151
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Jang JP, Kim GS, Oh TH, Park B, Kim M, Hwang GJ, Lee HW, Lee JG, Hong YS, Ahn JS, Ko SK, Jang JH. Jejuketomycins A and B, polyketide glycosides with cancer cell migration inhibitory activity from Streptomyces sp. KCB15JA151. RSC Adv 2022; 12:22360-22366. [PMID: 36105948 PMCID: PMC9364360 DOI: 10.1039/d2ra04039e] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2022] [Accepted: 07/30/2022] [Indexed: 11/21/2022] Open
Abstract
Two new polyketide glycosides jejuketomycins A (1) and B (2), were isolated from a culture of Streptomyces sp. KCB15JA151. Their chemical structures including the absolute configurations were determined by detailed analyses of the NMR and HRMS data and ECD calculations and spectral data. Compounds 1 and 2 possess an unusual 6/6/8 tricyclic ring system. Biological evaluation with the wound healing assay and time-lapse cell tracking analysis revealed that compounds 1 and 2 have significant inhibitory activities against cancer cell migration with low cytotoxicity. Two new polyketide glycosides jejuketomycins A (1) and B (2), were isolated from a culture of Streptomyces sp. KCB15JA151.![]()
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Affiliation(s)
- Jun-Pil Jang
- Chemical Biology Research Center, Korea Research Institute of Bioscience and Biotechnology, Cheongju 28116, Korea
| | - Gil Soo Kim
- Central Research and Development, HanpoongPharm. Co., LTD., Wanju 54843, Korea
| | - Tae Hoon Oh
- Chemical Biology Research Center, Korea Research Institute of Bioscience and Biotechnology, Cheongju 28116, Korea
- College of Pharmacy, Chungbuk National University, Cheongju, 28160, Korea
| | - Beomcheol Park
- Chemical Biology Research Center, Korea Research Institute of Bioscience and Biotechnology, Cheongju 28116, Korea
- College of Pharmacy, Chungbuk National University, Cheongju, 28160, Korea
| | - Minhee Kim
- Chemical Biology Research Center, Korea Research Institute of Bioscience and Biotechnology, Cheongju 28116, Korea
- College of Pharmacy, Chungbuk National University, Cheongju, 28160, Korea
| | - Gwi Ja Hwang
- Chemical Biology Research Center, Korea Research Institute of Bioscience and Biotechnology, Cheongju 28116, Korea
| | - Hyeok-Won Lee
- Biotechnology Process Engineering Center, Korea Research Institute of Bioscience and Biotechnology, Cheongju, 28116, Korea
| | - Jin-Gyeom Lee
- Biotechnology Process Engineering Center, Korea Research Institute of Bioscience and Biotechnology, Cheongju, 28116, Korea
| | - Young-Soo Hong
- Chemical Biology Research Center, Korea Research Institute of Bioscience and Biotechnology, Cheongju 28116, Korea
- Department of Biomolecular Science, KRIBB School of Bioscience, University of Science and Technology, Daejeon 34113, Korea
| | - Jong Seog Ahn
- Chemical Biology Research Center, Korea Research Institute of Bioscience and Biotechnology, Cheongju 28116, Korea
- Department of Biomolecular Science, KRIBB School of Bioscience, University of Science and Technology, Daejeon 34113, Korea
| | - Sung-Kyun Ko
- Chemical Biology Research Center, Korea Research Institute of Bioscience and Biotechnology, Cheongju 28116, Korea
- Department of Biomolecular Science, KRIBB School of Bioscience, University of Science and Technology, Daejeon 34113, Korea
| | - Jae-Hyuk Jang
- Chemical Biology Research Center, Korea Research Institute of Bioscience and Biotechnology, Cheongju 28116, Korea
- Department of Biomolecular Science, KRIBB School of Bioscience, University of Science and Technology, Daejeon 34113, Korea
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152
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Abdalla TH, Nasr AS, Bassioni G, Harding DR, Kandile NG. Fabrication of sustainable hydrogels-based chitosan Schiff base and their potential applications. ARAB J CHEM 2022. [DOI: 10.1016/j.arabjc.2021.103511] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022] Open
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153
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Negri T, Mantri S, Angelov A, Peter S, Muth G, Eustáquio AS, Ziemert N. A rapid and efficient strategy to identify and recover biosynthetic gene clusters from soil metagenomes. Appl Microbiol Biotechnol 2022; 106:3293-3306. [PMID: 35435454 PMCID: PMC9064862 DOI: 10.1007/s00253-022-11917-y] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2022] [Revised: 03/31/2022] [Accepted: 04/03/2022] [Indexed: 11/30/2022]
Abstract
Culture-independent metagenomic approaches offer a promising solution to the discovery of therapeutically relevant compounds such as antibiotics by enabling access to the hidden biosynthetic potential of microorganisms. These strategies, however, often entail laborious, multi-step, and time-consuming procedures to recover the biosynthetic gene clusters (BGCs) from soil metagenomes for subsequent heterologous expression. Here, we developed an efficient method we called single Nanopore read cluster mining (SNRCM), which enables the fast recovery of complete BGCs from a soil metagenome using long- and short-read sequencing. A metagenomic fosmid library of 83,700 clones was generated and sequenced using Nanopore as well as Illumina technologies. Hybrid assembled contigs of the sequenced fosmid library were subsequently analyzed to identify BGCs encoding secondary metabolites. Using SNRCM, we aligned the identified BGCs directly to Nanopore long-reads and were able to detect complete BGCs on single fosmids. This enabled us to select for and recover BGCs of interest for subsequent heterologous expression attempts. Additionally, the sequencing data of the fosmid library and its corresponding metagenomic DNA enabled us to assemble and recover a large nonribosomal peptide synthetase (NRPS) BGC from three different fosmids of our library and to directly amplify and recover a complete lasso peptide BGC from the high-quality metagenomic DNA. Overall, the strategies presented here provide a useful tool for accelerating and facilitating the identification and production of potentially interesting bioactive compounds from soil metagenomes. KEY POINTS: • An efficient approach for the recovery of BGCs from soil metagenomes was developed to facilitate natural product discovery. • A fosmid library was constructed from soil metagenomic HMW DNA and sequenced via Illumina and Nanopore. • Nanopore long-reads enabled the direct identification and recovery of complete BGCs on single fosmids.
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Affiliation(s)
- Timo Negri
- Interfaculty Institute of Microbiology and Infection Medicine Tübingen (IMIT), University of Tübingen, Tübingen, Germany
| | - Shrikant Mantri
- Interfaculty Institute of Microbiology and Infection Medicine Tübingen (IMIT), University of Tübingen, Tübingen, Germany ,Interfaculty Institute for Biomedical Informatics (IBMI), University of Tübingen, Tübingen, Germany ,Computational Biology Laboratory, National Agri-Food Biotechnology Institute (NABI), Mohali, Punjab India
| | - Angel Angelov
- NGS Competence Center Tübingen (NCCT), Institut Für Medizinische Mikrobiologie Und Hygiene, Universitätsklinikum Tübingen, Tübingen, Germany
| | - Silke Peter
- NGS Competence Center Tübingen (NCCT), Institut Für Medizinische Mikrobiologie Und Hygiene, Universitätsklinikum Tübingen, Tübingen, Germany
| | - Günther Muth
- Interfaculty Institute of Microbiology and Infection Medicine Tübingen (IMIT), University of Tübingen, Tübingen, Germany
| | | | - Nadine Ziemert
- Interfaculty Institute of Microbiology and Infection Medicine Tübingen (IMIT), University of Tübingen, Tübingen, Germany. .,Interfaculty Institute for Biomedical Informatics (IBMI), University of Tübingen, Tübingen, Germany. .,German Centre for Infection Research (DZIF), Partner Site Tübingen, Tübingen, Germany.
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154
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Narad P, Naresh G, Sengupta A. Metabolomics and flux balance analysis. Bioinformatics 2022. [DOI: 10.1016/b978-0-323-89775-4.00008-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022] Open
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155
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Sharma BR, Halami PM, Tamang JP. Novel pathways in bacteriocin synthesis by lactic acid bacteria with special reference to ethnic fermented foods. Food Sci Biotechnol 2022; 31:1-16. [PMID: 35059226 PMCID: PMC8733103 DOI: 10.1007/s10068-021-00986-w] [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: 06/28/2021] [Revised: 08/28/2021] [Accepted: 09/16/2021] [Indexed: 10/20/2022] Open
Abstract
Ethnic fermented foods are known for their unique aroma, flavour, taste, texture and other sensory properties preferred by every ethnic community in this world culturally as parts of their eatables. Some beneficial microorganisms associated with fermented foods have several functional properties and health-promoting benefits. Bacteriocins are the secondary metabolites produced by the microorganisms mostly lactic acid bacteria present in the fermented foods which can act as lantibiotics against the pathogen bacteria. Several studies have been conducted regarding the isolation and characterization of potent strains as well as their association with different types of bacteriocins. Collective information regarding the gene organizations responsible for the potent effect of bacteriocins as lantibiotics, mode of action on pathogen bacterial cells is not yet available. This review focuses on the gene organizations, pathways include for bacteriocin and their mode of action for various classes of bacteriocins produced by lactic acid bacteria in some ethnic fermented foods.
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Affiliation(s)
- Basista Rabina Sharma
- Microbiology and Fermentation Technology Department, CSIR-Central Food Technological Research Institute, Mysore, Karnataka 570020 India
| | - Prakash M. Halami
- Microbiology and Fermentation Technology Department, CSIR-Central Food Technological Research Institute, Mysore, Karnataka 570020 India
| | - Jyoti Prakash Tamang
- DAICENTER, Department of Microbiology, Sikkim University, Science Building, Tadong, Gangtok, Sikkim 737102 India
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156
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Measurements of drugs and metabolites in biological matrices using SFC and SFE-SFC-MS. SEP SCI TECHNOL 2022. [DOI: 10.1016/b978-0-323-88487-7.00004-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/04/2022]
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157
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Characterizing Selected Sorghum Grain Varieties and Evaluating the Suitability of Their Malt Extracts for Cultivating Microbial Biomass. INTERNATIONAL JOURNAL OF FOOD SCIENCE 2021; 2021:6658358. [PMID: 34957297 PMCID: PMC8709753 DOI: 10.1155/2021/6658358] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/02/2020] [Accepted: 12/02/2021] [Indexed: 11/19/2022]
Abstract
Microbial biomass is cultivated for different technological applications including food processing, medicine, waste management, and research. The conventional growth media used are generally expensive thus necessitating the development of more affordable alternatives. In this study, four sorghum grain varieties, SESO 1, SESO 3, Epuripur, and Eyera, and their malt extracts were characterized which is aimed at determining their suitability for growing microbial biomass. The varieties had kernel length, kernel width, kernel thickness, and thousand kernel weigh equivalent to 3.8-4.3 mm, 3.2-4.5 mm, 2.4-2.8 mm, and 12.4-20.2 g, respectively. SESO 1 and Epuripur had corneous endosperm textures whereas those of SESO 3 and Eyera were intermediate and floury, respectively. Varieties had germinative energies > 90% and total defects < 8%. SESO 3 had the highest (p < 0.05) crude protein (10.8 ± 0.3%) and dietary fiber (22.5 ± 0.4%) whereas Epuripur had the highest (p < 0.05) starch (81.6 ± 0.0%) and crude fat (2.9 ± 0.1%). There was no significant difference (p > 0.05) in the ash contents (2.1 ± 0.0%). The total sugars, free amino nitrogen, condensed tannins, and pH of the malt extracts were 106-116 g/L, 70-78 mg/L, 0.1-0.6 mg/mL, and 5.5-5.7, respectively. The composition of the sorghum malt extracts suggests their potential for use in cultivating microbial biomass.
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158
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Carruthers DN, Lee TS. Diversifying Isoprenoid Platforms via Atypical Carbon Substrates and Non-model Microorganisms. Front Microbiol 2021; 12:791089. [PMID: 34925299 PMCID: PMC8677530 DOI: 10.3389/fmicb.2021.791089] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2021] [Accepted: 11/10/2021] [Indexed: 01/07/2023] Open
Abstract
Isoprenoid compounds are biologically ubiquitous, and their characteristic modularity has afforded products ranging from pharmaceuticals to biofuels. Isoprenoid production has been largely successful in Escherichia coli and Saccharomyces cerevisiae with metabolic engineering of the mevalonate (MVA) and methylerythritol phosphate (MEP) pathways coupled with the expression of heterologous terpene synthases. Yet conventional microbial chassis pose several major obstacles to successful commercialization including the affordability of sugar substrates at scale, precursor flux limitations, and intermediate feedback-inhibition. Now, recent studies have challenged typical isoprenoid paradigms by expanding the boundaries of terpene biosynthesis and using non-model organisms including those capable of metabolizing atypical C1 substrates. Conversely, investigations of non-model organisms have historically informed optimization in conventional microbes by tuning heterologous gene expression. Here, we review advances in isoprenoid biosynthesis with specific focus on the synergy between model and non-model organisms that may elevate the commercial viability of isoprenoid platforms by addressing the dichotomy between high titer production and inexpensive substrates.
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Affiliation(s)
- David N Carruthers
- Joint BioEnergy Institute, Emeryville, CA, United States.,Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, CA, United States
| | - Taek Soon Lee
- Joint BioEnergy Institute, Emeryville, CA, United States.,Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, CA, United States
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159
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Jang JP, Jang M, Hwang GJ, Kim MH, Ahn JS, Ko SK, Jang JH. Streptooctatins A and B, fusicoccane-type diterpenoids with autophagic activity from Streptomyces sp. KCB17JA11. Bioorg Med Chem Lett 2021; 57:128504. [PMID: 34922027 DOI: 10.1016/j.bmcl.2021.128504] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2021] [Revised: 12/06/2021] [Accepted: 12/10/2021] [Indexed: 11/26/2022]
Abstract
Two new fusicoccane-type diterpenoids, streptooctatins A (1) and B (2), together with a known compound cyclooctatin (3) were isolated from Streptomyces sp. KCB17JA11. The structures of 1 and 2 were determined by analyzing spectroscopic and spectrometric data from 1D and 2D NMR and HRESIMS experiments. Compounds 1 and 2 induced EGFP-LC3 puncta indicating autophagic activities against HeLa cells without cytotoxicity.
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Affiliation(s)
- Jun-Pil Jang
- Anticancer Agent Research Center, Korea Research Institute of Bioscience and Biotechnology, Cheongju 28116, South Korea
| | - Mina Jang
- Anticancer Agent Research Center, Korea Research Institute of Bioscience and Biotechnology, Cheongju 28116, South Korea
| | - Gwi Ja Hwang
- Anticancer Agent Research Center, Korea Research Institute of Bioscience and Biotechnology, Cheongju 28116, South Korea; Department of Biomolecular Science, KRIBB School of Bioscience, Korea University of Science and Technology, Daejeon 34113, South Korea
| | - Min Hee Kim
- Anticancer Agent Research Center, Korea Research Institute of Bioscience and Biotechnology, Cheongju 28116, South Korea
| | - Jong Seog Ahn
- Anticancer Agent Research Center, Korea Research Institute of Bioscience and Biotechnology, Cheongju 28116, South Korea; Department of Biomolecular Science, KRIBB School of Bioscience, Korea University of Science and Technology, Daejeon 34113, South Korea.
| | - Sung-Kyun Ko
- Anticancer Agent Research Center, Korea Research Institute of Bioscience and Biotechnology, Cheongju 28116, South Korea; Department of Biomolecular Science, KRIBB School of Bioscience, Korea University of Science and Technology, Daejeon 34113, South Korea.
| | - Jae-Hyuk Jang
- Anticancer Agent Research Center, Korea Research Institute of Bioscience and Biotechnology, Cheongju 28116, South Korea; Department of Biomolecular Science, KRIBB School of Bioscience, Korea University of Science and Technology, Daejeon 34113, South Korea.
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160
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Romsdahl J, Schultzhaus Z, Cuomo CA, Dong H, Abeyratne-Perera H, Hervey WJ, Wang Z. Phenotypic Characterization and Comparative Genomics of the Melanin-Producing Yeast Exophiala lecanii-corni Reveals a Distinct Stress Tolerance Profile and Reduced Ribosomal Genetic Content. J Fungi (Basel) 2021; 7:1078. [PMID: 34947060 PMCID: PMC8709033 DOI: 10.3390/jof7121078] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2021] [Revised: 12/07/2021] [Accepted: 12/10/2021] [Indexed: 12/19/2022] Open
Abstract
The black yeast Exophiala lecanii-corni of the order Chaetothyriales is notable for its ability to produce abundant quantities of DHN-melanin. While many other Exophiala species are frequent causal agents of human infection, E. lecanii-corni CBS 102400 lacks the thermotolerance requirements that enable pathogenicity, making it appealing for use in targeted functional studies and biotechnological applications. Here, we report the stress tolerance characteristics of E. lecanii-corni, with an emphasis on the influence of melanin on its resistance to various forms of stress. We find that E. lecanii-corni has a distinct stress tolerance profile that includes variation in resistance to temperature, osmotic, and oxidative stress relative to the extremophilic and pathogenic black yeast Exophiala dermatitidis. Notably, the presence of melanin substantially impacts stress resistance in E. lecanii-corni, while this was not found to be the case in E. dermatitidis. The cellular context, therefore, influences the role of melanin in stress protection. In addition, we present a detailed analysis of the E. lecanii-corni genome, revealing key differences in functional genetic content relative to other ascomycetous species, including a significant decrease in abundance of genes encoding ribosomal proteins. In all, this study provides insight into how genetics and physiology may underlie stress tolerance and enhances understanding of the genetic diversity of black yeasts.
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Affiliation(s)
- Jillian Romsdahl
- National Research Council Postdoctoral Research Associate, U.S. Naval Research Laboratory, Washington, DC 20375, USA;
| | - Zachary Schultzhaus
- Center for Biomolecular Sciences and Engineering, U.S. Naval Research Laboratory, Washington, DC 20375, USA; (Z.S.); (W.J.H.IV)
| | - Christina A. Cuomo
- Infectious Disease and Microbiome Program, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA;
| | - Hong Dong
- Biotechnology Branch, CCDC Army Research Laboratory, Adelphi, MD 20783, USA;
| | - Hashanthi Abeyratne-Perera
- American Society for Engineering Education Postdoctoral Research Associate, U.S. Naval Research Laboratory, Washington, DC 20375, USA;
| | - W. Judson Hervey
- Center for Biomolecular Sciences and Engineering, U.S. Naval Research Laboratory, Washington, DC 20375, USA; (Z.S.); (W.J.H.IV)
| | - Zheng Wang
- Center for Biomolecular Sciences and Engineering, U.S. Naval Research Laboratory, Washington, DC 20375, USA; (Z.S.); (W.J.H.IV)
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161
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Genome Mining of Pseudomonas Species: Diversity and Evolution of Metabolic and Biosynthetic Potential. Molecules 2021; 26:molecules26247524. [PMID: 34946606 PMCID: PMC8704066 DOI: 10.3390/molecules26247524] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2021] [Revised: 12/07/2021] [Accepted: 12/08/2021] [Indexed: 11/17/2022] Open
Abstract
Microbial genome sequencing has uncovered a myriad of natural products (NPs) that have yet to be explored. Bacteria in the genus Pseudomonas serve as pathogens, plant growth promoters, and therapeutically, industrially, and environmentally important microorganisms. Though most species of Pseudomonas have a large number of NP biosynthetic gene clusters (BGCs) in their genomes, it is difficult to link many of these BGCs with products under current laboratory conditions. In order to gain new insights into the diversity, distribution, and evolution of these BGCs in Pseudomonas for the discovery of unexplored NPs, we applied several bioinformatic programming approaches to characterize BGCs from Pseudomonas reference genome sequences available in public databases along with phylogenetic and genomic comparison. Our research revealed that most BGCs in the genomes of Pseudomonas species have a high diversity for NPs at the species and subspecies levels and built the correlation of species with BGC taxonomic ranges. These data will pave the way for the algorithmic detection of species- and subspecies-specific pathways for NP development.
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162
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Jin L, Niu G, Guan L, Ramelow J, Zhan Z, Zhou X, Li J. Discovery of mosquitocides from fungal extracts through a high-throughput cytotoxicity-screening approach. Parasit Vectors 2021; 14:595. [PMID: 34863250 PMCID: PMC8643003 DOI: 10.1186/s13071-021-05089-3] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2021] [Accepted: 11/08/2021] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Mosquitoes transmit a variety of diseases. Due to widespread insecticide resistance, new effective pesticides are urgently needed. Entomopathogenic fungi are widely utilized to control pest insects in agriculture. We hypothesized that certain fungal metabolites may be effective insecticides against mosquitoes. METHODS A high-throughput cytotoxicity-based screening approach was developed to search for insecticidal compounds in our newly established global fungal extract library. We first determined cell survival rates after adding various fungal extracts. Candidate insecticides were further analyzed using traditional larval and adult survival bioassays. RESULTS Twelve ethyl acetate extracts from a total of 192 fungal extracts displayed > 85% inhibition of cabbage looper ovary cell proliferation. Ten of these 12 candidates were confirmed to be toxic to Anopheles gambiae Sua5B cell line, and six showed > 85% inhibition of Anopheles mosquito cell growth. Further bioassays determined a LC50, the lethal concentration that kills 50% of larval or adult mosquitoes, of 122 µg/mL and 1.7 µg/mosquito, respectively, after 24 h for extract 76F6 from Penicillium toxicarium. CONCLUSIONS We established a high-throughput MTT-based cytotoxicity screening approach for the discovery of new mosquitocides from fungal extracts. We discovered a candidate extract from P. toxicarium that exhibited high toxicity to mosquito larvae and adults, and thus were able to demonstrate the value of our recently developed approach. The active fungal extracts discovered here are ideal candidates for further development as mosquitocides.
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Affiliation(s)
- Liang Jin
- Department of Biological Sciences, Florida International University, Miami, FL, 33199, USA.
- Institute of Microbiology, Jiangxi Academy of Sciences, Nanchang, Jiangxi, China.
| | - Guodong Niu
- Department of Biological Sciences, Florida International University, Miami, FL, 33199, USA
- Biomolecular Sciences Institute, Florida International University, Miami, FL, 33199, USA
| | - Limei Guan
- Institute of Microbiology, Jiangxi Academy of Sciences, Nanchang, Jiangxi, China
| | - Julian Ramelow
- Herbert Wertheim College of Medicine, Florida International University, Miami, FL, 33199, USA
| | - Zhigao Zhan
- Institute of Microbiology, Jiangxi Academy of Sciences, Nanchang, Jiangxi, China
| | - Xi Zhou
- Institute of Microbiology, Jiangxi Academy of Sciences, Nanchang, Jiangxi, China
- Wuhan Institute of Virology, Chinese Academy of Sciences, Wuhan, 430071, Hubei, China
| | - Jun Li
- Department of Biological Sciences, Florida International University, Miami, FL, 33199, USA.
- Biomolecular Sciences Institute, Florida International University, Miami, FL, 33199, USA.
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163
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Soleimanizadeh A, Dinter H, Schindowski K. Central Nervous System Delivery of Antibodies and Their Single-Domain Antibodies and Variable Fragment Derivatives with Focus on Intranasal Nose to Brain Administration. Antibodies (Basel) 2021; 10:antib10040047. [PMID: 34939999 PMCID: PMC8699001 DOI: 10.3390/antib10040047] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2021] [Revised: 11/10/2021] [Accepted: 11/25/2021] [Indexed: 02/06/2023] Open
Abstract
IgG antibodies are some of the most important biopharmaceutical molecules with a high market volume. In spite of the fact that clinical therapies with antibodies are broadly utilized in oncology, immunology and hematology, their delivery strategies and biodistribution need improvement, their limitations being due to their size and poor ability to penetrate into tissues. In view of their small size, there is a rising interest in derivatives, such as single-domain antibodies and single-chain variable fragments, for clinical diagnostic but also therapeutic applications. Smaller antibody formats combine several benefits for clinical applications and can be manufactured at reduced production costs compared with full-length IgGs. Moreover, such formats have a relevant potential for targeted drug delivery that directs drug cargo to a specific tissue or across the blood–brain barrier. In this review, we give an overview of the challenges for antibody drug delivery in general and focus on intranasal delivery to the central nervous system with antibody formats of different sizes.
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Affiliation(s)
- Arghavan Soleimanizadeh
- Institute of Applied Biotechnology, Biberach University of Applied Science, 88400 Biberach, Germany; (A.S.); (H.D.)
- Faculty of Medicine, University of Ulm, 89081 Ulm, Germany
| | - Heiko Dinter
- Institute of Applied Biotechnology, Biberach University of Applied Science, 88400 Biberach, Germany; (A.S.); (H.D.)
- Department of Pharmacy and Biochemistry, University of Tübingen, 72076 Tübingen, Germany
| | - Katharina Schindowski
- Institute of Applied Biotechnology, Biberach University of Applied Science, 88400 Biberach, Germany; (A.S.); (H.D.)
- Correspondence:
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164
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Sarker S, Wankum B, Perey T, Mau MM, Shimizu J, Jones R, Terry B. A Novel Capsule-Delivered Enteric Drug-Injection Device for Delivery of Systemic Biologics: A Pilot Study in a Porcine Model. IEEE Trans Biomed Eng 2021; 69:1870-1879. [PMID: 34807818 DOI: 10.1109/tbme.2021.3129653] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
Abstract
Innovative swallowable capsule technologies such as drug-loaded, dissolvable microneedles, mucoadhesive patches, and various microdevices present unique drug-carrying capabilities to overcome challenges regarding oral delivery of biologics. Here, we report a swallowable capsule for intestinal drug delivery (SCIDD) with the potential of directly injecting biological therapeutics into the insensate small intestine wall. The design, optimization, and validation of the SCIDD's primary subsystems were performed both ex-vivo and in-vivo. The assembled capsule was further tested in vivo to validate the actuation sequence and showed a 70% (n=17) success rate in an animal model. Additionally, a drug delivery study indicated systemic uptake of adalimumab via SCIDD compared with luminal delivery in the small intestine. The pilot study presented here establishes that the novel platform could be used to orally deliver systemic biologics.
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165
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Synthetic Biology Advanced Natural Product Discovery. Metabolites 2021; 11:metabo11110785. [PMID: 34822443 PMCID: PMC8617713 DOI: 10.3390/metabo11110785] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2021] [Revised: 11/10/2021] [Accepted: 11/12/2021] [Indexed: 01/16/2023] Open
Abstract
A wide variety of bacteria, fungi and plants can produce bioactive secondary metabolites, which are often referred to as natural products. With the rapid development of DNA sequencing technology and bioinformatics, a large number of putative biosynthetic gene clusters have been reported. However, only a limited number of natural products have been discovered, as most biosynthetic gene clusters are not expressed or are expressed at extremely low levels under conventional laboratory conditions. With the rapid development of synthetic biology, advanced genome mining and engineering strategies have been reported and they provide new opportunities for discovery of natural products. This review discusses advances in recent years that can accelerate the design, build, test, and learn (DBTL) cycle of natural product discovery, and prospects trends and key challenges for future research directions.
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166
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Ganeshan S, Kim SH, Vujanovic V. Scaling-up production of plant endophytes in bioreactors: concepts, challenges and perspectives. BIORESOUR BIOPROCESS 2021; 8:63. [PMID: 34760435 PMCID: PMC8570317 DOI: 10.1186/s40643-021-00417-y] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2020] [Accepted: 07/09/2021] [Indexed: 11/11/2022] Open
Abstract
The benefit of microorganisms to humans, animals, insects and plants is increasingly recognized, with intensified microbial endophytes research indicative of this realization. In the agriculture industry, the benefits are tremendous to move towards sustainable crop production and minimize or circumvent the use of chemical fertilizers and pesticides. The research leading to the identification of potential plant endophytes is long and arduous and for many researchers the challenge is ultimately in scale-up production. While many of the larger agriculture and food industries have their own scale-up and manufacturing facilities, for many in academia and start-up companies the next steps towards production have been a stumbling block due to lack of information and understanding of the processes involved in scale-up fermentation. This review provides an overview of the fermentation process from shake flask cultures to scale-up and the manufacturing steps involved such as process development optimization (PDO), process hazard analysis (PHA), pre-, in- and post-production (PIP) challenges and finally the preparation of a technology transfer package (TTP) to transition the PDO to manufacturing. The focus is on submerged liquid fermentation (SLF) and plant endophytes production by providing original examples of fungal and bacterial endophytes, plant growth promoting Penicillium sp. and Streptomyces sp. bioinoculants, respectively. We also discuss the concepts, challenges and future perspectives of the scale-up microbial endophyte process technology based on the industrial and biosafety research platform for advancing a massive production of next-generation biologicals in bioreactors.
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Affiliation(s)
- Seedhabadee Ganeshan
- Department of Food and Bioproduct Sciences, University of Saskatchewan, 51 Campus Drive, Saskatoon, SK S7N 5A8 Canada
| | - Seon Hwa Kim
- Department of Food and Bioproduct Sciences, University of Saskatchewan, 51 Campus Drive, Saskatoon, SK S7N 5A8 Canada
| | - Vladimir Vujanovic
- Department of Food and Bioproduct Sciences, University of Saskatchewan, 51 Campus Drive, Saskatoon, SK S7N 5A8 Canada
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167
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Fadhilah QG, Santoso I, Maryanto AE, Abdullah S, Yasman Y. Evaluation of the antifungal activity of marine actinomycetes isolates against the phytopathogenic fungi Colletotrichum siamense KA: A preliminary study for new antifungal compound discovery. PHARMACIA 2021. [DOI: 10.3897/pharmacia.68.e72817] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
Marine actinomycetes are being explored to discover potential actinomycetes that produce antifungal compounds. In a previous study, marine actinomycetes isolates from the mangrove ecosystem were found to inhibit growth of the phytopathogenic fungi Colletotrichum siamense KA. In this study, the three of these isolates with the highest antagonistic activity—SM11, SM14, and SM15—were evaluated for their antifungal activity using antibiosis assay. The fermentation was performed in SCB:PDB medium (1:1) for 6, 9, and 12 days. The results showed that SM14 was the strongest potential isolate; it inhibited the growth of C. siamense KA on average up to 64.90% for 12 days on PDA filtrate medium. Molecular identification showed SM14 was closely related to Streptomyces sanyensis, but had differences in morphological and biochemical characteristics compared to SM11 or SM15. This indicated that the three isolates were different strains and may challenge further research on identifying and analyzing their antifungal compounds.
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168
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Deep learning strategies for active secondary metabolites biosynthesis from fungi: Harnessing artificial manipulation and application. BIOCATALYSIS AND AGRICULTURAL BIOTECHNOLOGY 2021. [DOI: 10.1016/j.bcab.2021.102195] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
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169
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Detection of biosynthetic genes of microbially-synthesized secondary metabolites in a contaminated tropical agricultural soil. Biologia (Bratisl) 2021. [DOI: 10.1007/s11756-021-00851-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
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170
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Qualitative and Quantitative Comparison of Liquid–Liquid Phase Extraction Using Ethyl Acetate and Liquid–Solid Phase Extraction Using Poly-Benzyl-Resin for Natural Products. APPLIED SCIENCES-BASEL 2021. [DOI: 10.3390/app112110241] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
A key step in the process of isolating microbial natural products is the preparation of an extract from a culture. This step determines which molecules will be available for detection in the subsequent chemical and biological analysis of a biodiscovery pipeline. In the present study we wanted to document potential differences in performance between liquid–liquid extraction using ethyl acetate and liquid–solid extraction using a poly-benzyl-resin. For the comparison of the two extraction protocols, we spiked a culture of Flavobacterium sp. with a diverse selection of natural products of microbial and plant origin to investigate whether the methods were comparable with respect to selectivity. We also investigated the efficiency of the two extraction methods quantitatively, using water spiked with a selection of natural products, and studied the quantitative effect of different pH levels of the aqueous solutions on the extraction yields of the two methods. The same compounds were extracted by the two methods, but the solid-phase extract contained more media components compared with the liquid-phase extract. Quantitatively, the two extraction methods varied in their recovery rates. We conclude that practical aspects could be more important when selecting one of the extraction protocols, as their efficiencies in extracting specific compounds were quite similar.
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171
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Liang Z, Lei F, Deng J, Zhang H, Wang Y, Li J, Shi T, Yang X, Wang Z. Design, synthesis and bioactivity evaluation of novel evodiamine derivatives with excellent potency against gastric cancer. Eur J Med Chem 2021; 228:113960. [PMID: 34774339 DOI: 10.1016/j.ejmech.2021.113960] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2021] [Revised: 10/19/2021] [Accepted: 10/26/2021] [Indexed: 12/12/2022]
Abstract
Gastric cancer represents a significant health burden worldwide. Previously, inspired by the traditional Chinese medicine Wu-Chu-Yu to treat the spleen and stomach system for thousands of years, we identified N14-phenyl substituted evodiamine derivatives as potential antitumor agents with favorable inhibition on Top1. Herein, structural optimization and structure-activity relationship studies (SARs) led us to discovering a highly active evodiamine derivative compound 6t against gastric cancer. Further anti-tumor mechanism studies revealed that compound 6t played as the inhibition of topoisomerase 1 (Top1), effectively induced apoptosis, obviously arrested the cell cycle at the G2/M phase, and significantly inhibited the migration and invasion of SGC-7901 and MGC-803 cell lines in a dose-dependent manner. Moreover, the compound 6t was low toxicity in vivo and exhibited excellent anti-tumor activity (TGI = 70.12%) in the MGC-803 xenograft models. In summary, compound 6t represents a promising candidate as a potential chemotherapeutic agent against gastric cancer.
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Affiliation(s)
- Ziyi Liang
- State Key Laboratory of Applied Organic Chemistry, College of Chemistry and Chemical Engineering, Lanzhou University, Lanzhou, 730000, China
| | - Fang Lei
- School of Pharmacy, Lanzhou University, Lanzhou, 730000, China
| | - Jiedan Deng
- School of Pharmacy, Lanzhou University, Lanzhou, 730000, China
| | - Honghua Zhang
- School of Pharmacy, Lanzhou University, Lanzhou, 730000, China
| | - Yuqing Wang
- School of Pharmacy, Lanzhou University, Lanzhou, 730000, China
| | - Junfang Li
- School of Pharmacy, Lanzhou University, Lanzhou, 730000, China
| | - Tao Shi
- School of Pharmacy, Lanzhou University, Lanzhou, 730000, China
| | - Xiaoyan Yang
- School of Pharmaceutical Science, Hengyang Medical School, University of South China, Hengyang, Hunan, 421001, China.
| | - Zhen Wang
- State Key Laboratory of Applied Organic Chemistry, College of Chemistry and Chemical Engineering, Lanzhou University, Lanzhou, 730000, China; School of Pharmaceutical Science, Hengyang Medical School, University of South China, Hengyang, Hunan, 421001, China; School of Pharmacy, Lanzhou University, Lanzhou, 730000, China.
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172
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Kennedy SJ, Atkinson CGF, Tomlinson BR, Hammond L, Eswara P, Baker BJ, Shaw LN. Phenogenomic Characterization of a Newly Domesticated and Novel Species from the Genus Verrucosispora. Appl Environ Microbiol 2021; 87:e0132721. [PMID: 34495705 PMCID: PMC8552891 DOI: 10.1128/aem.01327-21] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2021] [Accepted: 08/31/2021] [Indexed: 11/20/2022] Open
Abstract
The concept of bacterial dark matter stems from our inability to culture most microbes and represents a fundamental gap in our knowledge of microbial diversity. Here, we present the domestication of such an organism: a previously uncultured, novel species from the rare Actinomycetes genus Verrucosispora. Although initial recovery took >4 months, isolation of phenotypically distinct, domesticated generations occurred within weeks. Two isolates were subjected to phenogenomic analyses, revealing domestication correlated with enhanced growth rates in nutrient-rich media but diminished capacity to metabolize diverse amino acids. This is seemingly mediated by genomic atrophy through a mixed approach of pseudogenization and reversion of pseudogenization of amino acid metabolism genes. Conversely, later generational strains had enhanced spore germination rates, potentially through the reversion of a sporulation-associated kinase from pseudogene to true gene status. We observed that our most wild-type isolate had the greatest potential for antibacterial activity, which correlated with extensive mutational attrition of biosynthetic gene clusters in domesticated strains. Comparative analyses revealed wholesale genomic reordering in strains, with widespread single nucleotide polymorphism, indel, and pseudogene-impactful mutations observed. We hypothesize that domestication of this previously unculturable organism resulted from the shedding of genomic flexibility required for life in a dynamic marine environment, parsing out genetic redundancy to allow for a newfound cultivable amenability. IMPORTANCE The majority of environmental bacteria cannot be cultured within the laboratory. Understanding why only certain environmental isolates can be recovered is key to unlocking the abundant microbial dark matter that is widespread on our planet. In this study, we present not only the culturing but domestication of just such an organism. Although initial recovery took >4 months, we were able to isolate distinct, subpassaged offspring from the originating colony within mere weeks. A phenotypic and genotypic analysis of our generational strains revealed that adaptation to life in the lab occurred as a result of wholesale mutational changes. These permitted an enhanced ability for growth in nutrient rich media but came at the expense of reduced genomic flexibility. We suggest that without dynamic natural environmental stressors our domesticated strains effectively underwent genomic atrophy as they adapted to static conditions experienced in the laboratory.
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Affiliation(s)
- Sarah J. Kennedy
- Department of Cell Biology, Microbiology, and Molecular Biology, University of South Florida, Tampa, Florida, USA
| | - Celine Grace F. Atkinson
- Department of Cell Biology, Microbiology, and Molecular Biology, University of South Florida, Tampa, Florida, USA
| | - Brooke R. Tomlinson
- Department of Cell Biology, Microbiology, and Molecular Biology, University of South Florida, Tampa, Florida, USA
| | - Lauren Hammond
- Department of Cell Biology, Microbiology, and Molecular Biology, University of South Florida, Tampa, Florida, USA
| | - Prahathees Eswara
- Department of Cell Biology, Microbiology, and Molecular Biology, University of South Florida, Tampa, Florida, USA
| | - Bill J. Baker
- Department of Chemistry, University of South Florida, Tampa, Florida, USA
| | - Lindsey N. Shaw
- Department of Cell Biology, Microbiology, and Molecular Biology, University of South Florida, Tampa, Florida, USA
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173
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Schoenborn AA, Yannarell SM, Wallace ED, Clapper H, Weinstein IC, Shank EA. Defining the Expression, Production, and Signaling Roles of Specialized Metabolites during Bacillus subtilis Differentiation. J Bacteriol 2021; 203:e0033721. [PMID: 34460312 PMCID: PMC8544424 DOI: 10.1128/jb.00337-21] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2021] [Accepted: 08/11/2021] [Indexed: 11/20/2022] Open
Abstract
Bacterial specialized (or secondary) metabolites are structurally diverse molecules that mediate intra- and interspecies interactions by altering growth and cellular physiology and differentiation. Bacillus subtilis, a Gram-positive model bacterium commonly used to study biofilm formation and sporulation, has the capacity to produce more than 10 specialized metabolites. Some of these B. subtilis specialized metabolites have been investigated for their role in facilitating cellular differentiation, but only rarely has the behavior of multiple metabolites been simultaneously investigated. In this study, we explored the interconnectivity of differentiation (biofilm and sporulation) and specialized metabolites in B. subtilis. Specifically, we interrogated how development influences specialized metabolites and vice versa. Using the sporulation-inducing medium DSM, we found that the majority of the specialized metabolites examined are expressed and produced during biofilm formation and sporulation. Additionally, we found that six of these metabolites (surfactin, ComX, bacillibactin, bacilysin, subtilosin A, and plipastatin) are necessary signaling molecules for proper progression of B. subtilis differentiation. This study further supports the growing body of work demonstrating that specialized metabolites have essential physiological functions as cell-cell communication signals in bacteria. IMPORTANCE Bacterially produced specialized metabolites are frequently studied for their potential use as antibiotics and antifungals. However, a growing body of work has suggested that the antagonistic potential of specialized metabolites is not their only function. Here, using Bacillus subtilis as our model bacterium, we demonstrated that developmental processes such as biofilm formation and sporulation are tightly linked to specialized metabolite gene expression and production. Additionally, under our differentiation-inducing conditions, six out of the nine specialized metabolites investigated behave as intraspecific signals that impact B. subtilis physiology and influence biofilm formation and sporulation. Our work supports the viewpoint that specialized metabolites have a clear role as cell-cell signaling molecules within differentiated populations of bacteria.
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Affiliation(s)
- Alexi A. Schoenborn
- Department of Microbiology and Immunology, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA
- Department of Biology, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA
| | - Sarah M. Yannarell
- Department of Microbiology and Immunology, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA
- Department of Biology, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA
| | - E. Diane Wallace
- Department of Chemistry, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA
| | - Haley Clapper
- Department of Biology, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA
| | - Ilon C. Weinstein
- Department of Biology, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA
| | - Elizabeth A. Shank
- Program in Systems Biology, University of Massachusetts Medical School, Worcester, Massachusetts, USA
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174
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Boruta T, Ścigaczewska A, Bizukojć M. "Microbial Wars" in a Stirred Tank Bioreactor: Investigating the Co-Cultures of Streptomyces rimosus and Aspergillus terreus, Filamentous Microorganisms Equipped With a Rich Arsenal of Secondary Metabolites. Front Bioeng Biotechnol 2021; 9:713639. [PMID: 34660550 PMCID: PMC8511322 DOI: 10.3389/fbioe.2021.713639] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2021] [Accepted: 09/17/2021] [Indexed: 11/13/2022] Open
Abstract
Microbial co-cultivation is an approach frequently used for the induction of secondary metabolic pathways and the discovery of novel molecules. The studies of this kind are typically focused on the chemical and ecological aspects of inter-species interactions rather than on the bioprocess characterization. In the present work, the co-cultivation of two textbook producers of secondary metabolites, namely Aspergillus terreus (a filamentous fungus used for the manufacturing of lovastatin, a cholesterol-lowering drug) and Streptomyces rimosus (an actinobacterial producer of an antibiotic oxytetracycline) in a 5.5-L stirred tank bioreactor was investigated in the context of metabolic production, utilization of carbon substrates and dissolved oxygen levels. The cultivation runs differed in terms of the applied co-culture initiation strategy and the composition of growth medium. All the experiments were performed in three bioreactors running in parallel (corresponding to a co-culture and two respective monoculture controls). The analysis based upon mass spectrometry and liquid chromatography revealed a broad spectrum of more than 40 secondary metabolites, including the molecules identified as the oxidized derivatives of rimocidin and milbemycin that were observed solely under the conditions of co-cultivation. S. rimosus showed a tendency to dominate over A. terreus, except for the runs where S. rimosus was inoculated into the already developed bioreactor cultures of A. terreus. Despite being dominated, the less aggressive strain still had an observable influence on the production of secondary metabolites and the utilization of substrates in co-culture. The monitoring of dissolved oxygen levels was evaluated as a fast approach of identifying the dominant microorganism during the co-cultivation process.
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Affiliation(s)
- Tomasz Boruta
- Department of Bioprocess Engineering, Faculty of Process and Environmental Engineering, Lodz University of Technology, Lodz, Poland
| | - Anna Ścigaczewska
- Department of Bioprocess Engineering, Faculty of Process and Environmental Engineering, Lodz University of Technology, Lodz, Poland
| | - Marcin Bizukojć
- Department of Bioprocess Engineering, Faculty of Process and Environmental Engineering, Lodz University of Technology, Lodz, Poland
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175
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Caicedo-Montoya C, Manzo-Ruiz M, Ríos-Estepa R. Pan-Genome of the Genus Streptomyces and Prioritization of Biosynthetic Gene Clusters With Potential to Produce Antibiotic Compounds. Front Microbiol 2021; 12:677558. [PMID: 34659136 PMCID: PMC8510958 DOI: 10.3389/fmicb.2021.677558] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2021] [Accepted: 08/30/2021] [Indexed: 01/07/2023] Open
Abstract
Species of the genus Streptomyces are known for their ability to produce multiple secondary metabolites; their genomes have been extensively explored to discover new bioactive compounds. The richness of genomic data currently available allows filtering for high quality genomes, which in turn permits reliable comparative genomics studies and an improved prediction of biosynthetic gene clusters (BGCs) through genome mining approaches. In this work, we used 121 genome sequences of the genus Streptomyces in a comparative genomics study with the aim of estimating the genomic diversity by protein domains content, sequence similarity of proteins and conservation of Intergenic Regions (IGRs). We also searched for BGCs but prioritizing those with potential antibiotic activity. Our analysis revealed that the pan-genome of the genus Streptomyces is clearly open, with a high quantity of unique gene families across the different species and that the IGRs are rarely conserved. We also described the phylogenetic relationships of the analyzed genomes using multiple markers, obtaining a trustworthy tree whose relationships were further validated by Average Nucleotide Identity (ANI) calculations. Finally, 33 biosynthetic gene clusters were detected to have potential antibiotic activity and a predicted mode of action, which might serve up as a guide to formulation of related experimental studies.
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Affiliation(s)
- Carlos Caicedo-Montoya
- Grupo de Bioprocesos, Departamento de Ingeniería Química, Universidad de Antioquia (UdeA), Medellín, Colombia
| | - Monserrat Manzo-Ruiz
- Departamento de Biología Molecular y Biotecnología, Instituto de Investigaciones Biomédicas, Universidad Nacional Autónoma de México, Ciudad de México, Mexico
| | - Rigoberto Ríos-Estepa
- Grupo de Bioprocesos, Departamento de Ingeniería Química, Universidad de Antioquia (UdeA), Medellín, Colombia
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176
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La Maestra S, D'Agostini F, Geretto M, Micale RT. Microbial-based cleaning products as a potential risk to human health: A review. Toxicol Lett 2021; 353:60-70. [PMID: 34626814 DOI: 10.1016/j.toxlet.2021.09.013] [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: 06/09/2021] [Revised: 09/07/2021] [Accepted: 09/29/2021] [Indexed: 11/25/2022]
Abstract
Microbial-based cleaning products (MBCPs) have been introduced, on the market, as an alternative to traditional chemical cleaning. In addition to traditional detergents, MBCPs can perform their cleaning function, digesting the smallest particles of dirt and mitigating odours generated by environmental bacterium metabolic processes. Nevertheless, several aspects remain to be clarified and assessed, requiring further studies and new regulations to ensure safety. The particular composition of MBCPs makes it difficult to include these products in a specific class, making the European legal context incomplete and unclear. Moreover, MBCPs effects on human health are poorly documented. Exposure risks can be obtained indirectly by studies conducted in both microorganisms exposure and their metabolic products, such as enzymes, especially in workers. A further limiting factor for the accurate human health risk assessment due to MBCPs use is an incomplete indication about the MBCPs compositions. Moreover, additional factors such as host microorganisms, frequency and space of use, subject health condition, and age can determine different illness scenarios. The findings from the broad range of studies we have reviewed in this paper confirm the necessity of integrative investigation and regulation to address the use of MBCPs.
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Affiliation(s)
| | | | - Marta Geretto
- Department of Experimental Medicine, University of Genova, Italy
| | - Rosanna T Micale
- Department of Health Sciences, University of Genoa, Genoa, Italy
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177
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Rahman MS, Hoque MN, Puspo JA, Islam MR, Das N, Siddique MA, Hossain MA, Sultana M. Microbiome signature and diversity regulates the level of energy production under anaerobic condition. Sci Rep 2021; 11:19777. [PMID: 34611238 PMCID: PMC8492712 DOI: 10.1038/s41598-021-99104-3] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2021] [Accepted: 09/13/2021] [Indexed: 02/08/2023] Open
Abstract
The microbiome of the anaerobic digester (AD) regulates the level of energy production. To assess the microbiome diversity and composition in different stages of anaerobic digestion, we collected 16 samples from the AD of cow dung (CD) origin. The samples were categorized into four groups (Group-I, Group-II, Group-III and Group-IV) based on the level of energy production (CH4%), and sequenced through whole metagenome sequencing (WMS). Group-I (n = 2) belonged to initial time of energy production whereas Group-II (n = 5), Group-III (n = 5), and Group-IV (n = 4) had 21-34%, 47-58% and 71-74% of CH4, respectively. The physicochemical analysis revealed that level of energy production (CH4%) had significant positive correlation with digester pH (r = 0.92, p < 0.001), O2 level (%) (r = 0.54, p < 0.05), and environmental temperature (°C) (r = 0.57, p < 0.05). The WMS data mapped to 2800 distinct bacterial, archaeal and viral genomes through PathoScope (PS) and MG-RAST (MR) analyses. We detected 768, 1421, 1819 and 1774 bacterial strains in Group-I, Group-II, Group-III and Group-IV, respectively through PS analysis which were represented by Firmicutes, Bacteroidetes, Proteobacteria, Actinobacteria, Spirochaetes and Fibrobacteres phyla (> 93.0% of the total abundances). Simultaneously, 343 archaeal strains were detected, of which 95.90% strains shared across four metagenomes. We identified 43 dominant species including 31 bacterial and 12 archaeal species in AD microbiomes, of which only archaea showed positive correlation with digester pH, CH4 concentration, pressure and temperature (Spearman correlation; r > 0.6, p < 0.01). The indicator species analysis showed that the species Methanosarcina vacuolate, Dehalococcoides mccartyi, Methanosarcina sp. Kolksee and Methanosarcina barkeri were highly specific for energy production. The correlation network analysis showed that different strains of Euryarcheota and Firmicutes phyla exhibited significant correlation (p = 0.021, Kruskal-Wallis test; with a cutoff of 1.0) with the highest level (74.1%) of energy production (Group-IV). In addition, top CH4 producing microbiomes showed increased genomic functional activities related to one carbon and biotin metabolism, oxidative stress, proteolytic pathways, membrane-type-1-matrix-metalloproteinase (MT1-MMP) pericellular network, acetyl-CoA production, motility and chemotaxis. Importantly, the physicochemical properties of the AD including pH, CH4 concentration (%), pressure, temperature and environmental temperature were found to be positively correlated with these genomic functional potentials and distribution of ARGs and metal resistance pathways (Spearman correlation; r > 0.5, p < 0.01). This study reveals distinct changes in composition and diversity of the AD microbiomes including different indicator species, and their genomic features that are highly specific for energy production.
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Affiliation(s)
- M. Shaminur Rahman
- grid.8198.80000 0001 1498 6059Department of Microbiology, University of Dhaka, Dhaka, 1000 Bangladesh
| | - M. Nazmul Hoque
- grid.8198.80000 0001 1498 6059Department of Microbiology, University of Dhaka, Dhaka, 1000 Bangladesh ,grid.443108.a0000 0000 8550 5526Department of Gynecology, Obstetrics and Reproductive Health, Bangabandhu Sheikh Mujibur Rahman Agricultural University, Gazipur, 1706 Bangladesh
| | - Joynob Akter Puspo
- grid.8198.80000 0001 1498 6059Department of Microbiology, University of Dhaka, Dhaka, 1000 Bangladesh
| | - M. Rafiul Islam
- grid.8198.80000 0001 1498 6059Department of Microbiology, University of Dhaka, Dhaka, 1000 Bangladesh
| | - Niloy Das
- grid.8198.80000 0001 1498 6059Department of Microbiology, University of Dhaka, Dhaka, 1000 Bangladesh ,Surge Engineering (www.surgeengineering.com), Dhaka, 1205 Bangladesh
| | - Mohammad Anwar Siddique
- grid.8198.80000 0001 1498 6059Department of Microbiology, University of Dhaka, Dhaka, 1000 Bangladesh
| | - M. Anwar Hossain
- grid.8198.80000 0001 1498 6059Department of Microbiology, University of Dhaka, Dhaka, 1000 Bangladesh ,Present Address: Jashore University of Science and Technology, Jashore, 7408 Bangladesh
| | - Munawar Sultana
- grid.8198.80000 0001 1498 6059Department of Microbiology, University of Dhaka, Dhaka, 1000 Bangladesh
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178
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Stan D, Enciu AM, Mateescu AL, Ion AC, Brezeanu AC, Stan D, Tanase C. Natural Compounds With Antimicrobial and Antiviral Effect and Nanocarriers Used for Their Transportation. Front Pharmacol 2021; 12:723233. [PMID: 34552489 PMCID: PMC8450524 DOI: 10.3389/fphar.2021.723233] [Citation(s) in RCA: 61] [Impact Index Per Article: 20.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2021] [Accepted: 08/24/2021] [Indexed: 12/22/2022] Open
Abstract
Due to the increasing prevalence of life-threatening bacterial, fungal and viral infections and the ability of these human pathogens to develop resistance to current treatment strategies, there is a great need to find and develop new compunds to combat them. These molecules must have low toxicity, specific activity and high bioavailability. The most suitable compounds for this task are usually derived from natural sources (animal, plant or even microbial). In this review article, the latest and most promising natural compounds used to combat bacteria, filamentous fungi and viruses are presented and evaluated. These include plant extracts, essential oils, small antimicrobial peptides of animal origin, bacteriocins and various groups of plant compounds (triterpenoids; alkaloids; phenols; flavonoids) with antimicrobial and antiviral activity. Data are presented on the inhibitory activity of each natural antimicrobial substance and on the putative mechanism of action against bacterial and fungal strains. The results show that among the bioactive compounds studied, triterpenoids have significant inhibitory activity against coronaviruses, but flavonoids have also been shown to inhibit SARS-COV-2. The last chapter is devoted to nanocarriers used to improve stability, bioavailability, cellular uptake/internalization, pharmacokinetic profile and reduce toxicity of natural compunds. There are a number of nanocarriers such as liposomes, drug delivery microemulsion systems, nanocapsules, solid lipid nanoparticles, polymeric micelles, dendrimers, etc. However, some of the recent studies have focused on the incorporation of natural substances with antimicrobial/antiviral activity into polymeric nanoparticles, niosomes and silver nanoparticles (which have been shown to have intrinsic antimicrobial activity). The natural antimicrobials isolated from animals and microorganisms have been shown to have good inhibitory effect on a range of pathogens, however the plants remain the most prolific source. Even if the majority of the studies for the biological activity evaluation are in silico or in vitro, their internalization in the optimum nanocarriers represents the future of “green therapeutics” as shown by some of the recent work in the field.
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Affiliation(s)
- Diana Stan
- DDS Diagnostic, Bucharest, Romania.,Titu Maiorescu University, PhD Medical School, Bucharest, Romania
| | - Ana-Maria Enciu
- Victor Babes National Institute of Pathology, Biochemistry-Proteomics Department, Bucharest, Romania
| | | | | | - Ariana Cristina Brezeanu
- Carol Davila University of Medicine and Pharmacy-Department of Plastic Surgery, Bucharest, Romania
| | | | - Cristiana Tanase
- Victor Babes National Institute of Pathology, Biochemistry-Proteomics Department, Bucharest, Romania.,Titu Maiorescu University, Faculty of Medicine, Bucharest, Romania
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179
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Galanie S, Entwistle D, Lalonde J. Engineering biosynthetic enzymes for industrial natural product synthesis. Nat Prod Rep 2021; 37:1122-1143. [PMID: 32364202 DOI: 10.1039/c9np00071b] [Citation(s) in RCA: 45] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Covering: 2000 to 2020 Natural products and their derivatives are commercially important medicines, agrochemicals, flavors, fragrances, and food ingredients. Industrial strategies to produce these structurally complex molecules encompass varied combinations of chemical synthesis, biocatalysis, and extraction from natural sources. Interest in engineering natural product biosynthesis began with the advent of genetic tools for pathway discovery. Genes and strains can now readily be synthesized, mutated, recombined, and sequenced. Enzyme engineering has succeeded commercially due to the development of genetic methods, analytical technologies, and machine learning algorithms. Today, engineered biosynthetic enzymes from organisms spanning the tree of life are used industrially to produce diverse molecules. These biocatalytic processes include single enzymatic steps, multienzyme cascades, and engineered native and heterologous microbial strains. This review will describe how biosynthetic enzymes have been engineered to enable commercial and near-commercial syntheses of natural products and their analogs.
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Affiliation(s)
- Stephanie Galanie
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee, USA.
| | - David Entwistle
- Process Chemistry, Codexis, Inc., Redwood City, California, USA
| | - James Lalonde
- Microbial Digital Genome Engineering, Inscripta, Inc., Pleasanton, California, USA
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180
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Wei B, Du AQ, Zhou ZY, Lai C, Yu WC, Yu JB, Yu YL, Chen JW, Zhang HW, Xu XW, Wang H. An atlas of bacterial secondary metabolite biosynthesis gene clusters. Environ Microbiol 2021; 23:6981-6992. [PMID: 34490968 DOI: 10.1111/1462-2920.15761] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2021] [Accepted: 09/04/2021] [Indexed: 11/28/2022]
Abstract
Bacterial secondary metabolites are rich sources of novel drug leads. The diversity of secondary metabolite biosynthetic gene clusters (BGCs) in genome-sequenced bacteria, which will provide crucial information for the efficient discovery of novel natural products, has not been systematically investigated. Here, the distribution and genetic diversity of BGCs in 10 121 prokaryotic genomes (across 68 phyla) were obtained from their PRISM4 outputs using a custom python script. A total of 18 043 BGCs are detected from 5743 genomes with non-ribosomal peptide synthetases (25.4%) and polyketides (15.9%) as the dominant classes of BGCs. Bacterial strains harbouring the largest number of BGCs are revealed and BGC count in strains of some genera vary greatly, suggesting the necessity of individually evaluating the secondary metabolism potential. Additional analysis against 102 strains of discovered bacterial genera with abundant amounts of BGCs confirms that Kutzneria, Kibdelosporangium, Moorea, Saccharothrix, Cystobacter, Archangium, Actinosynnema, Kitasatospora, and Nocardia, may also be important sources of natural products and worthy of priority investigation. Comparative analysis of BGCs within these genera indicates the great diversity and novelty of the BGCs. This study presents an atlas of bacterial secondary metabolite BGCs that provides a lot of key information for the targeted discovery of novel natural products.
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Affiliation(s)
- Bin Wei
- College of Pharmaceutical Science & Collaborative Innovation Center of Yangtze River Delta Region Green Pharmaceuticals, Zhejiang University of Technology, Hangzhou, 310014, China.,Key Laboratory of Marine Ecosystem and Biogeochemistry, State Oceanic Administration & Second Institute of Oceanography, Ministry of Natural Resources, Hangzhou, 310012, China.,Key Laboratory of Marine Fishery Resources Exploitment & Utilization of Zhejiang Province, Hangzhou, 310014, China
| | - Ao-Qi Du
- College of Pharmaceutical Science & Collaborative Innovation Center of Yangtze River Delta Region Green Pharmaceuticals, Zhejiang University of Technology, Hangzhou, 310014, China
| | - Zhen-Yi Zhou
- College of Pharmaceutical Science & Collaborative Innovation Center of Yangtze River Delta Region Green Pharmaceuticals, Zhejiang University of Technology, Hangzhou, 310014, China
| | - Cong Lai
- College of Pharmaceutical Science & Collaborative Innovation Center of Yangtze River Delta Region Green Pharmaceuticals, Zhejiang University of Technology, Hangzhou, 310014, China
| | - Wen-Chao Yu
- College of Pharmaceutical Science & Collaborative Innovation Center of Yangtze River Delta Region Green Pharmaceuticals, Zhejiang University of Technology, Hangzhou, 310014, China
| | - Jin-Biao Yu
- College of Pharmaceutical Science & Collaborative Innovation Center of Yangtze River Delta Region Green Pharmaceuticals, Zhejiang University of Technology, Hangzhou, 310014, China
| | - Yan-Lei Yu
- College of Pharmaceutical Science & Collaborative Innovation Center of Yangtze River Delta Region Green Pharmaceuticals, Zhejiang University of Technology, Hangzhou, 310014, China
| | - Jian-Wei Chen
- College of Pharmaceutical Science & Collaborative Innovation Center of Yangtze River Delta Region Green Pharmaceuticals, Zhejiang University of Technology, Hangzhou, 310014, China
| | - Hua-Wei Zhang
- College of Pharmaceutical Science & Collaborative Innovation Center of Yangtze River Delta Region Green Pharmaceuticals, Zhejiang University of Technology, Hangzhou, 310014, China.,Key Laboratory of Marine Fishery Resources Exploitment & Utilization of Zhejiang Province, Hangzhou, 310014, China
| | - Xue-Wei Xu
- Key Laboratory of Marine Ecosystem and Biogeochemistry, State Oceanic Administration & Second Institute of Oceanography, Ministry of Natural Resources, Hangzhou, 310012, China
| | - Hong Wang
- College of Pharmaceutical Science & Collaborative Innovation Center of Yangtze River Delta Region Green Pharmaceuticals, Zhejiang University of Technology, Hangzhou, 310014, China.,Key Laboratory of Marine Fishery Resources Exploitment & Utilization of Zhejiang Province, Hangzhou, 310014, China
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181
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Raihan T, Rabbee MF, Roy P, Choudhury S, Baek KH, Azad AK. Microbial Metabolites: The Emerging Hotspot of Antiviral Compounds as Potential Candidates to Avert Viral Pandemic Alike COVID-19. Front Mol Biosci 2021; 8:732256. [PMID: 34557521 PMCID: PMC8452873 DOI: 10.3389/fmolb.2021.732256] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2021] [Accepted: 08/23/2021] [Indexed: 12/15/2022] Open
Abstract
The present global COVID-19 pandemic caused by the noble pleomorphic severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has created a vulnerable situation in the global healthcare and economy. In this pandemic situation, researchers all around the world are trying their level best to find suitable therapeutics from various sources to combat against the SARS-CoV-2. To date, numerous bioactive compounds from different sources have been tested to control many viral diseases. However, microbial metabolites are advantageous for drug development over metabolites from other sources. We herein retrieved and reviewed literatures from PubMed, Scopus and Google relevant to antiviral microbial metabolites by searching with the keywords "antiviral microbial metabolites," "microbial metabolite against virus," "microorganism with antiviral activity," "antiviral medicine from microbial metabolite," "antiviral bacterial metabolites," "antiviral fungal metabolites," "antiviral metabolites from microscopic algae' and so on. For the same purpose, the keywords "microbial metabolites against COVID-19 and SARS-CoV-2" and "plant metabolites against COVID-19 and SARS-CoV-2" were used. Only the full text literatures available in English and pertinent to the topic have been included and those which are not available as full text in English and pertinent to antiviral or anti-SARS-CoV-2 activity were excluded. In this review, we have accumulated microbial metabolites that can be used as antiviral agents against a broad range of viruses including SARS-CoV-2. Based on this concept, we have included 330 antiviral microbial metabolites so far available to date in the data bases and were previously isolated from fungi, bacteria and microalgae. The microbial source, chemical nature, targeted viruses, mechanism of actions and IC50/EC50 values of these metabolites are discussed although mechanisms of actions of many of them are not yet elucidated. Among these antiviral microbial metabolites, some compounds might be very potential against many other viruses including coronaviruses. However, these potential microbial metabolites need further research to be developed as effective antiviral drugs. This paper may provide the scientific community with the possible secret of microbial metabolites that could be an effective source of novel antiviral drugs to fight against many viruses including SARS-CoV-2 as well as the future viral pandemics.
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Affiliation(s)
- Topu Raihan
- Department of Genetic Engineering and Biotechnology, Shahjalal University of Science and Technology, Sylhet, Bangladesh
| | | | - Puja Roy
- Department of Genetic Engineering and Biotechnology, Shahjalal University of Science and Technology, Sylhet, Bangladesh
| | - Swapnila Choudhury
- Department of Genetic Engineering and Biotechnology, Jagannath University, Dhaka, Bangladesh
| | - Kwang-Hyun Baek
- Department of Biotechnology, Yeungnam University, Gyeongsan, South Korea
| | - Abul Kalam Azad
- Department of Genetic Engineering and Biotechnology, Shahjalal University of Science and Technology, Sylhet, Bangladesh
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182
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Iantas J, Savi DC, Schibelbein RDS, Noriler SA, Assad BM, Dilarri G, Ferreira H, Rohr J, Thorson JS, Shaaban KA, Glienke C. Endophytes of Brazilian Medicinal Plants With Activity Against Phytopathogens. Front Microbiol 2021; 12:714750. [PMID: 34539608 PMCID: PMC8442585 DOI: 10.3389/fmicb.2021.714750] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2021] [Accepted: 08/03/2021] [Indexed: 12/14/2022] Open
Abstract
Plant diseases caused by phytopathogens are responsible for significant crop losses worldwide. Resistance induction and biological control have been exploited in agriculture due to their enormous potential. In this study, we investigated the antimicrobial potential of endophytic fungi of leaves and petioles of medicinal plants Vochysia divergens and Stryphnodendron adstringens located in two regions of high diversity in Brazil, Pantanal, and Cerrado, respectively. We recovered 1,304 fungal isolates and based on the characteristics of the culture, were assigned to 159 phenotypes. One isolate was selected as representative of each phenotype and studied for antimicrobial activity against phytopathogens. Isolates with better biological activities were identified based on DNA sequences and phylogenetic analyzes. Among the 159 representative isolates, extracts from 12 endophytes that inhibited the mycelial growth (IG) of Colletotrichum abscissum (≥40%) were selected to expand the antimicrobial analysis. The minimum inhibitory concentrations (MIC) of the extracts were determined against citrus pathogens, C. abscissum, Phyllosticta citricarpa and Xanthomonas citri subsp. citri and the maize pathogen Fusarium graminearum. The highest activity against C. abscissum were from extracts of Pseudofusicoccum stromaticum CMRP4328 (IG: 83% and MIC: 40 μg/mL) and Diaporthe vochysiae CMRP4322 (IG: 75% and MIC: 1 μg/mL), both extracts also inhibited the development of post-bloom fruit drop symptoms in citrus flowers. The extracts were promising in inhibiting the mycelial growth of P. citricarpa and reducing the production of pycnidia in citrus leaves. Among the isolates that showed activity, the genus Diaporthe was the most common, including the new species D. cerradensis described in this study. In addition, high performance liquid chromatography, UV detection, and mass spectrometry and thin layer chromatography analyzes of extracts produced by endophytes that showed high activity, indicated D. vochysiae CMRP4322 and P. stromaticum CMRP4328 as promising strains that produce new bioactive natural products. We report here the capacity of endophytic fungi of medicinal plants to produce secondary metabolites with biological activities against phytopathogenic fungi and bacteria. The description of the new species D. cerradensis, reinforces the ability of medicinal plants found in Brazil to host a diverse group of fungi with biotechnological potential.
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Affiliation(s)
- Jucélia Iantas
- Postgraduate Program of Microbiology, Parasitology and Pathology, Department of Pathology, Federal University of Paraná, Curitiba, Brazil
| | - Daiani Cristina Savi
- Department of Biomedicine, Centro Universitário Católica de Santa Catarina, Joinville, Brazil
- Postgraduate Program of Genetics, Federal University of Paraná, Curitiba, Brazil
| | - Renata da Silva Schibelbein
- Postgraduate Program of Microbiology, Parasitology and Pathology, Department of Pathology, Federal University of Paraná, Curitiba, Brazil
| | - Sandriele Aparecida Noriler
- Postgraduate Program of Microbiology, Parasitology and Pathology, Department of Pathology, Federal University of Paraná, Curitiba, Brazil
| | | | - Guilherme Dilarri
- Department of General and Applied Biology, Biosciences Institute, State University of São Paulo, Rio Claro, Brazil
| | - Henrique Ferreira
- Department of General and Applied Biology, Biosciences Institute, State University of São Paulo, Rio Claro, Brazil
| | - Jürgen Rohr
- Department of Pharmaceutical Sciences, College of Pharmacy, University of Kentucky, Lexington, KY, United States
| | - Jon S. Thorson
- Department of Pharmaceutical Sciences, College of Pharmacy, University of Kentucky, Lexington, KY, United States
- Center for Pharmaceutical Research and Innovation, College of Pharmacy, University of Kentucky, Lexington, KY, United States
| | - Khaled A. Shaaban
- Department of Pharmaceutical Sciences, College of Pharmacy, University of Kentucky, Lexington, KY, United States
- Center for Pharmaceutical Research and Innovation, College of Pharmacy, University of Kentucky, Lexington, KY, United States
| | - Chirlei Glienke
- Postgraduate Program of Microbiology, Parasitology and Pathology, Department of Pathology, Federal University of Paraná, Curitiba, Brazil
- Postgraduate Program of Genetics, Federal University of Paraná, Curitiba, Brazil
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183
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Costa-Gutierrez SB, Saez JM, Aparicio JD, Raimondo EE, Benimeli CS, Polti MA. Glycerol as a substrate for actinobacteria of biotechnological interest: Advantages and perspectives in circular economy systems. CHEMOSPHERE 2021; 279:130505. [PMID: 33865166 DOI: 10.1016/j.chemosphere.2021.130505] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/09/2020] [Revised: 03/25/2021] [Accepted: 04/03/2021] [Indexed: 06/12/2023]
Abstract
Actinobacteria represent a ubiquitous group of microorganisms widely distributed in ecosystems. They have diverse physiological and metabolic properties, including the production of extracellular enzymes and a variety of secondary bioactive metabolites, such as antibiotics, immunosuppressants, and other compounds of industrial interest. Therefore, actinobacteria have been used for biotechnological purposes for more than three decades. The development of a biotechnological process requires the evaluation of its cost/benefit ratio, including the search for economic and efficient substrates for microorganisms development. Biodiesel is a clean, renewable, quality and economically viable source of energy, which also contributes to the conservation of the environment. Crude glycerol is the main by-product of biodiesel production and has many properties, so it has a commercial value that can be used to finance the biofuel production process. Actinobacteria can use glycerol as a source of carbon and energy, either pure o crude. A circular economy system aims to eliminate waste and pollution, keep products and materials in use, and regenerate natural systems. Although these principles are not yet met, some approaches are being made in this direction; the transformation of crude glycerol by actinobacteria is a process with great potential to be scaled on an industrial level. This review discusses the reports on glycerol as a promising source of carbon and energy for obtaining biomass and high-added value products by actinobacteria. Also, the factors influencing the biomass and secondary metabolites production in bioreactors are analyzed, and the tools available to overcome those that generate the main problems are discussed.
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Affiliation(s)
- Stefanie B Costa-Gutierrez
- Planta Piloto de Procesos Industriales Microbiológicos (PROIMI-CONICET), Avenida Belgrano y Pasaje Caseros, 4000, San Miguel de Tucumán, Tucumán, Argentina
| | - Juliana Maria Saez
- Planta Piloto de Procesos Industriales Microbiológicos (PROIMI-CONICET), Avenida Belgrano y Pasaje Caseros, 4000, San Miguel de Tucumán, Tucumán, Argentina; Facultad de Ciencias Naturales e Instituto Miguel Lillo, Universidad Nacional de Tucumán, Miguel Lillo 205, 4000, Tucumán, Argentina
| | - Juan Daniel Aparicio
- Planta Piloto de Procesos Industriales Microbiológicos (PROIMI-CONICET), Avenida Belgrano y Pasaje Caseros, 4000, San Miguel de Tucumán, Tucumán, Argentina; Facultad de Bioquímica, Química y Farmacia, Universidad Nacional de Tucumán, Ayacucho 491, 4000, Tucumán, Argentina
| | - Enzo E Raimondo
- Planta Piloto de Procesos Industriales Microbiológicos (PROIMI-CONICET), Avenida Belgrano y Pasaje Caseros, 4000, San Miguel de Tucumán, Tucumán, Argentina; Facultad de Bioquímica, Química y Farmacia, Universidad Nacional de Tucumán, Ayacucho 491, 4000, Tucumán, Argentina
| | - Claudia S Benimeli
- Planta Piloto de Procesos Industriales Microbiológicos (PROIMI-CONICET), Avenida Belgrano y Pasaje Caseros, 4000, San Miguel de Tucumán, Tucumán, Argentina; Facultad de Ciencias Exactas y Naturales, Universidad Nacional de Catamarca, Belgrano 300, 4700, Catamarca, Argentina
| | - Marta A Polti
- Planta Piloto de Procesos Industriales Microbiológicos (PROIMI-CONICET), Avenida Belgrano y Pasaje Caseros, 4000, San Miguel de Tucumán, Tucumán, Argentina; Facultad de Ciencias Naturales e Instituto Miguel Lillo, Universidad Nacional de Tucumán, Miguel Lillo 205, 4000, Tucumán, Argentina.
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184
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Eusebio N, Rego A, Glasser NR, Castelo-Branco R, Balskus EP, Leão PN. Distribution and diversity of dimetal-carboxylate halogenases in cyanobacteria. BMC Genomics 2021; 22:633. [PMID: 34461836 PMCID: PMC8406957 DOI: 10.1186/s12864-021-07939-x] [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: 05/18/2021] [Accepted: 08/14/2021] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Halogenation is a recurring feature in natural products, especially those from marine organisms. The selectivity with which halogenating enzymes act on their substrates renders halogenases interesting targets for biocatalyst development. Recently, CylC - the first predicted dimetal-carboxylate halogenase to be characterized - was shown to regio- and stereoselectively install a chlorine atom onto an unactivated carbon center during cylindrocyclophane biosynthesis. Homologs of CylC are also found in other characterized cyanobacterial secondary metabolite biosynthetic gene clusters. Due to its novelty in biological catalysis, selectivity and ability to perform C-H activation, this halogenase class is of considerable fundamental and applied interest. The study of CylC-like enzymes will provide insights into substrate scope, mechanism and catalytic partners, and will also enable engineering these biocatalysts for similar or additional C-H activating functions. Still, little is known regarding the diversity and distribution of these enzymes. RESULTS In this study, we used both genome mining and PCR-based screening to explore the genetic diversity of CylC homologs and their distribution in bacteria. While we found non-cyanobacterial homologs of these enzymes to be rare, we identified a large number of genes encoding CylC-like enzymes in publicly available cyanobacterial genomes and in our in-house culture collection of cyanobacteria. Genes encoding CylC homologs are widely distributed throughout the cyanobacterial tree of life, within biosynthetic gene clusters of distinct architectures (combination of unique gene groups). These enzymes are found in a variety of biosynthetic contexts, which include fatty-acid activating enzymes, type I or type III polyketide synthases, dialkylresorcinol-generating enzymes, monooxygenases or Rieske proteins. Our study also reveals that dimetal-carboxylate halogenases are among the most abundant types of halogenating enzymes in the phylum Cyanobacteria. CONCLUSIONS Our data show that dimetal-carboxylate halogenases are widely distributed throughout the Cyanobacteria phylum and that BGCs encoding CylC homologs are diverse and mostly uncharacterized. This work will help guide the search for new halogenating biocatalysts and natural product scaffolds.
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Affiliation(s)
- Nadia Eusebio
- Interdisciplinary Centre of Marine and Environmental Research (CIIMAR/CIMAR), University of Porto, Matosinhos, Portugal
| | - Adriana Rego
- Interdisciplinary Centre of Marine and Environmental Research (CIIMAR/CIMAR), University of Porto, Matosinhos, Portugal
| | - Nathaniel R Glasser
- Department of Chemistry and Chemical Biology, Harvard University, Cambridge, MA, USA
| | - Raquel Castelo-Branco
- Interdisciplinary Centre of Marine and Environmental Research (CIIMAR/CIMAR), University of Porto, Matosinhos, Portugal
| | - Emily P Balskus
- Department of Chemistry and Chemical Biology, Harvard University, Cambridge, MA, USA.
| | - Pedro N Leão
- Interdisciplinary Centre of Marine and Environmental Research (CIIMAR/CIMAR), University of Porto, Matosinhos, Portugal.
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185
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Pusparajah P, Letchumanan V, Law JWF, Ab Mutalib NS, Ong YS, Goh BH, Tan LTH, Lee LH. Streptomyces sp.-A Treasure Trove of Weapons to Combat Methicillin-Resistant Staphylococcus aureus Biofilm Associated with Biomedical Devices. Int J Mol Sci 2021; 22:ijms22179360. [PMID: 34502269 PMCID: PMC8431294 DOI: 10.3390/ijms22179360] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2021] [Revised: 08/23/2021] [Accepted: 08/26/2021] [Indexed: 11/16/2022] Open
Abstract
Biofilms formed by methicillin-resistant S. aureus (MRSA) are among the most frequent causes of biomedical device-related infection, which are difficult to treat and are often persistent and recurrent. Thus, new and effective antibiofilm agents are urgently needed. In this article, we review the most relevant literature of the recent years reporting on promising anti-MRSA biofilm agents derived from the genus Streptomyces bacteria, and discuss the potential contribution of these newly reported antibiofilm compounds to the current strategies in preventing biofilm formation and eradicating pre-existing biofilms of the clinically important pathogen MRSA. Many efforts are evidenced to address biofilm-related infections, and some novel strategies have been developed and demonstrated encouraging results in preclinical studies. Nevertheless, more in vivo studies with appropriate biofilm models and well-designed multicenter clinical trials are needed to assess the prospects of these strategies.
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Affiliation(s)
- Priyia Pusparajah
- Novel Bacteria and Drug Discovery Research Group (NBDD), Microbes and Bioresource Research Strength (MBRS), Jeffrey Cheah School of Medicine and Health Sciences, Monash University Malaysia, Bandar Sunway 47500, Malaysia; (P.P.); (V.L.); (J.W.-F.L.); (N.-S.A.M.)
| | - Vengadesh Letchumanan
- Novel Bacteria and Drug Discovery Research Group (NBDD), Microbes and Bioresource Research Strength (MBRS), Jeffrey Cheah School of Medicine and Health Sciences, Monash University Malaysia, Bandar Sunway 47500, Malaysia; (P.P.); (V.L.); (J.W.-F.L.); (N.-S.A.M.)
| | - Jodi Woan-Fei Law
- Novel Bacteria and Drug Discovery Research Group (NBDD), Microbes and Bioresource Research Strength (MBRS), Jeffrey Cheah School of Medicine and Health Sciences, Monash University Malaysia, Bandar Sunway 47500, Malaysia; (P.P.); (V.L.); (J.W.-F.L.); (N.-S.A.M.)
| | - Nurul-Syakima Ab Mutalib
- Novel Bacteria and Drug Discovery Research Group (NBDD), Microbes and Bioresource Research Strength (MBRS), Jeffrey Cheah School of Medicine and Health Sciences, Monash University Malaysia, Bandar Sunway 47500, Malaysia; (P.P.); (V.L.); (J.W.-F.L.); (N.-S.A.M.)
- UKM Medical Molecular Biology Institute (UMBI), UKM Medical Centre, Universiti Kebangsaan Malaysia, Kuala Lumpur 56000, Malaysia
| | - Yong Sze Ong
- Biofunctional Molecule Exploratory Research Group (BMEX), School of Pharmacy, Monash University Malaysia, Bandar Sunway 47500, Malaysia;
| | - Bey-Hing Goh
- Biofunctional Molecule Exploratory Research Group (BMEX), School of Pharmacy, Monash University Malaysia, Bandar Sunway 47500, Malaysia;
- College of Pharmaceutical Sciences, Zhejiang University, Hangzhou 310058, China
- Correspondence: (B.-H.G.); (L.T.-H.T.); (L.-H.L.)
| | - Loh Teng-Hern Tan
- Novel Bacteria and Drug Discovery Research Group (NBDD), Microbes and Bioresource Research Strength (MBRS), Jeffrey Cheah School of Medicine and Health Sciences, Monash University Malaysia, Bandar Sunway 47500, Malaysia; (P.P.); (V.L.); (J.W.-F.L.); (N.-S.A.M.)
- Clinical School Johor Bahru, Jeffrey Cheah School of Medicine and Health Sciences, Monash University Malaysia, Johor Bahru 80100, Malaysia
- Correspondence: (B.-H.G.); (L.T.-H.T.); (L.-H.L.)
| | - Learn-Han Lee
- Novel Bacteria and Drug Discovery Research Group (NBDD), Microbes and Bioresource Research Strength (MBRS), Jeffrey Cheah School of Medicine and Health Sciences, Monash University Malaysia, Bandar Sunway 47500, Malaysia; (P.P.); (V.L.); (J.W.-F.L.); (N.-S.A.M.)
- Correspondence: (B.-H.G.); (L.T.-H.T.); (L.-H.L.)
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186
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Miethke M, Pieroni M, Weber T, Brönstrup M, Hammann P, Halby L, Arimondo PB, Glaser P, Aigle B, Bode HB, Moreira R, Li Y, Luzhetskyy A, Medema MH, Pernodet JL, Stadler M, Tormo JR, Genilloud O, Truman AW, Weissman KJ, Takano E, Sabatini S, Stegmann E, Brötz-Oesterhelt H, Wohlleben W, Seemann M, Empting M, Hirsch AKH, Loretz B, Lehr CM, Titz A, Herrmann J, Jaeger T, Alt S, Hesterkamp T, Winterhalter M, Schiefer A, Pfarr K, Hoerauf A, Graz H, Graz M, Lindvall M, Ramurthy S, Karlén A, van Dongen M, Petkovic H, Keller A, Peyrane F, Donadio S, Fraisse L, Piddock LJV, Gilbert IH, Moser HE, Müller R. Towards the sustainable discovery and development of new antibiotics. Nat Rev Chem 2021; 5:726-749. [PMID: 34426795 PMCID: PMC8374425 DOI: 10.1038/s41570-021-00313-1] [Citation(s) in RCA: 427] [Impact Index Per Article: 142.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 07/01/2021] [Indexed: 02/08/2023]
Abstract
An ever-increasing demand for novel antimicrobials to treat life-threatening infections caused by the global spread of multidrug-resistant bacterial pathogens stands in stark contrast to the current level of investment in their development, particularly in the fields of natural-product-derived and synthetic small molecules. New agents displaying innovative chemistry and modes of action are desperately needed worldwide to tackle the public health menace posed by antimicrobial resistance. Here, our consortium presents a strategic blueprint to substantially improve our ability to discover and develop new antibiotics. We propose both short-term and long-term solutions to overcome the most urgent limitations in the various sectors of research and funding, aiming to bridge the gap between academic, industrial and political stakeholders, and to unite interdisciplinary expertise in order to efficiently fuel the translational pipeline for the benefit of future generations.
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Affiliation(s)
- Marcus Miethke
- Helmholtz Institute for Pharmaceutical Research Saarland (HIPS) - Helmholtz Centre for Infection Research (HZI), and Department of Pharmacy, Saarland University Campus E8.1, Saarbrücken, Germany
- German Center for Infection Research (DZIF), Braunschweig, Germany
| | - Marco Pieroni
- Food and Drug Department, University of Parma, Parma, Italy
| | - Tilmann Weber
- The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Lyngby, Denmark
| | - Mark Brönstrup
- German Center for Infection Research (DZIF), Braunschweig, Germany
- Department of Chemical Biology (CBIO), Helmholtz Centre for Infection Research (HZI), Braunschweig, Germany
| | - Peter Hammann
- Infectious Diseases & Natural Product Research at EVOTEC, and Justus Liebig University Giessen, Giessen, Germany
| | - Ludovic Halby
- Epigenetic Chemical Biology, Department of Structural Biology and Chemistry, Institut Pasteur, UMR n°3523, CNRS, Paris, France
| | - Paola B. Arimondo
- Epigenetic Chemical Biology, Department of Structural Biology and Chemistry, Institut Pasteur, UMR n°3523, CNRS, Paris, France
| | - Philippe Glaser
- Ecology and Evolution of Antibiotic Resistance Unit, Microbiology Department, Institut Pasteur, CNRS UMR3525, Paris, France
| | | | - Helge B. Bode
- Department of Biosciences, Goethe University Frankfurt, Frankfurt, Germany
- Max Planck Institute for Terrestrial Microbiology, Department of Natural Products in Organismic Interactions, Marburg, Germany
| | - Rui Moreira
- Faculty of Pharmacy, University of Lisbon, Lisbon, Portugal
| | - Yanyan Li
- Unit MCAM, CNRS, National Museum of Natural History (MNHN), Paris, France
| | - Andriy Luzhetskyy
- Pharmaceutical Biotechnology, Saarland University, Saarbrücken, Germany
| | - Marnix H. Medema
- Bioinformatics Group, Wageningen University and Research, Wageningen, Netherlands
| | - Jean-Luc Pernodet
- Institute for Integrative Biology of the Cell (I2BC) & Microbiology Department, University of Paris-Saclay, Gif-sur-Yvette, France
| | - Marc Stadler
- German Center for Infection Research (DZIF), Braunschweig, Germany
- Microbial Drugs (MWIS), Helmholtz Centre for Infection Research (HZI), Braunschweig, Germany
| | | | | | - Andrew W. Truman
- Department of Molecular Microbiology, John Innes Centre, Norwich, United Kingdom
| | - Kira J. Weissman
- Molecular and Structural Enzymology Group, Université de Lorraine, CNRS, IMoPA, Nancy, France
| | - Eriko Takano
- Manchester Institute of Biotechnology, Department of Chemistry, School of Natural Sciences, Faculty of Science and Engineering, University of Manchester, Manchester, United Kingdom
| | - Stefano Sabatini
- Department of Pharmaceutical Sciences, University of Perugia, Perugia, Italy
| | - Evi Stegmann
- German Center for Infection Research (DZIF), Braunschweig, Germany
- Department of Microbial Bioactive Compounds, Interfaculty Institute of Microbiology and Infection Medicine, University of Tübingen, Tübingen, Germany
| | - Heike Brötz-Oesterhelt
- German Center for Infection Research (DZIF), Braunschweig, Germany
- Department of Microbial Bioactive Compounds, Interfaculty Institute of Microbiology and Infection Medicine, University of Tübingen, Tübingen, Germany
| | - Wolfgang Wohlleben
- German Center for Infection Research (DZIF), Braunschweig, Germany
- Department of Microbiology/Biotechnology, Interfaculty Institute of Microbiology and Infection Medicine, University of Tübingen, Tübingen, Germany
| | - Myriam Seemann
- Institute for Chemistry UMR 7177, University of Strasbourg/CNRS, ITI InnoVec, Strasbourg, France
| | - Martin Empting
- Helmholtz Institute for Pharmaceutical Research Saarland (HIPS) - Helmholtz Centre for Infection Research (HZI), and Department of Pharmacy, Saarland University Campus E8.1, Saarbrücken, Germany
- German Center for Infection Research (DZIF), Braunschweig, Germany
| | - Anna K. H. Hirsch
- Helmholtz Institute for Pharmaceutical Research Saarland (HIPS) - Helmholtz Centre for Infection Research (HZI), and Department of Pharmacy, Saarland University Campus E8.1, Saarbrücken, Germany
- German Center for Infection Research (DZIF), Braunschweig, Germany
| | - Brigitta Loretz
- Helmholtz Institute for Pharmaceutical Research Saarland (HIPS) - Helmholtz Centre for Infection Research (HZI), and Department of Pharmacy, Saarland University Campus E8.1, Saarbrücken, Germany
| | - Claus-Michael Lehr
- Helmholtz Institute for Pharmaceutical Research Saarland (HIPS) - Helmholtz Centre for Infection Research (HZI), and Department of Pharmacy, Saarland University Campus E8.1, Saarbrücken, Germany
| | - Alexander Titz
- Helmholtz Institute for Pharmaceutical Research Saarland (HIPS) - Helmholtz Centre for Infection Research (HZI), and Department of Pharmacy, Saarland University Campus E8.1, Saarbrücken, Germany
- German Center for Infection Research (DZIF), Braunschweig, Germany
| | - Jennifer Herrmann
- Helmholtz Institute for Pharmaceutical Research Saarland (HIPS) - Helmholtz Centre for Infection Research (HZI), and Department of Pharmacy, Saarland University Campus E8.1, Saarbrücken, Germany
- German Center for Infection Research (DZIF), Braunschweig, Germany
| | - Timo Jaeger
- German Center for Infection Research (DZIF), Braunschweig, Germany
| | - Silke Alt
- German Center for Infection Research (DZIF), Braunschweig, Germany
| | | | | | - Andrea Schiefer
- German Center for Infection Research (DZIF), Braunschweig, Germany
- Institute of Medical Microbiology, Immunology and Parasitology (IMMIP), University Hospital Bonn, Bonn, Germany
| | - Kenneth Pfarr
- German Center for Infection Research (DZIF), Braunschweig, Germany
- Institute of Medical Microbiology, Immunology and Parasitology (IMMIP), University Hospital Bonn, Bonn, Germany
| | - Achim Hoerauf
- German Center for Infection Research (DZIF), Braunschweig, Germany
- Institute of Medical Microbiology, Immunology and Parasitology (IMMIP), University Hospital Bonn, Bonn, Germany
| | - Heather Graz
- Biophys Ltd., Usk, Monmouthshire, United Kingdom
| | - Michael Graz
- School of Law, University of Bristol, Bristol, United Kingdom
| | | | | | - Anders Karlén
- Department of Medicinal Chemistry, Uppsala University, Uppsala, Sweden
| | | | - Hrvoje Petkovic
- Department of Food Science and Technology, Biotechnical Faculty, University of Ljubljana, Ljubljana, Slovenia
| | - Andreas Keller
- Chair for Clinical Bioinformatics, Saarland University, University Hospital, Saarbrücken, Germany
| | | | | | - Laurent Fraisse
- Drugs for Neglected Diseases initiative (DNDi), Geneva, Switzerland
| | - Laura J. V. Piddock
- The Global Antibiotic Research and Development Partnership (GARDP), Geneva, Switzerland
| | - Ian H. Gilbert
- Division of Biological Chemistry and Drug Discovery, University of Dundee, Dundee, United Kingdom
| | - Heinz E. Moser
- Novartis Institutes for BioMedical Research (NIBR), Emeryville, CA USA
| | - Rolf Müller
- Helmholtz Institute for Pharmaceutical Research Saarland (HIPS) - Helmholtz Centre for Infection Research (HZI), and Department of Pharmacy, Saarland University Campus E8.1, Saarbrücken, Germany
- German Center for Infection Research (DZIF), Braunschweig, Germany
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187
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Advances in Microbial Fermentation Processes. Processes (Basel) 2021. [DOI: 10.3390/pr9081371] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022] Open
Abstract
In the food sector, fermentation processes have been the object of great interest in regard to enhancing the yield, the quality, and the safety of the final product [...]
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188
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Tandi M, Sundriyal S. Recent trends in the design of antimicrobial agents using Ugi-multicomponent reaction. J INDIAN CHEM SOC 2021. [DOI: 10.1016/j.jics.2021.100106] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
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189
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Antonio A, Wiedemann L, Galante E, Guimarães A, Matharu A, Veiga-Junior V. Efficacy and sustainability of natural products in COVID-19 treatment development: opportunities and challenges in using agro-industrial waste from Citrus and apple. Heliyon 2021; 7:e07816. [PMID: 34423146 PMCID: PMC8366044 DOI: 10.1016/j.heliyon.2021.e07816] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2021] [Revised: 07/13/2021] [Accepted: 08/13/2021] [Indexed: 12/24/2022] Open
Abstract
Natural products have been used in the treatment of illnesses throughout the history of humankind. Exploitation of bioactive compounds from natural sources can aid in the discovery of new drugs, provide the scaffold of new medicines. In the face of challenging diseases, such as the COVID-19 pandemic, for which there was no effective treatment, nature could offer insights as to novel therapeutic options for control measures. However, the environmental impact and supply chain of bioactive production must be carefully evaluated to ensure the detrimental effects will not outweigh the potential benefits gained. History has already proven that highly bioactive compounds can be rare and not suitable for medicinal exploitation; therefore, the sustainability must be accessed before expensive, time-demanding, and large trials can be initialized. A sustainable option to readily produce a phytotherapy with minimal environmental stress is the use of agro-industry wastes, a by-product produced in high quantities. In this review we evaluate the sustainability issues associated with the production of phytotherapy as a readily available tool for pandemic control.
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Affiliation(s)
- A.S. Antonio
- Chemical Engineering Section, Military Institute of Engineering, Praça General Tibúrcio, 80, Praia Vermelha, Urca, 22290-270, Rio de Janeiro, RJ, Brazil
- Chemistry Department, Institute of Exact Sciences, Amazonas Federal University, Avenida Rodrigo Otávio, 6200, Coroado, 69077-000, Manaus, AM, Brazil
| | - L.S.M. Wiedemann
- Chemistry Department, Institute of Exact Sciences, Amazonas Federal University, Avenida Rodrigo Otávio, 6200, Coroado, 69077-000, Manaus, AM, Brazil
| | - E.B.F. Galante
- Chemical Engineering Section, Military Institute of Engineering, Praça General Tibúrcio, 80, Praia Vermelha, Urca, 22290-270, Rio de Janeiro, RJ, Brazil
| | - A.C. Guimarães
- Chemistry Department, Institute of Exact Sciences, Amazonas Federal University, Avenida Rodrigo Otávio, 6200, Coroado, 69077-000, Manaus, AM, Brazil
| | - A.S. Matharu
- Green Chemistry Centre of Excellence, Department of Chemistry, University of York, York, YO10 5DD, UK
| | - V.F. Veiga-Junior
- Chemical Engineering Section, Military Institute of Engineering, Praça General Tibúrcio, 80, Praia Vermelha, Urca, 22290-270, Rio de Janeiro, RJ, Brazil
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190
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Iyer R, Damania A. Shotgun metagenomics of indigenous bacteria collected from the banks of the San Jacinto River for biodegradation of aromatic waste. FEMS Microbiol Lett 2021; 367:5881932. [PMID: 32761171 DOI: 10.1093/femsle/fnaa133] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2020] [Accepted: 08/04/2020] [Indexed: 12/24/2022] Open
Abstract
Several Eastern Harris County communities lie near the now enclosed San Jacinto River (SJR) Waste Pit Superfund, a dumping ground for chlorinated dioxins and other paper mill waste products. Currently, no active monitoring of the SJR is conducted for these toxins with the exact concentration and health impact to the area unknown. As such, remediation and monitoring efforts outside of the Superfund itself could be necessary. To better understand the possible environmental fate of these aromatics, here we provide a shotgun metagenomic analysis of the structural and putative functional diversity of the SJR microbiome from two impacted Channelview, Texas communities bordering the Superfund. Results show that the underlying SJR microbiome possesses a core of metabolic enzymes related to the β-ketoadipate and benzoate degradation pathways. This suggests possible endpoints for many aromatics found deposited in the SJR including dioxin-like compounds. However, degradation biomarkers related to the priming and initial cleavage of chlorinated dioxin-like aromatics while present, are poorly concentrated across sampled sites. This may be due in part to decreased coverage of low abundance bacterial species, but also be a contributing factor leading to increased recalcitrance of these compounds in this environment compared to other aromatics.
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Affiliation(s)
- Rupa Iyer
- Center for Life Sciences Technology, Engineering Technology, University of Houston, 300 Technology Building, Houston 77204, TX, USA
| | - Ashish Damania
- Department of Pediatrics-Tropical Medicine, Baylor College of Medicine, One Baylor Plaza, Houston 77030, TX, USA
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191
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Schneider YK. Bacterial Natural Product Drug Discovery for New Antibiotics: Strategies for Tackling the Problem of Antibiotic Resistance by Efficient Bioprospecting. Antibiotics (Basel) 2021; 10:antibiotics10070842. [PMID: 34356763 PMCID: PMC8300778 DOI: 10.3390/antibiotics10070842] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2021] [Revised: 07/05/2021] [Accepted: 07/08/2021] [Indexed: 12/25/2022] Open
Abstract
The problem of antibiotic resistance has become a challenge for our public health and society; it has allowed infectious diseases to re-emerge as a risk to human health. New antibiotics that are introduced to the market face the rise of resistant pathogens after a certain period of use. The relatively fast development of resistance against some antibiotics seems to be closely linked to their microbial origin and function in nature. Antibiotics in clinical use are merely products of microorganisms or derivatives of microbial products. The evolution of these antimicrobial compounds has progressed with the evolution of the respective resistance mechanisms in microbes for billions of years. Thus, antimicrobial resistance genes are present within the environment and can be taken up by pathogens through horizontal gene transfer. Natural products from bacteria are an important source of leads for drug development, and microbial natural products have contributed the most antibiotics in current clinical use. Bioprospecting for new antibiotics is a labor-intensive task as obstacles such as redetection of known compounds and low compound yields consume significant resources. The number of bacterial isolates one can theoretically investigate for new secondary metabolites is, on the other hand, immense. Therefore, the available capacity for biodiscovery should be focused on the most promising sources for chemical novelty and bioactivity, employing the appropriate scientific tools. This can be done by first looking into under- or unexplored environments for bacterial isolates and by focusing on the promising candidates to reduce the number of subjects.
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Affiliation(s)
- Yannik K Schneider
- Marbio, Faculty for Fisheries, Biosciences and Economy, UiT-The Arctic University of Norway, Breivika, N-9037 Tromsø, Norway
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192
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Kim GS, Jang JP, Oh TH, Kwon M, Lee B, Lee JS, Ko SK, Hong YS, Ahn JS, Jang JH. Angucyclines containing β-ᴅ-glucuronic acid from Streptomyces sp. KCB15JA151. Bioorg Med Chem Lett 2021; 48:128237. [PMID: 34216745 DOI: 10.1016/j.bmcl.2021.128237] [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: 04/27/2021] [Revised: 06/21/2021] [Accepted: 06/27/2021] [Indexed: 10/21/2022]
Abstract
Two angucyclines, pseudonocardones D (1) and E (2), were isolated from Streptomyces sp. KCB15JA151. The planar structure was elucidated by comprehensive spectroscopic analysis. The absolute configuration of the sugar unit was determined based on the basis of coupling constants, ROESY, chemical derivatization and HPLC analysis. The biological activities of compounds 1 and 2 were examined by performing a computational target prediction, which led to tests of the antiestrogenic activity. The result suggested that compound 1 might be an ERα antagonist.
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Affiliation(s)
- Gil Soo Kim
- Anticancer Agent Research Center, Korea Research Institute of Bioscience and Biotechnology, Cheongju 28116, Republic of Korea; Department of Biomolecular Science, KRIBB School of Bioscience, University of Science and Technology, Daejeon 34113, Republic of Korea
| | - Jun-Pil Jang
- Anticancer Agent Research Center, Korea Research Institute of Bioscience and Biotechnology, Cheongju 28116, Republic of Korea
| | - Tae Hoon Oh
- Anticancer Agent Research Center, Korea Research Institute of Bioscience and Biotechnology, Cheongju 28116, Republic of Korea; College of Pharmacy, Chungbuk National University, Cheongju 28160, Republic of Korea
| | - Mincheol Kwon
- Anticancer Agent Research Center, Korea Research Institute of Bioscience and Biotechnology, Cheongju 28116, Republic of Korea; Department of Biomolecular Science, KRIBB School of Bioscience, University of Science and Technology, Daejeon 34113, Republic of Korea
| | - Byeongsan Lee
- Anticancer Agent Research Center, Korea Research Institute of Bioscience and Biotechnology, Cheongju 28116, Republic of Korea; College of Pharmacy, Chungbuk National University, Cheongju 28160, Republic of Korea
| | - Jung-Sook Lee
- Korean Collection for Type Cultures, Korea Research Institute of Bioscience and Biotechnology, Jeongeup 56212, Republic of Korea
| | - Sung-Kyun Ko
- Anticancer Agent Research Center, Korea Research Institute of Bioscience and Biotechnology, Cheongju 28116, Republic of Korea
| | - Young-Soo Hong
- Anticancer Agent Research Center, Korea Research Institute of Bioscience and Biotechnology, Cheongju 28116, Republic of Korea; Department of Biomolecular Science, KRIBB School of Bioscience, University of Science and Technology, Daejeon 34113, Republic of Korea
| | - Jong Seog Ahn
- Anticancer Agent Research Center, Korea Research Institute of Bioscience and Biotechnology, Cheongju 28116, Republic of Korea; Department of Biomolecular Science, KRIBB School of Bioscience, University of Science and Technology, Daejeon 34113, Republic of Korea.
| | - Jae-Hyuk Jang
- Anticancer Agent Research Center, Korea Research Institute of Bioscience and Biotechnology, Cheongju 28116, Republic of Korea; Department of Biomolecular Science, KRIBB School of Bioscience, University of Science and Technology, Daejeon 34113, Republic of Korea.
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193
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Doan CT, Tran TN, Nguyen TT, Tran TPH, Nguyen VB, Tran TD, Nguyen AD, Wang SL. Production of Sucrolytic Enzyme by Bacillus licheniformis by the Bioconversion of Pomelo Albedo as a Carbon Source. Polymers (Basel) 2021; 13:polym13121959. [PMID: 34199171 PMCID: PMC8231626 DOI: 10.3390/polym13121959] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2021] [Revised: 06/10/2021] [Accepted: 06/10/2021] [Indexed: 11/30/2022] Open
Abstract
Recently, there has been increasing use of agro-byproducts in microbial fermentation to produce a variety of value-added products. In this study, among various kinds of agro-byproducts, pomelo albedo powder (PAP) was found to be the most effective carbon source for the production of sucrose hydrolyzing enzyme by Bacillus licheniformis TKU004. The optimal medium for sucrolytic enzyme production contained 2% PAP, 0.75% NH4NO3, 0.05% MgSO4, and 0.05% NaH2PO4 and the optimal culture conditions were pH 6.7, 35 °C, 150 rpm, and 24 h. Accordingly, the highest sucrolytic activity was 1.87 U/mL, 4.79-fold higher than that from standard conditions using sucrose as the carbon source. The purified sucrolytic enzyme (sleTKU004) is a 53 kDa monomeric protein and belongs to the glycoside hydrolase family 68. The optimum temperature and pH of sleTKU004 were 50 °C, and pH = 6, respectively. SleTKU004 could hydrolyze sucrose, raffinose, and stachyose by attacking the glycoside linkage between glucose and fructose molecules of the sucrose unit. The Km and Vmax of sleTKU004 were 1.16 M and 5.99 µmol/min, respectively. Finally, sleTKU004 showed strong sucrose tolerance and presented the highest hydrolytic activity at the sucrose concentration of 1.2 M–1.5 M.
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Affiliation(s)
- Chien Thang Doan
- Department of Chemistry, Tamkang University, New Taipei City 25137, Taiwan; (C.T.D.); (T.N.T.)
- Faculty of Natural Sciences and Technology, Tay Nguyen University, Buon Ma Thuot 630000, Vietnam; (T.T.N.); (T.P.H.T.); (T.D.T.)
| | - Thi Ngoc Tran
- Department of Chemistry, Tamkang University, New Taipei City 25137, Taiwan; (C.T.D.); (T.N.T.)
- Faculty of Natural Sciences and Technology, Tay Nguyen University, Buon Ma Thuot 630000, Vietnam; (T.T.N.); (T.P.H.T.); (T.D.T.)
| | - Thi Thanh Nguyen
- Faculty of Natural Sciences and Technology, Tay Nguyen University, Buon Ma Thuot 630000, Vietnam; (T.T.N.); (T.P.H.T.); (T.D.T.)
| | - Thi Phuong Hanh Tran
- Faculty of Natural Sciences and Technology, Tay Nguyen University, Buon Ma Thuot 630000, Vietnam; (T.T.N.); (T.P.H.T.); (T.D.T.)
| | - Van Bon Nguyen
- Institute of Biotechnology and Environment, Tay Nguyen University, Buon Ma Thuot 630000, Vietnam; (V.B.N.); (A.D.N.)
| | - Trung Dung Tran
- Faculty of Natural Sciences and Technology, Tay Nguyen University, Buon Ma Thuot 630000, Vietnam; (T.T.N.); (T.P.H.T.); (T.D.T.)
| | - Anh Dzung Nguyen
- Institute of Biotechnology and Environment, Tay Nguyen University, Buon Ma Thuot 630000, Vietnam; (V.B.N.); (A.D.N.)
| | - San-Lang Wang
- Department of Chemistry, Tamkang University, New Taipei City 25137, Taiwan; (C.T.D.); (T.N.T.)
- Life Science Development Center, Tamkang University, New Taipei City 25137, Taiwan
- Correspondence: ; Tel.: +886-2-2621-5656; Fax: +886-2-2620-9924
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194
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Jin Y, Wang Z, Dong AY, Huang YQ, Hao GF, Song BA. Web repositories of natural agents promote pests and pathogenic microbes management. Brief Bioinform 2021; 22:6294160. [PMID: 34098581 DOI: 10.1093/bib/bbab205] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2021] [Revised: 05/10/2021] [Accepted: 05/10/2021] [Indexed: 12/30/2022] Open
Abstract
The grand challenge to meet the increasing demands for food by a rapidly growing global population requires protecting crops from pests. Natural active substances play a significant role in the sustainable pests and pathogenic microbes management. In recent years, natural products- (NPs), antimicrobial peptides- (AMPs), medicinal plant- and plant essential oils (EOs)-related online resources have greatly facilitated the development of pests and pathogenic microbes control agents in an efficient and economical manner. However, a comprehensive comparison, analysis and summary of these existing web resources are still lacking. Here, we surveyed these databases of NPs, AMPs, medicinal plants and plant EOs with insecticidal, antibacterial, antiviral and antifungal activity, and we compared their functionality, data volume, data sources and applicability. We comprehensively discussed the limitation of these web resources. This study provides a toolbox for bench scientists working in the pesticide, botany, biomedical and pharmaceutical engineering fields. The aim of the review is to hope that these web resources will facilitate the discovery and development of potential active ingredients of pests and pathogenic microbes control agents.
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Affiliation(s)
- Yin Jin
- State Key Laboratory Breeding Base of Green Pesticide and Agricultural Bioengineering, Key Laboratory of Green Pesticide and Agricultural Bioengineering, Center for Research and Development of Fine Chemicals, Guizhou University, Guiyang 550025, P. R. China
| | - Zheng Wang
- State Key Laboratory Breeding Base of Green Pesticide and Agricultural Bioengineering, Key Laboratory of Green Pesticide and Agricultural Bioengineering, Center for Research and Development of Fine Chemicals, Guizhou University, Guiyang 550025, P. R. China
| | - An-Yu Dong
- State Key Laboratory Breeding Base of Green Pesticide and Agricultural Bioengineering, Key Laboratory of Green Pesticide and Agricultural Bioengineering, Center for Research and Development of Fine Chemicals, Guizhou University, Guiyang 550025, P. R. China
| | - Yuan-Qin Huang
- State Key Laboratory Breeding Base of Green Pesticide and Agricultural Bioengineering, Key Laboratory of Green Pesticide and Agricultural Bioengineering, Center for Research and Development of Fine Chemicals, Guizhou University, Guiyang 550025, P. R. China
| | - Ge-Fei Hao
- State Key Laboratory Breeding Base of Green Pesticide and Agricultural Bioengineering, Key Laboratory of Green Pesticide and Agricultural Bioengineering, Center for Research and Development of Fine Chemicals, Guizhou University, Guiyang 550025, P. R. China
| | - Bao-An Song
- State Key Laboratory Breeding Base of Green Pesticide and Agricultural Bioengineering, Key Laboratory of Green Pesticide and Agricultural Bioengineering, Center for Research and Development of Fine Chemicals, Guizhou University, Guiyang 550025, P. R. China
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195
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Kim MJ, Tagele SB, Jo H, Kim MC, Jung Y, Park YJ, So JH, Kim HJ, Kim HJ, Lee DG, Kang S, Shin JH. Effect of a bioconverted product of Lotus corniculatus seed on the axillary microbiome and body odor. Sci Rep 2021; 11:10138. [PMID: 33980951 PMCID: PMC8115508 DOI: 10.1038/s41598-021-89606-5] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2020] [Accepted: 04/07/2021] [Indexed: 02/01/2023] Open
Abstract
The skin microbiome, especially the axillary microbiome, consists of odor-causing bacteria that decompose odorless sweat into malodor compounds, which contributes to the formation of body odor. Plant-derived products are a cheap source of bioactive compounds that are common ingredients in cosmetics. Microbial bioconversion of natural products is an ecofriendly and economical method for production of new or improved biologically active compounds. Therefore, in this study, we tested the potential of a Lactobacillus acidophilus KNU-02-mediated bioconverted product (BLC) of Lotus corniculatus seed to reduce axillary malodor and its effect on the associated axillary microbiota. A chemical profile analysis revealed that benzoic acid was the most abundant chemical compound in BLC, which increased following bioconversion. Moreover, BLC treatment was found to reduce the intensity of axillary malodor. We tested the axillary microbiome of 18 study participants, divided equally into BLC and placebo groups, and revealed through 16S rRNA gene sequencing that Staphylococcus, Corynebacterium, and Anaerococcus were the dominant taxa, and some of these taxa were significantly associated with axillary malodor. After one week of BLC treatment, the abundance of Corynebacterium and Anaerococcus, which are associated with well-known odor-related genes that produce volatile fatty acids, had significantly reduced. Likewise, the identified odor-related genes decreased after the application of BLC. BLC treatment enhanced the richness and network density of the axillary microbial community. The placebo group, on the other hand, showed no difference in the microbial richness, odor associated taxa, and predicted functional genes after a week. The results demonstrated that BLC has the potential to reduce the axillary malodor and the associated odor-causing bacteria, which makes BLC a viable deodorant material in cosmetic products.
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Affiliation(s)
- Min-Ji Kim
- Department of Applied Biosciences, Kyungpook National University, Daegu, 41566, Republic of Korea
| | - Setu Bazie Tagele
- Department of Applied Biosciences, Kyungpook National University, Daegu, 41566, Republic of Korea
| | - HyungWoo Jo
- R&I Center, COSMAX BTI, Seongnam, 13486, Republic of Korea
| | - Min-Chul Kim
- Department of Applied Biosciences, Kyungpook National University, Daegu, 41566, Republic of Korea
| | - YeonGyun Jung
- Department of Applied Biosciences, Kyungpook National University, Daegu, 41566, Republic of Korea
| | - Yeong-Jun Park
- Department of Applied Biosciences, Kyungpook National University, Daegu, 41566, Republic of Korea
| | - Jai-Hyun So
- National Development Institute of Korean Medicine, 94, Hwarang-ro, Gyeongsan, Gyeongsangbuk-do, 38540, Republic of Korea
| | - Hae Jin Kim
- Experiment Research Institute, National Agricultural Products Quality Management Service, Gimcheon, Gyeongsangbuk-do, 39660, Republic of Korea
| | - Ho Jin Kim
- Experiment Research Institute, National Agricultural Products Quality Management Service, Gimcheon, Gyeongsangbuk-do, 39660, Republic of Korea
| | - Dong-Geol Lee
- R&I Center, COSMAX BTI, Seongnam, 13486, Republic of Korea
| | - Seunghyun Kang
- R&I Center, COSMAX BTI, Seongnam, 13486, Republic of Korea
| | - Jae-Ho Shin
- Department of Applied Biosciences, Kyungpook National University, Daegu, 41566, Republic of Korea.
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196
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Klamrak A, Nabnueangsap J, Nualkaew N. Biotransformation of Benzoate to 2,4,6-Trihydroxybenzophenone by Engineered Escherichia coli. Molecules 2021; 26:molecules26092779. [PMID: 34066831 PMCID: PMC8125937 DOI: 10.3390/molecules26092779] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2021] [Revised: 05/01/2021] [Accepted: 05/02/2021] [Indexed: 11/16/2022] Open
Abstract
The synthesis of natural products by E. coli is a challenging alternative method of environmentally friendly minimization of hazardous waste. Here, we establish a recombinant E. coli capable of transforming sodium benzoate into 2,4,6-trihydroxybenzophenone (2,4,6-TriHB), the intermediate of benzophenones and xanthones derivatives, based on the coexpression of benzoate-CoA ligase from Rhodopseudomonas palustris (BadA) and benzophenone synthase from Garcinia mangostana (GmBPS). It was found that the engineered E. coli accepted benzoate as the leading substrate for the formation of benzoyl CoA by the function of BadA and subsequently condensed, with the endogenous malonyl CoA by the catalytic function of BPS, into 2,4,6-TriHB. This metabolite was excreted into the culture medium and was detected by the high-resolution LC-ESI-QTOF-MS/MS. The structure was elucidated by in silico tools: Sirius 4.5 combined with CSI FingerID web service. The results suggested the potential of the new artificial pathway in E. coli to successfully catalyze the transformation of sodium benzoate into 2,4,6-TriHB. This system will lead to further syntheses of other benzophenone derivatives via the addition of various genes to catalyze for functional groups.
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Affiliation(s)
- Anuwatchakij Klamrak
- Faculty of Pharmaceutical Sciences, Khon Kaen University, Khon Kaen 40002, Thailand;
| | - Jaran Nabnueangsap
- Salaya Central Instrument Facility RSPG, Mahidol University, Nakhon Pathom 73170, Thailand;
| | - Natsajee Nualkaew
- Faculty of Pharmaceutical Sciences, Khon Kaen University, Khon Kaen 40002, Thailand;
- Correspondence:
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197
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Balachandran C, Vishali A, Nagendran NA, Baskar K, Hashem A, Abd_Allah EF. Optimization of protease production from Bacillus halodurans under solid state fermentation using agrowastes. Saudi J Biol Sci 2021; 28:4263-4269. [PMID: 34354408 PMCID: PMC8324923 DOI: 10.1016/j.sjbs.2021.04.069] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2021] [Revised: 03/08/2021] [Accepted: 04/21/2021] [Indexed: 11/30/2022] Open
Abstract
Marine microbes are potential source for novel metabolites. They are efficient in producing these metabolites utilizing agrowastes. Protease is one of the enzymes which find wide industrial applications. In the present study, protease producing bacteria was isolated from marine sediments and the organism was identified as Bacillus halodurans. The organism was subjected to protease production under solid state fermentation (SSF) using different agrowastes as substrates. Among the substrates used, wheat bran yielded maximum quantity of protease. The fermentation process was carried out under different cultural conditions to optimize the parameters influencing the enzyme production. The results of the stain removal studies by the enzyme revealed the increased efficiency of the microbial enzyme than the commercial detergent.
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Affiliation(s)
- Chellapandian Balachandran
- Department of Biotechnology, Thiagarajar College, Madurai 625 009, Tamil Nadu, India
- National Centre of Excellence (MHRD), Thiagarajar College, Madurai 625 009, Tamil Nadu, India
- Corresponding authors at: Department of Biotechnology, Thiagarajar College, Madurai 625 009, Tamil Nadu, India (Chellapandian Balachandran); Department of Ecotoxicology, Ross Lifescience, Pvt., Ltd., Bhosari, Pune, India (Kathirvelu Baskar).
| | - Alagumalai Vishali
- Department of Biotechnology, Thiagarajar College, Madurai 625 009, Tamil Nadu, India
| | - Natarajan Arun Nagendran
- National Centre of Excellence (MHRD), Thiagarajar College, Madurai 625 009, Tamil Nadu, India
- Department of Zoology, Thiagarajar College, Madurai 625 009, Tamil Nadu, India
| | - Kathirvelu Baskar
- Department of Ecotoxicology, Ross Lifescience, Pvt., Ltd., Bhosari, Pune, India
- Corresponding authors at: Department of Biotechnology, Thiagarajar College, Madurai 625 009, Tamil Nadu, India (Chellapandian Balachandran); Department of Ecotoxicology, Ross Lifescience, Pvt., Ltd., Bhosari, Pune, India (Kathirvelu Baskar).
| | - Abeer Hashem
- Botany and Microbiology Department, College of Science, King Saud University, P.O. Box. 2460, Riyadh 11451, Saudi Arabia
- Mycology and Plant Disease Survey Department, Plant Pathology Research Institute, ARC, Giza 12511, Egypt
| | - Elsayed Fathi Abd_Allah
- Plant Production Department, College of Food and Agricultural Sciences, King Saud University, P.O. Box. 2460, Riyadh 11451, Saudi Arabia
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198
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Bourrain M, Suzuki MT, Calvez A, West NJ, Lions J, Lebaron P. In-depth prospection of Avène Thermal Spring Water reveals an uncommon and stable microbial community. J Eur Acad Dermatol Venereol 2021; 34 Suppl 5:8-14. [PMID: 32870559 DOI: 10.1111/jdv.16599] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2020] [Revised: 04/24/2020] [Accepted: 04/30/2020] [Indexed: 01/04/2023]
Abstract
BACKGROUND Avène Thermal Spring Water (TSW) exhibits therapeutic properties in the treatment of skin pathologies. Arising from a dolomitic aquifer system, its physico-chemical properties are well-established and its bacteriological quality regularly monitored. The microbiota of this aquifer have been characterized. OBJECTIVES We aimed to describe the structure of the bacterial community inhabiting the deep aquifer and to examine its dynamics over time. METHODS The Avène TSW was collected at the catchment point and filtered through 0.1 µm pore size filters. The sampling was carried out every 3 months to generate a 4-year time series. The DNA extracted from filters was analysed using high-throughput 16S rRNA gene amplicon sequencing, and the microorganisms and their contribution were characterized by the taxonomic assignment of sequence variants generated from each sample. RESULTS Bacteria were distributed into 39 phyla. Nitrospirae and Proteobacteria were the most prevalent, accounting for 38% and 23% of the total community on average, respectively. A stable pattern was observed throughout the study. A few bacterial species were always detected, forming a core community of likely chemolithoautotrophic organisms which might use energy sources and nutrients produced from water-bedrock interactions. Most of the species were distantly related to organisms described to date. CONCLUSIONS Avène TSW provided by the deep aquifer system harbours a unique microbial community, shaped by the physico-chemical characteristics of the deep environment. Its remarkable stability over time has revealed a high level of confinement of the water resource.
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Affiliation(s)
- M Bourrain
- Pierre Fabre Dermo-Cosmétique R&D Center, Toulouse, France
| | - M T Suzuki
- Sorbonne Université, CNRS, Laboratoire de Biodiversité et Biotechnologies Microbiennes, LBBM, Observatoire Océanologique, Banyuls-sur-mer, France
| | - A Calvez
- Pierre Fabre Dermo-Cosmétique R&D Center, Toulouse, France
| | - N J West
- Sorbonne Université, CNRS, Observatoire Océanologique de Banyuls, Banyuls-sur-mer, France
| | - J Lions
- Pierre Fabre Dermo-Cosmétique R&D Center, Toulouse, France
| | - P Lebaron
- Sorbonne Université, CNRS, Laboratoire de Biodiversité et Biotechnologies Microbiennes, LBBM, Observatoire Océanologique, Banyuls-sur-mer, France
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199
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Alam K, Hao J, Zhang Y, Li A. Synthetic biology-inspired strategies and tools for engineering of microbial natural product biosynthetic pathways. Biotechnol Adv 2021; 49:107759. [PMID: 33930523 DOI: 10.1016/j.biotechadv.2021.107759] [Citation(s) in RCA: 26] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2020] [Revised: 03/28/2021] [Accepted: 04/23/2021] [Indexed: 02/08/2023]
Abstract
Microbial-derived natural products (NPs) and their derivative products are of great importance and used widely in many fields, especially in pharmaceutical industries. However, there is an immediate need to establish innovative approaches, strategies, and techniques to discover new NPs with novel or enhanced biological properties, due to the less productivity and higher cost on traditional drug discovery pipelines from natural bioresources. Revealing of untapped microbial cryptic biosynthetic gene clusters (BGCs) using DNA sequencing technology and bioinformatics tools makes genome mining possible for NP discovery from microorganisms. Meanwhile, new approaches and strategies in the area of synthetic biology offer great potentials for generation of new NPs by engineering or creating synthetic systems with improved and desired functions. Development of approaches, strategies and tools in synthetic biology can facilitate not only exploration and enhancement in supply, and also in the structural diversification of NPs. Here, we discussed recent advances in synthetic biology-inspired strategies, including bioinformatics and genetic engineering tools and approaches for identification, cloning, editing/refactoring of candidate biosynthetic pathways, construction of heterologous expression hosts, fitness optimization between target pathways and hosts and detection of NP production.
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Affiliation(s)
- Khorshed Alam
- Helmholtz International Lab for Anti-Infectives, Shandong University-Helmholtz Institute of Biotechnology, State Key Laboratory of Microbial Technology, Shandong University, Qingdao 266237, PR China.
| | - Jinfang Hao
- Helmholtz International Lab for Anti-Infectives, Shandong University-Helmholtz Institute of Biotechnology, State Key Laboratory of Microbial Technology, Shandong University, Qingdao 266237, PR China
| | - Youming Zhang
- Helmholtz International Lab for Anti-Infectives, Shandong University-Helmholtz Institute of Biotechnology, State Key Laboratory of Microbial Technology, Shandong University, Qingdao 266237, PR China.
| | - Aiying Li
- Helmholtz International Lab for Anti-Infectives, Shandong University-Helmholtz Institute of Biotechnology, State Key Laboratory of Microbial Technology, Shandong University, Qingdao 266237, PR China.
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200
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Hozzein WN, Mohany M, Alhawsawi SMM, Zaky MY, Al-Rejaie SS, Alkhalifah DHM. Flavonoids from Marine-Derived Actinobacteria as Anticancer Drugs. Curr Pharm Des 2021; 27:505-512. [PMID: 33327903 DOI: 10.2174/1381612826666201216160154] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2020] [Accepted: 10/05/2020] [Indexed: 12/24/2022]
Abstract
Flavonoids represent a large diverse group of natural products that are used as a traditional medicine against various infectious diseases. They possess many biological activities including antimicrobial, antioxidant, anti-inflammatory, anti-cancer and anti-diabetic activities. Commercially, flavonoids are mainly obtained from plants, however, several challenges are faced during their extraction. Microorganisms have been known as natural sources of a wide range of bioactive compounds including flavonoids. Actinobacteria are the most prolific group of microorganisms for the production of bioactive secondary metabolites, thus facilitating the production of flavonoids. The screening programs for bioactive compounds revealed the potential application of actinobacteria to produce flavonoids with interesting biological activities, especially anticancer activities. Since marine actinobacteria are recognized as a potential source of novel anticancer agents, they are highly expected to be potential producers of anticancer flavonoids with unusual structures and properties. In this review, we highlight the production of flavonoids by actinobacteria through classical fermentation, engineering of plant biosynthetic genes in a recombinant actinobacterium and the de novo biosynthesis approach. Through these approaches, we can control and improve the production of interesting flavonoids or their derivatives for the treatment of cancer.
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Affiliation(s)
- Wael N Hozzein
- Bioproducts Research Chair, Zoology Department, College of Science, King Saud University, Riyadh, Saudi Arabia
| | - Mohamed Mohany
- Department of Pharmacology and Toxicology, College of Pharmacy, King Saud University, Riyadh, 11451, Saudi Arabia
| | - Sana M M Alhawsawi
- Bioproducts Research Chair, Zoology Department, College of Science, King Saud University, Riyadh, Saudi Arabia
| | - Mohamed Y Zaky
- Molecular Physiology Division, Zoology Department, Faculty of Science, Beni-Suef University, Beni-Suef, Egypt
| | - Salim S Al-Rejaie
- Department of Pharmacology and Toxicology, College of Pharmacy, King Saud University, Riyadh, 11451, Saudi Arabia
| | - Dalal H M Alkhalifah
- Biology Department, College of Science, Princess Nourah Bint Abdulrahman University, Riyadh, Saudi Arabia
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