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Uncovering Lasonolide A Biosynthesis Using Genome-Resolved Metagenomics
Invertebrates, particularly sponges, have been a dominant source of new marine natural products. For example, lasonolide A (LSA) is a potential anticancer molecule isolated from the marine sponge Forcepia sp., with nanomolar growth inhibitory activity and a unique cytotoxicity profile against the Na...
Autores principales: | , , , , , , |
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Formato: | Online Artículo Texto |
Lenguaje: | English |
Publicado: |
American Society for Microbiology
2022
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Materias: | |
Acceso en línea: | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9600693/ https://www.ncbi.nlm.nih.gov/pubmed/36125273 http://dx.doi.org/10.1128/mbio.01524-22 |
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author | Uppal, Siddharth Metz, Jackie L. Xavier, René K. M. Nepal, Keshav Kumar Xu, Dongbo Wang, Guojun Kwan, Jason C. |
author_facet | Uppal, Siddharth Metz, Jackie L. Xavier, René K. M. Nepal, Keshav Kumar Xu, Dongbo Wang, Guojun Kwan, Jason C. |
author_sort | Uppal, Siddharth |
collection | PubMed |
description | Invertebrates, particularly sponges, have been a dominant source of new marine natural products. For example, lasonolide A (LSA) is a potential anticancer molecule isolated from the marine sponge Forcepia sp., with nanomolar growth inhibitory activity and a unique cytotoxicity profile against the National Cancer Institute 60-cell-line screen. Here, we identified the putative biosynthetic pathway for LSA. Genomic binning of the Forcepia sponge metagenome revealed a Gram-negative bacterium belonging to the phylum Verrucomicrobia as the candidate producer of LSA. Phylogenetic analysis showed that this bacterium, here named “Candidatus Thermopylae lasonolidus,” only has 88.78% 16S rRNA identity with the closest relative, Pedosphaera parvula Ellin514, indicating that it represents a new genus. The lasonolide A (las) biosynthetic gene cluster (BGC) was identified as a trans-acyltransferase (AT) polyketide synthase (PKS) pathway. Compared with its host genome, the las BGC exhibits a significantly different GC content and pentanucleotide frequency, suggesting a potential horizontal acquisition of the gene cluster. Furthermore, three copies of the putative las pathway were identified in the candidate producer genome. Differences between the three las repeats were observed, including the presence of three insertions, two single-nucleotide polymorphisms, and the absence of a stand-alone acyl carrier protein in one of the repeats. Even though the verrucomicrobial producer shows signs of genome reduction, its genome size is still fairly large (about 5 Mbp), and, compared to its closest free-living relative, it contains most of the primary metabolic pathways, suggesting that it is in the early stages of reduction. |
format | Online Article Text |
id | pubmed-9600693 |
institution | National Center for Biotechnology Information |
language | English |
publishDate | 2022 |
publisher | American Society for Microbiology |
record_format | MEDLINE/PubMed |
spelling | pubmed-96006932022-10-27 Uncovering Lasonolide A Biosynthesis Using Genome-Resolved Metagenomics Uppal, Siddharth Metz, Jackie L. Xavier, René K. M. Nepal, Keshav Kumar Xu, Dongbo Wang, Guojun Kwan, Jason C. mBio Research Article Invertebrates, particularly sponges, have been a dominant source of new marine natural products. For example, lasonolide A (LSA) is a potential anticancer molecule isolated from the marine sponge Forcepia sp., with nanomolar growth inhibitory activity and a unique cytotoxicity profile against the National Cancer Institute 60-cell-line screen. Here, we identified the putative biosynthetic pathway for LSA. Genomic binning of the Forcepia sponge metagenome revealed a Gram-negative bacterium belonging to the phylum Verrucomicrobia as the candidate producer of LSA. Phylogenetic analysis showed that this bacterium, here named “Candidatus Thermopylae lasonolidus,” only has 88.78% 16S rRNA identity with the closest relative, Pedosphaera parvula Ellin514, indicating that it represents a new genus. The lasonolide A (las) biosynthetic gene cluster (BGC) was identified as a trans-acyltransferase (AT) polyketide synthase (PKS) pathway. Compared with its host genome, the las BGC exhibits a significantly different GC content and pentanucleotide frequency, suggesting a potential horizontal acquisition of the gene cluster. Furthermore, three copies of the putative las pathway were identified in the candidate producer genome. Differences between the three las repeats were observed, including the presence of three insertions, two single-nucleotide polymorphisms, and the absence of a stand-alone acyl carrier protein in one of the repeats. Even though the verrucomicrobial producer shows signs of genome reduction, its genome size is still fairly large (about 5 Mbp), and, compared to its closest free-living relative, it contains most of the primary metabolic pathways, suggesting that it is in the early stages of reduction. American Society for Microbiology 2022-09-20 /pmc/articles/PMC9600693/ /pubmed/36125273 http://dx.doi.org/10.1128/mbio.01524-22 Text en Copyright © 2022 Uppal et al. https://creativecommons.org/licenses/by/4.0/This is an open-access article distributed under the terms of the Creative Commons Attribution 4.0 International license (https://creativecommons.org/licenses/by/4.0/) . |
spellingShingle | Research Article Uppal, Siddharth Metz, Jackie L. Xavier, René K. M. Nepal, Keshav Kumar Xu, Dongbo Wang, Guojun Kwan, Jason C. Uncovering Lasonolide A Biosynthesis Using Genome-Resolved Metagenomics |
title | Uncovering Lasonolide A Biosynthesis Using Genome-Resolved Metagenomics |
title_full | Uncovering Lasonolide A Biosynthesis Using Genome-Resolved Metagenomics |
title_fullStr | Uncovering Lasonolide A Biosynthesis Using Genome-Resolved Metagenomics |
title_full_unstemmed | Uncovering Lasonolide A Biosynthesis Using Genome-Resolved Metagenomics |
title_short | Uncovering Lasonolide A Biosynthesis Using Genome-Resolved Metagenomics |
title_sort | uncovering lasonolide a biosynthesis using genome-resolved metagenomics |
topic | Research Article |
url | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9600693/ https://www.ncbi.nlm.nih.gov/pubmed/36125273 http://dx.doi.org/10.1128/mbio.01524-22 |
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