V5A 1S6, Canada
| | - Vasuk Gautam
- Department of Biological Sciences, University of Alberta, Edmonton, AB T6G 2E9, Canada
| | - Harrison Peters
- Department of Biological Sciences, University of Alberta, Edmonton, AB T6G 2E9, Canada
| | - Tanvir Sajed
- Department of Biological Sciences, University of Alberta, Edmonton, AB T6G 2E9, Canada
| | - Brian L. Lee
- Department of Biological Sciences, University of Alberta, Edmonton, AB T6G 2E9, Canada
| | - Hailey A. Shreffler
- Earth and Biological Sciences Directorate, Pacific Northwest National Laboratory, Richland, WA, United States
| | - James T. Koller
- Interdisciplinary Plant Group, MU Metabolomics Center, Bond Life Sciences Center, Department of Biochemistry, University of Missouri, Columbia, MO 65211, USA
| | - Zachary M. Tretter
- Interdisciplinary Plant Group, MU Metabolomics Center, Bond Life Sciences Center, Department of Biochemistry, University of Missouri, Columbia, MO 65211, USA
| | - John R. Cort
- Earth and Biological Sciences Directorate, Pacific Northwest National Laboratory, Richland, WA, United States
| | - Lloyd W. Sumner
- Interdisciplinary Plant Group, MU Metabolomics Center, Bond Life Sciences Center, Department of Biochemistry, University of Missouri, Columbia, MO 65211, USA
| | - David S. Wishart
- Department of Biological Sciences, University of Alberta, Edmonton, AB T6G 2E9, Canada
| | - Roger G. Linington
- Department of Chemistry, Simon Fraser University, 8888 University Drive, Burnaby, BC, V5A 1S6, Canada
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12
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Benyamin MS, Perisin MP, Hellman CA, Schwalm ND, Jahnke JP, Sund CJ. Modeling control and transduction of electrochemical gradients in acid-stressed bacteria. iScience 2023; 26:107140. [PMID: 37404371 PMCID: PMC10316662 DOI: 10.1016/j.isci.2023.107140] [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: 09/15/2022] [Revised: 03/05/2023] [Accepted: 06/12/2023] [Indexed: 07/06/2023] Open
Abstract
Transmembrane electrochemical gradients drive solute uptake and constitute a substantial fraction of the cellular energy pool in bacteria. These gradients act not only as "homeostatic contributors," but also play a dynamic and keystone role in several bacterial functions, including sensing, stress response, and metabolism. At the system level, multiple gradients interact with ion transporters and bacterial behavior in a complex, rapid, and emergent manner; consequently, experiments alone cannot untangle their interdependencies. Electrochemical gradient modeling provides a general framework to understand these interactions and their underlying mechanisms. We quantify the generation, maintenance, and interactions of electrical, proton, and potassium potential gradients under lactic acid-stress and lactic acid fermentation. Further, we elucidate a gradient-mediated mechanism for intracellular pH sensing and stress response. We demonstrate that this gradient model can yield insights on the energetic limitations of membrane transport, and can predict bacterial behavior across changing environments.
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Affiliation(s)
- Marcus S. Benyamin
- Biological and Biotechnology Sciences Division, DEVCOM Army Research Laboratory, Adelphi, MD, USA
| | - Matthew P. Perisin
- Biological and Biotechnology Sciences Division, DEVCOM Army Research Laboratory, Adelphi, MD, USA
| | - Caleb A. Hellman
- Biological and Biotechnology Sciences Division, DEVCOM Army Research Laboratory, Adelphi, MD, USA
| | - Nathan D. Schwalm
- Biological and Biotechnology Sciences Division, DEVCOM Army Research Laboratory, Adelphi, MD, USA
| | - Justin P. Jahnke
- Biological and Biotechnology Sciences Division, DEVCOM Army Research Laboratory, Adelphi, MD, USA
| | - Christian J. Sund
- Biological and Biotechnology Sciences Division, DEVCOM Army Research Laboratory, Adelphi, MD, USA
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13
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Arnold A, Alexander J, Liu G, Stokes JM. Applications of machine learning in microbial natural product drug discovery. Expert Opin Drug Discov 2023; 18:1259-1272. [PMID: 37651150 DOI: 10.1080/17460441.2023.2251400] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2023] [Accepted: 08/21/2023] [Indexed: 09/01/2023]
Abstract
INTRODUCTION Natural products (NPs) are a desirable source of new therapeutics due to their structural diversity and evolutionarily optimized bioactivities. NPs and their derivatives account for roughly 70% of approved pharmaceuticals. However, the rate at which novel NPs are discovered has decreased. To accelerate the microbial NP discovery process, machine learning (ML) is being applied to numerous areas of NP discovery and development. AREAS COVERED This review explores the utility of ML at various phases of the microbial NP drug discovery pipeline, discussing concrete examples throughout each major phase: genome mining, dereplication, and biological target prediction. Moreover, the authors discuss how ML approaches can be applied to semi-synthetic approaches to drug discovery. EXPERT OPINION Despite the important role that microbial NPs play in the development of novel drugs, their discovery has declined due to challenges associated with the conventional discovery process. ML is positioned to overcome these limitations given its ability to model complex datasets and generalize to novel chemical and sequence space. Unsurprisingly, ML comes with its own limitations that must be considered for its successful implementation. The authors stress the importance of continuing to build high quality and open access NP datasets to further increase the utility of ML in NP discovery.
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Affiliation(s)
- Autumn Arnold
- Department of Biochemistry and Biomedical Sciences, McMaster University, Hamilton, OntarioCanada
- Michael G. DeGroote Institute for Infectious Disease Research, McMaster University, Hamilton,Ontario, Canada
- David Braley Centre for Antibiotic Discovery, McMaster University, Hamilton, Ontario Canada
| | - Jeremie Alexander
- Department of Biochemistry and Biomedical Sciences, McMaster University, Hamilton, OntarioCanada
- Michael G. DeGroote Institute for Infectious Disease Research, McMaster University, Hamilton,Ontario, Canada
- David Braley Centre for Antibiotic Discovery, McMaster University, Hamilton, Ontario Canada
| | - Gary Liu
- Department of Biochemistry and Biomedical Sciences, McMaster University, Hamilton, OntarioCanada
- Michael G. DeGroote Institute for Infectious Disease Research, McMaster University, Hamilton,Ontario, Canada
- David Braley Centre for Antibiotic Discovery, McMaster University, Hamilton, Ontario Canada
| | - Jonathan M Stokes
- Department of Biochemistry and Biomedical Sciences, McMaster University, Hamilton, OntarioCanada
- Michael G. DeGroote Institute for Infectious Disease Research, McMaster University, Hamilton,Ontario, Canada
- David Braley Centre for Antibiotic Discovery, McMaster University, Hamilton, Ontario Canada
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14
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Wei B, Hu GA, Zhou ZY, Yu WC, Du AQ, Yang CL, Yu YL, Chen JW, Zhang HW, Wu Q, Xuan Q, Xu XW, Wang H. Global analysis of the biosynthetic chemical space of marine prokaryotes. MICROBIOME 2023; 11:144. [PMID: 37370187 DOI: 10.1186/s40168-023-01573-3] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/13/2023] [Accepted: 05/15/2023] [Indexed: 06/29/2023]
Abstract
BACKGROUND Marine prokaryotes are a rich source of novel bioactive secondary metabolites for drug discovery. Recent genome mining studies have revealed their great potential to bio-synthesize novel secondary metabolites. However, the exact biosynthetic chemical space encoded by the marine prokaryotes has yet to be systematically evaluated. RESULTS We first investigated the secondary metabolic potential of marine prokaryotes by analyzing the diversity and novelty of the biosynthetic gene clusters (BGCs) in 7541 prokaryotic genomes from cultivated and single cells, along with 26,363 newly assembled medium-to-high-quality genomes from marine environmental samples. To quantitatively evaluate the unexplored biosynthetic chemical space of marine prokaryotes, the clustering thresholds for constructing the biosynthetic gene cluster and molecular networks were optimized to reach a similar level of the chemical similarity between the gene cluster family (GCF)-encoded metabolites and molecular family (MF) scaffolds using the MIBiG database. The global genome mining analysis demonstrated that the predicted 70,011 BGCs were organized into 24,536 mostly new (99.5%) GCFs, while the reported marine prokaryotic natural products were only classified into 778 MFs at the optimized clustering thresholds. The number of MF scaffolds is only 3.2% of the number of GCF-encoded scaffolds, suggesting that at least 96.8% of the secondary metabolic potential in marine prokaryotes is untapped. The unexplored biosynthetic chemical space of marine prokaryotes was illustrated by the 88 potential novel antimicrobial peptides encoded by ribosomally synthesized and post-translationally modified peptide BGCs. Furthermore, a sea-water-derived Aquimarina strain was selected to illustrate the diverse biosynthetic chemical space through untargeted metabolomics and genomics approaches, which identified the potential biosynthetic pathways of a group of novel polyketides and two known compounds (didemnilactone B and macrolactin A 15-ketone). CONCLUSIONS The present bioinformatics and cheminformatics analyses highlight the promising potential to explore the biosynthetic chemical diversity of marine prokaryotes and provide valuable knowledge for the targeted discovery and biosynthesis of novel marine prokaryotic natural products. Video Abstract.
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Affiliation(s)
- Bin Wei
- College of Pharmaceutical Science & Collaborative Innovation Center of Yangtze River Delta Region Green Pharmaceuticals, Key Laboratory of Marine Fishery Resources Exploitment & Utilization of Zhejiang Province, Zhejiang University of Technology, Hangzhou, 310014, China
- Key Laboratory of Marine Ecosystem and Biogeochemistry, Ministry of Natural Resources & Second Institute of Oceanography, Ministry of Natural Resources, Hangzhou, 310012, China
| | - Gang-Ao Hu
- College of Pharmaceutical Science & Collaborative Innovation Center of Yangtze River Delta Region Green Pharmaceuticals, Key Laboratory of Marine Fishery Resources Exploitment & Utilization of Zhejiang Province, Zhejiang University of Technology, Hangzhou, 310014, China
| | - Zhen-Yi Zhou
- College of Pharmaceutical Science & Collaborative Innovation Center of Yangtze River Delta Region Green Pharmaceuticals, Key Laboratory of Marine Fishery Resources Exploitment & Utilization of Zhejiang Province, Zhejiang University of Technology, Hangzhou, 310014, China
| | - Wen-Chao Yu
- College of Pharmaceutical Science & Collaborative Innovation Center of Yangtze River Delta Region Green Pharmaceuticals, Key Laboratory of Marine Fishery Resources Exploitment & Utilization of Zhejiang Province, Zhejiang University of Technology, Hangzhou, 310014, China
| | - Ao-Qi Du
- College of Pharmaceutical Science & Collaborative Innovation Center of Yangtze River Delta Region Green Pharmaceuticals, Key Laboratory of Marine Fishery Resources Exploitment & Utilization of Zhejiang Province, Zhejiang University of Technology, Hangzhou, 310014, China
| | - Cai-Ling Yang
- College of Pharmaceutical Science & Collaborative Innovation Center of Yangtze River Delta Region Green Pharmaceuticals, Key Laboratory of Marine Fishery Resources Exploitment & Utilization of Zhejiang Province, Zhejiang University of Technology, Hangzhou, 310014, China
| | - Yan-Lei Yu
- College of Pharmaceutical Science & Collaborative Innovation Center of Yangtze River Delta Region Green Pharmaceuticals, Key Laboratory of Marine Fishery Resources Exploitment & Utilization of Zhejiang Province, Zhejiang University of Technology, Hangzhou, 310014, China
| | - Jian-Wei Chen
- College of Pharmaceutical Science & Collaborative Innovation Center of Yangtze River Delta Region Green Pharmaceuticals, Key Laboratory of Marine Fishery Resources Exploitment & Utilization of Zhejiang Province, Zhejiang University of Technology, Hangzhou, 310014, China
| | - Hua-Wei Zhang
- College of Pharmaceutical Science & Collaborative Innovation Center of Yangtze River Delta Region Green Pharmaceuticals, Key Laboratory of Marine Fishery Resources Exploitment & Utilization of Zhejiang Province, Zhejiang University of Technology, Hangzhou, 310014, China
| | - Qihao Wu
- Department of Chemistry, Institute of Biomolecular Design & Discovery, Yale University, West Haven, CT, 06516, USA
| | - Qi Xuan
- Institute of Cyberspace Security, College of Information Engineering, Zhejiang University of Technology, Hangzhou, 310023, China.
| | - Xue-Wei Xu
- Key Laboratory of Marine Ecosystem and Biogeochemistry, Ministry of Natural Resources & Second Institute of Oceanography, Ministry of Natural Resources, Hangzhou, 310012, China.
| | - Hong Wang
- College of Pharmaceutical Science & Collaborative Innovation Center of Yangtze River Delta Region Green Pharmaceuticals, Key Laboratory of Marine Fishery Resources Exploitment & Utilization of Zhejiang Province, Zhejiang University of Technology, Hangzhou, 310014, China.
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15
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Gaudêncio SP, Bayram E, Lukić Bilela L, Cueto M, Díaz-Marrero AR, Haznedaroglu BZ, Jimenez C, Mandalakis M, Pereira F, Reyes F, Tasdemir D. Advanced Methods for Natural Products Discovery: Bioactivity Screening, Dereplication, Metabolomics Profiling, Genomic Sequencing, Databases and Informatic Tools, and Structure Elucidation. Mar Drugs 2023; 21:md21050308. [PMID: 37233502 DOI: 10.3390/md21050308] [Citation(s) in RCA: 20] [Impact Index Per Article: 20.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2023] [Revised: 05/11/2023] [Accepted: 05/12/2023] [Indexed: 05/27/2023] Open
Abstract
Natural Products (NP) are essential for the discovery of novel drugs and products for numerous biotechnological applications. The NP discovery process is expensive and time-consuming, having as major hurdles dereplication (early identification of known compounds) and structure elucidation, particularly the determination of the absolute configuration of metabolites with stereogenic centers. This review comprehensively focuses on recent technological and instrumental advances, highlighting the development of methods that alleviate these obstacles, paving the way for accelerating NP discovery towards biotechnological applications. Herein, we emphasize the most innovative high-throughput tools and methods for advancing bioactivity screening, NP chemical analysis, dereplication, metabolite profiling, metabolomics, genome sequencing and/or genomics approaches, databases, bioinformatics, chemoinformatics, and three-dimensional NP structure elucidation.
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Affiliation(s)
- Susana P Gaudêncio
- Associate Laboratory i4HB-Institute for Health and Bioeconomy, NOVA School of Science and Technology, NOVA University Lisbon, 2819-516 Caparica, Portugal
- UCIBIO-Applied Molecular Biosciences Unit, Chemistry Department, NOVA School of Science and Technology, NOVA University of Lisbon, 2819-516 Caparica, Portugal
| | - Engin Bayram
- Institute of Environmental Sciences, Room HKC-202, Hisar Campus, Bogazici University, Bebek, Istanbul 34342, Turkey
| | - Lada Lukić Bilela
- Department of Biology, Faculty of Science, University of Sarajevo, 71000 Sarajevo, Bosnia and Herzegovina
| | - Mercedes Cueto
- Instituto de Productos Naturales y Agrobiología-CSIC, 38206 La Laguna, Spain
| | - Ana R Díaz-Marrero
- Instituto de Productos Naturales y Agrobiología-CSIC, 38206 La Laguna, Spain
- Instituto Universitario de Bio-Orgánica (IUBO), Universidad de La Laguna, 38206 La Laguna, Spain
| | - Berat Z Haznedaroglu
- Institute of Environmental Sciences, Room HKC-202, Hisar Campus, Bogazici University, Bebek, Istanbul 34342, Turkey
| | - Carlos Jimenez
- CICA- Centro Interdisciplinar de Química e Bioloxía, Departamento de Química, Facultade de Ciencias, Universidade da Coruña, 15071 A Coruña, Spain
| | - Manolis Mandalakis
- Institute of Marine Biology, Biotechnology and Aquaculture, Hellenic Centre for Marine Research, HCMR Thalassocosmos, 71500 Gournes, Crete, Greece
| | - Florbela Pereira
- LAQV, REQUIMTE, Chemistry Department, NOVA School of Science and Technology, NOVA University of Lisbon, 2819-516 Caparica, Portugal
| | - Fernando Reyes
- Fundación MEDINA, Avda. del Conocimiento 34, 18016 Armilla, Spain
| | - Deniz Tasdemir
- GEOMAR Centre for Marine Biotechnology (GEOMAR-Biotech), Research Unit Marine Natural Products Chemistry, GEOMAR Helmholtz Centre for Ocean Research Kiel, Am Kiel-Kanal 44, 24106 Kiel, Germany
- Faculty of Mathematics and Natural Science, Kiel University, Christian-Albrechts-Platz 4, 24118 Kiel, Germany
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16
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Zhang LH, Gao WK, Li SW, Song XY, Wu HH, Wang HF, Chen G, Wang SX, Pei YH. Santalane-type sesquiterpenoids and isobenzofuranones from cultures of Paraconiothyrium sporulosum YK-03. PHYTOCHEMISTRY 2023; 211:113691. [PMID: 37100221 DOI: 10.1016/j.phytochem.2023.113691] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/30/2022] [Revised: 04/20/2023] [Accepted: 04/21/2023] [Indexed: 05/14/2023]
Abstract
Three undescribed santalane-type sesquiterpenoids (parasantalenoic acids A-C) and two undescribed epimeric isobenzofuranones (paraphthalides A and B) were isolated from cultures of the marine mud-associated fungus Paraconiothyrium sporulosum YK-03. Their structures were elucidated by analysis of the extensive spectroscopic and crystal X-ray diffraction data, combined with ECD calculations and comparison. Santalane-type sesquiterpenoids have been firstly found in the Paraconiothyrium species. Parasantalenoic acids A-C represent three rare polyhydroxylated santalane-type sesquiterpenoid carboxylic acids, and parasantalenoic acid A represents the first example of 2-chlorinated santalane-type sesquiterpenoid. A plausible biosynthetic pathway for parasantalenoic acids A-C was proposed. Additionally, the anti-neuroinflammatory activities of parasantalenoic acids A-C were investigated by evaluating their inhibitory effects on nitric oxide (NO) production in lipopolysaccharide (LPS)-stimulated BV-2 microglia cells. Among them, parasantalenoic acid C showed significant anti-neuroinflammatory activity with an inhibition of 86.45 ± 2.45% at 10 μM.
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Affiliation(s)
- Li-Hua Zhang
- State Key Laboratory of Component-based Chinese Medicine, Institute of Traditional Chinese Medicine, Tianjin University of Traditional Chinese Medicine, Tianjin, 301617, People's Republic of China
| | - Wen-Ke Gao
- State Key Laboratory of Component-based Chinese Medicine, Institute of Traditional Chinese Medicine, Tianjin University of Traditional Chinese Medicine, Tianjin, 301617, People's Republic of China
| | - Shi-Wei Li
- State Key Laboratory of Component-based Chinese Medicine, Institute of Traditional Chinese Medicine, Tianjin University of Traditional Chinese Medicine, Tianjin, 301617, People's Republic of China
| | - Xiao-Yan Song
- State Key Laboratory of Component-based Chinese Medicine, Institute of Traditional Chinese Medicine, Tianjin University of Traditional Chinese Medicine, Tianjin, 301617, People's Republic of China
| | - Hong-Hua Wu
- State Key Laboratory of Component-based Chinese Medicine, Institute of Traditional Chinese Medicine, Tianjin University of Traditional Chinese Medicine, Tianjin, 301617, People's Republic of China
| | - Hai-Feng Wang
- Key Laboratory of Structure-Based Drug Design & Discovery, Ministry of Education, School of Traditional Chinese Materia Medica, Shenyang Pharmaceutical University, Shenyang, 110016, People's Republic of China
| | - Gang Chen
- Key Laboratory of Structure-Based Drug Design & Discovery, Ministry of Education, School of Traditional Chinese Materia Medica, Shenyang Pharmaceutical University, Shenyang, 110016, People's Republic of China
| | - Shao-Xia Wang
- School of Integrative Medicine, Tianjin University of Traditional Chinese Medicine, Tianjin, 301617, People's Republic of China
| | - Yue-Hu Pei
- Department of Medicinal Chemistry and Natural Medicine Chemistry, College of Pharmacy, Harbin Medical University, Harbin, 150081, People's Republic of China.
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17
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Baranova AA, Alferova VA, Korshun VA, Tyurin AP. Modern Trends in Natural Antibiotic Discovery. Life (Basel) 2023; 13:1073. [PMID: 37240718 PMCID: PMC10221674 DOI: 10.3390/life13051073] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2023] [Revised: 04/10/2023] [Accepted: 04/21/2023] [Indexed: 05/28/2023] Open
Abstract
Natural scaffolds remain an important basis for drug development. Therefore, approaches to natural bioactive compound discovery attract significant attention. In this account, we summarize modern and emerging trends in the screening and identification of natural antibiotics. The methods are divided into three large groups: approaches based on microbiology, chemistry, and molecular biology. The scientific potential of the methods is illustrated with the most prominent and recent results.
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Affiliation(s)
- Anna A. Baranova
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Miklukho-Maklaya 16/10, 117997 Moscow, Russia; (A.A.B.); (V.A.A.)
- Gause Institute of New Antibiotics, Bolshaya Pirogovskaya 11, 119021 Moscow, Russia
| | - Vera A. Alferova
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Miklukho-Maklaya 16/10, 117997 Moscow, Russia; (A.A.B.); (V.A.A.)
- Gause Institute of New Antibiotics, Bolshaya Pirogovskaya 11, 119021 Moscow, Russia
| | - Vladimir A. Korshun
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Miklukho-Maklaya 16/10, 117997 Moscow, Russia; (A.A.B.); (V.A.A.)
| | - Anton P. Tyurin
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Miklukho-Maklaya 16/10, 117997 Moscow, Russia; (A.A.B.); (V.A.A.)
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18
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Cai P, Liu S, Zhang D, Xing H, Han M, Liu D, Gong L, Hu QN. SynBioTools: a one-stop facility for searching and selecting synthetic biology tools. BMC Bioinformatics 2023; 24:152. [PMID: 37069545 PMCID: PMC10111727 DOI: 10.1186/s12859-023-05281-5] [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: 01/09/2023] [Accepted: 04/11/2023] [Indexed: 04/19/2023] Open
Abstract
BACKGROUND The rapid development of synthetic biology relies heavily on the use of databases and computational tools, which are also developing rapidly. While many tool registries have been created to facilitate tool retrieval, sharing, and reuse, no relatively comprehensive tool registry or catalog addresses all aspects of synthetic biology. RESULTS We constructed SynBioTools, a comprehensive collection of synthetic biology databases, computational tools, and experimental methods, as a one-stop facility for searching and selecting synthetic biology tools. SynBioTools includes databases, computational tools, and methods extracted from reviews via SCIentific Table Extraction, a scientific table-extraction tool that we built. Approximately 57% of the resources that we located and included in SynBioTools are not mentioned in bio.tools, the dominant tool registry. To improve users' understanding of the tools and to enable them to make better choices, the tools are grouped into nine modules (each with subdivisions) based on their potential biosynthetic applications. Detailed comparisons of similar tools in every classification are included. The URLs, descriptions, source references, and the number of citations of the tools are also integrated into the system. CONCLUSIONS SynBioTools is freely available at https://synbiotools.lifesynther.com/ . It provides end-users and developers with a useful resource of categorized synthetic biology databases, tools, and methods to facilitate tool retrieval and selection.
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Affiliation(s)
- Pengli Cai
- 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
| | - Sheng Liu
- 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
| | - Dachuan Zhang
- Ecological Systems Design, Institute of Environmental Engineering, ETH Zurich, 8093, Zurich, Switzerland
| | - 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
| | - Mengying Han
- 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
| | - Dongliang Liu
- 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
| | - Linlin Gong
- 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
| | - Qian-Nan Hu
- 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.
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19
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Seyler LM, Kraus EA, McLean C, Spear JR, Templeton AS, Schrenk MO. An untargeted exometabolomics approach to characterize dissolved organic matter in groundwater of the Samail Ophiolite. Front Microbiol 2023; 14:1093372. [PMID: 36970670 PMCID: PMC10033605 DOI: 10.3389/fmicb.2023.1093372] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2022] [Accepted: 01/23/2023] [Indexed: 03/11/2023] Open
Abstract
The process of serpentinization supports life on Earth and gives rise to the habitability of other worlds in our Solar System. While numerous studies have provided clues to the survival strategies of microbial communities in serpentinizing environments on the modern Earth, characterizing microbial activity in such environments remains challenging due to low biomass and extreme conditions. Here, we used an untargeted metabolomics approach to characterize dissolved organic matter in groundwater in the Samail Ophiolite, the largest and best characterized example of actively serpentinizing uplifted ocean crust and mantle. We found that dissolved organic matter composition is strongly correlated with both fluid type and microbial community composition, and that the fluids that were most influenced by serpentinization contained the greatest number of unique compounds, none of which could be identified using the current metabolite databases. Using metabolomics in conjunction with metagenomic data, we detected numerous products and intermediates of microbial metabolic processes and identified potential biosignatures of microbial activity, including pigments, porphyrins, quinones, fatty acids, and metabolites involved in methanogenesis. Metabolomics techniques like the ones used in this study may be used to further our understanding of life in serpentinizing environments, and aid in the identification of biosignatures that can be used to search for life in serpentinizing systems on other worlds.
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Affiliation(s)
- Lauren M. Seyler
- Department of Earth and Environmental Sciences, Michigan State University, East Lansing, MI, United States
- Biology Program, School of Natural Sciences and Mathematics, Stockton University, Galloway, NJ, United States
- Blue Marble Space Institute of Science, Seattle, WA, United States
- *Correspondence: Lauren M. Seyler,
| | - Emily A. Kraus
- Department of Civil and Environmental Engineering, Colorado School of Mines, Golden, CO, United States
- Department of Environmental Engineering, University of Colorado, Boulder, Boulder, CO, United States
| | - Craig McLean
- Massachusetts Institute of Technology, Cambridge, MA, United States
| | - John R. Spear
- Department of Civil and Environmental Engineering, Colorado School of Mines, Golden, CO, United States
| | - Alexis S. Templeton
- Department of Geological Sciences, University of Colorado, Boulder, Boulder, CO, United States
| | - Matthew O. Schrenk
- Department of Earth and Environmental Sciences, Michigan State University, East Lansing, MI, United States
- Department of Microbiology and Molecular Genetics, Michigan State University, East Lansing, MI, United States
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20
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Abstract
Covering: January to December 2021This review covers the literature published in 2021 for marine natural products (MNPs), with 736 citations (724 for the period January to December 2021) referring to compounds isolated from marine microorganisms and phytoplankton, green, brown and red algae, sponges, cnidarians, bryozoans, molluscs, tunicates, echinoderms, mangroves and other intertidal plants and microorganisms. The emphasis is on new compounds (1425 in 416 papers for 2021), together with the relevant biological activities, source organisms and country of origin. Pertinent reviews, biosynthetic studies, first syntheses, and syntheses that led to the revision of structures or stereochemistries, have been included. An analysis of the number of authors, their affiliations, domestic and international collection locations, focus of MNP studies, citation metrics and journal choices is discussed.
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Affiliation(s)
- Anthony R Carroll
- School of Environment and Science, Griffith University, Gold Coast, Australia. .,Griffith Institute for Drug Discovery, Griffith University, Brisbane, Australia
| | - Brent R Copp
- School of Chemical Sciences, University of Auckland, Auckland, New Zealand
| | - Rohan A Davis
- Griffith Institute for Drug Discovery, Griffith University, Brisbane, Australia.,School of Enivironment and Science, Griffith University, Brisbane, Australia
| | - Robert A Keyzers
- Centre for Biodiscovery, and School of Chemical and Physical Sciences, Victoria University of Wellington, Wellington, New Zealand
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21
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Moore SJ, Lai HE, Li J, Freemont PS. Streptomyces cell-free systems for natural product discovery and engineering. Nat Prod Rep 2023; 40:228-236. [PMID: 36341536 PMCID: PMC9945932 DOI: 10.1039/d2np00057a] [Citation(s) in RCA: 11] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2022] [Indexed: 11/09/2022]
Abstract
Streptomyces bacteria are a major microbial source of natural products, which are encoded within so-called biosynthetic gene clusters (BGCs). This highlight discusses the emergence of native Streptomyces cell-free systems as a new tool to accelerate the study of the fundamental chemistry and biology of natural product biosynthesis from these bacteria. Cell-free systems provide a prototyping platform to study plug-and-play reactions in microscale reactions. So far, Streptomyces cell-free systems have been used to rapidly characterise gene expression regulation, access secondary metabolite biosynthetic enzymes, and catalyse cell-free transcription, translation, and biosynthesis of example natural products. With further progress, we anticipate the development of more complex systems to complement existing experimental tools for the discovery and engineering of natural product biosynthesis from Streptomyces and related high G + C (%) bacteria.
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Affiliation(s)
- Simon J Moore
- School of Biosciences, University of Kent, UK
- School of Biological and Behavioural Sciences, Queen Mary University of London, UK.
| | - Hung-En Lai
- School of Biological Sciences, Victoria University of Wellington, New Zealand
| | - Jian Li
- School of Physical Science and Technology, ShanghaiTech University, China
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22
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Zhang L, Wang C, Chen K, Zhong W, Xu Y, Molnár I. Engineering the biosynthesis of fungal nonribosomal peptides. Nat Prod Rep 2023; 40:62-88. [PMID: 35796260 DOI: 10.1039/d2np00036a] [Citation(s) in RCA: 17] [Impact Index Per Article: 17.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]
Abstract
Covering: 2011 up to the end of 2021.Fungal nonribosomal peptides (NRPs) and the related polyketide-nonribosomal peptide hybrid products (PK-NRPs) are a prolific source of bioactive compounds, some of which have been developed into essential drugs. The synthesis of these complex natural products (NPs) utilizes nonribosomal peptide synthetases (NRPSs), multidomain megaenzymes that assemble specific peptide products by sequential condensation of amino acids and amino acid-like substances, independent of the ribosome. NRPSs, collaborating polyketide synthase modules, and their associated tailoring enzymes involved in product maturation represent promising targets for NP structure diversification and the generation of small molecule unnatural products (uNPs) with improved or novel bioactivities. Indeed, reprogramming of NRPSs and recruiting of novel tailoring enzymes is the strategy by which nature evolves NRP products. The recent years have witnessed a rapid development in the discovery and identification of novel NRPs and PK-NRPs, and significant advances have also been made towards the engineering of fungal NRP assembly lines to generate uNP peptides. However, the intrinsic complexities of fungal NRP and PK-NRP biosynthesis, and the large size of the NRPSs still present formidable conceptual and technical challenges for the rational and efficient reprogramming of these pathways. This review examines key examples for the successful (and for some less-successful) re-engineering of fungal NRPS assembly lines to inform future efforts towards generating novel, biologically active peptides and PK-NRPs.
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Affiliation(s)
- Liwen Zhang
- Biotechnology Research Institute, The Chinese Academy of Agricultural Sciences, 12 Zhongguancun South Street, Beijing 100081, P. R. China.
| | - Chen Wang
- Biotechnology Research Institute, The Chinese Academy of Agricultural Sciences, 12 Zhongguancun South Street, Beijing 100081, P. R. China.
| | - Kang Chen
- Biotechnology Research Institute, The Chinese Academy of Agricultural Sciences, 12 Zhongguancun South Street, Beijing 100081, P. R. China.
| | - Weimao Zhong
- Southwest Center for Natural Products Research, University of Arizona, 250 E. Valencia Rd., Tucson, AZ 85706, USA
| | - Yuquan Xu
- Biotechnology Research Institute, The Chinese Academy of Agricultural Sciences, 12 Zhongguancun South Street, Beijing 100081, P. R. China.
| | - István Molnár
- Southwest Center for Natural Products Research, University of Arizona, 250 E. Valencia Rd., Tucson, AZ 85706, USA.,VTT Technical Research Centre of Finland, P.O. Box 1000, FI-02044 VTT, Espoo, Finland.
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23
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Stallforth P, Mittag M, Brakhage AA, Hertweck C, Hellmich UA. Functional modulation of chemical mediators in microbial communities. Trends Biochem Sci 2023; 48:71-81. [PMID: 35981931 DOI: 10.1016/j.tibs.2022.07.006] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2022] [Revised: 07/14/2022] [Accepted: 07/20/2022] [Indexed: 12/27/2022]
Abstract
Interactions between microorganisms are often mediated by specialized metabolites. Although the structures and biosynthesis of these compounds may have been elucidated, microbes exist within complex microbiomes and chemical signals can thus also be subject to community-dependent modifications. Increasingly powerful chemical and biological tools allow to shed light on this poorly understood aspect of chemical ecology. We provide an overview of loss-of-function and gain-of-function chemical mediator (CM) modifications within microbial multipartner relationships. Although loss-of-function modifications are abundant in the literature, few gain-of-function modifications have been described despite their important role in microbial interactions. Research in this field holds great potential for our understanding of microbial interactions and may also provide novel tools for targeted interference with microbial signaling.
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Affiliation(s)
- Pierre Stallforth
- Leibniz Institute for Natural Product Research and Infection Biology - Hans-Knöll Institute, Beutenbergstrasse 11a, 07745 Jena, Germany; Friedrich Schiller University Jena, Faculty of Chemistry and Earth Sciences, Institute of Organic Chemistry and Macromolecular Chemistry, Humboldtstrasse 10, 07743 Jena, Germany.
| | - Maria Mittag
- Matthias Schleiden Institute of Genetics, Bioinformatics and Molecular Botany, Friedrich Schiller University Jena, 07743 Jena, Germany
| | - Axel A Brakhage
- Leibniz Institute for Natural Product Research and Infection Biology - Hans-Knöll Institute, Beutenbergstrasse 11a, 07745 Jena, Germany; Institute of Microbiology, Friedrich Schiller University Jena, 07743 Jena, Germany
| | - Christian Hertweck
- Leibniz Institute for Natural Product Research and Infection Biology - Hans-Knöll Institute, Beutenbergstrasse 11a, 07745 Jena, Germany; Institute of Microbiology, Friedrich Schiller University Jena, 07743 Jena, Germany
| | - Ute A Hellmich
- Friedrich Schiller University Jena, Faculty of Chemistry and Earth Sciences, Institute of Organic Chemistry and Macromolecular Chemistry, Humboldtstrasse 10, 07743 Jena, Germany; Centre for Biomolecular Magnetic Resonance (BMRZ), Goethe-University Frankfurt, Max-von-Laue-Strasse 9, 60438 Frankfurt, Germany.
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24
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Moschny J, Daletos G, Proksch P, Hughes CC. Structure Elucidation of Antibiotics. Methods Mol Biol 2023; 2601:97-122. [PMID: 36445581 DOI: 10.1007/978-1-0716-2855-3_6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/16/2023]
Abstract
To date, there are hundreds of characterized natural products with antibacterial activity against pathogenic bacteria, and several have become bonafide antibiotic drugs. The development of antibacterial natural products into antibiotic drugs, both in the past and in the future, hinges upon an accurate description of the exact chemical structure of the compound. Bolstered by some form of mass spectrometry (MS), nuclear magnetic resonance (NMR) spectroscopy is the primary technique for elucidating the chemical structure of organic molecules including natural products. By combining various one-dimensional (1D) and two-dimensional (2D) experiments, the connectivity between atoms is established and a complete "picture" of the molecule is thereby revealed.
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Affiliation(s)
- Julia Moschny
- Department of Microbial Bioactive Compounds, Interfaculty Institute of Microbiology and Infection Medicine, University of Tübingen, Tübingen, Germany
| | - Georgios Daletos
- Institute of Pharmaceutical Biology and Biotechnology, Heinrich-Heine-University, Düsseldorf, Germany
| | - Peter Proksch
- Institute of Pharmaceutical Biology and Biotechnology, Heinrich-Heine-University, Düsseldorf, Germany
| | - Chambers C Hughes
- Department of Microbial Bioactive Compounds, Interfaculty Institute of Microbiology and Infection Medicine, University of Tübingen, Tübingen, Germany.
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25
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de Medeiros LS, de Araújo Júnior MB, Peres EG, da Silva JCI, Bassicheto MC, Di Gioia G, Veiga TAM, Koolen HHF. Discovering New Natural Products Using Metabolomics-Based Approaches. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2023; 1439:185-224. [PMID: 37843810 DOI: 10.1007/978-3-031-41741-2_8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/17/2023]
Abstract
The incessant search for new natural molecules with biological activities has forced researchers in the field of chemistry of natural products to seek different approaches for their prospection studies. In particular, researchers around the world are turning to approaches in metabolomics to avoid high rates of re-isolation of certain compounds, something recurrent in this branch of science. Thanks to the development of new technologies in the analytical instrumentation of spectroscopic and spectrometric techniques, as well as the advance in the computational processing modes of the results, metabolomics has been gaining more and more space in studies that involve the prospection of natural products. Thus, this chapter summarizes the precepts and good practices in the metabolomics of microbial natural products using mass spectrometry and nuclear magnetic resonance spectroscopy, and also summarizes several examples where this approach has been applied in the discovery of bioactive molecules.
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Affiliation(s)
- Lívia Soman de Medeiros
- Grupo de Pesquisas LaBiORG - Laboratório de Química Bio-orgânica Otto Richard Gottlieb, Universidade Federal de São Paulo, Diadema, Brazil.
| | - Moysés B de Araújo Júnior
- Grupo de Pesquisa em Metabolômica e Espectrometria de Massas, Universidade do Estado do Amazonas, Manaus, Brazil
| | - Eldrinei G Peres
- Grupo de Pesquisa em Metabolômica e Espectrometria de Massas, Universidade do Estado do Amazonas, Manaus, Brazil
| | | | - Milena Costa Bassicheto
- Grupo de Pesquisas LaBiORG - Laboratório de Química Bio-orgânica Otto Richard Gottlieb, Universidade Federal de São Paulo, Diadema, Brazil
| | - Giordanno Di Gioia
- Grupo de Pesquisas LaBiORG - Laboratório de Química Bio-orgânica Otto Richard Gottlieb, Universidade Federal de São Paulo, Diadema, Brazil
| | - Thiago André Moura Veiga
- Grupo de Pesquisas LaBiORG - Laboratório de Química Bio-orgânica Otto Richard Gottlieb, Universidade Federal de São Paulo, Diadema, Brazil
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26
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Sahayasheela VJ, Lankadasari MB, Dan VM, Dastager SG, Pandian GN, Sugiyama H. Artificial intelligence in microbial natural product drug discovery: current and emerging role. Nat Prod Rep 2022; 39:2215-2230. [PMID: 36017693 PMCID: PMC9931531 DOI: 10.1039/d2np00035k] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
Covering: up to the end of 2022Microorganisms are exceptional sources of a wide array of unique natural products and play a significant role in drug discovery. During the golden era, several life-saving antibiotics and anticancer agents were isolated from microbes; moreover, they are still widely used. However, difficulties in the isolation methods and repeated discoveries of the same molecules have caused a setback in the past. Artificial intelligence (AI) has had a profound impact on various research fields, and its application allows the effective performance of data analyses and predictions. With the advances in omics, it is possible to obtain a wealth of information for the identification, isolation, and target prediction of secondary metabolites. In this review, we discuss drug discovery based on natural products from microorganisms with the help of AI and machine learning.
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Affiliation(s)
- Vinodh J Sahayasheela
- Department of Chemistry, Graduate School of Science, Kyoto University, Kitashirakawa-Oiwakecho, Sakyo-Ku, Kyoto 606-8502, Japan.
| | - Manendra B Lankadasari
- Thoracic Service, Department of Surgery, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
| | - Vipin Mohan Dan
- Microbiology Division, Jawaharlal Nehru Tropical Botanic Garden and Research Institute, Thiruvananthapuram, Kerala, India
| | - Syed G Dastager
- NCIM Resource Centre, Division of Biochemical Sciences, CSIR - National Chemical Laboratory, Pune, Maharashtra, India
| | - Ganesh N Pandian
- Institute for Integrated Cell-Material Sciences (WPI-iCeMS), Kyoto University, Yoshida-Ushinomaecho, Sakyo-Ku, Kyoto 606-8501, Japan
| | - Hiroshi Sugiyama
- Department of Chemistry, Graduate School of Science, Kyoto University, Kitashirakawa-Oiwakecho, Sakyo-Ku, Kyoto 606-8502, Japan.
- Institute for Integrated Cell-Material Sciences (WPI-iCeMS), Kyoto University, Yoshida-Ushinomaecho, Sakyo-Ku, Kyoto 606-8501, Japan
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27
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Avalon NE, Murray AE, Baker BJ. Integrated Metabolomic-Genomic Workflows Accelerate Microbial Natural Product Discovery. Anal Chem 2022; 94:11959-11966. [PMID: 35994737 PMCID: PMC9453739 DOI: 10.1021/acs.analchem.2c02245] [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] [Indexed: 11/29/2022]
Abstract
The pairing of analytical chemistry with genomic techniques represents a new wave in natural product chemistry. With an increase in the availability of sequencing and assembly of microbial genomes, interrogation into the biosynthetic capability of producers with valuable secondary metabolites is possible. However, without the development of robust, accessible, and medium to high throughput tools, the bottleneck in pairing metabolic potential and compound isolation will continue. Several innovative approaches have proven useful in the nascent stages of microbial genome-informed drug discovery. Here, we consider a number of these approaches which have led to prioritization of strain targets and have mitigated rediscovery rates. Likewise, we discuss integration of principles of comparative evolutionary studies and retrobiosynthetic predictions to better understand biosynthetic mechanistic details and link genome sequence to structure. Lastly, we discuss advances in engineering, chemistry, and molecular networking and other computational approaches that are accelerating progress in the field of omic-informed natural product drug discovery. Together, these strategies enhance the synergy between cutting edge omics, chemical characterization, and computational technologies that pitch the discovery of natural products with pharmaceutical and other potential applications to the crest of the wave where progress is ripe for rapid advances.
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Affiliation(s)
- Nicole E Avalon
- Department of Chemistry, University of South Florida, Tampa, Florida 33620, United States
| | - Alison E Murray
- Division of Earth and Ecosystem Sciences, Desert Research Institute, Reno, Nevada 89512, United States
| | - Bill J Baker
- Department of Chemistry, University of South Florida, Tampa, Florida 33620, United States
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28
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A Candidate Gene Cluster for the Bioactive Natural Product Gyrophoric Acid in Lichen-Forming Fungi. Microbiol Spectr 2022; 10:e0010922. [PMID: 35867425 PMCID: PMC9430680 DOI: 10.1128/spectrum.00109-22] [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] [Indexed: 12/22/2022] Open
Abstract
Natural products of lichen-forming fungi are structurally diverse and have a variety of medicinal properties. Despite this, they have limited implementation in industry mostly because the corresponding genes are unknown for most of their natural products. Here, we implement a long-read sequencing and bioinformatic approach to identify the putative biosynthetic gene cluster of the bioactive natural product gyrophoric acid (GA). Using 15 high-quality genomes representing nine GA-producing species of the lichen-forming fungal genus Umbilicaria, we identify the most likely GA cluster and investigate the cluster gene organization and composition across the nine species. Our results show that GA clusters are promiscuous within Umbilicaria, and only three genes are conserved across species, including the polyketide synthase (PKS) gene. In addition, our results suggest that the same cluster codes for different, but structurally similar compounds, namely, GA, umbilicaric-, and hiascic acid, bringing new evidence that lichen metabolite diversity is also generated through regulatory mechanisms at the molecular level. Ours is the first study to identify the most likely GA cluster and, thus, provides essential information to open new avenues for biotechnological approaches to producing and modifying GA and similar lichen-derived compounds. GA PKS is the first tridepside PKS to be identified. IMPORTANCE The implementation of natural products in the pharmaceutical industry relies on the possibility of modifying the natural product (NP) pathway to optimize yields and pharmacological effects. Characterization of genes and pathways underlying natural product biosynthesis is a major bottleneck for exploiting the medicinal properties of the natural products. Genome mining is a promising and relatively cost- and time-effective approach to utilize unexplored NP resources for drug discovery. In this study, we identify the most likely gene cluster for the lichen-forming fungal depside gyrophoric acid in nine Umbilicaria species. This compound shows cytotoxic and antiproliferative properties against several cancer cell lines and is also a broad-spectrum antimicrobial agent. This information paves the way for generating GA analogs with modified properties by selective activation/deactivation of genes.
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29
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Brinkmann S, Kurz M, Patras MA, Hartwig C, Marner M, Leis B, Billion A, Kleiner Y, Bauer A, Toti L, Pöverlein C, Hammann PE, Vilcinskas A, Glaeser J, Spohn M, Schäberle TF. Genomic and Chemical Decryption of the Bacteroidetes Phylum for Its Potential to Biosynthesize Natural Products. Microbiol Spectr 2022; 10:e0247921. [PMID: 35442080 PMCID: PMC9248904 DOI: 10.1128/spectrum.02479-21] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2021] [Accepted: 03/29/2022] [Indexed: 12/04/2022] Open
Abstract
With progress in genome sequencing and data sharing, 1,000s of bacterial genomes are publicly available. Genome mining-using bioinformatics tools in terms of biosynthetic gene cluster (BGC) identification, analysis, and rating-has become a key technology to explore the capabilities for natural product (NP) biosynthesis. Comprehensively, analyzing the genetic potential of the phylum Bacteroidetes revealed Chitinophaga as the most talented genus in terms of BGC abundance and diversity. Guided by the computational predictions, we conducted a metabolomics and bioactivity driven NP discovery program on 25 Chitinophaga strains. High numbers of strain-specific metabolite buckets confirmed the upfront predicted biosynthetic potential and revealed a tremendous uncharted chemical space. Mining this data set, we isolated the new iron chelating nonribosomally synthesized cyclic tetradeca- and pentadecalipodepsipeptide antibiotics chitinopeptins with activity against Candida, produced by C. eiseniae DSM 22224 and C. flava KCTC 62435, respectively. IMPORTANCE The development of pipelines for anti-infectives to be applied in plant, animal, and human health management are dried up. However, the resistance development against compounds in use calls for new lead structures. To fill this gap and to enhance the probability of success for the discovery of new bioactive natural products, microbial taxa currently underinvestigated must be mined. This study investigates the potential within the bacterial phylum Bacteroidetes. A combination of omics-technologies revealed taxonomical hot spots for specialized metabolites. Genome- and metabolome-based analyses showed that the phylum covers a new chemical space compared with classic natural product producers. Members of the Bacteroidetes may thus present a promising bioresource for future screening and isolation campaigns.
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Affiliation(s)
- Stephan Brinkmann
- Fraunhofer Institute for Molecular Biology and Applied Ecology (IME), Branch for Bioresources, Giessen, Germany
| | - Michael Kurz
- Sanofi-Aventis Deutschland GmbH, Frankfurt am Main, Germany
| | - Maria A. Patras
- Fraunhofer Institute for Molecular Biology and Applied Ecology (IME), Branch for Bioresources, Giessen, Germany
| | - Christoph Hartwig
- Fraunhofer Institute for Molecular Biology and Applied Ecology (IME), Branch for Bioresources, Giessen, Germany
| | - Michael Marner
- Fraunhofer Institute for Molecular Biology and Applied Ecology (IME), Branch for Bioresources, Giessen, Germany
| | - Benedikt Leis
- Fraunhofer Institute for Molecular Biology and Applied Ecology (IME), Branch for Bioresources, Giessen, Germany
| | - André Billion
- Fraunhofer Institute for Molecular Biology and Applied Ecology (IME), Branch for Bioresources, Giessen, Germany
| | - Yolanda Kleiner
- Fraunhofer Institute for Molecular Biology and Applied Ecology (IME), Branch for Bioresources, Giessen, Germany
| | - Armin Bauer
- Sanofi-Aventis Deutschland GmbH, Frankfurt am Main, Germany
| | - Luigi Toti
- Sanofi-Aventis Deutschland GmbH, Frankfurt am Main, Germany
| | | | | | - Andreas Vilcinskas
- Fraunhofer Institute for Molecular Biology and Applied Ecology (IME), Branch for Bioresources, Giessen, Germany
- Institute for Insect Biotechnology, Justus-Liebig-University Giessen, Giessen, Germany
| | - Jens Glaeser
- Fraunhofer Institute for Molecular Biology and Applied Ecology (IME), Branch for Bioresources, Giessen, Germany
- Evotec International GmbH, Göttingen, Germany
| | - Marius Spohn
- Fraunhofer Institute for Molecular Biology and Applied Ecology (IME), Branch for Bioresources, Giessen, Germany
| | - Till F. Schäberle
- Fraunhofer Institute for Molecular Biology and Applied Ecology (IME), Branch for Bioresources, Giessen, Germany
- Institute for Insect Biotechnology, Justus-Liebig-University Giessen, Giessen, Germany
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30
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Chen S, Zhang C, Zhang L. Investigation of the Molecular Landscape of Bacterial Aromatic Polyketides by Global Analysis of Type II Polyketide Synthases. Angew Chem Int Ed Engl 2022; 61:e202202286. [PMID: 35384223 DOI: 10.1002/anie.202202286] [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: 02/11/2022] [Indexed: 12/17/2022]
Abstract
Aromatic polyketides biosynthesized by microorganisms are a prominent class of natural products widely used in clinical treatments. Although genome mining approaches have accelerated the discovery of these molecules, the molecular diversity, abundance, and distribution of bacterial aromatic polyketides at a global scale remain elusive. Here, we provide a global atlas of bacterial aromatic polyketides based on large-scale analysis of type II polyketide synthases. We first established the chain length factor protein as a marker that can predict both chemical class and molecular uniqueness of the biosynthetic product, and analyzed the abundance, taxonomic distribution, estimated structural diversity, and the total number of aromatic polyketides in bacteria. We further show the identification of oryzanaphthopyrans with an unprecedented angular naphthopyran scaffold from a rare actinobacterium by genome mining guided by the global atlas. These results serve as a compass for exploiting the entire type II polyketide synthase-derived aromatic polyketides in bacteria.
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Affiliation(s)
- Shanchong Chen
- Department of Chemistry, Zhejiang University, Hangzhou, 310027, Zhejiang Province, China.,Key Laboratory of Precise Synthesis of Functional Molecules of Zhejiang Province, School of Science, Westlake University, 18 Shilongshan Road, Hangzhou, 310024, Zhejiang Province, China
| | - Chi Zhang
- Key Laboratory of Precise Synthesis of Functional Molecules of Zhejiang Province, School of Science, Westlake University, 18 Shilongshan Road, Hangzhou, 310024, Zhejiang Province, China.,Institute of Natural Sciences, Westlake Institute for Advanced Study, 18 Shilongshan Road, Hangzhou, 310024, Zhejiang Province, China
| | - Lihan Zhang
- Key Laboratory of Precise Synthesis of Functional Molecules of Zhejiang Province, School of Science, Westlake University, 18 Shilongshan Road, Hangzhou, 310024, Zhejiang Province, China.,Institute of Natural Sciences, Westlake Institute for Advanced Study, 18 Shilongshan Road, Hangzhou, 310024, Zhejiang Province, China
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31
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Calado R, Mamede R, Cruz S, Leal MC. Updated Trends on the Biodiscovery of New Marine Natural Products from Invertebrates. Mar Drugs 2022; 20:md20060389. [PMID: 35736192 PMCID: PMC9228037 DOI: 10.3390/md20060389] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2022] [Revised: 06/06/2022] [Accepted: 06/07/2022] [Indexed: 01/27/2023] Open
Abstract
From 1990–2019, a total of 15,442 New Marine Natural Products from Invertebrates (NMNPIs) were reported. The 2010s saw the most prolific decade of biodiscovery, with 5630 NMNPIs recorded. The phyla that contributed most biomolecules were the Porifera (sponges) (47.2%, 2659 NMNPIs) and the Cnidaria (35.3%, 1989 NMNPIs). The prevalence of these two phyla as the main sources of NMNPIs became more pronounced in the 2010s. The tropical areas of the Pacific Ocean yielded more NMNPIs, most likely due to the remarkable biodiversity of coral reefs. The Indo-Burma biodiversity hotspot (BH) was the most relevant area for the biodiscovery of NMNPIs in the 2010s, accounting for nearly one-third (1819 NMNPIs) of the total and surpassing the top BH from the 1990s and the 2000s (the Sea of Japan and the Caribbean Islands, respectively). The Chinese exclusive economic zone (EEZ) alone contributed nearly one-quarter (24.7%) of all NMNPIs recorded during the 2010s, displacing Japan’s leading role from the 1990s and the 2000s. With the biodiscovery of these biomolecules steadily decreasing since 2012, it is uncertain whether this decline has been caused by lower bioprospecting efforts or the potential exhaustion of chemodiversity from traditional marine invertebrate sources.
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Chen S, Zhang C, Zhang L. Investigation of the Molecular Landscape of Bacterial Aromatic Polyketides by Global Analysis of Type II Polyketide Synthases. Angew Chem Int Ed Engl 2022. [DOI: 10.1002/ange.202202286] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
Affiliation(s)
- Shanchong Chen
- Zhejiang University Department of Chemistry Hangzhou CHINA
| | - Chi Zhang
- Westlake University School of Science Hangzhou CHINA
| | - Lihan Zhang
- Westlake University School of Science Shilongshan Rd.18Xihu District 310024 Hangzhou CHINA
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33
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Biosynthesis of Fungal Natural Products Involving Two Separate Pathway Crosstalk. J Fungi (Basel) 2022; 8:jof8030320. [PMID: 35330322 PMCID: PMC8948627 DOI: 10.3390/jof8030320] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2022] [Revised: 03/17/2022] [Accepted: 03/17/2022] [Indexed: 01/21/2023] Open
Abstract
Fungal natural products (NPs) usually possess complicated structures, exhibit satisfactory bioactivities, and are an outstanding source of drug leads, such as the cholesterol-lowering drug lovastatin and the immunosuppressive drug mycophenolic acid. The fungal NPs biosynthetic genes are always arranged within one single biosynthetic gene cluster (BGC). However, a rare but fascinating phenomenon that a crosstalk between two separate BGCs is indispensable to some fungal dimeric NPs biosynthesis has attracted increasing attention. The hybridization of two separate BGCs not only increases the structural complexity and chemical diversity of fungal NPs, but also expands the scope of bioactivities. More importantly, the underlying mechanism for this hybridization process is poorly understood and needs further exploration, especially the determination of BGCs for each building block construction and the identification of enzyme(s) catalyzing the two biosynthetic precursors coupling processes such as Diels–Alder cycloaddition and Michael addition. In this review, we summarized the fungal NPs produced by functional crosstalk of two discrete BGCs, and highlighted their biosynthetic processes, which might shed new light on genome mining for fungal NPs with unprecedented frameworks, and provide valuable insights into the investigation of mysterious biosynthetic mechanisms of fungal dimeric NPs which are constructed by collaboration of two separate BGCs.
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34
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Saati-Santamaría Z, Selem-Mojica N, Peral-Aranega E, Rivas R, García-Fraile P. Unveiling the genomic potential of Pseudomonas type strains for discovering new natural products. Microb Genom 2022; 8:000758. [PMID: 35195510 PMCID: PMC8942027 DOI: 10.1099/mgen.0.000758] [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: 06/08/2021] [Accepted: 12/07/2021] [Indexed: 12/20/2022] Open
Abstract
Microbes host a huge variety of biosynthetic gene clusters that produce an immeasurable array of secondary metabolites with many different biological activities such as antimicrobial, anticarcinogenic and antiviral. Despite the complex task of isolating and characterizing novel natural products, microbial genomic strategies can be useful for carrying out these types of studies. However, although genomic-based research on secondary metabolism is on the increase, there is still a lack of reports focusing specifically on the genus Pseudomonas. In this work, we aimed (i) to unveil the main biosynthetic systems related to secondary metabolism in Pseudomonas type strains, (ii) to study the evolutionary processes that drive the diversification of their coding regions and (iii) to select Pseudomonas strains showing promising results in the search for useful natural products. We performed a comparative genomic study on 194 Pseudomonas species, paying special attention to the evolution and distribution of different classes of biosynthetic gene clusters and the coding features of antimicrobial peptides. Using EvoMining, a bioinformatic approach for studying evolutionary processes related to secondary metabolism, we sought to decipher the protein expansion of enzymes related to the lipid metabolism, which may have evolved toward the biosynthesis of novel secondary metabolites in Pseudomonas. The types of metabolites encoded in Pseudomonas type strains were predominantly non-ribosomal peptide synthetases, bacteriocins, N-acetylglutaminylglutamine amides and ß-lactones. Also, the evolution of genes related to secondary metabolites was found to coincide with Pseudomonas species diversification. Interestingly, only a few Pseudomonas species encode polyketide synthases, which are related to the lipid metabolism broadly distributed among bacteria. Thus, our EvoMining-based search may help to discover new types of secondary metabolite gene clusters in which lipid-related enzymes are involved. This work provides information about uncharacterized metabolites produced by Pseudomonas type strains, whose gene clusters have evolved in a species-specific way. Our results provide novel insight into the secondary metabolism of Pseudomonas and will serve as a basis for the prioritization of the isolated strains. This article contains data hosted by Microreact.
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Affiliation(s)
- Zaki Saati-Santamaría
- Microbiology and Genetics Department, University of Salamanca, 37007 Salamanca, Spain
- Institute for Agribiotechnology Research (CIALE), 37185 Salamanca, Spain
| | | | - Ezequiel Peral-Aranega
- Microbiology and Genetics Department, University of Salamanca, 37007 Salamanca, Spain
- Institute for Agribiotechnology Research (CIALE), 37185 Salamanca, Spain
| | - Raúl Rivas
- Microbiology and Genetics Department, University of Salamanca, 37007 Salamanca, Spain
- Institute for Agribiotechnology Research (CIALE), 37185 Salamanca, Spain
- Associated Research Unit of Plant-Microorganism Interaction, University of Salamanca-IRNASA-CSIC, 37008 Salamanca, Spain
| | - Paula García-Fraile
- Microbiology and Genetics Department, University of Salamanca, 37007 Salamanca, Spain
- Institute for Agribiotechnology Research (CIALE), 37185 Salamanca, Spain
- Associated Research Unit of Plant-Microorganism Interaction, University of Salamanca-IRNASA-CSIC, 37008 Salamanca, Spain
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Chevrette MG, Selem-Mojica N, Aguilar C, Labby K, Bustos-Diaz ED, Handelsman J, Barona-Gómez F. Evolutionary Genome Mining for the Discovery and Engineering of Natural Product Biosynthesis. Methods Mol Biol 2022; 2489:129-155. [PMID: 35524049 DOI: 10.1007/978-1-0716-2273-5_8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/14/2023]
Abstract
Genome mining has become an invaluable tool in natural products research to quickly identify and characterize the biosynthetic pathways that assemble secondary or specialized metabolites. Recently, evolutionary principles have been incorporated into genome mining strategies in an effort to better assess and prioritize novelty and understand their chemical diversification for engineering purposes. Here, we provide an introduction to the principles underlying evolutionary genome mining, including bioinformatic strategies and natural product biosynthetic databases. We introduce workflows for traditional genome mining, focusing on the popular pipeline antiSMASH, and methods to predict enzyme substrate specificity from genomic information. We then provide an in-depth discussion of evolutionary genome mining workflows, including EvoMining, CORASON, ARTS, and others, as adopted by our group for the discovery and prioritization of natural products biosynthetic gene clusters and their products.
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Affiliation(s)
- Marc G Chevrette
- Wisconsin Institute for Discovery and Department of Plant Pathology, University of Wisconsin-Madison, Madison, WI, USA
| | - Nelly Selem-Mojica
- Evolution of Metabolic Diversity Laboratory, Unidad de Genómica Avanzada (Langebio), Cinvestav-IPN, Guanajuato, Mexico
- Centro de Ciencias Matemáticas, UNAM, Morelia, Michoacán, Mexico
| | - César Aguilar
- Evolution of Metabolic Diversity Laboratory, Unidad de Genómica Avanzada (Langebio), Cinvestav-IPN, Guanajuato, Mexico
- Department of Chemistry, Purdue University, West Lafayette, IN, USA
| | - Kristin Labby
- Department of Chemistry, Beloit College, Beloit, WI, USA
| | - Edder D Bustos-Diaz
- Evolution of Metabolic Diversity Laboratory, Unidad de Genómica Avanzada (Langebio), Cinvestav-IPN, Guanajuato, Mexico
| | - Jo Handelsman
- Wisconsin Institute for Discovery and Department of Plant Pathology, University of Wisconsin-Madison, Madison, WI, USA
| | - Francisco Barona-Gómez
- Evolution of Metabolic Diversity Laboratory, Unidad de Genómica Avanzada (Langebio), Cinvestav-IPN, Guanajuato, Mexico.
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Caesar LK, Montaser R, Keller NP, Kelleher NL. Metabolomics and genomics in natural products research: complementary tools for targeting new chemical entities. Nat Prod Rep 2021; 38:2041-2065. [PMID: 34787623 PMCID: PMC8691422 DOI: 10.1039/d1np00036e] [Citation(s) in RCA: 46] [Impact Index Per Article: 15.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
Abstract
Covering: 2010 to 2021Organisms in nature have evolved into proficient synthetic chemists, utilizing specialized enzymatic machinery to biosynthesize an inspiring diversity of secondary metabolites. Often serving to boost competitive advantage for their producers, these secondary metabolites have widespread human impacts as antibiotics, anti-inflammatories, and antifungal drugs. The natural products discovery field has begun a shift away from traditional activity-guided approaches and is beginning to take advantage of increasingly available metabolomics and genomics datasets to explore undiscovered chemical space. Major strides have been made and now enable -omics-informed prioritization of chemical structures for discovery, including the prospect of confidently linking metabolites to their biosynthetic pathways. Over the last decade, more integrated strategies now provide researchers with pipelines for simultaneous identification of expressed secondary metabolites and their biosynthetic machinery. However, continuous collaboration by the natural products community will be required to optimize strategies for effective evaluation of natural product biosynthetic gene clusters to accelerate discovery efforts. Here, we provide an evaluative guide to scientific literature as it relates to studying natural product biosynthesis using genomics, metabolomics, and their integrated datasets. Particular emphasis is placed on the unique insights that can be gained from large-scale integrated strategies, and we provide source organism-specific considerations to evaluate the gaps in our current knowledge.
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Affiliation(s)
- Lindsay K Caesar
- Department of Chemistry, Northwestern University, Evanston, IL, USA.
| | - Rana Montaser
- Department of Chemistry, Northwestern University, Evanston, IL, USA.
| | - Nancy P Keller
- Department of Medical Microbiology and Immunology and Bacteriology, University of Wisconsin-Madison, Madison, WI, USA
| | - Neil L Kelleher
- Department of Chemistry, Northwestern University, Evanston, IL, USA.
- Department of Molecular Biosciences, Northwestern University, Evanston, IL, USA
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37
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Jarmusch SA, van der Hooft JJJ, Dorrestein PC, Jarmusch AK. Advancements in capturing and mining mass spectrometry data are transforming natural products research. Nat Prod Rep 2021; 38:2066-2082. [PMID: 34612288 PMCID: PMC8667781 DOI: 10.1039/d1np00040c] [Citation(s) in RCA: 29] [Impact Index Per Article: 9.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
Covering: 2016 up to 2021Mass spectrometry (MS) is an essential technology in natural products research with MS fragmentation (MS/MS) approaches becoming a key tool. Recent advancements in MS yield dense metabolomics datasets which have been, conventionally, used by individual labs for individual projects; however, a shift is brewing. The movement towards open MS data (and other structural characterization data) and accessible data mining tools is emerging in natural products research. Over the past 5 years, this movement has rapidly expanded and evolved with no slowdown in sight; the capabilities of today vastly exceed those of 5 years ago. Herein, we address the analysis of individual datasets, a situation we are calling the '2021 status quo', and the emergent framework to systematically capture sample information (metadata) and perform repository-scale analyses. We evaluate public data deposition, discuss the challenges of working in the repository scale, highlight the challenges of metadata capture and provide illustrative examples of the power of utilizing repository data and the tools that enable it. We conclude that the advancements in MS data collection must be met with advancements in how we utilize data; therefore, we argue that open data and data mining is the next evolution in obtaining the maximum potential in natural products research.
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Affiliation(s)
- Scott A Jarmusch
- Department of Biotechnology and Biomedicine, Technical University of Denmark, Søltofts Plads 221, DK-2800 Kongens Lyngby, Denmark.
| | | | - Pieter C Dorrestein
- Collaborative Mass Spectrometry Innovation Center, Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California, San Diego, La Jolla, CA, 92093-0751, USA
| | - Alan K Jarmusch
- Collaborative Mass Spectrometry Innovation Center, Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California, San Diego, La Jolla, CA, 92093-0751, USA
- Immunity, Inflammation, and Disease Laboratory, Division of Intramural Research, National Institute of Environmental Health Sciences, National Institutes of Health, Research Triangle Park, NC 27709, USA
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38
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Nishimura S. Marine natural products targeting the eukaryotic cell membrane. J Antibiot (Tokyo) 2021; 74:769-785. [PMID: 34493848 DOI: 10.1038/s41429-021-00468-5] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2021] [Revised: 06/16/2021] [Accepted: 07/01/2021] [Indexed: 02/07/2023]
Abstract
The cell membrane, with high fluidity and alternative curvatures, maintains the robust integrity to distinguish inner and outer space of cells or organelles. Lipids are the main components of the cell membrane, but their functions are largely unknown. Even the visualization of lipids is not straightforward since modification of lipids often hampers its correct physical properties. Many natural products target cell membranes, some of which are used as pharmaceuticals and/or research tools. They show specific recognition on lipids, and thus exhibit desired pharmacological effects and unique biological phenotypes. This review is a catalog of marine natural products that target eukaryotic cell membranes. Chemical structures, biological activities, and molecular mechanisms are summarized. I hope that this review will be helpful for readers to notice the potential of marine natural products in the exploration of the function of lipids and the druggability of eukaryotic cell membranes.
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Affiliation(s)
- Shinichi Nishimura
- Department of Biotechnology, Collaborative Research Institute for Innovative Microbiology, The University of Tokyo, Tokyo, Japan.
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Activation of Cryptic Antibiotic Biosynthetic Gene Clusters Guided by RNA-seq Data from Both Streptomyces ansochromogenes and ΔwblA. Antibiotics (Basel) 2021; 10:antibiotics10091097. [PMID: 34572679 PMCID: PMC8465540 DOI: 10.3390/antibiotics10091097] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2021] [Revised: 08/27/2021] [Accepted: 09/07/2021] [Indexed: 12/13/2022] Open
Abstract
With the increase of drug resistance caused by the improper use and abuse of antibiotics, human beings are facing a global health crisis. Sequencing of Streptomyces genomes revealed the presence of an important reservoir of secondary metabolic gene clusters for previously unsuspected products with potentially valuable bioactivity. It has therefore become necessary to activate these cryptic pathways through various strategies. Here, we used RNA-seq data to perform a comparative transcriptome analysis of Streptomyces ansochromogenes (wild-type, WT) and its global regulatory gene disruption mutant ΔwblA, in which some differentially expressed genes are associated with the abolished nikkomycin biosynthesis and activated tylosin analogue compounds (TACs) production, and also with the oviedomycin production that is induced by the genetic manipulation of two differentially expressed genes (san7324 and san7324L) encoding RsbR. These results provide a significant clue for the discovery of new drug candidates and the activation of cryptic biosynthetic gene clusters.
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40
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Ntie-Kang F, Telukunta KK, Fobofou SAT, Chukwudi Osamor V, Egieyeh SA, Valli M, Djoumbou-Feunang Y, Sorokina M, Stork C, Mathai N, Zierep P, Chávez-Hernández AL, Duran-Frigola M, Babiaka SB, Tematio Fouedjou R, Eni DB, Akame S, Arreyetta-Bawak AB, Ebob OT, Metuge JA, Bekono BD, Isa MA, Onuku R, Shadrack DM, Musyoka TM, Patil VM, van der Hooft JJJ, da Silva Bolzani V, Medina-Franco JL, Kirchmair J, Weber T, Tastan Bishop Ö, Medema MH, Wessjohann LA, Ludwig-Müller J. Computational Applications in Secondary Metabolite Discovery (CAiSMD): an online workshop. J Cheminform 2021; 13:64. [PMID: 34488889 PMCID: PMC8419829 DOI: 10.1186/s13321-021-00546-8] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2021] [Accepted: 08/23/2021] [Indexed: 11/12/2022] Open
Abstract
We report the major conclusions of the online open-access workshop "Computational Applications in Secondary Metabolite Discovery (CAiSMD)" that took place from 08 to 10 March 2021. Invited speakers from academia and industry and about 200 registered participants from five continents (Africa, Asia, Europe, South America, and North America) took part in the workshop. The workshop highlighted the potential applications of computational methodologies in the search for secondary metabolites (SMs) or natural products (NPs) as potential drugs and drug leads. During 3 days, the participants of this online workshop received an overview of modern computer-based approaches for exploring NP discovery in the "omics" age. The invited experts gave keynote lectures, trained participants in hands-on sessions, and held round table discussions. This was followed by oral presentations with much interaction between the speakers and the audience. Selected applicants (early-career scientists) were offered the opportunity to give oral presentations (15 min) and present posters in the form of flash presentations (5 min) upon submission of an abstract. The final program available on the workshop website ( https://caismd.indiayouth.info/ ) comprised of 4 keynote lectures (KLs), 12 oral presentations (OPs), 2 round table discussions (RTDs), and 5 hands-on sessions (HSs). This meeting report also references internet resources for computational biology in the area of secondary metabolites that are of use outside of the workshop areas and will constitute a long-term valuable source for the community. The workshop concluded with an online survey form to be completed by speakers and participants for the goal of improving any subsequent editions.
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Affiliation(s)
- Fidele Ntie-Kang
- Department of Chemistry, University of Buea, P. O. Box 63, Buea, Cameroon
- Institute of Pharmacy, Martin-Luther University of Halle-Wittenberg, Kurt-Mothes-Str. 3, 06120 Halle, Germany
- Institute of Botany, Technische Universität Dresden, Zellescher Weg 20b, 01062 Dresden, Germany
| | - Kiran K. Telukunta
- Tarunavadaanenasaha Muktbharatonnayana Samstha Foundation, Hyderabad, India
| | - Serge A. T. Fobofou
- Institute of Pharmaceutical Biology, Technische Universität Braunschweig, Mendelssohnstrasse 1, 38106 Braunschweig, Germany
| | - Victor Chukwudi Osamor
- Department of Computer and Information Sciences, Colege of Science and Technology, Covenant University, Km. 10 Idiroko Rd, Ogun Ota, Nigeria
| | - Samuel A. Egieyeh
- School of Pharmacy, University of the Western Cape, Cape Town, 7535 South Africa
- South African Medical Research Council Bioinformatics Unit, South African National Bioinformatics Institute, University of the Western Cape, Cape Town, 7535 South Africa
| | - Marilia Valli
- Nuclei of Bioassays, Biosynthesis and Ecophysiology of Natural Products (NuBBE), Department of Organic Chemistry, Institute of Chemistry, Sao Paulo State University–UNESP, Araraquara, Brazil
| | | | - Maria Sorokina
- Institute for Inorganic and Analytical Chemistry, Friedrich Schiller University, Jena, Germany
| | - Conrad Stork
- Center for Bioinformatics, Universität Hamburg, 20146 Hamburg, Germany
| | - Neann Mathai
- Department of Chemistry and Computational Biology Unit (CBU), University of Bergen, 5020 Bergen, Norway
| | - Paul Zierep
- Pharmaceutical Bioinformatics, Albert-Ludwigs-University, Freiburg, Germany
| | - Ana L. Chávez-Hernández
- DIFACQUIM Research Group, Department of Pharmacy, School of Chemistry, Universidad Nacional Autónoma de México, Mexico City, Mexico
| | - Miquel Duran-Frigola
- Ersilia Open Source Initiative, Cambridge, UK
- Joint IRB-BSC-CRG Programme in Computational Biology, Institute for Research in Biomedicine (IRB Barcelona), The Barcelona Institute of Science and Technology, Barcelona, Catalonia Spain
| | - Smith B. Babiaka
- Department of Chemistry, University of Buea, P. O. Box 63, Buea, Cameroon
| | | | - Donatus B. Eni
- Department of Chemistry, University of Buea, P. O. Box 63, Buea, Cameroon
| | - Simeon Akame
- Department of Immunology, School of Health Sciences, Catholic University of Central Africa, BP 7871, Yaoundé, Cameroon
| | | | - Oyere T. Ebob
- Department of Chemistry, University of Buea, P. O. Box 63, Buea, Cameroon
| | - Jonathan A. Metuge
- Department of Biochemistry and Molecular Biology, University of Buea, P. O. Box 63, Buea, Cameroon
| | - Boris D. Bekono
- Department of Physics, Ecole Normale Supérieure, University of Yaoundé I, BP. 47, Yaoundé, Cameroon
| | - Mustafa A. Isa
- Bioinformatics and Computational Biology Lab, Department of Microbiology, Faculty of Sciences, University of Maiduguri, P.M.B. 1069, Maiduguri, Borno State Nigeria
| | - Raphael Onuku
- Department of Pharmaceutical and Medicinal Chemistry, Faculty of Pharmaceutical Sciences, University of Nigeria Nsukka, Nsukka, Nigeria
| | - Daniel M. Shadrack
- Department of Chemistry, St. John’s University of Tanzania, P. O. Box 47, Dodoma, Tanzania
| | - Thommas M. Musyoka
- Research Unit in Bioinformatics (RUBi), Department of Biochemistry and Microbiology, Rhodes University, Makhanda, 6140 South Africa
| | - Vaishali M. Patil
- Computer Aided Drug Design Lab, KIET Group of Institutions, Delhi-NCR, Ghaziabad, 201206 India
| | | | - Vanderlan da Silva Bolzani
- Nuclei of Bioassays, Biosynthesis and Ecophysiology of Natural Products (NuBBE), Department of Organic Chemistry, Institute of Chemistry, Sao Paulo State University–UNESP, Araraquara, Brazil
| | - José L. Medina-Franco
- DIFACQUIM Research Group, Department of Pharmacy, School of Chemistry, Universidad Nacional Autónoma de México, Mexico City, Mexico
| | - Johannes Kirchmair
- Department of Pharmaceutical Sciences, Division of Pharmaceutical Chemistry, University of Vienna, 1090 Vienna, Austria
| | - Tilmann Weber
- The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Kgs. Lyngby, Denmark
| | - Özlem Tastan Bishop
- Research Unit in Bioinformatics (RUBi), Department of Biochemistry and Microbiology, Rhodes University, Makhanda, 6140 South Africa
| | - Marnix H. Medema
- Bioinformatics Group, Wageningen University, Wageningen, The Netherlands
| | - Ludger A. Wessjohann
- Department of Bioorganic Chemistry, Leibniz Institute of Plant Biochemistry (IPB), Weinberg 3, 06120 Halle (Saale), Germany
- German Centre for Integrative Biodiversity Research (iDiv), Puschstraße 4, 04103 Leipzig, Germany
| | - Jutta Ludwig-Müller
- Institute of Botany, Technische Universität Dresden, Zellescher Weg 20b, 01062 Dresden, Germany
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Bach E, Passaglia LMP, Jiao J, Gross H. Burkholderia in the genomic era: from taxonomy to the discovery of new antimicrobial secondary metabolites. Crit Rev Microbiol 2021; 48:121-160. [PMID: 34346791 DOI: 10.1080/1040841x.2021.1946009] [Citation(s) in RCA: 22] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
Abstract
Species of Burkholderia are highly versatile being found not only abundantly in soil, but also as plants and animals' commensals or pathogens. Their complex multireplicon genomes harbour an impressive number of polyketide synthase (PKS) and nonribosomal peptide-synthetase (NRPS) genes coding for the production of antimicrobial secondary metabolites (SMs), which have been successfully deciphered by genome-guided tools. Moreover, genome metrics supported the split of this genus into Burkholderia sensu stricto (s.s.) and five new other genera. Here, we show that the successful antimicrobial SMs producers belong to Burkholderia s.s. Additionally, we reviewed the occurrence, bioactivities, modes of action, structural, and biosynthetic information of thirty-eight Burkholderia antimicrobial SMs shedding light on their diversity, complexity, and uniqueness as well as the importance of genome-guided strategies to facilitate their discovery. Several Burkholderia NRPS and PKS display unusual features, which are reflected in their structural diversity, important bioactivities, and varied modes of action. Up to now, it is possible to observe a general tendency of Burkholderia SMs being more active against fungi. Although the modes of action and biosynthetic gene clusters of many SMs remain unknown, we highlight the potential of Burkholderia SMs as alternatives to fight against new diseases and antibiotic resistance.
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Affiliation(s)
- Evelise Bach
- Departamento de Genética and Programa de Pós-graduação em Genética e Biologia Molecular, Instituto de Biociências, Universidade Federal do Rio Grande do Sul (UFRGS), Porto Alegre, Brazil
| | - Luciane Maria Pereira Passaglia
- Departamento de Genética and Programa de Pós-graduação em Genética e Biologia Molecular, Instituto de Biociências, Universidade Federal do Rio Grande do Sul (UFRGS), Porto Alegre, Brazil
| | - Junjing Jiao
- Department for Pharmaceutical Biology, Pharmaceutical Institute, University of Tübingen, Tübingen, Germany
| | - Harald Gross
- Department for Pharmaceutical Biology, Pharmaceutical Institute, University of Tübingen, Tübingen, Germany
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42
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Zdouc MM, Iorio M, Vind K, Simone M, Serina S, Brunati C, Monciardini P, Tocchetti A, Zarazúa GS, Crüsemann M, Maffioli SI, Sosio M, Donadio S. Effective approaches to discover new microbial metabolites in a large strain library. J Ind Microbiol Biotechnol 2021; 48:6144606. [PMID: 33599744 PMCID: PMC9113118 DOI: 10.1093/jimb/kuab017] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2020] [Accepted: 12/31/2020] [Indexed: 12/28/2022]
Abstract
Natural products have provided many molecules to treat and prevent illnesses in humans, animals and plants. While only a small fraction of the existing microbial diversity has been explored for bioactive metabolites, tens of thousands of molecules have been reported in the literature over the past 80 years. Thus, the main challenge in microbial metabolite screening is to avoid the re-discovery of known metabolites in a cost-effective manner. In this perspective, we report and discuss different approaches used in our laboratory over the past few years, ranging from bioactivity-based screening to looking for metabolic rarity in different datasets to deeply investigating a single Streptomyces strain. Our results show that it is possible to find novel chemistry through a limited screening effort, provided that appropriate selection criteria are in place.
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Affiliation(s)
- Mitja M Zdouc
- NAICONS Srl, 20139 Milan, Italy.,Swammerdam Institute for Life Sciences, University of Amsterdam, 1098 XH Amsterdam, The Netherlands
| | | | - Kristiina Vind
- NAICONS Srl, 20139 Milan, Italy.,Host-Microbe Interactomics Group, Wageningen University, 6708 WD Wageningen, The Netherlands
| | | | | | | | | | | | - Guadalupe S Zarazúa
- Institut für Pharmazeutische Biologie, Rheinische Friedrich-Wilhelms-Universität, 53115 Bonn, Germany
| | - Max Crüsemann
- Institut für Pharmazeutische Biologie, Rheinische Friedrich-Wilhelms-Universität, 53115 Bonn, Germany
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43
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Ntie-Kang F. Editorial: Advanced chemoinformatics applications at the service of natural product discovery. PHYSICAL SCIENCES REVIEWS 2021. [DOI: 10.1515/psr-2019-0077] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
Affiliation(s)
- Fidele Ntie-Kang
- Faculty of Science, Department of Chemistry , University of Buea , P.O. Box 63 , Buea , Cameroon
- Department of Pharmaceutical Chemistry , Martin-Luther University Halle-Wittenberg , Kurt-Mothes-Str. 3 , Halle (Saale) , 06120 Germany
- Institute of Botany , Technische Universität Dresden , Zellescher Weg 20b , Dresden , 01217 Germany
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44
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Biosynthesis and Heterologous Expression of Cacaoidin, the First Member of the Lanthidin Family of RiPPs. Antibiotics (Basel) 2021; 10:antibiotics10040403. [PMID: 33917820 PMCID: PMC8068269 DOI: 10.3390/antibiotics10040403] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2021] [Revised: 04/03/2021] [Accepted: 04/06/2021] [Indexed: 01/05/2023] Open
Abstract
Cacaoidin is produced by the strain Streptomyces cacaoi CA-170360 and represents the first member of the new lanthidin (class V lanthipeptides) RiPP family. In this work, we describe the complete identification, cloning and heterologous expression of the cacaoidin biosynthetic gene cluster, which shows unique RiPP genes whose functions were not predicted by any bioinformatic tool. We also describe that the cacaoidin pathway is restricted to strains of the subspecies Streptomyces cacaoi subsp. cacaoi found in public genome databases, where we have also identified the presence of other putative class V lanthipeptide pathways. This is the first report on the heterologous production of a class V lanthipeptide.
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45
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Panter F, Bader CD, Müller R. Synergizing the potential of bacterial genomics and metabolomics to find novel antibiotics. Chem Sci 2021; 12:5994-6010. [PMID: 33995996 PMCID: PMC8098685 DOI: 10.1039/d0sc06919a] [Citation(s) in RCA: 21] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2020] [Accepted: 03/22/2021] [Indexed: 12/13/2022] Open
Abstract
Antibiotic development based on natural products has faced a long lasting decline since the 1970s, while both the speed and the extent of antimicrobial resistance (AMR) development have been severely underestimated. The discovery of antimicrobial natural products of bacterial and fungal origin featuring new chemistry and previously unknown mode of actions is increasingly challenged by rediscovery issues. Natural products that are abundantly produced by the corresponding wild type organisms often featuring strong UV signals have been extensively characterized, especially the ones produced by extensively screened microbial genera such as streptomycetes. Purely synthetic chemistry approaches aiming to replace the declining supply from natural products as starting materials to develop novel antibiotics largely failed to provide significant numbers of antibiotic drug leads. To cope with this fundamental issue, microbial natural products science is being transformed from a 'grind-and-find' study to an integrated approach based on bacterial genomics and metabolomics. Novel technologies in instrumental analytics are increasingly employed to lower detection limits and expand the space of detectable substance classes, while broadening the scope of accessible and potentially bioactive natural products. Furthermore, the almost exponential increase in publicly available bacterial genome data has shown that the biosynthetic potential of the investigated strains by far exceeds the amount of detected metabolites. This can be judged by the discrepancy between the number of biosynthetic gene clusters (BGC) encoded in the genome of each microbial strain and the number of secondary metabolites actually detected, even when considering the increased sensitivity provided by novel analytical instrumentation. In silico annotation tools for biosynthetic gene cluster classification and analysis allow fast prioritization in BGC-to-compound workflows, which is highly important to be able to process the enormous underlying data volumes. BGC prioritization is currently accompanied by novel molecular biology-based approaches to access the so-called orphan BGCs not yet correlated with a secondary metabolite. Integration of metabolomics, in silico genomics and molecular biology approaches into the mainstream of natural product research will critically influence future success and impact the natural product field in pharmaceutical, nutritional and agrochemical applications and especially in anti-infective research.
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Affiliation(s)
- Fabian Panter
- Department of Microbial Natural Products, Helmholtz-Institute for Pharmaceutical Research Saarland (HIPS), Helmholtz Centre for Infection Research (HZI), Department of Pharmacy, Saarland University Campus E8 1 66123 Saarbrücken Germany
- German Centre for Infection Research (DZIF) Partner Site Hannover-Braunschweig Germany
- Helmholtz International Lab for Anti-infectives Campus E8 1 66123 Saarbrücken Germany
| | - Chantal D Bader
- Department of Microbial Natural Products, Helmholtz-Institute for Pharmaceutical Research Saarland (HIPS), Helmholtz Centre for Infection Research (HZI), Department of Pharmacy, Saarland University Campus E8 1 66123 Saarbrücken Germany
- German Centre for Infection Research (DZIF) Partner Site Hannover-Braunschweig Germany
| | - Rolf Müller
- Department of Microbial Natural Products, Helmholtz-Institute for Pharmaceutical Research Saarland (HIPS), Helmholtz Centre for Infection Research (HZI), Department of Pharmacy, Saarland University Campus E8 1 66123 Saarbrücken Germany
- German Centre for Infection Research (DZIF) Partner Site Hannover-Braunschweig Germany
- Helmholtz International Lab for Anti-infectives Campus E8 1 66123 Saarbrücken Germany
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46
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Liu Z, Zhao Y, Huang C, Luo Y. Recent Advances in Silent Gene Cluster Activation in Streptomyces. Front Bioeng Biotechnol 2021; 9:632230. [PMID: 33681170 PMCID: PMC7930741 DOI: 10.3389/fbioe.2021.632230] [Citation(s) in RCA: 42] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2020] [Accepted: 01/25/2021] [Indexed: 11/13/2022] Open
Abstract
Natural products (NPs) are critical sources of drug molecules for decades. About two-thirds of natural antibiotics are produced by Streptomyces. Streptomyces have a large number of secondary metabolite biosynthetic gene clusters (SM-BGCs) that may encode NPs. However, most of these BGCs are silent under standard laboratory conditions. Hence, activation of these silent BGCs is essential to current natural products discovery research. In this review, we described the commonly used strategies for silent BGC activation in Streptomyces from two aspects. One focused on the strategies applied in heterologous host, including methods to clone and reconstruct BGCs along with advances in chassis engineering; the other focused on methods applied in native host which includes engineering of promoters, regulatory factors, and ribosomes. With the metabolic network being elucidated more comprehensively and methods optimized more high-thoroughly, the discovery of NPs will be greatly accelerated.
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Affiliation(s)
- Zhenyu Liu
- Key Laboratory of Systems Bioengineering (Ministry of Education), Frontier Science Center for Synthetic Biology, School of Chemical Engineering and Technology, Tianjin University, Tianjin, China
| | - Yatong Zhao
- Key Laboratory of Systems Bioengineering (Ministry of Education), Frontier Science Center for Synthetic Biology, School of Chemical Engineering and Technology, Tianjin University, Tianjin, China
| | - Chaoqun Huang
- Key Laboratory of Systems Bioengineering (Ministry of Education), Frontier Science Center for Synthetic Biology, School of Chemical Engineering and Technology, Tianjin University, Tianjin, China
| | - Yunzi Luo
- Key Laboratory of Systems Bioengineering (Ministry of Education), Frontier Science Center for Synthetic Biology, School of Chemical Engineering and Technology, Tianjin University, Tianjin, China.,Collaborative Innovation Center of Chemical Science and Engineering (Tianjin), Tianjin University, Tianjin, China
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Soldatou S, Eldjárn GH, Ramsay A, van der Hooft JJJ, Hughes AH, Rogers S, Duncan KR. Comparative Metabologenomics Analysis of Polar Actinomycetes. Mar Drugs 2021; 19:103. [PMID: 33578887 PMCID: PMC7916644 DOI: 10.3390/md19020103] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2021] [Revised: 02/05/2021] [Accepted: 02/08/2021] [Indexed: 12/16/2022] Open
Abstract
Biosynthetic and chemical datasets are the two major pillars for microbial drug discovery in the omics era. Despite the advancement of analysis tools and platforms for multi-strain metabolomics and genomics, linking these information sources remains a considerable bottleneck in strain prioritisation and natural product discovery. In this study, molecular networking of the 100 metabolite extracts derived from applying the OSMAC approach to 25 Polar bacterial strains, showed growth media specificity and potential chemical novelty was suggested. Moreover, the metabolite extracts were screened for antibacterial activity and promising selective bioactivity against drug-persistent pathogens such as Klebsiella pneumoniae and Acinetobacter baumannii was observed. Genome sequencing data were combined with metabolomics experiments in the recently developed computational approach, NPLinker, which was used to link BGC and molecular features to prioritise strains for further investigation based on biosynthetic and chemical information. Herein, we putatively identified the known metabolites ectoine and chrloramphenicol which, through NPLinker, were linked to their associated BGCs. The metabologenomics approach followed in this study can potentially be applied to any large microbial datasets for accelerating the discovery of new (bioactive) specialised metabolites.
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Affiliation(s)
- Sylvia Soldatou
- Strathclyde Institute of Pharmacy and Biomedical Sciences, University of Strathclyde, Glasgow G4 0RE, UK; (S.S.); (A.H.H.)
| | | | - Andrew Ramsay
- School of Computing Science, University of Glasgow, Glasgow G12 8RZ, UK; (G.H.E.); (A.R.); (S.R.)
| | | | - Alison H. Hughes
- Strathclyde Institute of Pharmacy and Biomedical Sciences, University of Strathclyde, Glasgow G4 0RE, UK; (S.S.); (A.H.H.)
| | - Simon Rogers
- School of Computing Science, University of Glasgow, Glasgow G12 8RZ, UK; (G.H.E.); (A.R.); (S.R.)
| | - Katherine R. Duncan
- Strathclyde Institute of Pharmacy and Biomedical Sciences, University of Strathclyde, Glasgow G4 0RE, UK; (S.S.); (A.H.H.)
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