1
|
Maimone NM, Apaza-Castillo GA, Quecine MC, de Lira SP. Accessing the specialized metabolome of actinobacteria from the bulk soil of Paullinia cupana Mart. on the Brazilian Amazon: a promising source of bioactive compounds against soybean phytopathogens. Braz J Microbiol 2024; 55:1863-1882. [PMID: 38421597 PMCID: PMC11153476 DOI: 10.1007/s42770-024-01286-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2023] [Accepted: 02/10/2024] [Indexed: 03/02/2024] Open
Abstract
The Amazon rainforest, an incredibly biodiverse ecosystem, has been increasingly vulnerable to deforestation. Despite its undeniable importance and potential, the Amazonian microbiome has historically received limited study, particularly in relation to its unique arsenal of specialized metabolites. Therefore, in this study our aim was to assess the metabolic diversity and the antifungal activity of actinobacterial strains isolated from the bulk soil of Paullinia cupana, a native crop, in the Brazilian Amazon Rainforest. Extracts from 24 strains were subjected to UPLC-MS/MS analysis using an integrative approach that relied on the Chemical Structural and Compositional Similarity (CSCS) metric, GNPS molecular networking, and in silico dereplication tools. This procedure allowed the comprehensive understanding of the chemical space encompassed by these actinobacteria, which consists of features belonging to known bioactive metabolite classes and several unannotated molecular families. Among the evaluated strains, five isolates exhibited bioactivity against a panel of soybean fungal phytopathogens (Rhizoctonia solani, Macrophomina phaseolina, and Sclerotinia sclerotiorum). A focused inspection led to the annotation of pepstatins, oligomycins, hydroxamate siderophores and dorrigocins as metabolites produced by these bioactive strains, with potentially unknown compounds also comprising their metabolomes. This study introduces a pragmatic protocol grounded in established and readily available tools for the annotation of metabolites and the prioritization of strains to optimize further isolation of specialized metabolites. Conclusively, we demonstrate the relevance of the Amazonian actinobacteria as sources for bioactive metabolites useful for agriculture. We also emphasize the importance of preserving this biome and conducting more in-depth studies on its microbiota.
Collapse
Affiliation(s)
- Naydja Moralles Maimone
- College of Agriculture "Luiz de Queiroz", Department of Exact Sciences, University of São Paulo, Piracicaba, SP, 13418-900, Brazil
| | - Gladys Angélica Apaza-Castillo
- College of Agriculture "Luiz de Queiroz", Department of Genetics, University of São Paulo, Piracicaba, SP, 13418-900, Brazil
| | - Maria Carolina Quecine
- College of Agriculture "Luiz de Queiroz", Department of Genetics, University of São Paulo, Piracicaba, SP, 13418-900, Brazil
| | - Simone Possedente de Lira
- College of Agriculture "Luiz de Queiroz", Department of Exact Sciences, University of São Paulo, Piracicaba, SP, 13418-900, Brazil.
| |
Collapse
|
2
|
Thompson TP, Gilmore BF. Exploring halophilic environments as a source of new antibiotics. Crit Rev Microbiol 2024; 50:341-370. [PMID: 37079280 DOI: 10.1080/1040841x.2023.2197491] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2022] [Accepted: 03/25/2023] [Indexed: 04/21/2023]
Abstract
Microbial natural products from microbes in extreme environments, including haloarchaea, and halophilic bacteria, possess a huge capacity to produce novel antibiotics. Additionally, enhanced isolation techniques and improved tools for genomic mining have expanded the efficiencies in the antibiotic discovery process. This review article provides a detailed overview of known antimicrobial compounds produced by halophiles from all three domains of life. We summarize that while halophilic bacteria, in particular actinomycetes, contribute the vast majority of these compounds the importance of understudied halophiles from other domains of life requires additional consideration. Finally, we conclude by discussing upcoming technologies- enhanced isolation and metagenomic screening, as tools that will be required to overcome the barriers to antimicrobial drug discovery. This review highlights the potential of these microbes from extreme environments, and their importance to the wider scientific community, with the hope of provoking discussion and collaborations within halophile biodiscovery. Importantly, we emphasize the importance of bioprospecting from communities of lesser-studied halophilic and halotolerant microorganisms as sources of novel therapeutically relevant chemical diversity to combat the high rediscovery rates. The complexity of halophiles will necessitate a multitude of scientific disciplines to unravel their potential and therefore this review reflects these research communities.
Collapse
Affiliation(s)
- Thomas P Thompson
- Biofilm Research Group, School of Pharmacy, Queen's University Belfast, Belfast, UK
| | - Brendan F Gilmore
- Biofilm Research Group, School of Pharmacy, Queen's University Belfast, Belfast, UK
| |
Collapse
|
3
|
Liu SW, Zhai XX, Liu D, Liu YY, Sui LY, Luo KK, Yang Q, Li FN, Nikandrova AA, Imamutdinova AN, Lukianov DA, Osterman IA, Sergiev PV, Zhang BY, Zhang DJ, Xue CM, Sun CH. Bioprospecting of Actinobacterial Diversity and Antibacterial Secondary Metabolites from the Sediments of Four Saline Lakes on the Northern Tibetan Plateau. Microorganisms 2023; 11:2475. [PMID: 37894133 PMCID: PMC10609225 DOI: 10.3390/microorganisms11102475] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2023] [Revised: 09/28/2023] [Accepted: 09/29/2023] [Indexed: 10/29/2023] Open
Abstract
The Tibetan Plateau, known as the "Roof of the World" and "The Third Pole", harbors numerous saline lakes primarily distributed in the Northern Tibetan Plateau. However, the challenging conditions of high altitude, low oxygen level, and harsh climate have limited investigations into the actinobacteria from these saline lakes. This study focuses on investigating the biodiversity and bioactive secondary metabolites of cultivable actinobacteria isolated from the sediments of four saline lakes on the Northern Tibetan Plateau. A total of 255 actinobacterial strains affiliated with 21 genera in 12 families of 7 orders were recovered by using the pure culture technique and 16S rRNA gene phylogenetic analysis. To facilitate a high-throughput bioactivity evaluation, 192 isolates underwent OSMAC cultivation in a miniaturized 24-well microbioreactor system (MATRIX cultivation). The antibacterial activity of crude extracts was then evaluated in a 96-well plate antibacterial assay. Forty-six strains demonstrated antagonistic effects against at least one tested pathogen, and their underlying antibacterial mechanisms were further investigated through a dual-fluorescent reporter assay (pDualrep2). Two Streptomyces strains (378 and 549) that produce compounds triggering DNA damage were prioritized for subsequent chemical investigations. Metabolomics profiling involving HPLC-UV/vis, UPLC-QTOF-MS/MS, and molecular networking identified three types of bioactive metabolites belonging to the aromatic polyketide family, i.e., cosmomycin, kidamycin, and hedamycin. In-depth analysis of the metabolomic data unveiled some potentially novel anthracycline compounds. A genome mining study based on the whole-genome sequences of strains 378 and 549 identified gene clusters potentially responsible for cosmomycin and kidamycin biosynthesis. This work highlights the effectiveness of combining metabolomic and genomic approaches to rapidly identify bioactive chemicals within microbial extracts. The saline lakes on the Northern Tibetan Plateau present prospective sources for discovering novel actinobacteria and biologically active compounds.
Collapse
Affiliation(s)
- Shao-Wei Liu
- Department of Microbial Chemistry, Beijing Key Laboratory of Antimicrobial Agents, Institute of Medicinal Biotechnology, Chinese Academy of Medical Sciences, Peking Union Medical College, Beijing 100050, China; (S.-W.L.)
| | - Xiao-Xu Zhai
- Department of Microbial Chemistry, Beijing Key Laboratory of Antimicrobial Agents, Institute of Medicinal Biotechnology, Chinese Academy of Medical Sciences, Peking Union Medical College, Beijing 100050, China; (S.-W.L.)
- State Key Laboratory of Plateau Ecology and Agriculture, Qinghai University, Xining 810016, China
- College of Life Sciences, Jiamusi University, Jiamusi 154000, China
| | - Di Liu
- Department of Microbial Chemistry, Beijing Key Laboratory of Antimicrobial Agents, Institute of Medicinal Biotechnology, Chinese Academy of Medical Sciences, Peking Union Medical College, Beijing 100050, China; (S.-W.L.)
- College of Life Sciences, Jiamusi University, Jiamusi 154000, China
| | - Yu-Yu Liu
- Department of Microbial Chemistry, Beijing Key Laboratory of Antimicrobial Agents, Institute of Medicinal Biotechnology, Chinese Academy of Medical Sciences, Peking Union Medical College, Beijing 100050, China; (S.-W.L.)
| | - Li-Ying Sui
- College of Marine and Environmental Sciences, Tianjin University of Science and Technology, Tianjin 300457, China
| | - Ke-Ke Luo
- Department of Microbial Chemistry, Beijing Key Laboratory of Antimicrobial Agents, Institute of Medicinal Biotechnology, Chinese Academy of Medical Sciences, Peking Union Medical College, Beijing 100050, China; (S.-W.L.)
| | - Qin Yang
- Department of Microbial Chemistry, Beijing Key Laboratory of Antimicrobial Agents, Institute of Medicinal Biotechnology, Chinese Academy of Medical Sciences, Peking Union Medical College, Beijing 100050, China; (S.-W.L.)
| | - Fei-Na Li
- Laboratory of Respiratory Diseases, Beijing Key Laboratory of Pediatric Respiratory Infection Diseases, Beijing Pediatric Research Institute, Beijing Children’s Hospital, Capital Medical University, Key Laboratory of Major Diseases in Children, Ministry of Education, National Clinical Research Center for Respiratory Diseases, National Center for Children’s Health, Beijing 100045, China;
| | - Arina A. Nikandrova
- Center of Life Sciences, Skolkovo Institute of Science and Technology, 121205 Moscow, Russia
- Department of Biology, Lomonosov Moscow State University, 119991 Moscow, Russia
| | - Arina N. Imamutdinova
- Center of Life Sciences, Skolkovo Institute of Science and Technology, 121205 Moscow, Russia
- Department of Chemistry, Lomonosov Moscow State University, 119991 Moscow, Russia
| | - Dmitrii A. Lukianov
- Center of Life Sciences, Skolkovo Institute of Science and Technology, 121205 Moscow, Russia
- Department of Chemistry, Lomonosov Moscow State University, 119991 Moscow, Russia
| | - Ilya A. Osterman
- Center of Life Sciences, Skolkovo Institute of Science and Technology, 121205 Moscow, Russia
- Department of Chemistry, Lomonosov Moscow State University, 119991 Moscow, Russia
| | - Petr V. Sergiev
- Center of Life Sciences, Skolkovo Institute of Science and Technology, 121205 Moscow, Russia
- Department of Chemistry, Lomonosov Moscow State University, 119991 Moscow, Russia
| | - Ben-Yin Zhang
- College of Eco-Environmental Engineering, Qinghai University, Xining 810016, China; (B.-Y.Z.); (D.-J.Z.)
| | - De-Jun Zhang
- College of Eco-Environmental Engineering, Qinghai University, Xining 810016, China; (B.-Y.Z.); (D.-J.Z.)
| | - Chun-Mei Xue
- College of Life Sciences, Jiamusi University, Jiamusi 154000, China
| | - Cheng-Hang Sun
- Department of Microbial Chemistry, Beijing Key Laboratory of Antimicrobial Agents, Institute of Medicinal Biotechnology, Chinese Academy of Medical Sciences, Peking Union Medical College, Beijing 100050, China; (S.-W.L.)
- State Key Laboratory of Plateau Ecology and Agriculture, Qinghai University, Xining 810016, China
- College of Eco-Environmental Engineering, Qinghai University, Xining 810016, China; (B.-Y.Z.); (D.-J.Z.)
| |
Collapse
|
4
|
Boudjelal F, Zitouni A, Bouras N, Spröer C, Klenk HP, Smaoui S, Mathieu F. Rare Halophilic Nocardiopsis from Algerian Saharan Soils as Tools for Biotechnological Processes in Pharmaceutical Industry. BIOMED RESEARCH INTERNATIONAL 2023; 2023:1061176. [PMID: 37284028 PMCID: PMC10241594 DOI: 10.1155/2023/1061176] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/14/2022] [Revised: 05/01/2023] [Accepted: 05/15/2023] [Indexed: 06/08/2023]
Abstract
The Sahara Desert, one of the most extreme ecosystems in the planet, constitutes an unexplored source of microorganisms such as mycelial bacteria. In this study, we investigated the diversity of halophilic actinobacteria in soils collected from five regions of the Algerian Sahara. A total of 23 halophilic actinobacterial strains were isolated by using a humic-vitamin agar medium supplemented with 10% NaCl. The isolated halophilic strains were subjected to taxonomic analysis using a polyphasic approach, which included morphological, chemotaxonomic, physiological (numerical taxonomy), and phylogenetic analyses. The isolates showed abundant growth in CMA (complex medium agar) and TSA (tryptic soy agar) media containing 10% NaCl, and chemotaxonomic characteristics were consistent with their assignment to the genus Nocardiopsis. Analysis of the 16S rRNA sequence of 23 isolates showed five distinct clusters and a similarity level ranging between 98.4% and 99.8% within the Nocardiopsis species. Comparison of their physiological characteristics with the nearest species showed significant differences with the closely related species. Halophilic Nocardiopsis isolated from Algerian Sahara soil represents a distinct phyletic line suggesting a potential new species. Furthermore, the isolated strains of halophilic Nocardiopsis were screened for their antagonistic properties against a broad spectrum of microorganisms by the conventional agar method (agar cylinders method) and found to have the capacity to produce bioactive secondary metabolites. Except one isolate (AH37), all isolated Nocardiopsis showed moderate to high biological activities against Pseudomonas syringae and Salmonella enterica, and some isolates showed activities against Agrobacterium tumefaciens, Serratia marcescens, and Klebsiella pneumoniae. However, no isolates were active against Bacillus subtilis, Aspergillus flavus, or Aspergillus niger. The obtained finding implies that the unexplored extreme environments such as the Sahara contain many new bacterial species as a novel drug source for medical and industrial applications.
Collapse
Affiliation(s)
- Farida Boudjelal
- Laboratoire de Biologie des Systèmes Microbiens (LBSM), Ecole Normale Supérieure de Kouba, Algiers, Algeria
- Faculty of Biological Sciences (FSB), University of Sciences and Technologies Houari Boumediene (USTHB), BP 32 El Alia, Bab Ezzouar, 16111 Algiers, Algeria
| | - Abdelghani Zitouni
- Laboratoire de Biologie des Systèmes Microbiens (LBSM), Ecole Normale Supérieure de Kouba, Algiers, Algeria
| | - Noureddine Bouras
- Laboratoire de Biologie des Systèmes Microbiens (LBSM), Ecole Normale Supérieure de Kouba, Algiers, Algeria
- Laboratoire de Valorisation et Conservation des Écosystèmes Arides (LVCEA), Faculté des Sciences de la Nature et de la Vie et Sciences de la Terre, Université de Ghardaia, Ghardaia, Algeria
| | - Cathrin Spröer
- Department Bioinformatics and Databases, Leibniz Institute DSMZ-German Collection of Microorganisms and Cell Cultures GmbH, Brunswick, Germany
| | - Hans-Peter Klenk
- School of Natural and Environmental Sciences, Newcastle University, Newcastle upon Tyne, UK
| | - Slim Smaoui
- Laboratory of Microbial Biotechnology and Engineering Enzymes (LMBEE), Center of Biotechnology of Sfax (CBS), University of Sfax, Road of Sidi Mansour Km 6, P.O. Box 1177 3018 Sfax, Tunisia
| | - Florence Mathieu
- Laboratoire de Génie Chimique, UMR 5503 CNRS/INPT/UPS, INP-ENSAT, 1, Université de Toulouse, Avenue de l'Agrobiopôle, 31326 Castanet-Tolosan, France
| |
Collapse
|
5
|
Stupak A, Gęca T, Kwaśniewska A, Mlak R, Piwowarczyk P, Nawrot R, Goździcka-Józefiak A, Kwaśniewski W. Comparative Analysis of the Placental Microbiome in Pregnancies with Late Fetal Growth Restriction versus Physiological Pregnancies. Int J Mol Sci 2023; 24:ijms24086922. [PMID: 37108086 PMCID: PMC10139004 DOI: 10.3390/ijms24086922] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2023] [Revised: 04/03/2023] [Accepted: 04/06/2023] [Indexed: 04/29/2023] Open
Abstract
A comparative analysis of the placental microbiome in pregnancies with late fetal growth restriction (FGR) was performed with normal pregnancies to assess the impact of bacteria on placental development and function. The presence of microorganisms in the placenta, amniotic fluid, fetal membranes and umbilical cord blood throughout pregnancy disproves the theory of the "sterile uterus". FGR occurs when the fetus is unable to follow a biophysically determined growth path. Bacterial infections have been linked to maternal overproduction of pro-inflammatory cytokines, as well as various short- and long-term problems. Proteomics and bioinformatics studies of placental biomass allowed the development of new diagnostic options. In this study, the microbiome of normal and FGR placentas was analyzed by LC-ESI-MS/MS mass spectrometry, and the bacteria present in both placentas were identified by analysis of a set of bacterial proteins. Thirty-six pregnant Caucasian women participated in the study, including 18 women with normal pregnancy and eutrophic fetuses (EFW > 10th percentile) and 18 women with late FGR diagnosed after 32 weeks of gestation. Based on the analysis of the proteinogram, 166 bacterial proteins were detected in the material taken from the placentas in the study group. Of these, 21 proteins had an exponentially modified protein abundance index (emPAI) value of 0 and were not included in further analysis. Of the remaining 145 proteins, 52 were also present in the material from the control group. The remaining 93 proteins were present only in the material collected from the study group. Based on the proteinogram analysis, 732 bacterial proteins were detected in the material taken from the control group. Of these, 104 proteins had an emPAI value of 0 and were not included in further analysis. Of the remaining 628 proteins, 52 were also present in the material from the study group. The remaining 576 proteins were present only in the material taken from the control group. In both groups, we considered the result of ns prot ≥ 60 as the cut-off value for the agreement of the detected protein with its theoretical counterpart. Our study found significantly higher emPAI values of proteins representative of the following bacteria: Actinopolyspora erythraea, Listeria costaricensis, E. coli, Methylobacterium, Acidobacteria bacterium, Bacteroidetes bacterium, Paenisporsarcina sp., Thiodiazotropha endol oripes and Clostridiales bacterium. On the other hand, in the control group statistically more frequently, based on proteomic data, the following were found: Flavobacterial bacterium, Aureimonas sp. and Bacillus cereus. Our study showed that placental dysbiosis may be an important factor in the etiology of FGR. The presence of numerous bacterial proteins present in the control material may indicate their protective role, while the presence of bacterial proteins detected only in the material taken from the placentas of the study group may indicate their potentially pathogenic nature. This phenomenon is probably important in the development of the immune system in early life, and the placental microbiota and its metabolites may have great potential in the screening, prevention, diagnosis and treatment of FGR.
Collapse
Affiliation(s)
- Aleksandra Stupak
- Chair and Department of Obstetrics and Pathology of Pregnancy, Medical University of Lublin, 20-059 Lublin, Poland
| | - Tomasz Gęca
- Chair and Department of Obstetrics and Pathology of Pregnancy, Medical University of Lublin, 20-059 Lublin, Poland
| | - Anna Kwaśniewska
- Chair and Department of Obstetrics and Pathology of Pregnancy, Medical University of Lublin, 20-059 Lublin, Poland
| | - Radosław Mlak
- Body Composition Research Laboratory, Department of Preclinical Science, Medical University of Lublin, 20-059 Lublin, Poland
| | - Paweł Piwowarczyk
- 2nd Department of Anesthesiology and Intensive Care Unit, Medical University of Lublin, 20-059 Lublin, Poland
| | - Robert Nawrot
- Department of Molecular Virology, Institute of Experimental Biology, Adam Mickiewicz University in Poznan, 61-712 Poznań, Poland
| | - Anna Goździcka-Józefiak
- Department of Molecular Virology, Institute of Experimental Biology, Adam Mickiewicz University in Poznan, 61-712 Poznań, Poland
| | - Wojciech Kwaśniewski
- Department of Gynecologic Oncology and Gynecology, Medical University of Lublin, 20-059 Lublin, Poland
| |
Collapse
|
6
|
Menasria T, Monteoliva-Sánchez M, Benhadj M, Benammar L, Boukoucha M, Aguilera M. Unraveling the enzymatic and antibacterial potential of rare halophilic actinomycetes from Algerian hypersaline wetland ecosystems. J Basic Microbiol 2022; 62:1202-1215. [PMID: 35945171 DOI: 10.1002/jobm.202200085] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2022] [Revised: 06/18/2022] [Accepted: 07/10/2022] [Indexed: 11/07/2022]
Abstract
The study aimed to isolate rare halophilic actinomycetes from hypersaline soils of Algerian inland Wetland Ecosystems "Sebkhas-Chotts" located in arid and hot hyperarid lands with international importance under the Ramsar Convention and to explore their enzyme-producing and antibacterial abilities. The halophilic actinomycetes were selectively isolated using agar-rich media supplemented with 5, 10, and 15% (W/V) of total salts. Thirty-one isolates were obtained and 16S rRNA gene sequencing analysis revealed the presence of members affiliated to rare halophilic actinobacterial genera (Actinopolyspora and Nocardiopsis) accounting for 74.19% (23 isolates out of 31) and 25.8% (8 isolates), respectively. Both phylotypes are alkalitolerant and halophilic thermotolerant actinomycetes displaying significant hydrolytic activities relative to (amylase, asparaginase, cellulase, esterase, glutaminase, inulinase, protease, pectinase, xylanase), and over 96% of tested isolates exhibited all common enzymes, mainly active at 10% of growing salt. In addition, high antibacterial activity was observed against Bacillus cereus, Bacillus subtilis, Micrococcus luteus, and Staphylococcus aureus. The findings showed that saline wetlands ecosystems represent a rich reservoir for the isolation of significant rare halophilic actinomycetes with potential adaptive features and valuable sources for novel bioactive metabolites and biocatalysts of biotechnological interest.
Collapse
Affiliation(s)
- Taha Menasria
- Department of Applied Biology, Faculty of Exact Sciences and Natural and Life Sciences, University of Larbi Tebessi, Tebessa, Algeria.,Department of Microbiology, Faculty of Pharmacy, University of Granada, Granada, Spain
| | | | - Mabrouka Benhadj
- Department of Applied Biology, Faculty of Exact Sciences and Natural and Life Sciences, University of Larbi Tebessi, Tebessa, Algeria
| | - Leyla Benammar
- Department of Microbiology and Biochemistry, Faculty of Natural and Life Sciences University of Batna, Batna, Algeria
| | - Mourad Boukoucha
- Department of Applied Biology, Faculty of Exact Sciences and Natural and Life Sciences, University of Larbi Tebessi, Tebessa, Algeria
| | - Margarita Aguilera
- Department of Microbiology, Faculty of Pharmacy, University of Granada, Granada, Spain
| |
Collapse
|
7
|
Yu G, Sun P, Aierken R, Sun C, Zhang Z, Che Q, Zhang G, Zhu T, Gu Q, Li M, Li D. Linear polyketides produced by co-culture of Penicillium crustosum and Penicillium fellutanum. MARINE LIFE SCIENCE & TECHNOLOGY 2022; 4:237-244. [PMID: 37073220 PMCID: PMC10077197 DOI: 10.1007/s42995-021-00125-8] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/19/2021] [Accepted: 11/17/2021] [Indexed: 05/03/2023]
Abstract
Two new polyketides, penifellutins A (1) and B (2), possessing a 22 carbon linear skeleton, were isolated from a co-culture of the deep-sea-derived fungi Penicillium crustosum PRB-2 and Penicillium fellutanum HDN14-323. Meanwhile, two esterification products of 1, penifellutins C (3) and D (4), were obtained because compound 1 could be esterified spontaneously when stored in methanol. Their configurations were difficult to determine because of chiral central crowdedness, structural flexibility and instability. As such, we solved this issue by comprehensively using Mo2(OAc)4-based CD experiments, density functional theory calculation of 13C NMR, DP4 + probability analysis and many chemical reactions, including making acetonide derivative, Mosher's method, PGME method, etc. Compounds 1 and 2 show obvious inhibitory activity on the liver hyperplasia of zebrafish larvae at a concentration of 10 μmol/L, while 3 and 4 show no activity, indicating that two carboxyls in the structure are important active sites. Supplementary Information The online version contains supplementary material available at 10.1007/s42995-021-00125-8.
Collapse
Affiliation(s)
- Guihong Yu
- Key Laboratory of Marine Drugs, Chinese Ministry of Education, School of Medicine and Pharmacy, Ocean University of China, Qingdao, 266003 China
- School of Life Sciences, Shandong Province Key Laboratory of Applied Mycology, Qingdao Agricultural University, Qingdao, 266109 China
| | - Peng Sun
- Key Laboratory of Marine Drugs, Chinese Ministry of Education, School of Medicine and Pharmacy, Ocean University of China, Qingdao, 266003 China
| | - Reyilamu Aierken
- Fujian Provincial Key Laboratory of Innovative Drug Target Research, School of Pharmaceutical Science, Xiamen University, Xiamen, 361102 China
| | - Chunxiao Sun
- Key Laboratory of Marine Drugs, Chinese Ministry of Education, School of Medicine and Pharmacy, Ocean University of China, Qingdao, 266003 China
| | - Zhenzhen Zhang
- Key Laboratory of Marine Drugs, Chinese Ministry of Education, School of Medicine and Pharmacy, Ocean University of China, Qingdao, 266003 China
| | - Qian Che
- Key Laboratory of Marine Drugs, Chinese Ministry of Education, School of Medicine and Pharmacy, Ocean University of China, Qingdao, 266003 China
| | - Guojian Zhang
- Key Laboratory of Marine Drugs, Chinese Ministry of Education, School of Medicine and Pharmacy, Ocean University of China, Qingdao, 266003 China
- Laboratory for Marine Drugs and Bioproducts of Pilot National Laboratory for Marine Science and Technology (Qingdao), Qingdao, 266237 China
| | - Tianjiao Zhu
- Key Laboratory of Marine Drugs, Chinese Ministry of Education, School of Medicine and Pharmacy, Ocean University of China, Qingdao, 266003 China
- Laboratory for Marine Drugs and Bioproducts of Pilot National Laboratory for Marine Science and Technology (Qingdao), Qingdao, 266237 China
| | - Qianqun Gu
- Key Laboratory of Marine Drugs, Chinese Ministry of Education, School of Medicine and Pharmacy, Ocean University of China, Qingdao, 266003 China
| | - Mingyu Li
- Fujian Provincial Key Laboratory of Innovative Drug Target Research, School of Pharmaceutical Science, Xiamen University, Xiamen, 361102 China
| | - Dehai Li
- Key Laboratory of Marine Drugs, Chinese Ministry of Education, School of Medicine and Pharmacy, Ocean University of China, Qingdao, 266003 China
- Laboratory for Marine Drugs and Bioproducts of Pilot National Laboratory for Marine Science and Technology (Qingdao), Qingdao, 266237 China
| |
Collapse
|
8
|
Sponge-associated sp . RM66 metabolome induction with N-acetylglucosamine: Antibacterial, antifungal and anti-trypanosomal activities. Saudi J Biol Sci 2021; 28:4691-4698. [PMID: 34354456 PMCID: PMC8324951 DOI: 10.1016/j.sjbs.2021.04.082] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2021] [Revised: 04/23/2021] [Accepted: 04/26/2021] [Indexed: 11/22/2022] Open
Abstract
The marine sponge Amphimedon sp., collected from Hurghada (Egypt) was investigated for its sponge-derived actinomycetes diversity. Nineteen actinomycetes were cultivated and phylogenetically identified using 16S rDNA gene sequencing were carried out. The strains belong to genera Kocuria, Dietzia, Micrococcus, Microbacterium and Streptomyces. Many silent biosynthetic genes clusters were investigated using genome sequencing of actinomycete strains and has revealed in particular the genus Streptomyces that has indicated their exceptional capacity for the secondary metabolites production that not observed under classical cultivation conditions. In this study, the effect of N-acetylglucosamine on the metabolome of Streptomyces sp. RM66 was investigated using three actinomycetes media (ISP2, M1 and MA). In total, twelve extracts were produced using solid and liquid fermentation approaches. Liquid chromatography-high resolution tandem mass spectrometry (LC-HRMS/MS) data were analysed using metabolomics tools to compare natural product production across all crude extracts. Our study highlighted the elicitation effect of N-acetylglucosamine on the secondary metabolite profiles of Streptomyces sp. RM66. These results highlight the of N-acetylglucosamine application as an elicitor to induce the cryptic metabolites and for increasing the chemical diversity. All the twelve extracts were tested for their antibacterial activity was tested against Staphylococcus aureus NCTC 8325, antifungal activity against Candida albicans 5314 (ATCC 90028) and anti-trypanosomal activity against Trypanosoma brucei brucei. Extract St1 showed the most potent one with activities 2.3, 3.2 and 4.7 ug/ml as antibacterial, antifungal and anti-trypanosomal, respectively.
Collapse
|
9
|
Wilson ZE, Brimble MA. Molecules derived from the extremes of life: a decade later. Nat Prod Rep 2020; 38:24-82. [PMID: 32672280 DOI: 10.1039/d0np00021c] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
Covering: Early 2008 until the end of 2019Microorganisms which survive (extreme-tolerant) or even prefer (extremophilic) living at the limits of pH, temperature, salinity and pressure found on earth have proven to be a rich source of novel structures. In this update we summarise the wide variety of new molecules which have been isolated from extremophilic and extreme-tolerant microorganisms since our original 2009 review, highlighting the range of bioactivities these molecules have been reported to possess.
Collapse
Affiliation(s)
- Zoe E Wilson
- School of Chemical Sciences, The University of Auckland, 23 Symonds Street, Auckland 1010, New Zealand.
| | | |
Collapse
|
10
|
Corral P, Amoozegar MA, Ventosa A. Halophiles and Their Biomolecules: Recent Advances and Future Applications in Biomedicine. Mar Drugs 2019; 18:md18010033. [PMID: 31906001 PMCID: PMC7024382 DOI: 10.3390/md18010033] [Citation(s) in RCA: 64] [Impact Index Per Article: 12.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2019] [Revised: 12/21/2019] [Accepted: 12/28/2019] [Indexed: 12/18/2022] Open
Abstract
The organisms thriving under extreme conditions better than any other organism living on Earth, fascinate by their hostile growing parameters, physiological features, and their production of valuable bioactive metabolites. This is the case of microorganisms (bacteria, archaea, and fungi) that grow optimally at high salinities and are able to produce biomolecules of pharmaceutical interest for therapeutic applications. As along as the microbiota is being approached by massive sequencing, novel insights are revealing the environmental conditions on which the compounds are produced in the microbial community without more stress than sharing the same substratum with their peers, the salt. In this review are reported the molecules described and produced by halophilic microorganisms with a spectrum of action in vitro: antimicrobial and anticancer. The action mechanisms of these molecules, the urgent need to introduce alternative lead compounds and the current aspects on the exploitation and its limitations are discussed.
Collapse
Affiliation(s)
- Paulina Corral
- Department of Biology, University of Naples Federico II, 80126 Naples, Italy;
- Department of Microbiology and Parasitology, Faculty of Pharmacy, University of Sevilla, 41012 Sevilla, Spain
| | - Mohammad A. Amoozegar
- Department of Microbiology, School of Biology, College of Science, University of Tehran, Tehran 14155-6955, Iran;
| | - Antonio Ventosa
- Department of Microbiology and Parasitology, Faculty of Pharmacy, University of Sevilla, 41012 Sevilla, Spain
- Correspondence: ; Tel.: +34-954556765
| |
Collapse
|
11
|
Chen JJ, Rateb ME, Love MS, Xu Z, Yang D, Zhu X, Huang Y, Zhao LX, Jiang Y, Duan Y, McNamara CW, Shen B. Herbicidins from Streptomyces sp. CB01388 Showing Anti- Cryptosporidium Activity. JOURNAL OF NATURAL PRODUCTS 2018; 81:791-797. [PMID: 29469575 DOI: 10.1021/acs.jnatprod.7b00850] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/08/2023]
Abstract
A high-content imaging assay was used to screen the fraction collection of the Natural Product Library at The Scripps Research Institute for inhibitors of Cryptosporidium parvum. A chemical investigation of one strain, Streptomyces sp. CB01388, resulted in the isolation of six herbicidins (1-6), one of which is new (herbicidin L, 1). Five of the six herbicidins (1-3, 5, 6) showed moderate inhibitory activity against C. parvum, with 1 and 6 comparable to the FDA-approved drug nitazoxanide, and 2-6 showed no toxicity to the host HCT-8 cells and human HEK293T and HepG2 cells. These findings highlight the herbicidin scaffold for anti- Cryptosporidium drug development.
Collapse
Affiliation(s)
- Jian-Jun Chen
- Department of Chemistry , The Scripps Research Institute , Jupiter , Florida 33458 , United States
| | - Mostafa E Rateb
- Department of Chemistry , The Scripps Research Institute , Jupiter , Florida 33458 , United States
| | - Melissa S Love
- California Institute for Biomedical Research , La Jolla , California 92037 , United States
| | - Zhengren Xu
- Department of Chemistry , The Scripps Research Institute , Jupiter , Florida 33458 , United States
| | - Dong Yang
- Department of Chemistry , The Scripps Research Institute , Jupiter , Florida 33458 , United States
- Natural Products Library Initiative at The Scripps Research Institute , The Scripps Research Institute , Jupiter , Florida 33458 , United States
| | - Xiangcheng Zhu
- Xiangya International Academy of Translational Medicine , Central South University , Changsha , Hunan 410013 , People's Republic of China
- Hunan Engineering Research Center of Combinatorial Biosynthesis and Natural Product Drug Discovery , Changsha , Hunan 410013 , People's Republic of China
| | - Yong Huang
- Xiangya International Academy of Translational Medicine , Central South University , Changsha , Hunan 410013 , People's Republic of China
| | - Li-Xing Zhao
- Yunnan Institute of Microbiology , Yunnan University , Kunming , Yunnan 650091 , People's Republic of China
| | - Yi Jiang
- Yunnan Institute of Microbiology , Yunnan University , Kunming , Yunnan 650091 , People's Republic of China
| | - Yanwen Duan
- Xiangya International Academy of Translational Medicine , Central South University , Changsha , Hunan 410013 , People's Republic of China
- Hunan Engineering Research Center of Combinatorial Biosynthesis and Natural Product Drug Discovery , Changsha , Hunan 410013 , People's Republic of China
| | - Case W McNamara
- California Institute for Biomedical Research , La Jolla , California 92037 , United States
| | - Ben Shen
- Department of Chemistry , The Scripps Research Institute , Jupiter , Florida 33458 , United States
- Natural Products Library Initiative at The Scripps Research Institute , The Scripps Research Institute , Jupiter , Florida 33458 , United States
- Department of Molecular Medicine , The Scripps Research Institute , Jupiter , Florida 33458 , United States
| |
Collapse
|
12
|
Li C, Sarotti AM, Yoshida W, Cao S. Two new polyketides from Hawaiian endophytic fungus Pestalotiopsis sp. FT172. Tetrahedron Lett 2018. [DOI: 10.1016/j.tetlet.2017.11.045] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
|
13
|
Hill P, Heberlig GW, Boddy CN. Sampling Terrestrial Environments for Bacterial Polyketides. Molecules 2017; 22:E707. [PMID: 28468277 PMCID: PMC6154731 DOI: 10.3390/molecules22050707] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2017] [Revised: 04/14/2017] [Accepted: 04/18/2017] [Indexed: 12/17/2022] Open
Abstract
Bacterial polyketides are highly biologically active molecules that are frequently used as drugs, particularly as antibiotics and anticancer agents, thus the discovery of new polyketides is of major interest. Since the 1980s discovery of polyketides has slowed dramatically due in large part to the repeated rediscovery of known compounds. While recent scientific and technical advances have improved our ability to discover new polyketides, one key area has been under addressed, namely the distribution of polyketide-producing bacteria in the environment. Identifying environments where producing bacteria are abundant and diverse should improve our ability to discover (bioprospect) new polyketides. This review summarizes for the bioprospector the state-of-the-field in terrestrial microbial ecology. It provides insight into the scientific and technical challenges limiting the application of microbial ecology discoveries for bioprospecting and summarizes key developments in the field that will enable more effective bioprospecting. The major recent efforts by researchers to sample new environments for polyketide discovery is also reviewed and key emerging environments such as insect associated bacteria, desert soils, disease suppressive soils, and caves are highlighted. Finally strategies for taking and characterizing terrestrial samples to help maximize discovery efforts are proposed and the inclusion of non-actinomycetal bacteria in any terrestrial discovery strategy is recommended.
Collapse
Affiliation(s)
- Patrick Hill
- Department of Biology, University of Ottawa, Ottawa, ON K1N 6N5, Canada.
| | - Graham W Heberlig
- Department of Chemistry and Biomolecular Sciences, University of Ottawa, Ottawa, ON K1N 6N5, Canada.
| | - Christopher N Boddy
- Department of Biology, University of Ottawa, Ottawa, ON K1N 6N5, Canada.
- Department of Chemistry and Biomolecular Sciences, University of Ottawa, Ottawa, ON K1N 6N5, Canada.
| |
Collapse
|
14
|
New isofuranonaphthoquinones and isoindolequinones from Streptomyces sp. CB01883. J Antibiot (Tokyo) 2016; 70:414-422. [DOI: 10.1038/ja.2016.122] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2016] [Revised: 09/07/2016] [Accepted: 09/09/2016] [Indexed: 12/27/2022]
|
15
|
Sun MW, Zhang XM, Bi HL, Li WJ, Lu CH. Two new sesquiterpenoids produced by halophilic Nocardiopsis chromatogenes YIM 90109. Nat Prod Res 2016; 31:77-83. [DOI: 10.1080/14786419.2016.1214831] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Affiliation(s)
- Ming-Wei Sun
- Key Laboratory of Chemical Biology (Ministry of Education), School of Pharmaceutical Sciences, Shandong University, Jinan, China
| | - Xiao-Mei Zhang
- College of Basic Medicine, Yunnan University of Traditional Chinese Medicine, Kunming, China
| | - Hui-Li Bi
- Key Laboratory of Chemical Biology (Ministry of Education), School of Pharmaceutical Sciences, Shandong University, Jinan, China
| | - Wen-Jun Li
- State Key Laboratory of Biocontrol and Guangdong provincial Key Laboratory of Plant Resources, College of Ecology and Evolution, Sun Yat-Sen University, Guangzhou, China
- Key Laboratory of Biogeography and Bioresource in Arid Land, Xinjiang Institute of Ecology and Geography, Chinese Academy of Sciences, Urumqi, China
| | - Chun-Hua Lu
- Key Laboratory of Chemical Biology (Ministry of Education), School of Pharmaceutical Sciences, Shandong University, Jinan, China
| |
Collapse
|
16
|
Schmid T, Blees JS, Bajer MM, Wild J, Pescatori L, Cuzzucoli Crucitti G, Scipione L, Costi R, Henrich CJ, Brüne B, Colburn NH, Di Santo R. Diaryl Disulfides as Novel Stabilizers of Tumor Suppressor Pdcd4. PLoS One 2016; 11:e0151643. [PMID: 26982744 PMCID: PMC4794182 DOI: 10.1371/journal.pone.0151643] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2015] [Accepted: 03/02/2016] [Indexed: 01/01/2023] Open
Abstract
The translation inhibitor and tumor suppressor Pdcd4 was reported to be lost in various tumors and put forward as prognostic marker in tumorigenesis. Decreased Pdcd4 protein stability due to PI3K-mTOR-p70S6K1 dependent phosphorylation of Pdcd4 followed by β-TrCP1-mediated ubiquitination, and proteasomal destruction of the protein was characterized as a major mechanism contributing to the loss of Pdcd4 expression in tumors. In an attempt to identify stabilizers of Pdcd4, we used a luciferase-based high-throughput compatible cellular assay to monitor phosphorylation-dependent proteasomal degradation of Pdcd4 in response to mitogen stimulation. Following a screen of approximately 2000 compounds, we identified 1,2-bis(4-chlorophenyl)disulfide as a novel Pdcd4 stabilizer. To determine an initial structure-activity relationship, we used 3 additional compounds, synthesized according to previous reports, and 2 commercially available compounds for further testing, in which either the linker between the aryls was modified (compounds 2-4) or the chlorine residues were replaced by groups with different electronic properties (compounds 5 and 6). We observed that those compounds with alterations in the sulfide linker completely lost the Pdcd4 stabilizing potential. In contrast, modifications in the chlorine residues showed only minor effects on the Pdcd4 stabilizing activity. A reporter with a mutated phospho-degron verified the specificity of the compounds for stabilizing the Pdcd4 reporter. Interestingly, the active diaryl disulfides inhibited proliferation and viability at concentrations where they stabilized Pdcd4, suggesting that Pdcd4 stabilization might contribute to the anti-proliferative properties. Finally, computational modelling indicated that the flexibility of the disulfide linker might be necessary to exert the biological functions of the compounds, as the inactive compound appeared to be energetically more restricted.
Collapse
Affiliation(s)
- Tobias Schmid
- Institute of Biochemistry I, Faculty of Medicine, Goethe-University Frankfurt, 60590, Frankfurt, Germany
| | - Johanna S. Blees
- Institute of Biochemistry I, Faculty of Medicine, Goethe-University Frankfurt, 60590, Frankfurt, Germany
| | - Magdalena M. Bajer
- Institute of Biochemistry I, Faculty of Medicine, Goethe-University Frankfurt, 60590, Frankfurt, Germany
| | - Janine Wild
- Institute of Biochemistry I, Faculty of Medicine, Goethe-University Frankfurt, 60590, Frankfurt, Germany
| | - Luca Pescatori
- Dipartimento di Chimica e Tecnologie del Farmaco, Istituto Pasteur – Fondazione Cenci Bolognetti, “Sapienza” University of Rome, 00185, Rome, Italy
| | - Giuliana Cuzzucoli Crucitti
- Dipartimento di Chimica e Tecnologie del Farmaco, Istituto Pasteur – Fondazione Cenci Bolognetti, “Sapienza” University of Rome, 00185, Rome, Italy
| | - Luigi Scipione
- Dipartimento di Chimica e Tecnologie del Farmaco, Istituto Pasteur – Fondazione Cenci Bolognetti, “Sapienza” University of Rome, 00185, Rome, Italy
| | - Roberta Costi
- Dipartimento di Chimica e Tecnologie del Farmaco, Istituto Pasteur – Fondazione Cenci Bolognetti, “Sapienza” University of Rome, 00185, Rome, Italy
| | - Curtis J. Henrich
- Molecular Targets Laboratory, Center for Cancer Research, National Cancer Institute-Frederick, Frederick, MD, 21702, United States of America
- Basic Science Program, Leidos Biomedical Research, Inc., Frederick National Laboratory for Cancer Research, Frederick, MD, 21702, United States of America
| | - Bernhard Brüne
- Institute of Biochemistry I, Faculty of Medicine, Goethe-University Frankfurt, 60590, Frankfurt, Germany
| | - Nancy H. Colburn
- Laboratory of Cancer Prevention, Center for Cancer Research, National Cancer Institute-Frederick, Frederick, MD, 21702, United States of America
| | - Roberto Di Santo
- Dipartimento di Chimica e Tecnologie del Farmaco, Istituto Pasteur – Fondazione Cenci Bolognetti, “Sapienza” University of Rome, 00185, Rome, Italy
| |
Collapse
|
17
|
Smanski MJ, Schlatter DC, Kinkel LL. Leveraging ecological theory to guide natural product discovery. ACTA ACUST UNITED AC 2016; 43:115-28. [DOI: 10.1007/s10295-015-1683-9] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2015] [Accepted: 08/29/2015] [Indexed: 12/31/2022]
Abstract
Abstract
Technological improvements have accelerated natural product (NP) discovery and engineering to the point that systematic genome mining for new molecules is on the horizon. NP biosynthetic potential is not equally distributed across organisms, environments, or microbial life histories, but instead is enriched in a number of prolific clades. Also, NPs are not equally abundant in nature; some are quite common and others markedly rare. Armed with this knowledge, random ‘fishing expeditions’ for new NPs are increasingly harder to justify. Understanding the ecological and evolutionary pressures that drive the non-uniform distribution of NP biosynthesis provides a rational framework for the targeted isolation of strains enriched in new NP potential. Additionally, ecological theory leads to testable hypotheses regarding the roles of NPs in shaping ecosystems. Here we review several recent strain prioritization practices and discuss the ecological and evolutionary underpinnings for each. Finally, we offer perspectives on leveraging microbial ecology and evolutionary biology for future NP discovery.
Collapse
Affiliation(s)
- Michael J Smanski
- grid.17635.36 0000000419368657 Department of Biochemistry, Molecular Biology, and Biophysics University of Minnesota-Twin Cities 55108 Saint Paul MN USA
- grid.17635.36 0000000419368657 BioTechnology Institute University of Minnesota-Twin Cities 55108 Saint Paul MN USA
| | - Daniel C Schlatter
- grid.17635.36 0000000419368657 Department of Plant Pathology University of Minnesota-Twin Cities 55108 Saint Paul MN USA
| | - Linda L Kinkel
- grid.17635.36 0000000419368657 BioTechnology Institute University of Minnesota-Twin Cities 55108 Saint Paul MN USA
- grid.17635.36 0000000419368657 Department of Plant Pathology University of Minnesota-Twin Cities 55108 Saint Paul MN USA
| |
Collapse
|
18
|
Affiliation(s)
- Ming-Wei Sun
- Key Laboratory of Chemical Biology (Ministry of Education), School of Pharmaceutical Sciences, Shandong University, Jinan, PR China
| | - Zhi-Xing Guo
- Key Laboratory of Chemical Biology (Ministry of Education), School of Pharmaceutical Sciences, Shandong University, Jinan, PR China
| | - Chun-Hua Lu
- Key Laboratory of Chemical Biology (Ministry of Education), School of Pharmaceutical Sciences, Shandong University, Jinan, PR China
| |
Collapse
|
19
|
Ma M, Rateb ME, Teng Q, Yang D, Rudolf JD, Zhu X, Huang Y, Zhao LX, Jiang Y, Li X, Rader C, Duan Y, Shen B. Angucyclines and Angucyclinones from Streptomyces sp. CB01913 Featuring C-Ring Cleavage and Expansion. JOURNAL OF NATURAL PRODUCTS 2015; 78:2471-80. [PMID: 26335269 PMCID: PMC4845661 DOI: 10.1021/acs.jnatprod.5b00601] [Citation(s) in RCA: 37] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/28/2023]
Abstract
Angucyclines and angucyclinones are aromatic polyketides with a tetracyclic benz[a]anthracene skeleton. The benz[a]anthracene scaffold is biosynthesized by type II polyketide synthases that catalyze the decarboxylative condensation of a short acyl-CoA starter and nine extender units. Angucyclines and angucyclinones, the largest group of polycyclic aromatic polyketides, achieve structural diversity via subsequent oxidation, ring cleavage, amino acid incorporation, and glycosylation. We here report the discovery of 14 angucyclinones and two angucyclines (1-16) from Streptomyces sp. CB01913, identifying 12 new compounds featuring various oxidations on rings A and C (1, 2, and 4), different sugar moieties attached to rings A and B (3 and 6), and C-ring cleavage (5 and 10-14) and expansion (8). These new structural features, highlighted by C-ring cleavage and expansion, enrich the structural diversity of angucyclines and angucyclinones. All compounds were tested for cytotoxicity and antibacterial activities, with 1, 5, 15, and 16 showing moderate activities against selected cancer cell lines or bacterial strains.
Collapse
Affiliation(s)
- Ming Ma
- Department of Chemistry, The Scripps Research Institute, Jupiter, FL 33458, USA
| | - Mostafa E. Rateb
- Department of Chemistry, The Scripps Research Institute, Jupiter, FL 33458, USA
| | - Qihui Teng
- Department of Chemistry, The Scripps Research Institute, Jupiter, FL 33458, USA
| | - Dong Yang
- Department of Chemistry, The Scripps Research Institute, Jupiter, FL 33458, USA
| | - Jeffrey D. Rudolf
- Department of Chemistry, The Scripps Research Institute, Jupiter, FL 33458, USA
| | - Xiangcheng Zhu
- Xiangya International Academy of Translational Medicine, Central South University, Changsha, Hunan 410013, China
- Hunan Engineering Research Center of Combinatorial Biosynthesis and Natural Product Drug Discovery, Changsha, Hunan 410329, China
| | - Yong Huang
- Xiangya International Academy of Translational Medicine, Central South University, Changsha, Hunan 410013, China
| | - Li-Xing Zhao
- Yunnan Institute of Microbiology, Yunnan University, Kunming, Yunnan 650091, China
| | - Yi Jiang
- Yunnan Institute of Microbiology, Yunnan University, Kunming, Yunnan 650091, China
| | - Xiuling Li
- Department of Cancer Biology, The Scripps Research Institute, Jupiter, FL 33458, USA
| | - Christoph Rader
- Department of Cancer Biology, The Scripps Research Institute, Jupiter, FL 33458, USA
- Department of Molecular Therapeutics, The Scripps Research Institute, Jupiter, FL 33458, USA
| | - Yanwen Duan
- Xiangya International Academy of Translational Medicine, Central South University, Changsha, Hunan 410013, China
- Hunan Engineering Research Center of Combinatorial Biosynthesis and Natural Product Drug Discovery, Changsha, Hunan 410329, China
| | - Ben Shen
- Department of Chemistry, The Scripps Research Institute, Jupiter, FL 33458, USA
- Department of Molecular Therapeutics, The Scripps Research Institute, Jupiter, FL 33458, USA
- Natural Products Library Initiative, The Scripps Research Institute, Jupiter, FL 33458, USA
| |
Collapse
|
20
|
Abstract
A de novo asymmetric total synthesis of the guanidine alkaloid natural product (+)-monanchorin has been achieved in nine steps from the commodity chemicals furan and caproic acid. The asymmetry of the route was introduced by a Noyori reduction of an acylfuran. In addition, this route relies upon an Achmatowicz rearrangement, a diastereoselective palladium catalyzed glycosylation, reductive amination, and an acid catalyzed bicyclic guanidine mixed acetal formation.
Collapse
Affiliation(s)
- Yuzhi Ma
- Department of Chemistry and Chemical Biology, Northeastern University , Boston, Massachusetts 02115, United States
| | - George A O'Doherty
- Department of Chemistry and Chemical Biology, Northeastern University , Boston, Massachusetts 02115, United States
| |
Collapse
|
21
|
Sun M, Zhang X, Hao H, Li W, Lu C. Nocarbenzoxazoles A-G, Benzoxazoles Produced by Halophilic Nocardiopsis lucentensis DSM 44048. JOURNAL OF NATURAL PRODUCTS 2015; 78:2123-2127. [PMID: 26270803 DOI: 10.1021/acs.jnatprod.5b00031] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/04/2023]
Abstract
Seven new benzoxazole derivatives, nocarbenzoxazoles A-G (1-7), were isolated from the halophilic strain Nocardiopsis lucentensis DSM 44048. Their structures were elucidated on the basis of 1D and 2D NMR spectroscopic data, HRESIMS, and X-ray single-crystal diffraction. The isolated compounds were assayed for their cytotoxicity against a panel of human tumor cell lines (HepG2, MDA-MB-231, MDA-MB-435, HeLa, and PC3). Compounds 1-6 were found to have modest or no activity. Compound 7 showed selective activity against HepG2 and HeLa with IC₅₀ values of 3 and 1 μM, respectively.
Collapse
Affiliation(s)
- Mingwei Sun
- Key Laboratory of Chemical Biology (Ministry of Education), School of Pharmaceutical Sciences, Shandong University , No. 44 West Wenhua Road, Jinan, Shandong 250012, People's Republic of China
| | - Xiaomei Zhang
- Key Laboratory of Microbial Diversity in Southwest China, Ministry of Education and Laboratory for Conservation and Utilization of Bio-Resources, Yunnan Institute of Microbiology, Yunnan University , Kunming, Yunnan 650091, People's Republic of China
| | - Huilin Hao
- Key Laboratory of Chemical Biology (Ministry of Education), School of Pharmaceutical Sciences, Shandong University , No. 44 West Wenhua Road, Jinan, Shandong 250012, People's Republic of China
| | - Wenjun Li
- Key Laboratory of Microbial Diversity in Southwest China, Ministry of Education and Laboratory for Conservation and Utilization of Bio-Resources, Yunnan Institute of Microbiology, Yunnan University , Kunming, Yunnan 650091, People's Republic of China
| | - Chunhua Lu
- Key Laboratory of Chemical Biology (Ministry of Education), School of Pharmaceutical Sciences, Shandong University , No. 44 West Wenhua Road, Jinan, Shandong 250012, People's Republic of China
| |
Collapse
|
22
|
Bounagaea algeriensis gen. nov., sp. nov., an extremely halophilic actinobacterium isolated from a Saharan soil of Algeria. Antonie van Leeuwenhoek 2015; 108:473-82. [PMID: 26050246 DOI: 10.1007/s10482-015-0500-9] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/04/2015] [Accepted: 06/02/2015] [Indexed: 01/09/2023]
Abstract
A novel halophilic actinobacterium strain, designated H8(T), was isolated from a Saharan soil sample collected in El-Goléa, South Algeria. Strain H8(T) was identified as representing a new genus using a polyphasic taxonomic approach. Phylogenetic analysis revealed that strain H8(T) shared the highest degree of 16S rRNA gene sequence similarity with 'Mzabimyces algeriensis' DSM 46680(T) (93.0 %), Saccharopolyspora ghardaiensis DSM 45606(T) (91.2 %), Halopolyspora alba DSM 45976(T) (90.8 %) and Actinopolyspora mortivallis DSM 44261(T) (90.0 %). The strain was found to grow optimally at 28-35 °C, at pH 6.0-7.0, and in the presence of 15-25 % (w/v) NaCl. The substrate mycelium was observed to be well developed and fragmented in liquid medium and on solid medium. The aerial mycelium was observed to be moderately abundant and to form long chains with non-motile, smooth-surfaced and ovoid or spherical spores at maturity. The cell wall of strain H8(T) was found to contain meso-diaminopimelic acid. The whole-cell hydrolysates were found to mainly contain arabinose and galactose. The diagnostic phospholipid detected was phosphatidylcholine, and MK-9(H4), MK-9(H2) and MK-10(H2) were found to be the predominant menaquinones. The major cellular fatty acids were determined to be anteiso-C17:0 and iso-C15:0. The genomic DNA G+C content of strain H8(T) was determined to be 71.3 mol%. The genotypic and phenotypic data showed that the strain represents a novel genus and species, for which the name Bounagaea algeriensis gen. nov., sp. nov. is proposed, with the type strain H8(T) (=DSM 45966(T) = CECT 8470(T)).
Collapse
|
23
|
Chen D, Feng J, Huang L, Zhang Q, Wu J, Zhu X, Duan Y, Xu Z. Identification and characterization of a new erythromycin biosynthetic gene cluster in Actinopolyspora erythraea YIM90600, a novel erythronolide-producing halophilic actinomycete isolated from salt field. PLoS One 2014; 9:e108129. [PMID: 25250723 PMCID: PMC4176971 DOI: 10.1371/journal.pone.0108129] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2014] [Accepted: 08/25/2014] [Indexed: 12/20/2022] Open
Abstract
Erythromycins (Ers) are clinically potent macrolide antibiotics in treating pathogenic bacterial infections. Microorganisms capable of producing Ers, represented by Saccharopolyspora erythraea, are mainly soil-dwelling actinomycetes. So far, Actinopolyspora erythraea YIM90600, a halophilic actinomycete isolated from Baicheng salt field, is the only known Er-producing extremophile. In this study, we have reported the draft genome sequence of Ac. erythraea YIM90600, genome mining of which has revealed a new Er biosynthetic gene cluster encoding several novel Er metabolites. This Er gene cluster shares high identity and similarity with the one of Sa. erythraea NRRL2338, except for two absent genes, eryBI and eryG. By correlating genotype and chemotype, the biosynthetic pathways of 3'-demethyl-erythromycin C, erythronolide H (EH) and erythronolide I have been proposed. The formation of EH is supposed to be sequentially biosynthesized via C-6/C-18 epoxidation and C-14 hydroxylation from 6-deoxyerythronolide B. Although an in vitro enzymatic activity assay has provided limited evidence for the involvement of the cytochrome P450 oxidase EryFAc (derived from Ac. erythraea YIM90600) in the catalysis of a two-step oxidation, resulting in an epoxy moiety, the attempt to construct an EH-producing Sa. erythraea mutant via gene complementation was not successful. Characterization of EryKAc (derived from Ac. erythraea YIM90600) in vitro has confirmed its unique role as a C-12 hydroxylase, rather than a C-14 hydroxylase of the erythronolide. Genomic characterization of the halophile Ac. erythraea YIM90600 will assist us to explore the great potential of extremophiles, and promote the understanding of EH formation, which will shed new insights into the biosynthesis of Er metabolites.
Collapse
Affiliation(s)
- Dandan Chen
- Department of Chemical and Biological Engineering, Zhejiang University, Hangzhou, China
- Huzhou Center of Bio-synthetic Innovation, Shanghai Institute of Organic Chemistry, Chinese Academy of Sciences, Huzhou, China
| | - Junyin Feng
- Huzhou Center of Bio-synthetic Innovation, Shanghai Institute of Organic Chemistry, Chinese Academy of Sciences, Huzhou, China
| | - Lei Huang
- Department of Chemical and Biological Engineering, Zhejiang University, Hangzhou, China
| | - Qinglin Zhang
- Huzhou Center of Bio-synthetic Innovation, Shanghai Institute of Organic Chemistry, Chinese Academy of Sciences, Huzhou, China
| | - Jiequn Wu
- Huzhou Center of Bio-synthetic Innovation, Shanghai Institute of Organic Chemistry, Chinese Academy of Sciences, Huzhou, China
| | - Xiangcheng Zhu
- Hunan Engineering Research Center of Combinatorial Biosynthesis and Natural Product Drug Discovery, Changsha, Hunan, China
- Xiangya International Academy of Translational Medicine, Central South University, Changsha, Hunan, China
| | - Yanwen Duan
- Hunan Engineering Research Center of Combinatorial Biosynthesis and Natural Product Drug Discovery, Changsha, Hunan, China
- Xiangya International Academy of Translational Medicine, Central South University, Changsha, Hunan, China
| | - Zhinan Xu
- Department of Chemical and Biological Engineering, Zhejiang University, Hangzhou, China
- * E-mail:
| |
Collapse
|
24
|
Grkovic T, Blees JS, Bayer MM, Colburn NH, Thomas CL, Henrich CJ, Peach ML, McMahon JB, Schmid T, Gustafson KR. Tricyclic guanidine alkaloids from the marine sponge Acanthella cavernosa that stabilize the tumor suppressor PDCD4. Mar Drugs 2014; 12:4593-601. [PMID: 25196934 PMCID: PMC4145332 DOI: 10.3390/md12084593] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2014] [Revised: 06/25/2014] [Accepted: 07/24/2014] [Indexed: 01/14/2023] Open
Abstract
A cell-based high-throughput screen that assessed the cellular stability of a tumor suppressor protein PDCD4 (Programmed cell death 4) was used to identify a new guanidine-containing marine alkaloid mirabilin K (3), as well as the known compounds mirabilin G (1) and netamine M (2). The structures of these tricyclic guanidine alkaloids were established from extensive spectroscopic analyses. Compounds 1 and 2 inhibited cellular degradation of PDCD4 with EC50 values of 1.8 μg/mL and 2.8 μg/mL, respectively. Mirabilin G (1) and netamine M (2) are the first marine natural products reported to stabilize PDCD4 under tumor promoting conditions.
Collapse
Affiliation(s)
- Tanja Grkovic
- Molecular Targets Laboratory, Center for Cancer Research, National Cancer Institute, Frederick, MD 21702, USA.
| | - Johanna S Blees
- Molecular Targets Laboratory, Center for Cancer Research, National Cancer Institute, Frederick, MD 21702, USA.
| | - Magdalena M Bayer
- Institute of Biochemistry I, Faculty of Medicine, Goethe-University Frankfurt, 60590 Frankfurt, Germany.
| | - Nancy H Colburn
- Laboratory of Cancer Prevention, Center for Cancer Research, National Cancer Institute, Frederick, MD 21702, USA.
| | - Cheryl L Thomas
- Molecular Targets Laboratory, Center for Cancer Research, National Cancer Institute, Frederick, MD 21702, USA.
| | - Curtis J Henrich
- Molecular Targets Laboratory, Center for Cancer Research, National Cancer Institute, Frederick, MD 21702, USA.
| | - Megan L Peach
- Basic Science Program, Leidos Biomedical Research, Inc., Chemical Biology Laboratory, Frederick National Laboratory for Cancer Research, Frederick, MD 21702, USA.
| | - James B McMahon
- Molecular Targets Laboratory, Center for Cancer Research, National Cancer Institute, Frederick, MD 21702, USA.
| | - Tobias Schmid
- Institute of Biochemistry I, Faculty of Medicine, Goethe-University Frankfurt, 60590 Frankfurt, Germany.
| | - Kirk R Gustafson
- Molecular Targets Laboratory, Center for Cancer Research, National Cancer Institute, Frederick, MD 21702, USA.
| |
Collapse
|
25
|
Jose PA, Jebakumar SRD. Unexplored hypersaline habitats are sources of novel actinomycetes. Front Microbiol 2014; 5:242. [PMID: 24904555 PMCID: PMC4034035 DOI: 10.3389/fmicb.2014.00242] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2014] [Accepted: 05/04/2014] [Indexed: 11/13/2022] Open
Affiliation(s)
- Polpass Arul Jose
- Department of Molecular Microbiology, School of Biotechnology, Madurai Kamaraj University Madurai, India
| | | |
Collapse
|
26
|
Cuccarese MF, Wang Y, Beuning PJ, O’Doherty GA. Cryptocaryol Structure-Activity Relationship Study of Cancer Cell Cytotoxicity and Ability to Stabilize PDCD4. ACS Med Chem Lett 2014; 5:522-6. [PMID: 24900873 DOI: 10.1021/ml4005039] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2013] [Accepted: 02/17/2014] [Indexed: 12/11/2022] Open
Abstract
The synthetic cryptocaryols A and B and a series of their analogues have been evaluated for their cytotoxicity and their ability to stabilize the tumor suppressor PDCD4. Cytotoxicities in the 3 to 30 μM range were found. Both the cytotoxicity and PDCD4 stabilizing ability were tolerant of large stereochemical changes to the molecule. Co-dosing studies with cryptocaryols A and B and several known cancer drugs showed no measuable enhancement in cancer drug cytotoxicity.
Collapse
Affiliation(s)
- Michael F. Cuccarese
- Department of Chemistry
and
Chemical Biology, Northeastern University, Boston, Massachusetts 02115, United States
| | - Yanping Wang
- Department of Chemistry
and
Chemical Biology, Northeastern University, Boston, Massachusetts 02115, United States
| | - Penny J. Beuning
- Department of Chemistry
and
Chemical Biology, Northeastern University, Boston, Massachusetts 02115, United States
| | - George A. O’Doherty
- Department of Chemistry
and
Chemical Biology, Northeastern University, Boston, Massachusetts 02115, United States
| |
Collapse
|
27
|
Bajer MM, Kunze MM, Blees JS, Bokesch HR, Chen H, Brauss TF, Dong Z, Gustafson KR, Biondi RM, Henrich CJ, McMahon JB, Colburn NH, Schmid T, Brüne B. Characterization of pomiferin triacetate as a novel mTOR and translation inhibitor. Biochem Pharmacol 2014; 88:313-21. [PMID: 24513322 PMCID: PMC3978168 DOI: 10.1016/j.bcp.2014.01.034] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2013] [Revised: 01/08/2014] [Accepted: 01/24/2014] [Indexed: 01/03/2023]
Abstract
Deregulation of the phosphatidylinositol 3-kinase (PI3K)-Akt-mammalian target of rapamycin (mTOR)-70kDa ribosomal protein S6 kinase 1 (p70(S6K)) pathway is commonly observed in many tumors. This pathway controls proliferation, survival, and translation, and its overactivation is associated with poor prognosis for tumor-associated survival. Current efforts focus on the development of novel inhibitors of this pathway. In a cell-based high-throughput screening assay of 15,272 pure natural compounds, we identified pomiferin triacetate as a potent stabilizer of the tumor suppressor programmed cell death 4 (Pdcd4). Mechanistically, pomiferin triacetate appeared as a general inhibitor of the PI3K-Akt-mTOR-p70(S6K) cascade. Interference with this pathway occurred downstream of Akt but upstream of p70(S6K). Specifically, mTOR kinase emerged as the molecular target of pomiferin triacetate, with similar activities against mTOR complexes 1 and 2. In an in vitro mTOR kinase assay pomiferin triacetate dose-dependently inhibited mTOR with an IC50 of 6.2 μM. Molecular docking studies supported the interaction of the inhibitor with the catalytic site of mTOR. Importantly, pomiferin triacetate appeared to be highly selective for mTOR compared to a panel of 17 lipid and 50 protein kinases tested. As a consequence of the mTOR inhibition, pomiferin triacetate efficiently attenuated translation. In summary, pomiferin triacetate emerged as a novel and highly specific mTOR inhibitor with strong translation inhibitory effects. Thus, it might be an interesting lead structure for the development of mTOR- and translation-targeted anti-tumor therapies.
Collapse
Affiliation(s)
- Magdalena M Bajer
- Institute of Biochemistry I, Faculty of Medicine, Goethe-University Frankfurt, 60590 Frankfurt, Germany
| | - Michael M Kunze
- Institute of Biochemistry I, Faculty of Medicine, Goethe-University Frankfurt, 60590 Frankfurt, Germany
| | - Johanna S Blees
- Institute of Biochemistry I, Faculty of Medicine, Goethe-University Frankfurt, 60590 Frankfurt, Germany
| | - Heidi R Bokesch
- Molecular Targets Laboratory, Center for Cancer Research, National Cancer Institute-Frederick, Frederick, MD 21702, USA; Basic Science Program, Leidos Biomedical Research, Inc., Frederick National Laboratory for Cancer Research, Frederick, MD 21702, USA
| | - Hanyong Chen
- The Hormel Institute, University of Minnesota, Austin, MN 55912, USA
| | - Thilo F Brauss
- Institute of Biochemistry I, Faculty of Medicine, Goethe-University Frankfurt, 60590 Frankfurt, Germany
| | - Zigang Dong
- The Hormel Institute, University of Minnesota, Austin, MN 55912, USA
| | - Kirk R Gustafson
- Molecular Targets Laboratory, Center for Cancer Research, National Cancer Institute-Frederick, Frederick, MD 21702, USA
| | - Ricardo M Biondi
- Research Group PhosphoSites, Department of Internal Medicine I, University Clinic, 60590 Frankfurt, Germany
| | - Curtis J Henrich
- Molecular Targets Laboratory, Center for Cancer Research, National Cancer Institute-Frederick, Frederick, MD 21702, USA; Basic Science Program, Leidos Biomedical Research, Inc., Frederick National Laboratory for Cancer Research, Frederick, MD 21702, USA
| | - James B McMahon
- Molecular Targets Laboratory, Center for Cancer Research, National Cancer Institute-Frederick, Frederick, MD 21702, USA
| | - Nancy H Colburn
- Laboratory of Cancer Prevention, Center for Cancer Research, National Cancer Institute-Frederick, Frederick, MD 21702, USA
| | - Tobias Schmid
- Institute of Biochemistry I, Faculty of Medicine, Goethe-University Frankfurt, 60590 Frankfurt, Germany.
| | - Bernhard Brüne
- Institute of Biochemistry I, Faculty of Medicine, Goethe-University Frankfurt, 60590 Frankfurt, Germany
| |
Collapse
|
28
|
Xie P, Ma M, Rateb ME, Shaaban K, Yu Z, Huang SX, Zhao LX, Zhu X, Yan Y, Peterson R, Lohman JR, Yang D, Yin M, Rudolf JD, Jiang Y, Duan Y, Shen B. Biosynthetic potential-based strain prioritization for natural product discovery: a showcase for diterpenoid-producing actinomycetes. JOURNAL OF NATURAL PRODUCTS 2014; 77:377-87. [PMID: 24484381 PMCID: PMC3963700 DOI: 10.1021/np401063s] [Citation(s) in RCA: 41] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/17/2013] [Indexed: 05/09/2023]
Abstract
Natural products remain the best sources of drugs and drug leads and serve as outstanding small-molecule probes to dissect fundamental biological processes. A great challenge for the natural product community is to discover novel natural products efficiently and cost effectively. Here we report the development of a practical method to survey biosynthetic potential in microorganisms, thereby identifying the most promising strains and prioritizing them for natural product discovery. Central to our approach is the innovative preparation, by a two-tiered PCR method, of a pool of pathway-specific probes, thereby allowing the survey of all variants of the biosynthetic machineries for the targeted class of natural products. The utility of the method was demonstrated by surveying 100 strains, randomly selected from our actinomycete collection, for their biosynthetic potential of four classes of natural products, aromatic polyketides, reduced polyketides, nonribosomal peptides, and diterpenoids, identifying 16 talented strains. One of the talented strains, Streptomyces griseus CB00830, was finally chosen to showcase the discovery of the targeted classes of natural products, resulting in the isolation of three diterpenoids, six nonribosomal peptides and related metabolites, and three polyketides. Variations of this method should be applicable to the discovery of other classes of natural products.
Collapse
Affiliation(s)
- Pengfei Xie
- Department
of Chemistry, The Scripps Research Institute, Jupiter, Florida 33458, United States
| | - Ming Ma
- Department
of Chemistry, The Scripps Research Institute, Jupiter, Florida 33458, United States
| | - Mostafa E. Rateb
- Department
of Chemistry, The Scripps Research Institute, Jupiter, Florida 33458, United States
| | - Khaled
A. Shaaban
- Department
of Chemistry, The Scripps Research Institute, Jupiter, Florida 33458, United States
| | - Zhiguo Yu
- Department
of Chemistry, The Scripps Research Institute, Jupiter, Florida 33458, United States
| | - Sheng-Xiong Huang
- Department
of Chemistry, The Scripps Research Institute, Jupiter, Florida 33458, United States
| | - Li-Xing Zhao
- Yunnan
Institute of Microbiology, Yunnan University, Kunming, Yunnan 650091, People’s Republic
of China
| | - Xiangcheng Zhu
- Hunan
Engineering Research Center of Combinatorial Biosynthesis and Natural
Product Drug Discovery, Changsha, Hunan 410329, People’s Republic of China
- Xiangya
International Academy of Translational Medicine, Central South University, Changsha, Hunan 410013, People’s Republic of China
| | - Yijun Yan
- Department
of Chemistry, The Scripps Research Institute, Jupiter, Florida 33458, United States
| | - Ryan
M. Peterson
- Department
of Chemistry, The Scripps Research Institute, Jupiter, Florida 33458, United States
- Division
of Pharmaceutical Sciences, University of
Wisconsin−Madison, Madison, Wisconsin 53705, United States
| | - Jeremy R. Lohman
- Department
of Chemistry, The Scripps Research Institute, Jupiter, Florida 33458, United States
| | - Dong Yang
- Department
of Chemistry, The Scripps Research Institute, Jupiter, Florida 33458, United States
| | - Min Yin
- Department
of Chemistry, The Scripps Research Institute, Jupiter, Florida 33458, United States
| | - Jeffrey D. Rudolf
- Department
of Chemistry, The Scripps Research Institute, Jupiter, Florida 33458, United States
| | - Yi Jiang
- Yunnan
Institute of Microbiology, Yunnan University, Kunming, Yunnan 650091, People’s Republic
of China
| | - Yanwen Duan
- Hunan
Engineering Research Center of Combinatorial Biosynthesis and Natural
Product Drug Discovery, Changsha, Hunan 410329, People’s Republic of China
- Xiangya
International Academy of Translational Medicine, Central South University, Changsha, Hunan 410013, People’s Republic of China
| | - Ben Shen
- Hunan
Engineering Research Center of Combinatorial Biosynthesis and Natural
Product Drug Discovery, Changsha, Hunan 410329, People’s Republic of China
- Division
of Pharmaceutical Sciences, University of
Wisconsin−Madison, Madison, Wisconsin 53705, United States
- Department
of Molecular Therapeutics, The Scripps Research
Institute, Jupiter, Florida 33458, United
States
- Natural Products
Library Initiative, The Scripps Research
Institute, Jupiter, Florida 33458, United
States
| |
Collapse
|
29
|
Tian S, Yang Y, Liu K, Xiong Z, Xu L, Zhao L. Antimicrobial metabolites from a novel halophilic actinomycete Nocardiopsis terrae YIM 90022. Nat Prod Res 2013; 28:344-6. [PMID: 24236566 DOI: 10.1080/14786419.2013.858341] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Abstract
A quinoline alkaloid 1 and five known compounds (2-6) were isolated from a novel halophilic actinomycete Nocardiopsis terrae YIM 90022, and their structures were determined by spectroscopic studies as 4-oxo-1,4-dihydroquinoline-3-carboxamide (1), p-hydroxybenzoic acid (2), N-acetyl-anthranilic acid (3), indoly-3-carboxylic acid (4), cyclo(Trp-Gly) (5) and cyclo(Leu-Ala) (6). Compound 1 was isolated from natural resources for the first time. Compounds 1 and 3 showed antimicrobial activities against some plant pathogens.
Collapse
Affiliation(s)
- Shouzheng Tian
- a Key Laboratory of Microbial Diversity in Southwestern China of Ministry of Education and Laboratory for Conservation and Utilization of Bio-Resources, Yunnan Institute of Microbiology, Yunnan University , Kunming 650091 , P.R. China
| | | | | | | | | | | |
Collapse
|
30
|
Zhou H, Yang Y, Zhang J, Peng T, Zhao L, Xu L, Ding Z. Alkaloids from an Endophytic Streptomyces sp. YIM66017. Nat Prod Commun 2013. [DOI: 10.1177/1934578x1300801012] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022] Open
Abstract
Three alkaloids, flavensomycinoic acid (1), a linear polyketide, alpiniamide (2), and cyclo (L-Trp-L-Ala) (3), were isolated from the culture filtrate of endophytic Streptomyces sp. YIM66017 from Alpinia oxyphylla. Their structures were elucidated by spectroscopic analysis and the structure of 1 was confirmed by X-ray crystallographic analysis. Compound 1 was isolated from a natural source for the first time, and compound 2 is a new compound. Compound 1 showed cytotoxicity to MCF-7 with an IC 50 value of 17.0 μM.
Collapse
Affiliation(s)
- Hao Zhou
- Key Laboratory of Medicinal Chemistry for Natural Resource, Ministry of Education, School of Chemical Science and Technology, Yunnan University, Kunming 650091, China
| | - Yabin Yang
- Key Laboratory of Medicinal Chemistry for Natural Resource, Ministry of Education, School of Chemical Science and Technology, Yunnan University, Kunming 650091, China
| | - Jucheng Zhang
- Key Laboratory of Medicinal Chemistry for Natural Resource, Ministry of Education, School of Chemical Science and Technology, Yunnan University, Kunming 650091, China
| | - Tianfeng Peng
- Key Laboratory of Medicinal Chemistry for Natural Resource, Ministry of Education, School of Chemical Science and Technology, Yunnan University, Kunming 650091, China
| | - Lixing Zhao
- Yunnan Institute of Microbiology, Yunnan University, Kunming 650091, China
| | - Lihua Xu
- Yunnan Institute of Microbiology, Yunnan University, Kunming 650091, China
| | - Zhongtao Ding
- Key Laboratory of Medicinal Chemistry for Natural Resource, Ministry of Education, School of Chemical Science and Technology, Yunnan University, Kunming 650091, China
| |
Collapse
|
31
|
Tebbets B, Yu Z, Stewart D, Zhao LX, Jiang Y, Xu LH, Andes D, Shen B, Klein B. Identification of antifungal natural products via Saccharomyces cerevisiae bioassay: insights into macrotetrolide drug spectrum, potency and mode of action. Med Mycol 2013; 51:280-9. [PMID: 22928922 PMCID: PMC3594352 DOI: 10.3109/13693786.2012.710917] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023] Open
Abstract
Since current antifungal drugs have not kept pace with the escalating medical demands of fungal infections, new, effective medications are required. However, antifungal drug discovery is hindered by the evolutionary similarity of mammalian and fungal cells, which results in fungal drug targets having human homologs and drug non-selectivity. The group III hybrid histidine kinases (HHKs) are an attractive drug target since they are conserved in fungi and absent in mammals. We used a Saccharomyces cerevisiae reporter strain that conditionally expresses HHK to establish a high-throughput bioassay to screen microbial extracts natural products for antifungals. We identified macrotetrolides, a group of related ionophores thought to exhibit restricted antifungal activity. In addition to confirming the use of this bioassay for the discovery of antifungal natural products, we demonstrated broader, more potent fungistatic activity of the macrotetrolides against multiple Candida spp., Cryptococcus spp., and Candida albicans in biofilms. Macrotetrolides were also active in an animal model of C. albicans biofilm, but were found to have inconsistent activity against fluconazole-resistant C. albicans, with most isolates resistant to this natural product. The macrotetrolides do not directly target HHKs, but their selective activity against S. cerevisiae grown in galactose (regardless of Drk1 expression) revealed potential new insight into the role of ion transport in the mode of action of these promising antifungal compounds. Thus, this simple, high-throughput bioassay permitted us to screen microbial extracts, identify natural products as antifungal drugs, and expand our understanding of the activity of macrotetrolides.
Collapse
Affiliation(s)
- Brad Tebbets
- Department of Pediatrics, the University of Wisconsin School of Medicine and Public Health, Madison, WI
- Department of Medical Microbiology and Immunology, the University of Wisconsin School of Medicine and Public Health, Madison, WI
| | - Zhiguo Yu
- Department of Chemistry, The Scripps Research Institute, Jupiter, Florida, USA
| | - Douglas Stewart
- Department of Pediatrics, the University of Wisconsin School of Medicine and Public Health, Madison, WI
| | - Li-Xing Zhao
- Yunnan Institute of Microbiology, Yunnan University, Kunming, Yunnan, China
| | - Yi Jiang
- Yunnan Institute of Microbiology, Yunnan University, Kunming, Yunnan, China
| | - Li-Hua Xu
- Yunnan Institute of Microbiology, Yunnan University, Kunming, Yunnan, China
| | - David Andes
- Department of Internal Medicine, the University of Wisconsin School of Medicine and Public Health, Madison, WI
| | - Ben Shen
- Department of Chemistry, The Scripps Research Institute, Jupiter, Florida, USA
- Department of Molecular Therapeutics, The Scripps Research Institute, Jupiter, Florida, USA
| | - Bruce Klein
- Department of Pediatrics, the University of Wisconsin School of Medicine and Public Health, Madison, WI
- Department of Internal Medicine, the University of Wisconsin School of Medicine and Public Health, Madison, WI
- Department of Medical Microbiology and Immunology, the University of Wisconsin School of Medicine and Public Health, Madison, WI
| |
Collapse
|
32
|
Tian SZ, Pu X, Luo G, Zhao LX, Xu LH, Li WJ, Luo Y. Isolation and characterization of new p-Terphenyls with antifungal, antibacterial, and antioxidant activities from halophilic actinomycete Nocardiopsis gilva YIM 90087. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2013; 61:3006-3012. [PMID: 23441911 DOI: 10.1021/jf400718w] [Citation(s) in RCA: 75] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/01/2023]
Abstract
A new p-terphenyl 1 and a novel p-terphenyl derivative 3 bearing a benzothiazole moiety were isolated from halophilic actinomycete Nocardiopsis gilva YIM 90087, along with known p-terphenyl 2, antibiotic novobiocin 4, cyclodipeptides 5-13, and aromatic acids 14 and 15. Their structures were elucidated on the basis of the interpretation of spectral data and by comparison of the corresponding data with those reported previously. The p-terphenyl 1 showed antifungal activity against the three pathogenic fungi, including Fusarium avenaceum, Fusarium graminearum, and Fusarium culmorum, that caused Fusarium head blight with minimal inhibitory concentrations (MICs) of 8, 16, and 128 μg/mL, respectively. Compound 1 showed antifungal activity against Candida albicans with a MIC of 32 μg/mL and antibacterial activity against Bacillus subtilis with a MIC of 64 μg/mL. Novobiocin 4 showed antifungal activity against Pyricularia oryzae with a MIC of 16 μg/mL and antibacterial activity against B. subtilis with a MIC of 16 μg/mL and Staphylococcus aureus with a MIC of 64 μg/mL. The 1,1-diphenyl-2-picryl-hydrazyl assay suggested that 1, 3, and 4 exhibited 54.9% (2 mg/mL), 14.3% (4 mg/mL), and 47.7% (2 mg/mL) free radical scavenging activity, respectively. The positively charged 2,2'-azino-bis-3-ethylbenzothiazoline-6-sulfonic acid radical (ABTS(+•)) scavenging assay indicated that 1, 3, 4, and 8 exhibited 68.6% (1 mg/mL), 28.4% (2 mg/mL), 78.2% (0.5 mg/mL), and 54.6% (2 mg/mL) ABTS(+•) scavenging capacity, respectively. The superoxide anion radical scavenging assay suggested that 4 exhibited 77.9% superoxide anion radical scavenging capacity at 2 mg/mL. N. gilva YIM 90087 is a new resource for novobiocin 4.
Collapse
Affiliation(s)
- Shou-Zheng Tian
- Center for Natural Products Research, Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu 610041, People's Republic of China
| | | | | | | | | | | | | |
Collapse
|
33
|
Systematic and biotechnological aspects of halophilic and halotolerant actinomycetes. Extremophiles 2012; 17:1-13. [PMID: 23129307 DOI: 10.1007/s00792-012-0493-5] [Citation(s) in RCA: 54] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2012] [Accepted: 10/18/2012] [Indexed: 12/22/2022]
Abstract
More than 70 species of halotolerant and halophilic actinomycetes belonging to at least 24 genera have been validly described. Halophilic actinomycetes are a less explored source of actinomycetes for discovery of novel bioactive secondary metabolites. Degradation of aliphatic and aromatic organic compounds, detoxification of pollutants, production of new enzymes and other metabolites such as antibiotics, compatible solutes and polymers are other potential industrial applications of halophilic and halotolerant actinomycetes. Especially new bioactive secondary metabolites that are derived from only a small fraction of the investigated halophilic actinomycetes, mainly from marine habitats, have revealed the huge capacity of this physiological group in production of new bioactive chemical entities. Combined high metabolic capacities of actinomycetes and unique features related to extremophilic nature of the halophilic actinomycetes have conferred on them an influential role for future biotechnological applications.
Collapse
|
34
|
Blees JS, Bokesch HR, Rübsamen D, Schulz K, Milke L, Bajer MM, Gustafson KR, Henrich CJ, McMahon JB, Colburn NH, Schmid T, Brüne B. Erioflorin stabilizes the tumor suppressor Pdcd4 by inhibiting its interaction with the E3-ligase β-TrCP1. PLoS One 2012; 7:e46567. [PMID: 23056346 PMCID: PMC3462793 DOI: 10.1371/journal.pone.0046567] [Citation(s) in RCA: 39] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2012] [Accepted: 08/31/2012] [Indexed: 12/20/2022] Open
Abstract
Loss of the tumor suppressor Pdcd4 was reported for various tumor entities and proposed as a prognostic marker in tumorigenesis. We previously characterized decreased Pdcd4 protein stability in response to mitogenic stimuli, which resulted from p70(S6K1)-dependent protein phosphorylation, β-TrCP1-mediated ubiquitination, and proteasomal destruction. Following high-throughput screening of natural product extract libraries using a luciferase-based reporter assay to monitor phosphorylation-dependent proteasomal degradation of the tumor suppressor Pdcd4, we succeeded in showing that a crude extract from Eriophyllum lanatum stabilized Pdcd4 from TPA-induced degradation. Erioflorin was identified as the active component and inhibited not only degradation of the Pdcd4-luciferase-based reporter but also of endogenous Pdcd4 at low micromolar concentrations. Mechanistically, erioflorin interfered with the interaction between the E3-ubiquitin ligase β-TrCP1 and Pdcd4 in cell culture and in in vitro binding assays, consequently decreasing ubiquitination and degradation of Pdcd4. Interestingly, while erioflorin stabilized additional β-TrCP-targets (such as IκBα and β-catenin), it did not prevent the degradation of targets of other E3-ubiquitin ligases such as p21 (a Skp2-target) and HIF-1α (a pVHL-target), implying selectivity for β-TrCP. Moreover, erioflorin inhibited the tumor-associated activity of known Pdcd4- and IκBα-regulated αtranscription factors, that is, AP-1 and NF-κB, altered cell cycle progression and suppressed proliferation of various cancer cell lines. Our studies succeeded in identifying erioflorin as a novel Pdcd4 stabilizer that inhibits the interaction of Pdcd4 with the E3-ubiquitin ligase β-TrCP1. Inhibition of E3-ligase/target-protein interactions may offer the possibility to target degradation of specific proteins only as compared to general proteasome inhibition.
Collapse
Affiliation(s)
- Johanna S. Blees
- Institute of Biochemistry I, Faculty of Medicine, Goethe-University Frankfurt, Frankfurt, Germany
| | - Heidi R. Bokesch
- Molecular Targets Laboratory, Center for Cancer Research, National Cancer Institute, Frederick National Laboratory for Cancer Research, Frederick, Maryland, United States of America
- SAIC-Frederick, Inc., Frederick National Laboratory for Cancer Research, Frederick, Maryland, United States of America
| | - Daniela Rübsamen
- Institute of Biochemistry I, Faculty of Medicine, Goethe-University Frankfurt, Frankfurt, Germany
| | - Kathrin Schulz
- Institute of Biochemistry I, Faculty of Medicine, Goethe-University Frankfurt, Frankfurt, Germany
| | - Larissa Milke
- Institute of Biochemistry I, Faculty of Medicine, Goethe-University Frankfurt, Frankfurt, Germany
| | - Magdalena M. Bajer
- Institute of Biochemistry I, Faculty of Medicine, Goethe-University Frankfurt, Frankfurt, Germany
| | - Kirk R. Gustafson
- Molecular Targets Laboratory, Center for Cancer Research, National Cancer Institute, Frederick National Laboratory for Cancer Research, Frederick, Maryland, United States of America
| | - Curtis J. Henrich
- Molecular Targets Laboratory, Center for Cancer Research, National Cancer Institute, Frederick National Laboratory for Cancer Research, Frederick, Maryland, United States of America
- SAIC-Frederick, Inc., Frederick National Laboratory for Cancer Research, Frederick, Maryland, United States of America
| | - James B. McMahon
- Molecular Targets Laboratory, Center for Cancer Research, National Cancer Institute, Frederick National Laboratory for Cancer Research, Frederick, Maryland, United States of America
| | - Nancy H. Colburn
- Laboratory of Cancer Prevention, Center for Cancer Research, National Cancer Institute, Frederick National Laboratory for Cancer Research, Frederick, Maryland, United States of America
| | - Tobias Schmid
- Institute of Biochemistry I, Faculty of Medicine, Goethe-University Frankfurt, Frankfurt, Germany
| | - Bernhard Brüne
- Institute of Biochemistry I, Faculty of Medicine, Goethe-University Frankfurt, Frankfurt, Germany
| |
Collapse
|
35
|
Huang SX, Wang XJ, Yan Y, Wang JD, Zhang J, Liu CX, Xiang WS, Shen B. Neaumycin: a new macrolide from Streptomyces sp. NEAU-x211. Org Lett 2012; 14:1254-7. [PMID: 22332843 PMCID: PMC3293494 DOI: 10.1021/ol300074d] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Abstract
Neaumycin, a new 30-membered macrolide featuring an internal diester bridge, a molecular architecture that is unprecedented among known macrolide natural products, was isolated from a soil actinomycete strain Streptomyces sp. NEAU-x211. The structure of neaumycin was elucidated on the basis of comprehensive mass and NMR spectroscopic interpretation, including the relative stereochemistry of four independent coupling systems.
Collapse
Affiliation(s)
- Sheng-Xiong Huang
- Department of Chemistry, The Scripps Research Institute, Jupiter, Florida 33458, USA
| | | | | | | | | | | | | | | |
Collapse
|