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Pinto-Almeida A, Bauermeister A, Luppino L, Grilo IR, Oliveira J, Sousa JR, Petras D, Rodrigues CF, Prieto-Davó A, Tasdemir D, Sobral RG, Gaudêncio SP. The Diversity, Metabolomics Profiling, and the Pharmacological Potential of Actinomycetes Isolated from the Estremadura Spur Pockmarks (Portugal). Mar Drugs 2021; 20:21. [PMID: 35049876 PMCID: PMC8780274 DOI: 10.3390/md20010021] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2021] [Revised: 12/05/2021] [Accepted: 12/14/2021] [Indexed: 01/24/2023] Open
Abstract
The Estremadura Spur pockmarks are a unique and unexplored ecosystem located in the North Atlantic, off the coast of Portugal. A total of 85 marine-derived actinomycetes were isolated and cultured from sediments collected from this ecosystem at a depth of 200 to 350 m. Nine genera, Streptomyces, Micromonospora, Saccharopolyspora, Actinomadura, Actinopolymorpha, Nocardiopsis, Saccharomonospora, Stackebrandtia, and Verrucosispora were identified by 16S rRNA gene sequencing analyses, from which the first two were the most predominant. Non-targeted LC-MS/MS, in combination with molecular networking, revealed high metabolite diversity, including several known metabolites, such as surugamide, antimycin, etamycin, physostigmine, desferrioxamine, ikarugamycin, piericidine, and rakicidin derivatives, as well as numerous unidentified metabolites. Taxonomy was the strongest parameter influencing the metabolite production, highlighting the different biosynthetic potentials of phylogenetically related actinomycetes; the majority of the chemical classes can be used as chemotaxonomic markers, as the metabolite distribution was mostly genera-specific. The EtOAc extracts of the actinomycete isolates demonstrated antimicrobial and antioxidant activity. Altogether, this study demonstrates that the Estremadura Spur is a source of actinomycetes with potential applications for biotechnology. It highlights the importance of investigating actinomycetes from unique ecosystems, such as pockmarks, as the metabolite production reflects their adaptation to this habitat.
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Affiliation(s)
- António Pinto-Almeida
- Associate Laboratory i4HB—Institute for Health and Bioeconomy, NOVA School of Science and Technology, NOVA University Lisbon, 2819-516 Caparica, Portugal; (A.P.-A.); (L.L.); (I.R.G.); (J.O.); (J.R.S.); (R.G.S.)
- UCIBIO—Applied Molecular Biosciences Unit, NOVA School of Science and Technology, NOVA University of Lisbon, 2819-516 Caparica, Portugal
- Instituto de Engenharias e Ciências do Mar, Universidade Técnica do Atlântico, 163 Ribeira de Julião, 163 Mindelo, Cape Verde
| | - Anelize Bauermeister
- Skaggs School of Pharmacy & Pharmaceutical Science, University of California San Diego, La Jolla, CA 92093-075, USA;
| | - Luca Luppino
- Associate Laboratory i4HB—Institute for Health and Bioeconomy, NOVA School of Science and Technology, NOVA University Lisbon, 2819-516 Caparica, Portugal; (A.P.-A.); (L.L.); (I.R.G.); (J.O.); (J.R.S.); (R.G.S.)
- UCIBIO—Applied Molecular Biosciences Unit, NOVA School of Science and Technology, NOVA University of Lisbon, 2819-516 Caparica, Portugal
- Dipartimento di Scienze Della Vita, Università Degli Studi di Modena e Reggio Emilia, 41125 Modena, Italy
| | - Inês R. Grilo
- Associate Laboratory i4HB—Institute for Health and Bioeconomy, NOVA School of Science and Technology, NOVA University Lisbon, 2819-516 Caparica, Portugal; (A.P.-A.); (L.L.); (I.R.G.); (J.O.); (J.R.S.); (R.G.S.)
- UCIBIO—Applied Molecular Biosciences Unit, NOVA School of Science and Technology, NOVA University of Lisbon, 2819-516 Caparica, Portugal
| | - Juliana Oliveira
- Associate Laboratory i4HB—Institute for Health and Bioeconomy, NOVA School of Science and Technology, NOVA University Lisbon, 2819-516 Caparica, Portugal; (A.P.-A.); (L.L.); (I.R.G.); (J.O.); (J.R.S.); (R.G.S.)
- UCIBIO—Applied Molecular Biosciences Unit, NOVA School of Science and Technology, NOVA University of Lisbon, 2819-516 Caparica, Portugal
| | - Joana R. Sousa
- Associate Laboratory i4HB—Institute for Health and Bioeconomy, NOVA School of Science and Technology, NOVA University Lisbon, 2819-516 Caparica, Portugal; (A.P.-A.); (L.L.); (I.R.G.); (J.O.); (J.R.S.); (R.G.S.)
- UCIBIO—Applied Molecular Biosciences Unit, NOVA School of Science and Technology, NOVA University of Lisbon, 2819-516 Caparica, Portugal
| | - Daniel Petras
- CMFI Cluster of Excellence, Interfaculty Institute of Microbiology and Medicine, University of Tuebingen, Auf der Morgenstelle 24, 72076 Tuebingen, Germany;
| | - Clara F. Rodrigues
- CESAM—Centre for Environmental and Marine Studies, Department of Biology, University of Aveiro, 3810-193 Aveiro, Portugal;
| | - Alejandra Prieto-Davó
- Unidad de Química-Sisal, Facultad de Química, Universidad Nacional Autónoma de México, Sisal 97356, Mexico;
| | - Deniz Tasdemir
- GEOMAR Centre for Marine Biotechnology, Research Unit Marine Natural Products Chemistry, GEOMAR Helmholtz Centre for Ocean Research Kiel, 24106 Kiel, Germany;
- Faculty of Mathematics and Natural Sciences, Kiel University, Christian-Albrechts-Platz 4, 24118 Kiel, Germany
| | - Rita G. Sobral
- Associate Laboratory i4HB—Institute for Health and Bioeconomy, NOVA School of Science and Technology, NOVA University Lisbon, 2819-516 Caparica, Portugal; (A.P.-A.); (L.L.); (I.R.G.); (J.O.); (J.R.S.); (R.G.S.)
- UCIBIO—Applied Molecular Biosciences Unit, NOVA School of Science and Technology, NOVA University of Lisbon, 2819-516 Caparica, Portugal
| | - Susana P. Gaudêncio
- Associate Laboratory i4HB—Institute for Health and Bioeconomy, NOVA School of Science and Technology, NOVA University Lisbon, 2819-516 Caparica, Portugal; (A.P.-A.); (L.L.); (I.R.G.); (J.O.); (J.R.S.); (R.G.S.)
- UCIBIO—Applied Molecular Biosciences Unit, NOVA School of Science and Technology, NOVA University of Lisbon, 2819-516 Caparica, Portugal
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Comparative study of protease hydrolysis reaction demonstrating Normalized Peptide Bond Cleavage Frequency and Protease Substrate Broadness Index. PLoS One 2020; 15:e0239080. [PMID: 32956384 PMCID: PMC7505449 DOI: 10.1371/journal.pone.0239080] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2020] [Accepted: 08/28/2020] [Indexed: 01/01/2023] Open
Abstract
Two commercial proteases (subtilisin-typed FNA from Bacillus amyloliquefaciens, and chymotrypsin-like NPP from Nocardiopsis prasina), porcine pepsin, porcine pancreatin having protease activity and their combinations were studied in vitro by LC-MS for their ability to digest soy protein isolate (SPI) under conditions close to those found in the stomach (pH 3.7) and small intestine (pH 6.5). The total number of peptides generated, and their size distribution were obtained under each set of the digestion conditions. These peptides were grouped according to their C-terminal amino acid (AA) residue (P1) and mass, based on which two concepts were proposed, i.e., Normalized Peptide Bond Cleavage Frequency (NPBCF) and Protease Substrate Broadness Index (PSBI). At pH 3.7, FNA+pepsin increased PSBI vs. pepsin alone by 2.7 and 4.9 percentage points (p.p.) at a SPI:protease ratio of 20:1 and 100:1, respectively. At pH 6.5, FNA+pancreatin improved PSBI by 9.1 and 10.2 p.p. at SPI:protease 20:1 and 100:1, respectively, vs. pancreatin alone. NPP generated 38% more peptides than FNA when administered with pancreatin at SPI:protease 200:1:1 and pH 6.5, but FNA alone (28.9) or FNA+pancreatin (29.1) gave a higher PSBI than pancreatin (22.2), NPP (20.3) and NPP+pancreatin (22.0). At pH 3.7 FNA generated 59% and 39% of peptides of pepsin at SPI:protease of 20:1 and 100:1, respectively, and both groups of peptides had similar size distribution. At pH 6.5 more small sized peptides were generated by FNA or FNA+pancreatin than pancreatin and NPP alone or pancreatin+NPP. In conclusion, FNA showed complementary effects with pepsin and pancreatin in terms of PSBI and generated more small sized peptides compared to NPP.
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Bennur T, Kumar AR, Zinjarde S, Javdekar V. Nocardiopsis species: Incidence, ecological roles and adaptations. Microbiol Res 2015; 174:33-47. [PMID: 25946327 DOI: 10.1016/j.micres.2015.03.010] [Citation(s) in RCA: 69] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2014] [Revised: 03/13/2015] [Accepted: 03/16/2015] [Indexed: 12/23/2022]
Abstract
Members of the genus Nocardiopsis are ecologically versatile and biotechnologically important. They produce a variety of bioactive compounds such as antimicrobial agents, anticancer substances, tumor inducers, toxins and immunomodulators. They also secrete novel extracellular enzymes such as amylases, chitinases, cellulases, β-glucanases, inulinases, xylanases and proteases. Nocardiopsis species are aerobic, Gram-positive, non-acid-fast, catalase-positive actinomycetes with nocardioform substrate mycelia and their aerial mycelia bear long chains of spores. Their DNA possesses high contents of guanine and cytosine. There is a marked variation in properties of the isolates obtained from different ecological niches and their products. An important feature of several species is their halophilic or halotolerant nature. They are associated with a variety of marine and terrestrial biological forms wherein they produce antibiotics and toxins that help their hosts in evading pathogens and predators. Two Nocardiopsis species, namely, N. dassonvillei and N. synnemataformans (among the thirty nine reported ones) are opportunistic human pathogens and cause mycetoma, suppurative infections and abscesses. Nocardiopsis species are present in some plants (as endophytes or surface microflora) and their rhizospheres. Here, they are reported to produce enzymes such as α-amylases and antifungal agents that are effective in warding-off plant pathogens. They are prevalent as free-living entities in terrestrial locales, indoor locations, marine ecosystems and hypersaline habitats on account of their salt-, alkali- and desiccation-resistant behavior. In such natural locations, Nocardiopsis species mainly help in recycling organic compounds. Survival under these diverse conditions is mediated by the production of extracellular enzymes, antibiotics, surfactants, and the accumulation of compatible solutes. The accommodative genomic features of Nocardiopsis species support their existence under the diverse conditions where they prevail.
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Affiliation(s)
- Tahsin Bennur
- Institute of Bioinformatics and Biotechnology, Savitribai Phule Pune University, Pune 411007, India
| | - Ameeta Ravi Kumar
- Institute of Bioinformatics and Biotechnology, Savitribai Phule Pune University, Pune 411007, India
| | - Smita Zinjarde
- Institute of Bioinformatics and Biotechnology, Savitribai Phule Pune University, Pune 411007, India.
| | - Vaishali Javdekar
- Department of Biotechnology, Abasaheb Garware College, Pune 411004, India.
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Bennur T, Kumar AR, Zinjarde S, Javdekar V. Nocardiopsis species as potential sources of diverse and novel extracellular enzymes. Appl Microbiol Biotechnol 2014; 98:9173-85. [PMID: 25269602 DOI: 10.1007/s00253-014-6111-y] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2014] [Revised: 09/18/2014] [Accepted: 09/19/2014] [Indexed: 01/10/2023]
Abstract
Members of the genus Nocardiopsis are generally encountered in locations that are inherently extreme. They are present in frozen soils, desert sand, compost, saline or hypersaline habitats (marine systems, salterns and soils) and alkaline places (slag dumps, lake soils and sediments). In order to survive under these severe conditions, they produce novel and diverse enzymes that allow them to utilize the available nutrients and to thrive. The members of this genus are multifaceted and release an assortment of extracellular hydrolytic enzymes. They produce enzymes that are cold-adapted (α-amylases), thermotolerant (α-amylases and xylanases), thermoalkalotolerant (cellulases, β-1,3-glucanases), alkali-tolerant thermostable (inulinases), acid-stable (keratinase) and alkalophilic (serine proteases). Some of the enzymes derived from Nocardiopsis species act on insoluble polymers such as glucans (pachyman and curdlan), keratin (feathers and prion proteins) and polyhydroxyalkanoates. Extreme tolerance exhibited by proteases has been attributed to the presence of some amino acids (Asn and Pro) in loop structures, relocation of multiple salt bridges to outer regions of the protein or the presence of a distinct polyproline II helix. The range of novel enzymes is projected to increase in the forthcoming years, as new isolates are being continually reported, and the development of processes involving such enzymes is envisaged in the future.
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Affiliation(s)
- Tahsin Bennur
- Institute of Bioinformatics and Biotechnology, University of Pune, Pune, 411007, India
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