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Joshi J, Hanson AD. A pilot oral history of plant synthetic biology. PLANT PHYSIOLOGY 2024; 195:36-47. [PMID: 38163646 PMCID: PMC11060686 DOI: 10.1093/plphys/kiad585] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/31/2023] [Accepted: 09/15/2023] [Indexed: 01/03/2024]
Abstract
The whole field of synthetic biology (SynBio) is only about 20 years old, and plant SynBio is younger still. Nevertheless, within that short time, SynBio in general has drawn more scientific, philosophical, government, and private-sector interest than anything in biology since the recombinant DNA revolution. Plant SynBio, in particular, is now drawing more and more interest in relation to plants' potential to help solve planetary problems such as carbon capture and storage and replacing fossil fuels and feedstocks. As plant SynBio is so young and so fast-developing, we felt it was too soon to try to analyze its history. Instead, we set out to capture the essence of plant SynBio's origins and early development through interviews with 8 of the field's founders, representing 5 countries and 3 continents. We then distilled these founders' personal recollections and reflections into this review, centering the narrative on timelines for pivotal events, articles, funding programs, and quoting from interviews. We have archived the interview recordings and documented timeline entries. This work provides a resource for future historical scholarship.
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Affiliation(s)
- Jaya Joshi
- Department of Wood Science, University of British Columbia, 2424 Main Mall, Vancouver, BC V6T 1Z4, Canada
| | - Andrew D Hanson
- Horticultural Sciences Department, University of Florida, 2550 Hull Road, Gainesville, FL 32611, USA
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Frangedakis E, Shimamura M, Villarreal JC, Li FW, Tomaselli M, Waller M, Sakakibara K, Renzaglia KS, Szövényi P. The hornworts: morphology, evolution and development. THE NEW PHYTOLOGIST 2021; 229:735-754. [PMID: 32790880 PMCID: PMC7881058 DOI: 10.1111/nph.16874] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/17/2020] [Accepted: 07/28/2020] [Indexed: 05/12/2023]
Abstract
Extant land plants consist of two deeply divergent groups, tracheophytes and bryophytes, which shared a common ancestor some 500 million years ago. While information about vascular plants and the two of the three lineages of bryophytes, the mosses and liverworts, is steadily accumulating, the biology of hornworts remains poorly explored. Yet, as the sister group to liverworts and mosses, hornworts are critical in understanding the evolution of key land plant traits. Until recently, there was no hornwort model species amenable to systematic experimental investigation, which hampered detailed insight into the molecular biology and genetics of this unique group of land plants. The emerging hornwort model species, Anthoceros agrestis, is instrumental in our efforts to better understand not only hornwort biology but also fundamental questions of land plant evolution. To this end, here we provide an overview of hornwort biology and current research on the model plant A. agrestis to highlight its potential in answering key questions of land plant biology and evolution.
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Affiliation(s)
| | - Masaki Shimamura
- Graduate School of Integrated Sciences for Life, Hiroshima University, 739-8528, Japan
| | - Juan Carlos Villarreal
- Department of Biology, Laval University, Quebec City, Quebec, G1V 0A6, Canada
- Smithsonian Tropical Research Institute, Balboa, Ancon, Panamá
| | - Fay-Wei Li
- Boyce Thompson Institute, Ithaca, New York, 14853-1801, USA
- Plant Biology Section, Cornell University, Ithaca, New York, 14853-1801, USA
| | - Marta Tomaselli
- Department of Plant Sciences, University of Cambridge, Cambridge, CB3 EA, UK
| | - Manuel Waller
- Department of Systematic and Evolutionary Botany, University of Zurich, 8008, Switzerland
| | - Keiko Sakakibara
- Department of Life Science, Rikkyo University, Tokyo, 171-8501, Japan
| | - Karen S. Renzaglia
- Department of Plant Biology, Southern Illinois University, Illinois, 62901, USA
| | - Péter Szövényi
- Department of Systematic and Evolutionary Botany, University of Zurich, 8008, Switzerland
- Zurich-Basel Plant Science Center, Zurich, 8092, Switzerland
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Hanano S, Tomatsu H, Ohnishi A, Kobayashi K, Kondo Y, Betsuyaku S, Takita E, Ogata Y, Ozawa K, Suda K, Hosouchi T, Nagase T, Suzuki H, Sakurai N, Masumoto H, Fukuda H, Shibata D. An Artificial Conversion of Roots into Organs with Shoot Stem Characteristics by Inducing Two Transcription Factors. iScience 2020; 23:101332. [PMID: 32668199 PMCID: PMC7385925 DOI: 10.1016/j.isci.2020.101332] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2019] [Revised: 02/29/2020] [Accepted: 06/28/2020] [Indexed: 11/19/2022] Open
Abstract
Somatic plant cells can regenerate shoots and/or roots or adventitious embryonic calluses, which may induce organ formation under certain conditions. Such regenerations occur via dedifferentiation of somatic cells, induction of organs, and their subsequent outgrowth. Despite recent advances in understanding of plant regeneration, many details of shoot induction remain unclear. Here, we artificially induced shoot stem-like green organs (SSOs) in Arabidopsis thaliana roots via simultaneous induction of two transcription factors (TFs), ARABIDOPSIS THALIANA HOMEOBOX PROTEIN 25 (ATHB25, At5g65410) and the B3 family transcription factor REPRODUCTIVE MERISTEM 7 (REM7, At3g18960). The SSOs exhibited negative gravitropism and differentiated vascular bundle phenotypes. The ATHB25/REM7 induced the expression of genes controlling shoot stem characteristics by ectopic expression in roots. Intriguingly, the restoration of root growth was seen in the consecutive and adjacent parts of the SSOs under gene induction conditions. Our findings thus provide insights into the development and regeneration of plant shoot stems. Co-induction of ATHB25 and REM7 produces shoot stem-like organs (SSOs) in roots SSOs exhibit negative gravitropism and differentiated vascular bundles Shoot- and root-specific genes are up- and down-regulated, respectively, in SSOs The restoration of normal root growth follows the SSO formation
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Affiliation(s)
- Shigeru Hanano
- Kazusa DNA Research Institute, 2-6-7 Kazusa-Kamatari, Kisarazu, Chiba 292-0818, Japan.
| | - Hajime Tomatsu
- Kazusa DNA Research Institute, 2-6-7 Kazusa-Kamatari, Kisarazu, Chiba 292-0818, Japan
| | - Ai Ohnishi
- Graduate School of Arts and Sciences, The University of Tokyo, 3-8-1 Komaba, Meguro-ku, Tokyo 153-8902, Japan
| | - Koichi Kobayashi
- Graduate School of Arts and Sciences, The University of Tokyo, 3-8-1 Komaba, Meguro-ku, Tokyo 153-8902, Japan
| | - Yuki Kondo
- Department of Biological Sciences, Graduate School of Science, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-0033, Japan
| | - Shigeyuki Betsuyaku
- Department of Biological Sciences, Graduate School of Science, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-0033, Japan; Japan Science and Technology Agency (JST), PRESTO, 4-1-8 Honcho, Kawaguchi, Saitama 332-0012, Japan
| | - Eiji Takita
- Kazusa DNA Research Institute, 2-6-7 Kazusa-Kamatari, Kisarazu, Chiba 292-0818, Japan
| | - Yoshiyuki Ogata
- Kazusa DNA Research Institute, 2-6-7 Kazusa-Kamatari, Kisarazu, Chiba 292-0818, Japan
| | - Keishi Ozawa
- Kazusa DNA Research Institute, 2-6-7 Kazusa-Kamatari, Kisarazu, Chiba 292-0818, Japan
| | - Kunihiro Suda
- Kazusa DNA Research Institute, 2-6-7 Kazusa-Kamatari, Kisarazu, Chiba 292-0818, Japan
| | - Tsutomu Hosouchi
- Kazusa DNA Research Institute, 2-6-7 Kazusa-Kamatari, Kisarazu, Chiba 292-0818, Japan
| | - Takahiro Nagase
- Kazusa DNA Research Institute, 2-6-7 Kazusa-Kamatari, Kisarazu, Chiba 292-0818, Japan; The Kisarazu Laboratory, Graduate School of Life Sciences, Tohoku University, 2-6-7 Kazusa-Kamatari, Kisarazu, Chiba 292-0818, Japan
| | - Hideyuki Suzuki
- Kazusa DNA Research Institute, 2-6-7 Kazusa-Kamatari, Kisarazu, Chiba 292-0818, Japan
| | - Nozomu Sakurai
- Kazusa DNA Research Institute, 2-6-7 Kazusa-Kamatari, Kisarazu, Chiba 292-0818, Japan
| | - Hiroshi Masumoto
- Kazusa DNA Research Institute, 2-6-7 Kazusa-Kamatari, Kisarazu, Chiba 292-0818, Japan
| | - Hiroo Fukuda
- Department of Biological Sciences, Graduate School of Science, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-0033, Japan
| | - Daisuke Shibata
- Kazusa DNA Research Institute, 2-6-7 Kazusa-Kamatari, Kisarazu, Chiba 292-0818, Japan; The Kisarazu Laboratory, Graduate School of Life Sciences, Tohoku University, 2-6-7 Kazusa-Kamatari, Kisarazu, Chiba 292-0818, Japan.
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Han Y, Sun J, Yang J, Tan Z, Luo J, Lu D. Reconstitution of the plant ubiquitination cascade in bacteria using a synthetic biology approach. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2017; 91:766-776. [PMID: 28509348 DOI: 10.1111/tpj.13603] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/02/2017] [Accepted: 05/12/2017] [Indexed: 05/23/2023]
Abstract
Ubiquitination modulates nearly all aspects of plant life. Here, we reconstituted the Arabidopsis thaliana ubiquitination cascade in Escherichia coli using a synthetic biology approach. In this system, plant proteins are expressed and then immediately participate in ubiquitination reactions within E. coli cells. Additionally, the purification of individual ubiquitination components prior to setting up the ubiquitination reactions is omitted. To establish the reconstituted system, we co-expressed Arabidopsis ubiquitin (Ub) and ubiquitination substrates with E1, E2 and E3 enzymes in E. coli using the Duet expression vectors. The functionality of the system was evaluated by examining the auto-ubiquitination of a RING (really interesting new gene)-type E3 ligase AIP2 and the ubiquitination of its substrate ABI3. Our results demonstrated the fidelity and specificity of this system. In addition, we applied this system to assess a subset of Arabidopsis E2s in Ub chain formation using E2 conjugation assays. Affinity-tagged Ub allowed efficient purification of Ub conjugates in milligram quantities. Consistent with previous reports, distinct roles of various E2s in Ub chain assembly were also observed in this bacterial system. Therefore, this reconstituted system has multiple advantages, and it can be used to screen for targets of E3 ligases or to study plant ubiquitination in detail.
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Affiliation(s)
- Yufang Han
- State Key Laboratory of Plant Genomics, Center for Agricultural Research Resources, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Shijiazhuang, Hebei, 050021, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Jianhang Sun
- State Key Laboratory of Plant Genomics, Center for Agricultural Research Resources, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Shijiazhuang, Hebei, 050021, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Jun Yang
- State Key Laboratory of Plant Genomics, Center for Agricultural Research Resources, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Shijiazhuang, Hebei, 050021, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Zhaoyun Tan
- State Key Laboratory of Plant Genomics, Center for Agricultural Research Resources, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Shijiazhuang, Hebei, 050021, China
| | - Jijing Luo
- College of Life Science and Technology, Guangxi University, Nanning, Guangxi, 530004, China
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, Guangxi University, Nanning, Guangxi, 530004, China
| | - Dongping Lu
- State Key Laboratory of Plant Genomics, Center for Agricultural Research Resources, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Shijiazhuang, Hebei, 050021, China
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