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Pfotenhauer AC, Lenaghan SC. Phytosensors: harnessing plants to understand the world around us. Curr Opin Biotechnol 2024; 87:103134. [PMID: 38705091 DOI: 10.1016/j.copbio.2024.103134] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2024] [Revised: 04/04/2024] [Accepted: 04/09/2024] [Indexed: 05/07/2024]
Abstract
Although plants are sessile, their ubiquitous distribution, ability to harness energy from the sun, and ability to sense above and belowground signals make them ideal candidates for biosensor development. Synthetic biology has allowed scientists to reimagine biosensors as engineered devices that are focused on accomplishing novel tasks. As such, a new wave of plant-based sensors, phytosensors, are being engineered as multi-component sense-and-report devices that can alert human operators to a variety of hazards. While phytosensors are intrinsically tied to agriculture, a new generation of phytosensors has been envisioned to function in the built environment and even in austere environments, such as space. In this review, we will explore the current state of the art with regard to phytosensor engineering.
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Affiliation(s)
| | - Scott C Lenaghan
- Center for Agricultural Synthetic Biology, University of Tennessee, Knoxville, TN, USA; Department of Food Science, University of Tennessee, Knoxville, USA.
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2
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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] [What about the content of this article? (0)] [Affiliation(s)] [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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3
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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] [What about the content of this article? (0)] [Affiliation(s)] [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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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. Sci Adv 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] [What about the content of this article? (0)] [Affiliation(s)] [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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5
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Fenelon KD, Krause J, Koromila T. Opticool: Cutting-edge transgenic optical tools. PLoS Genet 2024; 20:e1011208. [PMID: 38517915 PMCID: PMC10959397 DOI: 10.1371/journal.pgen.1011208] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/24/2024] Open
Abstract
Only a few short decades have passed since the sequencing of GFP, yet the modern repertoire of transgenically encoded optical tools implies an exponential proliferation of ever improving constructions to interrogate the subcellular environment. A myriad of tags for labeling proteins, RNA, or DNA have arisen in the last few decades, facilitating unprecedented visualization of subcellular components and processes. Development of a broad array of modern genetically encoded sensors allows real-time, in vivo detection of molecule levels, pH, forces, enzyme activity, and other subcellular and extracellular phenomena in ever expanding contexts. Optogenetic, genetically encoded optically controlled manipulation systems have gained traction in the biological research community and facilitate single-cell, real-time modulation of protein function in vivo in ever broadening, novel applications. While this field continues to explosively expand, references are needed to assist scientists seeking to use and improve these transgenic devices in new and exciting ways to interrogate development and disease. In this review, we endeavor to highlight the state and trajectory of the field of in vivo transgenic optical tools.
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Affiliation(s)
- Kelli D. Fenelon
- Department of Biology, University of Texas at Arlington, Arlington, Texas, United States of America
| | - Julia Krause
- Department of Biology, University of Texas at Arlington, Arlington, Texas, United States of America
| | - Theodora Koromila
- Department of Biology, University of Texas at Arlington, Arlington, Texas, United States of America
- School of Biology, Aristotle University of Thessaloniki, Thessaloniki, Greece
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6
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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: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [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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Wang X, Wei J, Liu Z, Wang Y, Yuan X, Wang D, Niu J, Yang Y, Zhou J. Comparative genomic analysis of Sanghuangporus sanghuang with other Hymenochaetaceae species. Braz J Microbiol 2024; 55:87-100. [PMID: 38099978 PMCID: PMC10920484 DOI: 10.1007/s42770-023-01212-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2023] [Accepted: 12/03/2023] [Indexed: 03/09/2024] Open
Abstract
Sanghuangporus sanghuang is a medicinal macrofungus with antioxidant and antitumor activities, and it is enriched with secondary metabolites such as polysaccharides, terpenes, polyphenols, and styrylpyrone compounds. To explore the putative core genes and gene clusters involved in sanghuang biosynthesis, we sequenced and assembled a 40.5-Mb genome of S. sanghuang (SH1 strain). Using antiSMASH, local BLAST, and NCBI comparison, 12 terpene synthases (TPSs), 1 non-ribosomal peptide synthase, and five polyketide synthases (PKSs) were identified in SH1. Combining the transcriptome analysis with liquid chromatography mass spectrometry-ion trap-time of flight analysis, we determined that ShPKS1, one phenylalanine aminolyase (ShPAL), and one P450 monooxygenase (ShC4H1) were associated with hispidin biosynthesis. Structural domain comparison indicated that ShPKS2 and ShPKS3 are involved in the biosynthesis of orsellinic acid and 2-hydroxy-6-methylbenzoic acid, respectively. Furthermore, comparative genomic analysis of SH1 with 14 other fungi from the Hymenochaetaceae family showed variation in the number of TPSs among different genomes, with Coniferiporia weirii exhibiting only 9 TPSs and Inonotus obliquus having 20. The number of TPSs also differed among the genomes of three strains of S. sanghuang, namely Kangneng (16), MS2 (9), and SH1 (12). The type and number of PKSs also varied among species and even strains, ranging from two PKSs in Pyrrhoderma noxium to five PKSs in S. sanghuang SH1. Among the three strains of S. sanghuang, both the structural domains and the number of PKSs in strains MS2 and SH1 were consistent, whereas strain Kangneng exhibited only four PKSs and lacked the PKS with the structural domain KS-AT-DH-KR-ACP. Additionally, Sanghuangporus species exhibited more similar PKSs to Inonotus, with higher gene similarity around five PKSs, while showing differences from those of other fungi in the same family, including Phellinus lamaoensis. This result supports the independent taxonomic significance of the genus Sanghuangporus to some extent.
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Affiliation(s)
- Xinyue Wang
- School of Pharmaceutical Science and Yunnan Key Laboratory of Pharmacology for Natural Products, Kunming Medical University, 1168 Western Chunrong Road, Yuhua Street, Chenggong New City, Kunming, 650500, China
- Laboratory of Forest Plant Cultivation and Utilization, The Key Laboratory of Rare and Endangered Forest Plants of State Forestry Administration, Yunnan Academy of Forestry and Grassland, Kunming, 650201, China
| | - Jiansheng Wei
- Laboratory of Forest Plant Cultivation and Utilization, The Key Laboratory of Rare and Endangered Forest Plants of State Forestry Administration, Yunnan Academy of Forestry and Grassland, Kunming, 650201, China
- Haba Snow Mountain Provincial Nature Reserve Management and Protection Bureau, Diqing, 674402, China
| | - Zhenwen Liu
- Laboratory of Forest Plant Cultivation and Utilization, The Key Laboratory of Rare and Endangered Forest Plants of State Forestry Administration, Yunnan Academy of Forestry and Grassland, Kunming, 650201, China
| | - Yi Wang
- Laboratory of Forest Plant Cultivation and Utilization, The Key Laboratory of Rare and Endangered Forest Plants of State Forestry Administration, Yunnan Academy of Forestry and Grassland, Kunming, 650201, China.
| | - Xiaolong Yuan
- Laboratory of Forest Plant Cultivation and Utilization, The Key Laboratory of Rare and Endangered Forest Plants of State Forestry Administration, Yunnan Academy of Forestry and Grassland, Kunming, 650201, China
| | - Dong Wang
- Laboratory of Forest Plant Cultivation and Utilization, The Key Laboratory of Rare and Endangered Forest Plants of State Forestry Administration, Yunnan Academy of Forestry and Grassland, Kunming, 650201, China
- College of Forestry, Southwest Forestry University, Kunming, 650224, Yunnan, China
| | - Junmei Niu
- School of Pharmaceutical Science and Yunnan Key Laboratory of Pharmacology for Natural Products, Kunming Medical University, 1168 Western Chunrong Road, Yuhua Street, Chenggong New City, Kunming, 650500, China
| | - Yan Yang
- Institute of Edible Fungi, Shanghai Academy of Agricultural Sciences, Shanghai, 201106, China
| | - Jing Zhou
- School of Pharmaceutical Science and Yunnan Key Laboratory of Pharmacology for Natural Products, Kunming Medical University, 1168 Western Chunrong Road, Yuhua Street, Chenggong New City, Kunming, 650500, China.
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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] [What about the content of this article? (0)] [Affiliation(s)] [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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9
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Rabinowitch I, Colón-Ramos DA, Krieg M. Understanding neural circuit function through synaptic engineering. Nat Rev Neurosci 2024; 25:131-139. [PMID: 38172626 DOI: 10.1038/s41583-023-00777-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 11/29/2023] [Indexed: 01/05/2024]
Abstract
Synapses are a key component of neural circuits, facilitating rapid and specific signalling between neurons. Synaptic engineering - the synthetic insertion of new synaptic connections into in vivo neural circuits - is an emerging approach for neural circuit interrogation. This approach is especially powerful for establishing causality in neural circuit structure-function relationships, for emulating synaptic plasticity and for exploring novel patterns of circuit connectivity. Contrary to other approaches for neural circuit manipulation, synaptic engineering targets specific connections between neurons and functions autonomously with no user-controlled external activation. Synaptic engineering has been successfully implemented in several systems and in different forms, including electrical synapses constructed from ectopically expressed connexin gap junction proteins, synthetic optical synapses composed of presynaptic photon-emitting luciferase coupled with postsynaptic light-gated channels, and artificial neuropeptide signalling pathways. This Perspective describes these different methods and how they have been applied, and examines how the field may advance.
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Affiliation(s)
- Ithai Rabinowitch
- Department of Medical Neurobiology, Institute for Medical Research Israel-Canada, Faculty of Medicine, Hebrew University of Jerusalem, Jerusalem, Israel.
| | - Daniel A Colón-Ramos
- Wu Tsai Institute, Department of Neuroscience and Department of Cell Biology, Yale University School of Medicine, New Haven, CT, USA
| | - Michael Krieg
- ICFO - Institut de Ciencies Fotoniques, The Barcelona Institute of Science and Technology, Castelldefels, Spain
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10
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Bourzac K. Glow way! Bioluminescent houseplant hits US market for first time. Nature 2024; 626:701. [PMID: 38337056 DOI: 10.1038/d41586-024-00383-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/12/2024]
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11
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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] [What about the content of this article? (0)] [Affiliation(s)] [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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12
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Calvache C, Vazquez‐Vilar M, Moreno‐Giménez E, Orzaez D. A quantitative autonomous bioluminescence reporter system with a wide dynamic range for Plant Synthetic Biology. Plant Biotechnol J 2024; 22:37-47. [PMID: 37882352 PMCID: PMC10754000 DOI: 10.1111/pbi.14146] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/13/2023] [Revised: 06/24/2023] [Accepted: 07/24/2023] [Indexed: 10/27/2023]
Abstract
Plant Synthetic Biology aims to enhance the capacities of plants by designing and integrating synthetic gene circuits (SGCs). Quantitative reporting solutions that can produce quick, rich datasets affordably are necessary for SGC optimization. In this paper, we present a new, low-cost, and high-throughput reporter system for the quantitative measurement of gene expression in plants based on autonomous bioluminescence. This method eliminates the need for an exogenous supply of luciferase substrate by exploiting the entire Neonothopanus nambi fungal bioluminescence cyclic pathway to build a self-sustained reporter. The HispS gene, the pathway's limiting step, was set up as the reporter's transcriptional entry point as part of the new system's design, which significantly improved the output's dynamic range and brought it on par with that of the gold standard FLuc/RLuc reporter. Additionally, transient ratiometric measurements in N. benthamiana were made possible by the addition of an enhanced GFP as a normalizer. The performance of new NeoLuc/eGFP system was extensively validated with SGCs previously described, including phytohormone and optogenetic sensors. Furthermore, we employed NeoLuc/eGFP in the optimization of challenging SGCs, including new configurations for an agrochemical (copper) switch, a new blue optogenetic sensor, and a dual copper/red-light switch for tight regulation of metabolic pathways.
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Affiliation(s)
- Camilo Calvache
- Instituto de Biología Molecular y Celular de Plantas, Consejo Superior de Investigaciones CientíficasUniversitat Politècnica de ValénciaValenciaSpain
| | - Marta Vazquez‐Vilar
- Instituto de Biología Molecular y Celular de Plantas, Consejo Superior de Investigaciones CientíficasUniversitat Politècnica de ValénciaValenciaSpain
| | - Elena Moreno‐Giménez
- Instituto de Biología Molecular y Celular de Plantas, Consejo Superior de Investigaciones CientíficasUniversitat Politècnica de ValénciaValenciaSpain
| | - Diego Orzaez
- Instituto de Biología Molecular y Celular de Plantas, Consejo Superior de Investigaciones CientíficasUniversitat Politècnica de ValénciaValenciaSpain
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13
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Quan Z, Ohmiya Y, Liu YJ. Chemical Mechanism of Fireworm Bioluminescence - A Theoretical Proposition. J Phys Chem A 2023; 127:10851-10859. [PMID: 38103213 DOI: 10.1021/acs.jpca.3c07409] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2023]
Abstract
Odontosyllis undecimdonta is a marine worm, commonly known as a fireworm, that exhibits bluish-green bioluminescence (BL). The luciferin (L) and oxyluciferin (OL) during fireworm BL have been experimentally identified in vitro. The L and OL are the respective starting point and ending point of a series of complicated chemical reactions in the BL. However, the chemical mechanism of the fireworm BL remains largely unknown. Before the experiments provided strong evidence for the mechanism, based on our previously successful studies on several bioluminescent systems, we theoretically proposed the chemical mechanism of the fireworm BL in this article. By means of the spin-flip and time-dependent density functional calculations, we clearly described the complete process from L to OL: under the catalysis of luciferase, L undergoes deprotonation and reacts with 3O2 to form a dioxetanone anion via the single-electron transfer mechanism; the dioxetanone anion decomposes into the OL at the first singlet excited state (S1) by the gradually reversible charge-transfer-induced luminescence mechanism; and the S1-OL emits light and deexcites to OL in the ground state.
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Affiliation(s)
- Zhuo Quan
- Key Laboratory of Theoretical and Computational Photochemistry, Ministry of Education, College of Chemistry, Beijing Normal University, Beijing 100875, China
| | - Yoshihiro Ohmiya
- Osaka Institute of Technology (OIT), 5-16-1 Ohmiya, Asahi-ku, Osaka 535-8585, Japan
| | - Ya-Jun 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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14
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Nemergut M, Pluskal D, Horackova J, Sustrova T, Tulis J, Barta T, Baatallah R, Gagnot G, Novakova V, Majerova M, Sedlackova K, Marques SM, Toul M, Damborsky J, Prokop Z, Bednar D, Janin YL, Marek M. Illuminating the mechanism and allosteric behavior of NanoLuc luciferase. Nat Commun 2023; 14:7864. [PMID: 38030625 PMCID: PMC10687086 DOI: 10.1038/s41467-023-43403-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2022] [Accepted: 11/08/2023] [Indexed: 12/01/2023] Open
Abstract
NanoLuc, a superior β-barrel fold luciferase, was engineered 10 years ago but the nature of its catalysis remains puzzling. Here experimental and computational techniques are combined, revealing that imidazopyrazinone luciferins bind to an intra-barrel catalytic site but also to an allosteric site shaped on the enzyme surface. Structurally, binding to the allosteric site prevents simultaneous binding to the catalytic site, and vice versa, through concerted conformational changes. We demonstrate that restructuration of the allosteric site can boost the luminescent reaction in the remote active site. Mechanistically, an intra-barrel arginine coordinates the imidazopyrazinone component of luciferin, which reacts with O2 via a radical charge-transfer mechanism, and then it also protonates the resulting excited amide product to form a light-emitting neutral species. Concomitantly, an aspartate, supported by two tyrosines, fine-tunes the blue color emitter to secure a high emission intensity. This information is critical to engineering the next-generation of ultrasensitive bioluminescent reporters.
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Affiliation(s)
- Michal Nemergut
- Loschmidt Laboratories, Department of Experimental Biology and RECETOX, Faculty of Science, Masaryk University, Kamenice 5, Bld. C13, 625 00, Brno, Czech Republic
- International Clinical Research Center, St. Anne's University Hospital Brno, Pekarska 53, 656 91, Brno, Czech Republic
- Center for Interdisciplinary Biosciences, Technology and Innovation Park, P. J. Safarik University in Kosice, Trieda SNP 1, 04011, Kosice, Slovakia
| | - Daniel Pluskal
- Loschmidt Laboratories, Department of Experimental Biology and RECETOX, Faculty of Science, Masaryk University, Kamenice 5, Bld. C13, 625 00, Brno, Czech Republic
| | - Jana Horackova
- Loschmidt Laboratories, Department of Experimental Biology and RECETOX, Faculty of Science, Masaryk University, Kamenice 5, Bld. C13, 625 00, Brno, Czech Republic
| | - Tereza Sustrova
- Loschmidt Laboratories, Department of Experimental Biology and RECETOX, Faculty of Science, Masaryk University, Kamenice 5, Bld. C13, 625 00, Brno, Czech Republic
| | - Jan Tulis
- Loschmidt Laboratories, Department of Experimental Biology and RECETOX, Faculty of Science, Masaryk University, Kamenice 5, Bld. C13, 625 00, Brno, Czech Republic
| | - Tomas Barta
- Department of Histology and Embryology, Faculty of Medicine, Masaryk University, Kamenice 753/5, 625 00, Brno, Czech Republic
| | - Racha Baatallah
- Unité de Chimie et Biocatalyse, Institut Pasteur, UMR 3523, CNRS, 28 rue du Dr. Roux, 75724 Paris Cedex 15, Paris, France
| | - Glwadys Gagnot
- Unité de Chimie et Biocatalyse, Institut Pasteur, UMR 3523, CNRS, 28 rue du Dr. Roux, 75724 Paris Cedex 15, Paris, France
- Université de Paris, 12 rue de l'école de Médecine, 75006, Paris, France
| | - Veronika Novakova
- Loschmidt Laboratories, Department of Experimental Biology and RECETOX, Faculty of Science, Masaryk University, Kamenice 5, Bld. C13, 625 00, Brno, Czech Republic
- International Clinical Research Center, St. Anne's University Hospital Brno, Pekarska 53, 656 91, Brno, Czech Republic
| | - Marika Majerova
- Loschmidt Laboratories, Department of Experimental Biology and RECETOX, Faculty of Science, Masaryk University, Kamenice 5, Bld. C13, 625 00, Brno, Czech Republic
- International Clinical Research Center, St. Anne's University Hospital Brno, Pekarska 53, 656 91, Brno, Czech Republic
| | - Karolina Sedlackova
- Loschmidt Laboratories, Department of Experimental Biology and RECETOX, Faculty of Science, Masaryk University, Kamenice 5, Bld. C13, 625 00, Brno, Czech Republic
- International Clinical Research Center, St. Anne's University Hospital Brno, Pekarska 53, 656 91, Brno, Czech Republic
| | - Sérgio M Marques
- Loschmidt Laboratories, Department of Experimental Biology and RECETOX, Faculty of Science, Masaryk University, Kamenice 5, Bld. C13, 625 00, Brno, Czech Republic
- International Clinical Research Center, St. Anne's University Hospital Brno, Pekarska 53, 656 91, Brno, Czech Republic
| | - Martin Toul
- Loschmidt Laboratories, Department of Experimental Biology and RECETOX, Faculty of Science, Masaryk University, Kamenice 5, Bld. C13, 625 00, Brno, Czech Republic
- International Clinical Research Center, St. Anne's University Hospital Brno, Pekarska 53, 656 91, Brno, Czech Republic
| | - Jiri Damborsky
- Loschmidt Laboratories, Department of Experimental Biology and RECETOX, Faculty of Science, Masaryk University, Kamenice 5, Bld. C13, 625 00, Brno, Czech Republic
- International Clinical Research Center, St. Anne's University Hospital Brno, Pekarska 53, 656 91, Brno, Czech Republic
| | - Zbynek Prokop
- Loschmidt Laboratories, Department of Experimental Biology and RECETOX, Faculty of Science, Masaryk University, Kamenice 5, Bld. C13, 625 00, Brno, Czech Republic
- International Clinical Research Center, St. Anne's University Hospital Brno, Pekarska 53, 656 91, Brno, Czech Republic
| | - David Bednar
- Loschmidt Laboratories, Department of Experimental Biology and RECETOX, Faculty of Science, Masaryk University, Kamenice 5, Bld. C13, 625 00, Brno, Czech Republic.
- International Clinical Research Center, St. Anne's University Hospital Brno, Pekarska 53, 656 91, Brno, Czech Republic.
| | - Yves L Janin
- Structure et Instabilité des Génomes (StrInG), Muséum National d'Histoire Naturelle, INSERM, CNRS, Alliance Sorbonne Université, 75005, Paris, France.
| | - Martin Marek
- Loschmidt Laboratories, Department of Experimental Biology and RECETOX, Faculty of Science, Masaryk University, Kamenice 5, Bld. C13, 625 00, Brno, Czech Republic.
- International Clinical Research Center, St. Anne's University Hospital Brno, Pekarska 53, 656 91, Brno, Czech Republic.
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15
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Partap M, Verma V, Thakur M, Bhargava B. Designing of future ornamental crops: a biotechnological driven perspective. Hortic Res 2023; 10:uhad192. [PMID: 38023473 PMCID: PMC10681008 DOI: 10.1093/hr/uhad192] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 05/09/2023] [Accepted: 09/14/2023] [Indexed: 12/01/2023]
Abstract
With a basis in human appreciation of beauty and aesthetic values, the new era of ornamental crops is based on implementing innovative technologies and transforming symbols into tangible assets. Recent advances in plant biotechnology have attracted considerable scientific and industrial interest, particularly in terms of modifying desired plant traits and developing future ornamental crops. By utilizing omics approaches, genomic data, genetic engineering, and gene editing tools, scientists have successively explored the underlying molecular mechanism and potential gene(s) behind trait regulation such as floral induction, plant architecture, stress resistance, plasticity, adaptation, and phytoremediation in ornamental crop species. These signs of progress lay a theoretical and practical foundation for designing and enhancing the efficiency of ornamental plants for a wide range of applications. In this review, we briefly summarized the existing literature and advances in biotechnological approaches for the improvement of vital traits in ornamental plants. The future ornamental plants, such as light-emitting plants, biotic/abiotic stress detectors, and pollution abatement, and the introduction of new ornamental varieties via domestication of wild species are also discussed.
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Affiliation(s)
- Mahinder Partap
- Floriculture Laboratory, Agrotechnology Division, Council of Scientific and Industrial Research (CSIR), Institute of Himalayan Bioresource Technology (IHBT), Post Box No. 6, 176 061 (HP) Palampur, India
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, 201002, Uttar Pradesh, India
| | - Vipasha Verma
- Floriculture Laboratory, Agrotechnology Division, Council of Scientific and Industrial Research (CSIR), Institute of Himalayan Bioresource Technology (IHBT), Post Box No. 6, 176 061 (HP) Palampur, India
| | - Meenakshi Thakur
- Floriculture Laboratory, Agrotechnology Division, Council of Scientific and Industrial Research (CSIR), Institute of Himalayan Bioresource Technology (IHBT), Post Box No. 6, 176 061 (HP) Palampur, India
| | - Bhavya Bhargava
- Floriculture Laboratory, Agrotechnology Division, Council of Scientific and Industrial Research (CSIR), Institute of Himalayan Bioresource Technology (IHBT), Post Box No. 6, 176 061 (HP) Palampur, India
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, 201002, Uttar Pradesh, India
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16
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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. Adv Mater 2023:e2305828. [PMID: 37677048 DOI: 10.1002/adma.202305828] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [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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17
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Ranawaka B, An J, Lorenc MT, Jung H, Sulli M, Aprea G, Roden S, Llaca V, Hayashi S, Asadyar L, LeBlanc Z, Ahmed Z, Naim F, de Campos SB, Cooper T, de Felippes FF, Dong P, Zhong S, Garcia-Carpintero V, Orzaez D, Dudley KJ, Bombarely A, Bally J, Winefield C, Giuliano G, Waterhouse PM. A multi-omic Nicotiana benthamiana resource for fundamental research and biotechnology. Nat Plants 2023; 9:1558-1571. [PMID: 37563457 PMCID: PMC10505560 DOI: 10.1038/s41477-023-01489-8] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/01/2023] [Accepted: 07/11/2023] [Indexed: 08/12/2023]
Abstract
Nicotiana benthamiana is an invaluable model plant and biotechnology platform with a ~3 Gb allotetraploid genome. To further improve its usefulness and versatility, we have produced high-quality chromosome-level genome assemblies, coupled with transcriptome, epigenome, microRNA and transposable element datasets, for the ubiquitously used LAB strain and a related wild accession, QLD. In addition, single nucleotide polymorphism maps have been produced for a further two laboratory strains and four wild accessions. Despite the loss of five chromosomes from the ancestral tetraploid, expansion of intergenic regions, widespread segmental allopolyploidy, advanced diploidization and evidence of recent bursts of Copia pseudovirus (Copia) mobility not seen in other Nicotiana genomes, the two subgenomes of N. benthamiana show large regions of synteny across the Solanaceae. LAB and QLD have many genetic, metabolic and phenotypic differences, including disparate RNA interference responses, but are highly interfertile and amenable to genome editing and both transient and stable transformation. The LAB/QLD combination has the potential to be as useful as the Columbia-0/Landsberg errecta partnership, utilized from the early pioneering days of Arabidopsis genomics to today.
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Affiliation(s)
- Buddhini Ranawaka
- Centre for Agriculture and the Bioeconomy, Queensland University of Technology (QUT), Brisbane, Queensland, Australia
- ARC Centre of Excellence for Plant Success in Nature & Agriculture, Brisbane, Queensland, Australia
| | - Jiyuan An
- Centre for Agriculture and the Bioeconomy, Queensland University of Technology (QUT), Brisbane, Queensland, Australia.
- ARC Centre of Excellence for Plant Success in Nature & Agriculture, Brisbane, Queensland, Australia.
| | - Michał T Lorenc
- Centre for Agriculture and the Bioeconomy, Queensland University of Technology (QUT), Brisbane, Queensland, Australia
| | - Hyungtaek Jung
- Centre for Agriculture and the Bioeconomy, Queensland University of Technology (QUT), Brisbane, Queensland, Australia
- Centre for Animal Science, Queensland Alliance for Agriculture and Food Innovation (QAAFI), The University of Queensland, Brisbane, Queensland, Australia
| | - Maria Sulli
- Italian National Agency for New Technologies, Energy and Sustainable Economic Development (ENEA), Casaccia Research Centre, Rome, Italy
| | - Giuseppe Aprea
- Italian National Agency for New Technologies, Energy and Sustainable Economic Development (ENEA), Casaccia Research Centre, Rome, Italy
| | - Sally Roden
- Centre for Agriculture and the Bioeconomy, Queensland University of Technology (QUT), Brisbane, Queensland, Australia
- ARC Centre of Excellence for Plant Success in Nature & Agriculture, Brisbane, Queensland, Australia
| | - Victor Llaca
- Genomics Technologies, Corteva Agriscience, Johnston, IA, USA
| | - Satomi Hayashi
- Centre for Agriculture and the Bioeconomy, Queensland University of Technology (QUT), Brisbane, Queensland, Australia
- ARC Centre of Excellence for Plant Success in Nature & Agriculture, Brisbane, Queensland, Australia
| | - Leila Asadyar
- Centre for Agriculture and the Bioeconomy, Queensland University of Technology (QUT), Brisbane, Queensland, Australia
- ARC Centre of Excellence for Plant Success in Nature & Agriculture, Brisbane, Queensland, Australia
| | - Zacharie LeBlanc
- Centre for Agriculture and the Bioeconomy, Queensland University of Technology (QUT), Brisbane, Queensland, Australia
| | - Zuba Ahmed
- Centre for Agriculture and the Bioeconomy, Queensland University of Technology (QUT), Brisbane, Queensland, Australia
- ARC Centre of Excellence for Plant Success in Nature & Agriculture, Brisbane, Queensland, Australia
| | - Fatima Naim
- Centre for Agriculture and the Bioeconomy, Queensland University of Technology (QUT), Brisbane, Queensland, Australia
- Centre for Crop and Disease Management, School of Molecular and Life Sciences, Curtin University, Bentley, Western Australia, Australia
| | - Samanta Bolzan de Campos
- Centre for Agriculture and the Bioeconomy, Queensland University of Technology (QUT), Brisbane, Queensland, Australia
| | - Tal Cooper
- Centre for Agriculture and the Bioeconomy, Queensland University of Technology (QUT), Brisbane, Queensland, Australia
| | - Felipe F de Felippes
- Centre for Agriculture and the Bioeconomy, Queensland University of Technology (QUT), Brisbane, Queensland, Australia
| | - Pengfei Dong
- State Key Laboratory of Agrobiotechnology, School of Life Sciences, The Chinese University of Hong Kong, Hong Kong, China
| | - Silin Zhong
- State Key Laboratory of Agrobiotechnology, School of Life Sciences, The Chinese University of Hong Kong, Hong Kong, China
| | - Victor Garcia-Carpintero
- Instituto de Biología Molecular y Celular de Plantas (IBMCP), Consejo Superior de Investigaciones Científicas (CSIC), Universidad Politècnica de Valencia, Valencia, Spain
| | - Diego Orzaez
- Instituto de Biología Molecular y Celular de Plantas (IBMCP), Consejo Superior de Investigaciones Científicas (CSIC), Universidad Politècnica de Valencia, Valencia, Spain
| | - Kevin J Dudley
- School of Biology and Environmental Science, Queensland University of Technology (QUT), Brisbane, Queensland, Australia
- QUT Central Analytical Research Facility, Queensland University of Technology (QUT), Brisbane, Queensland, Australia
| | - Aureliano Bombarely
- Instituto de Biología Molecular y Celular de Plantas (IBMCP), Consejo Superior de Investigaciones Científicas (CSIC), Universidad Politècnica de Valencia, Valencia, Spain
- Università degli Studi di Milano, Milan, Italy
| | - Julia Bally
- Centre for Agriculture and the Bioeconomy, Queensland University of Technology (QUT), Brisbane, Queensland, Australia
- ARC Centre of Excellence for Plant Success in Nature & Agriculture, Brisbane, Queensland, Australia
| | - Christopher Winefield
- ARC Centre of Excellence for Plant Success in Nature & Agriculture, Brisbane, Queensland, Australia.
- Department of Wine Food and Molecular Biosciences, Lincoln University, Lincoln, New Zealand.
| | - Giovanni Giuliano
- Italian National Agency for New Technologies, Energy and Sustainable Economic Development (ENEA), Casaccia Research Centre, Rome, Italy
| | - Peter M Waterhouse
- Centre for Agriculture and the Bioeconomy, Queensland University of Technology (QUT), Brisbane, Queensland, Australia.
- ARC Centre of Excellence for Plant Success in Nature & Agriculture, Brisbane, Queensland, Australia.
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18
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Kanjanapokin C, Thiravetyan P, Krobthong S, Aonbangkhen C, Yingchutrakul Y, Kittipornkul P, Treesubsuntorn C. Possibility to Apply Strontium Aluminate to Produce Light-Emitting Plants: Efficiency and Safety. Chem Biodivers 2023; 20:e202300552. [PMID: 37345919 DOI: 10.1002/cbdv.202300552] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2023] [Revised: 06/17/2023] [Accepted: 06/20/2023] [Indexed: 06/23/2023]
Abstract
Light-emitting plants (LEPs) provides light in areas without electricity. The phosphorescent compound was used as a lighting material for LEP development. However, using the phosphorescent compound for LEPs development required optimization and phytotoxicity evaluation. Strontium aluminate (SrAl2 O4 ) is a phosphorescent compound that can glow for a long time and is easily recharged by visible light. In this study, using SrAl2 O4 to develop LEPs was evaluated. Additionally, plant stress under SrAl2 O4 was investigated. Metabolomic analysis can explain the possible mechanism of plants' stress under SrAl2 O4 . After, injecting 3 mL of 5 % (w/v) SrAl2 O4 products 1, 2, and 3 into the stem of Ipomoea aquatica, the result showed that SrAl2 O4 products 2 and 3 caused oxidative stress. The metabolomic analysis also indicated that I. aquatica responded to SrAl2 O4 product 1 by increasing pipecolic acid and salicylic acid, while I. aquatica injected with SrAl2 O4 products 2 and 3 showed a decrease in salicylic acid around 0.005 and 0.061-fold, respectively, compared to control plants. and an excess accumulation of MDA around 10.00-12.00 μmol g-1 FW. A 15 % concentration of SrAl2 O4 can be used for LEPs development, enabling photoemission 18-fold for 50 min. SrAl2 O4 product 1 has the potential to be a material for LEPs.
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Affiliation(s)
- Chutipa Kanjanapokin
- School of Bioresources and Technology, King Mongkut's University of Technology Thonburi, Bangkok, 10150, Thailand
| | - Paitip Thiravetyan
- School of Bioresources and Technology, King Mongkut's University of Technology Thonburi, Bangkok, 10150, Thailand
- Pilot Plant Development and Training Institute, King Mongkut's University of Technology Thonburi, Bangkok, 10150, Thailand
| | - Sucheewin Krobthong
- Center of Excellence in Natural Products Chemistry (CENP), Department of Chemistry, Faculty of Science, Chulalongkorn University, Bangkok, 10330, Thailand
| | - Chanat Aonbangkhen
- Center of Excellence in Natural Products Chemistry (CENP), Department of Chemistry, Faculty of Science, Chulalongkorn University, Bangkok, 10330, Thailand
| | | | - Piyatida Kittipornkul
- Pilot Plant Development and Training Institute, King Mongkut's University of Technology Thonburi, Bangkok, 10150, Thailand
| | - Chairat Treesubsuntorn
- School of Bioresources and Technology, King Mongkut's University of Technology Thonburi, Bangkok, 10150, Thailand
- 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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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. Environ Sci Pollut Res Int 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] [What about the content of this article? (0)] [Affiliation(s)] [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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20
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Brooks EG, Elorriaga E, Liu Y, Duduit JR, Yuan G, Tsai CJ, Tuskan GA, Ranney TG, Yang X, Liu W. Plant Promoters and Terminators for High-Precision Bioengineering. Biodes Res 2023; 5:0013. [PMID: 37849460 PMCID: PMC10328392 DOI: 10.34133/bdr.0013] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2023] [Accepted: 06/12/2023] [Indexed: 10/19/2023] Open
Abstract
High-precision bioengineering and synthetic biology require fine-tuning gene expression at both transcriptional and posttranscriptional levels. Gene transcription is tightly regulated by promoters and terminators. Promoters determine the timing, tissues and cells, and levels of the expression of genes. Terminators mediate transcription termination of genes and affect mRNA levels posttranscriptionally, e.g., the 3'-end processing, stability, translation efficiency, and nuclear to cytoplasmic export of mRNAs. The promoter and terminator combination affects gene expression. In the present article, we review the function and features of plant core promoters, proximal and distal promoters, and terminators, and their effects on and benchmarking strategies for regulating gene expression.
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Affiliation(s)
- Emily G. Brooks
- Department of Horticultural Science, North Carolina State University, Raleigh, NC 27607, USA
| | - Estefania Elorriaga
- Department of Horticultural Science, North Carolina State University, Raleigh, NC 27607, USA
| | - Yang Liu
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN 37831, USA
- The Center for Bioenergy Innovation, Oak Ridge National Laboratory, Oak Ridge, TN 37831, USA
| | - James R. Duduit
- Department of Horticultural Science, North Carolina State University, Raleigh, NC 27607, USA
| | - Guoliang Yuan
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN 37831, USA
- The Center for Bioenergy Innovation, Oak Ridge National Laboratory, Oak Ridge, TN 37831, USA
| | - Chung-Jui Tsai
- The Center for Bioenergy Innovation, Oak Ridge National Laboratory, Oak Ridge, TN 37831, USA
- Warnell School of Forestry and Natural Resource, University of Georgia, Athens, GA 30602, USA
- Department of Plant Biology, University of Georgia, Athens, GA 30602, USA
- Department of Genetics, University of Georgia, Athens, GA 30602, USA
| | - Gerald A. Tuskan
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN 37831, USA
- The Center for Bioenergy Innovation, Oak Ridge National Laboratory, Oak Ridge, TN 37831, USA
| | - Thomas G. Ranney
- Mountain Crop Improvement Lab, Department of Horticultural Science, Mountain Horticultural Crops Research and Extension Center, North Carolina State University, Mills River, NC 28759, USA
| | - Xiaohan Yang
- The Center for Bioenergy Innovation, Oak Ridge National Laboratory, Oak Ridge, TN 37831, USA
- Warnell School of Forestry and Natural Resource, University of Georgia, Athens, GA 30602, USA
| | - Wusheng Liu
- Department of Horticultural Science, North Carolina State University, Raleigh, NC 27607, USA
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21
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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] [What about the content of this article? (0)] [Affiliation(s)] [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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22
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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 Biotechnol J 2023. [PMID: 37155328 PMCID: PMC10363767 DOI: 10.1111/pbi.14068] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [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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23
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Porta-de-la-Riva M, Gonzalez AC, Sanfeliu-Cerdán N, Karimi S, Malaiwong N, Pidde A, Morales-Curiel LF, Fernandez P, González-Bolívar S, Hurth C, Krieg M. Neural engineering with photons as synaptic transmitters. Nat Methods 2023; 20:761-769. [PMID: 37024651 DOI: 10.1038/s41592-023-01836-9] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2021] [Accepted: 03/03/2023] [Indexed: 04/08/2023]
Abstract
Neuronal computation is achieved through connections of individual neurons into a larger network. To expand the repertoire of endogenous cellular communication, we developed a synthetic, photon-assisted synaptic transmission (PhAST) system. PhAST is based on luciferases and channelrhodopsins that enable the transmission of a neuronal state across space, using photons as neurotransmitters. PhAST overcomes synaptic barriers and rescues the behavioral deficit of a glutamate mutant with conditional, calcium-triggered photon emission between two neurons of the Caenorhabditis elegans nociceptive avoidance circuit. To demonstrate versatility and flexibility, we generated de novo synaptic transmission between two unconnected cells in a sexually dimorphic neuronal circuit, suppressed endogenous nocifensive response through activation of an anion channelrhodopsin and switched attractive to aversive behavior in an olfactory circuit. Finally, we applied PhAST to dissect the calcium dynamics of the temporal pattern generator in a motor circuit for ovipositioning. In summary, we established photon-based synaptic transmission that facilitates the modification of animal behavior.
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Affiliation(s)
| | | | | | - Shadi Karimi
- Institut de Ciències Fotòniques, Castelldefels, Spain
| | | | | | | | | | | | - Cedric Hurth
- Institut de Ciències Fotòniques, Castelldefels, Spain
| | - Michael Krieg
- Institut de Ciències Fotòniques, Castelldefels, Spain.
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24
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Photon-based communication between two neurons in Caenorhabditis elegans. Nat Methods 2023. [PMID: 37024655 DOI: 10.1038/s41592-023-01837-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/08/2023]
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25
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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] [What about the content of this article? (0)] [Affiliation(s)] [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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26
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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. Mol Plant Microbe Interact 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] [What about the content of this article? (0)] [Affiliation(s)] [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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27
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Quan W, Zhao X, Zhao C, Duan H, Ding G. Characterization of 35 Masson pine (Pinus massoniana) half-sib families from two provinces based on metabolite properties. Front Ecol Evol 2023. [DOI: 10.3389/fevo.2023.1107597] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023] Open
Abstract
Plant metabolism is an important functional trait, and its metabolites have physiological and ecological functions to adapt to the growth environment. However, the physiological and ecological functions of metabolites from different provinces of the same plant species are still unclear. Therefore, this study aimed to determine whether metabolites from different provinces of Masson pine (Pinus massoniana Lamb.) have the corresponding metabolic traits. The gas chromatography–mass spectrometry technique and metabonomic analysis methods were used to characterize 35 Masson pine half-sib families from two provinces. A total of 116 metabolites were putatively identified in 35 families of Masson pine, among which the average content of organic acids was the highest, followed by saccharides and alcohols, and phosphoric acids. Comparative analysis of metabolite groups showed that organic acids, amines, and others were significantly different between the Masson pine families from Guangxi and Guizhou provinces. Six differential metabolites were found between the provinces from Guizhou and Guangxi, namely caffeic acid, L-ascorbic acid, gentiobiose, xylitol, d-pinitol, and β-sitosterol. The most significantly enriched pathways among differentially expressed metabolites between the two provinces were steroid biosynthesis, phenylpropanoid biosynthesis, glutathione metabolism, pentose and glucuronate interconversions. Overall, the results showed that Masson pine half-sib families from different geographical provinces have different metabolite profiles and their metabolites are affected by geographical provenance and growth environment adaptability. This study revealed that the breeding of Masson pine families from different provinces changed the metabolite profiles, providing a reference for the multipurpose breeding of Masson pine.
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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: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [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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Schenkmayerova A, Toul M, Pluskal D, Baatallah R, Gagnot G, Pinto GP, Santana VT, Stuchla M, Neugebauer P, Chaiyen P, Damborsky J, Bednar D, Janin YL, Prokop Z, Marek M. Catalytic mechanism for Renilla-type luciferases. Nat Catal 2023. [DOI: 10.1038/s41929-022-00895-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
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Ma X, Li X, Li Z. Transgene-Free Genome Editing in Nicotiana benthamiana with CRISPR/Cas9 Delivered by a Rhabdovirus Vector. Methods Mol Biol 2023; 2653:173-185. [PMID: 36995626 DOI: 10.1007/978-1-0716-3131-7_11] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/28/2023]
Abstract
The clustered regularly interspersed short palindromic repeats (CRISPR)/Cas systems have become the most widely adopted genome editing platform owing to their unprecedented simplicity, efficiency, and versatility. Typically, the genome editing enzyme is expressed in plant cells from an integrated transgene delivered by either Agrobacterium-mediated or biolistic transformation. Recently, plant virus vectors have emerged as promising tools for the in planta delivery of CRISPR/Cas reagent. Here, we provide a protocol for CRISPR/Cas9-mediated genome editing in the model tobacco plant Nicotiana benthamiana using a recombinant negative-stranded RNA rhabdovirus vector. The method is based on infection of N. benthamiana with a Sonchus yellow net virus (SYNV)-based vector that carries the Cas9 and guide RNA expression cassettes to target specific genome loci for mutagenesis. With this method, mutant plants free of foreign DNA can be obtained within 4-5 months.
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Affiliation(s)
- Xiaonan Ma
- State Key Laboratory of Rice Biology, Institute of Biotechnology, Zhejiang University, Hangzhou, China
- Ministry of Agriculture Key Laboratory of Molecular Biology of Crop Pathogens and Insect Pests, Zhejiang University, Hangzhou, China
- Key Laboratory of Biology of Crop Pathogens and Insects of Zhejiang Province, Zhejiang University, Hangzhou, China
| | - Xuemei Li
- Technology Center, China Tobacco Yunnan Industrial Co. LTD, Kunming, Yunnan, China
| | - Zhenghe Li
- State Key Laboratory of Rice Biology, Institute of Biotechnology, Zhejiang University, Hangzhou, China.
- Ministry of Agriculture Key Laboratory of Molecular Biology of Crop Pathogens and Insect Pests, Zhejiang University, Hangzhou, China.
- Key Laboratory of Biology of Crop Pathogens and Insects of Zhejiang Province, Zhejiang University, Hangzhou, China.
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Peng Q, Zhao J, Xiang S, Li J, He C, Huang X, Bao M, Wang J, Zhu G, Larkin RM, Luo H, Ning G. Producing fluorescent plants to lure and trap insect pests. Plant Biotechnol J 2022; 20:1847-1849. [PMID: 35796633 PMCID: PMC9491452 DOI: 10.1111/pbi.13887] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 03/08/2022] [Revised: 06/20/2022] [Accepted: 07/02/2022] [Indexed: 06/15/2023]
Affiliation(s)
- Qinglin Peng
- Key laboratory of Horticultural Plant Biology, Ministry of EducationHuazhong Agricultural UniversityWuhanChina
| | - Jing Zhao
- College of Plant Science and TechnologyHuazhong Agricultural UniversityWuhanChina
| | - Siya Xiang
- Key laboratory of Horticultural Plant Biology, Ministry of EducationHuazhong Agricultural UniversityWuhanChina
| | - Jiajia Li
- Key laboratory of Horticultural Plant Biology, Ministry of EducationHuazhong Agricultural UniversityWuhanChina
| | - Chaochao He
- Key laboratory of Horticultural Plant Biology, Ministry of EducationHuazhong Agricultural UniversityWuhanChina
| | - Xingting Huang
- College of Plant Science and TechnologyHuazhong Agricultural UniversityWuhanChina
| | - ManZhu Bao
- Key laboratory of Horticultural Plant Biology, Ministry of EducationHuazhong Agricultural UniversityWuhanChina
| | - Jihua Wang
- Flower Research Institute of Yunnan Academy of Agricultural SciencesNational Engineering Research Center For Ornamental HorticultureKunmingChina
| | - Genfa Zhu
- Guangdong Key Laboratory of Ornamental Plant Germplasm Innovation and UtilizationInstitute of Environmental Horticulture, Guangdong Academy of Agricultural SciencesGuangzhouChina
| | - Robert M. Larkin
- Key laboratory of Horticultural Plant Biology, Ministry of EducationHuazhong Agricultural UniversityWuhanChina
| | - Hong Luo
- Department of Genetics and BiochemistryClemson UniversityClemsonSCUSA
| | - Guogui Ning
- Key laboratory of Horticultural Plant Biology, Ministry of EducationHuazhong Agricultural UniversityWuhanChina
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Davis W, Endo M, Locke JCW. Spatially specific mechanisms and functions of the plant circadian clock. Plant Physiol 2022; 190:938-951. [PMID: 35640123 PMCID: PMC9516738 DOI: 10.1093/plphys/kiac236] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 01/03/2022] [Accepted: 04/22/2022] [Indexed: 06/15/2023]
Abstract
Like many organisms, plants have evolved a genetic network, the circadian clock, to coordinate processes with day/night cycles. In plants, the clock is a pervasive regulator of development and modulates many aspects of physiology. Clock-regulated processes range from the correct timing of growth and cell division to interactions with the root microbiome. Recently developed techniques, such as single-cell time-lapse microscopy and single-cell RNA-seq, are beginning to revolutionize our understanding of this clock regulation, revealing a surprising degree of organ, tissue, and cell-type specificity. In this review, we highlight recent advances in our spatial view of the clock across the plant, both in terms of how it is regulated and how it regulates a diversity of output processes. We outline how understanding these spatially specific functions will help reveal the range of ways that the clock provides a fitness benefit for the plant.
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Affiliation(s)
- William Davis
- Sainsbury Laboratory, University of Cambridge, Cambridge, UK
| | - Motomu Endo
- Authors for correspondence: (M.E.); (J.C.W.L.)
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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] [What about the content of this article? (0)] [Affiliation(s)] [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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34
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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] [What about the content of this article? (0)] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
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Sato W, Rasmussen M, Deich C, Engelhart AE, Adamala KP. Expanding luciferase reporter systems for cell-free protein expression. Sci Rep 2022; 12:11489. [PMID: 35798760 DOI: 10.1038/s41598-022-15624-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [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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Jin K, Jin C, Wu Y. Synthetic biology-powered microbial co-culture strategy and application of bacterial cellulose-based composite materials. Carbohydr Polym 2022; 283:119171. [DOI: 10.1016/j.carbpol.2022.119171] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2021] [Revised: 01/18/2022] [Accepted: 01/19/2022] [Indexed: 11/18/2022]
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Oba Y, Schultz DT. Firefly genomes illuminate the evolution of beetle bioluminescent systems. Curr Opin Insect Sci 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] [What about the content of this article? (0)] [Affiliation(s)] [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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Qu C, Wang J, Wang Y, He F, Shi X, Zhang Z, Wang Y. Multimodality imaging in the assessment of bone marrow-derived mesenchymal stem cell therapy for doxorubicin-induced cardiomyopathy. Am J Cancer Res 2022; 12:574-584. [PMID: 35261788 PMCID: PMC8899982] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2021] [Accepted: 12/22/2021] [Indexed: 06/14/2023] Open
Abstract
Due to their broad-spectrum effects and high antitumor efficacies, anthracycline-based chemotherapies are commonly prescribed in various solid and hematological malignancies. Doxorubicin (DOX) is one of the most highly used anthracyclines but has been shown to cause lethal cardiomyopathy in clinical practice. Studies have demonstrated that bone marrow-derived mesenchymal stem cells (BMSCs) have the ability to rescue DOX-induced cardiomyopathy (DIC). However, novel molecular imaging techniques are required to explore the biological behaviors, safety, eventual viability, and environmental interactions of transplanted stem cells during therapy. To investigate the biological behaviors of transplanted BMSCs, we applied bioluminescence imaging (BLI) and magnetic resonance imaging (MRI) techniques to trace firefly luciferase (Fluc) and ultrasmall superparamagnetic iron oxide (USPIO) double-labeled mouse BMSCs after injection into the heart apex in a chronic DIC mouse model. Then, we determined the optimal BMSC number for transplantation into the heart and optimized MRI parameters to evaluate transplanted BMSCs in vitro and in vivo. Our results showed that the BLI trace signal could last 7 days in the DIC mouse model, whereas the MRI signal lasted up to 3 days. However, MRI provided more detailed pathophysiological information on DIC than BLI, such as inflammation and fibrosis signs. The optimal in vivo cell number for BLI and MRI was determined to be 1×106. In conclusion, BLI combined with multimodality MRI could be used to monitor the biological behavior of BMSCs transplanted into a chronic DIC mouse model in a visual and dynamic manner.
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Affiliation(s)
- Chanjuan Qu
- Department of Radiology, State Key Laboratory of Complex Severe and Rare Diseases, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences and Peking Union Medical CollegeBeijing 100730, China
| | - Jian Wang
- Department of Radiology, State Key Laboratory of Complex Severe and Rare Diseases, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences and Peking Union Medical CollegeBeijing 100730, China
| | - Yuqing Wang
- Tsinghua Laboratory of Brain and Intelligence, Tsinghua UniversityBeijing 100084, China
| | - Fangfei He
- National Center for Nanoscience and Technology (NCNST)Beijing 100190, China
| | - Xudong Shi
- Key Laboratory of Human Disease Comparative Medicine, National Health Commission of China (NHC), Institute of Laboratory Animal Sciences, Peking Union Medicine College, Chinese Academy of Medical SciencesBeijing 100021, China
| | - Zhuoli Zhang
- Radiology & Biomedical Engineering Chao Family Comprehensive Cancer, University of CaliforniaIrvine, USA
| | - Yining Wang
- Department of Radiology, State Key Laboratory of Complex Severe and Rare Diseases, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences and Peking Union Medical CollegeBeijing 100730, China
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40
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Kaschuk JJ, Al Haj Y, Rojas OJ, Miettunen K, Abitbol T, Vapaavuori J. Plant-Based Structures as an Opportunity to Engineer Optical Functions in Next-Generation Light Management. Adv Mater 2022; 34:e2104473. [PMID: 34699648 DOI: 10.1002/adma.202104473] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/11/2021] [Revised: 10/13/2021] [Indexed: 06/13/2023]
Abstract
This review addresses the reconstruction of structural plant components (cellulose, lignin, and hemicelluloses) into materials displaying advanced optical properties. The strategies to isolate the main building blocks are discussed, and the effects of fibrillation, fibril alignment, densification, self-assembly, surface-patterning, and compositing are presented considering their role in engineering optical performance. Then, key elements that enable lignocellulosic to be translated into materials that present optical functionality, such as transparency, haze, reflectance, UV-blocking, luminescence, and structural colors, are described. Mapping the optical landscape that is accessible from lignocellulosics is shown as an essential step toward their utilization in smart devices. Advanced materials built from sustainable resources, including those obtained from industrial or agricultural side streams, demonstrate enormous promise in optoelectronics due to their potentially lower cost, while meeting or even exceeding current demands in performance. The requirements are summarized for the production and application of plant-based optically functional materials in different smart material applications and the review is concluded with a perspective about this active field of knowledge.
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Affiliation(s)
- Joice Jaqueline Kaschuk
- Department of Bioproducts and Biosystems, School of Chemical Engineering, Aalto University, Box 16300, Aalto, Espoo, 00076, Finland
| | - Yazan Al Haj
- Department of Chemistry and Materials Science, School of Chemical Engineering, Aalto University, Aalto, FI-00076, Finland
| | - Orlando J Rojas
- Department of Bioproducts and Biosystems, School of Chemical Engineering, Aalto University, Box 16300, Aalto, Espoo, 00076, Finland
- Bioproducts Institute, Departments of Chemical Engineering, Department of Biological Engineering, Department of Chemistry, Department of Wood Science, 2360 East Mall, The University of British Columbia, Vancouver, BC, V6T 1Z3, Canada
| | - Kati Miettunen
- Department of Mechanical and Materials Engineering, Faculty of Technology, University of Turku, Turku, FI-20500, Finland
| | - Tiffany Abitbol
- RISE Research Institutes of Sweden, Stockholm, SE-114 28, Sweden
| | - Jaana Vapaavuori
- Department of Chemistry and Materials Science, School of Chemical Engineering, Aalto University, Aalto, FI-00076, Finland
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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] [What about the content of this article? (0)] [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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Dufil G, Bernacka-Wojcik I, Armada-Moreira A, Stavrinidou E. Plant Bioelectronics and Biohybrids: The Growing Contribution of Organic Electronic and Carbon-Based Materials. Chem Rev 2021; 122:4847-4883. [PMID: 34928592 PMCID: PMC8874897 DOI: 10.1021/acs.chemrev.1c00525] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Abstract
Life in our planet is highly dependent on plants as they are the primary source of food, regulators of the atmosphere, and providers of a variety of materials. In this work, we review the progress on bioelectronic devices for plants and biohybrid systems based on plants, therefore discussing advancements that view plants either from a biological or a technological perspective, respectively. We give an overview on wearable and implantable bioelectronic devices for monitoring and modulating plant physiology that can be used as tools in basic plant science or find application in agriculture. Furthermore, we discuss plant-wearable devices for monitoring a plant's microenvironment that will enable optimization of growth conditions. The review then covers plant biohybrid systems where plants are an integral part of devices or are converted to devices upon functionalization with smart materials, including self-organized electronics, plant nanobionics, and energy applications. The review focuses on advancements based on organic electronic and carbon-based materials and discusses opportunities, challenges, as well as future steps.
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Affiliation(s)
- Gwennaël Dufil
- Laboratory of Organic Electronics, Department of Science and Technology, Linköping University, SE-601 74 Norrköping, Sweden
| | - Iwona Bernacka-Wojcik
- Laboratory of Organic Electronics, Department of Science and Technology, Linköping University, SE-601 74 Norrköping, Sweden
| | - Adam Armada-Moreira
- Laboratory of Organic Electronics, Department of Science and Technology, Linköping University, SE-601 74 Norrköping, Sweden
| | - Eleni Stavrinidou
- Laboratory of Organic Electronics, Department of Science and Technology, Linköping University, SE-601 74 Norrköping, Sweden.,Wallenberg Wood Science Center, Department of Science and Technology, Linköping University, SE-60174 Norrköping, Sweden.,Umeå Plant Science Centre, Department of Forest Genetics and Plant Physiology, Swedish University of Agricultural Sciences, Campus Umeå, SE-901 83 Umeå, Sweden
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Nóbrega BB, Soares DMM, Zamuner CK, Stevani CV. Optimized methodology for obtention of high-yield and -quality RNA from the mycelium of the bioluminescent fungus Neonothopanus gardneri. J Microbiol Methods 2021; 191:106348. [PMID: 34699864 DOI: 10.1016/j.mimet.2021.106348] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2021] [Revised: 10/18/2021] [Accepted: 10/18/2021] [Indexed: 10/20/2022]
Abstract
Neonothopanus gardneri, also known as coconut flower mushroom (flor-de-coco), is a Brazilian bioluminescent basidiomycete found in Palm Forest, a transitional biome between the Amazonian Forest and Caatinga (Savanna-like vegetation) in Northeast Brazil, especially in Piauí State. Recent advances toward the elucidation of fungal bioluminescence have contributed to the discovery of four genes (hisps, h3h, luz and cph) involved with the bioluminescence process, the so-called Caffeic Acid Cycle (CAC) and to develop biotechnological applications such autoluminescent tobacco plants and luciferase-based reporter genes. High-yield and -quality RNA-extraction methods are required for most of these purposes. Herein, four methods for RNA isolation from the mycelium of N. gardneri were evaluated: RNeasy® kit (QIAGEN), TRI+, TRI18G+, and TRI26G+. Highest RNA yield was observed for TRI18G+ and TRI26G+ methods, an increase of ~130% in comparison to the RNeasy® method and of ~40% to the TRI+ protocol. All the RNA samples showed good purity and integrity, except by gDNA contamination in RNA samples produced with the RNeasy® method. High quality of RNA samples was confirmed by successful cDNA synthesis and PCR amplification of the coding sequence of h3h gene, responsible for the hydroxylation of the precursor of fungal luciferin (3-hydroxyhispidin). Similarly, RT-qPCR amplification of ef-tu gene, related to the protein biosynthesis in the cell, was demonstrated from RNA samples. This is the first report of a reproducible, time-saving and low-cost optimized method for isolation of high-quality and -yield, DNA-free RNA from a bioluminescent fungus, but that can also be useful for other basidiomycetes.
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Affiliation(s)
- Bianca B Nóbrega
- Departamento de Bioquímica, Instituto de Química, Universidade de São Paulo, São Paulo, Brazil; Departamento de Química Fundamental, Instituto de Química, Universidade de São Paulo, São Paulo, Brazil
| | - Douglas M M Soares
- Departamento de Química Fundamental, Instituto de Química, Universidade de São Paulo, São Paulo, Brazil.
| | - Caio K Zamuner
- Departamento de Química Fundamental, Instituto de Química, Universidade de São Paulo, São Paulo, Brazil
| | - Cassius V Stevani
- Departamento de Química Fundamental, Instituto de Química, Universidade de São Paulo, São Paulo, Brazil.
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44
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Li Y, He X, Zhu W, Li H, Wang W. Bacterial bioluminescence assay for bioanalysis and bioimaging. Anal Bioanal Chem 2021. [PMID: 34693470 DOI: 10.1007/s00216-021-03695-9] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2021] [Revised: 08/31/2021] [Accepted: 09/24/2021] [Indexed: 10/20/2022]
Abstract
Bioluminescence occurs through a chemical reaction in organisms that spontaneously produce light. Luminescent bacteria are unique among bioluminescent organisms. Their bioluminescence intensity is an indicator of their metabolic activity, which can directly reflect the influence of environmental factors on cell viability. Moreover, the whole bioluminescence process is totally gene encoded without the addition of extra substrates. As a result, bacterial bioluminescence has been a powerful tool for whole-cell biosensors and bio-reporters in bioanalysis and bioimaging. This review aims to cover the applications of wild-type and recombinant luminescent bacteria to detect the toxicity of environmental pollutants and biological molecules. The bacterial bioluminescence analytical assay has characteristics such as high sensitivity, short-term detection, and easy operation. Meanwhile, due to the development of gene engineering and optical technology, bacterial luciferase as a reporter protein has been successfully expressed in prokaryotic and eukaryotic cells, tissues, and organs of animals. The major applications for bacterial luciferase-based bioluminescence imaging, such as infectious diseases, cancer therapy, and stem cell tracing, are discussed in this review.
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45
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Li Y, Wang S, He X, Li S, Zheng T, Chen YP, Cui H, Wang W. Imaging the oxygen wave with a single bioluminescent bacterium. Chem Sci 2021; 12:12400-12406. [PMID: 34603670 PMCID: PMC8480313 DOI: 10.1039/d1sc03310g] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2021] [Accepted: 08/12/2021] [Indexed: 01/03/2023] Open
Abstract
We developed a capability of a monolayer of bioluminescent (BL) bacteria for spatiotemporally visualizing the heterogeneous distribution and dynamic evolution of interfacial oxygen concentration, resulting in the discovery of spontaneous and stochastic oxygen waves at the interface between the substrate and an undisturbed, apparently still solution. Wild type bacteria, P. phosphoreum, spontaneously emit light during the native metabolism processes, i.e., bioluminescence. The emission intensity is sensitively regulated by oxygen concentration. By taking the electrolysis of water as a model, it was demonstrated that time-lapsed BL imaging of a bacterial monolayer allowed for visualizing the dynamic distribution of oxygen. The results were quantitatively understood with a physical model involving the diffusion equation and Michaelis-Menten equation. Unexpectedly, further study uncovered a spontaneous and stochastic oxygen wave in a standard well of a microtiter plate, which was subsequently attributed to the inevitable micro-convections induced by inhomogeneous evaporation and thermal fluctuation. Because of the wide application of microtiter plates, this study sheds new light to better understand the apparent heterogeneity in cell-culture and bio-assays.
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Affiliation(s)
- Yaohua Li
- State Key Laboratory of Analytical Chemistry for Life Science, School of Chemistry and Chemical Engineering, ChemBIC (Chemistry and Biomedicine Innovation Center), Nanjing University 210023 Nanjing Jiangsu China
| | - Sa Wang
- State Key Laboratory of Analytical Chemistry for Life Science, School of Chemistry and Chemical Engineering, ChemBIC (Chemistry and Biomedicine Innovation Center), Nanjing University 210023 Nanjing Jiangsu China
| | - Xinyu He
- State Key Laboratory of Analytical Chemistry for Life Science, School of Chemistry and Chemical Engineering, ChemBIC (Chemistry and Biomedicine Innovation Center), Nanjing University 210023 Nanjing Jiangsu China
| | - Shijun Li
- Key Laboratory of the Three Gorges Reservoir Region's Eco-Environment of Ministry of Education, Chongqing University 400045 Chongqing China
| | - Tianhua Zheng
- CAS Key Laboratory of Soft Matter Chemistry, iChEM (Collaborative Innovation Center of Chemistry for Energy Materials), Department of Chemistry, University of Science and Technology of China 230026 Hefei Anhui China
| | - You-Peng Chen
- Key Laboratory of the Three Gorges Reservoir Region's Eco-Environment of Ministry of Education, Chongqing University 400045 Chongqing China
| | - Hua Cui
- CAS Key Laboratory of Soft Matter Chemistry, iChEM (Collaborative Innovation Center of Chemistry for Energy Materials), Department of Chemistry, University of Science and Technology of China 230026 Hefei Anhui China
| | - Wei Wang
- State Key Laboratory of Analytical Chemistry for Life Science, School of Chemistry and Chemical Engineering, ChemBIC (Chemistry and Biomedicine Innovation Center), Nanjing University 210023 Nanjing Jiangsu China
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Gordiichuk P, Coleman S, Zhang G, Kuehne M, Lew TTS, Park M, Cui J, Brooks AM, Hudson K, Graziano AM, Marshall DJM, Karsan Z, Kennedy S, Strano MS. Augmenting the living plant mesophyll into a photonic capacitor. Sci Adv 2021; 7:eabe9733. [PMID: 34516870 PMCID: PMC8442876 DOI: 10.1126/sciadv.abe9733] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/25/2020] [Accepted: 07/20/2021] [Indexed: 06/13/2023]
Abstract
Living plants provide an opportunity to rethink the design and fabrication of devices ordinarily produced from plastic and circuit boards and ultimately disposed of as waste. The spongy mesophyll is a high -surface area composition of parenchyma cells that supports gas and liquid exchange through stomata pores within the surface of most leaves. Here, we investigate the mesophyll of living plants as biocompatible substrates for the photonic display of thin nanophosphorescent films for photonic applications. Size-sorted, silica-coated 650 ± 290 -nm strontium aluminate nanoparticles are infused into five diverse plant species with conformal display of 2-μm films on the mesophyll enabling photoemission of up to 4.8 × 1013 photons/second. Chlorophyll measurements over 9 days and functional testing over 2 weeks at 2016 excitation/emission cycles confirm biocompatibility. This work establishes methods to transform living plants into photonic substrates for applications in plant-based reflectance devices, signaling, and the augmentation of plant-based lighting.
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Affiliation(s)
- Pavlo Gordiichuk
- Department of Chemical Engineering, Massachusetts Institute of Technology, Cambridge, MA 02141, USA
| | - Sarah Coleman
- Department of Chemical Engineering, Massachusetts Institute of Technology, Cambridge, MA 02141, USA
- Department of Chemical Engineering, University of Texas at Austin, Austin, TX 78712, USA
| | - Ge Zhang
- Department of Chemical Engineering, Massachusetts Institute of Technology, Cambridge, MA 02141, USA
| | - Matthias Kuehne
- Department of Chemical Engineering, Massachusetts Institute of Technology, Cambridge, MA 02141, USA
| | - Tedrick T. S. Lew
- Department of Chemical Engineering, Massachusetts Institute of Technology, Cambridge, MA 02141, USA
- Institute of Materials Research and Engineering, Agency for Science, Technology and Research (A*STAR), Singapore 138634, Singapore
| | - Minkyung Park
- Department of Chemical Engineering, Massachusetts Institute of Technology, Cambridge, MA 02141, USA
| | - Jianqiao Cui
- Department of Chemical Engineering, Massachusetts Institute of Technology, Cambridge, MA 02141, USA
| | - Allan M. Brooks
- Department of Chemical Engineering, Massachusetts Institute of Technology, Cambridge, MA 02141, USA
| | - Karaghen Hudson
- Department of Architecture, Massachusetts Institute of Technology, Cambridge, MA 02141, USA
| | - Anne M. Graziano
- Department of Architecture, Massachusetts Institute of Technology, Cambridge, MA 02141, USA
| | - Daniel J. M. Marshall
- Department of Architecture, Massachusetts Institute of Technology, Cambridge, MA 02141, USA
| | - Zain Karsan
- Department of Architecture, Massachusetts Institute of Technology, Cambridge, MA 02141, USA
| | - Sheila Kennedy
- Department of Architecture, Massachusetts Institute of Technology, Cambridge, MA 02141, USA
| | - Michael S. Strano
- Department of Chemical Engineering, Massachusetts Institute of Technology, Cambridge, MA 02141, USA
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Li B, Chen R, Zhu C, Kong F. Glowing plants can light up the night sky? A review. Biotechnol Bioeng 2021; 118:3706-3715. [PMID: 34251679 DOI: 10.1002/bit.27884] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2021] [Revised: 07/04/2021] [Accepted: 07/09/2021] [Indexed: 11/10/2022]
Abstract
Luminescence, a physical phenomenon that producing cool light in vivo, has been found in bacteria, fungi, and animals but not yet in terrestrial higher plants. Through genetic engineering, it is feasible to introduce luminescence systems into living plant cells as biomarkers. Recently, some plants transformed with luminescent systems can glimmer in darkness, which can be observed by our naked eyes and provides a novel lighting resource. In this review, we summarized the bioassay development of luminescence in plant cells, followed by exampling the successful cases of glowing plants transformed with diverse luminescent systems. The potential key factors to design or optimize a glowing plant were also discussed. Our review is useful for the creation of the optimized glowing plants, which can be used not only in scientific research, but also as promising substitutes of artificial light sources in the future.
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Affiliation(s)
- Bolong Li
- School of Bioengineering, Dalian University of Technology, Dalian, China
| | - Ru Chen
- School of Bioengineering, Dalian University of Technology, Dalian, China
| | - Chenba Zhu
- School of Bioengineering, Dalian University of Technology, Dalian, China.,Institute of Biotechnology, RWTH Aachen University, Aachen, Germany
| | - Fantao Kong
- School of Bioengineering, Dalian University of Technology, Dalian, China
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48
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Rathbun CM, Ionkina AA, Yao Z, Jones KA, Porterfield WB, Prescher JA. Rapid Multicomponent Bioluminescence Imaging via Substrate Unmixing. ACS Chem Biol 2021; 16:682-690. [PMID: 33729750 DOI: 10.1021/acschembio.0c00959] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
Studies of biological function demand probes that can report on processes in real time and in physiological environments. Bioluminescent tools are uniquely suited for this purpose, as they enable sensitive imaging in cells and tissues. Bioluminescent reporters can also be monitored continuously over time without detriment, as excitation light is not required. Rather, light emission derives from luciferase-luciferin reactions. Several engineered luciferases and luciferins have expanded the scope of bioluminescence imaging in recent years. Multicomponent tracking remains challenging, though, due to a lack of streamlined methods to visualize combinations of bioluminescent reporters. Conventional approaches image one luciferase at a time. Consequently, short-term changes in cell growth or gene expression cannot be easily captured. Here, we report a strategy for rapid, multiplexed imaging with a wide range of luciferases and luciferins. Sequential addition of orthogonal luciferins, followed by substrate unmixing, enabled facile detection of multiple luciferases in vitro and in vivo. Multicomponent imaging in mice was also achieved on the minutes-to-hours time scale.
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DeVree BT, Steiner LM, Głazowska S, Ruhnow F, Herburger K, Persson S, Mravec J. Current and future advances in fluorescence-based visualization of plant cell wall components and cell wall biosynthetic machineries. Biotechnol Biofuels 2021; 14:78. [PMID: 33781321 PMCID: PMC8008654 DOI: 10.1186/s13068-021-01922-0] [Citation(s) in RCA: 28] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/17/2020] [Accepted: 03/05/2021] [Indexed: 05/18/2023]
Abstract
Plant cell wall-derived biomass serves as a renewable source of energy and materials with increasing importance. The cell walls are biomacromolecular assemblies defined by a fine arrangement of different classes of polysaccharides, proteoglycans, and aromatic polymers and are one of the most complex structures in Nature. One of the most challenging tasks of cell biology and biomass biotechnology research is to image the structure and organization of this complex matrix, as well as to visualize the compartmentalized, multiplayer biosynthetic machineries that build the elaborate cell wall architecture. Better knowledge of the plant cells, cell walls, and whole tissue is essential for bioengineering efforts and for designing efficient strategies of industrial deconstruction of the cell wall-derived biomass and its saccharification. Cell wall-directed molecular probes and analysis by light microscopy, which is capable of imaging with a high level of specificity, little sample processing, and often in real time, are important tools to understand cell wall assemblies. This review provides a comprehensive overview about the possibilities for fluorescence label-based imaging techniques and a variety of probing methods, discussing both well-established and emerging tools. Examples of applications of these tools are provided. We also list and discuss the advantages and limitations of the methods. Specifically, we elaborate on what are the most important considerations when applying a particular technique for plants, the potential for future development, and how the plant cell wall field might be inspired by advances in the biomedical and general cell biology fields.
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Affiliation(s)
- Brian T DeVree
- Department of Plant and Environmental Sciences, University of Copenhagen, Thorvaldsensvej 40, 1871 Frederiksberg, Denmark
| | - Lisa M Steiner
- Department of Plant and Environmental Sciences, University of Copenhagen, Thorvaldsensvej 40, 1871 Frederiksberg, Denmark
| | - Sylwia Głazowska
- Department of Plant and Environmental Sciences, University of Copenhagen, Thorvaldsensvej 40, 1871 Frederiksberg, Denmark
| | - Felix Ruhnow
- Department of Plant and Environmental Sciences, University of Copenhagen, Thorvaldsensvej 40, 1871 Frederiksberg, Denmark
| | - Klaus Herburger
- Department of Plant and Environmental Sciences, University of Copenhagen, Thorvaldsensvej 40, 1871 Frederiksberg, Denmark
| | - Staffan Persson
- Department of Plant and Environmental Sciences, University of Copenhagen, Thorvaldsensvej 40, 1871 Frederiksberg, Denmark
- Joint International Research Laboratory of Metabolic and Developmental Sciences, State Key Laboratory of Hybrid Rice, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, China
| | - Jozef Mravec
- Department of Plant and Environmental Sciences, University of Copenhagen, Thorvaldsensvej 40, 1871 Frederiksberg, Denmark
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Zambito G, Chawda C, Mezzanotte L. Emerging tools for bioluminescence imaging. Curr Opin Chem Biol 2021; 63:86-94. [PMID: 33770744 DOI: 10.1016/j.cbpa.2021.02.005] [Citation(s) in RCA: 30] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2020] [Revised: 01/27/2021] [Accepted: 02/15/2021] [Indexed: 02/08/2023]
Abstract
Bioluminescence (BL) relies on the enzymatic reaction between luciferase, a substrate conventionally named luciferin, and various cofactors. BL imaging has become a widely used technique to interrogate gene expression and cell fate, both in small and large animal models of research. Recent developments include the generation of improved luciferase-luciferin systems for deeper and more sensitive imaging as well as new caged luciferins to report on enzymatic activity and other intracellular functions. Here, we critically evaluate the emerging tools for BL imaging aiming to provide the reader with an updated compendium of the latest developments (2018-2020) and their notable applications.
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