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National Committee on Marine Sciences (NCMS)

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Author: search.filters.author.Salvador-Reyes, LilibethSDG: search.filters.sdg.SDG 14 - Life below water

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    Genome mining of a novel marine sponge symbiont Nocardia sp. BML-15-R-026U reveals high biosynthetic potential for secondary metabolites, including a non-ribosomal peptide and a polyketide of high novelty
    Gloria, Paul Christian; Romines, Elaine; Punzalan, Marc Jeremie; Florece, Christine Marie; Cadorna, Kreighton; Salvador-Reyes, Lilibeth; Lluisma, Arturo (Philippine-American Academy of Science and Engineering, 2023-11-28)
    Antibiotic and drug resistance poses serious global public health threats, leading to substantial infections and fatalities annually. Addressing these issues requires the discovery of novel bioactive compounds and a faster and more cost-effective discovery process. However, traditional approaches, which require isolation and multi-step purification of compounds from organisms and running of initial assays, suffer from serious limitations such as the need for substantial amounts of biological material and high rates of compound rediscoveries. Because the biosynthetic capabilities of organisms are encoded in their genomes, genome mining provides a promising solution that would complement traditional approaches. This study conducted long-read whole genome sequencing on a marine sponge symbiont, Nocardia sp. BML-15-R-026U, to explore its genomic repertoire of secondary metabolite-encoding Biosynthetic Gene Clusters (BGCs). A four-contig genome assembly was generated for this isolate with a high degree of completeness and an estimated genome size of 4.84 Mbp. Its genome displays remarkable biosynthetic potential by containing at least 34 distinct secondary metabolite BGCs, predominantly Non-Ribosomal Peptide Synthetase (NRPS) and Polyketide Synthase (PKS) systems capable of producing novel chemical structures. Further analysis was focused on two genomic regions. In region 3.10, the study predicted a BGC for a novel, serine-rich non-ribosomal peptide with a predicted molecular weight of 2754 g/mol. Region 3.12 contained an iterative type-I PKS BGC, suggesting the potential synthesis of a polyketide compound with oxidoreductase-inhibiting properties. This study highlights genome mining as a productive early-phase approach for identifying promising drug leads and has identified the most promising candidates among this isolate’s BGCs for experimental validation.
    The study was funded by the Philippine Council for Health Research and Development – Department of Science and Technology under the “Anti-infective and Anticancer Drug Candidates from Marine Microorganisms and Sponges: Discovery and Development” project, Marine Science Institute – UP Diliman. The authors would like to thank the researchers of the Marine Genomics and Molecular Genetics Laboratory, MSI. The authors would also like to thank the researchers of the Discovery and Development of Health Products – Marine Component Phase I and researchers of the Marine Pharmacognosy Laboratory for the collection and initial analysis of the sample used in this study and storage and maintenance of the bacterial cultures. Sample collection was done under Gratuitous Permit No. GP-0084-15.
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    Genistein and daidzein from a sponge-associated fungus (Family: Microstromataceae) show dose and incubation time-dependent Ca2+ influx activity variation
    Azcuna, Miguel Enrique Ma.; Acyatan, Zildjian; Manzano, Geminne; Yu, Clairecynth; Aliño, Porfirio Alexander M.; Altamia, Marvin; Salvador-Reyes, Lilibeth; Concepcion, Gisela P. (Philippine Association for the Advancement of Science and Technology, 2023-10-31)
    The compounds genistein and daidzein were obtained from the broth culture of a fungus isolated from the Philippine blue sponge Xestospongia sp. Genomic sequencing (18S rRNA) resulted in no exact hits and low sequence similarity (91%) to two species of fungi under the family Microstromataceae: Sympodiomycopsis vantaiensis and Microstromatales sp. Genistein has gained attention in recent years because of its potential to delay the onset of Alzheimer’s disease. This is the first report of genistein and daidzein isolated from a marine-derived fungus. Genistein and daidzein have a wide range of biological activities (e.g., neuroprotective, antimicrobial, anticancer), and this study reports a variation in intracellular [Ca2+] levels in dorsal root ganglion cells (DRGs) post-administration depending on dose and incubation time. An incubation time of 10 min resulted in a block effect, which was evidenced by decreased intracellular [Ca2+] levels. A dose-response was observed as the intensity of intracellular [Ca2+] decreased further at a higher dose. Conversely, an incubation time of 5 min resulted in an increase effect which was evidenced by decreased intracellular [Ca2+] levels. The similarity of these compounds with potent estrogens indicates that estrogen-mediated receptor signaling is the mechanism of action for the increase effect. The block effect, however, could be caused by a variety of factors, such as neurotoxicity or an ER stress response that results in the release of pro- and anti-apoptotic proteins. These findings confirm the ability of genistein to regulate [Ca2+] influx and the expression of apoptosis-related proteins. Further studies should investigate these mechanisms to understand the neuroprotective activities of genistein and daidzein.
    We thank the Drug Discovery and Health Products (DDHP) – Marine Component Project 1 for providing the sponge sample for fungal isolation. We thank Dr. Eizadora Yu of the Institute of Chemistry, University of the Philippines Diliman for providing fungal primers for DNA extraction and obtaining DNA sequences from the fungal sample.