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Gribble GW. Naturally Occurring Organohalogen Compounds-A Comprehensive Review. PROGRESS IN THE CHEMISTRY OF ORGANIC NATURAL PRODUCTS 2023; 121:1-546. [PMID: 37488466 DOI: 10.1007/978-3-031-26629-4_1] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/26/2023]
Abstract
The present volume is the third in a trilogy that documents naturally occurring organohalogen compounds, bringing the total number-from fewer than 25 in 1968-to approximately 8000 compounds to date. Nearly all of these natural products contain chlorine or bromine, with a few containing iodine and, fewer still, fluorine. Produced by ubiquitous marine (algae, sponges, corals, bryozoa, nudibranchs, fungi, bacteria) and terrestrial organisms (plants, fungi, bacteria, insects, higher animals) and universal abiotic processes (volcanos, forest fires, geothermal events), organohalogens pervade the global ecosystem. Newly identified extraterrestrial sources are also documented. In addition to chemical structures, biological activity, biohalogenation, biodegradation, natural function, and future outlook are presented.
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Affiliation(s)
- Gordon W Gribble
- Department of Chemistry, Dartmouth College, Hanover, NH, 03755, USA.
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2
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Ribeiro I, Antunes JT, Alexandrino DAM, Tomasino MP, Almeida E, Hilário A, Urbatzka R, Leão PN, Mucha AP, Carvalho MF. Actinobacteria from Arctic and Atlantic deep-sea sediments-Biodiversity and bioactive potential. Front Microbiol 2023; 14:1158441. [PMID: 37065153 PMCID: PMC10100589 DOI: 10.3389/fmicb.2023.1158441] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2023] [Accepted: 03/07/2023] [Indexed: 04/18/2023] Open
Abstract
The deep-sea covers over 70% of the Earth's surface and harbors predominantly uncharacterized bacterial communities. Actinobacteria are the major prokaryotic source of bioactive natural products that find their way into drug discovery programs, and the deep-sea is a promising source of biotechnologically relevant actinobacteria. Previous studies on actinobacteria in deep-sea sediments were either regionally restricted or did not combine a community characterization with the analysis of their bioactive potential. Here we characterized the actinobacterial communities of upper layers of deep-sea sediments from the Arctic and the Atlantic (Azores and Madeira) ocean basins, employing 16S rRNA metabarcoding, and studied the biosynthetic potential of cultivable actinobacteria retrieved from those samples. Metabarcoding analysis showed that the actinobacterial composition varied between the sampled regions, with higher abundance in the Arctic samples but higher diversity in the Atlantic ones. Twenty actinobacterial genera were detected using metabarcoding, as a culture-independent method, while culture-dependent methods only allowed the identification of nine genera. Isolation of actinobacteria resulted on the retrieval of 44 isolates, mainly associated with Brachybacterium, Microbacterium, and Brevibacterium genera. Some of these isolates were only identified on a specific sampled region. Chemical extracts of the actinobacterial isolates were subsequently screened for their antimicrobial, anticancer and anti-inflammatory activities. Extracts from two Streptomyces strains demonstrated activity against Candida albicans. Additionally, eight extracts (obtained from Brachybacterium, Brevibacterium, Microbacterium, Rhodococcus, and Streptomyces isolates) showed significant activity against at least one of the tested cancer cell lines (HepG2 and T-47D). Furthermore, 15 actinobacterial extracts showed anti-inflammatory potential in the RAW 264.4 cell model assay, with no concomitant cytotoxic response. Dereplication and molecular networking analysis of the bioactive actinobacterial extracts showed the presence of some metabolites associated with known natural products, but one of the analyzed clusters did not show any match with the natural products described as responsible for these bioactivities. Overall, we were able to recover taxonomically diverse actinobacteria with different bioactivities from the studied deep-sea samples. The conjugation of culture-dependent and -independent methods allows a better understanding of the actinobacterial diversity of deep-sea environments, which is important for the optimization of approaches to obtain novel chemically-rich isolates.
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Affiliation(s)
- Inês Ribeiro
- CIIMAR - Interdisciplinary Centre of Marine and Environmental Research, University of Porto, Porto, Portugal
- School of Medicine and Biomedical Sciences (ICBAS), University of Porto, Porto, Portugal
- *Correspondence: Inês Ribeiro,
| | - Jorge T. Antunes
- CIIMAR - Interdisciplinary Centre of Marine and Environmental Research, University of Porto, Porto, Portugal
| | - Diogo A. M. Alexandrino
- CIIMAR - Interdisciplinary Centre of Marine and Environmental Research, University of Porto, Porto, Portugal
- Department of Environmental Health, School of Health, Polytechnic of Porto, Porto, Portugal
| | - Maria Paola Tomasino
- CIIMAR - Interdisciplinary Centre of Marine and Environmental Research, University of Porto, Porto, Portugal
| | - Eduarda Almeida
- CIIMAR - Interdisciplinary Centre of Marine and Environmental Research, University of Porto, Porto, Portugal
- Department of Biology, FCUP - Faculty of Sciences of the University of Porto, Porto, Portugal
| | - Ana Hilário
- Centre for Environmental and Marine Studies and Department of Biology, University of Aveiro, Aveiro, Portugal
| | - Ralph Urbatzka
- CIIMAR - Interdisciplinary Centre of Marine and Environmental Research, University of Porto, Porto, Portugal
| | - Pedro N. Leão
- CIIMAR - Interdisciplinary Centre of Marine and Environmental Research, University of Porto, Porto, Portugal
| | - Ana P. Mucha
- CIIMAR - Interdisciplinary Centre of Marine and Environmental Research, University of Porto, Porto, Portugal
- Department of Biology, FCUP - Faculty of Sciences of the University of Porto, Porto, Portugal
| | - Maria F. Carvalho
- CIIMAR - Interdisciplinary Centre of Marine and Environmental Research, University of Porto, Porto, Portugal
- School of Medicine and Biomedical Sciences (ICBAS), University of Porto, Porto, Portugal
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3
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Ji X, Nie J, Peng X, Hu J, Xu X, Huang Y, Li Y, Jiang H. Palladium-Catalyzed Cross Haloalkynylation of Haloalkynes. Org Lett 2022; 24:3384-3388. [PMID: 35481743 DOI: 10.1021/acs.orglett.2c01161] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Herein, we have developed a robust Pd-catalyzed haloalkynylation of haloalkynes for the synthesis of dihaloalkenyne derivatives. This cross-haloalkynylation reaction proceeds in a highly chemo- and regioselective manner under mild conditions in the presence of two slightly structurally different haloalkynes and shows strong functional group tolerance under ligand- and base-free conditions.
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Affiliation(s)
- Xiaoliang Ji
- School of Biotechnology and Health Sciences, Wuyi University, Jiangmen, Guangdong 529090, China
| | - Jinli Nie
- School of Biotechnology and Health Sciences, Wuyi University, Jiangmen, Guangdong 529090, China
| | - Xin Peng
- School of Biotechnology and Health Sciences, Wuyi University, Jiangmen, Guangdong 529090, China
| | - Jinhui Hu
- School of Biotechnology and Health Sciences, Wuyi University, Jiangmen, Guangdong 529090, China
| | - Xuetao Xu
- School of Biotechnology and Health Sciences, Wuyi University, Jiangmen, Guangdong 529090, China
| | - Yubing Huang
- School of Biotechnology and Health Sciences, Wuyi University, Jiangmen, Guangdong 529090, China
| | - Yibiao Li
- School of Biotechnology and Health Sciences, Wuyi University, Jiangmen, Guangdong 529090, China
| | - Huanfeng Jiang
- Key Lab of Functional Molecular Engineering of Guangdong Province, School of Chemistry and Chemical Engineering, South China University of Technology, Guangzhou 510641, China
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4
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Girija A, Vijayanathan M, Sreekumar S, Basheer J, Menon TG, Krishnankutty RE, Soniya EV. Harnessing the natural pool of polyketide and non-ribosomal peptide family: A route map towards novel drug development. Curr Mol Pharmacol 2021; 15:265-291. [PMID: 33745440 DOI: 10.2174/1874467214666210319145816] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2020] [Revised: 12/10/2020] [Accepted: 12/31/2020] [Indexed: 11/22/2022]
Abstract
Emergence of communicable and non-communicable diseases possess health challenge to millions of people worldwide and is a major threat to the economic and social development in the coming century. The occurrence of recent pandemic, SARS-CoV-2 caused by lethal severe acute respiratory syndrome coronavirus 2 is one such example. Rapid research and development of drugs for the treatment and management of these diseases has been an incredibly challenging task for the pharmaceutical industry. Although, substantial focus has been made in the discovery of therapeutic compounds from natural sources having significant medicinal potential, their synthesis has shown a slow progress. Hence, the discovery of new targets by the application of the latest biotechnological and synthetic biology approaches is very much the need of the hour. Polyketides (PKs) and non-ribosomal peptides (NRPs) found in bacteria, fungi and plants are a large diverse family of natural products synthesized by two classes of enzymes: polyketide synthases (PKS) and non-ribosomal peptide synthetases (NRPS). These enzymes possess immense biomedical potential due to their simple architecture, catalytic capacity, as well as diversity. With the advent of latest in-silico and in-vitro strategies, these enzymes and their related metabolic pathways, if targeted, can contribute highly towards the biosynthesis of an array of potentially natural drug leads that have antagonist effects on biopolymers associated with various human diseases. In the face of the rising threat from the multidrug-resistant pathogens, this will further open new avenues for the discovery of novel and improved drugs by combining the natural and the synthetic approaches. This review discusses the relevance of polyketides and non-ribosomal peptides and the improvement strategies for the development of their derivatives and scaffolds, and how they will be beneficial to the future bioprospecting and drug discovery.
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Affiliation(s)
- Aiswarya Girija
- Transdisciplinary Biology, Rajiv Gandhi Centre for Biotechnology (RGCB), Thiruvananthapuram, Kerala, India.,Institute of Biological Environmental Rural Sciences (IBERS), Aberystwyth University, United Kingdom
| | - Mallika Vijayanathan
- Transdisciplinary Biology, Rajiv Gandhi Centre for Biotechnology (RGCB), Thiruvananthapuram, Kerala, India.,Biology Centre - Institute of Plant Molecular Biology, Czech Academy of Sciences, České Budějovice, 370 05, Czech Republic
| | - Sweda Sreekumar
- Transdisciplinary Biology, Rajiv Gandhi Centre for Biotechnology (RGCB), Thiruvananthapuram, Kerala, India.,Research Centre, University of Kerala, India
| | - Jasim Basheer
- School of Biosciences, Mahatma Gandhi University, PD Hills, Kottayam, Kerala, India.,Department of Cell Biology, Centre of the Region Haná for Biotechnological and Agricultural Research, Palacky University, Olomouc, Czech Republic
| | - Tara G Menon
- Transdisciplinary Biology, Rajiv Gandhi Centre for Biotechnology (RGCB), Thiruvananthapuram, Kerala, India
| | | | - Eppurathu Vasudevan Soniya
- Transdisciplinary Biology, Rajiv Gandhi Centre for Biotechnology (RGCB), Thiruvananthapuram, Kerala, India
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6
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Menon BRK, Richmond D, Menon N. Halogenases for biosynthetic pathway engineering: Toward new routes to naturals and non-naturals. CATALYSIS REVIEWS-SCIENCE AND ENGINEERING 2020. [DOI: 10.1080/01614940.2020.1823788] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Affiliation(s)
- Binuraj R. K. Menon
- Warwick Integrative Synthetic Biology Centre, School of Life Sciences, University of Warwick, Coventry, UK
| | - Daniel Richmond
- Warwick Integrative Synthetic Biology Centre, School of Life Sciences, University of Warwick, Coventry, UK
| | - Navya Menon
- Warwick Integrative Synthetic Biology Centre, School of Life Sciences, University of Warwick, Coventry, UK
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7
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Morgan KT, Zheng J, McCafferty DG. Discovery of Six Ramoplanin Family Gene Clusters and the Lipoglycodepsipeptide Chersinamycin*. Chembiochem 2020; 22:176-185. [PMID: 32805078 DOI: 10.1002/cbic.202000555] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2020] [Indexed: 11/10/2022]
Abstract
Ramoplanins and enduracidins are peptidoglycan lipid intermediate II-binding lipodepsipeptides with broad-spectrum activity against methicillin- and vancomycin-resistant Gram-positive pathogens. Targeted genome mining using probes from conserved sequences within the ramoplanin/enduracidin biosynthetic gene clusters (BGCs) was used to identify six microorganisms with BGCs predicted to produce unique lipodepsipeptide congeners of ramoplanin and enduracidin. Fermentation of Micromonospora chersina yielded a novel lipoglycodepsipeptide, called chersinamycin, which exhibited good antibiotic activity against Gram-positive bacteria (1-2 μg/mL) similar to the ramoplanins and enduracidins. The covalent structure of chersinamycin was determined by NMR spectroscopy and tandem mass spectrometry in conjunction with chemical degradation studies. These six new BGCs and isolation of a new antimicrobial peptide provide much-needed tools to investigate the fundamental aspects of lipodepsipeptide biosynthesis and to facilitate efforts to produce novel antibiotics capable of combating antibiotic-resistant infections.
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Affiliation(s)
- Kelsey T Morgan
- Department of Chemistry, Duke University, Durham, NC 27708, USA
| | - Jeffrey Zheng
- Department of Chemistry, Duke University, Durham, NC 27708, USA
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8
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Semi-rational mutagenesis of an industrial Streptomyces fungicidicus strain for improved enduracidin productivity. Appl Microbiol Biotechnol 2020; 104:3459-3471. [DOI: 10.1007/s00253-020-10488-0] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2020] [Revised: 02/14/2020] [Accepted: 02/18/2020] [Indexed: 12/21/2022]
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9
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Chen YW, Liu XC, Lv FX, Li P. Characterization of three regulatory genes involved in enduracidin biosynthesis and improvement of enduracidin production in Streptomyces fungicidicus. J Appl Microbiol 2019; 127:1698-1705. [PMID: 31424146 DOI: 10.1111/jam.14417] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2019] [Revised: 07/27/2019] [Accepted: 07/30/2019] [Indexed: 12/25/2022]
Abstract
AIMS To increase enduracidin production in Streptomyces fungicidicus ATCC 31731 by overexpressing positive regulators in enduracidin biosynthesis. METHODS AND RESULTS Genes orf22 and orf42 were knocked out by in-frame deletion based on CRISPR/Cas9 strategy, while the orf41 gene was inactivated by replacing it with the apramycin resistance gene cassette aac(3)IV using a fast screening blue/white system. The integrative plasmid pSET152ermE was used for the overexpression of orf22, orf41 and orf42 individually. The constructed plasmids were transformed into wild-type strain Streptomyces fungicidicus ATCC 31731. Three gene inactivation mutants Δorf22, Δorf41 and Δorf42 and three recombinant strains overexpressing orf22, orf41 and orf42 were all fermented and the enduracidin production of each strain was detected and compared by HPLC analysis. Two resulting engineered strains were generated through overexpression of gene orf22 and orf42 in Streptomyces fungicidicus, respectively, and in these strains the enduracidins titres were increased by approximately 4·0-fold and 2·3-fold higher than that of the wild-type strain. CONCLUSIONS The functions of three regulatory genes orf22, orf41 and orf42 in the enduracidin gene cluster in Streptomyces fungicidicus ATCC 31731 were examined. The orf22 gene, encoding a SARP family protein, was proposed to act in a positive manner. The proteins encoded by genes orf41 and orf42 were proposed to compose a two-component regulation system, in which the response protein Orf41 was characterized as a repressor, and the kinase Orf42 was shown to be an activator. The production of enduracidins was improved considerably by overexpression of the two positive regulatory genes orf22 and orf42 respectively. SIGNIFICANCE AND IMPACT OF THE STUDY The production of enduracidins was successfully improved by manipulating the regulatory genes involving in enduracidin biosynthesis, providing an efficient approach to improve enduracidin production further for fermentation industry and synthetic biological research.
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Affiliation(s)
- Y-W Chen
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China.,Hebei Shuangge Food Co. Ltd, Shijiazhuang, China
| | - X-C Liu
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China.,College of Food Science and Technology, Nanjing Agricultural University, Nanjing, China
| | - F-X Lv
- College of Food Science and Technology, Nanjing Agricultural University, Nanjing, China
| | - P Li
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China.,University of Chinese Academy of Sciences, Beijing, China
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10
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Kaniusaite M, Tailhades J, Marschall EA, Goode RJA, Schittenhelm RB, Cryle MJ. A proof-reading mechanism for non-proteinogenic amino acid incorporation into glycopeptide antibiotics. Chem Sci 2019; 10:9466-9482. [PMID: 32055321 PMCID: PMC6993612 DOI: 10.1039/c9sc03678d] [Citation(s) in RCA: 34] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2019] [Accepted: 08/29/2019] [Indexed: 01/09/2023] Open
Abstract
A complex interplay of non-ribosomal peptide synthetase domains works together with trans-acting enzymes to ensure effective GPA biosynthesis.
Non-ribosomal peptide biosynthesis produces highly diverse natural products through a complex cascade of enzymatic reactions that together function with high selectivity to produce bioactive peptides. The modification of non-ribosomal peptide synthetase (NRPS)-bound amino acids can introduce significant structural diversity into these peptides and has exciting potential for biosynthetic redesign. However, the control mechanisms ensuring selective modification of specific residues during NRPS biosynthesis have previously been unclear. Here, we have characterised the incorporation of the non-proteinogenic amino acid 3-chloro-β-hydroxytyrosine during glycopeptide antibiotic (GPA) biosynthesis. Our results demonstrate that the modification of this residue by trans-acting enzymes is controlled by the selectivity of the upstream condensation domain responsible for peptide synthesis. A proofreading thioesterase works together with this process to ensure that effective peptide biosynthesis proceeds even when the selectivity of key amino acid activation domains within the NRPS is low. Furthermore, the exchange of condensation domains with altered amino acid specificities allows the modification of such residues within NRPS biosynthesis to be controlled, which will doubtless prove important for reengineering of these assembly lines. Taken together, our results indicate the importance of the complex interplay of NRPS domains and trans-acting enzymes to ensure effective GPA biosynthesis, and in doing so reveals a process that is mechanistically comparable to the hydrolytic proofreading function of tRNA synthetases in ribosomal protein synthesis.
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Affiliation(s)
- Milda Kaniusaite
- The Monash Biomedicine Discovery Institute , Department of Biochemistry and Molecular Biology , Monash University , Clayton , Victoria 3800 , Australia . .,EMBL Australia , Monash University , Clayton , Victoria 3800 , Australia
| | - Julien Tailhades
- The Monash Biomedicine Discovery Institute , Department of Biochemistry and Molecular Biology , Monash University , Clayton , Victoria 3800 , Australia . .,EMBL Australia , Monash University , Clayton , Victoria 3800 , Australia
| | - Edward A Marschall
- The Monash Biomedicine Discovery Institute , Department of Biochemistry and Molecular Biology , Monash University , Clayton , Victoria 3800 , Australia . .,EMBL Australia , Monash University , Clayton , Victoria 3800 , Australia
| | - Robert J A Goode
- The Monash Biomedicine Discovery Institute , Department of Biochemistry and Molecular Biology , Monash University , Clayton , Victoria 3800 , Australia . .,Monash Proteomics and Metabolomics Facility , Monash University , Clayton , Victoria 3800 , Australia
| | - Ralf B Schittenhelm
- The Monash Biomedicine Discovery Institute , Department of Biochemistry and Molecular Biology , Monash University , Clayton , Victoria 3800 , Australia . .,Monash Proteomics and Metabolomics Facility , Monash University , Clayton , Victoria 3800 , Australia
| | - Max J Cryle
- The Monash Biomedicine Discovery Institute , Department of Biochemistry and Molecular Biology , Monash University , Clayton , Victoria 3800 , Australia . .,EMBL Australia , Monash University , Clayton , Victoria 3800 , Australia
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11
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Agrawal S, Acharya D, Adholeya A, Barrow CJ, Deshmukh SK. Nonribosomal Peptides from Marine Microbes and Their Antimicrobial and Anticancer Potential. Front Pharmacol 2017; 8:828. [PMID: 29209209 PMCID: PMC5702503 DOI: 10.3389/fphar.2017.00828] [Citation(s) in RCA: 88] [Impact Index Per Article: 12.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2017] [Accepted: 10/31/2017] [Indexed: 11/13/2022] Open
Abstract
Marine environments are largely unexplored and can be a source of new molecules for the treatment of many diseases such as malaria, cancer, tuberculosis, HIV etc. The Marine environment is one of the untapped bioresource of getting pharmacologically active nonribosomal peptides (NRPs). Bioprospecting of marine microbes have achieved many remarkable milestones in pharmaceutics. Till date, more than 50% of drugs which are in clinical use belong to the nonribosomal peptide or mixed polyketide-nonribosomal peptide families of natural products isolated from marine bacteria, cyanobacteria and fungi. In recent years large numbers of nonribosomal have been discovered from marine microbes using multi-disciplinary approaches. The present review covers the NRPs discovered from marine microbes and their pharmacological potential along with role of genomics, proteomics and bioinformatics in discovery and development of nonribosomal peptides drugs.
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Affiliation(s)
- Shivankar Agrawal
- Biotechnology and Management of Bioresources Division, TERI-Deakin Nano Biotechnology Centre, Energy and Resources Institute, New Delhi, India.,Centre for Chemistry and Biotechnology, School of Life and Environmental Sciences, Deakin University, Waurn Ponds, VIC, Australia
| | - Debabrata Acharya
- Biotechnology and Management of Bioresources Division, TERI-Deakin Nano Biotechnology Centre, Energy and Resources Institute, New Delhi, India
| | - Alok Adholeya
- Biotechnology and Management of Bioresources Division, TERI-Deakin Nano Biotechnology Centre, Energy and Resources Institute, New Delhi, India
| | - Colin J Barrow
- Centre for Chemistry and Biotechnology, School of Life and Environmental Sciences, Deakin University, Waurn Ponds, VIC, Australia
| | - Sunil K Deshmukh
- Biotechnology and Management of Bioresources Division, TERI-Deakin Nano Biotechnology Centre, Energy and Resources Institute, New Delhi, India
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12
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Kittilä T, Kittel C, Tailhades J, Butz D, Schoppet M, Büttner A, Goode RJA, Schittenhelm RB, van Pee KH, Süssmuth RD, Wohlleben W, Cryle MJ, Stegmann E. Halogenation of glycopeptide antibiotics occurs at the amino acid level during non-ribosomal peptide synthesis. Chem Sci 2017; 8:5992-6004. [PMID: 28989629 PMCID: PMC5620994 DOI: 10.1039/c7sc00460e] [Citation(s) in RCA: 38] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2017] [Accepted: 06/20/2017] [Indexed: 12/30/2022] Open
Abstract
Halogenation plays a significant role in the activity of the glycopeptide antibiotics (GPAs), although up until now the timing and therefore exact substrate involved was unclear. Here, we present results combined from in vivo and in vitro studies that reveal the substrates for the halogenase enzymes from GPA biosynthesis as amino acid residues bound to peptidyl carrier protein (PCP)-domains from the non-ribosomal peptide synthetase machinery: no activity was detected upon either free amino acids or PCP-bound peptides. Furthermore, we show that the selectivity of GPA halogenase enzymes depends upon both the structure of the bound amino acid and the PCP domain, rather than being driven solely via the PCP domain. These studies provide the first detailed understanding of how halogenation is performed during GPA biosynthesis and highlight the importance and versatility of trans-acting enzymes that operate during peptide assembly by non-ribosomal peptide synthetases.
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Affiliation(s)
- Tiia Kittilä
- Department of Biomolecular Mechanisms , Max Planck Institute for Medical Research , Jahnstrasse 29 , 69120 Heidelberg , Germany
| | - Claudia Kittel
- Interfaculty Institute of Microbiology and Infection Medicine Tuebingen , Microbiology/Biotechnology , University of Tuebingen , Auf der Morgenstelle 28 , 72076 Tuebingen , Germany .
| | - Julien Tailhades
- EMBL Australia , Monash University , Clayton , Victoria 3800 , Australia .
- The Monash Biomedicine Discovery Institute , Department of Biochemistry and Molecular Biology , Monash University , Clayton , Victoria 3800 , Australia
| | - Diane Butz
- Institut für Chemie , Technische Universität Berlin , 10623 Berlin , Germany
| | - Melanie Schoppet
- Department of Biomolecular Mechanisms , Max Planck Institute for Medical Research , Jahnstrasse 29 , 69120 Heidelberg , Germany
- EMBL Australia , Monash University , Clayton , Victoria 3800 , Australia .
- The Monash Biomedicine Discovery Institute , Department of Biochemistry and Molecular Biology , Monash University , Clayton , Victoria 3800 , Australia
| | - Anita Büttner
- Allgemeine Biochemie , TU Dresden , 01062 Dresden , Germany
| | - Rob J A Goode
- The Monash Biomedicine Discovery Institute , Department of Biochemistry and Molecular Biology , Monash University , Clayton , Victoria 3800 , Australia
- Monash Biomedical Proteomics Facility , Monash University , Clayton , Victoria 3800 , Australia
| | - Ralf B Schittenhelm
- The Monash Biomedicine Discovery Institute , Department of Biochemistry and Molecular Biology , Monash University , Clayton , Victoria 3800 , Australia
- Monash Biomedical Proteomics Facility , Monash University , Clayton , Victoria 3800 , Australia
| | - Karl-Heinz van Pee
- Institut für Chemie , Technische Universität Berlin , 10623 Berlin , Germany
| | | | - Wolfgang Wohlleben
- Interfaculty Institute of Microbiology and Infection Medicine Tuebingen , Microbiology/Biotechnology , University of Tuebingen , Auf der Morgenstelle 28 , 72076 Tuebingen , Germany .
- German Centre for Infection Research (DZIF) , Partner Site Tuebingen , Tuebingen , Germany
| | - Max J Cryle
- Department of Biomolecular Mechanisms , Max Planck Institute for Medical Research , Jahnstrasse 29 , 69120 Heidelberg , Germany
- EMBL Australia , Monash University , Clayton , Victoria 3800 , Australia .
- The Monash Biomedicine Discovery Institute , Department of Biochemistry and Molecular Biology , Monash University , Clayton , Victoria 3800 , Australia
- ARC Centre of Excellence in Advanced Molecular Imaging , Monash University , Clayton , Victoria 3800 , Australia
| | - Evi Stegmann
- Interfaculty Institute of Microbiology and Infection Medicine Tuebingen , Microbiology/Biotechnology , University of Tuebingen , Auf der Morgenstelle 28 , 72076 Tuebingen , Germany .
- German Centre for Infection Research (DZIF) , Partner Site Tuebingen , Tuebingen , Germany
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Latham J, Brandenburger E, Shepherd SA, Menon BRK, Micklefield J. Development of Halogenase Enzymes for Use in Synthesis. Chem Rev 2017; 118:232-269. [PMID: 28466644 DOI: 10.1021/acs.chemrev.7b00032] [Citation(s) in RCA: 207] [Impact Index Per Article: 29.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
Nature has evolved halogenase enzymes to regioselectively halogenate a diverse range of biosynthetic precursors, with the halogens introduced often having a profound effect on the biological activity of the resulting natural products. Synthetic endeavors to create non-natural bioactive small molecules for pharmaceutical and agrochemical applications have also arrived at a similar conclusion: halogens can dramatically improve the properties of organic molecules for selective modulation of biological targets in vivo. Consequently, a high proportion of pharmaceuticals and agrochemicals on the market today possess halogens. Halogenated organic compounds are also common intermediates in synthesis and are particularly valuable in metal-catalyzed cross-coupling reactions. Despite the potential utility of organohalogens, traditional nonenzymatic halogenation chemistry utilizes deleterious reagents and often lacks regiocontrol. Reliable, facile, and cleaner methods for the regioselective halogenation of organic compounds are therefore essential in the development of economical and environmentally friendly industrial processes. A potential avenue toward such methods is the use of halogenase enzymes, responsible for the biosynthesis of halogenated natural products, as biocatalysts. This Review will discuss advances in developing halogenases for biocatalysis, potential untapped sources of such biocatalysts and how further optimization of these enzymes is required to achieve the goal of industrial scale biohalogenation.
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Affiliation(s)
- Jonathan Latham
- School of Chemistry and Manchester Institute of Biotechnology, The University of Manchester , 131 Princess Street, Manchester M1 7DN, United Kingdom
| | - Eileen Brandenburger
- School of Chemistry and Manchester Institute of Biotechnology, The University of Manchester , 131 Princess Street, Manchester M1 7DN, United Kingdom
| | - Sarah A Shepherd
- School of Chemistry and Manchester Institute of Biotechnology, The University of Manchester , 131 Princess Street, Manchester M1 7DN, United Kingdom
| | - Binuraj R K Menon
- School of Chemistry and Manchester Institute of Biotechnology, The University of Manchester , 131 Princess Street, Manchester M1 7DN, United Kingdom
| | - Jason Micklefield
- School of Chemistry and Manchester Institute of Biotechnology, The University of Manchester , 131 Princess Street, Manchester M1 7DN, United Kingdom
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Agarwal V, Miles ZD, Winter JM, Eustáquio AS, El Gamal AA, Moore BS. Enzymatic Halogenation and Dehalogenation Reactions: Pervasive and Mechanistically Diverse. Chem Rev 2017; 117:5619-5674. [PMID: 28106994 PMCID: PMC5575885 DOI: 10.1021/acs.chemrev.6b00571] [Citation(s) in RCA: 248] [Impact Index Per Article: 35.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Abstract
Naturally produced halogenated compounds are ubiquitous across all domains of life where they perform a multitude of biological functions and adopt a diversity of chemical structures. Accordingly, a diverse collection of enzyme catalysts to install and remove halogens from organic scaffolds has evolved in nature. Accounting for the different chemical properties of the four halogen atoms (fluorine, chlorine, bromine, and iodine) and the diversity and chemical reactivity of their organic substrates, enzymes performing biosynthetic and degradative halogenation chemistry utilize numerous mechanistic strategies involving oxidation, reduction, and substitution. Biosynthetic halogenation reactions range from simple aromatic substitutions to stereoselective C-H functionalizations on remote carbon centers and can initiate the formation of simple to complex ring structures. Dehalogenating enzymes, on the other hand, are best known for removing halogen atoms from man-made organohalogens, yet also function naturally, albeit rarely, in metabolic pathways. This review details the scope and mechanism of nature's halogenation and dehalogenation enzymatic strategies, highlights gaps in our understanding, and posits where new advances in the field might arise in the near future.
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Affiliation(s)
- Vinayak Agarwal
- Center for Oceans and Human Health, Scripps Institution of Oceanography, University of California, San Diego
| | - Zachary D. Miles
- Center for Marine Biotechnology and Biomedicine, Scripps Institution of Oceanography, University of California, San Diego
| | | | - Alessandra S. Eustáquio
- College of Pharmacy, Department of Medicinal Chemistry & Pharmacognosy and Center for Biomolecular Sciences, University of Illinois at Chicago
| | - Abrahim A. El Gamal
- Center for Oceans and Human Health, Scripps Institution of Oceanography, University of California, San Diego
| | - Bradley S. Moore
- Center for Oceans and Human Health, Scripps Institution of Oceanography, University of California, San Diego
- Center for Marine Biotechnology and Biomedicine, Scripps Institution of Oceanography, University of California, San Diego
- Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California, San Diego
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15
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Atkinson DJ, Naysmith BJ, Furkert DP, Brimble MA. Enduracididine, a rare amino acid component of peptide antibiotics: Natural products and synthesis. Beilstein J Org Chem 2016; 12:2325-2342. [PMID: 28144300 PMCID: PMC5238550 DOI: 10.3762/bjoc.12.226] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2016] [Accepted: 10/20/2016] [Indexed: 11/23/2022] Open
Abstract
Rising resistance to current clinical antibacterial agents is an imminent threat to global public health and highlights the demand for new lead compounds for drug discovery. One such potential lead compound, the peptide antibiotic teixobactin, was recently isolated from an uncultured bacterial source, and demonstrates remarkably high potency against a wide range of resistant pathogens without apparent development of resistance. A rare amino acid residue component of teixobactin, enduracididine, is only known to occur in a small number of natural products that also possess promising antibiotic activity. This review highlights the presence of enduracididine in natural products, its biosynthesis together with a review of analogues of enduracididine. Reported synthetic approaches to the cyclic guanidine structure of enduracididine are discussed, illustrating the challenges encountered to date in the development of efficient synthetic routes to facilitate drug discovery efforts inspired by the discovery of teixobactin.
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Affiliation(s)
- Darcy J Atkinson
- School of Chemical Sciences, The University of Auckland, 23 Symonds Street, Auckland, New Zealand
- Maurice Wilkins Centre for Molecular Biodiscovery, The University of Auckland, 3 Symonds Street, Auckland, New Zealand
| | - Briar J Naysmith
- School of Chemical Sciences, The University of Auckland, 23 Symonds Street, Auckland, New Zealand
- Maurice Wilkins Centre for Molecular Biodiscovery, The University of Auckland, 3 Symonds Street, Auckland, New Zealand
| | - Daniel P Furkert
- School of Chemical Sciences, The University of Auckland, 23 Symonds Street, Auckland, New Zealand
- Maurice Wilkins Centre for Molecular Biodiscovery, The University of Auckland, 3 Symonds Street, Auckland, New Zealand
| | - Margaret A Brimble
- School of Chemical Sciences, The University of Auckland, 23 Symonds Street, Auckland, New Zealand
- Maurice Wilkins Centre for Molecular Biodiscovery, The University of Auckland, 3 Symonds Street, Auckland, New Zealand
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16
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Winn M, Fyans JK, Zhuo Y, Micklefield J. Recent advances in engineering nonribosomal peptide assembly lines. Nat Prod Rep 2016; 33:317-47. [PMID: 26699732 DOI: 10.1039/c5np00099h] [Citation(s) in RCA: 177] [Impact Index Per Article: 22.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
Nonribosomal peptides are amongst the most widespread and structurally diverse secondary metabolites in nature with many possessing bioactivity that can be exploited for therapeutic applications. Due to the major challenges associated with total- and semi-synthesis, bioengineering approaches have been developed to increase yields and generate modified peptides with improved physicochemical properties or altered bioactivity. Here we review the major advances that have been made over the last decade in engineering the biosynthesis of nonribosomal peptides. Structural diversity has been introduced by the modification of enzymes required for the supply of precursors or by heterologous expression of tailoring enzymes. The modularity of nonribosomal peptide synthetase (NRPS) assembly lines further supports module or domain swapping methodologies to achieve changes in the amino acid sequence of nonribosomal peptides. We also review the new synthetic biology technologies promising to speed up the process, enabling the creation and optimisation of many more assembly lines for heterologous expression, offering new opportunities for engineering the biosynthesis of novel nonribosomal peptides.
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Affiliation(s)
- M Winn
- School of Chemistry and Manchester Institute of Biotechnology, The University of Manchester, 131 Princess Street, Manchester M1 7DN, UK.
| | - J K Fyans
- School of Chemistry and Manchester Institute of Biotechnology, The University of Manchester, 131 Princess Street, Manchester M1 7DN, UK.
| | - Y Zhuo
- School of Chemistry and Manchester Institute of Biotechnology, The University of Manchester, 131 Princess Street, Manchester M1 7DN, UK.
| | - J Micklefield
- School of Chemistry and Manchester Institute of Biotechnology, The University of Manchester, 131 Princess Street, Manchester M1 7DN, UK.
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17
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Investigation of halogenation during the biosynthesis of ramoplanin in Actinoplanes sp. ATCC33076. Appl Microbiol Biotechnol 2015; 100:289-98. [DOI: 10.1007/s00253-015-7014-2] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2015] [Revised: 08/17/2015] [Accepted: 09/15/2015] [Indexed: 10/23/2022]
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18
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Al Toma RS, Brieke C, Cryle MJ, Süssmuth RD. Structural aspects of phenylglycines, their biosynthesis and occurrence in peptide natural products. Nat Prod Rep 2015; 32:1207-35. [DOI: 10.1039/c5np00025d] [Citation(s) in RCA: 73] [Impact Index Per Article: 8.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
Phenylglycine-type amino acids occur in a wide variety of peptide natural products. Herein structures and properties of these peptides as well as the biosynthetic origin and incorporation of phenylglycines are discussed.
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Affiliation(s)
| | - Clara Brieke
- Max Planck Institute for Medical Research
- Department of Biomolecular Mechanisms
- 69120 Heidelberg
- Germany
| | - Max J. Cryle
- Max Planck Institute for Medical Research
- Department of Biomolecular Mechanisms
- 69120 Heidelberg
- Germany
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19
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Promoter analysis and transcription regulation of fus gene cluster responsible for fusaricidin synthesis of Paenibacillus polymyxa SQR-21. Appl Microbiol Biotechnol 2013; 97:9479-89. [PMID: 24072159 DOI: 10.1007/s00253-013-5157-6] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2013] [Revised: 06/25/2013] [Accepted: 07/27/2013] [Indexed: 10/26/2022]
Abstract
Fusaricidins produced by Paenibacillus polymyxa are lipopeptide antibiotics with outstanding antifungal activity. In this study, the whole gene cluster responsible for fusaricidin biosynthesis (fusA) was isolated and identified from the cDNA library of one biocontrol agent P. polymyxa SQR-21 (SQR-21). MALDI-TOF MS analysis confirmed that SQR-21 could produce four kinds of fusaricidins: A, B, C, and D. A central promoter that drove the transcription of fusGFEDCBA was revealed by mapping of the fus promoter region by 5' deletions. The disruption of fusA in SQR-21 led to the abolishment of fusaricidin production and antifungal activity. The direct interaction between a potential regulator, AbrB, and the promoter region of fus gene cluster was confirmed by electrophoretic mobility shift assays. One abrB disruption mutant showed significantly higher antifungal activity compared with the wild type. These results revealed a pathway for the transcriptional regulation of the fus gene cluster in P. polymyxa.
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20
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Bionda N, Pitteloud JP, Cudic P. Cyclic lipodepsipeptides: a new class of antibacterial agents in the battle against resistant bacteria. Future Med Chem 2013; 5:1311-30. [PMID: 23859209 PMCID: PMC3845972 DOI: 10.4155/fmc.13.86] [Citation(s) in RCA: 51] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/03/2023] Open
Abstract
In order to provide effective treatment options for infections caused by multidrug-resistant bacteria, innovative antibiotics are necessary, preferably with novel modes of action and/or belonging to novel classes of drugs. Naturally occurring cyclic lipodepsipeptides, which contain one or more ester bonds along with the amide bonds, have emerged as promising candidates for the development of new antibiotics. Some of these natural products are either already marketed or in advanced stages of clinical development. However, despite the progress in the development of new antibacterial agents, it is inevitable that resistant strains of bacteria will emerge in response to the widespread use of a particular antibiotic and limit its lifetime. Therefore, development of new antibiotics remains our most efficient way to counteract bacterial resistance.
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Affiliation(s)
- Nina Bionda
- Torrey Pines Institute for Molecular Studies, 11350 SW Village Parkway, Post St Lucie, FL 34987, USA
| | - Jean-Philippe Pitteloud
- Torrey Pines Institute for Molecular Studies, 11350 SW Village Parkway, Post St Lucie, FL 34987, USA
| | - Predrag Cudic
- Torrey Pines Institute for Molecular Studies, 11350 SW Village Parkway, Post St Lucie, FL 34987, USA
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21
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Bioengineering natural product biosynthetic pathways for therapeutic applications. Curr Opin Biotechnol 2012; 23:931-40. [DOI: 10.1016/j.copbio.2012.03.008] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2012] [Accepted: 03/13/2012] [Indexed: 01/05/2023]
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23
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Wang J, Xiong Z, Meng H, Wang Y, Wang Y. Synthetic biology triggers new era of antibiotics development. Subcell Biochem 2012; 64:95-114. [PMID: 23080247 DOI: 10.1007/978-94-007-5055-5_5] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
As a discipline to design and construct organisms with desired properties, synthetic biology has generated rapid progresses in the last decade. Combined synthetic biology with the traditional process, a new universal workflow for drug development has been becoming more and more attractive. The new methodology exhibits more efficient and inexpensive comparing to traditional methods in every aspect, such as new compounds discovery & screening, process design & drug manufacturing. This article reviews the application of synthetic biology in antibiotics development, including new drug discovery and screening, combinatorial biosynthesis to generate more analogues and heterologous expression of biosynthetic gene clusters with systematic engineering the recombinant microbial systems for large scale production.
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Affiliation(s)
- Jianfeng Wang
- Key Laboratory of Synthetic Biology, Institute of Plant Physiology and Ecology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, 300 Fenglin Road, Shanghai, 200032, China
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Molecular cloning and identification of the laspartomycin biosynthetic gene cluster from Streptomyces viridochromogenes. Gene 2011; 483:11-21. [PMID: 21640802 DOI: 10.1016/j.gene.2011.05.005] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2011] [Revised: 05/10/2011] [Accepted: 05/10/2011] [Indexed: 11/21/2022]
Abstract
The biosynthetic gene cluster for laspartomycins, a family of 11 amino acid peptide antibiotics, has been cloned and sequenced from Streptomyces viridochromogenes ATCC 29814. Annotation of a segment of 88912bp of S. viridochromogenes genomic sequence revealed the putative lpm cluster and its flanking regions which harbor 43 open reading frames. The lpm cluster, which spans approximately 60 kb, consists of 21 open reading frames. Those include four NRPS genes (lpmA/orf18, lpmB/orf25, lpmC/orf26 and lpmD/orf27), four genes (orfs 21, 22, 24 and 29) involved in the lipid tail biosynthesis and attachment, four regulatory genes (orfs 13, 19, 32 and 33) and three putative exporters or self-resistance genes (orfs 14, 20 and 30). In addition, the gene involved in the biosynthesis of the nonproteinogenic amino acid Pip was also identified in the lpm cluster while the genes necessary for the biosynthesis of the rare residue diaminopropionic acid (Dap) were found to reside elsewhere on the chromosome. Interestingly, the dabA, dabB and dabC genes predicted to code for the biosynthesis of the unusual amino acid diaminobutyric acid (Dab) are organized into the lpm cluster even though the Dab residue was not found in the laspartomycins. Disruption of the NRPS lpmC gene completely abolished laspartomycin production in the corresponding mutant strain. These findings will allow molecular engineering and combinatorial biosynthesis approaches to expand the structural diversity of the amphomycin-group peptide antibiotics including the laspartomycins and friulimicins.
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