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Nag N, Ray T, Tapader R, Gope A, Das R, Mahapatra E, Saha S, Pal A, Prasad P, Pal A. Metallo-protease Peptidase M84 from Bacillusaltitudinis induces ROS-dependent apoptosis in ovarian cancer cells by targeting PAR-1. iScience 2024; 27:109828. [PMID: 38799586 PMCID: PMC11126781 DOI: 10.1016/j.isci.2024.109828] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2023] [Revised: 01/02/2024] [Accepted: 04/24/2024] [Indexed: 05/29/2024] Open
Abstract
We have purified Peptidase M84 from Bacillus altitudinis in an effort to isolate anticancer proteases from environmental microbial isolates. This metallo-protease had no discernible impact on normal cell survival, but it specifically induced apoptosis in ovarian cancer cells. PAR-1, a GPCR which is reported to be overexpressed in ovarian cancer cells, was identified as a target of Peptidase M84. We observed that Peptidase M84 induced PAR-1 overexpression along with activating its downstream signaling effectors NF-κB and MAPK to promote excessive reactive oxygen species (ROS) generation. This evoked apoptotic death of the ovarian cancer cells through the intrinsic route. In in vivo set-up, weekly intraperitoneal administration of Peptidase M84 in syngeneic mice significantly diminished ascites accumulation, increasing murine survival rates by 60%. Collectively, our findings suggested that Peptidase M84 triggered PAR-1-mediated oxidative stress to act as an apoptosis inducer. This established Peptidase M84 as a drug candidate for receptor mediated targeted-therapy of ovarian cancer.
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Affiliation(s)
- Niraj Nag
- Division of Molecular Pathophysiology, ICMR-National Institute of Cholera and Enteric Diseases (ICMR-NICED), P-33, CIT Road, Scheme-XM, Beliaghata, Kolkata, West Bengal 700010, India
| | - Tanusree Ray
- Division of Molecular Pathophysiology, ICMR-National Institute of Cholera and Enteric Diseases (ICMR-NICED), P-33, CIT Road, Scheme-XM, Beliaghata, Kolkata, West Bengal 700010, India
| | - Rima Tapader
- Division of Molecular Pathophysiology, ICMR-National Institute of Cholera and Enteric Diseases (ICMR-NICED), P-33, CIT Road, Scheme-XM, Beliaghata, Kolkata, West Bengal 700010, India
| | - Animesh Gope
- Division of Clinical Medicine, ICMR-National Institute of Cholera and Enteric Diseases (ICMR-NICED), P-33, CIT Road, Scheme-XM, Beliaghata, Kolkata, West Bengal 700010, India
| | - Rajdeep Das
- Molecular Cell Biology of Autophagy Lab, The Francis Crick Institute, 1, Midland Road, London NW1 1AT, UK
| | - Elizabeth Mahapatra
- Department of Environmental Carcinogenesis and Toxicology, Chittaranjan National Cancer Institute, 37, S.P. Mukherjee Road, Kolkata, West Bengal 700026, India
| | - Saibal Saha
- Division of Molecular Pathophysiology, ICMR-National Institute of Cholera and Enteric Diseases (ICMR-NICED), P-33, CIT Road, Scheme-XM, Beliaghata, Kolkata, West Bengal 700010, India
| | - Ananda Pal
- Division of Clinical Medicine, ICMR-National Institute of Cholera and Enteric Diseases (ICMR-NICED), P-33, CIT Road, Scheme-XM, Beliaghata, Kolkata, West Bengal 700010, India
| | - Parash Prasad
- Division of Experimental Hematology and Cancer Biology, Cincinnati Children’s Hospital and Medical Center, 3333 Burnet Avenue, Cincinnati 45229-3026, OH, USA
| | - Amit Pal
- Division of Molecular Pathophysiology, ICMR-National Institute of Cholera and Enteric Diseases (ICMR-NICED), P-33, CIT Road, Scheme-XM, Beliaghata, Kolkata, West Bengal 700010, India
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2
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Bogdanov A, Salib MN, Chase AB, Hammerlindl H, Muskat MN, Luedtke S, da Silva EB, O'Donoghue AJ, Wu LF, Altschuler SJ, Molinski TF, Jensen PR. Small molecule in situ resin capture provides a compound first approach to natural product discovery. Nat Commun 2024; 15:5230. [PMID: 38898025 PMCID: PMC11187115 DOI: 10.1038/s41467-024-49367-x] [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: 08/24/2023] [Accepted: 06/04/2024] [Indexed: 06/21/2024] Open
Abstract
Culture-based microbial natural product discovery strategies fail to realize the extraordinary biosynthetic potential detected across earth's microbiomes. Here we introduce Small Molecule In situ Resin Capture (SMIRC), a culture-independent method to obtain natural products directly from the environments in which they are produced. We use SMIRC to capture numerous compounds including two new carbon skeletons that were characterized using NMR and contain structural features that are, to the best of our knowledge, unprecedented among natural products. Applications across diverse marine habitats reveal biome-specific metabolomic signatures and levels of chemical diversity in concordance with sequence-based predictions. Expanded deployments, in situ cultivation, and metagenomics facilitate compound discovery, enhance yields, and link compounds to candidate producing organisms, although microbial community complexity creates challenges for the later. This compound-first approach to natural product discovery provides access to poorly explored chemical space and has implications for drug discovery and the detection of chemically mediated biotic interactions.
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Affiliation(s)
- Alexander Bogdanov
- Scripps Institution of Oceanography, University of California, San Diego, La Jolla, CA, 92093, USA
| | - Mariam N Salib
- Department of Chemistry and Biochemistry, University of California, San Diego, La Jolla, CA, 92093, USA
| | - Alexander B Chase
- Scripps Institution of Oceanography, University of California, San Diego, La Jolla, CA, 92093, USA
- Department of Earth Sciences, Southern Methodist University, Dallas, TX, 75275, USA
| | - Heinz Hammerlindl
- Department of Pharmaceutical Chemistry, University of California, San Francisco, San Francisco, CA, 94158, USA
| | - Mitchell N Muskat
- Scripps Institution of Oceanography, University of California, San Diego, La Jolla, CA, 92093, USA
| | - Stephanie Luedtke
- Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California, San Diego, La Jolla, CA, 92093, USA
| | - Elany Barbosa da Silva
- Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California, San Diego, La Jolla, CA, 92093, USA
| | - Anthony J O'Donoghue
- Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California, San Diego, La Jolla, CA, 92093, USA
| | - Lani F Wu
- Department of Pharmaceutical Chemistry, University of California, San Francisco, San Francisco, CA, 94158, USA
| | - Steven J Altschuler
- Department of Pharmaceutical Chemistry, University of California, San Francisco, San Francisco, CA, 94158, USA
| | - Tadeusz F Molinski
- Department of Chemistry and Biochemistry, University of California, San Diego, La Jolla, CA, 92093, USA.
| | - Paul R Jensen
- Scripps Institution of Oceanography, University of California, San Diego, La Jolla, CA, 92093, USA.
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3
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Parmar D, Rosado-Rosa JM, Shrout JD, Sweedler JV. Metabolic insights from mass spectrometry imaging of biofilms: A perspective from model microorganisms. Methods 2024; 224:21-34. [PMID: 38295894 PMCID: PMC11149699 DOI: 10.1016/j.ymeth.2024.01.014] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2023] [Revised: 12/17/2023] [Accepted: 01/16/2024] [Indexed: 02/05/2024] Open
Abstract
Biofilms are dense aggregates of bacterial colonies embedded inside a self-produced polymeric matrix. Biofilms have received increasing attention in medical, industrial, and environmental settings due to their enhanced survival. Their characterization using microscopy techniques has revealed the presence of structural and cellular heterogeneity in many bacterial systems. However, these techniques provide limited chemical detail and lack information about the molecules important for bacterial communication and virulence. Mass spectrometry imaging (MSI) bridges the gap by generating spatial chemical information with unmatched chemical detail, making it an irreplaceable analytical platform in the multi-modal imaging of biofilms. In the last two decades, over 30 species of biofilm-forming bacteria have been studied using MSI in different environments. The literature conveys both analytical advancements and an improved understanding of the effects of environmental variables such as host surface characteristics, antibiotics, and other species of microorganisms on biofilms. This review summarizes the insights from frequently studied model microorganisms. We share a detailed list of organism-wide metabolites, commonly observed mass spectral adducts, culture conditions, strains of bacteria, substrate, broad problem definition, and details of the MS instrumentation, such as ionization sources and matrix, to facilitate future studies. We also compared the spatial characteristics of the secretome under different study designs to highlight changes because of various environmental influences. In addition, we highlight the current limitations of MSI in relation to biofilm characterization to enable cross-comparison between experiments. Overall, MSI has emerged to become an important approach for the spatial/chemical characterization of bacterial biofilms and its use will continue to grow as MSI becomes more accessible.
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Affiliation(s)
- Dharmeshkumar Parmar
- Department of Chemistry and Beckman Institute for Advanced Science and Technology, University of Illinois at Urbana-Champaign, Urbana, IL 61801, United States
| | - Joenisse M Rosado-Rosa
- Department of Chemistry and Beckman Institute for Advanced Science and Technology, University of Illinois at Urbana-Champaign, Urbana, IL 61801, United States
| | - Joshua D Shrout
- Department of Civil and Environmental Engineering and Earth Sciences, University of Notre Dame, Notre Dame, IN 46556, United States; Department of Biological Sciences, University of Notre Dame, Notre Dame, IN 46556, United States
| | - Jonathan V Sweedler
- Department of Chemistry and Beckman Institute for Advanced Science and Technology, University of Illinois at Urbana-Champaign, Urbana, IL 61801, United States.
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4
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Zhang H, Li X, Hui Z, Huang S, Cai M, Shi W, Lin Y, Shen J, Sui M, Lai Q, Shao Z, Dou J, Luo X, Ge Y, Tang X. A Semisynthesis Platform for the Efficient Production and Exploration of Didemnin-Based Drugs. Angew Chem Int Ed Engl 2024; 63:e202318784. [PMID: 38291557 DOI: 10.1002/anie.202318784] [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: 12/26/2023] [Revised: 01/28/2024] [Accepted: 01/30/2024] [Indexed: 02/01/2024]
Abstract
Plitidepsin (or dehydrodidemnin B), an approved anticancer drug, belongs to the didemnin family of cyclic depsipeptides, which are found in limited quantities in marine tunicate extracts. Herein, we introduce a new approach that integrates microbial and chemical synthesis to generate plitidepsin and its analogues. We screened a Tistrella strain library to identify a potent didemnin B producer, and then introduced a second copy of the didemnin biosynthetic gene cluster into its genome, resulting in a didemnin B titer of approximately 75 mg/L. Next, we developed two straightforward chemical strategies to convert didemnin B into plitidepsin, one of which involved a one-step synthetic route giving over 90 % overall yield. Furthermore, we synthesized 13 new didemnin derivatives and three didemnin probes, enabling research into structure-activity relationships and interactions between didemnin and proteins. Our study highlights the synergistic potential of biosynthesis and chemical synthesis in overcoming the challenge of producing complex natural products sustainably and at scale.
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Affiliation(s)
- Haili Zhang
- Institute of Chemical Biology, Shenzhen Bay Laboratory, 518132, Shenzhen, China
| | - Xuyang Li
- Institute of Chemical Biology, Shenzhen Bay Laboratory, 518132, Shenzhen, China
| | - Zhen Hui
- Institute of Chemical Biology, Shenzhen Bay Laboratory, 518132, Shenzhen, China
| | - Shipeng Huang
- Institute of Chemical Biology, Shenzhen Bay Laboratory, 518132, Shenzhen, China
- Department of Chemistry and Shenzhen Grubbs Institute, Southern University of Science and Technology, 518000, Shenzhen, China
| | - Mingwei Cai
- Institute of Chemical Biology, Shenzhen Bay Laboratory, 518132, Shenzhen, China
| | - Wenguang Shi
- Institute of Chemical Biology, Shenzhen Bay Laboratory, 518132, Shenzhen, China
| | - Yang Lin
- Institute of Chemical Biology, Shenzhen Bay Laboratory, 518132, Shenzhen, China
| | - Jie Shen
- College of Life Science and Technology, China Pharmaceutical University, 211198, Nanjing, China
| | - Minghao Sui
- College of Life Science and Technology, China Pharmaceutical University, 211198, Nanjing, China
| | - Qiliang Lai
- Key Laboratory of Marine Genetic Resources, Third Institute of Oceanography, Ministry of Natural Resources, 184 Daxue Road, 361005, Xiamen, China
| | - Zongze Shao
- Key Laboratory of Marine Genetic Resources, Third Institute of Oceanography, Ministry of Natural Resources, 184 Daxue Road, 361005, Xiamen, China
| | - Jie Dou
- College of Life Science and Technology, China Pharmaceutical University, 211198, Nanjing, China
| | - Xiaozhou Luo
- Center for Synthetic Biochemistry, Shenzhen Institute of Synthetic Biology, Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences, 518055, Shenzhen, China
| | - Yun Ge
- Institute of Chemical Biology, Shenzhen Bay Laboratory, 518132, Shenzhen, China
- State Key Laboratory of Chemical Oncogenomics, School of Chemical Biology and Biotechnology, Peking University Shenzhen Graduate School, 518055, Shenzhen, China
| | - Xiaoyu Tang
- Institute of Chemical Biology, Shenzhen Bay Laboratory, 518132, Shenzhen, China
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5
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Ngo TE, Ecker A, Ryu B, Guild A, Remmel A, Boudreau PD, Alexander KL, Naman CB, Glukhov E, Avalon NE, Shende VV, Thomas L, Dahesh S, Nizet V, Gerwick L, Gerwick WH. Structure and Biosynthesis of Hectoramide B, a Linear Depsipeptide from Marine Cyanobacterium Moorena producens JHB Discovered via Coculture with Candida albicans. ACS Chem Biol 2024; 19:619-628. [PMID: 38330248 PMCID: PMC10949194 DOI: 10.1021/acschembio.3c00391] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2023] [Revised: 01/17/2024] [Accepted: 01/18/2024] [Indexed: 02/10/2024]
Abstract
The tropical marine cyanobacterium Moorena producens JHB is a prolific source of secondary metabolites with potential biomedical utility. Previous studies on this strain led to the discovery of several novel compounds such as hectochlorins and jamaicamides. However, bioinformatic analyses of its genome indicate the presence of numerous cryptic biosynthetic gene clusters that have yet to be characterized. To potentially stimulate the production of novel compounds from this strain, it was cocultured with Candida albicans. From this experiment, we observed the increased production of a new compound that we characterize here as hectoramide B. Bioinformatic analysis of the M. producens JHB genome enabled the identification of a putative biosynthetic gene cluster responsible for hectoramide B biosynthesis. This work demonstrates that coculture competition experiments can be a valuable method to facilitate the discovery of novel natural products from cyanobacteria.
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Affiliation(s)
- Thuan-Ethan Ngo
- Center
for Marine Biotechnology and Biomedicine, Scripps Institution of Oceanography, University of California San Diego, 9500 Gilman Drive, La Jolla, California 92093, United States
| | - Andrew Ecker
- Center
for Marine Biotechnology and Biomedicine, Scripps Institution of Oceanography, University of California San Diego, 9500 Gilman Drive, La Jolla, California 92093, United States
- Department
of Pharmaceutical Chemistry, Cardiovascular Research Institute, University of California San Francisco, San Francisco, California 94143, United States
| | - Byeol Ryu
- Center
for Marine Biotechnology and Biomedicine, Scripps Institution of Oceanography, University of California San Diego, 9500 Gilman Drive, La Jolla, California 92093, United States
| | - Aurora Guild
- Center
for Marine Biotechnology and Biomedicine, Scripps Institution of Oceanography, University of California San Diego, 9500 Gilman Drive, La Jolla, California 92093, United States
| | - Ariana Remmel
- Center
for Marine Biotechnology and Biomedicine, Scripps Institution of Oceanography, University of California San Diego, 9500 Gilman Drive, La Jolla, California 92093, United States
| | - Paul D. Boudreau
- Center
for Marine Biotechnology and Biomedicine, Scripps Institution of Oceanography, University of California San Diego, 9500 Gilman Drive, La Jolla, California 92093, United States
- Department
of BioMolecular Sciences,University of Mississippi,
School of Pharmacy, University, Mississippi 38677, United States
| | - Kelsey L. Alexander
- Center
for Marine Biotechnology and Biomedicine, Scripps Institution of Oceanography, University of California San Diego, 9500 Gilman Drive, La Jolla, California 92093, United States
- Department
of Chemistry, University of California San
Diego, 9500 Gilman Drive, La Jolla, California 92093, United States
| | - C. Benjamin Naman
- Center
for Marine Biotechnology and Biomedicine, Scripps Institution of Oceanography, University of California San Diego, 9500 Gilman Drive, La Jolla, California 92093, United States
- Department
of Science and Conservation, San Diego Botanic
Garden, 300 Quail Gardens
Drive, Encinitas, California 92024, United States
| | - Evgenia Glukhov
- Center
for Marine Biotechnology and Biomedicine, Scripps Institution of Oceanography, University of California San Diego, 9500 Gilman Drive, La Jolla, California 92093, United States
| | - Nicole E. Avalon
- Center
for Marine Biotechnology and Biomedicine, Scripps Institution of Oceanography, University of California San Diego, 9500 Gilman Drive, La Jolla, California 92093, United States
| | - Vikram V. Shende
- Center
for Marine Biotechnology and Biomedicine, Scripps Institution of Oceanography, University of California San Diego, 9500 Gilman Drive, La Jolla, California 92093, United States
| | - Lamar Thomas
- Department
of Pediatrics, University of California,
San Diego, 9500 Gilman
Drive, La Jolla, California 92093, United States
| | - Samira Dahesh
- Department
of Pediatrics, University of California,
San Diego, 9500 Gilman
Drive, La Jolla, California 92093, United States
| | - Victor Nizet
- Department
of Pediatrics, University of California,
San Diego, 9500 Gilman
Drive, La Jolla, California 92093, United States
- Skaggs
School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, 9500 Gilman Drive, La Jolla, California 92093, United States
| | - Lena Gerwick
- Center
for Marine Biotechnology and Biomedicine, Scripps Institution of Oceanography, University of California San Diego, 9500 Gilman Drive, La Jolla, California 92093, United States
| | - William H. Gerwick
- Center
for Marine Biotechnology and Biomedicine, Scripps Institution of Oceanography, University of California San Diego, 9500 Gilman Drive, La Jolla, California 92093, United States
- Skaggs
School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, 9500 Gilman Drive, La Jolla, California 92093, United States
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6
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Chekan JR, Mydy LS, Pasquale MA, Kersten RD. Plant peptides - redefining an area of ribosomally synthesized and post-translationally modified peptides. Nat Prod Rep 2024. [PMID: 38411572 DOI: 10.1039/d3np00042g] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/28/2024]
Abstract
Covering 1965 to February 2024Plants are prolific peptide chemists and are known to make thousands of different peptidic molecules. These peptides vary dramatically in their size, chemistry, and bioactivity. Despite their differences, all plant peptides to date are biosynthesized as ribosomally synthesized and post-translationally modified peptides (RiPPs). Decades of research in plant RiPP biosynthesis have extended the definition and scope of RiPPs from microbial sources, establishing paradigms and discovering new families of biosynthetic enzymes. The discovery and elucidation of plant peptide pathways is challenging due to repurposing and evolution of housekeeping genes as both precursor peptides and biosynthetic enzymes and due to the low rates of gene clustering in plants. In this review, we highlight the chemistry, biosynthesis, and function of the known RiPP classes from plants and recommend a nomenclature for the recent addition of BURP-domain-derived RiPPs termed burpitides. Burpitides are an emerging family of cyclic plant RiPPs characterized by macrocyclic crosslinks between tyrosine or tryptophan side chains and other amino acid side chains or their peptide backbone that are formed by copper-dependent BURP-domain-containing proteins termed burpitide cyclases. Finally, we review the discovery of plant RiPPs through bioactivity-guided, structure-guided, and gene-guided approaches.
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Affiliation(s)
- Jonathan R Chekan
- Department of Chemistry and Biochemistry, University of North Carolina at Greensboro, Greensboro, NC, USA.
| | - Lisa S Mydy
- Department of Medicinal Chemistry, University of Michigan, Ann Arbor, MI, USA.
| | - Michael A Pasquale
- Department of Chemistry and Biochemistry, University of North Carolina at Greensboro, Greensboro, NC, USA.
| | - Roland D Kersten
- Department of Medicinal Chemistry, University of Michigan, Ann Arbor, MI, USA.
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7
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Bauermeister A, Furtado LC, Ferreira EG, Moreira EA, Jimenez PC, Lopes NP, Araújo WL, Olchanheski LR, Monteiro da Cruz Lotufo T, Costa-Lotufo LV. Chemical and microbial diversity of a tropical intertidal ascidian holobiont. MARINE ENVIRONMENTAL RESEARCH 2024; 194:106303. [PMID: 38150785 DOI: 10.1016/j.marenvres.2023.106303] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/29/2023] [Revised: 12/07/2023] [Accepted: 12/10/2023] [Indexed: 12/29/2023]
Abstract
The tropical ascidian Eudistoma vannamei, endemic to the northeastern coast of Brazil, is considered a prolific source of secondary metabolites and hosts Actinomycetota that produce bioactive compounds. Herein, we used an omics approach to study the ascidian as a holobiont, including the microbial diversity through 16S rRNA gene sequencing and metabolite production using mass spectrometry-based metabolomics. Gene sequencing analysis revealed all samples of E. vannamei shared about 50% of the observed ASVs, and Pseudomonadota (50.7%), Planctomycetota (9.58%), Actinomycetota (10.34%), Bacteroidota (12.05%) were the most abundant bacterial phyla. Analysis of tandem mass spectrometry (MS/MS) data allowed annotation of compounds, including phospholipids, amino acids, and pyrimidine alkaloids, such as staurosporine, a member of a well-known chemical class recognized as a microbial metabolite. Isolated bacteria, mainly belonging to Streptomyces and Micromonospora genera, were cultivated and extracted with ethyl acetate. MS/MS analysis of bacterial extracts allowed annotation of compounds not detected in the ascidian tissue, including marineosin and dihydroergotamine, yielding about 30% overlapped ions between host and isolated bacteria. This study reveals E. vannamei as a rich source of microbial and chemical diversity and, furthermore, highlights the importance of omic tools for a comprehensive investigation of holobiont systems.
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Affiliation(s)
- Anelize Bauermeister
- Departamento de Farmacologia, Instituto de Ciências Biomédicas, Universidade de São Paulo, São Paulo, SP, 05508-000, Brazil; Departamento de Física e Química, Faculdade de Ciências Farmacêuticas de Ribeirão Preto, Universidade de São Paulo, Ribeirão Preto, SP, 14040-903, Brazil
| | - Luciana Costa Furtado
- Departamento de Farmacologia, Instituto de Ciências Biomédicas, Universidade de São Paulo, São Paulo, SP, 05508-000, Brazil
| | - Elthon G Ferreira
- Departamento de Química Orgânica e Inorgânica, Universidade Federal do Ceará, Fortaleza, CE, 60451-970, Brazil
| | - Eduarda Antunes Moreira
- Departamento de Física e Química, Faculdade de Ciências Farmacêuticas de Ribeirão Preto, Universidade de São Paulo, Ribeirão Preto, SP, 14040-903, Brazil
| | | | - Norberto Peporine Lopes
- Departamento de Física e Química, Faculdade de Ciências Farmacêuticas de Ribeirão Preto, Universidade de São Paulo, Ribeirão Preto, SP, 14040-903, Brazil
| | - Welington Luiz Araújo
- Departamento de Microbiologia, Instituto de Ciências Biomédicas, Universidade de São Paulo, São Paulo, SP, 05508-900, Brazil
| | - Luiz Ricardo Olchanheski
- Departamento de Microbiologia, Instituto de Ciências Biomédicas, Universidade de São Paulo, São Paulo, SP, 05508-900, Brazil
| | | | - Leticia Veras Costa-Lotufo
- Departamento de Farmacologia, Instituto de Ciências Biomédicas, Universidade de São Paulo, São Paulo, SP, 05508-000, Brazil.
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8
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Zou X, Hui Z, Shepherd RA, Zhao S, Wu Y, Shen Z, Pang C, Zhou S, Yu Z, Zhou J, Moore BS, Sanchez LM, Tang X. Unveiling a CAAX Protease-Like Protein Involved in Didemnin Drug Maturation and Secretion. ADVANCED SCIENCE (WEINHEIM, BADEN-WURTTEMBERG, GERMANY) 2024; 11:e2306044. [PMID: 38032137 PMCID: PMC10811503 DOI: 10.1002/advs.202306044] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/24/2023] [Revised: 10/29/2023] [Indexed: 12/01/2023]
Abstract
The assembly line biosynthesis of the powerful anticancer-antiviral didemnin cyclic peptides is proposed to follow a prodrug release mechanism in Tristella bacteria. This strategy commences with the formation of N-terminal prodrug scaffolds and culminates in their cleavage during the cellular export of the mature products. In this study, a comprehensive exploration of the genetic and biochemical aspects of the enzymes responsible for both the assembly and cleavage of the acylated peptide prodrug scaffolds is provided. This process involves the assembly of N-acyl-polyglutamine moieties orchestrated by the nonribosomal peptide synthetase DidA and the cleavage of these components at the post-assembly stage by DidK, a transmembrane CAAX hydrolase homolog. The findings not only shed light on the complex prodrug mechanism that underlies the synthesis and secretion of didemnin compounds but also offer novel insights into the expanded role of CAAX hydrolases in microbes. Furthermore, this knowledge can be leveraged for the strategic design of genome mining approaches aimed at discovering new bioactive natural products that employ similar prodrug biochemical strategies.
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Affiliation(s)
- Xiaolin Zou
- Institute of Chemical BiologyShenzhen Bay LaboratoryShenzhen518132China
| | - Zhen Hui
- Institute of Chemical BiologyShenzhen Bay LaboratoryShenzhen518132China
| | - Robert A. Shepherd
- Department of Chemistry and BiochemistryUniversity of California Santa CruzSanta CruzCA95064USA
| | - Shuaiqiang Zhao
- Institute of Chemical BiologyShenzhen Bay LaboratoryShenzhen518132China
| | - Yanfei Wu
- CAS Key Laboratory of Quantitative Engineering BiologyShenzhen Institute of Synthetic BiologyShenzhen Institute of Advanced TechnologyChinese Academy of SciencesShenzhen518055China
| | - Zhuanglin Shen
- CAS Key Laboratory of Quantitative Engineering BiologyShenzhen Institute of Synthetic BiologyShenzhen Institute of Advanced TechnologyChinese Academy of SciencesShenzhen518055China
| | - Cuiping Pang
- CAS Key Laboratory of Quantitative Engineering BiologyShenzhen Institute of Synthetic BiologyShenzhen Institute of Advanced TechnologyChinese Academy of SciencesShenzhen518055China
| | - Shipeng Zhou
- Institute of Chemical BiologyShenzhen Bay LaboratoryShenzhen518132China
| | - Zehai Yu
- Institute of Chemical BiologyShenzhen Bay LaboratoryShenzhen518132China
| | - Jiahai Zhou
- CAS Key Laboratory of Quantitative Engineering BiologyShenzhen Institute of Synthetic BiologyShenzhen Institute of Advanced TechnologyChinese Academy of SciencesShenzhen518055China
| | - Bradly S. Moore
- Scripps Institution of OceanographyUniversity of California San DiegoLa JollaCA92093USA
- Skaggs School of Pharmacy and Pharmaceutical SciencesUniversity of California San DiegoLa JollaCA92093USA
| | - Laura M. Sanchez
- Department of Chemistry and BiochemistryUniversity of California Santa CruzSanta CruzCA95064USA
| | - Xiaoyu Tang
- Institute of Chemical BiologyShenzhen Bay LaboratoryShenzhen518132China
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9
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Jia K, Wang J, Zhai R, Du Y, Kira J, Wu C, Qian PY, Zhang W. Abi Family Protein, DidK, Is Involved in the Maturation of Anticancer Depsipeptide, Didemnin B. ACS Chem Biol 2023; 18:2300-2308. [PMID: 37773034 DOI: 10.1021/acschembio.3c00393] [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: 09/30/2023]
Abstract
Didemnin B is a marine-derived depsipeptide with potent antiviral and anticancer activities. A prodrug activation mechanism was previously proposed for the biosynthesis of didemnin B by the nonribosomal peptide synthetase/polyketide synthase (NRPS/PKS) assembly line, but the enzyme involved in the maturation process remained unknown. Herein, we demonstrated that DidA, a dimodular NRPS predicted with unrelated activity to didemnin B structure assembly, was indispensable to produce didemnin B, confirming the prodrug mechanism in didemnin B biosynthesis. We further identified an Abi family transmembrane protease, DidK, that functioned as an esterase in the maturation step of didemnin B by in vivo gene knockout and heterologous expression. DidK is structurally distinct from other known hydrolytic enzymes involved in the maturation of bacterial nonribosomal peptides and is the first Abi family protein known to participate in NRPS/PKS-derived natural product production. Further bioinformatic analysis revealed more than 20 DidK homologues encoded in bacterial NRPS/PKS BGCs, suggesting that the involvement of Abi family proteins in natural product biosynthesis might not be rare. These results not only clarify the priming and maturation steps of didemnin B biosynthesis but also expand the function scope of Abi family proteins.
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Affiliation(s)
- Kaimin Jia
- Department of Chemical and Biomolecular Engineering, University of California Berkeley, Berkeley, California 94720, United States
- California Institute for Quantitative Biosciences, University of California Berkeley, Berkeley, California 94720, United States
| | - Jiayu Wang
- Department of Chemistry, University of California Berkeley, Berkeley, California 94720, United States
| | - Rui Zhai
- Department of Chemical and Biomolecular Engineering, University of California Berkeley, Berkeley, California 94720, United States
- California Institute for Quantitative Biosciences, University of California Berkeley, Berkeley, California 94720, United States
| | - Yongle Du
- Department of Chemical and Biomolecular Engineering, University of California Berkeley, Berkeley, California 94720, United States
- California Institute for Quantitative Biosciences, University of California Berkeley, Berkeley, California 94720, United States
| | - Jenna Kira
- Department of Chemical and Biomolecular Engineering, University of California Berkeley, Berkeley, California 94720, United States
| | - Chuanhai Wu
- Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou), Guangzhou 511458, China
- Department of Ocean Science, The Hong Kong University of Science and Technology, Clear Water Bay, Kowloon, Hong Kong 999077, China
| | - Pei-Yuan Qian
- Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou), Guangzhou 511458, China
- Department of Ocean Science, The Hong Kong University of Science and Technology, Clear Water Bay, Kowloon, Hong Kong 999077, China
| | - Wenjun Zhang
- Department of Chemical and Biomolecular Engineering, University of California Berkeley, Berkeley, California 94720, United States
- California Institute for Quantitative Biosciences, University of California Berkeley, Berkeley, California 94720, United States
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10
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Cooreman K, De Spiegeleer B, Van Poucke C, Vanavermaete D, Delbare D, Wynendaele E, De Witte B. Emerging pharmaceutical therapies of Ascidian-derived natural products and derivatives. ENVIRONMENTAL TOXICOLOGY AND PHARMACOLOGY 2023; 102:104254. [PMID: 37648122 DOI: 10.1016/j.etap.2023.104254] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/02/2023] [Revised: 08/22/2023] [Accepted: 08/23/2023] [Indexed: 09/01/2023]
Abstract
In a growing multidrug-resistant environment, the identification of potential new drug candidates with an acceptable safety profile is a substantial crux in pharmaceutical discovery. This review discusses several aspects and properties of approved marine natural products derived from ascidian sources (phylum Chordata, subphylum Tunicata) and/or their deduced analogues including their biosynthetic origin, (bio)chemical preclinical assessments and known efficacy-safety profiles, clinical status in trials, but also translational developments, opportunities and final conclusions. The review also describes the preclinical assessments of a large number of other ascidian compounds that have not been involved in clinical trials yet. Finally, the emerging research on the connectivity of the ascidian hosts and their independent or obligate symbiotic guests is discussed. The review covers the latest information on the topic of ascidian-derived marine natural products over the last two decades including 2022, with the majority of publications published in the last decade.
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Affiliation(s)
- Kris Cooreman
- Aquatic Environment and Quality, Animal Sciences Unit, Flanders Research Institute for Agriculture, Fisheries and Food, Jacobsenstraat 1, BE-8400 Ostend, Belgium
| | - Bart De Spiegeleer
- Faculty of Pharmaceutical Sciences, Drug Quality and Registration Group, Ghent University, Ottergemsesteenweg 460, BE-9000 Ghent, Belgium
| | - Christof Van Poucke
- Technology and Food Science Unit, Flanders Research Institute for Agriculture, Fisheries and Food, Brusselsesteenweg 370, BE-9090 Melle, Belgium
| | - David Vanavermaete
- Aquatic Environment and Quality, Animal Sciences Unit, Flanders Research Institute for Agriculture, Fisheries and Food, Jacobsenstraat 1, BE-8400 Ostend, Belgium
| | - Daan Delbare
- Aquatic Environment and Quality, Animal Sciences Unit, Flanders Research Institute for Agriculture, Fisheries and Food, Jacobsenstraat 1, BE-8400 Ostend, Belgium
| | - Evelien Wynendaele
- Faculty of Pharmaceutical Sciences, Drug Quality and Registration Group, Ghent University, Ottergemsesteenweg 460, BE-9000 Ghent, Belgium
| | - Bavo De Witte
- Aquatic Environment and Quality, Animal Sciences Unit, Flanders Research Institute for Agriculture, Fisheries and Food, Jacobsenstraat 1, BE-8400 Ostend, Belgium.
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11
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Makris C, Leckrone JK, Butler A. Tistrellabactins A and B Are Photoreactive C-Diazeniumdiolate Siderophores from the Marine-Derived Strain Tistrella mobilis KA081020-065. JOURNAL OF NATURAL PRODUCTS 2023; 86:1770-1778. [PMID: 37341506 PMCID: PMC10391617 DOI: 10.1021/acs.jnatprod.3c00230] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/22/2023] [Indexed: 06/22/2023]
Abstract
The C-diazeniumdiolate group in the amino acid graminine is emerging as a new microbially produced Fe(III) coordinating ligand in siderophores, which is photoreactive. While the few siderophores reported from this class have only been isolated from soil-associated microbes, here we report the first C-diazeniumdiolate siderophores tistrellabactins A and B, isolated from the bioactive marine-derived strain Tistrella mobilis KA081020-065. The structural characterization of the tistrellabactins reveals unique biosynthetic features including an NRPS module iteratively loading glutamine residues and a promiscuous adenylation domain yielding either tistrellabactin A with an asparagine residue or tistrellabactin B with an aspartic acid residue at analogous positions. Beyond the function of scavenging Fe(III) for growth, these siderophores are photoreactive upon irradiation with UV light, releasing the equivalent of nitric oxide (NO) and an H atom from the C-diazeniumdiolate group. Fe(III)-tistrellabactin is also photoreactive, with both the C-diazeniumdiolate and the β-hydroxyaspartate residues undergoing photoreactions, resulting in a photoproduct without the ability to chelate Fe(III).
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Affiliation(s)
- Christina Makris
- Department of Chemistry &
Biochemistry, University of California, Santa Barbara, California 93106-9510, United States
| | - Jamie K. Leckrone
- Department of Chemistry &
Biochemistry, University of California, Santa Barbara, California 93106-9510, United States
| | - Alison Butler
- Department of Chemistry &
Biochemistry, University of California, Santa Barbara, California 93106-9510, United States
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12
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Ngo TE, Ecker A, Guild A, Remmel A, Boudreau PD, Alexander KL, Naman CB, Glukhov E, Avalon NE, Shende VV, Gerwick L, Gerwick WH. Structure and Biosynthesis of Hectoramide B, a Linear Depsipeptide from the Marine Cyanobacterium Moorena producens JHB Discovered via Co-culture with Candida albicans. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.07.06.547815. [PMID: 37461655 PMCID: PMC10350029 DOI: 10.1101/2023.07.06.547815] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 07/25/2023]
Abstract
The tropical marine cyanobacterium Moorena producens JHB is a prolific source of secondary metabolites with potential biomedical utility. Previous studies of this strain led to the discovery of several novel compounds such as the hectochlorins and jamaicamides; however, bioinformatic analyses of its genome suggested that there were many more cryptic biosynthetic gene clusters yet to be characterized. To potentially stimulate the production of novel compounds from this strain, it was co-cultured with Candida albicans. From this experiment, we observed the increased production of a new compound that we characterize here as hectoramide B. Bioinformatic analysis of the M. producens JHB genome enabled the identification of a putative biosynthetic gene cluster responsible for hectoramide B biosynthesis. This work demonstrates that co-culture competition experiments can be a valuable method to facilitate the discovery of novel natural products from cyanobacteria.
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Affiliation(s)
- Thuan-Ethan Ngo
- Center for Marine Biotechnology and Biomedicine, Scripps Institution of Oceanography, University of California San Diego, 9500 Gilman Drive, La Jolla, CA, 92093, USA
| | - Andrew Ecker
- Center for Marine Biotechnology and Biomedicine, Scripps Institution of Oceanography, University of California San Diego, 9500 Gilman Drive, La Jolla, CA, 92093, USA
- Department of Pharmaceutical Chemistry, Cardiovascular Research Institute, University of California, San Francisco, San Francisco, CA, USA
| | - Aurora Guild
- Center for Marine Biotechnology and Biomedicine, Scripps Institution of Oceanography, University of California San Diego, 9500 Gilman Drive, La Jolla, CA, 92093, USA
| | - Ariana Remmel
- Center for Marine Biotechnology and Biomedicine, Scripps Institution of Oceanography, University of California San Diego, 9500 Gilman Drive, La Jolla, CA, 92093, USA
| | - Paul D Boudreau
- Center for Marine Biotechnology and Biomedicine, Scripps Institution of Oceanography, University of California San Diego, 9500 Gilman Drive, La Jolla, CA, 92093, USA
- Department of BioMolecular Sciences, University of Mississippi School of Pharmacy, University, Mississippi 38677, USA
| | - Kelsey L Alexander
- Center for Marine Biotechnology and Biomedicine, Scripps Institution of Oceanography, University of California San Diego, 9500 Gilman Drive, La Jolla, CA, 92093, USA
- Department of Chemistry, University of California San Diego, 9500 Gilman Drive, La Jolla, CA 92093, USA
| | - C Benjamin Naman
- Center for Marine Biotechnology and Biomedicine, Scripps Institution of Oceanography, University of California San Diego, 9500 Gilman Drive, La Jolla, CA, 92093, USA
- Department of Science and Conservation, San Diego Botanic Garden, 300 Quail Gardens Drive, Encinitas, CA, 92024, USA
| | - Evgenia Glukhov
- Center for Marine Biotechnology and Biomedicine, Scripps Institution of Oceanography, University of California San Diego, 9500 Gilman Drive, La Jolla, CA, 92093, USA
| | - Nicole E Avalon
- Center for Marine Biotechnology and Biomedicine, Scripps Institution of Oceanography, University of California San Diego, 9500 Gilman Drive, La Jolla, CA, 92093, USA
| | - Vikram V Shende
- Center for Marine Biotechnology and Biomedicine, Scripps Institution of Oceanography, University of California San Diego, 9500 Gilman Drive, La Jolla, CA, 92093, USA
| | - Lena Gerwick
- Center for Marine Biotechnology and Biomedicine, Scripps Institution of Oceanography, University of California San Diego, 9500 Gilman Drive, La Jolla, CA, 92093, USA
| | - William H Gerwick
- Center for Marine Biotechnology and Biomedicine, Scripps Institution of Oceanography, University of California San Diego, 9500 Gilman Drive, La Jolla, CA, 92093, USA
- Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, 9500 Gilman Drive, La Jolla, CA, 92093, USA
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13
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Hu JS, He YP, Zhou FG, Wu PP, Chen LY, Ni C, Zhang ZK, Xiao XJ, An LK, He XX, Zhang CX. New Indole Diketopiperazine Alkaloids from Soft Coral-Associated Epiphytic Fungus Aspergillus versicolor CGF 9-1-2. Chem Biodivers 2023; 20:e202300301. [PMID: 37097072 DOI: 10.1002/cbdv.202300301] [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: 02/28/2023] [Revised: 04/23/2023] [Accepted: 04/23/2023] [Indexed: 04/26/2023]
Abstract
Two new indole diketopiperazine alkaloids (IDAs), (+)19-epi-sclerotiamide (1) and (-)19-epi-sclerotiamide (2), along with 13 known analogs (3-15), were isolated from a soft coral-associated epiphytic fungus Aspergillus versicolor CGF 9-1-2. The structures of two new compounds were established based on the combination of HR-ESI-MS, 1D and 2D NMR spectroscopy, optical rotation measurements and quantum chemical 13 C-NMR, the absolute configurations were determined by experimental and electronic circular dichroism (ECD) calculations. The results of molecular docking showed that all the compounds had a good binding with TDP1, TDP2, TOP1, TOP2, Ache, NLRP3, EGFR, EGFR L858R, EGFR T790M and EGFR T790/L858. Biological evaluation of compounds 3, 6, 8, 11 showed that 3 exerted a strong inhibitory effect on TDP2 with a rate of 81.72 %.
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Affiliation(s)
- Jin-Shan Hu
- School of Pharmaceutical Sciences, Guangzhou University of Chinese Medicine, Guangzhou, 510006, P. R. China
- The First Compulsory Isolated Detoxification Center of Shenzhen, Municipal Bureau of Justice, Shenzhen, 518024, P. R. China
| | - Yu-Pei He
- School of Pharmaceutical Sciences, Guangzhou University of Chinese Medicine, Guangzhou, 510006, P. R. China
| | - Feng-Guo Zhou
- School of Pharmaceutical Sciences, Guangzhou University of Chinese Medicine, Guangzhou, 510006, P. R. China
| | - Ping-Ping Wu
- School of Pharmaceutical Sciences, Guangzhou University of Chinese Medicine, Guangzhou, 510006, P. R. China
| | - Le-Yi Chen
- School of Pharmaceutical Sciences, Guangzhou University of Chinese Medicine, Guangzhou, 510006, P. R. China
| | - Cheng Ni
- School of Pharmaceutical Sciences, Guangzhou University of Chinese Medicine, Guangzhou, 510006, P. R. China
| | - Ze-Kun Zhang
- School of Pharmaceutical Sciences, Guangzhou University of Chinese Medicine, Guangzhou, 510006, P. R. China
| | - Xi-Ji Xiao
- School of Pharmaceutical Sciences, Guangzhou University of Chinese Medicine, Guangzhou, 510006, P. R. China
| | - Lin-Kun An
- School of Pharmaceutical Sciences, Sun Yat-Sen University, Guangzhou, 510006, P. R. China
| | - Xi-Xin He
- School of Pharmaceutical Sciences, Guangzhou University of Chinese Medicine, Guangzhou, 510006, P. R. China
| | - Cui-Xian Zhang
- School of Pharmaceutical Sciences, Guangzhou University of Chinese Medicine, Guangzhou, 510006, P. R. China
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14
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Bogdanov A, Salib MN, Chase AB, Hammerlindl H, Muskat MN, Luedtke S, Barbosa da Silva E, O’Donoghue AJ, Wu LF, Altschuler SJ, Molinski TF, Jensen PR. Small Molecule in situ Resin Capture - A Compound First Approach to Natural Product Discovery. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.03.02.530684. [PMID: 37398257 PMCID: PMC10312467 DOI: 10.1101/2023.03.02.530684] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/04/2023]
Abstract
Microbial natural products remain an important resource for drug discovery. Yet, commonly employed discovery techniques are plagued by the rediscovery of known compounds, the relatively few microbes that can be cultured, and laboratory growth conditions that do not elicit biosynthetic gene expression among myriad other challenges. Here we introduce a culture independent approach to natural product discovery that we call the Small Molecule In situ Resin Capture (SMIRC) technique. SMIRC exploits in situ environmental conditions to elicit compound production and represents a new approach to access poorly explored chemical space by capturing natural products directly from the environments in which they are produced. In contrast to traditional methods, this compound-first approach can capture structurally complex small molecules across all domains of life in a single deployment while relying on Nature to provide the complex and poorly understood environmental cues needed to elicit biosynthetic gene expression. We illustrate the effectiveness of SMIRC in marine habitats with the discovery of numerous new compounds and demonstrate that sufficient compound yields can be obtained for NMR-based structure assignment. Two new compound classes are reported including one novel carbon skeleton that possesses a functional group not previously observed among natural products and a second that possesses potent biological activity. We introduce expanded deployments, in situ cultivation, and metagenomics as methods to facilitate compound discovery, enhance yields, and link compounds to producing organisms. This compound first approach can provide unprecedented access to new natural product chemotypes with broad implications for drug discovery.
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Affiliation(s)
- Alexander Bogdanov
- Scripps Institution of Oceanography, University of California, San Diego, La Jolla, CA 92093, USA
| | - Mariam N. Salib
- Department of Chemistry and Biochemistry, University of California, San Diego, La Jolla, CA 92093, USA
| | - Alexander B. Chase
- Scripps Institution of Oceanography, University of California, San Diego, La Jolla, CA 92093, USA
- Department of Earth Sciences, Southern Methodist University, Dallas, TX 75275, USA
| | - Heinz Hammerlindl
- Department of Pharmaceutical Chemistry, University of California, San Francisco, San Francisco, CA 94158, USA
| | - Mitchell N. Muskat
- Scripps Institution of Oceanography, University of California, San Diego, La Jolla, CA 92093, USA
| | - Stephanie Luedtke
- Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California, San Diego, La Jolla, CA 92093
| | - Elany Barbosa da Silva
- Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California, San Diego, La Jolla, CA 92093
| | - Anthony J. O’Donoghue
- Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California, San Diego, La Jolla, CA 92093
| | - Lani F. Wu
- Department of Pharmaceutical Chemistry, University of California, San Francisco, San Francisco, CA 94158, USA
| | - Steven J. Altschuler
- Department of Pharmaceutical Chemistry, University of California, San Francisco, San Francisco, CA 94158, USA
| | - Tadeusz F. Molinski
- Department of Chemistry and Biochemistry, University of California, San Diego, La Jolla, CA 92093, USA
| | - Paul R. Jensen
- Scripps Institution of Oceanography, University of California, San Diego, La Jolla, CA 92093, USA
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15
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Impact of Marine Chemical Ecology Research on the Discovery and Development of New Pharmaceuticals. Mar Drugs 2023; 21:md21030174. [PMID: 36976223 PMCID: PMC10055925 DOI: 10.3390/md21030174] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2023] [Revised: 03/04/2023] [Accepted: 03/08/2023] [Indexed: 03/12/2023] Open
Abstract
Diverse ecologically important metabolites, such as allelochemicals, infochemicals and volatile organic chemicals, are involved in marine organismal interactions. Chemically mediated interactions between intra- and interspecific organisms can have a significant impact on community organization, population structure and ecosystem functioning. Advances in analytical techniques, microscopy and genomics are providing insights on the chemistry and functional roles of the metabolites involved in such interactions. This review highlights the targeted translational value of several marine chemical ecology-driven research studies and their impact on the sustainable discovery of novel therapeutic agents. These chemical ecology-based approaches include activated defense, allelochemicals arising from organismal interactions, spatio-temporal variations of allelochemicals and phylogeny-based approaches. In addition, innovative analytical techniques used in the mapping of surface metabolites as well as in metabolite translocation within marine holobionts are summarized. Chemical information related to the maintenance of the marine symbioses and biosyntheses of specialized compounds can be harnessed for biomedical applications, particularly in microbial fermentation and compound production. Furthermore, the impact of climate change on the chemical ecology of marine organisms—especially on the production, functionality and perception of allelochemicals—and its implications on drug discovery efforts will be presented.
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16
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Botryllin, a Novel Antimicrobial Peptide from the Colonial Ascidian Botryllus schlosseri. Mar Drugs 2023; 21:md21020074. [PMID: 36827115 PMCID: PMC9966394 DOI: 10.3390/md21020074] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2022] [Revised: 01/12/2023] [Accepted: 01/18/2023] [Indexed: 01/24/2023] Open
Abstract
By mining the transcriptome of the colonial ascidian Botryllus schlosseri, we identified a transcript for a novel styelin-like antimicrobial peptide, which we named botryllin. The gene is constitutively transcribed by circulating cytotoxic morula cells (MCs) as a pre-propeptide that is then cleaved to mature peptide. The synthetic peptide, obtained from in silico translation of the transcript, shows robust killing activity of bacterial and unicellular yeast cells, causing breakages of both the plasma membrane and the cell wall. Specific monoclonal antibodies were raised against the epitopes of the putative amino acid sequence of the propeptide and the mature peptide; in both cases, they label the MC granular content. Upon MC degranulation induced by the presence of nonself, the antibodies recognise the extracellular nets with entrapped bacteria nearby MC remains. The obtained results suggest that the botryllin gene carries the information for the synthesis of an AMP involved in the protection of B. schlosseri from invading foreign cells.
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17
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Stankey RJ, Johnson D, Duggan BM, Mead DA, La Clair JJ. A Survey of Didemnin Depsipeptide Production in Tistrella. Mar Drugs 2023; 21:md21020056. [PMID: 36827097 PMCID: PMC9964501 DOI: 10.3390/md21020056] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2022] [Revised: 01/07/2023] [Accepted: 01/12/2023] [Indexed: 01/19/2023] Open
Abstract
As one of the first families of marine natural products to undergo clinical trials, the didemnin depsipeptides have played a significant role in inspiring the discovery of marine drugs. Originally developed as anticancer therapeutics, the recent re-evaluation of these compounds including synthetically derived dehydrodidemnin B or Aplidine, has led to their advancement towards antiviral applications. While conventionally associated with production in colonial tunicates of the family Didemnidae, recent studies have identified their biosynthetic gene clusters from the marine-derived bacteria Tistrella mobilis. While these studies confirm the production of didemnin X/Y, the low titer and general lack of understanding of their biosynthesis in Tistrella currently prevents the development of effective microbial or synthetic biological approaches for their production. To this end, we conducted a survey of known species of Tistrella and report on their ability to produce the didemnin depsipeptides. These data were used to develop conditions to produce didemnin B at titers over 15 mg/L.
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Affiliation(s)
| | - Don Johnson
- Terra Bioworks Inc., Middleton, WI 53562, USA
| | - Brendan M. Duggan
- Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California, 9500 Gilman Drive, San Diego, CA 92093-0657, USA
| | - David A. Mead
- Terra Bioworks Inc., Middleton, WI 53562, USA
- Correspondence: (D.A.M.); (J.J.L.C.)
| | - James J. La Clair
- Department of Chemistry and Biochemistry, University of California, San Diego, CA 92093-0358, USA
- Xenobe Research Institute, P.O. Box 3052, San Diego, CA 92163-1052, USA
- Correspondence: (D.A.M.); (J.J.L.C.)
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18
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Yu J, Hermann M, Smith R, Tomm H, Metwally H, Kolwich J, Liu C, Le Blanc JCY, Covey TR, Ross AC, Oleschuk R. Hyperspectral Visualization-Based Mass Spectrometry Imaging by LMJ-SSP: A Novel Strategy for Rapid Natural Product Profiling in Bacteria. Anal Chem 2023; 95:2020-2028. [PMID: 36634199 DOI: 10.1021/acs.analchem.2c04550] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023]
Abstract
Mass spectrometry imaging (MSI) has been widely used to discover natural products (NPs) from underexplored microbiological sources. However, the technique is limited by incompatibility with complicated/uneven surface topography and labor-intensive sample preparation, as well as lengthy compound profiling procedures. Here, liquid micro-junction surface sampling probe (LMJ-SSP)-based MSI is used for rapid profiling of natural products from Gram-negative marine bacteria Pseudoalteromonas on nutrient agar media without any sample preparation. A conductance-based autosampling platform with 1 mm spatial resolution and an innovative multivariant analysis-driven method was used to create one hyperspectral image for the sampling area. NP discovery requires general spatial correlation between m/z and colony location but not highly precise spatial resolution. The hyperspectral image was used to annotate different m/z by straightforward color differences without the need to directly interrogate the spectra. To demonstrate the utility of our approach, the rapid analysis of Pseudoalteromonas rubra DSM6842, Pseudoalteromonas tunicata DSM14096, Pseudoalteromonas piscicida JCM20779, and Pseudoalteromonas elyakovii ATCC700519 cultures was directly performed on Agar. Various natural products, including prodiginine and tambjamine analogues, were quickly identified from the hyperspectral image, and the dynamic extracellular environment was shown with compound heatmaps. Hyperspectral visualization-based MSI is an efficient and sensitive strategy for direct and rapid natural product profiling from different Pseudoalteromonas strains.
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Affiliation(s)
- Jian Yu
- Department of Chemistry, Queen's University, Kingston, Ontario K7L 3N6, Canada
| | - Matthias Hermann
- Department of Chemistry, Queen's University, Kingston, Ontario K7L 3N6, Canada
| | - Rachael Smith
- Department of Chemistry, Queen's University, Kingston, Ontario K7L 3N6, Canada
| | - Hailey Tomm
- Department of Chemistry, Queen's University, Kingston, Ontario K7L 3N6, Canada
| | - Haidy Metwally
- Department of Chemistry, Queen's University, Kingston, Ontario K7L 3N6, Canada
| | - Jennifer Kolwich
- Department of Chemistry, Queen's University, Kingston, Ontario K7L 3N6, Canada
| | - Chang Liu
- SCIEX, Concord, Ontario L4K 4 V8, Canada
| | | | | | - Avena C Ross
- Department of Chemistry, Queen's University, Kingston, Ontario K7L 3N6, Canada
| | - Richard Oleschuk
- Department of Chemistry, Queen's University, Kingston, Ontario K7L 3N6, Canada
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19
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Li H, Li Z. The Exploration of Microbial Natural Products and Metabolic Interaction Guided by Mass Spectrometry Imaging. Bioengineering (Basel) 2022; 9:707. [PMID: 36421108 PMCID: PMC9687252 DOI: 10.3390/bioengineering9110707] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2022] [Revised: 11/02/2022] [Accepted: 11/12/2022] [Indexed: 10/17/2023] Open
Abstract
As an impressive mass spectrometry technology, mass spectrometric imaging (MSI) can provide mass spectra data and spatial distribution of analytes simultaneously. MSI has been widely used in diverse fields such as clinical diagnosis, the pharmaceutical industry and environmental study due to its accuracy, high resolution and developing reproducibility. Natural products (NPs) have been a critical source of leading drugs; almost half of marketed drugs are derived from NPs or their derivatives. The continuous search for bioactive NPs from microorganisms or microbiomes has always been attractive. MSI allows us to analyze and characterize NPs directly in monocultured microorganisms or a microbial community. In this review, we briefly introduce current mainstream ionization technologies for microbial samples and the key issue of sample preparation, and then summarize some applications of MSI in the exploration of microbial NPs and metabolic interaction, especially NPs from marine microbes. Additionally, remaining challenges and future prospects are discussed.
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Affiliation(s)
| | - Zhiyong Li
- State Key Laboratory of Microbial Metabolism, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai 200240, China
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20
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Yu Y, van der Donk WA. Biosynthesis of 3-thia-α-amino acids on a carrier peptide. Proc Natl Acad Sci U S A 2022; 119:e2205285119. [PMID: 35787182 PMCID: PMC9303977 DOI: 10.1073/pnas.2205285119] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2022] [Accepted: 05/23/2022] [Indexed: 11/18/2022] Open
Abstract
A subset of natural products, such as polyketides and nonribosomal peptides, is biosynthesized while tethered to a carrier peptide via a thioester linkage. Recently, we reported that the biosyntheses of 3-thiaglutamate and ammosamide, single amino acid-derived natural products, employ a very different type of carrier peptide to which the biosynthetic intermediates are bound via an amide linkage. During their biosyntheses, a peptide aminoacyl-transfer ribonucleic acid (tRNA) ligase (PEARL) first loads an amino acid to the C terminus of the carrier peptide for subsequent modification by other enzymes. Proteolytic removal of the modified C-terminal amino acid yields the mature product. We termed natural products that are biosynthesized using such pathways pearlins. To investigate the diversity of pearlins, in this study we experimentally characterized another PEARL-encoding biosynthetic gene cluster (BGC) from Tistrella mobilis (tmo). The enzymes encoded in the tmo BGC transformed cysteine into 3-thiahomoleucine both in vitro and in Escherichia coli. During this process, a cobalamin-dependent radical S-adenosylmethionine (SAM) enzyme catalyzes C-isopropylation. This work illustrates that the biosynthesis of amino acid-derived natural products on a carrier peptide is a widespread strategy in nature and expands the spectrum of thiahemiaminal analogs of amino acids that may serve a broader, currently unknown function.
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Affiliation(s)
- Yue Yu
- Department of Chemistry, University of Illinois at Urbana–Champaign, Urbana, IL 61801
- HHMI, University of Illinois at Urbana–Champaign, Urbana, IL 61801
| | - Wilfred A. van der Donk
- Department of Chemistry, University of Illinois at Urbana–Champaign, Urbana, IL 61801
- HHMI, University of Illinois at Urbana–Champaign, Urbana, IL 61801
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21
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Nuzzo G, Senese G, Gallo C, Albiani F, Romano L, d’Ippolito G, Manzo E, Fontana A. Antitumor Potential of Immunomodulatory Natural Products. Mar Drugs 2022; 20:md20060386. [PMID: 35736189 PMCID: PMC9229642 DOI: 10.3390/md20060386] [Citation(s) in RCA: 15] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2022] [Revised: 05/23/2022] [Accepted: 05/24/2022] [Indexed: 12/11/2022] Open
Abstract
Cancer is one of the leading causes of death globally. Anticancer drugs aim to block tumor growth by killing cancerous cells in order to prevent tumor progression and metastasis. Efficient anticancer drugs should also minimize general toxicity towards organs and healthy cells. Tumor growth can also be successfully restrained by targeting and modulating immune response. Cancer immunotherapy is assuming a growing relevance in the fight against cancer and has recently aroused much interest for its wider safety and the capability to complement conventional chemotherapeutic approaches. Natural products are a traditional source of molecules with relevant potential in the pharmacological field. The huge structural diversity of metabolites with low molecular weight (small molecules) from terrestrial and marine organisms has provided lead compounds for the discovery of many modern anticancer drugs. Many natural products combine chemo-protective and immunomodulant activity, thus offering the potential to be used alone or in association with conventional cancer therapy. In this review, we report the natural products known to possess antitumor properties by interaction with immune system, as well as discuss the possible immunomodulatory mechanisms of these molecules.
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Affiliation(s)
- Genoveffa Nuzzo
- Bio-Organic Chemistry Unit, Institute of Biomolecular Chemistry-CNR, Via Campi Flegrei 34, 80078 Pozzuoli, Italy; (G.S.); (C.G.); (F.A.); (L.R.); (G.d.); (A.F.)
- Correspondence: (G.N.); (E.M.); Tel.: +39-081-8675104 (G.N.); +39-081-8675177 (E.M.)
| | - Giuseppina Senese
- Bio-Organic Chemistry Unit, Institute of Biomolecular Chemistry-CNR, Via Campi Flegrei 34, 80078 Pozzuoli, Italy; (G.S.); (C.G.); (F.A.); (L.R.); (G.d.); (A.F.)
| | - Carmela Gallo
- Bio-Organic Chemistry Unit, Institute of Biomolecular Chemistry-CNR, Via Campi Flegrei 34, 80078 Pozzuoli, Italy; (G.S.); (C.G.); (F.A.); (L.R.); (G.d.); (A.F.)
| | - Federica Albiani
- Bio-Organic Chemistry Unit, Institute of Biomolecular Chemistry-CNR, Via Campi Flegrei 34, 80078 Pozzuoli, Italy; (G.S.); (C.G.); (F.A.); (L.R.); (G.d.); (A.F.)
| | - Lucia Romano
- Bio-Organic Chemistry Unit, Institute of Biomolecular Chemistry-CNR, Via Campi Flegrei 34, 80078 Pozzuoli, Italy; (G.S.); (C.G.); (F.A.); (L.R.); (G.d.); (A.F.)
| | - Giuliana d’Ippolito
- Bio-Organic Chemistry Unit, Institute of Biomolecular Chemistry-CNR, Via Campi Flegrei 34, 80078 Pozzuoli, Italy; (G.S.); (C.G.); (F.A.); (L.R.); (G.d.); (A.F.)
| | - Emiliano Manzo
- Bio-Organic Chemistry Unit, Institute of Biomolecular Chemistry-CNR, Via Campi Flegrei 34, 80078 Pozzuoli, Italy; (G.S.); (C.G.); (F.A.); (L.R.); (G.d.); (A.F.)
- Correspondence: (G.N.); (E.M.); Tel.: +39-081-8675104 (G.N.); +39-081-8675177 (E.M.)
| | - Angelo Fontana
- Bio-Organic Chemistry Unit, Institute of Biomolecular Chemistry-CNR, Via Campi Flegrei 34, 80078 Pozzuoli, Italy; (G.S.); (C.G.); (F.A.); (L.R.); (G.d.); (A.F.)
- Department of Biology, University of Naples Federico II, Via Cinthia–Bld. 7, 80126 Napoli, Italy
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22
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Kolodiazhnyi О, Kolodiazhna A, Grishkun E, Prysiazhnuk D, Kolodiazhna O, Sheiko S. Achievements in developments of organophosphorus stereochemistry. PHOSPHORUS SULFUR 2022. [DOI: 10.1080/10426507.2021.2011874] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
Affiliation(s)
- Оleg Kolodiazhnyi
- V.P. Kukhar Institute of Bioorganic Chemistry and Petrochemistry, NAS of Ukraine, Kiev, Ukraine
| | - Anastasy Kolodiazhna
- V.P. Kukhar Institute of Bioorganic Chemistry and Petrochemistry, NAS of Ukraine, Kiev, Ukraine
| | - Evgen Grishkun
- V.P. Kukhar Institute of Bioorganic Chemistry and Petrochemistry, NAS of Ukraine, Kiev, Ukraine
| | - Dmitry Prysiazhnuk
- V.P. Kukhar Institute of Bioorganic Chemistry and Petrochemistry, NAS of Ukraine, Kiev, Ukraine
| | - Olga Kolodiazhna
- V.P. Kukhar Institute of Bioorganic Chemistry and Petrochemistry, NAS of Ukraine, Kiev, Ukraine
| | - Sergei Sheiko
- V.P. Kukhar Institute of Bioorganic Chemistry and Petrochemistry, NAS of Ukraine, Kiev, Ukraine
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23
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Falco A, Adamek M, Pereiro P, Hoole D, Encinar JA, Novoa B, Mallavia R. The Immune System of Marine Organisms as Source for Drugs against Infectious Diseases. Mar Drugs 2022; 20:md20060363. [PMID: 35736166 PMCID: PMC9230875 DOI: 10.3390/md20060363] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2022] [Revised: 05/23/2022] [Accepted: 05/26/2022] [Indexed: 11/16/2022] Open
Abstract
The high proliferation of microorganisms in aquatic environments has allowed their coevolution for billions of years with other living beings that also inhabit these niches. Among the different existing types of interaction, the eternal competition for supremacy between the susceptible species and their pathogens has selected, as part of the effector division of the immune system of the former ones, a vast and varied arsenal of efficient antimicrobial molecules, which is highly amplified by the broad biodiversity radiated, above any others, at the marine habitats. At present, the great recent scientific and technological advances already allow the massive discovery and exploitation of these defense compounds for therapeutic purposes against infectious diseases of our interest. Among them, antimicrobial peptides and antimicrobial metabolites stand out because of the wide dimensions of their structural diversities, mechanisms of action, and target pathogen ranges. This revision work contextualizes the research in this field and serves as a presentation and scope identification of the Special Issue from Marine Drugs journal “The Immune System of Marine Organisms as Source for Drugs against Infectious Diseases”.
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Affiliation(s)
- Alberto Falco
- Institute of Research, Development, and Innovation in Healthcare Biotechnology in Elche (IDiBE), Miguel Hernández University (UMH), 03202 Elche, Spain; (J.A.E.); (R.M.)
- Correspondence: (A.F.); (M.A.)
| | - Mikolaj Adamek
- Fish Disease Research Unit, Institute for Parasitology, University of Veterinary Medicine, 30559 Hannover, Germany
- Correspondence: (A.F.); (M.A.)
| | - Patricia Pereiro
- Institute of Marine Research, Consejo Superior de Investigaciones Científicas (IIM-CSIC), 36208 Vigo, Spain; (P.P.); (B.N.)
| | - David Hoole
- School of Life Sciences, Keele University, Keele ST5 5BG, UK;
| | - José Antonio Encinar
- Institute of Research, Development, and Innovation in Healthcare Biotechnology in Elche (IDiBE), Miguel Hernández University (UMH), 03202 Elche, Spain; (J.A.E.); (R.M.)
| | - Beatriz Novoa
- Institute of Marine Research, Consejo Superior de Investigaciones Científicas (IIM-CSIC), 36208 Vigo, Spain; (P.P.); (B.N.)
| | - Ricardo Mallavia
- Institute of Research, Development, and Innovation in Healthcare Biotechnology in Elche (IDiBE), Miguel Hernández University (UMH), 03202 Elche, Spain; (J.A.E.); (R.M.)
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24
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Romano G, Almeida M, Varela Coelho A, Cutignano A, Gonçalves LG, Hansen E, Khnykin D, Mass T, Ramšak A, Rocha MS, Silva TH, Sugni M, Ballarin L, Genevière AM. Biomaterials and Bioactive Natural Products from Marine Invertebrates: From Basic Research to Innovative Applications. Mar Drugs 2022; 20:md20040219. [PMID: 35447892 PMCID: PMC9027906 DOI: 10.3390/md20040219] [Citation(s) in RCA: 19] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2022] [Revised: 03/16/2022] [Accepted: 03/16/2022] [Indexed: 12/22/2022] Open
Abstract
Aquatic invertebrates are a major source of biomaterials and bioactive natural products that can find applications as pharmaceutics, nutraceutics, cosmetics, antibiotics, antifouling products and biomaterials. Symbiotic microorganisms are often the real producers of many secondary metabolites initially isolated from marine invertebrates; however, a certain number of them are actually synthesized by the macro-organisms. In this review, we analysed the literature of the years 2010–2019 on natural products (bioactive molecules and biomaterials) from the main phyla of marine invertebrates explored so far, including sponges, cnidarians, molluscs, echinoderms and ascidians, and present relevant examples of natural products of interest to public and private stakeholders. We also describe omics tools that have been more relevant in identifying and understanding mechanisms and processes underlying the biosynthesis of secondary metabolites in marine invertebrates. Since there is increasing attention on finding new solutions for a sustainable large-scale supply of bioactive compounds, we propose that a possible improvement in the biodiscovery pipeline might also come from the study and utilization of aquatic invertebrate stem cells.
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Affiliation(s)
- Giovanna Romano
- Marine Biotechnology Department, Stazione Zoologica Anton Dohrn, Villa Comunale, 80121 Naples, Italy;
- Correspondence: (G.R.); (L.B.)
| | - Mariana Almeida
- 3B’s Research Group, I3B’s—Research Institute on Biomaterials, Biodegradables and Biomimetics of University of Minho, Headquarters of the European Institute of Excellence on Tissue Engineering and Regenerative Medicine, AvePark—Parque de Ciência e Tecnologia, Barco, 4805-017 Guimarães, Portugal; (M.A.); (M.S.R.); (T.H.S.)
- ICVS/3B´s—PT Government Associate Laboratory, 4710-057 Braga, Portugal
| | - Ana Varela Coelho
- ITQB NOVA, Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa, Av. da República, 2780-157 Oeiras, Portugal; (A.V.C.); (L.G.G.)
| | - Adele Cutignano
- Marine Biotechnology Department, Stazione Zoologica Anton Dohrn, Villa Comunale, 80121 Naples, Italy;
- CNR-Institute of Biomolecular Chemistry, Via Campi Flegrei 34, 80078 Pozzuoli, Italy
| | - Luis G Gonçalves
- ITQB NOVA, Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa, Av. da República, 2780-157 Oeiras, Portugal; (A.V.C.); (L.G.G.)
| | - Espen Hansen
- Marbio, UiT-The Arctic University of Norway, 9037 Tromso, Norway;
| | - Denis Khnykin
- Laboratory for Immunohistochemistry and Immunopathology (LIIPAT), Department of Pathology, Oslo University Hospital-Rikshospitalet, 0450 Oslo, Norway;
| | - Tali Mass
- Faculty of Natural Science, Department of Marine Biology, Charney School of Marine Sciences, University of Haifa, Haifa 3498838, Israel;
| | - Andreja Ramšak
- National Institute of Biology, Marine Biology Station, Fornače 41, SI-6330 Piran, Slovenia;
| | - Miguel S. Rocha
- 3B’s Research Group, I3B’s—Research Institute on Biomaterials, Biodegradables and Biomimetics of University of Minho, Headquarters of the European Institute of Excellence on Tissue Engineering and Regenerative Medicine, AvePark—Parque de Ciência e Tecnologia, Barco, 4805-017 Guimarães, Portugal; (M.A.); (M.S.R.); (T.H.S.)
- ICVS/3B´s—PT Government Associate Laboratory, 4710-057 Braga, Portugal
| | - Tiago H. Silva
- 3B’s Research Group, I3B’s—Research Institute on Biomaterials, Biodegradables and Biomimetics of University of Minho, Headquarters of the European Institute of Excellence on Tissue Engineering and Regenerative Medicine, AvePark—Parque de Ciência e Tecnologia, Barco, 4805-017 Guimarães, Portugal; (M.A.); (M.S.R.); (T.H.S.)
- ICVS/3B´s—PT Government Associate Laboratory, 4710-057 Braga, Portugal
| | - Michela Sugni
- Department of Environmental Science and Policy, University of Milan, Via Celoria, 2, 20133 Milan, Italy;
| | - Loriano Ballarin
- Department of Biology, University of Padova, Via U. Bassi 58/B, 35100 Padova, Italy
- Correspondence: (G.R.); (L.B.)
| | - Anne-Marie Genevière
- Biologie Intégrative des Organismes Marins (BIOM), Observatoire Océanologique de Banyuls-sur-Mer, Sorbonne Université, CNRS, 1 Avenue Pierre Fabre, 66650 Banyuls-sur-Mer, France;
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25
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Santos-Aberturas J, Vior NM. Beyond Soil-Dwelling Actinobacteria: Fantastic Antibiotics and Where to Find Them. Antibiotics (Basel) 2022; 11:195. [PMID: 35203798 PMCID: PMC8868522 DOI: 10.3390/antibiotics11020195] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2021] [Revised: 01/27/2022] [Accepted: 01/29/2022] [Indexed: 12/10/2022] Open
Abstract
Bacterial secondary metabolites represent an invaluable source of bioactive molecules for the pharmaceutical and agrochemical industries. Although screening campaigns for the discovery of new compounds have traditionally been strongly biased towards the study of soil-dwelling Actinobacteria, the current antibiotic resistance and discovery crisis has brought a considerable amount of attention to the study of previously neglected bacterial sources of secondary metabolites. The development and application of new screening, sequencing, genetic manipulation, cultivation and bioinformatic techniques have revealed several other groups of bacteria as producers of striking chemical novelty. Biosynthetic machineries evolved from independent taxonomic origins and under completely different ecological requirements and selective pressures are responsible for these structural innovations. In this review, we summarize the most important discoveries related to secondary metabolites from alternative bacterial sources, trying to provide the reader with a broad perspective on how technical novelties have facilitated the access to the bacterial metabolic dark matter.
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Affiliation(s)
| | - Natalia M. Vior
- Department of Molecular Microbiology, John Innes Centre, Norwich NR7 4UH, UK
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26
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Papon N, Copp BR, Courdavault V. Marine drugs: Biology, pipelines, current and future prospects for production. Biotechnol Adv 2021; 54:107871. [PMID: 34801661 DOI: 10.1016/j.biotechadv.2021.107871] [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] [Received: 08/02/2021] [Revised: 11/02/2021] [Accepted: 11/15/2021] [Indexed: 12/17/2022]
Abstract
The marine environment is a huge reservoir of biodiversity and represents an excellent source of chemical compounds, some of which have large economical values. In the urgent quest for new pharmaceuticals, marine-based drug discovery has progressed significantly over the past several decades and we now benefit from a series of approved marine natural products (MNPs) to treat cancer and pain while an additional collection of promising leads are in clinical trials. However, the discovery and supply of MNPs has always been challenging given their low bioavailability and structural complexity. Their manufacture for pre-clinical and clinical development but also commercialization mainly relies upon marine source extraction and chemical synthesis, which are associated with high costs, unsustainability and severe environmental problems. In this review, we discuss how metabolic engineering now raises reasonable expectations for the implementation of microbial cell factories, which may provide a sustainable approach for MNP-based drug supply in the near future.
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Affiliation(s)
- Nicolas Papon
- Univ. Angers, Univ. Brest, GEIHP, SFR ICAT, F-49000 Angers, France.
| | - Brent R Copp
- School of Chemical Sciences, The University of Auckland, Private Bag 92019, Auckland 1142, New Zealand.
| | - Vincent Courdavault
- Université de Tours, EA2106 Biomolécules et Biotechnologies Végétales, Tours, France.
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27
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Nerpa: A Tool for Discovering Biosynthetic Gene Clusters of Bacterial Nonribosomal Peptides. Metabolites 2021; 11:metabo11100693. [PMID: 34677408 PMCID: PMC8541647 DOI: 10.3390/metabo11100693] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2021] [Revised: 10/01/2021] [Accepted: 10/01/2021] [Indexed: 11/16/2022] Open
Abstract
Microbial natural products are a major source of bioactive compounds for drug discovery. Among these molecules, nonribosomal peptides (NRPs) represent a diverse class of natural products that include antibiotics, immunosuppressants, and anticancer agents. Recent breakthroughs in natural product discovery have revealed the chemical structure of several thousand NRPs. However, biosynthetic gene clusters (BGCs) encoding them are known only for a few hundred compounds. Here, we developed Nerpa, a computational method for the high-throughput discovery of novel BGCs responsible for producing known NRPs. After searching 13,399 representative bacterial genomes from the RefSeq repository against 8368 known NRPs, Nerpa linked 117 BGCs to their products. We further experimentally validated the predicted BGC of ngercheumicin from Photobacterium galatheae via mass spectrometry. Nerpa supports searching new genomes against thousands of known NRP structures, and novel molecular structures against tens of thousands of bacterial genomes. The availability of these tools can enhance our understanding of NRP synthesis and the function of their biosynthetic enzymes.
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28
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Kim H, Lee TG, Yang I, Wang W, Chin J, Lee J, Rho BJ, Choi H, Nam SJ, Hahn D, Kang H. Antibacterial Bicyclic Fatty Acids from a Korean Colonial Tunicate Didemnum sp. Mar Drugs 2021; 19:521. [PMID: 34564183 PMCID: PMC8465582 DOI: 10.3390/md19090521] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2021] [Revised: 09/14/2021] [Accepted: 09/14/2021] [Indexed: 11/16/2022] Open
Abstract
Five new bicyclic carboxylic acids were obtained by antibacterial activity-guided isolation from a Korean colonial tunicate Didemnum sp. Their structures were elucidated by the interpretation of NMR, MS and CD spectroscopic data. They all belong to the class of aplidic acids. Three of them were amide derivatives (1-3), and the other two were dicarboxylic derivatives (4 and 5). The absolute configurations were determined by a bisignate pattern of CD spectroscopy, which revealed that the absolute configurations of amides were opposite to those of dicarboxylates at every stereogenic centers. Compound 2 exhibited the most potent antibacterial activity (MIC, 2 μg/mL).
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Affiliation(s)
- Hiyoung Kim
- Laboratory of Marine Drugs, School of Earth and Environmental Sciences, Seoul National University, NS-80, Seoul 08826, Korea; (H.K.); (W.W.); (J.L.)
- Department of Biomedical Science and Engineering, Konkuk University, Seoul 05029, Korea
| | - Tae Gu Lee
- Safety Research Team, Crop Protection Research Institute, FarmHannong Co., Ltd., Nonsan 33010, Korea;
| | - Inho Yang
- Department of Convergence Study on the Ocean Science and Technology, Korea Maritime and Ocean University, Busan 49112, Korea;
| | - Weihong Wang
- Laboratory of Marine Drugs, School of Earth and Environmental Sciences, Seoul National University, NS-80, Seoul 08826, Korea; (H.K.); (W.W.); (J.L.)
- Research Institute of Oceanography, Seoul National University, Seoul 08826, Korea
| | - Jungwook Chin
- New Drug Development Center, Daegu-Gyeongbuk Medical Innovation Foundation, Daegu 41061, Korea;
| | - Jusung Lee
- Laboratory of Marine Drugs, School of Earth and Environmental Sciences, Seoul National University, NS-80, Seoul 08826, Korea; (H.K.); (W.W.); (J.L.)
| | - Boon Jo Rho
- Natural History Museum, Ewha Womans University, Seoul 03760, Korea;
| | - Hyukjae Choi
- College of Pharmacy, Yeungnam University, Gyeongsan 38541, Korea;
| | - Sang-Jip Nam
- Department of Chemistry and Nano Science, Ewha Womans University, Seoul 03760, Korea;
| | - Dongyup Hahn
- School of Food Science and Biotechnology & Department of Integrative Biology, Kyungpook National University, Daegu 41566, Korea
| | - Heonjoong Kang
- Laboratory of Marine Drugs, School of Earth and Environmental Sciences, Seoul National University, NS-80, Seoul 08826, Korea; (H.K.); (W.W.); (J.L.)
- Research Institute of Oceanography, Seoul National University, Seoul 08826, Korea
- Interdisciplinary Graduate Program in Genetic Engineering, Seoul National University, NS-80, Seoul 08826, Korea
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29
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Brönstrup M, Sasse F. Natural products targeting the elongation phase of eukaryotic protein biosynthesis. Nat Prod Rep 2021; 37:752-762. [PMID: 32428051 DOI: 10.1039/d0np00011f] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
Covering: 2000 to 2020 The translation of mRNA into proteins is a precisely regulated, complex process that can be divided into three main stages, i.e. initiation, elongation, termination, and recycling. This contribution is intended to highlight how natural products interfere with the elongation phase of eukaryotic protein biosynthesis. Cycloheximide, isolated from Streptomyces griseus, has long been the prototype inhibitor of eukaryotic translation elongation. In the last three decades, a variety of natural products from different origins were discovered to also address the elongation step in different manners, including interference with the elongation factors eEF1 and eEF2 as well as binding to A-, P- or E-sites of the ribosome itself. Recent advances in the crystallization of the ribosomal machinery together with natural product inhibitors allowed characterizing similarities as well as differences in their mode of action. Since aberrations in protein synthesis are commonly observed in tumors, and malfunction or overexpression of translation factors can cause cellular transformation, the protein synthesis machinery has been realized as an attractive target for anticancer drugs. The therapeutic use of the first natural products that reached market approval, plitidepsin (Aplidin®) and homoharringtonine (Synribo®), will be introduced. In addition, we will highlight two other potential indications for translation elongation inhibitors, i.e. viral infections and genetic disorders caused by premature termination of translation.
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Affiliation(s)
- Mark Brönstrup
- Department of Chemical Biology, Helmholtz Centre for Infection Research, 38124 Braunschweig, Germany. and Center of Biomolecular Drug Research (BMWZ), Leibniz University, 30159 Hannover, Germany and German Center for Infection Research (DZIF), partner site Hannover-Braunschweig, Germany
| | - Florenz Sasse
- Department of Chemical Biology, Helmholtz Centre for Infection Research, 38124 Braunschweig, Germany.
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30
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Ramesh C, Tulasi BR, Raju M, Thakur N, Dufossé L. Marine Natural Products from Tunicates and Their Associated Microbes. Mar Drugs 2021; 19:308. [PMID: 34073515 PMCID: PMC8228501 DOI: 10.3390/md19060308] [Citation(s) in RCA: 23] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2021] [Revised: 05/22/2021] [Accepted: 05/24/2021] [Indexed: 12/17/2022] Open
Abstract
Marine tunicates are identified as a potential source of marine natural products (MNPs), demonstrating a wide range of biological properties, like antimicrobial and anticancer activities. The symbiotic relationship between tunicates and specific microbial groups has revealed the acquisition of microbial compounds by tunicates for defensive purpose. For instance, yellow pigmented compounds, "tambjamines", produced by the tunicate, Sigillina signifera (Sluiter, 1909), primarily originated from their bacterial symbionts, which are involved in their chemical defense function, indicating the ecological role of symbiotic microbial association with tunicates. This review has garnered comprehensive literature on MNPs produced by tunicates and their symbiotic microbionts. Various sections covered in this review include tunicates' ecological functions, biological activities, such as antimicrobial, antitumor, and anticancer activities, metabolic origins, utilization of invasive tunicates, and research gaps. Apart from the literature content, 20 different chemical databases were explored to identify tunicates-derived MNPs. In addition, the management and exploitation of tunicate resources in the global oceans are detailed for their ecological and biotechnological implications.
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Affiliation(s)
- Chatragadda Ramesh
- Biological Oceanography Division (BOD), CSIR-National Institute of Oceanography (CSIR-NIO), Dona Paula 403004, India
- Department of Ocean Studies and Marine Biology, Pondicherry Central University, Brookshabad Campus, Port Blair 744102, India;
| | - Bhushan Rao Tulasi
- Zoology Division, Sri Gurajada Appa Rao Government Degree College, Yellamanchili 531055, India;
| | - Mohanraju Raju
- Department of Ocean Studies and Marine Biology, Pondicherry Central University, Brookshabad Campus, Port Blair 744102, India;
| | - Narsinh Thakur
- Chemical Oceanography Division (COD), CSIR-National Institute of Oceanography (CSIR-NIO), Dona Paula 403004, India;
| | - Laurent Dufossé
- Laboratoire de Chimie et Biotechnologie des Produits Naturels (CHEMBIOPRO), Université de La Réunion, ESIROI Agroalimentaire, 15 Avenue René Cassin, CS 92003, CEDEX 9, F-97744 Saint-Denis, Ile de La Réunion, France
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Mutalipassi M, Riccio G, Mazzella V, Galasso C, Somma E, Chiarore A, de Pascale D, Zupo V. Symbioses of Cyanobacteria in Marine Environments: Ecological Insights and Biotechnological Perspectives. Mar Drugs 2021; 19:227. [PMID: 33923826 PMCID: PMC8074062 DOI: 10.3390/md19040227] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2021] [Revised: 04/14/2021] [Accepted: 04/15/2021] [Indexed: 01/07/2023] Open
Abstract
Cyanobacteria are a diversified phylum of nitrogen-fixing, photo-oxygenic bacteria able to colonize a wide array of environments. In addition to their fundamental role as diazotrophs, they produce a plethora of bioactive molecules, often as secondary metabolites, exhibiting various biological and ecological functions to be further investigated. Among all the identified species, cyanobacteria are capable to embrace symbiotic relationships in marine environments with organisms such as protozoans, macroalgae, seagrasses, and sponges, up to ascidians and other invertebrates. These symbioses have been demonstrated to dramatically change the cyanobacteria physiology, inducing the production of usually unexpressed bioactive molecules. Indeed, metabolic changes in cyanobacteria engaged in a symbiotic relationship are triggered by an exchange of infochemicals and activate silenced pathways. Drug discovery studies demonstrated that those molecules have interesting biotechnological perspectives. In this review, we explore the cyanobacterial symbioses in marine environments, considering them not only as diazotrophs but taking into consideration exchanges of infochemicals as well and emphasizing both the chemical ecology of relationship and the candidate biotechnological value for pharmaceutical and nutraceutical applications.
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Affiliation(s)
- Mirko Mutalipassi
- Department of Marine Biotechnology, Stazione Zoologica Anton Dohrn, Villa Comunale, 80121 Naples, Italy; (G.R.); (C.G.); (D.d.P.)
| | - Gennaro Riccio
- Department of Marine Biotechnology, Stazione Zoologica Anton Dohrn, Villa Comunale, 80121 Naples, Italy; (G.R.); (C.G.); (D.d.P.)
| | - Valerio Mazzella
- Department of Integrated Marine Ecology, Stazione Zoologica Anton Dohrn, Villa Comunale, 80121 Naples, Italy;
| | - Christian Galasso
- Department of Marine Biotechnology, Stazione Zoologica Anton Dohrn, Villa Comunale, 80121 Naples, Italy; (G.R.); (C.G.); (D.d.P.)
| | - Emanuele Somma
- Department of Life Sciences, University of Trieste, Via Licio Giorgieri, 34127 Trieste, Italy;
- Department of Marine Biotechnology, Ischia Marine Centre, Stazione Zoologica Anton Dohrn, Punta San Pietro, 80077 Naples, Italy;
| | - Antonia Chiarore
- Department of Biology, University of Naples Federico II, Via Cinthia, 80126 Naples, Italy;
| | - Donatella de Pascale
- Department of Marine Biotechnology, Stazione Zoologica Anton Dohrn, Villa Comunale, 80121 Naples, Italy; (G.R.); (C.G.); (D.d.P.)
| | - Valerio Zupo
- Department of Marine Biotechnology, Ischia Marine Centre, Stazione Zoologica Anton Dohrn, Punta San Pietro, 80077 Naples, Italy;
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Salikin NH, Nappi J, Majzoub ME, Egan S. Combating Parasitic Nematode Infections, Newly Discovered Antinematode Compounds from Marine Epiphytic Bacteria. Microorganisms 2020; 8:E1963. [PMID: 33322253 PMCID: PMC7764037 DOI: 10.3390/microorganisms8121963] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2020] [Revised: 12/08/2020] [Accepted: 12/08/2020] [Indexed: 02/06/2023] Open
Abstract
Parasitic nematode infections cause debilitating diseases and impede economic productivity. Antinematode chemotherapies are fundamental to modern medicine and are also important for industries including agriculture, aquaculture and animal health. However, the lack of suitable treatments for some diseases and the rise of nematode resistance to many available therapies necessitates the discovery and development of new drugs. Here, marine epiphytic bacteria represent a promising repository of newly discovered antinematode compounds. Epiphytic bacteria are ubiquitous on marine surfaces where they are under constant pressure of grazing by bacterivorous predators (e.g., protozoans and nematodes). Studies have shown that these bacteria have developed defense strategies to prevent grazers by producing toxic bioactive compounds. Although several active metabolites against nematodes have been identified from marine bacteria, drug discovery from marine microorganisms remains underexplored. In this review, we aim to provide further insight into the need and potential for marine epiphytic bacteria to become a new source of antinematode drugs. We discuss current and emerging strategies, including culture-independent high throughput screening and the utilization of Caenorhabditis elegans as a model target organism, which will be required to advance antinematode drug discovery and development from marine microbial sources.
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Affiliation(s)
- Nor Hawani Salikin
- Centre for Marine Science and Innovation, School of Biological, Earth and Environmental Sciences, UNSW, Sydney, NSW 2052, Australia; (N.H.S.); (J.N.); (M.E.M.)
- School of Industrial Technology, Universiti Sains Malaysia, USM, 11800 Penang, Malaysia
| | - Jadranka Nappi
- Centre for Marine Science and Innovation, School of Biological, Earth and Environmental Sciences, UNSW, Sydney, NSW 2052, Australia; (N.H.S.); (J.N.); (M.E.M.)
| | - Marwan E. Majzoub
- Centre for Marine Science and Innovation, School of Biological, Earth and Environmental Sciences, UNSW, Sydney, NSW 2052, Australia; (N.H.S.); (J.N.); (M.E.M.)
| | - Suhelen Egan
- Centre for Marine Science and Innovation, School of Biological, Earth and Environmental Sciences, UNSW, Sydney, NSW 2052, Australia; (N.H.S.); (J.N.); (M.E.M.)
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Culture-Dependent Microbiome of the Ciona intestinalis Tunic: Isolation, Bioactivity Profiling and Untargeted Metabolomics. Microorganisms 2020; 8:microorganisms8111732. [PMID: 33167375 PMCID: PMC7694362 DOI: 10.3390/microorganisms8111732] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2020] [Revised: 11/01/2020] [Accepted: 11/03/2020] [Indexed: 01/28/2023] Open
Abstract
Ascidians and their associated microbiota are prolific producers of bioactive marine natural products. Recent culture-independent studies have revealed that the tunic of the solitary ascidian Cionaintestinalis (sea vase) is colonized by a diverse bacterial community, however, the biotechnological potential of this community has remained largely unexplored. In this study, we aimed at isolating the culturable microbiota associated with the tunic of C.intestinalis collected from the North and Baltic Seas, to investigate their antimicrobial and anticancer activities, and to gain first insights into their metabolite repertoire. The tunic of the sea vase was found to harbor a rich microbial community, from which 89 bacterial and 22 fungal strains were isolated. The diversity of the tunic-associated microbiota differed from that of the ambient seawater samples, but also between sampling sites. Fungi were isolated for the first time from the tunic of Ciona. The proportion of bioactive extracts was high, since 45% of the microbial extracts inhibited the growth of human pathogenic bacteria, fungi or cancer cell lines. In a subsequent bioactivity- and metabolite profiling-based approach, seven microbial extracts were prioritized for in-depth chemical investigations. Untargeted metabolomics analyses of the selected extracts by a UPLC-MS/MS-based molecular networking approach revealed a vast chemical diversity with compounds assigned to 22 natural product families, plus many metabolites that remained unidentified. This initial study indicates that bacteria and fungi associated with the tunic of C.intestinalis represent an untapped source of putatively new marine natural products with pharmacological relevance.
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Alonzo DA, Schmeing TM. Biosynthesis of depsipeptides, or Depsi: The peptides with varied generations. Protein Sci 2020; 29:2316-2347. [PMID: 33073901 DOI: 10.1002/pro.3979] [Citation(s) in RCA: 23] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2020] [Revised: 10/11/2020] [Accepted: 10/13/2020] [Indexed: 12/11/2022]
Abstract
Depsipeptides are compounds that contain both ester bonds and amide bonds. Important natural product depsipeptides include the piscicide antimycin, the K+ ionophores cereulide and valinomycin, the anticancer agent cryptophycin, and the antimicrobial kutzneride. Furthermore, database searches return hundreds of uncharacterized systems likely to produce novel depsipeptides. These compounds are made by specialized nonribosomal peptide synthetases (NRPSs). NRPSs are biosynthetic megaenzymes that use a module architecture and multi-step catalytic cycle to assemble monomer substrates into peptides, or in the case of specialized depsipeptide synthetases, depsipeptides. Two NRPS domains, the condensation domain and the thioesterase domain, catalyze ester bond formation, and ester bonds are introduced into depsipeptides in several different ways. The two most common occur during cyclization, in a reaction between a hydroxy-containing side chain and the C-terminal amino acid residue in a peptide intermediate, and during incorporation into the growing peptide chain of an α-hydroxy acyl moiety, recruited either by direct selection of an α-hydroxy acid substrate or by selection of an α-keto acid substrate that is reduced in situ. In this article, we discuss how and when these esters are introduced during depsipeptide synthesis, survey notable depsipeptide synthetases, and review insight into bacterial depsipeptide synthetases recently gained from structural studies.
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Affiliation(s)
- Diego A Alonzo
- Department of Biochemistry and Centre de Recherche en Biologie Structurale, McGill University, Montréal, Quebec, Canada
| | - T Martin Schmeing
- Department of Biochemistry and Centre de Recherche en Biologie Structurale, McGill University, Montréal, Quebec, Canada
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Miyako K, Yasuno Y, Shinada T, Fujita MJ, Sakai R. Diverse Aromatic Metabolites in the Solitary Tunicate Cnemidocarpa irene. JOURNAL OF NATURAL PRODUCTS 2020; 83:3156-3165. [PMID: 33030894 DOI: 10.1021/acs.jnatprod.0c00789] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/11/2023]
Abstract
Fourteen aromatic metabolites (6-19) were isolated from an aqueous extract of the solitary tunicate Cnemidocarpa irene collected in Hokkaido, Japan. The structures of the metabolites were determined based on the spectroscopic interpretations, including one- and two-dimensional NMR, mass spectra, UV, and circular dichroism data. The biopterin analogue 10 modulated the behavior of mice after intracerebroventricular injection and showed a weak affinity to ionotropic glutamate receptor subtypes. Analyses of fluorescent coelomic fluid of the tunicate revealed that pterin 12 was responsible for the fluorescence of the blood cells, while β-carbolines 1 and 3 were fluorescent compounds in the serum. The metabolic profiles in adults, juveniles, larvae, and eggs of the animal differed substantially, suggesting that the metabolism of the animal, especially biosynthesis of aromatic secondary metabolites, changes over different life stages.
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Affiliation(s)
- Kei Miyako
- Faculty and Graduate School of Fisheries Sciences, Hokkaido University, 3-1-1 Minato-cho, Hakodate, Hokkaido 041-8611, Japan
| | - Yoko Yasuno
- Graduate School of Science, Osaka City University, 3-3-138, Sugimoto, Sumiyoshi, Osaka 558-8585, Japan
| | - Tetsuro Shinada
- Graduate School of Science, Osaka City University, 3-3-138, Sugimoto, Sumiyoshi, Osaka 558-8585, Japan
| | - Masaki J Fujita
- Faculty and Graduate School of Fisheries Sciences, Hokkaido University, 3-1-1 Minato-cho, Hakodate, Hokkaido 041-8611, Japan
| | - Ryuichi Sakai
- Faculty and Graduate School of Fisheries Sciences, Hokkaido University, 3-1-1 Minato-cho, Hakodate, Hokkaido 041-8611, Japan
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Mori S, Garneau-Tsodikova S, Tsodikov OV. Unimodular Methylation by Adenylation-Thiolation Domains Containing an Embedded Methyltransferase. J Mol Biol 2020; 432:5802-5808. [PMID: 32920052 DOI: 10.1016/j.jmb.2020.09.004] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2020] [Revised: 08/16/2020] [Accepted: 09/03/2020] [Indexed: 10/23/2022]
Abstract
Nonribosomal peptides (NRPs) are natural products that are biosynthesized by large multi-enzyme assembly lines called nonribosomal peptide synthetases (NRPSs). We have previously discovered that backbone or side chain methylation of NRP residues is carried out by an interrupted adenylation (A) domain that contains an internal methyltransferase (M) domain, while maintaining a monolithic AMA fold of the bifunctional enzyme. A key question that has remained unanswered is at which step of the assembly line mechanism the methylation by these embedded M domains takes place. Does the M domain methylate an amino acid residue tethered to a thiolation (T) domain on same NRPS module (in cis), or does it methylate this residue on a nascent peptide tethered to a T domain on another module (in trans)? In this study, we investigated the kinetics of methylation by wild-type AMAT tridomains from two NRPSs involved in biosynthesis of anticancer depsipeptides thiocoraline and echinomycin, and by mutants of these domains, for which methylation can occur only in trans. The analysis of the methylation kinetics unequivocally demonstrated that the wild-type AMATs methylate overwhelmingly in cis, strongly suggesting that this is also the case in the context of the entire NRPS assembly line process. The mechanistic insight gained in this study will facilitate rational genetic engineering of NRPS to generate unnaturally methylated NRPs.
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Affiliation(s)
- Shogo Mori
- Department of Pharmaceutical Sciences, College of Pharmacy, University of Kentucky, Lexington, KY 40536-0596, USA
| | - Sylvie Garneau-Tsodikova
- Department of Pharmaceutical Sciences, College of Pharmacy, University of Kentucky, Lexington, KY 40536-0596, USA.
| | - Oleg V Tsodikov
- Department of Pharmaceutical Sciences, College of Pharmacy, University of Kentucky, Lexington, KY 40536-0596, USA.
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Lundy TA, Mori S, Garneau-Tsodikova S. A thorough analysis and categorization of bacterial interrupted adenylation domains, including previously unidentified families. RSC Chem Biol 2020; 1:233-250. [PMID: 34458763 PMCID: PMC8341866 DOI: 10.1039/d0cb00092b] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2020] [Accepted: 08/04/2020] [Indexed: 11/25/2022] Open
Abstract
Interrupted adenylation (A) domains are key to the immense structural diversity seen in the nonribosomal peptide (NRP) class of natural products (NPs). Interrupted A domains are A domains that contain within them the catalytic portion of another domain, most commonly a methylation (M) domain. It has been well documented that methylation events occur with extreme specificity on either the backbone (N-) or side chain (O- or S-) of the amino acid (or amino acid-like) building blocks of NRPs. Here, through taxonomic and phylogenetic analyses as well as multiple sequence alignments, we evaluated the similarities and differences between interrupted A domains. We probed their taxonomic distribution amongst bacterial organisms, their evolutionary relatedness, and described conserved motifs of each type of M domain found to be embedded in interrupted A domains. Additionally, we categorized interrupted A domains and the M domains within them into a total of seven distinct families and six different types, respectively. The families of interrupted A domains include two new families, 6 and 7, that possess new architectures. Rather than being interrupted between the previously described a2–a3 or a8–a9 of the ten conserved A domain sequence motifs (a1–a10), family 6 contains an M domain between a6–a7, a previously unknown interruption site. Family 7 demonstrates that di-interrupted A domains exist in Nature, containing an M domain between a2–a3 as well as one between a6–a7, displaying a novel arrangement. These in-depth investigations of amino acid sequences deposited in the NCBI database highlighted the prevalence of interrupted A domains in bacterial organisms, with each family of interrupted A domains having a different taxonomic distribution. They also emphasized the importance of utilizing a broad range of bacteria for NP discovery. Categorization of the families of interrupted A domains and types of M domains allowed for a better understanding of the trends of naturally occurring interrupted A domains, which illuminated patterns and insights on how to harness them for future engineering studies. In-depth study of intriguing bacterial interrupted adenylation domains from seven distinct families and six different types.![]()
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Affiliation(s)
- Taylor A Lundy
- University of Kentucky, Department of Pharmaceutical Sciences, College of Pharmacy Lexington KY 40536-0596 USA
| | - Shogo Mori
- University of Kentucky, Department of Pharmaceutical Sciences, College of Pharmacy Lexington KY 40536-0596 USA
| | - Sylvie Garneau-Tsodikova
- University of Kentucky, Department of Pharmaceutical Sciences, College of Pharmacy Lexington KY 40536-0596 USA
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The Ascidian-Derived Metabolites with Antimicrobial Properties. Antibiotics (Basel) 2020; 9:antibiotics9080510. [PMID: 32823633 PMCID: PMC7460354 DOI: 10.3390/antibiotics9080510] [Citation(s) in RCA: 33] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2020] [Revised: 08/07/2020] [Accepted: 08/11/2020] [Indexed: 12/21/2022] Open
Abstract
Among the sub-phylum of Tunicate, ascidians represent the most abundant class of marine invertebrates, with 3000 species by heterogeneous habitat, that is, from shallow water to deep sea, already reported. The chemistry of these sessile filter-feeding organisms is an attractive reservoir of varied and peculiar bioactive compounds. Most secondary metabolites isolated from ascidians stand out for their potential as putative therapeutic agents in the treatment of several illnesses like microbial infections. In this review, we present and discuss the antibacterial activity shown by the main groups of ascidian-derived products, such as sulfur-containing compounds, meroterpenes, alkaloids, peptides, furanones, and their derivatives. Moreover, the direct evidence of a symbiotic association between marine ascidians and microorganisms shed light on the real producers of many extremely potent marine natural compounds. Hence, we also report the antibacterial potential, joined to antifungal and antiviral activity, of metabolites isolated from ascidian-associate microorganisms by culture-dependent methods.
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Marine microbial natural products: the evolution of a new field of science. J Antibiot (Tokyo) 2020; 73:481-487. [PMID: 32713942 DOI: 10.1038/s41429-020-0331-4] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2020] [Accepted: 05/21/2020] [Indexed: 12/29/2022]
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Highlights of marine natural products having parallel scaffolds found from marine-derived bacteria, sponges, and tunicates. J Antibiot (Tokyo) 2020; 73:504-525. [PMID: 32507851 PMCID: PMC7276339 DOI: 10.1038/s41429-020-0330-5] [Citation(s) in RCA: 23] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2020] [Revised: 05/16/2020] [Accepted: 05/18/2020] [Indexed: 12/11/2022]
Abstract
Marine-derived bacteria are a prolific source of a wide range of structurally diverse natural products. This review, dedicated to Professor William Fenical, begins by showcasing many seminal discoveries made at the University of California San Diego from marine-derived actinomycetes. Discussed early on is the 20-year journey of discovery and advancement of the seminal actinomycetes natural product salinosporamide A into Phase III anticancer clinical trials. There are many fascinating parallels discussed that were gleaned from the comparative literature of marine sponge, tunicate, and bacteria-derived natural products. Identifying bacterial biosynthetic machinery housed in sponge and tunicate holobionts through both culture-independent and culture-dependent approaches is another important and expanding subject that is analyzed. Work reviewed herein also evaluates the hypotheses that many marine invertebrate-derived natural products are biosynthesised by associated or symbiotic bacteria. The insights and outcomes from metagenomic sequencing and synthetic biology to expand molecule discovery continue to provide exciting outcomes and they are predicted to be the source of the next generation of novel marine natural product chemical scaffolds.
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In Vitro Efficacy for Chlorpyrifos Degradation by Novel Isolate Tistrella sp. AUC10 Isolated from Chlorpyrifos Contaminated Field. Curr Microbiol 2020; 77:2226-2232. [PMID: 32361846 DOI: 10.1007/s00284-020-01998-1] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2019] [Accepted: 04/15/2020] [Indexed: 10/24/2022]
Abstract
Chlorpyrifos, an organophosphate (OP) pesticide, possess broad-spectrum insecticidal activity against Lepidoptera, Diptera, Homoptera, Coleoptera, Orthoptera, Hymenoptera, and Hemiptera. Organophosphate pesticides have acute neurotoxicity because they suppress acetylcholine esterase (AChE) which regulates the enzyme of neurotransmitters by reducing acetylcholine concentration at synaptic junctions. On exposure to OP, AChE is inactivated and leads to accumulation of acetylcholine in the junction. Moreover, due to their persistence nature they biomagnify at different food chain levels. In the present study, a newly isolated indigenous bacterial strain Tistrella sp. AUC10 was exploited for its ability to degrade chlorpyrifos pesticide. The isolate completely degrades (99.86%) chlorpyrifos. The degraded metabolites of chlorpyrifos by Tistrella sp. AUC10 were identified by GC-MS analysis. Based on the GC-MS analysis, a putative pathway of degradation of chlorpyrifos by Tistrella sp. AUC10 has been proposed. It emulsified various hydrocarbons and also confirms biosurfactant production on CTAB agar. This study is the first report on elucidation of the mechanism of degradation of chlorpyrifos by Tistrella sp. Furthermore, phytotoxicity studies of the parent compound and the biodegraded chlorpyrifos products revealed drastic reduction in the toxicity of metabolites as compared to the parent chlorpyrifos. This implies that the biodegraded metabolites of chlorpyrifos are of non-toxic nature. This study thus indicates the efficacy of Tistrella sp. AUC10 for the treatment of chlorpyrifos contaminated agricultural fields.
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Cuadrat RRC, Sorokina M, Andrade BG, Goris T, Dávila AMR. Global ocean resistome revealed: Exploring antibiotic resistance gene abundance and distribution in TARA Oceans samples. Gigascience 2020; 9:giaa046. [PMID: 32391909 PMCID: PMC7213576 DOI: 10.1093/gigascience/giaa046] [Citation(s) in RCA: 49] [Impact Index Per Article: 12.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2019] [Revised: 03/13/2020] [Accepted: 04/16/2020] [Indexed: 12/13/2022] Open
Abstract
BACKGROUND The rise of antibiotic resistance (AR) in clinical settings is of great concern. Therefore, the understanding of AR mechanisms, evolution, and global distribution is a priority for patient survival. Despite all efforts in the elucidation of AR mechanisms in clinical strains, little is known about its prevalence and evolution in environmental microorganisms. We used 293 metagenomic samples from the TARA Oceans project to detect and quantify environmental antibiotic resistance genes (ARGs) using machine learning tools. RESULTS After manual curation of ARGs, their abundance and distribution in the global ocean are presented. Additionally, the potential of horizontal ARG transfer by plasmids and their correlation with environmental and geographical parameters is shown. A total of 99,205 environmental open reading frames (ORFs) were classified as 1 of 560 different ARGs conferring resistance to 26 antibiotic classes. We found 24,567 ORFs in putative plasmid sequences, suggesting the importance of mobile genetic elements in the dynamics of environmental ARG transmission. Moreover, 4,804 contigs with >=2 putative ARGs were found, including 2 plasmid-like contigs with 5 different ARGs, highlighting the potential presence of multi-resistant microorganisms in the natural ocean environment. Finally, we identified ARGs conferring resistance to some of the most relevant clinical antibiotics, revealing the presence of 15 ARGs similar to mobilized colistin resistance genes (mcr) with high abundance on polar biomes. Of these, 5 are assigned to Psychrobacter, a genus including opportunistic human pathogens. CONCLUSIONS This study uncovers the diversity and abundance of ARGs in the global ocean metagenome. Our results are available on Zenodo in MySQL database dump format, and all the code used for the analyses, including a Jupyter notebook js avaliable on Github. We also developed a dashboard web application (http://www.resistomedb.com) for data visualization.
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Affiliation(s)
- Rafael R C Cuadrat
- Department of Molecular Epidemiology, German Institute of Human Nutrition Potsdam-Rehbruecke - DIfE, Arthur-Scheunert-Allee 114–116, 14558 Nuthetal, Germany
| | - Maria Sorokina
- Institute for Inorganic and Analytical Chemistry, Friedrich-Schiller University, Lessingstrasse 8, 07743 Jena, Germany
| | - Bruno G Andrade
- Animal Biotechnology Laboratory, Embrapa Southeast Livestock, EMBRAPA, Rodovia Washington Luiz, Km 234 s/n°, 13560-970 São Carlos, SP, Brazil
| | - Tobias Goris
- Department of Molecular Toxicology, Research Group Intestinal Microbiology, German Institute of Human Nutrition Potsdam-Rehbruecke - DIfE, Arthur-Scheunert-Allee 114–116, 14558 Nuthetal, Germany
| | - Alberto M R Dávila
- Computational and Systems Biology Laboratory, Oswaldo Cruz Institute, FIOCRUZ, Av Brasil 4365, 21040-900 Rio de Janeiro, RJ, Brazil
- Graduate Program in Biodiversity and Health, Oswaldo Cruz Institute, FIOCRUZ, Av. Brasil 4365, 21040-900 Rio de Janeiro, RJ, Brazil
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Sigrist R, Luhavaya H, McKinnie SMK, Ferreira da Silva A, Jurberg ID, Moore BS, Gonzaga de Oliveira L. Nonlinear Biosynthetic Assembly of Alpiniamide by a Hybrid cis/ trans-AT PKS-NRPS. ACS Chem Biol 2020; 15:1067-1077. [PMID: 32195572 DOI: 10.1021/acschembio.0c00081] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Alpiniamide A is a linear polyketide produced by Streptomyces endophytic bacteria. Despite its relatively simple chemical structure suggestive of a linear assembly line biosynthetic construction involving a hybrid polyketide synthase-nonribosomal peptide synthetase enzymatic protein machine, we report an unexpected nonlinear synthesis of this bacterial natural product. Using a combination of genomics, heterologous expression, mutagenesis, isotope-labeling, and chain terminator experiments, we propose that alpiniamide A is assembled in two halves and then ligated into the mature molecule. We show that each polyketide half is constructed using orthogonal biosynthetic strategies, employing either cis- or trans-acyl transferase mechanisms, thus prompting an alternative proposal for the operation of this PKS-NRPS.
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Affiliation(s)
- Renata Sigrist
- Department of Organic Chemistry, Institute of Chemistry, University of Campinas (UNICAMP), Campinas, São Paulo 13083-970, Brazil
| | - Hanna Luhavaya
- Center for Marine Biotechnology and Biomedicine, Scripps Institution of Oceanography, University of California, San Diego, La Jolla, California 92093, United States
| | - Shaun M. K. McKinnie
- Center for Marine Biotechnology and Biomedicine, Scripps Institution of Oceanography, University of California, San Diego, La Jolla, California 92093, United States
| | - Amanda Ferreira da Silva
- Department of Organic Chemistry, Institute of Chemistry, University of Campinas (UNICAMP), Campinas, São Paulo 13083-970, Brazil
| | - Igor D. Jurberg
- Department of Organic Chemistry, Institute of Chemistry, University of Campinas (UNICAMP), Campinas, São Paulo 13083-970, Brazil
| | - Bradley S. Moore
- Center for Marine Biotechnology and Biomedicine, Scripps Institution of Oceanography, University of California, San Diego, La Jolla, California 92093, United States
- Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California, San Diego, La Jolla, California 92093, United States
| | - Luciana Gonzaga de Oliveira
- Department of Organic Chemistry, Institute of Chemistry, University of Campinas (UNICAMP), Campinas, São Paulo 13083-970, Brazil
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Lundy TA, Mori S, Garneau-Tsodikova S. Lessons learned in engineering interrupted adenylation domains when attempting to create trifunctional enzymes from three independent monofunctional ones. RSC Adv 2020; 10:34299-34307. [PMID: 35519055 PMCID: PMC9056781 DOI: 10.1039/d0ra05490a] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2020] [Accepted: 09/07/2020] [Indexed: 11/21/2022] Open
Abstract
Interrupted adenylation (A) domains are fascinating examples of multifunctional enzymes. They are found in nonribosomal peptide synthetases (NRPSs), which biosynthesize nonribosomal peptides (NRPs), a major class of medically relevant natural products (NPs). Interrupted A domains contain the catalytic portion of another domain within them, typically a methylation (M) domain, thus combining both adenylation and methylation capabilities. In recent years, interrupted A domains have demonstrated tremendous enzyme engineering potential as they are able to be constructed artificially in a laboratory setting by combining the A and M domains of two separate NRPS proteins. A recent discovery and characterization of a naturally occurring interrupted A domain that harbored two M domains back-to-back, a trifunctional protein, showed the ingenuity of Nature to both N- and O-methylate amino acids, the building blocks of NRPs. Since we have shown that a single M domain could be added to an uninterrupted A domain to create an artificial interrupted A domain, we set out to investigate if: (i) an A domain could be engineered to contain two back-to-back M domains and (ii) the added M domains would have to reflect the pattern in Nature, a side chain (O-) methylating M domain (Ms) followed by a backbone (N-) methylating M domain (Mb), or if the order of the M domains could be reversed. To address these questions, we set out to create our own AMsMbA and AMbMsA engineered interrupted A domains. We evaluated these engineered proteins connected (in cis) and/or disconnected (in trans) from the native thiolation (T) domain, through a series of radiometric assays, high performance liquid chromatography (HPLC), and mass spectrometry (MS) for adenylation, loading, and methylation ability. We found that although adenylation activity was preserved in both versions (AMsMbA and AMbMsA), addition of the M domains, in natural and unnatural order, did not result in the desired added methylation capability. This study offers valuable insights into the limits of constructing engineered interrupted A domains as potential tools for modifications of NRPs. Interrupted adenylation (A) domains are fascinating examples of multifunctional enzymes with high potential for engineering. Here, limits were established in engineering trifunctional interrupted A domains.![]()
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Affiliation(s)
- Taylor A. Lundy
- Department of Pharmaceutical Sciences
- University of Kentucky
- College of Pharmacy
- Lexington
- USA
| | - Shogo Mori
- Department of Pharmaceutical Sciences
- University of Kentucky
- College of Pharmacy
- Lexington
- USA
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Phylogenetic Analysis and Screening of Antimicrobial and Antiproliferative Activities of Culturable Bacteria Associated with the Ascidian Styela clava from the Yellow Sea, China. BIOMED RESEARCH INTERNATIONAL 2019; 2019:7851251. [PMID: 31559313 PMCID: PMC6735190 DOI: 10.1155/2019/7851251] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/24/2019] [Revised: 07/04/2019] [Accepted: 07/28/2019] [Indexed: 01/01/2023]
Abstract
Over 1,000 compounds, including ecteinascidin-743 and didemnin B, have been isolated from ascidians, with most having bioactive properties such as antimicrobial, antitumor, and enzyme-inhibiting activities. In recent years, direct and indirect evidence has shown that some bioactive compounds isolated from ascidians are not produced by ascidians themselves but by their symbiotic microorganisms. Isolated culturable bacteria associated with ascidians and investigating their potential bioactivity are an important approach for discovering novel compounds. In this study, a total of 269 bacteria were isolated from the ascidian Styela clava collected from the coast of Weihai in the north of the Yellow Sea, China. Phylogenetic relationships among 183 isolates were determined using their 16S rRNA gene sequences. Isolates were tested for antimicrobial activity against seven indicator strains, and an antiproliferative activity assay was performed to test for inhibition of human hepatocellular carcinoma Bel 7402 and human cervical carcinoma HeLa cell proliferation. Our results showed that the isolates belonged to 26 genera from 18 families in four phyla (Firmicutes, Actinobacteria, Proteobacteria, and Bacteroidetes). Bacillus and Streptomyces were the most dominant genera; 146 strains had potent antimicrobial activities and inhibited at least one of the indicator strains. Crude extracts from 29 strains showed antiproliferative activity against Bel 7402 cells with IC50 values below 500 μg·mL-1, and 53 strains showed antiproliferative activity against HeLa cells, with IC50 values less than 500 μg·mL-1. Our results suggest that culturable bacteria associated with the ascidian Styela clava may be a promising source of novel bioactive compounds.
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Marine Biosurfactants: Biosynthesis, Structural Diversity and Biotechnological Applications. Mar Drugs 2019; 17:md17070408. [PMID: 31323998 PMCID: PMC6669457 DOI: 10.3390/md17070408] [Citation(s) in RCA: 54] [Impact Index Per Article: 10.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2019] [Revised: 07/04/2019] [Accepted: 07/07/2019] [Indexed: 11/16/2022] Open
Abstract
Biosurfactants are amphiphilic secondary metabolites produced by microorganisms. Marine bacteria have recently emerged as a rich source for these natural products which exhibit surface-active properties, making them useful for diverse applications such as detergents, wetting and foaming agents, solubilisers, emulsifiers and dispersants. Although precise structural data are often lacking, the already available information deduced from biochemical analyses and genome sequences of marine microbes indicates a high structural diversity including a broad spectrum of fatty acid derivatives, lipoamino acids, lipopeptides and glycolipids. This review aims to summarise biosyntheses and structures with an emphasis on low molecular weight biosurfactants produced by marine microorganisms and describes various biotechnological applications with special emphasis on their role in the bioremediation of oil-contaminated environments. Furthermore, novel exploitation strategies are suggested in an attempt to extend the existing biosurfactant portfolio.
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Degli Esposti M, Lozano L, Martínez-Romero E. Current phylogeny of Rhodospirillaceae: A multi-approach study. Mol Phylogenet Evol 2019; 139:106546. [PMID: 31279965 DOI: 10.1016/j.ympev.2019.106546] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2018] [Revised: 06/27/2019] [Accepted: 06/27/2019] [Indexed: 10/26/2022]
Abstract
Rhodospirillaceae represents a major family of the class alphaproteobacteria that includes an increasing number of functionally diverse taxa. The aim of this work is to evaluate the present phylogenetic diversity of the Rhodospirillaceae, which includes several metagenome-assembled genomes of uncultivated bacteria, as well as cultivated bacteria that were previously classified in different families. Various methodological approaches have been followed to discern the phylogenetic diversity of the taxa associated with the Rhodospirillaceae, which are grouped in three major sub-divisions and several other taxonomic entities that are currently confined to the genus rank. These genera include Tistrella, Elstera, Dongia and Ferrovibrio among cultivated organisms and alphaproteobacteria bacterium 41-28 among uncultivated bacteria. Overall, this study adds at least 11 genera and over 40 species to the current set of taxa belonging to the Rhodospirillaceae, a taxonomic term that clearly requires amendment. We propose to re-classify all taxa associated with the Rhodospirillaceae family under the new order, Diaforabacterales ord. nov. (from the Greek word for diversity, διάφορα). This study also uncovers the likely root of Rhodospirillaceae among recently reported metagenome-assembled genomes of uncultivated marine and groundwater bacteria.
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Affiliation(s)
- Mauro Degli Esposti
- Center for Genomic Sciences, UNAM Campus de Cuernavaca, Cuernavaca 62130, Morelos, Mexico.
| | - Luis Lozano
- Center for Genomic Sciences, UNAM Campus de Cuernavaca, Cuernavaca 62130, Morelos, Mexico
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Nigam M, Suleria HAR, Farzaei MH, Mishra AP. Marine anticancer drugs and their relevant targets: a treasure from the ocean. Daru 2019; 27:491-515. [PMID: 31165439 PMCID: PMC6593002 DOI: 10.1007/s40199-019-00273-4] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2018] [Accepted: 05/08/2019] [Indexed: 02/07/2023] Open
Abstract
Marine organisms comprising animals and plants are wealthiest sources of bioactive compounds possessing various pharmacological properties specifically: free radical scavenging, antitumor, antimicrobial, analgesic, neuroprotective and immunomodulatory. Marine drugs provide an alternative source to meet the demand of effective, safe and low-cost drugs that are rising with the continuously growing world population. Cancer is one of the leading reasons of mortality in western nations in contrast to communicable diseases of developing nations. In spite of outstanding developments in cancer therapy in past three decades, there is still an insistent necessity for innovative drugs in the area of cancer biology, especially in the unexplored area of marine anticancer compounds. However, recent technological innovations in structure revelation, synthetic creation of new compounds and biological assays have made possible the isolation and clinical assessment of innumerable unique anticancer compounds from marine environment. This review provides an insight into the anticancer research so far conducted in the area of the marine natural products/synthetic derivatives, their possible molecular targets and the current challenges in the drug development. Graphical abstract.
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Affiliation(s)
- Manisha Nigam
- Department of Biochemistry, H. N. B. Garhwal (A Central) University, Srinagar Garhwal, Uttarakhand 246174 India
| | - Hafiz Ansar Rasul Suleria
- Centre for Chemistry and Biotechnology, School of Life and Environmental Sciences, Deakin University, Pigdons Road, Waurn Ponds, Victoria 3216 Australia
- UQ Diamantina Institute, Translational Research Institute, Faculty of Medicine, The University of Queensland, 37 Kent Street Woolloongabba, Brisbane, QLD 4102 Australia
- Department of Food, Nutrition, Dietetics and Health, Kansas State University, Manhattan, KS 66506 USA
| | - Mohammad Hosein Farzaei
- Pharmaceutical Sciences Research Center, Health Institute, Kermanshah University of Medical Sciences, Kermanshah, Iran
| | - Abhay Prakash Mishra
- Department of Pharmaceutical Chemistry, H. N. B. Garhwal (A Central) University, Srinagar Garhwal, Uttarakhand 246174 India
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Kaysser L. Built to bind: biosynthetic strategies for the formation of small-molecule protease inhibitors. Nat Prod Rep 2019; 36:1654-1686. [DOI: 10.1039/c8np00095f] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
Abstract
The discovery and characterization of natural product protease inhibitors has inspired the development of numerous pharmaceutical agents.
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Affiliation(s)
- Leonard Kaysser
- Department of Pharmaceutical Biology
- University of Tübingen
- 72076 Tübingen
- Germany
- German Centre for Infection Research (DZIF)
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50
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Auerbach D, Yan F, Zhang Y, Müller R. Characterization of an Unusual Glycerate Esterification Process in Vioprolide Biosynthesis. ACS Chem Biol 2018; 13:3123-3130. [PMID: 30286293 DOI: 10.1021/acschembio.8b00826] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Abstract
Bacteria produce a large number of secondary metabolites with extraordinary chemical structures and bioactivities. Vioprolides are promising anticancer and antifungal lead compounds produced by the myxobacterium Cystobacter violaceus Cb vi35, which are initially synthesized as acylated precursors (previoprolides) by nonribosomal peptide synthetases (NRPS). Here, we describe and characterize an unprecedented glycerate esterification process in the biosynthesis of vioprolides. In vitro biochemical investigations revealed that the fatty acyl chain of previoprolides is adenylated by the starting fatty acyl-AMP ligase (FAAL) domain, while the glycerate moiety is incorporated by the FkbH domain. An unusual ester-bond forming condensation domain is shown responsible for the acylation of glycerate. LC-MS analysis and bioactivity assays suggest that the acylation serves for directed membrane transport rather than representing a prodrug mechanism.
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Affiliation(s)
- David Auerbach
- Helmholtz Institute for Pharmaceutical Research Saarland (HIPS), Helmholtz Centre for Infection Research and Department of Pharmacy, Saarland University, Saarland University Campus, Building E8.1, 66123 Saarbrücken, Germany
| | - Fu Yan
- Helmholtz Institute for Pharmaceutical Research Saarland (HIPS), Helmholtz Centre for Infection Research and Department of Pharmacy, Saarland University, Saarland University Campus, Building E8.1, 66123 Saarbrücken, Germany
| | - Youming Zhang
- Shandong University-Helmholtz Joint Institute of Biotechnology, State Key Laboratory of Microbial Technology, School of Life Science, Shandong University, Qingdao, People’s Republic of China
| | - Rolf Müller
- Helmholtz Institute for Pharmaceutical Research Saarland (HIPS), Helmholtz Centre for Infection Research and Department of Pharmacy, Saarland University, Saarland University Campus, Building E8.1, 66123 Saarbrücken, Germany
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