1
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Löhr NA, Platz L, Hoffmeister D, Müller M. From the forest floor to the lab: Insights into the diversity and complexity of mushroom polyketide synthases. Curr Opin Chem Biol 2024; 82:102510. [PMID: 39128325 DOI: 10.1016/j.cbpa.2024.102510] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2024] [Revised: 07/12/2024] [Accepted: 07/15/2024] [Indexed: 08/13/2024]
Abstract
Mushroom-forming fungi exhibit a distinctive ecology, which is unsurprisingly also reflected in unique and divergent biosynthetic pathways. We review this phenomenon through the lens of the polyketide metabolism, where mushrooms often deviate from established principles and challenge conventional paradigms. This is evident not only by non-canonical enzyme architectures and functions but also by their propensity for multi-product synthases rather than single-product pathways. Nevertheless, mushrooms also feature many polyketides familiar from plants, bacteria, and fungi of their sister division Ascomycota, which, however, are the result of an independent evolution. In this regard, the captivating biosynthetic pathways of mushrooms might even help us understand the biological pressures that led to the simultaneous production of the same natural products (via convergent evolution, co-evolution, and/or metaevolution) and thus address the question of their raison d'être.
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Affiliation(s)
- Nikolai A Löhr
- Institute of Pharmacy, Department of Pharmaceutical Microbiology, Friedrich Schiller University Jena, Winzerlaer Strasse 2, 07745 Jena, Germany; Department of Pharmaceutical Microbiology, Leibniz Institute for Natural Product Research and Infection Biology - Hans Knöll Institute, Winzerlaer Strasse 2, 07745 Jena, Germany
| | - Lukas Platz
- Institute of Pharmaceutical Sciences, Albert-Ludwigs-Universität Freiburg, Albertstrasse 25, 79104 Freiburg, Germany
| | - Dirk Hoffmeister
- Institute of Pharmacy, Department of Pharmaceutical Microbiology, Friedrich Schiller University Jena, Winzerlaer Strasse 2, 07745 Jena, Germany; Department of Pharmaceutical Microbiology, Leibniz Institute for Natural Product Research and Infection Biology - Hans Knöll Institute, Winzerlaer Strasse 2, 07745 Jena, Germany
| | - Michael Müller
- Institute of Pharmaceutical Sciences, Albert-Ludwigs-Universität Freiburg, Albertstrasse 25, 79104 Freiburg, Germany.
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2
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Yudenko A, Bazhenov SV, Aleksenko VA, Goncharov IM, Semenov O, Remeeva A, Nazarenko VV, Kuznetsova E, Fomin VV, Konopleva MN, Al Ebrahim R, Sluchanko NN, Ryzhykau Y, Semenov YS, Kuklin A, Manukhov IV, Gushchin I. luxA Gene From Enhygromyxa salina Encodes a Functional Homodimeric Luciferase. Proteins 2024. [PMID: 39171358 DOI: 10.1002/prot.26739] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2024] [Revised: 07/20/2024] [Accepted: 08/05/2024] [Indexed: 08/23/2024]
Abstract
Several clades of luminescent bacteria are known currently. They all contain similar lux operons, which include the genes luxA and luxB encoding a heterodimeric luciferase. The aldehyde oxygenation reaction is presumed to be catalyzed primarily by the subunit LuxA, whereas LuxB is required for efficiency and stability of the complex. Recently, genomic analysis identified a subset of bacterial species with rearranged lux operons lacking luxB. Here, we show that the product of the luxA gene from the reduced luxACDE operon of Enhygromyxa salina is luminescent upon addition of aldehydes both in vivo in Escherichia coli and in vitro. Overall, EsLuxA is much less bright compared with luciferases from Aliivibrio fischeri (AfLuxAB) and Photorhabdus luminescens (PlLuxAB), and most active with medium-chain C4-C9 aldehydes. Crystal structure of EsLuxA determined at the resolution of 2.71 Å reveals a (β/α)8 TIM-barrel fold, characteristic for other bacterial luciferases, and the protein preferentially forms a dimer in solution. The mobile loop residues 264-293, which form a β-hairpin or a coil in Vibrio harveyi LuxA, form α-helices in EsLuxA. Phylogenetic analysis shows EsLuxA and related proteins may be bacterial protoluciferases that arose prior to duplication of the luxA gene and its speciation to luxA and luxB in the previously described luminescent bacteria. Our work paves the way for the development of new bacterial luciferases that have an advantage of being encoded by a single gene.
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Affiliation(s)
- Anna Yudenko
- Research Center for Molecular Mechanisms of Aging and Age-Related Diseases, Moscow Institute of Physics and Technology, Dolgoprudny, Russia
| | - Sergey V Bazhenov
- Research Center for Molecular Mechanisms of Aging and Age-Related Diseases, Moscow Institute of Physics and Technology, Dolgoprudny, Russia
| | - Vladimir A Aleksenko
- Research Center for Molecular Mechanisms of Aging and Age-Related Diseases, Moscow Institute of Physics and Technology, Dolgoprudny, Russia
| | - Ivan M Goncharov
- Research Center for Molecular Mechanisms of Aging and Age-Related Diseases, Moscow Institute of Physics and Technology, Dolgoprudny, Russia
| | - Oleg Semenov
- Research Center for Molecular Mechanisms of Aging and Age-Related Diseases, Moscow Institute of Physics and Technology, Dolgoprudny, Russia
| | - Alina Remeeva
- Research Center for Molecular Mechanisms of Aging and Age-Related Diseases, Moscow Institute of Physics and Technology, Dolgoprudny, Russia
| | - Vera V Nazarenko
- Research Center for Molecular Mechanisms of Aging and Age-Related Diseases, Moscow Institute of Physics and Technology, Dolgoprudny, Russia
| | - Elizaveta Kuznetsova
- Research Center for Molecular Mechanisms of Aging and Age-Related Diseases, Moscow Institute of Physics and Technology, Dolgoprudny, Russia
| | - Vadim V Fomin
- Research Center for Molecular Mechanisms of Aging and Age-Related Diseases, Moscow Institute of Physics and Technology, Dolgoprudny, Russia
| | - Maria N Konopleva
- Research Center for Molecular Mechanisms of Aging and Age-Related Diseases, Moscow Institute of Physics and Technology, Dolgoprudny, Russia
| | - Rahaf Al Ebrahim
- Research Center for Molecular Mechanisms of Aging and Age-Related Diseases, Moscow Institute of Physics and Technology, Dolgoprudny, Russia
| | - Nikolai N Sluchanko
- A.N. Bach Institute of Biochemistry, Federal Research Center of Biotechnology of the Russian Academy of Sciences, Moscow, Russia
| | - Yury Ryzhykau
- Research Center for Molecular Mechanisms of Aging and Age-Related Diseases, Moscow Institute of Physics and Technology, Dolgoprudny, Russia
- Frank Laboratory of Neutron Physics, Joint Institute for Nuclear Research, Dubna, Russia
| | - Yury S Semenov
- Research Center for Molecular Mechanisms of Aging and Age-Related Diseases, Moscow Institute of Physics and Technology, Dolgoprudny, Russia
| | - Alexander Kuklin
- Research Center for Molecular Mechanisms of Aging and Age-Related Diseases, Moscow Institute of Physics and Technology, Dolgoprudny, Russia
- Frank Laboratory of Neutron Physics, Joint Institute for Nuclear Research, Dubna, Russia
| | - Ilya V Manukhov
- Research Center for Molecular Mechanisms of Aging and Age-Related Diseases, Moscow Institute of Physics and Technology, Dolgoprudny, Russia
| | - Ivan Gushchin
- Research Center for Molecular Mechanisms of Aging and Age-Related Diseases, Moscow Institute of Physics and Technology, Dolgoprudny, Russia
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3
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Yu G, Fu X, Mo X, Tan L, Yang S. Multi-target anti-diabetic styrylpyrones from Phellinus igniarius: Inhibition of α-glucosidase, protein glycation, and oxidative stress. Int J Biol Macromol 2024; 278:134854. [PMID: 39168223 DOI: 10.1016/j.ijbiomac.2024.134854] [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: 05/03/2024] [Revised: 08/15/2024] [Accepted: 08/16/2024] [Indexed: 08/23/2024]
Abstract
Bioactivity screening revealed that the EtOAc extract from the culture broth of Phellinus igniarius SY489 exhibited remarkable α-glucosidase inhibitory activity, with an IC50 value of 1.92 μg/mL. Activity- and ultraviolet (UV) profile-guided isolation led to the discovery of four anti-diabetic styrylpyrones (1-4), including two novel compounds, phelignidins A (1) and B (2). Compounds 1 and 2 represent a rare structural type of styrylpyrone dimer, in which one of the pyrone moieties exists in an open-ring state. The absolute configurations of the new compounds 1 and 2, as well as the previously unresolved compound 3, were established. Compounds 1-4 were effective in α-glucosidase inhibition, anti-glycation, and antioxidant assays, surpassing or being comparable to the positive control drugs, with minimal cytotoxicity. Furthermore, studies on α-glucosidase inhibition mechanisms suggested that these compounds interact with α-glucosidase at a single binding site, causing secondary structure unfolding and exerting inhibitory activity via a mixed-type mechanism. These results provide an important basis for developing novel, low-toxicity, multi-target anti-diabetic drugs from edible and medicinal fungi.
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Affiliation(s)
- Guihong Yu
- School of Life Sciences, Shandong Province Key Laboratory of Applied Mycology, Qingdao International Center on Microbes Utilizing Biogas, Qingdao Agricultural University, Qingdao 266109, Shandong Province, People's Republic of China.
| | - Xiangji Fu
- School of Life Sciences, Shandong Province Key Laboratory of Applied Mycology, Qingdao International Center on Microbes Utilizing Biogas, Qingdao Agricultural University, Qingdao 266109, Shandong Province, People's Republic of China
| | - Xuhua Mo
- School of Life Sciences, Shandong Province Key Laboratory of Applied Mycology, Qingdao International Center on Microbes Utilizing Biogas, Qingdao Agricultural University, Qingdao 266109, Shandong Province, People's Republic of China
| | - Lingling Tan
- School of Life Sciences, Shandong Province Key Laboratory of Applied Mycology, Qingdao International Center on Microbes Utilizing Biogas, Qingdao Agricultural University, Qingdao 266109, Shandong Province, People's Republic of China
| | - Song Yang
- School of Life Sciences, Shandong Province Key Laboratory of Applied Mycology, Qingdao International Center on Microbes Utilizing Biogas, Qingdao Agricultural University, Qingdao 266109, Shandong Province, People's Republic of China.
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4
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Amaral DT, Kaplan RA, Takishita TKE, de Souza DR, Oliveira AG, Rosa SP. Glowing wonders: exploring the diversity and ecological significance of bioluminescent organisms in Brazil. Photochem Photobiol Sci 2024; 23:1373-1392. [PMID: 38733516 DOI: 10.1007/s43630-024-00590-x] [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: 12/11/2023] [Accepted: 04/27/2024] [Indexed: 05/13/2024]
Abstract
Bioluminescence, the emission of light by living organisms, is a captivating and widespread phenomenon with diverse ecological functions. This comprehensive review explores the biodiversity, mechanisms, ecological roles, and conservation challenges of bioluminescent organisms in Brazil, a country known for its vast and diverse ecosystems. From the enchanting glow of fireflies and glow-in-the-dark mushrooms to the mesmerizing displays of marine dinoflagellates and cnidarians, Brazil showcases a remarkable array of bioluminescent species. Understanding the biochemical mechanisms and enzymes involved in bioluminescence enhances our knowledge of their evolutionary adaptations and ecological functions. However, habitat loss, climate change, and photopollution pose significant threats to these bioluminescent organisms. Conservation measures, interdisciplinary collaborations, and responsible lighting practices are crucial for their survival. Future research should focus on identifying endemic species, studying environmental factors influencing bioluminescence, and developing effective conservation strategies. Through interdisciplinary collaborations, advanced technologies, and increased funding, Brazil can unravel the mysteries of its bioluminescent biodiversity, drive scientific advancements, and ensure the long-term preservation of these captivating organisms.
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Affiliation(s)
- Danilo T Amaral
- Centro de Ciências Naturais E Humanas, Universidade Federal Do ABC (UFABC), Santo André, São Paulo, Brazil.
- Programa de Pós Graduação Em Biotecnociência, Universidade Federal Do ABC (UFABC), Avenida Dos Estados, Bloco A, Room 504-3. ZIP 09210-580, Santo André, São Paulo, 5001, Brazil.
| | - Rachel A Kaplan
- Department of Chemistry and Biochemistry, Yeshiva University, 245 Lexington Avenue, New York, NY, 10016, USA
| | | | - Daniel R de Souza
- Laboratório de Estudos Avançados Em Jornalismo, Universidade Estadual de Campinas (Unicamp), Campinas, São Paulo, Brazil
| | - Anderson G Oliveira
- Department of Chemistry and Biochemistry, Yeshiva University, 245 Lexington Avenue, New York, NY, 10016, USA
| | - Simone Policena Rosa
- Instituto de Recursos Naturais (IRN), Universidade Federal de Itajubá (UNIFEI), Itajubá, MG, Brazil
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5
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Wang PC, Deng H, Xu R, Du JL, Tao R. Improvement in Tol2 transposon for efficient large-cargo capacity transgene applications in cultured cells and zebrafish ( Danio rerio). Zool Res 2024; 45:567-574. [PMID: 38757224 PMCID: PMC11188598 DOI: 10.24272/j.issn.2095-8137.2024.026] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2024] [Accepted: 04/26/2024] [Indexed: 05/18/2024] Open
Abstract
Most viruses and transposons serve as effective carriers for the introduction of foreign DNA up to 11 kb into vertebrate genomes. However, their activity markedly diminishes with payloads exceeding 11 kb. Expanding the payload capacity of transposons could facilitate more sophisticated cargo designs, improving the regulation of expression and minimizing mutagenic risks associated with molecular therapeutics, metabolic engineering, and transgenic animal production. In this study, we improved the Tol2 transposon by increasing protein expression levels using a translational enhancer ( QBI SP163, ST) and enhanced the nuclear targeting ability using the nuclear localization protein H2B (SHT). The modified Tol2 and ST transposon efficiently integrated large DNA cargos into human cell cultures (H1299), comparable to the well-established super PiggyBac system. Furthermore, mRNA from ST and SHT showed a significant increase in transgene delivery efficiency of large DNA payloads (8 kb, 14 kb, and 24 kb) into zebrafish ( Danio rerio). This study presents a modified Tol2 transposon as an enhanced nonviral vector for the delivery of large DNA payloads in transgenic applications.
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Affiliation(s)
- Peng-Cheng Wang
- Department of Pediatric Cardiology, Xinhua Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai 200092, China
- Institute of Neuroscience, State Key Laboratory of Neuroscience, Center for Excellence in Brain Science and Intelligence Technology, Chinese Academy of Sciences, Shanghai 200031, China
| | - Hao Deng
- Institute of Neuroscience, State Key Laboratory of Neuroscience, Center for Excellence in Brain Science and Intelligence Technology, Chinese Academy of Sciences, Shanghai 200031, China
- Medical School, Kunming University of Science and Technology, Kunming, Yunnan 650500, China
| | - Rang Xu
- Scientific Research Center, Xinhua Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai 200092, China. E-mail:
| | - Jiu-Lin Du
- Institute of Neuroscience, State Key Laboratory of Neuroscience, Center for Excellence in Brain Science and Intelligence Technology, Chinese Academy of Sciences, Shanghai 200031, China
- University of Chinese Academy of Sciences, Beijing 100049, China
- School of Life Science and Technology, ShanghaiTech University, Shanghai 200031, China. E-mail:
| | - Rongkun Tao
- Institute of Neuroscience, State Key Laboratory of Neuroscience, Center for Excellence in Brain Science and Intelligence Technology, Chinese Academy of Sciences, Shanghai 200031, China. E-mail:
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6
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Schramm S, Weiß D. Bioluminescence - The Vibrant Glow of Nature and its Chemical Mechanisms. Chembiochem 2024; 25:e202400106. [PMID: 38469601 DOI: 10.1002/cbic.202400106] [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: 02/01/2024] [Revised: 03/09/2024] [Accepted: 03/11/2024] [Indexed: 03/13/2024]
Abstract
Bioluminescence, the mesmerizing natural phenomenon where living organisms produce light through chemical reactions, has long captivated scientists and laypersons alike, offering a rich tapestry of insights into biological function, ecology, evolution as well as the underlying chemistry. This comprehensive introductory review systematically explores the phenomenon of bioluminescence, addressing its historical context, geographic dispersion, and ecological significance with a focus on their chemical mechanisms. Our examination begins with terrestrial bioluminescence, discussing organisms from different habitats. We analyze thefireflies of Central Europe's meadows and the fungi in the Atlantic rainforest of Brazil. Additionally, we inspect bioluminescent species in New Zealand, specifically river-dwelling snails and mosquito larvae found in Waitomo Caves. Our exploration concludes in the Siberian Steppes, highlighting the area's luminescent insects and annelids. Transitioning to the marine realm, the second part of this review examines marine bioluminescent organisms. We explore this phenomenon in deep-sea jellyfish and their role in the ecosystem. We then move to Toyama Bay, Japan, where seasonal bioluminescence of dinoflagellates and ostracods present a unique case study. We also delve into the bacterial world, discussing how bioluminescent bacteria contribute to symbiotic relationships. For each organism, we contextualize its bioluminescence, providing details about its discovery, ecological function, and geographical distribution. A special focus lies on the examination of the underlying chemical mechanisms that enables these biological light displays. Concluding this review, we present a series of practical bioluminescence and chemiluminescence experiments, providing a resource for educational demonstrations and student research projects. Our goal with this review is to provide a summary of bioluminescence across the diverse ecological contexts, contributing to the broader understanding of this unique biological phenomenon and its chemical mechanisms serving researchers new to the field, educators and students alike.
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Affiliation(s)
- Stefan Schramm
- University of Applied Sciences Dresden (HTW Dresden), Friedrich-List-Platz 1, 01069, Dresden, Germany
| | - Dieter Weiß
- Institut für Organische und Makromolekulare Chemie, Friedrich-Schiller-Universität Jena, Humboldtstraße 10, 07743, Jena, Germany
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7
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Porta-de-la-Riva M, Morales-Curiel LF, Carolina Gonzalez A, Krieg M. Bioluminescence as a functional tool for visualizing and controlling neuronal activity in vivo. NEUROPHOTONICS 2024; 11:024203. [PMID: 38348359 PMCID: PMC10861157 DOI: 10.1117/1.nph.11.2.024203] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/03/2023] [Revised: 01/18/2024] [Accepted: 01/19/2024] [Indexed: 02/15/2024]
Abstract
The use of bioluminescence as a reporter for physiology in neuroscience is as old as the discovery of the calcium-dependent photon emission of aequorin. Over the years, luciferases have been largely replaced by fluorescent reporters, but recently, the field has seen a renaissance of bioluminescent probes, catalyzed by unique developments in imaging technology, bioengineering, and biochemistry to produce luciferases with previously unseen colors and intensity. This is not surprising as the advantages of bioluminescence make luciferases very attractive for noninvasive, longitudinal in vivo observations without the need of an excitation light source. Here, we review how the development of dedicated and specific sensor-luciferases afforded, among others, transcranial imaging of calcium and neurotransmitters, or cellular metabolites and physical quantities such as forces and membrane voltage. Further, the increased versatility and light output of luciferases have paved the way for a new field of functional bioluminescence optogenetics, in which the photon emission of the luciferase is coupled to the gating of a photosensor, e.g., a channelrhodopsin and we review how they have been successfully used to engineer synthetic neuronal connections. Finally, we provide a primer to consider important factors in setting up functional bioluminescence experiments, with a particular focus on the genetic model Caenorhabditis elegans, and discuss the leading challenges that the field needs to overcome to regain a competitive advantage over fluorescence modalities. Together, our paper caters to experienced users of bioluminescence as well as novices who would like to experience the advantages of luciferases in their own hand.
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Affiliation(s)
- Montserrat Porta-de-la-Riva
- ICFO—Institut de Ciències Fotòniques, The Barcelona Institute of Science and Technology, Castelldefels, Barcelona, Spain
| | - Luis-Felipe Morales-Curiel
- ICFO—Institut de Ciències Fotòniques, The Barcelona Institute of Science and Technology, Castelldefels, Barcelona, Spain
| | - Adriana Carolina Gonzalez
- ICFO—Institut de Ciències Fotòniques, The Barcelona Institute of Science and Technology, Castelldefels, Barcelona, Spain
| | - Michael Krieg
- ICFO—Institut de Ciències Fotòniques, The Barcelona Institute of Science and Technology, Castelldefels, Barcelona, Spain
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8
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Palkina KA, Karataeva TA, Perfilov MM, Fakhranurova LI, Markina NM, Somermeyer LG, Garcia-Perez E, Vazquez-Vilar M, Rodriguez-Rodriguez M, Vazquez-Vilriales V, Shakhova ES, Mitiouchkina T, Belozerova OA, Kovalchuk SI, Alekberova A, Malyshevskaia AK, Bugaeva EN, Guglya EB, Balakireva A, Sytov N, Bezlikhotnova A, Boldyreva DI, Babenko VV, Kondrashov FA, Choob VV, Orzaez D, Yampolsky IV, Mishin AS, Sarkisyan KS. A hybrid pathway for self-sustained luminescence. SCIENCE ADVANCES 2024; 10:eadk1992. [PMID: 38457503 PMCID: PMC10923510 DOI: 10.1126/sciadv.adk1992] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/11/2023] [Accepted: 02/01/2024] [Indexed: 03/10/2024]
Abstract
The fungal bioluminescence pathway can be reconstituted in other organisms allowing luminescence imaging without exogenously supplied substrate. The pathway starts from hispidin biosynthesis-a step catalyzed by a large fungal polyketide synthase that requires a posttranslational modification for activity. Here, we report identification of alternative compact hispidin synthases encoded by a phylogenetically diverse group of plants. A hybrid bioluminescence pathway that combines plant and fungal genes is more compact, not dependent on availability of machinery for posttranslational modifications, and confers autonomous bioluminescence in yeast, mammalian, and plant hosts. The compact size of plant hispidin synthases enables additional modes of delivery of autoluminescence, such as delivery with viral vectors.
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Affiliation(s)
- Kseniia A. Palkina
- Planta LLC, 121205 Moscow, Russia
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, 117997 Moscow, Russia
| | - Tatiana A. Karataeva
- Planta LLC, 121205 Moscow, Russia
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, 117997 Moscow, Russia
| | - Maxim M. Perfilov
- Planta LLC, 121205 Moscow, Russia
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, 117997 Moscow, Russia
| | - Liliia I. Fakhranurova
- Planta LLC, 121205 Moscow, Russia
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, 117997 Moscow, Russia
| | - Nadezhda M. Markina
- Planta LLC, 121205 Moscow, Russia
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, 117997 Moscow, Russia
| | | | - Elena Garcia-Perez
- Instituto de Biología Molecular y Celular de Plantas (IBMCP), Consejo Superior de Investigaciones Científicas (CSIC), Universitat Politècnica de Valéncia, 46022 Valencia, Spain
| | - Marta Vazquez-Vilar
- Instituto de Biología Molecular y Celular de Plantas (IBMCP), Consejo Superior de Investigaciones Científicas (CSIC), Universitat Politècnica de Valéncia, 46022 Valencia, Spain
| | - Marta Rodriguez-Rodriguez
- Instituto de Biología Molecular y Celular de Plantas (IBMCP), Consejo Superior de Investigaciones Científicas (CSIC), Universitat Politècnica de Valéncia, 46022 Valencia, Spain
| | - Victor Vazquez-Vilriales
- Instituto de Biología Molecular y Celular de Plantas (IBMCP), Consejo Superior de Investigaciones Científicas (CSIC), Universitat Politècnica de Valéncia, 46022 Valencia, Spain
| | - Ekaterina S. Shakhova
- Planta LLC, 121205 Moscow, Russia
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, 117997 Moscow, Russia
| | - Tatiana Mitiouchkina
- Planta LLC, 121205 Moscow, Russia
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, 117997 Moscow, Russia
| | - Olga A. Belozerova
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, 117997 Moscow, Russia
| | - Sergey I. Kovalchuk
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, 117997 Moscow, Russia
| | - Anna Alekberova
- Planta LLC, 121205 Moscow, Russia
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, 117997 Moscow, Russia
| | - Alena K. Malyshevskaia
- Planta LLC, 121205 Moscow, Russia
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, 117997 Moscow, Russia
| | | | - Elena B. Guglya
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, 117997 Moscow, Russia
- Pirogov Russian National Research Medical University, Ostrovityanova 1, Moscow 117997, Russia
| | - Anastasia Balakireva
- Planta LLC, 121205 Moscow, Russia
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, 117997 Moscow, Russia
| | - Nikita Sytov
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, 117997 Moscow, Russia
| | | | - Daria I. Boldyreva
- Lopukhin Federal Research and Clinical Center of Physical-Chemical Medicine of Federal Medical Biological Agency, Moscow, Russia
| | - Vladislav V. Babenko
- Lopukhin Federal Research and Clinical Center of Physical-Chemical Medicine of Federal Medical Biological Agency, Moscow, Russia
| | - Fyodor A. Kondrashov
- Okinawa Institute of Science and Technology Graduate University, Okinawa 904-0412, Japan
| | - Vladimir V. Choob
- Botanical Garden of Lomonosov Moscow State University, Vorobievy Gory 1 b.12, Moscow 119234 Russia
| | - Diego Orzaez
- Instituto de Biología Molecular y Celular de Plantas (IBMCP), Consejo Superior de Investigaciones Científicas (CSIC), Universitat Politècnica de Valéncia, 46022 Valencia, Spain
| | - Ilia V. Yampolsky
- Planta LLC, 121205 Moscow, Russia
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, 117997 Moscow, Russia
- Pirogov Russian National Research Medical University, Ostrovityanova 1, Moscow 117997, Russia
- Light Bio Inc., Ketchum, ID, USA
| | - Alexander S. Mishin
- Planta LLC, 121205 Moscow, Russia
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, 117997 Moscow, Russia
| | - Karen S. Sarkisyan
- Planta LLC, 121205 Moscow, Russia
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, 117997 Moscow, Russia
- Light Bio Inc., Ketchum, ID, USA
- Synthetic Biology Group, MRC Laboratory of Medical Sciences, London, UK
- Institute of Clinical Sciences, Faculty of Medicine and Imperial College Centre for Synthetic Biology, Imperial College London, London, UK
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9
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Shakhova ES, Karataeva TA, Markina NM, Mitiouchkina T, Palkina KA, Perfilov MM, Wood MG, Hoang TT, Hall MP, Fakhranurova LI, Alekberova AE, Malyshevskaia AK, Gorbachev DA, Bugaeva EN, Pletneva LK, Babenko VV, Boldyreva DI, Gorokhovatsky AY, Balakireva AV, Gao F, Choob VV, Encell LP, Wood KV, Yampolsky IV, Sarkisyan KS, Mishin AS. An improved pathway for autonomous bioluminescence imaging in eukaryotes. Nat Methods 2024; 21:406-410. [PMID: 38253843 PMCID: PMC10927554 DOI: 10.1038/s41592-023-02152-y] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2023] [Accepted: 12/13/2023] [Indexed: 01/24/2024]
Abstract
The discovery of the bioluminescence pathway in the fungus Neonothopanus nambi enabled engineering of eukaryotes with self-sustained luminescence. However, the brightness of luminescence in heterologous hosts was limited by performance of the native fungal enzymes. Here we report optimized versions of the pathway that enhance bioluminescence by one to two orders of magnitude in plant, fungal and mammalian hosts, and enable longitudinal video-rate imaging.
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Affiliation(s)
- Ekaterina S Shakhova
- Planta LLC, Moscow, Russia
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Moscow, Russia
| | - Tatiana A Karataeva
- Planta LLC, Moscow, Russia
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Moscow, Russia
| | - Nadezhda M Markina
- Planta LLC, Moscow, Russia
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Moscow, Russia
| | - Tatiana Mitiouchkina
- Planta LLC, Moscow, Russia
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Moscow, Russia
| | - Kseniia A Palkina
- Planta LLC, Moscow, Russia
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Moscow, Russia
| | - Maxim M Perfilov
- Planta LLC, Moscow, Russia
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Moscow, Russia
| | | | | | | | | | - Anna E Alekberova
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Moscow, Russia
| | - Alena K Malyshevskaia
- Planta LLC, Moscow, Russia
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Moscow, Russia
| | - Dmitry A Gorbachev
- Planta LLC, Moscow, Russia
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Moscow, Russia
| | | | | | - Vladislav V Babenko
- Lopukhin Federal Research and Clinical Center of Physical-Chemical Medicine of Federal Medical Biological Agency, Moscow, Russia
| | - Daria I Boldyreva
- Lopukhin Federal Research and Clinical Center of Physical-Chemical Medicine of Federal Medical Biological Agency, Moscow, Russia
| | - Andrey Y Gorokhovatsky
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Moscow, Russia
| | - Anastasia V Balakireva
- Planta LLC, Moscow, Russia
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Moscow, Russia
| | - Feng Gao
- Synthetic Biology Group, MRC Laboratory of Medical Sciences, London, UK
- Institute of Clinical Sciences, Faculty of Medicine and Imperial College Centre for Synthetic Biology, Imperial College London, London, UK
| | - Vladimir V Choob
- Planta LLC, Moscow, Russia
- Botanical Garden of Lomonosov Moscow State University, Moscow, Russia
| | | | | | - Ilia V Yampolsky
- Planta LLC, Moscow, Russia
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Moscow, Russia
- Light Bio Inc, Ketchum, ID, USA
- Pirogov Russian National Research Medical University, Moscow, Russia
| | - Karen S Sarkisyan
- Planta LLC, Moscow, Russia.
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Moscow, Russia.
- Synthetic Biology Group, MRC Laboratory of Medical Sciences, London, UK.
- Institute of Clinical Sciences, Faculty of Medicine and Imperial College Centre for Synthetic Biology, Imperial College London, London, UK.
- Light Bio Inc, Ketchum, ID, USA.
| | - Alexander S Mishin
- Planta LLC, Moscow, Russia.
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Moscow, Russia.
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10
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Mujawar A, Dimri S, Palkina KA, Markina NM, Sarkisyan KS, Balakireva AV, Yampolsky IV, De A. Novel BRET combination for detection of rapamycin-induced protein dimerization using luciferase from fungus Neonothopanusnambi. Heliyon 2024; 10:e25553. [PMID: 38384550 PMCID: PMC10878866 DOI: 10.1016/j.heliyon.2024.e25553] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2023] [Revised: 01/18/2024] [Accepted: 01/29/2024] [Indexed: 02/23/2024] Open
Abstract
Bioluminescence resonance energy transfer (BRET) is one of the most promising approaches used for noninvasive imaging of protein-protein interactions in vivo. Recently, our team has discovered a genetically encodable bioluminescent system from the fungus Neonothopanus nambi and identified a novel luciferase that represents an imaging tool orthogonal to other luciferin-luciferase systems. We demonstrated the possibility of using the fungal luciferase as a new BRET donor by creating fused pairs with acceptor red fluorescent proteins, of which tdTomato provided the highest BRET efficiency. Using this new BRET system, we also designed a mTOR pathway specific rapamycin biosensor by integrating the FRB and FKBP12 protein dimerization system. We demonstrated the specificity and efficacy of the new fungal luciferase-based BRET combination for application in mammalian cell culture that will provide the unique opportunity to perform multiplexed BRET assessment in the future.
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Affiliation(s)
- Aaiyas Mujawar
- Advanced Center for Treatment Research and Education in Cancer (ACTREC), Sector-22, Kharghar, Navi Mumbai 410210, India
- Life Science, Homi Bhabha National Institute, Mumbai, India
| | - Shalini Dimri
- Advanced Center for Treatment Research and Education in Cancer (ACTREC), Sector-22, Kharghar, Navi Mumbai 410210, India
- Life Science, Homi Bhabha National Institute, Mumbai, India
| | - Ksenia A. Palkina
- Planta LLC, Bolshoi Boulevard, 42 Str 1, Moscow, Russia
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry of the Russian Academy of Sciences, Miklukho-Maklaya, 16/10, Moscow, Russia
| | - Nadezhda M. Markina
- Planta LLC, Bolshoi Boulevard, 42 Str 1, Moscow, Russia
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry of the Russian Academy of Sciences, Miklukho-Maklaya, 16/10, Moscow, Russia
| | - Karen S. Sarkisyan
- Planta LLC, Bolshoi Boulevard, 42 Str 1, Moscow, Russia
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry of the Russian Academy of Sciences, Miklukho-Maklaya, 16/10, Moscow, Russia
- Synthetic Biology Group, MRC London Institute of Medical Sciences, London W12 0NN, UK
| | - Anastasia V. Balakireva
- Planta LLC, Bolshoi Boulevard, 42 Str 1, Moscow, Russia
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry of the Russian Academy of Sciences, Miklukho-Maklaya, 16/10, Moscow, Russia
| | - Ilia V. Yampolsky
- Planta LLC, Bolshoi Boulevard, 42 Str 1, Moscow, Russia
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry of the Russian Academy of Sciences, Miklukho-Maklaya, 16/10, Moscow, Russia
| | - Abhijit De
- Advanced Center for Treatment Research and Education in Cancer (ACTREC), Sector-22, Kharghar, Navi Mumbai 410210, India
- Life Science, Homi Bhabha National Institute, Mumbai, India
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11
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Dunuweera AN, Dunuweera SP, Ranganathan K. A Comprehensive Exploration of Bioluminescence Systems, Mechanisms, and Advanced Assays for Versatile Applications. Biochem Res Int 2024; 2024:8273237. [PMID: 38347947 PMCID: PMC10861286 DOI: 10.1155/2024/8273237] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2023] [Revised: 10/10/2023] [Accepted: 01/21/2024] [Indexed: 02/15/2024] Open
Abstract
Bioluminescence has been a fascinating natural phenomenon of light emission from living creatures. It happens when the enzyme luciferase facilitates the oxidation of luciferin, resulting in the creation of an excited-state species that emits light. Although there are many bioluminescent systems, few have been identified. D-luciferin-dependent systems, coelenterazine-dependent systems, Cypridina luciferin-based systems, tetrapyrrole-based luciferins, bacterial bioluminescent systems, and fungal bioluminescent systems are natural bioluminescent systems. Since different bioluminescence systems, such as various combinations of luciferin-luciferase pair reactions, have different light emission wavelengths, they benefit industrial applications such as drug discovery, protein-protein interactions, in vivo imaging in small animals, and controlling neurons. Due to the expression of luciferase and easy permeation of luciferin into most cells and tissues, bioluminescence assays are applied nowadays with modern technologies in most cell and tissue types. It is a versatile technique in a variety of biomedical research. Furthermore, there are some investigated blue-sky research projects, such as bioluminescent plants and lamps. This review article is mainly based on the theory of diverse bioluminescence systems and their past, present, and future applications.
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Affiliation(s)
| | | | - K. Ranganathan
- Department of Botany, University of Jaffna, Jaffna 40000, Sri Lanka
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12
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Park MJ, Kim E, Kim MJ, Jang Y, Ryoo R, Ka KH. Cloning and Expression Analysis of Bioluminescence Genes in Omphalotus guepiniiformis Reveal Stress-Dependent Regulation of Bioluminescence. MYCOBIOLOGY 2024; 52:42-50. [PMID: 38415178 PMCID: PMC10896133 DOI: 10.1080/12298093.2024.2302661] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/29/2023] [Accepted: 01/03/2024] [Indexed: 02/29/2024]
Abstract
Bioluminescence is a type of chemiluminescence that arises from a luciferase-catalyzed oxidation reaction of luciferin. Molecular biology and comparative genomics have recently elucidated the genes involved in fungal bioluminescence and the evolutionary history of their clusters. However, most studies on fungal bioluminescence have been limited to observing the changes in light intensity under various conditions. To understand the molecular basis of bioluminescent responses in Omphalotus guepiniiformis under different environmental conditions, we cloned and sequenced the genes of hispidin synthase, hispidin-3-hydroxylase, and luciferase enzymes, which are pivotal in the fungal bioluminescence pathway. Each gene showed high sequence similarity to that of other luminous fungal species. Furthermore, we investigated their transcriptional changes in response to abiotic stresses. Wound stress enhanced the bioluminescence intensity by increasing the expression of bioluminescence pathway genes, while temperature stress suppressed the bioluminescence intensity via the non-transcriptional pathway. Our data suggested that O. guepiniiformis regulates bioluminescence to respond differentially to specific environmental stresses. To our knowledge, this is the first study on fungal bioluminescence at the gene expression level. Further studies are required to address the biological and ecological meaning of different bioluminescence responses in changing environments, and O. quepiniiformis could be a potential model species.
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Affiliation(s)
- Mi-Jeong Park
- Forest Microbiology Division, Department of Forest Bio-Resources, National Institute of Forest Science, Suwon, Republic of Korea
| | - Eunjin Kim
- Forest Microbiology Division, Department of Forest Bio-Resources, National Institute of Forest Science, Suwon, Republic of Korea
| | - Min-Jun Kim
- Forest Microbiology Division, Department of Forest Bio-Resources, National Institute of Forest Science, Suwon, Republic of Korea
| | - Yeongseon Jang
- Forest Microbiology Division, Department of Forest Bio-Resources, National Institute of Forest Science, Suwon, Republic of Korea
| | - Rhim Ryoo
- Forest Microbiology Division, Department of Forest Bio-Resources, National Institute of Forest Science, Suwon, Republic of Korea
| | - Kang-Hyeon Ka
- Forest Microbiology Division, Department of Forest Bio-Resources, National Institute of Forest Science, Suwon, Republic of Korea
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13
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Calabretta MM, Gregucci D, Michelini E. New synthetic red- and orange-emitting luciferases to upgrade in vitro and 3D cell biosensing. Analyst 2023; 148:5642-5649. [PMID: 37791570 DOI: 10.1039/d3an01251d] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/05/2023]
Abstract
Bioluminescence (BL), i.e., the emission of light in living organisms, has become an indispensable tool for a plethora of applications including bioassays, biosensors, and in vivo imaging. Current efforts are focused on the obtainment of new luciferases having optimized properties, such as improved thermostability at 37 °C, pH-insensitive emission, high quantum yield, extended kinetics and red-shifted emission. To address these issues we have obtained two new synthetic luciferases, an orange and a red-emitting luciferase, which were designed to achieve high sensitivity (BoLuc) and multiplexing capability (BrLuc) for in vitro and in vivo biosensing using as a starting template a recently developed thermostable synthetic luciferase (BgLuc). Both luciferases were characterized in terms of emission behaviour and thermal and pH stability showing promising features as reporter proteins and BL probes. As proof-of-principle application, an inflammation assay based on Human Embryonic Kidney (HEK293T) 3D cell cultures was developed using either the orange or the red-emitting mutant. The assay provided good analytical performance, with limits of detection for Tumor Necrosis Factor (TNFα) of 0.06 and 0.12 ng mL-1 for BoLuc and BrLuc, respectively. Moreover, since these luciferases require the same substrate, D-luciferin, they can be easily implemented in dual-color assays with a significant reduction of total cost per assay.
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Affiliation(s)
- Maria Maddalena Calabretta
- Department of Chemistry "Giacomo Ciamician", University of Bologna, Via Selmi 2, 40126, Bologna, Italy.
- Center for Applied Biomedical Research (CRBA), Azienda Ospedaliero-Universitaria Policlinico S. Orso-la-Malpighi, 40138 Bologna, Italy
| | - Denise Gregucci
- Department of Chemistry "Giacomo Ciamician", University of Bologna, Via Selmi 2, 40126, Bologna, Italy.
- Center for Applied Biomedical Research (CRBA), Azienda Ospedaliero-Universitaria Policlinico S. Orso-la-Malpighi, 40138 Bologna, Italy
| | - Elisa Michelini
- Department of Chemistry "Giacomo Ciamician", University of Bologna, Via Selmi 2, 40126, Bologna, Italy.
- Center for Applied Biomedical Research (CRBA), Azienda Ospedaliero-Universitaria Policlinico S. Orso-la-Malpighi, 40138 Bologna, Italy
- Health Sciences and Technologies Interdepartmental Center for Industrial Research (HSTICIR), University of Bologna, 40126, Bologna, Italy
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14
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Silva-Filho AGS, Mombert A, Nascimento CC, Nóbrega BB, Soares DMM, Martins AGS, Domingos AHR, Santos I, Della-Torre OHP, Perry BA, Desjardin DE, Stevani CV, Menolli N. Eoscyphella luciurceolata gen. and sp. nov. (Agaricomycetes) Shed Light on Cyphellopsidaceae with a New Lineage of Bioluminescent Fungi. J Fungi (Basel) 2023; 9:1004. [PMID: 37888262 PMCID: PMC10608165 DOI: 10.3390/jof9101004] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2023] [Revised: 08/22/2023] [Accepted: 10/06/2023] [Indexed: 10/28/2023] Open
Abstract
During nocturnal field expeditions in the Brazilian Atlantic Rainforest, an unexpected bioluminescent fungus with reduced form was found. Based on morphological data, the taxon was first identified as belonging to the cyphelloid genus Maireina, but in our phylogenetic analyses, Maireina was recovered and confirmed as a paraphyletic group related to genera Merismodes and Cyphellopsis. Maireina filipendula, Ma. monacha, and Ma. subsphaerospora are herein transferred to Merismodes. Based upon morphological and molecular characters, the bioluminescent cyphelloid taxon is described as the new genus Eoscyphella, characterized by a vasiform to urceolate basidiomata, subglobose to broadly ellipsoid basidiospores, being pigmented, weakly to densely encrusted external hyphae, regularly bi-spored basidia, unclamped hyphae, and an absence of both conspicuous long external hairs and hymenial cystidia. Phylogenetic analyses based on ITS rDNA and LSU rDNA support the proposal of the new genus and confirm its position in Cyphellopsidaceae. Eoscyphella luciurceolata represents a new lineage of bioluminescent basidiomycetes with reduced forms.
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Affiliation(s)
- Alexandre G. S. Silva-Filho
- IFungiLab, Departamento de Ciências da Natureza e Matemática (DCM), Subárea de Biologia (SAB), Instituto Federal de Educação, Ciência e Tecnologia de São Paulo (IFSP), Campus São Paulo (SPO), São Paulo 01109-010, SP, Brazil; (A.G.S.S.-F.); (C.C.N.)
| | | | - Cristiano C. Nascimento
- IFungiLab, Departamento de Ciências da Natureza e Matemática (DCM), Subárea de Biologia (SAB), Instituto Federal de Educação, Ciência e Tecnologia de São Paulo (IFSP), Campus São Paulo (SPO), São Paulo 01109-010, SP, Brazil; (A.G.S.S.-F.); (C.C.N.)
| | - Bianca B. Nóbrega
- Departamento de Bioquímica, Instituto de Química, Universidade de São Paulo, São Paulo 05508-000, SP, Brazil;
- Departamento de Química Fundamental, Instituto de Química, Universidade de São Paulo, São Paulo 05508-000, SP, Brazil;
| | - Douglas M. M. Soares
- Departamento de Química Fundamental, Instituto de Química, Universidade de São Paulo, São Paulo 05508-000, SP, Brazil;
| | - Ana G. S. Martins
- Instituto de Pesquisa da Biodiversidade (IPBio), Iporanga 18330-000, SP, Brazil; (A.G.S.M.); (A.H.R.D.); (I.S.); (O.H.P.D.-T.)
| | - Adão H. R. Domingos
- Instituto de Pesquisa da Biodiversidade (IPBio), Iporanga 18330-000, SP, Brazil; (A.G.S.M.); (A.H.R.D.); (I.S.); (O.H.P.D.-T.)
| | - Isaias Santos
- Instituto de Pesquisa da Biodiversidade (IPBio), Iporanga 18330-000, SP, Brazil; (A.G.S.M.); (A.H.R.D.); (I.S.); (O.H.P.D.-T.)
| | - Olavo H. P. Della-Torre
- Instituto de Pesquisa da Biodiversidade (IPBio), Iporanga 18330-000, SP, Brazil; (A.G.S.M.); (A.H.R.D.); (I.S.); (O.H.P.D.-T.)
| | - Brian A. Perry
- Department of Biological Sciences, California State University, East Bay, Hayward, CA 94542, USA;
| | - Dennis E. Desjardin
- Department of Biology, San Francisco State University, San Francisco, CA 94132, USA;
| | - Cassius V. Stevani
- Departamento de Bioquímica, Instituto de Química, Universidade de São Paulo, São Paulo 05508-000, SP, Brazil;
- Departamento de Química Fundamental, Instituto de Química, Universidade de São Paulo, São Paulo 05508-000, SP, Brazil;
| | - Nelson Menolli
- IFungiLab, Departamento de Ciências da Natureza e Matemática (DCM), Subárea de Biologia (SAB), Instituto Federal de Educação, Ciência e Tecnologia de São Paulo (IFSP), Campus São Paulo (SPO), São Paulo 01109-010, SP, Brazil; (A.G.S.S.-F.); (C.C.N.)
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15
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Ramírez Martínez C, Gómez-Pérez LS, Ordaz A, Torres-Huerta AL, Antonio-Perez A. Current Trends of Bacterial and Fungal Optoproteins for Novel Optical Applications. Int J Mol Sci 2023; 24:14741. [PMID: 37834188 PMCID: PMC10572898 DOI: 10.3390/ijms241914741] [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: 08/31/2023] [Revised: 09/13/2023] [Accepted: 09/15/2023] [Indexed: 10/15/2023] Open
Abstract
Photoproteins, luminescent proteins or optoproteins are a kind of light-response protein responsible for the conversion of light into biochemical energy that is used by some bacteria or fungi to regulate specific biological processes. Within these specific proteins, there are groups such as the photoreceptors that respond to a given light wavelength and generate reactions susceptible to being used for the development of high-novel applications, such as the optocontrol of metabolic pathways. Photoswitchable proteins play important roles during the development of new materials due to their capacity to change their conformational structure by providing/eliminating a specific light stimulus. Additionally, there are bioluminescent proteins that produce light during a heatless chemical reaction and are useful to be employed as biomarkers in several fields such as imaging, cell biology, disease tracking and pollutant detection. The classification of these optoproteins from bacteria and fungi as photoreceptors or photoresponse elements according to the excitation-emission spectrum (UV-Vis-IR), as well as their potential use in novel applications, is addressed in this article by providing a structured scheme for this broad area of knowledge.
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Affiliation(s)
| | | | | | | | - Aurora Antonio-Perez
- Escuela de Ingeniería y Ciencias, Tecnológico de Monterrey, Campus Estado de México, Av. Lago de Guadalupe KM 3.5, Margarita Maza de Juárez, Ciudad López Mateos, Atizapán de Zaragoza 52926, Estado de México, Mexico; (C.R.M.); (L.S.G.-P.); (A.O.); (A.L.T.-H.)
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16
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Pholyotha A, Yano D, Mizuno G, Sutcharit C, Tongkerd P, Oba Y, Panha S. A new discovery of the bioluminescent terrestrial snail genus Phuphania (Gastropoda: Dyakiidae). Sci Rep 2023; 13:15137. [PMID: 37704646 PMCID: PMC10499882 DOI: 10.1038/s41598-023-42364-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2023] [Accepted: 09/09/2023] [Indexed: 09/15/2023] Open
Abstract
The mysterious world of the bioluminescent molluscs in terrestrial ecosystems is mesmerizing, but Quantula striata was previously the only terrestrial mollusc known to be luminescent. Here, we document the new discovery of bioluminescence in four land snails, namely Phuphania crossei, P. globosa, P. carinata, and P. costata. Our observations establish clearly that these four species of Phuphania produce a continuous greenish light from the light-emitting cells located within the mantle and the foot, and that its bright luminescence is intracellular and is not due to any luminous secretion. Although both Quantula and Phuphania can produce a green light, the luminescence patterns are different. The luminescence displayed by Quantula is rhythmical blinking or flashing, while Phuphania glows continuously. In addition, the bioluminescence in Q. weinkauffiana is confirmed, which is similar to that in the related species, Q. striata.
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Affiliation(s)
- Arthit Pholyotha
- Animal Systematics Research Unit, Department of Biology, Faculty of Science, Chulalongkorn University, Bangkok, 10330, Thailand
| | - Daichi Yano
- Animal Systematics Research Unit, Department of Biology, Faculty of Science, Chulalongkorn University, Bangkok, 10330, Thailand
| | - Gaku Mizuno
- Department of Environmental Biology, Chubu University, Kasugai, 487‑8501, Japan
| | - Chirasak Sutcharit
- Animal Systematics Research Unit, Department of Biology, Faculty of Science, Chulalongkorn University, Bangkok, 10330, Thailand
| | - Piyoros Tongkerd
- Animal Systematics Research Unit, Department of Biology, Faculty of Science, Chulalongkorn University, Bangkok, 10330, Thailand
| | - Yuichi Oba
- Department of Environmental Biology, Chubu University, Kasugai, 487‑8501, Japan.
| | - Somsak Panha
- Animal Systematics Research Unit, Department of Biology, Faculty of Science, Chulalongkorn University, Bangkok, 10330, Thailand.
- Academy of Science, The Royal Society of Thailand, Bangkok, 10300, Thailand.
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17
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Wang Q, Hu Z, Li Z, Liu T, Bian G. Exploring the Application and Prospects of Synthetic Biology in Engineered Living Materials. ADVANCED MATERIALS (DEERFIELD BEACH, FLA.) 2023:e2305828. [PMID: 37677048 DOI: 10.1002/adma.202305828] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/16/2023] [Revised: 09/05/2023] [Indexed: 09/09/2023]
Abstract
At the intersection of synthetic biology and materials science, engineered living materials (ELMs) exhibit unprecedented potential. Possessing unique "living" attributes, ELMs represent a significant paradigm shift in material design, showcasing self-organization, self-repair, adaptability, and evolvability, surpassing conventional synthetic materials. This review focuses on reviewing the applications of ELMs derived from bacteria, fungi, and plants in environmental remediation, eco-friendly architecture, and sustainable energy. The review provides a comprehensive overview of the latest research progress and emerging design strategies for ELMs in various application fields from the perspectives of synthetic biology and materials science. In addition, the review provides valuable references for the design of novel ELMs, extending the potential applications of future ELMs. The investigation into the synergistic application possibilities amongst different species of ELMs offers beneficial reference information for researchers and practitioners in this field. Finally, future trends and development challenges of synthetic biology for ELMs in the coming years are discussed in detail.
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Affiliation(s)
- Qiwen Wang
- Department of Urology, Zhongnan Hospital of Wuhan University, School of Pharmaceutical Sciences, Wuhan University, Wuhan, 430071, China
- Center of Materials Synthetic Biology, CAS Key Laboratory of Quantitative Engineering Biology, Shenzhen Institute of Synthetic Biology, Shenzhen Institutes of Advanced Technology, Chinese Academy of Sciences, Shenzhen, 518055, China
| | - Zhehui Hu
- Center of Materials Synthetic Biology, CAS Key Laboratory of Quantitative Engineering Biology, Shenzhen Institute of Synthetic Biology, Shenzhen Institutes of Advanced Technology, Chinese Academy of Sciences, Shenzhen, 518055, China
- National Key Laboratory for Germplasm Innovation & Utilization of Horticultural Crops, College of Horticulture and Forestry, Huazhong Agricultural University, Wuhan, 430071, China
| | - Zhixuan Li
- Center of Materials Synthetic Biology, CAS Key Laboratory of Quantitative Engineering Biology, Shenzhen Institute of Synthetic Biology, Shenzhen Institutes of Advanced Technology, Chinese Academy of Sciences, Shenzhen, 518055, China
| | - Tiangang Liu
- Department of Urology, Zhongnan Hospital of Wuhan University, School of Pharmaceutical Sciences, Wuhan University, Wuhan, 430071, China
| | - Guangkai Bian
- Center of Materials Synthetic Biology, CAS Key Laboratory of Quantitative Engineering Biology, Shenzhen Institute of Synthetic Biology, Shenzhen Institutes of Advanced Technology, Chinese Academy of Sciences, Shenzhen, 518055, China
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18
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Thar HM, Treesubsuntorn C, Thiravetyan P, Dolphen R. Development of light-emitting Episcia lilacina leaf by applying Vibrio campbellii RMT1 and extending the glowing by CaCl 2 and yeast extract. ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH INTERNATIONAL 2023:10.1007/s11356-023-28657-9. [PMID: 37421531 DOI: 10.1007/s11356-023-28657-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/25/2023] [Accepted: 07/03/2023] [Indexed: 07/10/2023]
Abstract
Glowing Episcia lilacina was generated through foliar application of the bioluminescent bacterium Vibrio campbellii RMT1. Firstly, different nutrient formulas were tested, incorporating yeast extract and various inorganic salts, such as CaCl2, MgCl2, MgSO4, KH2PO4, K2HPO4, and NaCl, in order to enhance bacterial growth and light emission. The combination of 0.15% of yeast extract and 0.3% of CaCl2 in a nutrient broth (NB) + 1% NaCl medium extended light emission to 24 h and resulted in higher light intensity compared to other combinations of yeast extract and inorganic salts. The peak intensity reached approximately 1.26 × 108 relative light units (RLU) at 7 h. The optimal presence of inorganic salt ions likely contributed to enhanced light emission, while the yeast extract acted as a nutrient source. Secondly, the effect of proline on salt-induced stress symptoms was investigated by applying 20 mM proline to the glowing plant. Additionally, a 0.5% agar nutrient was spread on the leaves prior to bacteria application to support bacterial growth and penetration. Exogenous proline application led to a significant accumulation of proline in plant cells, resulting in decreased malondialdehyde (MDA) levels. However, the proline accumulation also reduced the light intensity of the bioluminescent bacteria. This study demonstrates the potential for generating light on a living plant using bioluminescent bacteria. Further understanding of the interaction between plants and light-emitting bacteria could contribute to the development of sustainably light-emitting plants.
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Affiliation(s)
- Hsu Myat Thar
- Division of Biotechnology, Schools of Bioresources and Technology, King Mongkut's University of Technology Thonburi, Bangkok, 10150, Thailand
| | - Chairat Treesubsuntorn
- Division of Biotechnology, Schools of Bioresources and Technology, King Mongkut's University of Technology Thonburi, Bangkok, 10150, Thailand
| | - Paitip Thiravetyan
- Division of Biotechnology, Schools of Bioresources and Technology, King Mongkut's University of Technology Thonburi, Bangkok, 10150, Thailand
| | - Rujira Dolphen
- Pilot Plant Development and Training Institute, King Mongkut's University of Technology Thonburi, Bangkok, 10150, Thailand.
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19
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Oba Y, Hosaka K. The Luminous Fungi of Japan. J Fungi (Basel) 2023; 9:615. [PMID: 37367550 DOI: 10.3390/jof9060615] [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: 04/30/2023] [Revised: 05/17/2023] [Accepted: 05/24/2023] [Indexed: 06/28/2023] Open
Abstract
Luminous fungi have long attracted public attention in Japan, from old folklore and fiction to current tourism, children's toys, games, and picture books. At present, 25 species of luminous fungi have been discovered in Japan, which correspond to approximately one-fourth of the globally recognized species. This species richness is arguably due to the abundant presence of mycophiles looking to find new mushroom species and a tradition of night-time activities, such as firefly watching, in Japan. Bioluminescence, a field of bioscience focused on luminous organisms, has long been studied by many Japanese researchers, including the biochemistry and chemistry of luminous fungi. A Japanese Nobel Prize winner, Osamu Shimomura (1928-2018), primarily focused on the bioluminescence system of luminous fungi in the latter part of his life, and total elucidation of the mechanism was finally accomplished by an international research team with representatives from Russia, Brazil, and Japan in 2018. In this review, we focused on multiple aspects related to luminous fungi of Japan, including myth, taxonomy, and modern sciences.
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Affiliation(s)
- Yuichi Oba
- Department of Environmental Biology, Chubu University, Kasugai 487-8501, Aichi, Japan
| | - Kentaro Hosaka
- Department of Botany, National Museum of Nature and Science, Tsukuba 305-0005, Ibaraki, Japan
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20
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Zheng P, Ge J, Ji J, Zhong J, Chen H, Luo D, Li W, Bi B, Ma Y, Tong W, Han L, Ma S, Zhang Y, Wu J, Zhao Y, Pan R, Fan P, Lu M, Du H. Metabolic engineering and mechanical investigation of enhanced plant autoluminescence. PLANT BIOTECHNOLOGY JOURNAL 2023. [PMID: 37155328 PMCID: PMC10363767 DOI: 10.1111/pbi.14068] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/01/2023] [Revised: 04/18/2023] [Accepted: 04/24/2023] [Indexed: 05/10/2023]
Abstract
The fungal bioluminescence pathway (FBP) was identified from glowing fungi, which releases self-sustained visible green luminescence. However, weak bioluminescence limits the potential application of the bioluminescence system. Here, we screened and characterized a C3'H1 (4-coumaroyl shikimate/quinate 3'-hydroxylase) gene from Brassica napus, which efficiently converts p-coumaroyl shikimate to caffeic acid and hispidin. Simultaneous expression of BnC3'H1 and NPGA (null-pigment mutant in A. nidulans) produces more caffeic acid and hispidin as the natural precursor of luciferin and significantly intensifies the original fungal bioluminescence pathway (oFBP). Thus, we successfully created enhanced FBP (eFBP) plants emitting 3 × 1011 photons/min/cm2 , sufficient to illuminate its surroundings and visualize words clearly in the dark. The glowing plants provide sustainable and bio-renewable illumination for the naked eyes, and manifest distinct responses to diverse environmental conditions via caffeic acid biosynthesis pathway. Importantly, we revealed that the biosynthesis of caffeic acid and hispidin in eFBP plants derived from the sugar pathway, and the inhibitors of the energy production system significantly reduced the luminescence signal rapidly from eFBP plants, suggesting that the FBP system coupled with the luciferin metabolic flux functions in an energy-driven way. These findings lay the groundwork for genetically creating stronger eFBP plants and developing more powerful biological tools with the FBP system.
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Affiliation(s)
- Peng Zheng
- College of Agriculture and Biotechnology, Zhejiang University, Hangzhou, China
- ZJU-Hangzhou Global Scientific and Technological Innovation Center, Zhejiang University, Hangzhou, China
| | - Jieyu Ge
- College of Agriculture and Biotechnology, Zhejiang University, Hangzhou, China
| | - Jiayi Ji
- College of Agriculture and Biotechnology, Zhejiang University, Hangzhou, China
| | - Jingling Zhong
- College of Agriculture and Biotechnology, Zhejiang University, Hangzhou, China
- Hainan Institute of Zhejiang University, Sanya, China
| | - Hongyu Chen
- College of Agriculture and Biotechnology, Zhejiang University, Hangzhou, China
| | - Daren Luo
- College of Agriculture and Biotechnology, Zhejiang University, Hangzhou, China
| | - Wei Li
- College of Agriculture and Biotechnology, Zhejiang University, Hangzhou, China
- ZJU-Hangzhou Global Scientific and Technological Innovation Center, Zhejiang University, Hangzhou, China
| | - Bo Bi
- College of Agriculture and Biotechnology, Zhejiang University, Hangzhou, China
- ZJU-Hangzhou Global Scientific and Technological Innovation Center, Zhejiang University, Hangzhou, China
| | - Yongjun Ma
- College of Agriculture and Biotechnology, Zhejiang University, Hangzhou, China
| | - Wanghui Tong
- College of Agriculture and Biotechnology, Zhejiang University, Hangzhou, China
| | - Leiqin Han
- College of Agriculture and Biotechnology, Zhejiang University, Hangzhou, China
| | - Siqi Ma
- Marine Agriculture Research Center, Tobacco Research Institute of Chinese Academy of Agricultural Sciences, Qingdao, China
| | - Yuqi Zhang
- Key Laboratory of Structural Biology of Zhejiang Province, School of Life Sciences, Westlake University, Westlake Laboratory of Life Sciences and Biomedicine, Institute of Biology, Westlake Institute for Advanced Study, Hangzhou, China
| | - Jianping Wu
- Key Laboratory of Structural Biology of Zhejiang Province, School of Life Sciences, Westlake University, Westlake Laboratory of Life Sciences and Biomedicine, Institute of Biology, Westlake Institute for Advanced Study, Hangzhou, China
| | - Yanqiu Zhao
- State Key Laboratory of Subtropical Silviculture, Zhejiang A&F University, Hangzhou, China
| | - Ronghui Pan
- College of Agriculture and Biotechnology, Zhejiang University, Hangzhou, China
- ZJU-Hangzhou Global Scientific and Technological Innovation Center, Zhejiang University, Hangzhou, China
| | - Pengxiang Fan
- College of Agriculture and Biotechnology, Zhejiang University, Hangzhou, China
| | - Mengzhu Lu
- State Key Laboratory of Subtropical Silviculture, Zhejiang A&F University, Hangzhou, China
| | - Hao Du
- College of Agriculture and Biotechnology, Zhejiang University, Hangzhou, China
- ZJU-Hangzhou Global Scientific and Technological Innovation Center, Zhejiang University, Hangzhou, China
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21
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Affiliation(s)
- Vadim R Viviani
- Department of Physics, Chemistry and Mathematics (DFQM), Center for Sustainable Sciences and Technologies (CCTS), Federal University of São Carlos (UFSCar), Sorocaba, São Paulo, Brazil.
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22
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Liu X, Wang M, Liu Y. Chemistry in Fungal Bioluminescence: Theoretical Studies on Biosynthesis of Luciferin from Caffeic Acid and Regeneration of Caffeic Acid from Oxidized Luciferin. J Fungi (Basel) 2023; 9:jof9030369. [PMID: 36983537 PMCID: PMC10053366 DOI: 10.3390/jof9030369] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2023] [Revised: 03/11/2023] [Accepted: 03/16/2023] [Indexed: 03/30/2023] Open
Abstract
Fungal bioluminescence is widely distributed in the terrestrial environment. At a specific stage of growth, luminescent fungi shine green light at the fruiting body or mycelium. From the viewpoint of chemistry, fungal bioluminescence involves an in vivo cycle of caffeic acid. The complete cycle is composed of three stages: biosynthesis of luciferin from caffeic acid, luminescence process from luciferin to oxidized luciferin, and regeneration of caffeic acid from oxidized luciferin. Experimental studies roughly proposed this cycle but not the detailed reaction process and mechanism. Our previous theoretical study clearly described the mechanism of the middle stage. The present article attempts to describe the reaction processes and mechanisms of the other two stages by theoretical calculations. A complete theoretical study on the chemistry in the entire process of fungal bioluminescence is helpful to deeply understand fungal bioluminescence.
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Affiliation(s)
- Xiayu Liu
- Key Laboratory of Theoretical and Computational Photochemistry Ministry of Education, College of Chemistry Beijing Normal University, Beijing 100875, China
| | - Mingyu Wang
- School of Science, Hainan University, Haikou 570228, China
| | - Yajun Liu
- Key Laboratory of Theoretical and Computational Photochemistry Ministry of Education, College of Chemistry Beijing Normal University, Beijing 100875, China
- Center for Advanced Materials Research, Beijing Normal University, Zhuhai 519087, China
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23
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Jiang T, Song J, Zhang Y. Coelenterazine-Type Bioluminescence-Induced Optical Probes for Sensing and Controlling Biological Processes. Int J Mol Sci 2023; 24:ijms24065074. [PMID: 36982148 PMCID: PMC10049153 DOI: 10.3390/ijms24065074] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2023] [Revised: 02/21/2023] [Accepted: 03/02/2023] [Indexed: 03/09/2023] Open
Abstract
Bioluminescence-based probes have long been used to quantify and visualize biological processes in vitro and in vivo. Over the past years, we have witnessed the trend of bioluminescence-driven optogenetic systems. Typically, bioluminescence emitted from coelenterazine-type luciferin–luciferase reactions activate light-sensitive proteins, which induce downstream events. The development of coelenterazine-type bioluminescence-induced photosensory domain-based probes has been applied in the imaging, sensing, and control of cellular activities, signaling pathways, and synthetic genetic circuits in vitro and in vivo. This strategy can not only shed light on the mechanisms of diseases, but also promote interrelated therapy development. Here, this review provides an overview of these optical probes for sensing and controlling biological processes, highlights their applications and optimizations, and discusses the possible future directions.
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Affiliation(s)
- Tianyu Jiang
- Helmholtz International Lab for Anti-Infectives, Shandong University–Helmholtz Institute of Biotechnology, State Key Laboratory of Microbial Technology, Shandong University, Qingdao 266237, China
- Shenzhen Research Institute of Shandong University, Shenzhen 518000, China
- Correspondence: (T.J.); (Y.Z.)
| | - Jingwen Song
- Helmholtz International Lab for Anti-Infectives, Shandong University–Helmholtz Institute of Biotechnology, State Key Laboratory of Microbial Technology, Shandong University, Qingdao 266237, China
- School of Life Sciences, Shandong University, Qingdao 266237, China
| | - Youming Zhang
- Helmholtz International Lab for Anti-Infectives, Shandong University–Helmholtz Institute of Biotechnology, State Key Laboratory of Microbial Technology, Shandong University, Qingdao 266237, China
- Chinese Academy of Sciences (CAS) Key Laboratory of Quantitative Engineering Biology, Shenzhen Institute of Synthetic Biology, Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences, Shenzhen 518055, China
- Correspondence: (T.J.); (Y.Z.)
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24
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Garcia AGK, Steinbrenner AD. Bringing Plant Immunity to Light: A Genetically Encoded, Bioluminescent Reporter of Pattern-Triggered Immunity in Nicotiana benthamiana. MOLECULAR PLANT-MICROBE INTERACTIONS : MPMI 2023; 36:139-149. [PMID: 36583694 DOI: 10.1094/mpmi-07-22-0160-ta] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/17/2023]
Abstract
Plants rely on innate immune systems to defend against a wide variety of biotic attackers. Key components of innate immunity include cell-surface pattern-recognition receptors (PRRs), which recognize pest- and pathogen-associated molecular patterns (PAMPs). Unlike other classes of receptors that often have visible cell-death immune outputs upon activation, PRRs generally lack rapid methods for assessing function. Here, we describe a genetically encoded bioluminescent reporter of immune activation by heterologously expressed PRRs in the model organism Nicotiana benthamiana. We characterized N. benthamiana transcriptome changes in response to Agrobacterium tumefaciens and subsequent PAMP treatment to identify pattern-triggered immunity (PTI)-associated marker genes, which were then used to generate promoter-luciferase fusion fungal bioluminescence pathway (FBP) constructs. A reporter construct termed pFBP_2xNbLYS1::LUZ allows for robust detection of PTI activation by heterologously expressed PRRs. Consistent with known PTI signaling pathways, reporter activation by receptor-like protein (RLP) PRRs is dependent on the known adaptor of RLP PRRs, i.e., SOBIR1. The FBP reporter minimizes the amount of labor, reagents, and time needed to assay function of PRRs and displays robust sensitivity at biologically relevant PAMP concentrations, making it ideal for high throughput screens. The tools described in this paper will be powerful for investigations of PRR function and characterization of the structure-function of plant cell-surface receptors. [Formula: see text] The author(s) have dedicated the work to the public domain under the Creative Commons CC0 "No Rights Reserved" license by waiving all of his or her rights to the work worldwide under copyright law, including all related and neighboring rights, to the extent allowed by law, 2023.
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Affiliation(s)
- Anthony G K Garcia
- Department of Biology, University of Washington, Seattle, WA 98195, U.S.A
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25
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Furumura S, Ozaki T, Sugawara A, Morishita Y, Tsukada K, Ikuta T, Inoue A, Asai T. Identification and Functional Characterization of Fungal Chalcone Synthase and Chalcone Isomerase. JOURNAL OF NATURAL PRODUCTS 2023; 86:398-405. [PMID: 36762727 PMCID: PMC9972472 DOI: 10.1021/acs.jnatprod.2c01027] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/11/2022] [Indexed: 05/23/2023]
Abstract
By mining fungal genomic information, a noncanonical iterative type I PKS fused with an N-terminal adenylation-thiolation didomain, which catalyzes the formation of naringenin chalcone, was found. Structural prediction and molecular docking analysis indicated that a C-terminal thioesterase domain was involved in the Claisen-type cyclization. An enzyme responsible for formation of (2S)-flavanone in the biosynthesis of fungal flavonoids was also identified. Collectively, these findings demonstrate unprecedented fungal biosynthetic machinery leading to plant-like metabolites.
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26
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Motoyama T, Nogawa T, Shimizu T, Kawatani M, Kashiwa T, Yun CS, Hashizume D, Osada H. Fungal NRPS-PKS Hybrid Enzymes Biosynthesize New γ-Lactam Compounds, Taslactams A-D, Analogous to Actinomycete Proteasome Inhibitors. ACS Chem Biol 2023; 18:396-403. [PMID: 36692171 DOI: 10.1021/acschembio.2c00830] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023]
Abstract
Proteasome inhibitors with γ-lactam structure, such as lactacystin and salinosporamide A, have been isolated from actinomycetes and have attracted attention as lead compounds for anticancer drugs. Previously, we identified a unique enzyme TAS1, which is the first reported fungal NRPS-PKS hybrid enzyme, from the filamentous fungus Pyricularia oryzae for the biosynthesis of a mycotoxin tenuazonic acid, a tetramic acid compound without γ-lactam structure. Homologues of TAS1 have been identified in several fungal genomes and classified into four groups (A-D). Here, we show that the group D TAS1 homologues from two filamentous fungi can biosynthesize γ-lactam compounds, taslactams A-D, with high similarity to actinomycete proteasome inhibitors. One of the γ-lactam compounds, taslactam C, showed potent proteasome inhibitory activity. In contrast to actinomycete γ-lactam compounds which require multiple enzymes for biosynthesis, the TAS1 homologue alone was sufficient for the biosynthesis of the fungal γ-lactam compounds.
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Affiliation(s)
- Takayuki Motoyama
- Chemical Biology Research Group, RIKEN Center for Sustainable Resource Science (CSRS), 2-1 Hirosawa, Saitama 351-0198, Japan
| | - Toshihiko Nogawa
- Molecular Structure Characterization Unit, RIKEN Center for Sustainable Resource Science (CSRS), 2-1 Hirosawa, Saitama 351-0198, Japan
| | - Takeshi Shimizu
- Chemical Biology Research Group, RIKEN Center for Sustainable Resource Science (CSRS), 2-1 Hirosawa, Saitama 351-0198, Japan
| | - Makoto Kawatani
- Chemical Biology Research Group, RIKEN Center for Sustainable Resource Science (CSRS), 2-1 Hirosawa, Saitama 351-0198, Japan.,Biomolecular Characterization Unit, RIKEN Center for Sustainable Resource Science (CSRS), 2-1 Hirosawa, Saitama 351-0198, Japan.,Chemical Resource Development Research Unit, RIKEN Center for Sustainable Resource Science (CSRS), 2-1 Hirosawa, Saitama 351-0198, Japan
| | - Takeshi Kashiwa
- Chemical Biology Research Group, RIKEN Center for Sustainable Resource Science (CSRS), 2-1 Hirosawa, Saitama 351-0198, Japan
| | - Choong-Soo Yun
- Chemical Biology Research Group, RIKEN Center for Sustainable Resource Science (CSRS), 2-1 Hirosawa, Saitama 351-0198, Japan
| | - Daisuke Hashizume
- Materials Characterization Support Team, RIKEN Center for Emergent Matter Science (CEMS), 2-1 Hirosawa, Saitama 351-0198, Japan
| | - Hiroyuki Osada
- Chemical Biology Research Group, RIKEN Center for Sustainable Resource Science (CSRS), 2-1 Hirosawa, Saitama 351-0198, Japan.,Chemical Resource Development Research Unit, RIKEN Center for Sustainable Resource Science (CSRS), 2-1 Hirosawa, Saitama 351-0198, Japan.,Department of Pharmaceutical Sciences, University of Shizuoka, 52-1 Yata, Suruga-ku, Shizuoka 422-8526, Japan
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27
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Zhang L, Wang C, Chen K, Zhong W, Xu Y, Molnár I. Engineering the biosynthesis of fungal nonribosomal peptides. Nat Prod Rep 2023; 40:62-88. [PMID: 35796260 DOI: 10.1039/d2np00036a] [Citation(s) in RCA: 13] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]
Abstract
Covering: 2011 up to the end of 2021.Fungal nonribosomal peptides (NRPs) and the related polyketide-nonribosomal peptide hybrid products (PK-NRPs) are a prolific source of bioactive compounds, some of which have been developed into essential drugs. The synthesis of these complex natural products (NPs) utilizes nonribosomal peptide synthetases (NRPSs), multidomain megaenzymes that assemble specific peptide products by sequential condensation of amino acids and amino acid-like substances, independent of the ribosome. NRPSs, collaborating polyketide synthase modules, and their associated tailoring enzymes involved in product maturation represent promising targets for NP structure diversification and the generation of small molecule unnatural products (uNPs) with improved or novel bioactivities. Indeed, reprogramming of NRPSs and recruiting of novel tailoring enzymes is the strategy by which nature evolves NRP products. The recent years have witnessed a rapid development in the discovery and identification of novel NRPs and PK-NRPs, and significant advances have also been made towards the engineering of fungal NRP assembly lines to generate uNP peptides. However, the intrinsic complexities of fungal NRP and PK-NRP biosynthesis, and the large size of the NRPSs still present formidable conceptual and technical challenges for the rational and efficient reprogramming of these pathways. This review examines key examples for the successful (and for some less-successful) re-engineering of fungal NRPS assembly lines to inform future efforts towards generating novel, biologically active peptides and PK-NRPs.
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Affiliation(s)
- Liwen Zhang
- Biotechnology Research Institute, The Chinese Academy of Agricultural Sciences, 12 Zhongguancun South Street, Beijing 100081, P. R. China.
| | - Chen Wang
- Biotechnology Research Institute, The Chinese Academy of Agricultural Sciences, 12 Zhongguancun South Street, Beijing 100081, P. R. China.
| | - Kang Chen
- Biotechnology Research Institute, The Chinese Academy of Agricultural Sciences, 12 Zhongguancun South Street, Beijing 100081, P. R. China.
| | - Weimao Zhong
- Southwest Center for Natural Products Research, University of Arizona, 250 E. Valencia Rd., Tucson, AZ 85706, USA
| | - Yuquan Xu
- Biotechnology Research Institute, The Chinese Academy of Agricultural Sciences, 12 Zhongguancun South Street, Beijing 100081, P. R. China.
| | - István Molnár
- Southwest Center for Natural Products Research, University of Arizona, 250 E. Valencia Rd., Tucson, AZ 85706, USA.,VTT Technical Research Centre of Finland, P.O. Box 1000, FI-02044 VTT, Espoo, Finland.
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28
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Palkina KA, Balakireva AV, Belozerova OA, Chepurnykh TV, Markina NM, Kovalchuk SI, Tsarkova AS, Mishin AS, Yampolsky IV, Sarkisyan KS. Domain Truncation in Hispidin Synthase Orthologs from Non-Bioluminescent Fungi Does Not Lead to Hispidin Biosynthesis. Int J Mol Sci 2023; 24:1317. [PMID: 36674833 PMCID: PMC9866795 DOI: 10.3390/ijms24021317] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2022] [Revised: 12/22/2022] [Accepted: 01/07/2023] [Indexed: 01/12/2023] Open
Abstract
Hispidin is a polyketide found in plants and fungi. In bioluminescent fungi, hispidin serves as a precursor of luciferin and is produced by hispidin synthases. Previous studies revealed that hispidin synthases differ in orthologous polyketide synthases from non-bioluminescent fungi by the absence of two domains with predicted ketoreductase and dehydratase activities. Here, we investigated the hypothesis that the loss of these domains in evolution led to the production of hispidin and the emergence of bioluminescence. We cloned three orthologous polyketide synthases from non-bioluminescent fungi, as well as their truncated variants, and assessed their ability to produce hispidin in a bioluminescence assay in yeast. Interestingly, expression of the full-length enzyme hsPKS resulted in dim luminescence, indicating that small amounts of hispidin are likely being produced as side products of the main reaction. Deletion of the ketoreductase and dehydratase domains resulted in no luminescence. Thus, domain truncation by itself does not appear to be a sufficient step for the emergence of efficient hispidin synthases from orthologous polyketide synthases. At the same time, the production of small amounts of hispidin or related compounds by full-length enzymes suggests that ancestral fungal species were well-positioned for the evolution of bioluminescence.
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Affiliation(s)
- Kseniia A. Palkina
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, 117997 Moscow, Russia
- Planta LLC., 121205 Moscow, Russia
| | - Anastasia V. Balakireva
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, 117997 Moscow, Russia
- Planta LLC., 121205 Moscow, Russia
| | - Olga A. Belozerova
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, 117997 Moscow, Russia
- Institute of Translational Medicine, Pirogov Russian National Research Medical University, 117997 Moscow, Russia
| | - Tatiana V. Chepurnykh
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, 117997 Moscow, Russia
| | - Nadezhda M. Markina
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, 117997 Moscow, Russia
- Planta LLC., 121205 Moscow, Russia
| | - Sergey I. Kovalchuk
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, 117997 Moscow, Russia
| | - Aleksandra S. Tsarkova
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, 117997 Moscow, Russia
- Institute of Translational Medicine, Pirogov Russian National Research Medical University, 117997 Moscow, Russia
| | - Alexander S. Mishin
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, 117997 Moscow, Russia
- Planta LLC., 121205 Moscow, Russia
| | - Ilia V. Yampolsky
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, 117997 Moscow, Russia
- Institute of Translational Medicine, Pirogov Russian National Research Medical University, 117997 Moscow, Russia
| | - Karen S. Sarkisyan
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, 117997 Moscow, Russia
- Planta LLC., 121205 Moscow, Russia
- Synthetic Biology Group, MRC London Institute of Medical Sciences, London W12 0NN, UK
- Institute of Clinical Sciences, Faculty of Medicine and Imperial College Centre for Synthetic Biology, Imperial College London, London SW7 2AZ, UK
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29
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Zhang RQ, Feng XL, Wang ZX, Xie TC, Duan Y, Liu C, Gao JM, Qi J. Genomic and Metabolomic Analyses of the Medicinal Fungus Inonotus hispidus for Its Metabolite's Biosynthesis and Medicinal Application. J Fungi (Basel) 2022; 8:1245. [PMID: 36547578 PMCID: PMC9787987 DOI: 10.3390/jof8121245] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2022] [Revised: 11/11/2022] [Accepted: 11/21/2022] [Indexed: 11/27/2022] Open
Abstract
Inonotus hispidus mushroom is a traditional medicinal fungus with anti-cancer, antioxidation, and immunomodulatory activities, and it is used in folk medicine as a treatment for indigestion, cancer, diabetes, and gastric illnesses. Although I. hispidus is recognized as a rare edible medicinal macrofungi, its genomic sequence and biosynthesis potential of secondary metabolites have not been investigated. In this study, using Illumina NovaSeq combined with the PacBio platform, we sequenced and de novo assembled the whole genome of NPCB_001, a wild I. hispidus isolate from the Aksu area of Xinjiang Province, China. Comparative genomic and phylogenomic analyses reveal interspecific differences and evolutionary traits in the genus Inonotus. Bioinformatics analysis identified candidate genes associated with mating type, polysaccharide synthesis, carbohydrate-active enzymes, and secondary metabolite biosynthesis. Additionally, molecular networks of metabolites exhibit differences in chemical composition and content between fruiting bodies and mycelium, as well as association clusters of related compounds. The deciphering of the genome of I. hispidus will deepen the understanding of the biosynthesis of bioactive components, open the path for future biosynthesis research, and promote the application of Inonotus in the fields of drug research and functional food manufacturing.
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Affiliation(s)
- Rui-Qi Zhang
- Shaanxi Key Laboratory of Natural Products & Chemical Biology, College of Chemistry & Pharmacy, Northwest A&F University, Yangling, Xianyang 712100, China
| | - Xi-Long Feng
- Shaanxi Key Laboratory of Natural Products & Chemical Biology, College of Chemistry & Pharmacy, Northwest A&F University, Yangling, Xianyang 712100, China
| | - Zhen-Xin Wang
- Shaanxi Key Laboratory of Natural Products & Chemical Biology, College of Chemistry & Pharmacy, Northwest A&F University, Yangling, Xianyang 712100, China
| | - Tian-Chen Xie
- Shaanxi Key Laboratory of Natural Products & Chemical Biology, College of Chemistry & Pharmacy, Northwest A&F University, Yangling, Xianyang 712100, China
| | - Yingce Duan
- Key Laboratory for Enzyme and Enzyme-like Material Engineering of Heilongjiang, College of Life Science, Northeast Forestry University, Harbin 150040, China
| | - Chengwei Liu
- Key Laboratory for Enzyme and Enzyme-like Material Engineering of Heilongjiang, College of Life Science, Northeast Forestry University, Harbin 150040, China
| | - Jin-Ming Gao
- Shaanxi Key Laboratory of Natural Products & Chemical Biology, College of Chemistry & Pharmacy, Northwest A&F University, Yangling, Xianyang 712100, China
| | - Jianzhao Qi
- Shaanxi Key Laboratory of Natural Products & Chemical Biology, College of Chemistry & Pharmacy, Northwest A&F University, Yangling, Xianyang 712100, China
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30
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Noriler S, Navarro-Muñoz JC, Glienke C, Collemare J. Evolutionary relationships of adenylation domains in fungi. Genomics 2022; 114:110525. [PMID: 36423773 DOI: 10.1016/j.ygeno.2022.110525] [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: 09/26/2022] [Revised: 11/11/2022] [Accepted: 11/20/2022] [Indexed: 11/23/2022]
Abstract
Non-ribosomal peptide synthetases (NRPSs) and NRPS-like enzymes are abundant in microbes as they are involved in the production of primary and secondary metabolites. In contrast to the well-studied NRPSs, known to produce non-ribosomal peptides, NRPS-like enzymes exhibit more diverse activities and their evolutionary relationships are unclear. Here, we present the first in-depth phylogenetic analysis of fungal NRPS-like A domains from functionally characterized pathways, and their relationships to characterized A domains found in fungal NRPSs. This study clearly differentiated amino acid reductases, including NRPSs, from CoA/AMP ligases, which could be divided into 10 distinct phylogenetic clades that reflect their conserved domain organization, substrate specificity and enzymatic activity. In particular, evolutionary relationships of adenylate forming reductases could be refined and explained the substrate specificity difference. Consistent with their phylogeny, the deduced amino acid code of A domains differentiated amino acid reductases from other enzymes. However, a diagnostic code was found for α-keto acid reductases and clade 7 CoA/AMP ligases only. Comparative genomics of loci containing these enzymes revealed that they can be independently recruited as tailoring genes in diverse secondary metabolite pathways. Based on these results, we propose a refined and clear phylogeny-based classification of A domain-containing enzymes, which will provide a robust framework for future functional analyses and engineering of these enzymes to produce new bioactive molecules.
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Affiliation(s)
- Sandriele Noriler
- Postgraduate Program of Microbiology, Parasitology and Pathology, Department of Pathology, Universidade Federal do Parana, Av. Coronel Francisco Heráclito dos Santos, 210, CEP: 81531-970, Curitiba, PR, Brazil
| | - Jorge C Navarro-Muñoz
- Westerdijk Fungal Biodiversity Institute, Uppsalalaan 8, 3584, CT, Utrecht, the Netherlands
| | - Chirlei Glienke
- Postgraduate Program of Microbiology, Parasitology and Pathology, Department of Pathology, Universidade Federal do Parana, Av. Coronel Francisco Heráclito dos Santos, 210, CEP: 81531-970, Curitiba, PR, Brazil; Postgraduate Program of Genetics, Department of Genetics, Universidade Federal do Parana, Av. Coronel Francisco Heráclito dos Santos, 210, CEP: 81531-970, Curitiba, PR, Brazil
| | - Jérôme Collemare
- Westerdijk Fungal Biodiversity Institute, Uppsalalaan 8, 3584, CT, Utrecht, the Netherlands.
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Kim J, Park MJ, Shim D, Ryoo R. De novo genome assembly of the bioluminescent mushroom Omphalotus guepiniiformis reveals an Omphalotus-specific lineage of the luciferase gene block. Genomics 2022; 114:110514. [PMID: 36332840 DOI: 10.1016/j.ygeno.2022.110514] [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: 07/07/2022] [Revised: 10/04/2022] [Accepted: 10/23/2022] [Indexed: 11/05/2022]
Abstract
Omphalotus guepiniiformis, a bioluminescent mushroom species, is a source of the potentially valuable anticancer chemical. To provide genome information, we de novo assembled the high-quality O. guepiniiformis genome using two Next-Generation sequencing techniques, PacBio and Illumina sequencing. Our draft O. guepiniiformis genome comprises 42.5 Mbp of sequence with only 80 contigs and an N50 sequence length of over 1 Mbp. There were 15,554 predicted coding genes, and 7693 genes were functionally annotated with Gene Ontology terms. We performed a genomic study focusing on mushroom bioluminescent pathway cluster genes by comparing 17 luminescent and 23 non-luminescent Agaricales species belonging to 23 genera. Synteny analysis of genomic regions near the luminescent pathway cluster genes inferred that the Omphalotus lineage was genus-specific. In summary, our de novo assembled O. guepiniiformis genome provides significant biological insights into this organism, including the evolution of the luciferase gene block, and forms the basis for future analyses.
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Affiliation(s)
- Jaewook Kim
- Department of Biological Sciences, Chungnam National University, 34134 Daejeon, Republic of Korea
| | - Mi-Jeong Park
- Forest Microbiology Division, Department of Forest Bio-Resources, National Institute of Forest Science, 16631 Suwon, Republic of Korea
| | - Donghwan Shim
- Department of Biological Sciences, Chungnam National University, 34134 Daejeon, Republic of Korea.
| | - Rhim Ryoo
- Forest Microbiology Division, Department of Forest Bio-Resources, National Institute of Forest Science, 16631 Suwon, Republic of Korea.
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Ghobad-Nejhad M, Antonín V, Moghaddam M, Langer E. Resources of Iranian agarics (Basidiomycota) with an outlook on their antioxidant potential. Front Microbiol 2022; 13:1015440. [DOI: 10.3389/fmicb.2022.1015440] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2022] [Accepted: 09/20/2022] [Indexed: 11/13/2022] Open
Abstract
Agaric fungi are an important group of macromycetes with diverse ecological and functional properties, yet are poorly studied in many parts of the world. Here, we comprehensively analyzed 558 agaric species in Iran to reveal their resources of edible and poisonous species as well as their ecological guilds and luminescence potential. We also made a thorough survey of the antioxidant activity of the species. Phylogenetic relationships were reconstructed based on nuclear ribosomal LSU and ITS sequences. Our results reveal that agarics of Iran comprise about 189 edible, 128 poisonous, 254 soil saprotrophic, 172 ectomycorrhizal, 146 wood-inhabiting, 18 leaf/litter-inhabiting, 9 parasitic, and 19 luminescent species. Twenty percent of the Iranian agaric species possess antioxidant activity, phylogenetically distributed in four orders and 21 agaric families. About 5% of the antioxidant species can be considered strong antioxidants, many of which are also edible and could be utilized to develop functional foods. This is the first study combining phylogeny and antioxidant potential of agaric mushrooms in a large scale, and the obtained results would guide the selection of agaric taxa to be examined in the future for taxonomic revisions, biotechnological applications, and applied phylogeny studies.
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Zhang H, Li Z, Zhou S, Li SM, Ran H, Song Z, Yu T, Yin WB. A fungal NRPS-PKS enzyme catalyses the formation of the flavonoid naringenin. Nat Commun 2022; 13:6361. [PMID: 36289208 PMCID: PMC9606254 DOI: 10.1038/s41467-022-34150-7] [Citation(s) in RCA: 16] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2022] [Accepted: 10/14/2022] [Indexed: 12/25/2022] Open
Abstract
Biosynthesis of the flavonoid naringenin in plants and bacteria is commonly catalysed by a type III polyketide synthase (PKS) using one p-coumaroyl-CoA and three malonyl-CoA molecules as substrates. Here, we report a fungal non-ribosomal peptide synthetase -polyketide synthase (NRPS-PKS) hybrid FnsA for the naringenin formation. Feeding experiments with isotope-labelled precursors demonstrate that FnsA accepts not only p-coumaric acid (p-CA), but also p-hydroxybenzoic acid (p-HBA) as starter units, with three or four malonyl-CoA molecules for elongation, respectively. In vitro assays and MS/MS analysis prove that both p-CA and p-HBA are firstly activated by the adenylation domain of FnsA. Phylogenetic analysis reveals that the PKS portion of FnsA shares high sequence homology with type I PKSs. Refactoring the biosynthetic pathway in yeast with the involvement of fnsA provides an alternative approach for the production of flavonoids such as isorhamnetin and acacetin.
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Affiliation(s)
- Hongjiao Zhang
- State Key Laboratory of Mycology, Institute of Microbiology, Chinese Academy of Sciences, Beijing, 100101, China
- Savaid Medical School, University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Zixin Li
- State Key Laboratory of Mycology, Institute of Microbiology, Chinese Academy of Sciences, Beijing, 100101, China
- Savaid Medical School, University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Shuang Zhou
- State Key Laboratory of Mycology, Institute of Microbiology, Chinese Academy of Sciences, Beijing, 100101, China
- Savaid Medical School, University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Shu-Ming Li
- Institut für Pharmazeutische Biologie und Biotechnologie, Fachbereich Pharmazie, Philipps-Universität Marburg, Marburg, 35037, Germany
| | - Huomiao Ran
- State Key Laboratory of Mycology, Institute of Microbiology, Chinese Academy of Sciences, Beijing, 100101, China
| | - Zili Song
- State Key Laboratory of Mycology, Institute of Microbiology, Chinese Academy of Sciences, Beijing, 100101, China
- Savaid Medical School, University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Tao Yu
- Center for Synthetic Biochemistry, CAS Key Laboratory of Quantitative Engineering Biology, Shenzhen Institute of Synthetic Biology, Shenzhen Institutes for Advanced Technology, Chinese Academy of Sciences, Shenzhen, 518055, China
| | - Wen-Bing Yin
- State Key Laboratory of Mycology, Institute of Microbiology, Chinese Academy of Sciences, Beijing, 100101, China.
- Savaid Medical School, University of Chinese Academy of Sciences, Beijing, 100049, China.
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Moreno-Giménez E, Selma S, Calvache C, Orzáez D. GB_SynP: A Modular dCas9-Regulated Synthetic Promoter Collection for Fine-Tuned Recombinant Gene Expression in Plants. ACS Synth Biol 2022; 11:3037-3048. [PMID: 36044643 PMCID: PMC9486966 DOI: 10.1021/acssynbio.2c00238] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2022] [Indexed: 01/24/2023]
Abstract
Programmable transcriptional factors based on the CRISPR architecture are becoming commonly used in plants for endogenous gene regulation. In plants, a potent CRISPR tool for gene induction is the so-called dCasEV2.1 activation system, which has shown remarkable genome-wide specificity combined with a strong activation capacity. To explore the ability of dCasEV2.1 to act as a transactivator for orthogonal synthetic promoters, a collection of DNA parts was created (GB_SynP) for combinatorial synthetic promoter building. The collection includes (i) minimal promoter parts with the TATA box and 5'UTR regions, (ii) proximal parts containing single or multiple copies of the target sequence for the gRNA, thus functioning as regulatory cis boxes, and (iii) sequence-randomized distal parts that ensure the adequate length of the resulting promoter. A total of 35 promoters were assembled using the GB_SynP collection, showing in all cases minimal background and predictable activation levels depending on the proximal parts used. GB_SynP was also employed in a combinatorial expression analysis of an autoluminescence pathway in Nicotiana benthamiana, showing the value of this tool in extracting important biological information such as the determination of the limiting steps in an enzymatic pathway.
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Affiliation(s)
- Elena Moreno-Giménez
- Instituto
de Biología Molecular y Celular de Plantas (IBMCP), Consejo
Superior de Investigaciones Científicas, Universidad Politécnica de Valencia, Camino de Vera s/n, Valencia 46022, Spain
| | - Sara Selma
- Instituto
de Biología Molecular y Celular de Plantas (IBMCP), Consejo
Superior de Investigaciones Científicas, Universidad Politécnica de Valencia, Camino de Vera s/n, Valencia 46022, Spain
| | - Camilo Calvache
- Instituto
de Biología Molecular y Celular de Plantas (IBMCP), Consejo
Superior de Investigaciones Científicas, Universidad Politécnica de Valencia, Camino de Vera s/n, Valencia 46022, Spain
| | - Diego Orzáez
- Instituto
de Biología Molecular y Celular de Plantas (IBMCP), Consejo
Superior de Investigaciones Científicas, Universidad Politécnica de Valencia, Camino de Vera s/n, Valencia 46022, Spain
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Huang Y, Zhang W, Zhang C, Cui N, Xiao Z, Wang R, Su X. Rapid and reagent-free bioassay using autobioluminescent yeasts to detect agonistic and antagonistic activities of bisphenols against rat androgen receptor and progesterone receptor. J Steroid Biochem Mol Biol 2022; 222:106151. [PMID: 35787454 DOI: 10.1016/j.jsbmb.2022.106151] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/25/2022] [Revised: 06/20/2022] [Accepted: 06/29/2022] [Indexed: 11/17/2022]
Abstract
Bisphenol A (BPA) and its analogues have been classified as endocrine disruptors via binding to nuclear receptors. Two novel bioassays, BLYrARS and BLYrPRS, were developed for rapid detection of agonistic and antagonistic activities of BPA and five of its analogues binding rat androgen receptor (rAR) and rat progesterone receptor (rPR). The reporter bioassay was based on two autonomously bioluminescent strains of the yeast Saccharomyces cerevisiae, recombined with a bacterial luciferase reporter gene cassette (lux) that can produce autofluorescence, regulated by the corresponding hormone response element acting as the responsive promoter. The bioluminescent signal is autonomous and continuous without cell lysis or addition of exogenous reagents. The AR agonist R1881 could be detected at 4 h with a half-maximal effective concentration (EC50) of ~9.4 nM. The PR agonist progesterone could be determined at 4 h with an EC50 of ~2.74 nM. None of the sixteen bisphenols presented agonistic activities against rAR and rPR. However, thirteen BPs were rAR antagonists and eleven BPs acted as rPR antagonists with different potency. The BLYrARS and BLYrPRS bioassay characterized by automated signal acquisition without additional manipulations or cost can be applied for simple and rapid detection of agonistic and antagonistic activities of BPs and other compounds acting as agonists or antagonists of rAR and rPR. Based on data derived by use of this bioassay endocrine-disrupting activities of some BPA analogues are more potent than BPA.
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Affiliation(s)
- Yuan Huang
- Institute of Quality Standards and Testing Technology for Agro-Products, Chinese Academy of Agricultural Sciences, Beijing 10081, China.
| | - Wei Zhang
- Institute of Quality Standards and Testing Technology for Agro-Products, Chinese Academy of Agricultural Sciences, Beijing 10081, China.
| | - Chengdong Zhang
- Beijing Biorise Biotechnology Co., Ltd, Beijing 102206, China.
| | - Na Cui
- Institute of Quality Standards and Testing Technology for Agro-Products, Chinese Academy of Agricultural Sciences, Beijing 10081, China.
| | - Zhiming Xiao
- Institute of Quality Standards and Testing Technology for Agro-Products, Chinese Academy of Agricultural Sciences, Beijing 10081, China.
| | - Ruiguo Wang
- Institute of Quality Standards and Testing Technology for Agro-Products, Chinese Academy of Agricultural Sciences, Beijing 10081, China.
| | - Xiaoou Su
- Institute of Quality Standards and Testing Technology for Agro-Products, Chinese Academy of Agricultural Sciences, Beijing 10081, China.
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36
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Liu YJ. Understanding the complete bioluminescence cycle from a multiscale computational perspective: A review. JOURNAL OF PHOTOCHEMISTRY AND PHOTOBIOLOGY C: PHOTOCHEMISTRY REVIEWS 2022. [DOI: 10.1016/j.jphotochemrev.2022.100537] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
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37
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Rao L, Shi HC, Zou Y. A fungal nonribosomal peptide-polyketide hybrid synthase synthesizes 2-pyrrolidinone alkaloid. Tetrahedron 2022. [DOI: 10.1016/j.tet.2022.133060] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
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38
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Huang Y, Hoefgen S, Gherlone F, Valiante V. Intrinsic Ability of the β‐Oxidation Pathway To Produce Bioactive Styrylpyrones. Angew Chem Int Ed Engl 2022; 61:e202206851. [PMID: 35726672 PMCID: PMC9541201 DOI: 10.1002/anie.202206851] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2022] [Indexed: 11/09/2022]
Abstract
Naturally occurring α‐pyrones with biological activities are mostly synthesised by polyketide synthases (PKSs) via iterative decarboxylative Claisen condensation steps. Remarkably, we found that some enzymes related to the fatty acid β‐oxidation pathway in Escherichia coli, namely the CoA ligase FadD and the thiolases FadA and FadI, can synthesise styrylpyrones with phenylpropionic acids in vivo. The two thiolases directly utilise acetyl‐CoA as an extender unit for carbon‐chain elongation through a non‐decarboxylative Claisen condensation, thus making the overall reaction more efficient in terms of carbon and energy consumption. Moreover, using a cell‐free approach, different styrylpyrones were synthesised in vitro. Finally, targeted feeding experiments led to the detection of styrylpyrones in other species, demonstrating that the intrinsic ability of the β‐oxidation pathway allows for the synthesis of such molecules in bacteria, revealing an important biological feature hitherto neglected.
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Affiliation(s)
- Ying Huang
- Independent Junior Research Group Biobricks of Microbial Natural Product Syntheses Leibniz Institute for Natural Product Research and Infection Biology Hans Knöll Institute (HKI) Beutenbergstrasse 11a 07745 Jena Germany
| | - Sandra Hoefgen
- Independent Junior Research Group Biobricks of Microbial Natural Product Syntheses Leibniz Institute for Natural Product Research and Infection Biology Hans Knöll Institute (HKI) Beutenbergstrasse 11a 07745 Jena Germany
| | - Fabio Gherlone
- Independent Junior Research Group Biobricks of Microbial Natural Product Syntheses Leibniz Institute for Natural Product Research and Infection Biology Hans Knöll Institute (HKI) Beutenbergstrasse 11a 07745 Jena Germany
| | - Vito Valiante
- Independent Junior Research Group Biobricks of Microbial Natural Product Syntheses Leibniz Institute for Natural Product Research and Infection Biology Hans Knöll Institute (HKI) Beutenbergstrasse 11a 07745 Jena Germany
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39
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Dörner S, Rogge K, Fricke J, Schäfer T, Wurlitzer JM, Gressler M, Pham DNK, Manke DR, Chadeayne AR, Hoffmeister D. Genetic Survey of Psilocybe Natural Products. Chembiochem 2022; 23:e202200249. [PMID: 35583969 PMCID: PMC9400892 DOI: 10.1002/cbic.202200249] [Citation(s) in RCA: 16] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2022] [Revised: 05/17/2022] [Indexed: 11/07/2022]
Abstract
Psilocybe magic mushrooms are best known for their main natural product, psilocybin, and its dephosphorylated congener, the psychedelic metabolite psilocin. Beyond tryptamines, the secondary metabolome of these fungi is poorly understood. The genomes of five species (P. azurescens, P. cubensis, P. cyanescens, P. mexicana, and P. serbica) were browsed to understand more profoundly common and species-specific metabolic capacities. The genomic analyses revealed a much greater and yet unexplored metabolic diversity than evident from parallel chemical analyses. P. cyanescens and P. mexicana were identified as aeruginascin producers. Lumichrome and verpacamide A were also detected as Psilocybe metabolites. The observations concerning the potential secondary metabolome of this fungal genus support pharmacological and toxicological efforts to find a rational basis for yet elusive phenomena, such as paralytic effects, attributed to consumption of some magic mushrooms.
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Affiliation(s)
- Sebastian Dörner
- Department Pharmaceutical Microbiology at the Hans-Knöll-InstituteFriedrich-Schiller-UniversitätBeutenbergstrasse 11a07745JenaGermany
| | - Kai Rogge
- Department Pharmaceutical Microbiology at the Hans-Knöll-InstituteFriedrich-Schiller-UniversitätBeutenbergstrasse 11a07745JenaGermany
| | - Janis Fricke
- Department Pharmaceutical Microbiology at the Hans-Knöll-InstituteFriedrich-Schiller-UniversitätBeutenbergstrasse 11a07745JenaGermany
| | - Tim Schäfer
- Department Pharmaceutical Microbiology at the Hans-Knöll-InstituteFriedrich-Schiller-UniversitätBeutenbergstrasse 11a07745JenaGermany
| | - Jacob M. Wurlitzer
- Department Pharmaceutical Microbiology at the Hans-Knöll-InstituteFriedrich-Schiller-UniversitätBeutenbergstrasse 11a07745JenaGermany
| | - Markus Gressler
- Department Pharmaceutical Microbiology at the Hans-Knöll-InstituteFriedrich-Schiller-UniversitätBeutenbergstrasse 11a07745JenaGermany
| | - Duyen N. K. Pham
- Department of Chemistry & BiochemistryUniversity of Massachusetts285 Old Westport RoadDartmouthMA02747USA
| | - David R. Manke
- Department of Chemistry & BiochemistryUniversity of Massachusetts285 Old Westport RoadDartmouthMA02747USA
| | | | - Dirk Hoffmeister
- Department Pharmaceutical Microbiology at the Hans-Knöll-InstituteFriedrich-Schiller-UniversitätBeutenbergstrasse 11a07745JenaGermany
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40
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Expanding luciferase reporter systems for cell-free protein expression. Sci Rep 2022; 12:11489. [PMID: 35798760 PMCID: PMC9263134 DOI: 10.1038/s41598-022-15624-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2022] [Accepted: 06/27/2022] [Indexed: 11/08/2022] Open
Abstract
Luciferases are often used as a sensitive, versatile reporter in cell-free transcription-translation (TXTL) systems, for research and practical applications such as engineering genetic parts, validating genetic circuits, and biosensor outputs. Currently, only two luciferases (Firefly and Renilla) are commonly used without substrate cross-talk. Here we demonstrate the expansion of the cell-free luciferase reporter system, with two orthogonal luciferase reporters: N. nambi luciferase (Luz) and LuxAB. These luciferases do not have cross-reactivity with the Firefly and Renilla substrates. We also demonstrate a substrate regeneration pathway for one of the new luciferases, enabling long-term time courses of protein expression monitoring in the cell-free system. Furthermore, we reduced the number of genes required in TXTL expression, by engineering a cell extract containing part of the luciferase enzymes. Our findings lead to an expanded platform with multiple orthogonal luminescence translation readouts for in vitro protein expression.
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41
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Chen L, Tang JW, Liu YY, Matsuda Y. Aspcandine: A Pyrrolobenzazepine Alkaloid Synthesized by a Fungal Nonribosomal Peptide Synthetase-Polyketide Synthase Hybrid. Org Lett 2022; 24:4816-4819. [PMID: 35748771 DOI: 10.1021/acs.orglett.2c01918] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Characterization of an orphan biosynthetic gene cluster found in the fungus Aspergillus candidus CBS 102.13 resulted in the discovery of a pyrrolobenzazepine alkaloid, aspcandine (1). The unique molecular scaffold of 1 is synthesized by the nonribosomal peptide synthetase-polyketide synthase hybrid AcdB, which unusually incorporates 3-hydroxy-l-kynurenine as a building block. AcdB subsequently performs one round of chain elongation using malonyl-CoA, which is followed by the chain release to furnish the tricyclic system of 1.
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Affiliation(s)
- Lin Chen
- Department of Chemistry, City University of Hong Kong, Tat Chee Avenue, Kowloon, Hong Kong SAR, China
| | - Jian-Wei Tang
- Department of Ocean Science and Hong Kong Branch of Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou), The Hong Kong University of Science and Technology, Kowloon, Hong Kong SAR, China
| | - Yan Yee Liu
- Department of Chemistry, City University of Hong Kong, Tat Chee Avenue, Kowloon, Hong Kong SAR, China
| | - Yudai Matsuda
- Department of Chemistry, City University of Hong Kong, Tat Chee Avenue, Kowloon, Hong Kong SAR, China
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42
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Valiante V, Huang Y, Hoefgen S, Gherlone F. Intrinsic Ability of the ß‐Oxidation Pathway To Produce Bioactive Styrylpyrones. Angew Chem Int Ed Engl 2022. [DOI: 10.1002/ange.202206851] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Affiliation(s)
- Vito Valiante
- Leibniz-Institut für Naturstoff-Forschung und Infektionsbiologie eV Hans-Knöll-Institut Biobricks of Microbial Natural Product Syntheses Adolf-Reichwein-Str. 23 07745 Jena GERMANY
| | - Ying Huang
- Leibniz Institute for Natural Product Research and Infection BiologyHans Knöll Institute: Leibniz-Institut fur Naturstoff-Forschung und Infektionsbiologie eV Hans-Knoll-Institut Biobricks of Microbial Natural Product Syntheses 07745 Jena GERMANY
| | - Sandra Hoefgen
- Leibniz-Institut für Naturstoff-Forschung und Infektionsbiologie eV Hans-Knöll-Institut: Leibniz-Institut fur Naturstoff-Forschung und Infektionsbiologie eV Hans-Knoll-Institut Biobricks of Microbial Natural Product Syntheses 07745 Jena GERMANY
| | - Fabio Gherlone
- Leibniz-Institut für Naturstoff-Forschung und Infektionsbiologie eV Hans-Knöll-Institut: Leibniz-Institut fur Naturstoff-Forschung und Infektionsbiologie eV Hans-Knoll-Institut Biobricks of Microbial Natural Product Syntheses 07745 Jena GERMANY
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43
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Ronzhin NO, Posokhina ED, Mogilnaya OA, Bondar VS. Finding the Light Emission Stimulator of Neonothopanus nambi Basidiomycete and Studying Its Properties. DOKL BIOCHEM BIOPHYS 2022; 503:80-84. [PMID: 35538283 DOI: 10.1134/s1607672922020120] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2021] [Revised: 12/23/2021] [Accepted: 12/23/2021] [Indexed: 11/23/2022]
Abstract
A stimulator of light emission of the fungus was found in an aqueous extract from mycelium of the luminous basidiomycete Neonothopanus nambi after its treatment with β-glucosidase. The addition of the extract to the luminous mycelium increases the level of light emission from several times to 1.5 orders of magnitude or more. The luminescence stimulator is a low-molecular-weight thermostable compound: it is detected in the permeate after filtering the extract through a 10-kDa cutoff membrane and it retains the stimulating effect after heat treatment at 100°C for 5 min. In the absorption spectrum of the aqueous sample of the stimulator, two main peaks are observed in the shortwave region (205 and 260 nm) and a shoulder in the range of 350-370 nm can be seen. The luminescence stimulator exhibits blue fluorescence with an emission maximum at 440 nm when excited at 360 nm. It was established that the luminescence-stimulating component is not a substrate (or its precursor) of the luminescent system of the N. nambi fungus.
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Affiliation(s)
- N O Ronzhin
- Institute of Biophysics, Federal Research Center "Krasnoyarsk Scientific Center", Siberian Branch, Russian Academy of Sciences, Krasnoyarsk, Russia.
| | - E D Posokhina
- Institute of Biophysics, Federal Research Center "Krasnoyarsk Scientific Center", Siberian Branch, Russian Academy of Sciences, Krasnoyarsk, Russia
| | - O A Mogilnaya
- Institute of Biophysics, Federal Research Center "Krasnoyarsk Scientific Center", Siberian Branch, Russian Academy of Sciences, Krasnoyarsk, Russia
| | - V S Bondar
- Institute of Biophysics, Federal Research Center "Krasnoyarsk Scientific Center", Siberian Branch, Russian Academy of Sciences, Krasnoyarsk, Russia
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44
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Effect of excited state inter- or intra-proton transfers on the fluorescence behaviors of firefly fluorescein analogues. Chem Phys Lett 2022. [DOI: 10.1016/j.cplett.2022.139551] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
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Tian Q, Wu J, Xu H, Hu Z, Huo Y, Wang L. Cryo-EM structure of the fatty acid reductase LuxC-LuxE complex provides insights into bacterial bioluminescence. J Biol Chem 2022; 298:102006. [PMID: 35504354 PMCID: PMC9157457 DOI: 10.1016/j.jbc.2022.102006] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2022] [Revised: 04/26/2022] [Accepted: 04/27/2022] [Indexed: 11/25/2022] Open
Abstract
The discovery of reduced flavin mononucleotide and fatty aldehydes as essential factors of light emission facilitated study of bacterial luminescence. Although the molecular mechanisms underlying bacterial luminescence have been studied for more than 60 years, the structure of the bacterial fatty acid reductase complex remains unclear. Here, we report the cryo-EM structure of the Photobacterium phosphoreum fatty acid reductase complex LuxC–LuxE to a resolution of 2.79 Å. We show that the active site Lys238/Arg355 pair of LuxE is >30 Å from the active site Cys296 of LuxC, implying that catalysis relies on a large conformational change. Furthermore, mutagenesis and biochemical experiments support that the L-shaped cleft inside LuxC plays an important role in substrate binding and reaction. We obtained a series of mutants with significantly improved activity as measured by in vitro bioluminescence assays and demonstrated that the double mutant W111A/F483K displayed the highest activity (370% of the WT). Our results indicated that the activity of LuxC significantly affects the bacterial bioluminescence reaction. Finally, we expressed this mutated lux operon in Escherichia coli but observed that the in vivo concentrations of ATP and NADPH limited the enzyme activity; thus, we conclude that the luminous intensity mainly depends on the level of metabolic energy.
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Affiliation(s)
- Qingwei Tian
- Shenzhen Key Laboratory of Marine Bioresource and Eco-Environmental Science, College of Life Sciences and Oceanography, Shenzhen University, Shenzhen, China; Key Laboratory of Optoelectronic Devices and Systems, College of Physics and Optoelectronic Engineering, Shenzhen University, Shenzhen, China
| | - Jingting Wu
- Shenzhen Key Laboratory of Marine Bioresource and Eco-Environmental Science, College of Life Sciences and Oceanography, Shenzhen University, Shenzhen, China
| | - Haifeng Xu
- National Laboratory of Macromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing, China; University of Chinese Academy of Sciences, Beijing, China
| | - Zhangli Hu
- Shenzhen Key Laboratory of Marine Bioresource and Eco-Environmental Science, College of Life Sciences and Oceanography, Shenzhen University, Shenzhen, China; Key Laboratory of Optoelectronic Devices and Systems, College of Physics and Optoelectronic Engineering, Shenzhen University, Shenzhen, China
| | - Yangao Huo
- National Laboratory of Macromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing, China.
| | - Liyan Wang
- Shenzhen Key Laboratory of Marine Bioresource and Eco-Environmental Science, College of Life Sciences and Oceanography, Shenzhen University, Shenzhen, China.
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Oba Y, Schultz DT. Firefly genomes illuminate the evolution of beetle bioluminescent systems. CURRENT OPINION IN INSECT SCIENCE 2022; 50:100879. [PMID: 35091104 DOI: 10.1016/j.cois.2022.100879] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/17/2021] [Revised: 12/30/2021] [Accepted: 01/20/2022] [Indexed: 06/14/2023]
Abstract
Fireflies are one of the best-known bioluminescent organisms, and the reaction mechanism and ecological utility of bioluminescence have been well-studied. Genome assemblies of six species of bioluminescent beetles have recently been published. These studies have focused on the evolution of novelties; luciferase, and the biosynthesis of luciferin and defensive chemicals. For example, clustering of the luciferase gene with acyl-CoA synthetase genes on a chromosome in luminous beetle genomes suggests the involvement of tandem gene duplications and neofunctionalization during the evolution of beetle bioluminescence. Several candidate genes for critical roles in beetle bioluminescence have been identified, but their functional analyses are still ongoing. The establishment of a long-term mass-rearing system and strain will be the key for the post-genome research on bioluminescent beetles. Lastly, the application of contemporary chromosome-scale genome assembly techniques to luminous beetles will help resolve outstanding evolutionary questions, such as how many times bioluminescence evolved in this clade.
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Affiliation(s)
- Yuichi Oba
- Department of Environmental Biology, Chubu University, Kasugai 487-8501, Japan.
| | - Darrin T Schultz
- Monterey Bay Aquarium Research Institute, Moss Landing, CA 95039, United States
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Tanner F, Tonn S, de Wit J, Van den Ackerveken G, Berger B, Plett D. Sensor-based phenotyping of above-ground plant-pathogen interactions. PLANT METHODS 2022; 18:35. [PMID: 35313920 PMCID: PMC8935837 DOI: 10.1186/s13007-022-00853-7] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/29/2021] [Accepted: 02/08/2022] [Indexed: 05/20/2023]
Abstract
Plant pathogens cause yield losses in crops worldwide. Breeding for improved disease resistance and management by precision agriculture are two approaches to limit such yield losses. Both rely on detecting and quantifying signs and symptoms of plant disease. To achieve this, the field of plant phenotyping makes use of non-invasive sensor technology. Compared to invasive methods, this can offer improved throughput and allow for repeated measurements on living plants. Abiotic stress responses and yield components have been successfully measured with phenotyping technologies, whereas phenotyping methods for biotic stresses are less developed, despite the relevance of plant disease in crop production. The interactions between plants and pathogens can lead to a variety of signs (when the pathogen itself can be detected) and diverse symptoms (detectable responses of the plant). Here, we review the strengths and weaknesses of a broad range of sensor technologies that are being used for sensing of signs and symptoms on plant shoots, including monochrome, RGB, hyperspectral, fluorescence, chlorophyll fluorescence and thermal sensors, as well as Raman spectroscopy, X-ray computed tomography, and optical coherence tomography. We argue that choosing and combining appropriate sensors for each plant-pathosystem and measuring with sufficient spatial resolution can enable specific and accurate measurements of above-ground signs and symptoms of plant disease.
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Affiliation(s)
- Florian Tanner
- Australian Plant Phenomics Facility, School of Agriculture, Food and Wine, University of Adelaide, Urrbrae, SA Australia
| | - Sebastian Tonn
- Department of Biology, Plant-Microbe Interactions, Utrecht University, 3584CH Utrecht, The Netherlands
| | - Jos de Wit
- Department of Imaging Physics, Delft University of Technology, Lorentzweg 1, 2628 CJ Delft, The Netherlands
| | - Guido Van den Ackerveken
- Department of Biology, Plant-Microbe Interactions, Utrecht University, 3584CH Utrecht, The Netherlands
| | - Bettina Berger
- Australian Plant Phenomics Facility, School of Agriculture, Food and Wine, University of Adelaide, Urrbrae, SA Australia
| | - Darren Plett
- Australian Plant Phenomics Facility, School of Agriculture, Food and Wine, University of Adelaide, Urrbrae, SA Australia
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De novo biosynthesis of diverse plant-derived styrylpyrones in Saccharomyces cerevisiae. Metab Eng Commun 2022; 14:e00195. [PMID: 35287355 PMCID: PMC8917298 DOI: 10.1016/j.mec.2022.e00195] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2021] [Revised: 02/28/2022] [Accepted: 03/02/2022] [Indexed: 12/28/2022] Open
Abstract
Plant styrylpyrones exerting well-established neuroprotective properties have attracted increasing attention in recent years. The ability to synthesize each individual styrylpyrone in engineered microorganisms is important to understanding the biological activity of medicinal plants and the complex mixtures they produce. Microbial biomanufacturing of diverse plant-derived styrylpyrones also provides a sustainable and efficient approach for the production of valuable plant styrylpyrones as daily supplements or potential drugs complementary to the prevalent agriculture-based approach. In this study, we firstly demonstrated the heterogenous biosynthesis of two 7,8-saturated styrylpyrones (7,8-dihydro-5,6-dehydrokavain (DDK) and 7,8-dihydroyangonin (DHY)) and two 7,8-unsaturated styrylpyrones (desmethoxyyangonin (DMY) and yangonin (Y)), in Saccharomyces cerevisiae. Although plant styrylpyrone biosynthetic pathways have not been fully elucidated, we functionally reconstructed the recently discovered kava styrylpyrone biosynthetic pathway that has high substrate promiscuity in yeast, and combined it with upstream hydroxycinnamic acid biosynthetic pathways to produce diverse plant-derived styrylpyrones without the native plant enzymes. We optimized the de novo pathways by engineering yeast endogenous aromatic amino acid metabolism and endogenous double bond reductases and by CRISPR-mediated δ-integration to overexpress the rate-limiting pathway genes. These combinatorial engineering efforts led to the first three yeast strains that can produce diverse plant-derived styrylpyrones de novo, with the titers of DDK, DMY and Y at 4.40 μM, 1.28 μM and 0.10 μM, respectively. This work has laid the foundation for larger-scale styrylpyrone biomanufacturing and the complete biosynthesis of more complicated plant styrylpyrones. Complete biosynthesis of plant styrylpyrones was firstly achieved in yeast. Yeast enzyme replaces unknown plant enzymes to produce 7,8-saturated styrylpyrones. CRISPR-based δ-integration led to stable styrylpyrone overproduction in rich medium.
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Calabretta MM, Lopreside A, Montali L, Zangheri M, Evangelisti L, D'Elia M, Michelini E. Portable light detectors for bioluminescence biosensing applications: A comprehensive review from the analytical chemist's perspective. Anal Chim Acta 2022; 1200:339583. [DOI: 10.1016/j.aca.2022.339583] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2021] [Revised: 02/02/2022] [Accepted: 02/04/2022] [Indexed: 12/11/2022]
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Gregor C. Imaging of Autonomous Bioluminescence Emission From Single Mammalian Cells. Methods Mol Biol 2022; 2524:163-172. [PMID: 35821470 DOI: 10.1007/978-1-0716-2453-1_12] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/15/2023]
Abstract
The bioluminescent visualization of individual mammalian cells usually requires the addition of a luciferin substrate. This chapter describes the microscopic imaging of single cells by their bioluminescence (BL) emission generated without an external luciferin. Imaging is based on the expression of codon-optimized lux (co lux) genes and does not require manipulation of the cells apart from transfection. Due to the high brightness of the co lux system, light emission from single cells can be observed continuously for many hours using a specialized microscope.
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Affiliation(s)
- Carola Gregor
- Department of Optical Nanoscopy, Institut für Nanophotonik Göttingen e.V, Göttingen, Germany.
- Department of NanoBiophotonics, Max Planck Institute for Biophysical Chemistry, Göttingen, Germany.
- Cluster of Excellence "Multiscale Bioimaging: from Molecular Machines to Networks of Excitable Cells" (MBExC), University of Göttingen, Göttingen, Germany.
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