1
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Wang R, Bao Y, Dong Y, Dong Y, Li H. Genome-directed discovery of antiproliferative bafilomycins from a deepsea-derived Streptomyces samsunensis. Bioorg Chem 2023; 138:106599. [PMID: 37320913 DOI: 10.1016/j.bioorg.2023.106599] [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: 04/12/2023] [Revised: 04/25/2023] [Accepted: 05/04/2023] [Indexed: 06/17/2023]
Abstract
Genomic bioinformatics analysis identified a bafilomycin biosynthetic gene cluster (named bfl) in the deepsea-derived S. samsunensis OUCT16-12, from which two new (1 and 2, named bafilomycins R and S) along with four known (3-6) bafilomycins were targetly obtained. The structure of 3 was clearly identified for the first time, thus named bafilomycin T herein. Differ from the fumarate substitution at C-21 of known bafilomycins, its location on C-23 is a unique feature of 1 and 2. The stereochemistry of the compounds was established based on NOE correlations, ketoreductase (KR)-types in PKS modules of bfl, and ECD calculations. Moreover, a detailed biosynthetic model of 1-6 in S. samsunensis OUCT16-12 was provided based on the gene function prediction and sequence identity. Compared with the positive control doxorubicin, 1-6 showed more potent antiproliferative activities against drug-resistant lung cancer cell line A549-Taxol, with IC50 values ranging from 0.07 μM to 1.79 μM, which arrested cell cycle in G0/G1 phase to hinder proliferation.
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Affiliation(s)
- Runyi Wang
- Key Laboratory of Marine Drugs, Ministry of Education, School of Medicine and Pharmacy, Ocean University of China, Qingdao 266003, China
| | - Yilei Bao
- Key Laboratory of Marine Drugs, Ministry of Education, School of Medicine and Pharmacy, Ocean University of China, Qingdao 266003, China
| | - Yujing Dong
- Key Laboratory of Marine Drugs, Ministry of Education, School of Medicine and Pharmacy, Ocean University of China, Qingdao 266003, China
| | - Yun Dong
- Key Laboratory of Marine Drugs, Ministry of Education, School of Medicine and Pharmacy, Ocean University of China, Qingdao 266003, China
| | - Huayue Li
- Key Laboratory of Marine Drugs, Ministry of Education, School of Medicine and Pharmacy, Ocean University of China, Qingdao 266003, China; Laboratory for Marine Drugs and Bioproducts of Qingdao National Laboratory for Marine Science and Technology, Qingdao 266237, China.
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2
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Herisse M, Ishida K, Staiger-Creed J, Judd L, Williams SJ, Howden BP, Stinear TP, Dahse HM, Voigt K, Hertweck C, Pidot SJ. Discovery and Biosynthesis of the Cytotoxic Polyene Terpenomycin in Human Pathogenic Nocardia. ACS Chem Biol 2023; 18:1872-1879. [PMID: 37498707 DOI: 10.1021/acschembio.3c00311] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/29/2023]
Abstract
Nocardia are opportunistic human pathogens that can cause a range of debilitating and difficult to treat infections of the lungs, brain, skin, and soft tissues. Despite their close relationship to the well-known secondary metabolite-producing genus, Streptomyces, comparatively few natural products are known from the Nocardia, and even less is known about their involvement in the pathogenesis. Here, we combine chemistry, genomics, and molecular microbiology to reveal the production of terpenomycin, a new cytotoxic and antifungal polyene from a human pathogenic Nocardia terpenica isolate. We unveil the polyketide synthase (PKS) responsible for terpenomycin biosynthesis and show that it combines several unusual features, including "split", skipped, and iteratively used modules, and the use of the unusual extender unit methoxymalonate as a starter unit. To link genes to molecules, we constructed a transposon mutant library in N. terpenica, identifying a terpenomycin-null mutant with an inactivated terpenomycin PKS. Our findings show that the neglected actinomycetes have an unappreciated capacity for the production of bioactive molecules with unique biosynthetic pathways waiting to be uncovered and highlights these organisms as producers of diverse natural products.
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Affiliation(s)
- Marion Herisse
- Department of Microbiology and Immunology, Doherty Institute for Infection and Immunity, University of Melbourne, Melbourne, Victoria 3000, Australia
| | - Keishi Ishida
- Department of Biomolecular Chemistry, Leibniz Institute, for Natural Product Chemistry and Infection Biology (HKI), Beutenbergstrasse 11a, Jena 07745, Germany
| | - Jordan Staiger-Creed
- Department of Microbiology and Immunology, Doherty Institute for Infection and Immunity, University of Melbourne, Melbourne, Victoria 3000, Australia
| | - Louise Judd
- Department of Microbiology and Immunology, Doherty Institute for Infection and Immunity, University of Melbourne, Melbourne, Victoria 3000, Australia
| | - Spencer J Williams
- School of Chemistry, University of Melbourne, Melbourne, Victoria 3000, Australia
- Bio21 Molecular Science and Biotechnology Institute, University of Melbourne, Melbourne, Victoria 3000, Australia
| | - Benjamin P Howden
- Department of Microbiology and Immunology, Doherty Institute for Infection and Immunity, University of Melbourne, Melbourne, Victoria 3000, Australia
- Microbiological Diagnostic Unit Public Health Laboratory, Department of Microbiology and Immunology, Doherty Institute for Infection and Immunity, University of Melbourne, Melbourne, Victoria3000, Australia
| | - Timothy P Stinear
- Department of Microbiology and Immunology, Doherty Institute for Infection and Immunity, University of Melbourne, Melbourne, Victoria 3000, Australia
| | - Hans-Martin Dahse
- Department of Infection Biology, Leibniz Institute, for Natural Product Chemistry and Infection Biology (HKI), Beutenbergstrasse 11a, Jena 07745, Germany
| | - Kerstin Voigt
- Jena Microbial Resource Collection, Leibniz Institute for Natural Product Research and Infection Biology (HKI), Beutenbergstrasse 11a, Jena 07745, Germany
- Institute of Microbiology, Friedrich Schiller University Jena, 07743 Jena, Germany
| | - Christian Hertweck
- Department of Biomolecular Chemistry, Leibniz Institute, for Natural Product Chemistry and Infection Biology (HKI), Beutenbergstrasse 11a, Jena 07745, Germany
- Natural Product Chemistry, Faculty of Biological Sciences, Friedrich Schiller University Jena, Jena 07743, Germany
| | - Sacha J Pidot
- Department of Microbiology and Immunology, Doherty Institute for Infection and Immunity, University of Melbourne, Melbourne, Victoria 3000, Australia
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3
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Chiu CF, Chiu SJ, Bai LY, Feng CH, Hu JL, Lin WY, Huang HY, Weng JR. A macrolide from Streptomyces sp. modulates apoptosis and autophagy through Mcl-1 downregulation in human breast cancer cells. ENVIRONMENTAL TOXICOLOGY 2021; 36:1316-1325. [PMID: 33713530 DOI: 10.1002/tox.23128] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/23/2020] [Revised: 02/08/2021] [Accepted: 03/04/2021] [Indexed: 06/12/2023]
Abstract
Secondary metabolites in marine organisms exhibit various pharmacological activities against diseases, such as cancer. In this study, the anti-proliferative effect of JBIR-100, a macrolide isolated from Streptomyces sp., was investigated in breast cancer cells. Cell growth was inhibited in response to JBIR-100 treatment concentration- and time-dependently in both MCF-7 and MDA-MB-231 breast cancer cells. JBIR-100 caused apoptosis, as verified by caspase activation and the cleavage of PARP. Western blotting revealed that JBIR-100 modulated the expression of Akt/NF-κB signaling components and Bcl-2 family members. Overexpression of Mcl-1 partially rescued MCF-7 cells from JBIR-100-induced cytotoxicity. In addition, transmission electron microscopy analyses, confocal analysis, and western blot assay indicated that JBIR-100 inhibited autophagy in MCF-7 cells. Exposure to the autophagy inhibitor did not synergize JBIR-100-induced apoptosis. In summary, our results suggested that JBIR-100 may be potentially used for breast cancer therapy.
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Affiliation(s)
- Chang-Fang Chiu
- Division of Hematology and Oncology, Department of Internal Medicine, China Medical University Hospital, Taichung, Taiwan
- Cancer Center, China Medical University Hospital, Taichung, Taiwan
- College of Medicine, China Medical University, Taichung, Taiwan
| | - Shih-Jiuan Chiu
- School of Pharmacy, Taipei Medical University, Taipei, Taiwan
| | - Li-Yuan Bai
- Division of Hematology and Oncology, Department of Internal Medicine, China Medical University Hospital, Taichung, Taiwan
- College of Medicine, China Medical University, Taichung, Taiwan
| | - Chia-Hsien Feng
- Department of Fragrance and Cosmetic Science, College of Pharmacy, Kaohsiung Medical University, Kaohsiung, Taiwan
| | - Jing-Lan Hu
- Cancer Center, China Medical University Hospital, Taichung, Taiwan
| | - Wei-Yu Lin
- Department of Pharmacy, Kinmen Hospital, Ministry of Health and Welfare, Kinmen, Taiwan
| | - Hao-Yu Huang
- Department of Marine Biotechnology and Resources, National Sun Yat-sen University, Kaohsiung, Taiwan
| | - Jing-Ru Weng
- Department of Marine Biotechnology and Resources, National Sun Yat-sen University, Kaohsiung, Taiwan
- Doctoral Degree Program in Marine Biotechnology, National Sun Yat-sen University, Kaohsiung, Taiwan
- Department of Biotechnology, Kaohsiung Medical University, Kaohsiung, Taiwan
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4
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Guo X, Zhang J, Li X, Xiao E, Lange JD, Rienstra CM, Burke MD, Mitchell DA. Sterol Sponge Mechanism Is Conserved for Glycosylated Polyene Macrolides. ACS CENTRAL SCIENCE 2021; 7:781-791. [PMID: 34079896 PMCID: PMC8161476 DOI: 10.1021/acscentsci.1c00148] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/31/2021] [Indexed: 05/07/2023]
Abstract
Amphotericin-like glycosylated polyene macrolides (GPMs) are a clinically and industrially important family of natural products, but the mechanisms by which they exert their extraordinary biological activities have remained unclear for more than half a century. Amphotericin B exerts fungicidal action primarily via self-assembly into an extramembranous sponge that rapidly extracts ergosterol from fungal membranes, but it has remained unclear whether this mechanism is applicable to other GPMs. Using a highly conserved polyene-hemiketal region of GPMs that we hypothesized to represent a conserved ergosterol-binding domain, we bioinformatically mapped the entirety of the GPM sequence-function space and expanded the number of GPM biosynthetic gene clusters (BGCs) by 10-fold. We further leveraged bioinformatic predictions and tetrazine-based reactivity screening targeting the electron-rich polyene region of GPMs to discover a first-in-class methyltetraene- and diepoxide-containing GPM, kineosporicin, and to assign BGCs to many new producers of previously reported members. Leveraging a range of structurally diverse known and newly discovered GPMs, we found that the sterol sponge mechanism of fungicidal action is conserved.
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Affiliation(s)
- Xiaorui Guo
- Department
of Chemistry, Roger Adams Laboratory, University
of Illinois at Urbana−Champaign, 600 South Mathews Avenue, Urbana, Illinois 61801, United States
| | - Jiabao Zhang
- Department
of Chemistry, Roger Adams Laboratory, University
of Illinois at Urbana−Champaign, 600 South Mathews Avenue, Urbana, Illinois 61801, United States
- Carl
R. Woese Institute for Genomic Biology, University of Illinois at Urbana−Champaign, 1206 W. Gregory Avenue, Urbana, Illinois 61801, United States
| | - Xinyi Li
- Department
of Biochemistry, Roger Adams Laboratory, University of Illinois at Urbana−Champaign, 600 South Mathews Avenue, Urbana, Illinois 61801, United States
| | - Emily Xiao
- Department
of Chemistry, Roger Adams Laboratory, University
of Illinois at Urbana−Champaign, 600 South Mathews Avenue, Urbana, Illinois 61801, United States
| | - Justin D. Lange
- Department
of Chemistry, Roger Adams Laboratory, University
of Illinois at Urbana−Champaign, 600 South Mathews Avenue, Urbana, Illinois 61801, United States
- Carl
R. Woese Institute for Genomic Biology, University of Illinois at Urbana−Champaign, 1206 W. Gregory Avenue, Urbana, Illinois 61801, United States
| | - Chad M. Rienstra
- Department
of Biochemistry and National Magnetic Resonance Facility at Madison, DeLuca Biochemistry Laboratories, 433 Babcock Drive, Madison, Wisconsin 53706, United States
| | - Martin D. Burke
- Department
of Chemistry, Roger Adams Laboratory, University
of Illinois at Urbana−Champaign, 600 South Mathews Avenue, Urbana, Illinois 61801, United States
- Carl
R. Woese Institute for Genomic Biology, University of Illinois at Urbana−Champaign, 1206 W. Gregory Avenue, Urbana, Illinois 61801, United States
- Department
of Biochemistry, Roger Adams Laboratory, University of Illinois at Urbana−Champaign, 600 South Mathews Avenue, Urbana, Illinois 61801, United States
- Beckman
Institute for Advanced Science and Technology, University of Illinois at Urbana−Champaign, Urbana, Illinois 61801 United States
| | - Douglas A. Mitchell
- Department
of Chemistry, Roger Adams Laboratory, University
of Illinois at Urbana−Champaign, 600 South Mathews Avenue, Urbana, Illinois 61801, United States
- Carl
R. Woese Institute for Genomic Biology, University of Illinois at Urbana−Champaign, 1206 W. Gregory Avenue, Urbana, Illinois 61801, United States
- Department
of Microbiology, University of Illinois
at Urbana−Champaign, Urbana, Illinois 61801, United States
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5
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Harris LA, Saint-Vincent PMB, Guo X, Hudson GA, DiCaprio AJ, Zhu L, Mitchell DA. Reactivity-Based Screening for Citrulline-Containing Natural Products Reveals a Family of Bacterial Peptidyl Arginine Deiminases. ACS Chem Biol 2020; 15:3167-3175. [PMID: 33249828 DOI: 10.1021/acschembio.0c00685] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
Ribosomally synthesized and post-translationally modified peptides (RiPPs) are a family of natural products defined by a genetically encoded precursor peptide that is processed by associated biosynthetic enzymes to form the mature product. Lasso peptides are a class of RiPP defined by an isopeptide linkage between the N-terminal amine and an internal Asp/Glu residue with the C-terminal sequence threaded through the macrocycle. This unique lariat topology, which typically provides considerable stability toward heat and proteases, has stimulated interest in lasso peptides as potential therapeutics. Post-translational modifications beyond the class-defining, threaded macrolactam have been reported, including one example of Arg deimination to yield citrulline (Cit). Although a Cit-containing lasso peptide (i.e., citrulassin) was serendipitously discovered during a genome-guided campaign, the gene(s) responsible for Arg deimination has remained unknown. Herein, we describe the use of reactivity-based screening to discriminate bacterial strains that produce Arg- versus Cit-bearing citrulassins, yielding 13 new lasso peptide variants. Partial phylogenetic profiling identified a distally encoded peptidyl arginine deiminase (PAD) gene ubiquitous to the Cit-containing variants. Absence of this gene correlated strongly with lasso peptide variants only containing Arg (i.e., des-citrulassin). Heterologous expression of the PAD gene in a des-citrulassin producer resulted in the production of the deiminated analog, confirming PAD involvement in Arg deimination. The PADs were then bioinformatically surveyed to provide a deeper understanding of their taxonomic distribution and genomic contexts and to facilitate future studies that will evaluate any additional biochemical roles for the superfamily.
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6
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Ayed A, Wibberg D, Zendah El Euch I, Frese M, Limam F, Sewald N. Draft genome sequence of Streptomyces tunisialbus DSM 105760 T. Arch Microbiol 2020; 202:2013-2017. [PMID: 32474644 PMCID: PMC7385001 DOI: 10.1007/s00203-020-01913-z] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2019] [Revised: 04/27/2020] [Accepted: 05/14/2020] [Indexed: 11/28/2022]
Abstract
Streptomyces strains are well known as promising source of bioactive secondary metabolites, important in ecology, biotechnology and medicine. In this study, we present the draft genome of the new type strain Streptomyces tunisialbus DSM 105760T (= JCM 32165T), a rhizospheric bacterium with antimicrobial activity. The genome is 6,880,753 bp in size (average GC content, 71.85%) and encodes 5802 protein-coding genes. Preliminary analysis with antiSMASH 5.1.2. reveals 34 predicted gene clusters for the synthesis of potential secondary metabolites, which was compared with those of Streptomyces varsoviensis NRRL ISP-5346.
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Affiliation(s)
- Ameni Ayed
- Laboratory of Bioactive Substances, Biotechnology Center of Borj-Cedria (CBBC), BP-901, 2050, Hammam-Lif, Tunisia
| | - Daniel Wibberg
- Center for Biotechnology (CeBiTec), Bielefeld University, 33501, Bielefeld, Germany
| | - Imène Zendah El Euch
- Organic and Bioorganic Chemistry, Faculty of Chemistry, Bielefeld University, 33615, Bielefeld, Germany
| | - Marcel Frese
- Organic and Bioorganic Chemistry, Faculty of Chemistry, Bielefeld University, 33615, Bielefeld, Germany
| | - Ferid Limam
- Laboratory of Bioactive Substances, Biotechnology Center of Borj-Cedria (CBBC), BP-901, 2050, Hammam-Lif, Tunisia
| | - Norbert Sewald
- Organic and Bioorganic Chemistry, Faculty of Chemistry, Bielefeld University, 33615, Bielefeld, Germany.
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7
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Jiang Q, Zhu Z, Shou P, Teng F, Zhu Y, Zhao H, Yang B. Targeting pharmacophore with probe-reactivity-guided fractionation to precisely identify electrophilic sesquiterpenes and its activity of anti-TNBC. PHYTOCHEMICAL ANALYSIS : PCA 2020; 31:322-332. [PMID: 31849131 DOI: 10.1002/pca.2898] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/26/2019] [Revised: 10/13/2019] [Accepted: 10/15/2019] [Indexed: 06/10/2023]
Abstract
INTRODUCTION Innovative strategy is urgently needed to precisely discover novel natural products as lead compounds for development of new drugs against orphan diseases such as triple-negative breast cancer (TNBC). Herein, we describe a targeting pharmacophore with probe-reactivity-guided strategy for the discovery of electrophilic sesquiterpene (ES), a class of bioactive natural product. OBJECTIVE This study aimed to identify pharmacophore, based on pharmacophore with probe-reactivity-guided strategy for precisely discovering ESs from ethyl acetate extract of Eupatorium chinense L. (EEEChL) METHODOLOGY: MTT assay combined with ultra-performance liquid chromatography (UPLC) analysis was used to identify pharmacophore. UPLC-mass spectrometry (MS) was applied to carefully compare the intrinsic reactivity characteristics of two chemoselective nucleophilic probes: glutathione (GSH) and 4-bromothiophenol (BTP) reaction with ESs. ESs was isolated and identified from EEEChL by phytochemical methods. Furthermore, stoichiometric ratio and binding site of one typical ES 8β-[4'-hydroxytigloyloxy]-5-desoxy-8-desacyleuparotin (HDDE) reaction with BTP were studied by UPLC-quadrupole time-of-flight (Q-TOF)-MS and two-dimensional nuclear magnetic resonance (NMR). RESULTS Eleven ESs were identified from EEEChL, MTT assay illustrated that all of the 11 ESs possess fairly good anti-TNBC activity CONCLUSIONS: Electrophilic groups were confirmed as pharmacophore of bioactive compounds contained in EEEChL. An optimised halogenated aromatic probe BTP furnishes ES-BTP conjugates that are highly conspicuous via MS by virtue of a unique isotopic bromine signature, conjugates also have a considerable separation on C18 column. The new probe-reactivity-guided strategy can effectively improve the traditional bioassay-guided approaches, and significantly increase the probability of obtaining designated bioactive compounds.
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Affiliation(s)
- QingLi Jiang
- College of Pharmaceutical Sciences, Zhejiang Chinese Medical University, No. 260 Baichuan Street, Hangzhou, 311402, P. R. China
| | - ZhiHui Zhu
- College of Pharmaceutical Sciences, Zhejiang Chinese Medical University, No. 260 Baichuan Street, Hangzhou, 311402, P. R. China
| | - PanTing Shou
- College of Pharmaceutical Sciences, Zhejiang Chinese Medical University, No. 260 Baichuan Street, Hangzhou, 311402, P. R. China
| | - Fei Teng
- College of Pharmaceutical Sciences, Zhejiang Chinese Medical University, No. 260 Baichuan Street, Hangzhou, 311402, P. R. China
| | - Ying Zhu
- College of Pharmaceutical Sciences, Zhejiang Chinese Medical University, No. 260 Baichuan Street, Hangzhou, 311402, P. R. China
| | - HuaJun Zhao
- College of Pharmaceutical Sciences, Zhejiang Chinese Medical University, No. 260 Baichuan Street, Hangzhou, 311402, P. R. China
| | - Bo Yang
- College of Pharmaceutical Sciences, Zhejiang Chinese Medical University, No. 260 Baichuan Street, Hangzhou, 311402, P. R. China
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8
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Massicard JM, Soligot C, Weissman KJ, Jacob C. Manipulating polyketide stereochemistry by exchange of polyketide synthase modules. Chem Commun (Camb) 2020; 56:12749-12752. [DOI: 10.1039/d0cc05068g] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023]
Abstract
Exchange of polyketide synthase (PKS) modules by genetic engineering leads to efficient modification of polyketide stereochemistry.
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Affiliation(s)
| | - Claire Soligot
- Université de Lorraine
- UR AFPA
- USC 340 INRAE
- F-54000 Nancy
- France
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9
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Konaklieva MI. Addressing Antimicrobial Resistance through New Medicinal and Synthetic Chemistry Strategies. SLAS DISCOVERY 2018; 24:419-439. [PMID: 30523713 DOI: 10.1177/2472555218812657] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
Over the past century, a multitude of derivatives of structural scaffolds with established antimicrobial potential have been prepared and tested, and a variety of new scaffolds have emerged. The effectiveness of antibiotics, however, is in sharp decline because of the emergence of drug-resistant microorganisms. The prevalence of drug resistance, both in clinical and community settings, is a consequence of bacterial ingenuity in altering pathways and/or cell morphology, making it a persistent threat to human health. The fundamental ability of pathogens to survive in a multitude of habitats can be triggered by recognition of chemical signals that warn organisms of exposure to a potentially harmful environment. Host immune defenses, including reactive oxygen intermediates and antibacterial substances, are among the multitude of chemical signals that can subsequently trigger expression of phenotypes better adapted for survival in that hostile environment. Thus, resistance development appears to be unavoidable, which leads to the conclusion that developing an alternative perspective for treatment options is vital. This review will discuss emerging medicinal chemistry approaches for addressing the global multidrug resistance in the 21st century.
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10
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Gerlt JA. Genomic Enzymology: Web Tools for Leveraging Protein Family Sequence-Function Space and Genome Context to Discover Novel Functions. Biochemistry 2017; 56:4293-4308. [PMID: 28826221 PMCID: PMC5569362 DOI: 10.1021/acs.biochem.7b00614] [Citation(s) in RCA: 140] [Impact Index Per Article: 20.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
![]()
The exponentially increasing number
of protein and nucleic acid
sequences provides opportunities to discover novel enzymes, metabolic
pathways, and metabolites/natural products, thereby adding to our
knowledge of biochemistry and biology. The challenge has evolved from
generating sequence information to mining the databases to integrating
and leveraging the available information, i.e., the availability of
“genomic enzymology” web tools. Web tools that allow
identification of biosynthetic gene clusters are widely used by the
natural products/synthetic biology community, thereby facilitating
the discovery of novel natural products and the enzymes responsible
for their biosynthesis. However, many novel enzymes with interesting
mechanisms participate in uncharacterized small-molecule metabolic
pathways; their discovery and functional characterization also can
be accomplished by leveraging information in protein and nucleic acid
databases. This Perspective focuses on two genomic enzymology web
tools that assist the discovery novel metabolic pathways: (1) Enzyme
Function Initiative-Enzyme Similarity Tool (EFI-EST) for generating
sequence similarity networks to visualize and analyze sequence–function
space in protein families and (2) Enzyme Function Initiative-Genome
Neighborhood Tool (EFI-GNT) for generating genome neighborhood networks
to visualize and analyze the genome context in microbial and fungal
genomes. Both tools have been adapted to other applications to facilitate
target selection for enzyme discovery and functional characterization.
As the natural products community has demonstrated, the enzymology
community needs to embrace the essential role of web tools that allow
the protein and genome sequence databases to be leveraged for novel
insights into enzymological problems.
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Affiliation(s)
- John A Gerlt
- Departments of Biochemistry and Chemistry, Institute for Genomic Biology, University of Illinois , Urbana-Champaign Urbana, Illinois 61801, United States
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11
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Tietz JI, Schwalen CJ, Patel PS, Maxson T, Blair PM, Tai HC, Zakai UI, Mitchell DA. A new genome-mining tool redefines the lasso peptide biosynthetic landscape. Nat Chem Biol 2017; 13:470-478. [PMID: 28244986 PMCID: PMC5391289 DOI: 10.1038/nchembio.2319] [Citation(s) in RCA: 289] [Impact Index Per Article: 41.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2016] [Accepted: 12/06/2016] [Indexed: 12/14/2022]
Abstract
Ribosomally synthesized and post-translationally modified peptide (RiPP) natural products are attractive for genome-driven discovery and re-engineering, but limitations in bioinformatic methods and exponentially increasing genomic data make large-scale mining of RiPP data difficult. We report RODEO (Rapid ORF Description and Evaluation Online), which combines hidden-Markov-model-based analysis, heuristic scoring, and machine learning to identify biosynthetic gene clusters and predict RiPP precursor peptides. We initially focused on lasso peptides, which display intriguing physicochemical properties and bioactivities, but their hypervariability renders them challenging prospects for automated mining. Our approach yielded the most comprehensive mapping to date of lasso peptide space, revealing >1,300 compounds. We characterized the structures and bioactivities of six lasso peptides, prioritized based on predicted structural novelty, including one with an unprecedented handcuff-like topology and another with a citrulline modification exceptionally rare among bacteria. These combined insights significantly expand the knowledge of lasso peptides and, more broadly, provide a framework for future genome-mining efforts.
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Affiliation(s)
- Jonathan I Tietz
- Department of Chemistry, University of Illinois at Urbana-Champaign, Urbana, Illinois, USA
| | - Christopher J Schwalen
- Department of Chemistry, University of Illinois at Urbana-Champaign, Urbana, Illinois, USA
| | - Parth S Patel
- Department of Chemistry, University of Illinois at Urbana-Champaign, Urbana, Illinois, USA
| | - Tucker Maxson
- Department of Chemistry, University of Illinois at Urbana-Champaign, Urbana, Illinois, USA
| | - Patricia M Blair
- Department of Chemistry, University of Illinois at Urbana-Champaign, Urbana, Illinois, USA
| | - Hua-Chia Tai
- Department of Chemistry, University of Illinois at Urbana-Champaign, Urbana, Illinois, USA
| | - Uzma I Zakai
- Department of Chemistry, University of Illinois at Urbana-Champaign, Urbana, Illinois, USA
| | - Douglas A Mitchell
- Department of Chemistry, University of Illinois at Urbana-Champaign, Urbana, Illinois, USA.,Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, Illinois, USA.,Department of Microbiology, University of Illinois at Urbana-Champaign, Urbana, Illinois, USA
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12
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Weissman KJ. Polyketide stereocontrol: a study in chemical biology. Beilstein J Org Chem 2017; 13:348-371. [PMID: 28326145 PMCID: PMC5331325 DOI: 10.3762/bjoc.13.39] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2016] [Accepted: 02/01/2017] [Indexed: 11/23/2022] Open
Abstract
The biosynthesis of reduced polyketides in bacteria by modular polyketide synthases (PKSs) proceeds with exquisite stereocontrol. As the stereochemistry is intimately linked to the strong bioactivity of these molecules, the origins of stereochemical control are of significant interest in attempts to create derivatives of these compounds by genetic engineering. In this review, we discuss the current state of knowledge regarding this key aspect of the biosynthetic pathways. Given that much of this information has been obtained using chemical biology tools, work in this area serves as a showcase for the power of this approach to provide answers to fundamental biological questions.
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Affiliation(s)
- Kira J Weissman
- UMR 7365, Ingénierie Moléculaire et Physiopathologie Articulaire (IMoPA), CNRS-Université de Lorraine, Biopôle de l’Université de Lorraine, Campus Biologie Santé, Avenue de la Forêt de Haye, BP 50184, 54505 Vandœuvre-lès-Nancy Cedex, France
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Maxson T, Tietz JI, Hudson GA, Guo XR, Tai HC, Mitchell DA. Targeting Reactive Carbonyls for Identifying Natural Products and Their Biosynthetic Origins. J Am Chem Soc 2016; 138:15157-15166. [PMID: 27797509 DOI: 10.1021/jacs.6b06848] [Citation(s) in RCA: 38] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
Abstract
Natural products (NPs) serve important roles as drug candidates and as tools for chemical biology. However, traditional NP discovery, largely based on bioassay-guided approaches, is biased toward abundant compounds and rediscovery rates are high. Orthogonal methods to facilitate discovery of new NPs are thus needed, and herein we describe an isotope tag-based expansion of reactivity-based NP screening to address these shortcomings. Reactivity-based screening is a directed discovery approach in which a specific reactive handle on the NP is targeted by a chemoselective probe to enable its detection by mass spectrometry. In this study, we have developed an aminooxy-containing probe to guide the discovery of aldehyde- and ketone-containing NPs. To facilitate the detection of labeling events, the probe was dibrominated, imparting a unique isotopic signature to distinguish labeled metabolites from spectral noise. As a proof of concept, the probe was then utilized to screen a collection of bacterial extracts, leading to the identification of a new analogue of antipain, deimino-antipain. The bacterial producer of deimino-antipain was sequenced and the responsible biosynthetic gene cluster was identified by bioinformatic analysis and heterologous expression. These data reveal the previously undetermined genetic basis for a well-known family of aldehyde-containing, peptidic protease inhibitors, including antipain, chymostatin, leupeptin, elastatinal, and microbial alkaline protease inhibitor, which have been widely used for over 40 years.
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Affiliation(s)
- Tucker Maxson
- Department of Chemistry, University of Illinois at Urbana-Champaign , Urbana, Illinois 61801, United States
| | - Jonathan I Tietz
- Department of Chemistry, University of Illinois at Urbana-Champaign , Urbana, Illinois 61801, United States
| | - Graham A Hudson
- Department of Chemistry, University of Illinois at Urbana-Champaign , Urbana, Illinois 61801, United States
| | - Xiao Rui Guo
- Department of Chemistry, University of Illinois at Urbana-Champaign , Urbana, Illinois 61801, United States
| | - Hua-Chia Tai
- Department of Chemistry, University of Illinois at Urbana-Champaign , Urbana, Illinois 61801, United States
| | - Douglas A Mitchell
- Department of Chemistry, University of Illinois at Urbana-Champaign , Urbana, Illinois 61801, United States.,Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign , Urbana, Illinois 61801, United States.,Department of Microbiology, University of Illinois at Urbana-Champaign , Urbana, Illinois 61801, United States
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