1
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Chen M, Xia L, Wu C, Wang Z, Ding L, Xie Y, Feng W, Chen Y. Microbe-material hybrids for therapeutic applications. Chem Soc Rev 2024. [PMID: 39005165 DOI: 10.1039/d3cs00655g] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/16/2024]
Abstract
As natural living substances, microorganisms have emerged as useful resources in medicine for creating microbe-material hybrids ranging from nano to macro dimensions. The engineering of microbe-involved nanomedicine capitalizes on the distinctive physiological attributes of microbes, particularly their intrinsic "living" properties such as hypoxia tendency and oxygen production capabilities. Exploiting these remarkable characteristics in combination with other functional materials or molecules enables synergistic enhancements that hold tremendous promise for improved drug delivery, site-specific therapy, and enhanced monitoring of treatment outcomes, presenting substantial opportunities for amplifying the efficacy of disease treatments. This comprehensive review outlines the microorganisms and microbial derivatives used in biomedicine and their specific advantages for therapeutic application. In addition, we delineate the fundamental strategies and mechanisms employed for constructing microbe-material hybrids. The diverse biomedical applications of the constructed microbe-material hybrids, encompassing bioimaging, anti-tumor, anti-bacteria, anti-inflammation and other diseases therapy are exhaustively illustrated. We also discuss the current challenges and prospects associated with the clinical translation of microbe-material hybrid platforms. Therefore, the unique versatility and potential exhibited by microbe-material hybrids position them as promising candidates for the development of next-generation nanomedicine and biomaterials with unique theranostic properties and functionalities.
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Affiliation(s)
- Meng Chen
- Materdicine Lab, School of Life Sciences, Shanghai University, Shanghai 200444, P. R. China.
- School of Medicine, Shanghai University, Shanghai 200444, P. R. China.
| | - Lili Xia
- Materdicine Lab, School of Life Sciences, Shanghai University, Shanghai 200444, P. R. China.
| | - Chenyao Wu
- Materdicine Lab, School of Life Sciences, Shanghai University, Shanghai 200444, P. R. China.
| | - Zeyu Wang
- Materdicine Lab, School of Life Sciences, Shanghai University, Shanghai 200444, P. R. China.
| | - Li Ding
- Department of Medical Ultrasound, National Clinical Research Center of Interventional Medicine, Shanghai Tenth People's Hospital, Tongji University Cancer Center, Tongji University School of Medicine, Tongji University, Shanghai, 200072, P. R. China.
| | - Yujie Xie
- School of Medicine, Shanghai University, Shanghai 200444, P. R. China.
| | - Wei Feng
- Materdicine Lab, School of Life Sciences, Shanghai University, Shanghai 200444, P. R. China.
| | - Yu Chen
- Materdicine Lab, School of Life Sciences, Shanghai University, Shanghai 200444, P. R. China.
- Shanghai Institute of Materdicine, Shanghai 200051, P. R. China
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2
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Jalali E, Wang F, Overbay BR, Miller MD, Shaaban KA, Ponomareva LV, Ye Q, Saghaeiannejad-Esfahani H, Bhardwaj M, Steele AD, Teijaro CN, Shen B, Van Lanen SG, She QB, Voss SR, Phillips GN, Thorson JS. Biochemical and Structural Studies of the Carminomycin 4- O-Methyltransferase DnrK. JOURNAL OF NATURAL PRODUCTS 2024. [PMID: 38412432 DOI: 10.1021/acs.jnatprod.3c00947] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/29/2024]
Abstract
Structural and functional studies of the carminomycin 4-O-methyltransferase DnrK are described, with an emphasis on interrogating the acceptor substrate scope of DnrK. Specifically, the evaluation of 100 structurally and functionally diverse natural products and natural product mimetics revealed an array of pharmacophores as productive DnrK substrates. Representative newly identified DnrK substrates from this study included anthracyclines, angucyclines, anthraquinone-fused enediynes, flavonoids, pyranonaphthoquinones, and polyketides. The ligand-bound structure of DnrK bound to a non-native fluorescent hydroxycoumarin acceptor, 4-methylumbelliferone, along with corresponding DnrK kinetic parameters for 4-methylumbelliferone and native acceptor carminomycin are also reported for the first time. The demonstrated unique permissivity of DnrK highlights the potential for DnrK as a new tool in future biocatalytic and/or strain engineering applications. In addition, the comparative bioactivity assessment (cancer cell line cytotoxicity, 4E-BP1 phosphorylation, and axolotl embryo tail regeneration) of a select set of DnrK substrates/products highlights the ability of anthracycline 4-O-methylation to dictate diverse functional outcomes.
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Affiliation(s)
| | - Fengbin Wang
- Department of Biosciences, Rice University, Houston, Texas 77030, United States
| | | | - Mitchell D Miller
- Department of Biosciences, Rice University, Houston, Texas 77030, United States
| | | | | | - Qing Ye
- Markey Cancer Center, Department of Pharmacology and Nutritional Sciences, College of Medicine, University of Kentucky, Lexington, Kentucky 40536, United States
| | | | | | | | | | | | | | - Qing-Bai She
- Markey Cancer Center, Department of Pharmacology and Nutritional Sciences, College of Medicine, University of Kentucky, Lexington, Kentucky 40536, United States
| | - S Randal Voss
- Department of Neuroscience, University of Kentucky, Lexington, Kentucky 40536, United States
- Ambystoma Genetic Stock Center, University of Kentucky, Lexington, Kentucky 40536, United States
- Spinal Cord and Brain Injury Research Center, University of Kentucky, Lexington, Kentucky 40536, United States
| | - George N Phillips
- Department of Biosciences, Rice University, Houston, Texas 77030, United States
- Department of Chemistry, Rice University, Houston, Texas 77030, United States
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3
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Arsın S, Delbaje E, Jokela J, Wahlsten M, Farrar ZM, Permi P, Fewer D. A Plastic Biosynthetic Pathway for the Production of Structurally Distinct Microbial Sunscreens. ACS Chem Biol 2023; 18:1959-1967. [PMID: 37603862 PMCID: PMC10510106 DOI: 10.1021/acschembio.3c00112] [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] [Received: 02/20/2023] [Accepted: 08/07/2023] [Indexed: 08/23/2023]
Abstract
Mycosporine-like amino acids (MAAs) are small, colorless, and water-soluble secondary metabolites. They have high molar extinction coefficients and a unique UV radiation absorption mechanism that make them effective sunscreens. Here we report the discovery of two structurally distinct MAAs from the lichen symbiont strain Nostoc sp. UHCC 0926. We identified these MAAs as aplysiapalythine E (C23H38N2O15) and tricore B (C34H53N4O15) using a combination of high-resolution liquid chromatography-mass spectrometry (HR-LCMS) analysis and nuclear magnetic resonance (NMR) spectroscopy. We obtained a 8.3 Mb complete genome sequence of Nostoc sp. UHCC 0926 to gain insights into the genetic basis for the biosynthesis of these two structural distinct MAAs. We identified MAA biosynthetic genes encoded in three separate locations of the genome. The organization of biosynthetic enzymes in Nostoc sp. UHCC 0926 necessitates a branched biosynthetic pathway to produce two structurally distinct MAAs. We detected the presence of such discontiguous MAA biosynthetic gene clusters in 12% of the publicly available complete cyanobacterial genomes. Bioinformatic analysis of public MAA biosynthetic gene clusters suggests that they are subject to rapid evolutionary processes resulting in highly plastic biosynthetic pathways that are responsible for the chemical diversity in this family of microbial sunscreens.
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Affiliation(s)
- Sıla Arsın
- University
of Helsinki, Department of Microbiology,
Faculty of Agriculture and Forestry, 00014 Helsinki, Finland
| | - Endrews Delbaje
- University
of São Paulo, Center for Nuclear
Energy in Agriculture, Avenida Centenário 303, 13400-970 Piracicaba, São Paulo, Brazil
| | - Jouni Jokela
- University
of Helsinki, Department of Microbiology,
Faculty of Agriculture and Forestry, 00014 Helsinki, Finland
| | - Matti Wahlsten
- University
of Helsinki, Department of Microbiology,
Faculty of Agriculture and Forestry, 00014 Helsinki, Finland
| | - Zoë M. Farrar
- University
of Helsinki, Department of Microbiology,
Faculty of Agriculture and Forestry, 00014 Helsinki, Finland
| | - Perttu Permi
- Department
of Chemistry, University of Jyväskylä, 40014 Jyväskylä, Finland
- Department
of Biological and Environmental Science, Nanoscience Center, University of Jyväskylä, 40014 Jyväskylä, Finland
| | - David Fewer
- University
of Helsinki, Department of Microbiology,
Faculty of Agriculture and Forestry, 00014 Helsinki, Finland
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4
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Bundela R, Cameron RC, Singh AJ, McLellan RM, Richardson AT, Berry D, Nicholson MJ, Parker EJ. Generation of Alternate Indole Diterpene Architectures in Two Species of Aspergilli. J Am Chem Soc 2023; 145:2754-2758. [PMID: 36710518 PMCID: PMC9913125 DOI: 10.1021/jacs.2c11170] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2022] [Indexed: 01/31/2023]
Abstract
The significant structural diversity and potent bioactivity of the fungal indole diterpenes (IDTs) has attracted considerable interest in their biosynthesis. Although substantial skeletal diversity is generated by the action of noncanonical terpene cyclases, comparatively little is known about these enzymes, particularly those involved in the generation of the subgroup containing emindole SA and DA, which show alternate terpenoid skeletons. Here, we describe the IDT biosynthetic machinery generating these unusual IDT architectures from Aspergillus striatus and Aspergillus desertorum. The function of four putative cyclases was interrogated via heterologous expression. Two specific cyclases were identified that catalyze the formation of epimers emindole SA and DA from A. striatus and A. desertorum, respectively. These cyclases are both clustered along with all the elements required for basic IDT biosynthesis yet catalyze an unusual Markovnikov-like cyclization cascade with alternate stereochemical control. Their identification reveals that these alternate architectures are not generated by mechanistically sloppy or promiscuous enzymes, but by cyclases capable of delivering precise regio- and stereospecificities.
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Affiliation(s)
- Rudranuj Bundela
- Ferrier
Research Institute, Victoria University
of Wellington, PO Box 600, Wellington 6140, New Zealand
- Maurice
Wilkins Centre for Molecular Biodiscovery, Victoria University of Wellington, PO Box 600, Wellington 6140, New Zealand
| | - Rosannah C. Cameron
- Ferrier
Research Institute, Victoria University
of Wellington, PO Box 600, Wellington 6140, New Zealand
- Maurice
Wilkins Centre for Molecular Biodiscovery, Victoria University of Wellington, PO Box 600, Wellington 6140, New Zealand
| | - A. Jonathan Singh
- Ferrier
Research Institute, Victoria University
of Wellington, PO Box 600, Wellington 6140, New Zealand
- Maurice
Wilkins Centre for Molecular Biodiscovery, Victoria University of Wellington, PO Box 600, Wellington 6140, New Zealand
| | - Rose M. McLellan
- Ferrier
Research Institute, Victoria University
of Wellington, PO Box 600, Wellington 6140, New Zealand
- Maurice
Wilkins Centre for Molecular Biodiscovery, Victoria University of Wellington, PO Box 600, Wellington 6140, New Zealand
| | - Alistair T. Richardson
- Ferrier
Research Institute, Victoria University
of Wellington, PO Box 600, Wellington 6140, New Zealand
- Maurice
Wilkins Centre for Molecular Biodiscovery, Victoria University of Wellington, PO Box 600, Wellington 6140, New Zealand
| | - Daniel Berry
- Ferrier
Research Institute, Victoria University
of Wellington, PO Box 600, Wellington 6140, New Zealand
- Maurice
Wilkins Centre for Molecular Biodiscovery, Victoria University of Wellington, PO Box 600, Wellington 6140, New Zealand
| | - Matthew J. Nicholson
- Ferrier
Research Institute, Victoria University
of Wellington, PO Box 600, Wellington 6140, New Zealand
| | - Emily J. Parker
- Ferrier
Research Institute, Victoria University
of Wellington, PO Box 600, Wellington 6140, New Zealand
- Maurice
Wilkins Centre for Molecular Biodiscovery, Victoria University of Wellington, PO Box 600, Wellington 6140, New Zealand
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5
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Baral B, Matroodi S, Siitonen V, Thapa K, Akhgari A, Yamada K, Nuutila A, Metsä-Ketelä M. Co-factor independent oxidases ncnN and actVA-3 are involved in the dimerization of benzoisochromanequinone antibiotics in naphthocyclinone and actinorhodin biosynthesis. FEMS Microbiol Lett 2023; 370:fnad123. [PMID: 37989784 PMCID: PMC10697411 DOI: 10.1093/femsle/fnad123] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2023] [Revised: 10/19/2023] [Accepted: 11/20/2023] [Indexed: 11/23/2023] Open
Abstract
Streptomyces produce complex bioactive secondary metabolites with remarkable chemical diversity. Benzoisochromanequinone polyketides actinorhodin and naphthocyclinone are formed through dimerization of half-molecules via single or double carbon-carbon bonds, respectively. Here we sequenced the genome of S. arenae DSM40737 to identify the naphthocyclinone gene cluster and established heterologous production in S. albus J1074 by utilizing direct cluster capture techniques. Comparative sequence analysis uncovered ncnN and ncnM gene products as putative enzymes responsible for dimerization. Inactivation of ncnN that is homologous to atypical co-factor independent oxidases resulted in the accumulation of fogacin, which is likely a reduced shunt product of the true substrate for naphthocyclinone dimerization. In agreement, inactivation of the homologous actVA-3 in S. coelicolor M145 also led to significantly reduced production of actinorhodin. Previous work has identified the NAD(P)H-dependent reductase ActVA-4 as the key enzyme in actinorhodin dimerization, but surprisingly inactivation of the homologous ncnM did not abolish naphthocyclinone formation and the mutation may have been complemented by an endogenous gene product. Our data suggests that dimerization of benzoisochromanequinone polyketides require two-component reductase-oxidase systems.
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Affiliation(s)
- Bikash Baral
- Department of Life Technologies, University of Turku, FIN-20014 Turku, Finland
| | - Soheila Matroodi
- Department of Life Technologies, University of Turku, FIN-20014 Turku, Finland
- Laboratory of Biotechnology, Department of Marine Biology, Faculty of Marine Science and Oceanography, University of Marine Science and Technology, 64199-34619 Khorramshahr, Iran
| | - Vilja Siitonen
- Department of Life Technologies, University of Turku, FIN-20014 Turku, Finland
| | - Keshav Thapa
- Department of Life Technologies, University of Turku, FIN-20014 Turku, Finland
| | - Amir Akhgari
- Department of Life Technologies, University of Turku, FIN-20014 Turku, Finland
| | - Keith Yamada
- Department of Life Technologies, University of Turku, FIN-20014 Turku, Finland
| | - Aleksi Nuutila
- Department of Life Technologies, University of Turku, FIN-20014 Turku, Finland
| | - Mikko Metsä-Ketelä
- Department of Life Technologies, University of Turku, FIN-20014 Turku, Finland
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6
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Sharma G, Curtis PD. The Impacts of Microgravity on Bacterial Metabolism. Life (Basel) 2022; 12:life12060774. [PMID: 35743807 PMCID: PMC9225508 DOI: 10.3390/life12060774] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2022] [Revised: 05/18/2022] [Accepted: 05/20/2022] [Indexed: 12/15/2022] Open
Abstract
The inside of a space-faring vehicle provides a set of conditions unlike anything experienced by bacteria on Earth. The low-shear, diffusion-limited microenvironment with accompanying high levels of ionizing radiation create high stress in bacterial cells, and results in many physiological adaptations. This review gives an overview of the effect spaceflight in general, and real or simulated microgravity in particular, has on primary and secondary metabolism. Some broad trends in primary metabolic responses can be identified. These include increases in carbohydrate metabolism, changes in carbon substrate utilization range, and changes in amino acid metabolism that reflect increased oxidative stress. However, another important trend is that there is no universal bacterial response to microgravity, as different bacteria often have contradictory responses to the same stress. This is exemplified in many of the observed secondary metabolite responses where secondary metabolites may have increased, decreased, or unchanged production in microgravity. Different secondary metabolites in the same organism can even show drastically different production responses. Microgravity can also impact the production profile and localization of secondary metabolites. The inconsistency of bacterial responses to real or simulated microgravity underscores the importance of further research in this area to better understand how microbes can impact the people and systems aboard spacecraft.
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7
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Hulst MB, Grocholski T, Neefjes JJC, van Wezel GP, Metsä-Ketelä M. Anthracyclines: biosynthesis, engineering and clinical applications. Nat Prod Rep 2021; 39:814-841. [PMID: 34951423 DOI: 10.1039/d1np00059d] [Citation(s) in RCA: 37] [Impact Index Per Article: 12.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
Covering: January 1995 to June 2021Anthracyclines are glycosylated microbial natural products that harbour potent antiproliferative activities. Doxorubicin has been widely used as an anticancer agent in the clinic for several decades, but its use is restricted due to severe side-effects such as cardiotoxicity. Recent studies into the mode-of-action of anthracyclines have revealed that effective cardiotoxicity-free anthracyclines can be generated by focusing on histone eviction activity, instead of canonical topoisomerase II poisoning leading to double strand breaks in DNA. These developments have coincided with an increased understanding of the biosynthesis of anthracyclines, which has allowed generation of novel compound libraries by metabolic engineering and combinatorial biosynthesis. Coupled to the continued discovery of new congeners from rare Actinobacteria, a better understanding of the biology of Streptomyces and improved production methodologies, the stage is set for the development of novel anthracyclines that can finally surpass doxorubicin at the forefront of cancer chemotherapy.
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Affiliation(s)
- Mandy B Hulst
- Institute of Biology, Leiden University, Sylviusweg 72, 2333 BE Leiden, The Netherlands.
| | - Thadee Grocholski
- Department of Life Technologies, University of Turku, FIN-20014 Turku, Finland
| | - Jacques J C Neefjes
- Department of Cell and Chemical Biology and Oncode Institute, Leiden University Medical Centre, Leiden, The Netherlands
| | - Gilles P van Wezel
- Institute of Biology, Leiden University, Sylviusweg 72, 2333 BE Leiden, The Netherlands.
| | - Mikko Metsä-Ketelä
- Department of Life Technologies, University of Turku, FIN-20014 Turku, Finland
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8
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Vertical Inheritance Facilitates Interspecies Diversification in Biosynthetic Gene Clusters and Specialized Metabolites. mBio 2021; 12:e0270021. [PMID: 34809466 PMCID: PMC8609351 DOI: 10.1128/mbio.02700-21] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022] Open
Abstract
While specialized metabolites are thought to mediate ecological interactions, the evolutionary processes driving chemical diversification, particularly among closely related lineages, remain poorly understood. Here, we examine the evolutionary dynamics governing the distribution of natural product biosynthetic gene clusters (BGCs) among 118 strains representing all nine currently named species of the marine actinobacterial genus Salinispora. While much attention has been given to the role of horizontal gene transfer (HGT) in structuring BGC distributions, we find that vertical descent facilitates interspecies BGC diversification over evolutionary timescales. Moreover, we identified a distinct phylogenetic signal among Salinispora species at both the BGC and metabolite level, indicating that specialized metabolism represents a conserved phylogenetic trait. Using a combination of genomic analyses and liquid chromatography–high-resolution tandem mass spectrometry (LC-MS/MS) targeting nine experimentally characterized BGCs and their small molecule products, we identified gene gain/loss events, constrained interspecies recombination, and other evolutionary processes associated with vertical inheritance as major contributors to BGC diversification. These evolutionary dynamics had direct consequences for the compounds produced, as exemplified by species-level differences in salinosporamide production. Together, our results support the concept that specialized metabolites, and their cognate BGCs, can represent phylogenetically conserved functional traits with chemical diversification proceeding in species-specific patterns over evolutionary time frames.
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9
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Bonitto EP, McKeown BT, Goralski KB. Jadomycins: A potential chemotherapy for multi-drug resistant metastatic breast cancer. Pharmacol Res Perspect 2021; 9:e00886. [PMID: 34708587 PMCID: PMC8551564 DOI: 10.1002/prp2.886] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2021] [Accepted: 09/30/2021] [Indexed: 12/24/2022] Open
Abstract
Breast cancer causes the most cancer fatalities in women worldwide. Approximately one-third of breast cancers metastasize, or spread from primary tumors to other tissues, and have a 70% 5-year mortality rate. Current breast cancer treatments like doxorubicin and paclitaxel become ineffective when breast cancer cells develop multi-drug resistance and overexpress ATP-binding cassette transporters, as the transporters cause a substantial efflux of the chemotherapies. Jadomycins, a group of molecules isolated from Streptomyces venezuelae ISP5230, are shown to be cytotoxic against a variety of cancers, especially breast cancer. Furthermore, jadomycins retain their cytotoxic properties in multi-drug resistant breast cancer cells, as they are not expelled through ATP-binding cassette transporters. Here, we describe the research that supports the potential use of jadomycins as a novel chemotherapy in the treatment of multi-drug resistant, metastatic breast cancer. We present the supportive findings, as well as the mechanisms of action investigated thus far. These include copper-mediated reactive oxygen species generation, aurora B kinase inhibition, and topoisomerase IIα and IIβ inhibition. We also suggest future directions of jadomycin research, which will help to determine if jadomycins can be used as a breast cancer chemotherapy in clinical practice.
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Affiliation(s)
- Esther P. Bonitto
- Department of PharmacologyDalhousie UniversityHalifaxNova ScotiaCanada
| | - Brendan T. McKeown
- Department of PharmacologyDalhousie UniversityHalifaxNova ScotiaCanada
- Beatrice Hunter Cancer Research InstituteHalifaxNova ScotiaCanada
| | - Kerry B. Goralski
- Department of PharmacologyDalhousie UniversityHalifaxNova ScotiaCanada
- Beatrice Hunter Cancer Research InstituteHalifaxNova ScotiaCanada
- College of PharmacyDalhousie UniversityHalifaxNova ScotiaCanada
- Department of PediatricsDalhousie UniversityHalifaxNova ScotiaCanada
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10
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Fewer DP, Jokela J, Heinilä L, Aesoy R, Sivonen K, Galica T, Hrouzek P, Herfindal L. Chemical diversity and cellular effects of antifungal cyclic lipopeptides from cyanobacteria. PHYSIOLOGIA PLANTARUM 2021; 173:639-650. [PMID: 34145585 DOI: 10.1111/ppl.13484] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/15/2021] [Revised: 06/07/2021] [Accepted: 06/16/2021] [Indexed: 05/11/2023]
Abstract
Cyanobacteria produce a variety of chemically diverse cyclic lipopeptides with potent antifungal activities. These cyclic lipopeptides have an amphipathic structure comprised of a polar peptide cycle and hydrophobic fatty acid side chain. Many have antibiotic activity against a range of human and plant fungal pathogens. This review article aims to summarize the present knowledge on the chemical diversity and cellular effects of cyanobacterial cyclic lipopeptides that display antifungal activity. Cyclic antifungal lipopeptides from cyanobacteria commonly fall into four structural classes; hassallidins, puwainaphycins, laxaphycins, and anabaenolysins. Many of these antifungal cyclic lipopeptides act through cholesterol and ergosterol-dependent disruption of membranes. In many cases, the cyclic lipopeptides also exert cytotoxicity in human cells, and a more extensive examination of their biological activity and structure-activity relationship is warranted. The hassallidin, puwainaphycin, laxaphycin, and anabaenolysin structural classes are unified through shared complex biosynthetic pathways that encode a variety of unusual lipoinitiation mechanisms and branched biosynthesis that promote their chemical diversity. However, the biosynthetic origins of some cyanobacterial cyclic lipopeptides and the mechanisms, which drive their structural diversification in general, remain poorly understood. The strong functional convergence of differently organized chemical structures suggests that the production of lipopeptide confers benefits for their producer. Whether these benefits originate from their antifungal activity or some other physiological function remains to be answered in the future. However, it is clear that cyanobacteria encode a wealth of new cyclic lipopeptides with novel biotechnological and therapeutic applications.
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Affiliation(s)
- David P Fewer
- Department of Microbiology, University of Helsinki, Helsinki, Finland
| | - Jouni Jokela
- Department of Microbiology, University of Helsinki, Helsinki, Finland
| | - Lassi Heinilä
- Department of Microbiology, University of Helsinki, Helsinki, Finland
| | - Reidun Aesoy
- Centre for Pharmacy, Department of Clinical Science, University of Bergen, Bergen, Norway
| | - Kaarina Sivonen
- Department of Microbiology, University of Helsinki, Helsinki, Finland
| | - Tomáš Galica
- Academy of Science of the Czech Republic, Institute of Microbiology, Centre Algatech, Třeboň, Czech Republic
| | - Pavel Hrouzek
- Academy of Science of the Czech Republic, Institute of Microbiology, Centre Algatech, Třeboň, Czech Republic
| | - Lars Herfindal
- Centre for Pharmacy, Department of Clinical Science, University of Bergen, Bergen, Norway
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11
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Hermes C, König GM, Crüsemann M. The chromodepsins - chemistry, biology and biosynthesis of a selective Gq inhibitor natural product family. Nat Prod Rep 2021; 38:2276-2292. [PMID: 33998635 DOI: 10.1039/d1np00005e] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
Covering: up to April 2021The bacterial cyclic depsipeptides FR900359 (FR) and YM-254890 (YM) were shown to selectively inhibit Gαq proteins with high potency and selectivity and have recently emerged as valuable pharmacological tools due to their effective mechanism of action. Here, we summarize important aspects of this small and specialized natural product family, for which we propose the name chromodepsins, starting from their discovery, producing organisms and structural variety. We then review biosynthesis, structure-activity relationships and ecological and evolutionary aspects of the chromodepsins. Lastly, we discuss their mechanism of action, potential medicinal applications and future opportunities and challenges for further use and development of these complex inhibitor molecules from nature.
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Affiliation(s)
- Cornelia Hermes
- Institute of Pharmaceutical Biology, Rheinische Friedrich-Wilhelms-University of Bonn, 53115 Bonn, Germany.
| | - Gabriele M König
- Institute of Pharmaceutical Biology, Rheinische Friedrich-Wilhelms-University of Bonn, 53115 Bonn, Germany.
| | - Max Crüsemann
- Institute of Pharmaceutical Biology, Rheinische Friedrich-Wilhelms-University of Bonn, 53115 Bonn, Germany.
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12
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13
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Mikhaylov AA, Ikonnikova VA, Solyev PN. Disclosing biosynthetic connections and functions of atypical angucyclinones with a fragmented C-ring. Nat Prod Rep 2021; 38:1506-1517. [PMID: 33480893 DOI: 10.1039/d0np00082e] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
This review on atypical angucyclinones possessing an aromatic cleavage of the C-ring covers literature between 1995 and early 2020.The unusual framework of the middle C-ring, "broken" as a result of biotransformations and oxidations in vivo and bearing an sp3-C connection, is of interest for biosynthetic investigations. The reported 39 natural compounds (55 including stereoisomers) have been analyzed and arranged into three structural groups. The biosynthetic origin of all these compounds has been thoroughly reviewed and revised, based on the found connections with oxidized angucyclinone structures. The data on biological activities has been summarized. Careful consideration of the origin of the structure allowed us to outline a hypothesis on the biological function as well as prospective applications of such atypical angucyclinones.
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Affiliation(s)
- Andrey A Mikhaylov
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry of the Russian Academy of Sciences, 16/10 Miklukho-Maklaya St., Moscow, 117997, Russia.
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14
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Abstract
This Special Issue is composed of 10 reviews that delve into the intricacies behind enzyme promiscuity and evolution, an area that is of increasing interest in the biological research community. In particular, the reviews in this Special Issue explore enzyme promiscuity and evolution in the context of cellular metabolism, as discussed in this introductory Editorial. It is our hope that you enjoy these fascinating and informative reviews and we wish to thank the authors for their compelling contributions to The FEBS Journal. doi: 10.1111/febs.12650.
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Affiliation(s)
- Dan S Tawfik
- Department of Biomolecular Sciences, The Weizmann Institute of Science, Rehovot, Israel
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15
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Hermes C, Richarz R, Wirtz DA, Patt J, Hanke W, Kehraus S, Voß JH, Küppers J, Ohbayashi T, Namasivayam V, Alenfelder J, Inoue A, Mergaert P, Gütschow M, Müller CE, Kostenis E, König GM, Crüsemann M. Thioesterase-mediated side chain transesterification generates potent Gq signaling inhibitor FR900359. Nat Commun 2021; 12:144. [PMID: 33420046 PMCID: PMC7794379 DOI: 10.1038/s41467-020-20418-3] [Citation(s) in RCA: 27] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2020] [Accepted: 12/01/2020] [Indexed: 12/18/2022] Open
Abstract
The potent and selective Gq protein inhibitor depsipeptide FR900359 (FR), originally discovered as the product of an uncultivable plant endosymbiont, is synthesized by a complex biosynthetic system comprising two nonribosomal peptide synthetase (NRPS) assembly lines. Here we characterize a cultivable bacterial FR producer, enabling detailed investigations into biosynthesis and attachment of the functionally important FR side chain. We reconstitute side chain assembly by the monomodular NRPS FrsA and the non-heme monooxygenase FrsH, and characterize intermolecular side chain transesterification to the final macrocyclic intermediate FR-Core, mediated by the FrsA thioesterase domain. We harness FrsA substrate promiscuity to generate FR analogs with altered side chains and demonstrate indispensability of the FR side chain for efficient Gq inhibition by comparative bioactivity, toxicity and docking studies. Finally, evolution of FR and side chain biosynthesis is discussed based on bioinformatics analyses. Side chain transesterification boosts potency and target affinity of selective Gq inhibitor natural products. FR900359 (FR) is a Gq protein inhibitor depsipeptide isolated from an uncultivable plant endosymbiont and synthesized by non-ribosomal peptide synthetases. Here, the authors discover a cultivable bacterial FR producer and show that FrsA thioesterase domain catalyses intermolecular transesterification of the FR side chain to the depsipeptide core during biosynthesis, improving Gq inhibition properties.
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Affiliation(s)
- Cornelia Hermes
- Institute of Pharmaceutical Biology, University of Bonn, Nussallee 6, 53115, Bonn, Germany
| | - René Richarz
- Institute of Pharmaceutical Biology, University of Bonn, Nussallee 6, 53115, Bonn, Germany
| | - Daniel A Wirtz
- Institute of Pharmaceutical Biology, University of Bonn, Nussallee 6, 53115, Bonn, Germany
| | - Julian Patt
- Institute of Pharmaceutical Biology, University of Bonn, Nussallee 6, 53115, Bonn, Germany
| | - Wiebke Hanke
- Institute of Pharmaceutical Biology, University of Bonn, Nussallee 6, 53115, Bonn, Germany
| | - Stefan Kehraus
- Institute of Pharmaceutical Biology, University of Bonn, Nussallee 6, 53115, Bonn, Germany
| | - Jan Hendrik Voß
- Pharmaceutical Institute, Pharmaceutical & Medicinal Chemistry, University of Bonn, An der Immenburg 4, 53121, Bonn, Germany
| | - Jim Küppers
- Pharmaceutical Institute, Pharmaceutical & Medicinal Chemistry, University of Bonn, An der Immenburg 4, 53121, Bonn, Germany
| | - Tsubasa Ohbayashi
- University of Paris-Saclay, CEA, CNRS, Institute for Integrative Biology of the Cell (I2BC), Avenue de la Terrasse, Gif-sur-Yvette, 91198, France.,Institute for Agro-Environmental Sciences, National Agriculture and Food Research Organization (NARO), Tsukuba, 305-8604, Japan
| | - Vigneshwaran Namasivayam
- Pharmaceutical Institute, Pharmaceutical & Medicinal Chemistry, University of Bonn, An der Immenburg 4, 53121, Bonn, Germany
| | - Judith Alenfelder
- Institute of Pharmaceutical Biology, University of Bonn, Nussallee 6, 53115, Bonn, Germany
| | - Asuka Inoue
- Graduate School of Pharmaceutical Sciences, Tohoku University, Sendai, 980-8578, Japan
| | - Peter Mergaert
- University of Paris-Saclay, CEA, CNRS, Institute for Integrative Biology of the Cell (I2BC), Avenue de la Terrasse, Gif-sur-Yvette, 91198, France
| | - Michael Gütschow
- Pharmaceutical Institute, Pharmaceutical & Medicinal Chemistry, University of Bonn, An der Immenburg 4, 53121, Bonn, Germany
| | - Christa E Müller
- Pharmaceutical Institute, Pharmaceutical & Medicinal Chemistry, University of Bonn, An der Immenburg 4, 53121, Bonn, Germany
| | - Evi Kostenis
- Institute of Pharmaceutical Biology, University of Bonn, Nussallee 6, 53115, Bonn, Germany
| | - Gabriele M König
- Institute of Pharmaceutical Biology, University of Bonn, Nussallee 6, 53115, Bonn, Germany
| | - Max Crüsemann
- Institute of Pharmaceutical Biology, University of Bonn, Nussallee 6, 53115, Bonn, Germany.
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16
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Martin SJ. The FEBS Journal in 2021: a sharp reminder that science really matters. FEBS J 2021; 288:4-9. [PMID: 33393713 DOI: 10.1111/febs.15679] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2020] [Revised: 12/18/2020] [Accepted: 12/18/2020] [Indexed: 11/29/2022]
Abstract
The FEBS Journal, a leading multidisciplinary journal in the life sciences, continues to grow in visibility and impact. Here, the Editor-in-Chief Seamus Martin discusses developments at the journal over the past year and the impact of the COVID-19 crisis on research activities.
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Affiliation(s)
- Seamus J Martin
- The FEBS Journal Editorial Office, Cambridge, UK.,Department of Genetics, Trinity College, Dublin 2, Ireland
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17
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Noda-Garcia L, Tawfik DS. Enzyme evolution in natural products biosynthesis: target- or diversity-oriented? Curr Opin Chem Biol 2020; 59:147-154. [PMID: 32771972 DOI: 10.1016/j.cbpa.2020.05.011] [Citation(s) in RCA: 23] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2020] [Revised: 05/27/2020] [Accepted: 05/28/2020] [Indexed: 12/12/2022]
Abstract
Natural product biosynthesis (NPB) is the Panda's Thumb of evolutionary biochemistry. Arm races between organisms, and ever-changing environments, result in relentless innovation. This review focusses on enzyme evolution in NPB. First, we review cases of de novo emergence, whereby a completely new enzymatic activity arose in a ligand-binding protein, or a new enzyme emerged including a completely new scaffold. Second, we briefly review the current models for enzyme evolution, and how they explain the inherent promiscuity of NPB enzymes and their tendency to produce multiple related products. We thus suggest that NPB enzymes a priori evolved to generate a specific product; they are, however, trapped in a multifunctional, generalist evolutionary state and thereby produce a diversity of products.
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Affiliation(s)
- Lianet Noda-Garcia
- Department of Plant Pathology and Microbiology, Faculty of Agriculture, Food and Environment, The Hebrew University of Jerusalem, Rehovot, Israel
| | - Dan S Tawfik
- Department of Biomolecular Sciences, The Weizmann Institute of Science, Rehovot, 76100, Israel.
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18
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Nji Wandi B, Siitonen V, Dinis P, Vukic V, Salminen TA, Metsä-Ketelä M. Evolution-guided engineering of non-heme iron enzymes involved in nogalamycin biosynthesis. FEBS J 2020; 287:2998-3011. [PMID: 31876382 DOI: 10.1111/febs.15192] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2019] [Revised: 11/20/2019] [Accepted: 12/20/2019] [Indexed: 01/05/2023]
Abstract
Microbes are competent chemists that are able to generate thousands of chemically complex natural products with potent biological activities. The key to the formation of this chemical diversity has been the rapid evolution of secondary metabolism. Many enzymes residing on these metabolic pathways have acquired atypical catalytic properties in comparison with their counterparts found in primary metabolism. The biosynthetic pathway of the anthracycline nogalamycin contains two such proteins, SnoK and SnoN, belonging to nonheme iron and 2-oxoglutarate-dependent mono-oxygenases. In spite of structural similarity, the two proteins catalyze distinct chemical reactions; SnoK is a C2-C5″ carbocyclase, whereas SnoN catalyzes stereoinversion at the adjacent C4″ position. Here, we have identified four structural regions involved in the functional differentiation and generated 30 chimeric enzymes to probe catalysis. Our analyses indicate that the carbocyclase SnoK is the ancestral form of the enzyme from which SnoN has evolved to catalyze stereoinversion at the neighboring carbon. The critical step in the appearance of epimerization activity has likely been the insertion of three residues near the C-terminus, which allow repositioning of the substrate in front of the iron center. The loss of the original carbocyclization activity has then occurred with changes in four amino acids near the iron center that prohibit alignment of the substrate for the formation of the C2-C5″ bond. Our study provides detailed insights into the evolutionary processes that have enabled Streptomyces soil bacteria to become the major source of antibiotics and antiproliferative agents. ENZYMES: EC number 1.14.11.
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Affiliation(s)
| | - Vilja Siitonen
- Department of Biochemistry, University of Turku, Finland
| | - Pedro Dinis
- Department of Biochemistry, University of Turku, Finland
| | - Vladimir Vukic
- Structural Bioinformatics Laboratory, Biochemistry, Faculty of Science and Engineering, Åbo Akademi University, Turku, Finland.,Faculty of Technology Novi Sad, University of Novi Sad, Serbia
| | - Tiina A Salminen
- Structural Bioinformatics Laboratory, Biochemistry, Faculty of Science and Engineering, Åbo Akademi University, Turku, Finland
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