Global Genome Mining Reveals the Distribution of Diverse Thioamidated RiPP Biosynthesis Gene Clusters
Thioamidated ribosomally synthesized and post-translationally modified peptides (RiPPs) are recently characterized natural products with wide range of potent bioactivities, such as antibiotic, antiproliferative, and cytotoxic activities. These peptides are distinguished by the presence of thioamide...
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| Format: | Article |
| Language: | English |
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Frontiers Media S.A.
2021-04-01
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| Series: | Frontiers in Microbiology |
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| Online Access: | https://www.frontiersin.org/articles/10.3389/fmicb.2021.635389/full |
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| author | Jessie James Limlingan Malit Chuanhai Wu Ling-Li Liu Ling-Li Liu Pei-Yuan Qian |
| author_facet | Jessie James Limlingan Malit Chuanhai Wu Ling-Li Liu Ling-Li Liu Pei-Yuan Qian |
| author_sort | Jessie James Limlingan Malit |
| collection | DOAJ |
| description | Thioamidated ribosomally synthesized and post-translationally modified peptides (RiPPs) are recently characterized natural products with wide range of potent bioactivities, such as antibiotic, antiproliferative, and cytotoxic activities. These peptides are distinguished by the presence of thioamide bonds in the peptide backbone catalyzed by the YcaO-TfuA protein pair with its genes adjacent to each other. Genome mining has facilitated an in silico approach to identify biosynthesis gene clusters (BGCs) responsible for thioamidated RiPP production. In this work, publicly available genomic data was used to detect and illustrate the diversity of putative BGCs encoding for thioamidated RiPPs. AntiSMASH and RiPPER analysis identified 613 unique TfuA-related gene cluster families (GCFs) and 797 precursor peptide families, even on phyla where the presence of these clusters have not been previously described. Several additional biosynthesis genes are colocalized with the detected BGCs, suggesting an array of possible chemical modifications. This study shows that thioamidated RiPPs occupy a widely unexplored chemical landscape. |
| first_indexed | 2024-12-21T10:17:44Z |
| format | Article |
| id | doaj.art-f8966a3a3bbb417e9df46ce38be1af6f |
| institution | Directory Open Access Journal |
| issn | 1664-302X |
| language | English |
| last_indexed | 2024-12-21T10:17:44Z |
| publishDate | 2021-04-01 |
| publisher | Frontiers Media S.A. |
| record_format | Article |
| series | Frontiers in Microbiology |
| spelling | doaj.art-f8966a3a3bbb417e9df46ce38be1af6f2022-12-21T19:07:32ZengFrontiers Media S.A.Frontiers in Microbiology1664-302X2021-04-011210.3389/fmicb.2021.635389635389Global Genome Mining Reveals the Distribution of Diverse Thioamidated RiPP Biosynthesis Gene ClustersJessie James Limlingan Malit0Chuanhai Wu1Ling-Li Liu2Ling-Li Liu3Pei-Yuan Qian4Department of Ocean Science and Hong Kong Branch of Southern Marine Science and Engineering Guangdong Laboratory, The Hong Kong University of Science and Technology, Hong Kong, ChinaDepartment of Ocean Science and Hong Kong Branch of Southern Marine Science and Engineering Guangdong Laboratory, The Hong Kong University of Science and Technology, Hong Kong, ChinaDepartment of Ocean Science and Hong Kong Branch of Southern Marine Science and Engineering Guangdong Laboratory, The Hong Kong University of Science and Technology, Hong Kong, ChinaShaanxi Key Laboratory of Natural Products and Chemical Biology, College of Chemistry and Pharmacy, Northwest A&F University, Yangling, ChinaDepartment of Ocean Science and Hong Kong Branch of Southern Marine Science and Engineering Guangdong Laboratory, The Hong Kong University of Science and Technology, Hong Kong, ChinaThioamidated ribosomally synthesized and post-translationally modified peptides (RiPPs) are recently characterized natural products with wide range of potent bioactivities, such as antibiotic, antiproliferative, and cytotoxic activities. These peptides are distinguished by the presence of thioamide bonds in the peptide backbone catalyzed by the YcaO-TfuA protein pair with its genes adjacent to each other. Genome mining has facilitated an in silico approach to identify biosynthesis gene clusters (BGCs) responsible for thioamidated RiPP production. In this work, publicly available genomic data was used to detect and illustrate the diversity of putative BGCs encoding for thioamidated RiPPs. AntiSMASH and RiPPER analysis identified 613 unique TfuA-related gene cluster families (GCFs) and 797 precursor peptide families, even on phyla where the presence of these clusters have not been previously described. Several additional biosynthesis genes are colocalized with the detected BGCs, suggesting an array of possible chemical modifications. This study shows that thioamidated RiPPs occupy a widely unexplored chemical landscape.https://www.frontiersin.org/articles/10.3389/fmicb.2021.635389/fullTfuARiPPsgenome miningYcaObiosynthesis pathwaythioamide |
| spellingShingle | Jessie James Limlingan Malit Chuanhai Wu Ling-Li Liu Ling-Li Liu Pei-Yuan Qian Global Genome Mining Reveals the Distribution of Diverse Thioamidated RiPP Biosynthesis Gene Clusters Frontiers in Microbiology TfuA RiPPs genome mining YcaO biosynthesis pathway thioamide |
| title | Global Genome Mining Reveals the Distribution of Diverse Thioamidated RiPP Biosynthesis Gene Clusters |
| title_full | Global Genome Mining Reveals the Distribution of Diverse Thioamidated RiPP Biosynthesis Gene Clusters |
| title_fullStr | Global Genome Mining Reveals the Distribution of Diverse Thioamidated RiPP Biosynthesis Gene Clusters |
| title_full_unstemmed | Global Genome Mining Reveals the Distribution of Diverse Thioamidated RiPP Biosynthesis Gene Clusters |
| title_short | Global Genome Mining Reveals the Distribution of Diverse Thioamidated RiPP Biosynthesis Gene Clusters |
| title_sort | global genome mining reveals the distribution of diverse thioamidated ripp biosynthesis gene clusters |
| topic | TfuA RiPPs genome mining YcaO biosynthesis pathway thioamide |
| url | https://www.frontiersin.org/articles/10.3389/fmicb.2021.635389/full |
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