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Yi Y, Liang L, de Jong A, Kuipers OP. A systematic comparison of natural product potential, with an emphasis on RiPPs, by mining of bacteria of three large ecosystems. Genomics 2024; 116:110880. [PMID: 38857812 DOI: 10.1016/j.ygeno.2024.110880] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2024] [Revised: 04/22/2024] [Accepted: 06/05/2024] [Indexed: 06/12/2024]
Abstract
The implementation of several global microbiome studies has yielded extensive insights into the biosynthetic potential of natural microbial communities. However, studies on the distribution of several classes of ribosomally synthesized and post-translationally modified peptides (RiPPs), non-ribosomal peptides (NRPs) and polyketides (PKs) in different large microbial ecosystems have been very limited. Here, we collected a large set of metagenome-assembled bacterial genomes from marine, freshwater and terrestrial ecosystems to investigate the biosynthetic potential of these bacteria. We demonstrate the utility of public dataset collections for revealing the different secondary metabolite biosynthetic potentials among these different living environments. We show that there is a higher occurrence of RiPPs in terrestrial systems, while in marine systems, we found relatively more terpene-, NRP-, and PK encoding gene clusters. Among the many new biosynthetic gene clusters (BGCs) identified, we analyzed various Nif-11-like and nitrile hydratase leader peptide (NHLP) containing gene clusters that would merit further study, including promising products, such as mersacidin-, LAP- and proteusin analogs. This research highlights the significance of public datasets in elucidating the biosynthetic potential of microbes in different living environments and underscores the wide bioengineering opportunities within the RiPP family.
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Affiliation(s)
- Yunhai Yi
- Department of Molecular Genetics, University of Groningen, Groningen 9747AG, the Netherlands
| | | | - Anne de Jong
- Department of Molecular Genetics, University of Groningen, Groningen 9747AG, the Netherlands
| | - Oscar P Kuipers
- Department of Molecular Genetics, University of Groningen, Groningen 9747AG, the Netherlands.
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Girão M, Murillo-Alba J, Martín J, Pérez-Victoria I, Leite RB, Urbatzka R, Leão PN, Carvalho MF, Reyes F. Cellulamides: A New Family of Marine-Sourced Linear Peptides from the Underexplored Cellulosimicrobium Genus. Mar Drugs 2024; 22:268. [PMID: 38921579 PMCID: PMC11204466 DOI: 10.3390/md22060268] [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: 05/08/2024] [Revised: 06/04/2024] [Accepted: 06/06/2024] [Indexed: 06/27/2024] Open
Abstract
Bioprospecting the secondary metabolism of underexplored Actinomycetota taxa is a prolific route to uncover novel chemistry. In this work, we report the isolation, structure elucidation, and bioactivity screening of cellulamides A and B (1 and 2), two novel linear peptides obtained from the culture of the macroalga-associated Cellulosimicrobium funkei CT-R177. The host of this microorganism, the Chlorophyta Codium tomentosum, was collected in the northern Portuguese coast and, in the scope of a bioprospecting study focused on its associated actinobacterial community, strain CT-R177 was isolated, taxonomically identified, and screened for the production of antimicrobial and anticancer compounds. Dereplication of a crude extract of this strain using LC-HRMS(/MS) analysis unveiled a putative novel natural product, cellulamide A (1), that was isolated following mass spectrometry-guided fractionation. An additional analog, cellulamide B (2) was obtained during the chromatographic process and chemically characterized. The chemical structures of the novel linear peptides, including their absolute configurations, were elucidated using a combination of HRMS, 1D/2D NMR spectroscopy, and Marfey's analysis. Cellulamide A (1) was subjected to a set of bioactivity screenings, but no significant biological activity was observed. The cellulamides represent the first family of natural products reported from the Actinomycetota genus Cellulosimicrobium, showcasing not only the potential of less-explored taxa but also of host-associated marine strains for novel chemistry discovery.
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Affiliation(s)
- Mariana Girão
- CIIMAR—Interdisciplinary Centre of Marine and Environmental Research, Terminal de Cruzeiros do Porto de Leixões, University of Porto, 4450-208 Matosinhos, Portugal; (R.U.); (P.N.L.); (M.F.C.)
- ICBAS—School of Medicine and Biomedical Sciences, University of Porto, 4050-313 Porto, Portugal
| | - José Murillo-Alba
- Fundación MEDINA, Centro de Excelencia en Investigación de Medicamentos Innovadores en Andalucía, Parque Tecnológico de Ciencias de la Salud, 18016 Armilla, Spain; (J.M.-A.); (J.M.); (I.P.-V.)
| | - Jesús Martín
- Fundación MEDINA, Centro de Excelencia en Investigación de Medicamentos Innovadores en Andalucía, Parque Tecnológico de Ciencias de la Salud, 18016 Armilla, Spain; (J.M.-A.); (J.M.); (I.P.-V.)
| | - Ignacio Pérez-Victoria
- Fundación MEDINA, Centro de Excelencia en Investigación de Medicamentos Innovadores en Andalucía, Parque Tecnológico de Ciencias de la Salud, 18016 Armilla, Spain; (J.M.-A.); (J.M.); (I.P.-V.)
| | - Ricardo B. Leite
- Genomics Unit, Instituto Gulbenkian de Ciência, 2780-156 Oeiras, Portugal;
| | - Ralph Urbatzka
- CIIMAR—Interdisciplinary Centre of Marine and Environmental Research, Terminal de Cruzeiros do Porto de Leixões, University of Porto, 4450-208 Matosinhos, Portugal; (R.U.); (P.N.L.); (M.F.C.)
| | - Pedro N. Leão
- CIIMAR—Interdisciplinary Centre of Marine and Environmental Research, Terminal de Cruzeiros do Porto de Leixões, University of Porto, 4450-208 Matosinhos, Portugal; (R.U.); (P.N.L.); (M.F.C.)
| | - Maria F. Carvalho
- CIIMAR—Interdisciplinary Centre of Marine and Environmental Research, Terminal de Cruzeiros do Porto de Leixões, University of Porto, 4450-208 Matosinhos, Portugal; (R.U.); (P.N.L.); (M.F.C.)
- ICBAS—School of Medicine and Biomedical Sciences, University of Porto, 4050-313 Porto, Portugal
| | - Fernando Reyes
- Fundación MEDINA, Centro de Excelencia en Investigación de Medicamentos Innovadores en Andalucía, Parque Tecnológico de Ciencias de la Salud, 18016 Armilla, Spain; (J.M.-A.); (J.M.); (I.P.-V.)
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Cumsille A, Serna-Cardona N, González V, Claverías F, Undabarrena A, Molina V, Salvà-Serra F, Moore ERB, Cámara B. Exploring the biosynthetic gene clusters in Brevibacterium: a comparative genomic analysis of diversity and distribution. BMC Genomics 2023; 24:622. [PMID: 37858045 PMCID: PMC10588199 DOI: 10.1186/s12864-023-09694-7] [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: 06/11/2023] [Accepted: 09/21/2023] [Indexed: 10/21/2023] Open
Abstract
Exploring Brevibacterium strains from various ecosystems may lead to the discovery of new antibiotic-producing strains. Brevibacterium sp. H-BE7, a strain isolated from marine sediments from Northern Patagonia, Chile, had its genome sequenced to study the biosynthetic potential to produce novel natural products within the Brevibacterium genus. The genome sequences of 98 Brevibacterium strains, including strain H-BE7, were selected for a genomic analysis. A phylogenomic cladogram was generated, which divided the Brevibacterium strains into four major clades. A total of 25 strains are potentially unique new species according to Average Nucleotide Identity (ANIb) values. These strains were isolated from various environments, emphasizing the importance of exploring diverse ecosystems to discover the full diversity of Brevibacterium. Pangenome analysis of Brevibacterium strains revealed that only 2.5% of gene clusters are included within the core genome, and most gene clusters occur either as singletons or as cloud genes present in less than ten strains. Brevibacterium strains from various phylogenomic clades exhibit diverse BGCs. Specific groups of BGCs show clade-specific distribution patterns, such as siderophore BGCs and carotenoid-related BGCs. A group of clade IV-A Brevibacterium strains possess a clade-specific Polyketide synthase (PKS) BGCs that connects with phenazine-related BGCs. Within the PKS BGC, five genes, including the biosynthetic PKS gene, participate in the mevalonate pathway and exhibit similarities with the phenazine A BGC. However, additional core biosynthetic phenazine genes were exclusively discovered in nine Brevibacterium strains, primarily isolated from cheese. Evaluating the antibacterial activity of strain H-BE7, it exhibited antimicrobial activity against Salmonella enterica and Listeria monocytogenes. Chemical dereplication identified bioactive compounds, such as 1-methoxyphenazine in the crude extracts of strain H-BE7, which could be responsible of the observed antibacterial activity. While strain H-BE7 lacks the core phenazine biosynthetic genes, it produces 1-methoxyphenazine, indicating the presence of an unknown biosynthetic pathway for this compound. This suggests the existence of alternative biosynthetic pathways or promiscuous enzymes within H-BE7's genome.
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Affiliation(s)
- Andrés Cumsille
- Centro de Biotecnología DAL, Universidad Técnica Federico Santa María, Valparaíso, Chile
| | - Néstor Serna-Cardona
- Centro de Biotecnología DAL, Universidad Técnica Federico Santa María, Valparaíso, Chile
| | - Valentina González
- Centro de Biotecnología DAL, Universidad Técnica Federico Santa María, Valparaíso, Chile
| | - Fernanda Claverías
- Centro de Biotecnología DAL, Universidad Técnica Federico Santa María, Valparaíso, Chile
| | - Agustina Undabarrena
- Centro de Biotecnología DAL, Universidad Técnica Federico Santa María, Valparaíso, Chile
| | - Vania Molina
- Centro de Biotecnología DAL, Universidad Técnica Federico Santa María, Valparaíso, Chile
| | - Francisco Salvà-Serra
- Department of Infectious Diseases, Institute for Biomedicine, Sahlgrenska Academy, University of Gothenburg, Gothenburg, Sweden
- Department of Clinical Microbiology, Region Västra Götaland and Sahlgrenska Academy, Culture Collection University of Gothenburg (CCUG), Sahlgrenska University Hospital, University of Gothenburg, Gothenburg, Sweden
- Centre for Antibiotic Resistance Research (CARe), University of Gothenburg, Gothenburg, Sweden
| | - Edward R B Moore
- Department of Infectious Diseases, Institute for Biomedicine, Sahlgrenska Academy, University of Gothenburg, Gothenburg, Sweden
- Department of Clinical Microbiology, Region Västra Götaland and Sahlgrenska Academy, Culture Collection University of Gothenburg (CCUG), Sahlgrenska University Hospital, University of Gothenburg, Gothenburg, Sweden
- Microbiology, Department of Biology, University of the Balearic Islands, Palma de Mallorca, Spain
| | - Beatriz Cámara
- Centro de Biotecnología DAL, Universidad Técnica Federico Santa María, Valparaíso, Chile.
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Gao S, Jiang X, Wang L, Jiang S, Luo H, Chen Y, Peng C. The pathogenesis of liver cancer and the therapeutic potential of bioactive substances. Front Pharmacol 2022; 13:1029601. [PMID: 36278230 PMCID: PMC9581229 DOI: 10.3389/fphar.2022.1029601] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2022] [Accepted: 09/20/2022] [Indexed: 11/13/2022] Open
Abstract
Liver cancer is the third most common cause of cancer-related deaths in the world and has become an urgent problem for global public health. Bioactive substances are widely used for the treatment of liver cancer due to their widespread availability and reduced side effects. This review summarizes the main pathogenic factors involved in the development of liver cancer, including metabolic fatty liver disease, viral infection, and alcoholic cirrhosis, and focuses on the mechanism of action of bioactive components such as polysaccharides, alkaloids, phenols, peptides, and active bacteria/fungi. In addition, we also summarize transformation methods, combined therapy and modification of bioactive substances to improve the treatment efficiency against liver cancer, highlighting new ideas in this field.
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Affiliation(s)
- Song Gao
- State Key Laboratory of Southwestern Chinese Medicine Resources, Chengdu, China
- School of Public Health, Chengdu University of Traditional Chinese Medicine, Chengdu, China
| | - Xingyue Jiang
- School of Public Health, Chengdu University of Traditional Chinese Medicine, Chengdu, China
| | - Liang Wang
- School of Public Health, Chengdu University of Traditional Chinese Medicine, Chengdu, China
| | - Shanshan Jiang
- School of Public Health, Chengdu University of Traditional Chinese Medicine, Chengdu, China
| | - Hanyuan Luo
- School of Public Health, Chengdu University of Traditional Chinese Medicine, Chengdu, China
| | - Yan Chen
- State Key Laboratory of Southwestern Chinese Medicine Resources, Chengdu, China
- School of Public Health, Chengdu University of Traditional Chinese Medicine, Chengdu, China
- College of Pharmacy, Chengdu University of Traditional Chinese Medicine, Chengdu, China
- *Correspondence: Yan Chen, ; Cheng Peng,
| | - Cheng Peng
- State Key Laboratory of Southwestern Chinese Medicine Resources, Chengdu, China
- College of Pharmacy, Chengdu University of Traditional Chinese Medicine, Chengdu, China
- *Correspondence: Yan Chen, ; Cheng Peng,
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