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Harper CP, Day A, Tsingos M, Ding E, Zeng E, Stumpf SD, Qi Y, Robinson A, Greif J, Blodgett JAV. Critical analysis of polycyclic tetramate macrolactam biosynthetic gene cluster phylogeny and functional diversity. Appl Environ Microbiol 2024; 90:e0060024. [PMID: 38771054 PMCID: PMC11218653 DOI: 10.1128/aem.00600-24] [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: 04/06/2024] [Accepted: 04/25/2024] [Indexed: 05/22/2024] Open
Abstract
Polycyclic tetramate macrolactams (PTMs) are bioactive natural products commonly associated with certain actinobacterial and proteobacterial lineages. These molecules have been the subject of numerous structure-activity investigations since the 1970s. New members continue to be pursued in wild and engineered bacterial strains, and advances in PTM biosynthesis suggest their outwardly simplistic biosynthetic gene clusters (BGCs) belie unexpected product complexity. To address the origins of this complexity and understand its influence on PTM discovery, we engaged in a combination of bioinformatics to systematically classify PTM BGCs and PTM-targeted metabolomics to compare the products of select BGC types. By comparing groups of producers and BGC mutants, we exposed knowledge gaps that complicate bioinformatics-driven product predictions. In sum, we provide new insights into the evolution of PTM BGCs while systematically accounting for the PTMs discovered thus far. The combined computational and metabologenomic findings presented here should prove useful for guiding future discovery.IMPORTANCEPolycyclic tetramate macrolactam (PTM) pathways are frequently found within the genomes of biotechnologically important bacteria, including Streptomyces and Lysobacter spp. Their molecular products are typically bioactive, having substantial agricultural and therapeutic interest. Leveraging bacterial genomics for the discovery of new related molecules is thus desirable, but drawing accurate structural predictions from bioinformatics alone remains challenging. This difficulty stems from a combination of previously underappreciated biosynthetic complexity and remaining knowledge gaps, compounded by a stream of yet-uncharacterized PTM biosynthetic loci gleaned from recently sequenced bacterial genomes. We engaged in the following study to create a useful framework for cataloging historic PTM clusters, identifying new cluster variations, and tracing evolutionary paths for these molecules. Our data suggest new PTM chemistry remains discoverable in nature. However, our metabolomic and mutational analyses emphasize the practical limitations of genomics-based discovery by exposing hidden complexity.
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Affiliation(s)
| | - Anna Day
- Department of Biology, Washington University in St. Louis, St. Louis, Missouri, USA
| | - Maya Tsingos
- Department of Biology, Washington University in St. Louis, St. Louis, Missouri, USA
| | - Edward Ding
- Department of Biology, Washington University in St. Louis, St. Louis, Missouri, USA
| | - Elizabeth Zeng
- Department of Biology, Washington University in St. Louis, St. Louis, Missouri, USA
| | - Spencer D. Stumpf
- Department of Biology, Washington University in St. Louis, St. Louis, Missouri, USA
| | - Yunci Qi
- Department of Biology, Washington University in St. Louis, St. Louis, Missouri, USA
| | - Adam Robinson
- Department of Biology, Washington University in St. Louis, St. Louis, Missouri, USA
| | - Jennifer Greif
- Department of Biology, Washington University in St. Louis, St. Louis, Missouri, USA
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Tay DWP, Tan LL, Heng E, Zulkarnain N, Ching KC, Wibowo M, Chin EJ, Tan ZYQ, Leong CY, Ng VWP, Yang LK, Seow DCS, Lim YW, Koh W, Koduru L, Kanagasundaram Y, Ng SB, Lim YH, Wong FT. Exploring a general multi-pronged activation strategy for natural product discovery in Actinomycetes. Commun Biol 2024; 7:50. [PMID: 38184720 PMCID: PMC10771470 DOI: 10.1038/s42003-023-05648-7] [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: 08/16/2023] [Accepted: 11/29/2023] [Indexed: 01/08/2024] Open
Abstract
Natural products possess significant therapeutic potential but remain underutilized despite advances in genomics and bioinformatics. While there are approaches to activate and upregulate natural product biosynthesis in both native and heterologous microbial strains, a comprehensive strategy to elicit production of natural products as well as a generalizable and efficient method to interrogate diverse native strains collection, remains lacking. Here, we explore a flexible and robust integrase-mediated multi-pronged activation approach to reliably perturb and globally trigger antibiotics production in actinobacteria. Across 54 actinobacterial strains, our approach yielded 124 distinct activator-strain combinations which consistently outperform wild type. Our approach expands accessible metabolite space by nearly two-fold and increases selected metabolite yields by up to >200-fold, enabling discovery of Gram-negative bioactivity in tetramic acid analogs. We envision these findings as a gateway towards a more streamlined, accelerated, and scalable strategy to unlock the full potential of Nature's chemical repertoire.
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Grants
- NRF-CRP19-2017-05-00 National Research Foundation Singapore (National Research Foundation-Prime Minister's office, Republic of Singapore)
- NRF-CRP19-2017-05-00 National Research Foundation Singapore (National Research Foundation-Prime Minister's office, Republic of Singapore)
- NRF-CRP19-2017-05-00 National Research Foundation Singapore (National Research Foundation-Prime Minister's office, Republic of Singapore)
- NRF-CRP19-2017-05-00 National Research Foundation Singapore (National Research Foundation-Prime Minister's office, Republic of Singapore)
- NRF-CRP19-2017-05-00 National Research Foundation Singapore (National Research Foundation-Prime Minister's office, Republic of Singapore)
- NRF-CRP19-2017-05-00 National Research Foundation Singapore (National Research Foundation-Prime Minister's office, Republic of Singapore)
- NRF-CRP19-2017-05-00 National Research Foundation Singapore (National Research Foundation-Prime Minister's office, Republic of Singapore)
- NRF-CRP19-2017-05-00 National Research Foundation Singapore (National Research Foundation-Prime Minister's office, Republic of Singapore)
- C211917006 Agency for Science, Technology and Research (A*STAR)
- C233017006 Agency for Science, Technology and Research (A*STAR)
- C211917003 Agency for Science, Technology and Research (A*STAR)
- C211917006 Agency for Science, Technology and Research (A*STAR)
- C233017006 Agency for Science, Technology and Research (A*STAR)
- C211917006 Agency for Science, Technology and Research (A*STAR)
- National Research Foundation Singapore (National Research Foundation-Prime Minister’s office, Republic of Singapore)
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Affiliation(s)
- Dillon W P Tay
- Institute of Sustainability for Chemicals, Energy and Environment (ISCE2), Agency for Science, Technology and Research (A*STAR), 8 Biomedical Grove, #07-01 Neuros Building, Singapore, 138665, Republic of Singapore
| | - Lee Ling Tan
- Molecular Engineering Lab, Institute of Molecular and Cell Biology (IMCB), Agency for Science, Technology and Research (A*STAR), 61 Biopolis Drive, #07-06, Proteos, Singapore, 138673, Republic of Singapore
| | - Elena Heng
- Molecular Engineering Lab, Institute of Molecular and Cell Biology (IMCB), Agency for Science, Technology and Research (A*STAR), 61 Biopolis Drive, #07-06, Proteos, Singapore, 138673, Republic of Singapore
| | - Nadiah Zulkarnain
- Molecular Engineering Lab, Institute of Molecular and Cell Biology (IMCB), Agency for Science, Technology and Research (A*STAR), 61 Biopolis Drive, #07-06, Proteos, Singapore, 138673, Republic of Singapore
| | - Kuan Chieh Ching
- Singapore Institute of Food and Biotechnology Innovation (SIFBI), Agency for Science, Technology and Research (A*STAR), 31 Biopolis Way, #01-02, Nanos, Singapore, 138669, Republic of Singapore
| | - Mario Wibowo
- Singapore Institute of Food and Biotechnology Innovation (SIFBI), Agency for Science, Technology and Research (A*STAR), 31 Biopolis Way, #01-02, Nanos, Singapore, 138669, Republic of Singapore
| | - Elaine Jinfeng Chin
- Singapore Institute of Food and Biotechnology Innovation (SIFBI), Agency for Science, Technology and Research (A*STAR), 31 Biopolis Way, #01-02, Nanos, Singapore, 138669, Republic of Singapore
| | - Zann Yi Qi Tan
- Singapore Institute of Food and Biotechnology Innovation (SIFBI), Agency for Science, Technology and Research (A*STAR), 31 Biopolis Way, #01-02, Nanos, Singapore, 138669, Republic of Singapore
| | - Chung Yan Leong
- Singapore Institute of Food and Biotechnology Innovation (SIFBI), Agency for Science, Technology and Research (A*STAR), 31 Biopolis Way, #01-02, Nanos, Singapore, 138669, Republic of Singapore
| | - Veronica Wee Pin Ng
- Singapore Institute of Food and Biotechnology Innovation (SIFBI), Agency for Science, Technology and Research (A*STAR), 31 Biopolis Way, #01-02, Nanos, Singapore, 138669, Republic of Singapore
| | - Lay Kien Yang
- Singapore Institute of Food and Biotechnology Innovation (SIFBI), Agency for Science, Technology and Research (A*STAR), 31 Biopolis Way, #01-02, Nanos, Singapore, 138669, Republic of Singapore
| | - Deborah C S Seow
- Singapore Institute of Food and Biotechnology Innovation (SIFBI), Agency for Science, Technology and Research (A*STAR), 31 Biopolis Way, #01-02, Nanos, Singapore, 138669, Republic of Singapore
| | - Yi Wee Lim
- Institute of Sustainability for Chemicals, Energy and Environment (ISCE2), Agency for Science, Technology and Research (A*STAR), 8 Biomedical Grove, #07-01 Neuros Building, Singapore, 138665, Republic of Singapore
| | - Winston Koh
- Bioinformatics Institute (BII), Agency of Science, Technology and Research (A*STAR), 30 Biopolis Street, #07-01, Matrix, Singapore, 138671, Republic of Singapore
| | - Lokanand Koduru
- Molecular Engineering Lab, Institute of Molecular and Cell Biology (IMCB), Agency for Science, Technology and Research (A*STAR), 61 Biopolis Drive, #07-06, Proteos, Singapore, 138673, Republic of Singapore
| | - Yoganathan Kanagasundaram
- Singapore Institute of Food and Biotechnology Innovation (SIFBI), Agency for Science, Technology and Research (A*STAR), 31 Biopolis Way, #01-02, Nanos, Singapore, 138669, Republic of Singapore
| | - Siew Bee Ng
- Singapore Institute of Food and Biotechnology Innovation (SIFBI), Agency for Science, Technology and Research (A*STAR), 31 Biopolis Way, #01-02, Nanos, Singapore, 138669, Republic of Singapore
| | - Yee Hwee Lim
- Institute of Sustainability for Chemicals, Energy and Environment (ISCE2), Agency for Science, Technology and Research (A*STAR), 8 Biomedical Grove, #07-01 Neuros Building, Singapore, 138665, Republic of Singapore.
- Synthetic Biology Translational Research Program, Yong Loo Lin School of Medicine, National University of Singapore, 10 Medical Drive, Singapore, 117597, Republic of Singapore.
| | - Fong Tian Wong
- Institute of Sustainability for Chemicals, Energy and Environment (ISCE2), Agency for Science, Technology and Research (A*STAR), 8 Biomedical Grove, #07-01 Neuros Building, Singapore, 138665, Republic of Singapore.
- Molecular Engineering Lab, Institute of Molecular and Cell Biology (IMCB), Agency for Science, Technology and Research (A*STAR), 61 Biopolis Drive, #07-06, Proteos, Singapore, 138673, Republic of Singapore.
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Li T, Morselli M, Su T, Million M, Larauche M, Pellegrini M, Taché Y, Yuan PQ. Comparative transcriptomics reveals highly conserved regional programs between porcine and human colonic enteric nervous system. Commun Biol 2023; 6:98. [PMID: 36693960 PMCID: PMC9872754 DOI: 10.1038/s42003-023-04478-x] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2022] [Accepted: 01/12/2023] [Indexed: 01/26/2023] Open
Abstract
The porcine gut is increasingly regarded as a useful translational model. The enteric nervous system in the colon coordinates diverse functions. However, knowledge of the molecular profiling of porcine enteric nerve system and its similarity to that of human is still lacking. We identified the distinct transcriptional programs associated with functional characteristics between inner submucosal and myenteric ganglia in porcine proximal and distal colon using bulk RNA and single-cell RNA sequencing. Comparative transcriptomics of myenteric ganglia in corresponding colonic regions of pig and human revealed highly conserved programs in porcine proximal and distal colon, which explained >96% of their transcriptomic responses to vagal nerve stimulation, suggesting that porcine proximal and distal colon could serve as predictors in translational studies. The conserved programs specific for inflammatory modulation were displayed in pigs with vagal nerve stimulation. This study provides a valuable transcriptomic resource for understanding of human colonic functions and neuromodulation using porcine model.
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Affiliation(s)
- Tao Li
- grid.19006.3e0000 0000 9632 6718CURE/Digestive Diseases Research Center, Vatche and Tamar Manoukian Digestive Diseases Division, Department of Medicine, David Geffen School of Medicine, University of California at Los Angeles (UCLA), Los Angeles, USA
| | - Marco Morselli
- grid.19006.3e0000 0000 9632 6718Department of Molecular, Cell, & Developmental Biology, UCLA, Los Angeles, USA
| | - Trent Su
- grid.19006.3e0000 0000 9632 6718Department of Biological Chemistry, UCLA, Los Angeles, USA
| | - Mulugeta Million
- grid.19006.3e0000 0000 9632 6718CURE/Digestive Diseases Research Center, Vatche and Tamar Manoukian Digestive Diseases Division, Department of Medicine, David Geffen School of Medicine, University of California at Los Angeles (UCLA), Los Angeles, USA
| | - Muriel Larauche
- grid.19006.3e0000 0000 9632 6718CURE/Digestive Diseases Research Center, Vatche and Tamar Manoukian Digestive Diseases Division, Department of Medicine, David Geffen School of Medicine, University of California at Los Angeles (UCLA), Los Angeles, USA
| | - Matteo Pellegrini
- grid.19006.3e0000 0000 9632 6718Department of Molecular, Cell, & Developmental Biology, UCLA, Los Angeles, USA
| | - Yvette Taché
- grid.19006.3e0000 0000 9632 6718CURE/Digestive Diseases Research Center, Vatche and Tamar Manoukian Digestive Diseases Division, Department of Medicine, David Geffen School of Medicine, University of California at Los Angeles (UCLA), Los Angeles, USA ,grid.417119.b0000 0001 0384 5381VA Greater Los Angeles Healthcare System, Los Angeles, USA
| | - Pu-Qing Yuan
- grid.19006.3e0000 0000 9632 6718CURE/Digestive Diseases Research Center, Vatche and Tamar Manoukian Digestive Diseases Division, Department of Medicine, David Geffen School of Medicine, University of California at Los Angeles (UCLA), Los Angeles, USA ,grid.417119.b0000 0001 0384 5381VA Greater Los Angeles Healthcare System, Los Angeles, USA
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