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Lin H, Ning X, Wang D, Wang Q, Bai Y, Qu J. Quorum-sensing gene regulates hormetic effects induced by sulfonamides in Comamonadaceae. Appl Environ Microbiol 2023; 89:e0166223. [PMID: 38047646 PMCID: PMC10734536 DOI: 10.1128/aem.01662-23] [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: 09/20/2023] [Accepted: 10/17/2023] [Indexed: 12/05/2023] Open
Abstract
IMPORTANCE Antibiotics can induce dose-dependent hormetic effects on bacterial cell proliferation, i.e., low-dose stimulation and high-dose inhibition. However, the underlying molecular basis has yet to be clarified. Here, we showed that sulfonamides play dual roles as a weapon and signal against Comamonas testosteroni that can modulate cell physiology and phenotype. Subsequently, through investigating the hormesis mechanism, we proposed a comprehensive regulatory pathway for the hormetic effects of Comamonas testosteroni low-level sulfonamides and determined the generality of the observed regulatory model in the Comamonadaceae family. Considering the prevalence of Comamonadaceae in human guts and environmental ecosystems, we provide critical insights into the health and ecological effects of antibiotics.
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Affiliation(s)
- Hui Lin
- Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing, China
- University of Chinese Academy of Science, Beijing, China
| | - Xue Ning
- MaREI Centre, Environmental Research Institute, School of Engineering, University College Cork, Cork, Ireland
| | - Donglin Wang
- Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing, China
| | - Qiaojuan Wang
- Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing, China
- University of Chinese Academy of Science, Beijing, China
| | - Yaohui Bai
- Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing, China
| | - Jiuhui Qu
- Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing, China
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Yoshimura A, Saeki R, Nakada R, Tomimoto S, Jomori T, Suganuma K, Wakimoto T. Membrane-Vesicle-Mediated Interbacterial Communication Activates Silent Secondary Metabolite Production. Angew Chem Int Ed Engl 2023; 62:e202307304. [PMID: 37449463 DOI: 10.1002/anie.202307304] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2023] [Revised: 07/12/2023] [Accepted: 07/12/2023] [Indexed: 07/18/2023]
Abstract
Most bacterial biosynthetic gene clusters (BGCs) are "silent BGCs" that are expressed poorly or not at all under normal culture conditions. However, silent BGCs, even in part, may be conditionally expressed in response to external stimuli in the original bacterial habitats. The growing knowledge of bacterial membrane vesicles (MVs) suggests that they could be promising imitators of the exogenous stimulants, especially given their functions as signaling mediators in bacterial cell-to-cell communication. Therefore, we envisioned that MVs added to bacterial cultures could activate diverse silent BGCs. Herein, we employed Burkholderia multivorans MVs, which induced silent metabolites in a wide range of bacteria in Actinobacteria, Bacteroidetes and Proteobacteria phyla. A mechanistic analysis of MV-induced metabolite production in Xenorhabdus innexi suggested that the B. multivorans MVs activate silent metabolite production by inhibiting quorum sensing in X. innexi. In turn, the X. innexi MVs carrying some MV-induced peptides suppressed the growth of B. multivorans, highlighting the interspecies communication between B. multivorans and X. innexi through MV exchange.
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Affiliation(s)
- Aya Yoshimura
- Faculty of Pharmaceutical Sciences, Hokkaido University, Kita-12, Nishi-6, Kita-ku, Sapporo, 060-0812, Japan
| | - Rio Saeki
- Faculty of Pharmaceutical Sciences, Hokkaido University, Kita-12, Nishi-6, Kita-ku, Sapporo, 060-0812, Japan
| | - Ryusuke Nakada
- Faculty of Pharmaceutical Sciences, Hokkaido University, Kita-12, Nishi-6, Kita-ku, Sapporo, 060-0812, Japan
| | - Shota Tomimoto
- Faculty of Pharmaceutical Sciences, Hokkaido University, Kita-12, Nishi-6, Kita-ku, Sapporo, 060-0812, Japan
| | - Takahiro Jomori
- Faculty of Pharmaceutical Sciences, Hokkaido University, Kita-12, Nishi-6, Kita-ku, Sapporo, 060-0812, Japan
- Faculty of Science, University of the Ryukyus, 1-Senbaru, Nishihara, Nakagami, Okinawa, 903-0213, Japan
| | - Keisuke Suganuma
- National Research Center for Protozoan Diseases, Obihiro University of Agriculture and Veterinary Medicine, Inada, Obihiro, 080-8555, Japan
- Research Center for Global Agromedicine, Obihiro University of Agriculture and Veterinary Medicine Inada, Obihiro, 080-8555, Japan
| | - Toshiyuki Wakimoto
- Faculty of Pharmaceutical Sciences, Hokkaido University, Kita-12, Nishi-6, Kita-ku, Sapporo, 060-0812, Japan
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Han EJ, Lee SR, Townsend CA, Seyedsayamdost MR. Targeted Discovery of Cryptic Enediyne Natural Products via FRET-Coupled High-Throughput Elicitor Screening. ACS Chem Biol 2023; 18:1854-1862. [PMID: 37463302 PMCID: PMC11062413 DOI: 10.1021/acschembio.3c00281] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/20/2023]
Abstract
Enediyne antibiotics are a striking family of DNA-cleaving natural products with high degrees of cytotoxicity and structural complexity. Microbial genome sequences, which have recently accumulated, point to an untapped trove of "cryptic" enediynes. Most of the cognate biosynthetic gene clusters (BGCs) are sparingly expressed under standard growth conditions, making it difficult to characterize their products. Herein, we report a fluorescence-based DNA cleavage assay coupled with high-throughput elicitor screening for the rapid, targeted discovery of cryptic enediyne metabolites. We applied the approach to Streptomyces clavuligerus, which harbors two such BGCs with unknown products, identified steroids as effective elicitors, and characterized 10 cryptic enediyne-derived natural products, termed clavulynes A-J with unusual carbonate and terminal olefin functionalities, with one of these congeners matching the recently reported jejucarboside. Our results contribute to the growing repertoire of enediynes and provide a blueprint for identifying additional ones in the future.
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Affiliation(s)
- Esther J Han
- Department of Chemistry, Princeton University, Princeton, New Jersey 08544, United States
| | - Seoung Rak Lee
- Department of Chemistry, Princeton University, Princeton, New Jersey 08544, United States
| | - Craig A Townsend
- Department of Chemistry, Johns Hopkins University, Baltimore, Maryland 21218, United States
| | - Mohammad R Seyedsayamdost
- Department of Chemistry, Princeton University, Princeton, New Jersey 08544, United States
- Department of Molecular Biology, Princeton University, Princeton, New Jersey 08544, United States
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Han EJ, Lee SR, Hoshino S, Seyedsayamdost MR. Targeted Discovery of Cryptic Metabolites with Antiproliferative Activity. ACS Chem Biol 2022; 17:3121-3130. [PMID: 36228140 PMCID: PMC10171914 DOI: 10.1021/acschembio.2c00588] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023]
Abstract
Microorganisms have provided a rich source of therapeutically valuable natural products. Recent advances in whole genome sequencing and bioinformatics have revealed immense untapped potential for new natural products in the form of silent or "cryptic" biosynthetic genes. We herein conducted high-throughput elicitor screening (HiTES) in conjunction with cytotoxicity assays against selected cancer cell lines with the goal of uncovering otherwise undetectable cryptic metabolites with antiproliferative activity. Application to Streptomyces clavuligerus facilitated identification of clavamates A and B, two bioactive metabolites with unusual structural features, as well as facile activation of a gene cluster coding for tunicamycin, which exhibited strong growth-inhibitory activity. The elicitor we identified was pleiotropic, additionally leading to the discovery of a modified, bicyclic pentapeptide natural product. Our results highlight the utility of this approach in identifying new molecules with antiproliferative activity from even overexploited microbial strains.
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Affiliation(s)
- Esther J. Han
- Department of Chemistry, Princeton University, Princeton, NJ 08544, United States
- These authors contributed equally
| | - Seoung Rak Lee
- Department of Chemistry, Princeton University, Princeton, NJ 08544, United States
- These authors contributed equally
| | - Shotaro Hoshino
- Department of Chemistry, Princeton University, Princeton, NJ 08544, United States
| | - Mohammad R. Seyedsayamdost
- Department of Chemistry, Princeton University, Princeton, NJ 08544, United States
- Department of Molecular Biology, Princeton University, Princeton, NJ 08544, United States
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Li Y, Lee SR, Han EJ, Seyedsayamdost MR. Momomycin, an Antiproliferative Cryptic Metabolite from the Oxytetracycline Producer Streptomyces rimosus. Angew Chem Int Ed Engl 2022; 61:e202208573. [PMID: 35903822 PMCID: PMC9489664 DOI: 10.1002/anie.202208573] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2022] [Indexed: 08/27/2023]
Abstract
Natural products provide an important source of pharmaceuticals and chemical tools. Traditionally, assessment of unexplored microbial phyla has led to new natural products. However, with every new microbe, the number of orphan biosynthetic gene clusters (BGC) grows. As such, the more difficult proposition is finding new molecules from well-studied strains. Herein, we targeted Streptomyces rimosus, the widely-used oxytetracycline producer, for the discovery of new natural products. Using MALDI-MS-guided high-throughput elicitor screening (HiTES), we mapped the global secondary metabolome of S. rimosus and structurally characterized products of three cryptic BGCs, including momomycin, an unusual cyclic peptide natural product with backbone modifications and several non-canonical amino acids. We elucidated important aspects of its biosynthesis and evaluated its bioactivity. Our studies showcase HiTES as an effective approach for unearthing new chemical matter from "drained" strains.
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Affiliation(s)
- Yuchen Li
- Department of Chemistry, Princeton University, Princeton, NJ 08544 (USA)
| | - Seoung Rak Lee
- Department of Chemistry, Princeton University, Princeton, NJ 08544 (USA)
| | - Esther J. Han
- Department of Chemistry, Princeton University, Princeton, NJ 08544 (USA)
| | - Mohammad R. Seyedsayamdost
- Department of Chemistry, Princeton University, Princeton, NJ 08544 (USA)
- Department of Molecular Biology, Princeton University, Princeton, NJ 08544 (USA)
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Li Y, Lee SR, Han EJ, Seyedsayamdost MR. Momomycin, an Antiproliferative Cryptic Metabolite from the Oxytetracycline Producer Streptomyces rimosus. Angew Chem Int Ed Engl 2022. [DOI: 10.1002/ange.202208573] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Affiliation(s)
- Yuchen Li
- Princeton University Chemistry UNITED STATES
| | | | | | - Mohammad R. Seyedsayamdost
- Princeton University Chemistry Washington UniversityFrick Chemistry Lab, Room 333 08544 Princeton UNITED STATES
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Henriksen NNSE, Lindqvist LL, Wibowo M, Sonnenschein EC, Bentzon-Tilia M, Gram L. OUP accepted manuscript. FEMS Microbiol Rev 2022; 46:6517774. [PMID: 35099011 PMCID: PMC9075582 DOI: 10.1093/femsre/fuac007] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2021] [Revised: 01/24/2022] [Accepted: 01/27/2022] [Indexed: 11/13/2022] Open
Abstract
Many microbial secondary metabolites have been studied for decades primarily because of their antimicrobial properties. However, several of these metabolites also possess nonantimicrobial functions, both influencing the physiology of the producer and their ecological neighbors. An example of a versatile bacterial secondary metabolite with multiple functions is the tropone derivative tropodithietic acid (TDA). TDA is a broad-spectrum antimicrobial compound produced by several members of the Rhodobacteraceae family, a major marine bacterial lineage, within the genera Phaeobacter, Tritonibacter, and Pseudovibrio. The production of TDA is governed by the mode of growth and influenced by the availability of nutrient sources. The antibacterial effect of TDA is caused by disruption of the proton motive force of target microorganisms and, potentially, by its iron-chelating properties. TDA also acts as a signaling molecule, affecting gene expression in other bacteria, and altering phenotypic traits such as motility, biofilm formation, and antibiotic production in the producer. In microbial communities, TDA-producing bacteria cause a reduction of the relative abundance of closely related species and some fast-growing heterotrophic bacteria. Here, we summarize the current understanding of the chemical ecology of TDA, including the environmental niches of TDA-producing bacteria, and the molecular mechanisms governing the function and regulation of TDA.
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Affiliation(s)
| | | | - Mario Wibowo
- Department of Biotechnology and Biomedicine, Technical University of Denmark, Søltofts, Plads Bldg. 221, DK-2800 Kgs. Lyngby, Denmark
| | - Eva C Sonnenschein
- Department of Biotechnology and Biomedicine, Technical University of Denmark, Søltofts, Plads Bldg. 221, DK-2800 Kgs. Lyngby, Denmark
| | - Mikkel Bentzon-Tilia
- Department of Biotechnology and Biomedicine, Technical University of Denmark, Søltofts, Plads Bldg. 221, DK-2800 Kgs. Lyngby, Denmark
| | - Lone Gram
- Corresponding author: Department of Bioechnology and Biomedicine, Technical University of Denmark, Søltofts Plads Bldg. 221, DK-2800 Kgs. Lyngby, Denmark. Tel: +45 23688295; E-mail:
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