1
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Borowsky AT, Bailey-Serres J. Rewiring gene circuitry for plant improvement. Nat Genet 2024:10.1038/s41588-024-01806-7. [PMID: 39075207 DOI: 10.1038/s41588-024-01806-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2024] [Accepted: 05/17/2024] [Indexed: 07/31/2024]
Abstract
Aspirations for high crop growth and yield, nutritional quality and bioproduction of materials are challenged by climate change and limited adoption of new technologies. Here, we review recent advances in approaches to profile and model gene regulatory activity over developmental and response time in specific cells, which have revealed the basis of variation in plant phenotypes: both redeployment of key regulators to new contexts and their repurposing to control different slates of genes. New synthetic biology tools allow tunable, spatiotemporal regulation of transgenes, while recent gene-editing technologies enable manipulation of the regulation of native genes. Ultimately, understanding how gene circuitry is wired to control form and function across varied plant species, combined with advanced technology to rewire that circuitry, will unlock solutions to our greatest challenges in agriculture, energy and the environment.
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Affiliation(s)
- Alexander T Borowsky
- Center for Plant Cell Biology, Department of Botany and Plant Sciences, University of California, Riverside, Riverside, CA, USA
| | - Julia Bailey-Serres
- Center for Plant Cell Biology, Department of Botany and Plant Sciences, University of California, Riverside, Riverside, CA, USA.
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2
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Böhm CV, Inckemann R, Burgis M, Baumann J, Brinkmann CK, Lipinska KE, Gilles S, Freudigmann J, Seiler VN, Clark LG, Jewett MC, Voll LM, Niederholtmeyer H. Chloroplast Cell-Free Systems from Different Plant Species as a Rapid Prototyping Platform. ACS Synth Biol 2024. [PMID: 39028299 DOI: 10.1021/acssynbio.4c00117] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/20/2024]
Abstract
Climate change poses a significant threat to global agriculture, necessitating innovative solutions. Plant synthetic biology, particularly chloroplast engineering, holds promise as a viable approach to this challenge. Chloroplasts present a variety of advantageous traits for genetic engineering, but the development of genetic tools and genetic part characterization in these organelles is hindered by the lengthy time scales required to generate transplastomic organisms. To address these challenges, we have established a versatile protocol for generating highly active chloroplast-based cell-free gene expression (CFE) systems derived from a diverse range of plant species, including wheat (monocot), spinach, and poplar trees (dicots). We show that these systems work with conventionally used T7 RNA polymerase as well as the endogenous chloroplast polymerases, allowing for detailed characterization and prototyping of regulatory sequences at both transcription and translation levels. To demonstrate the platform for characterization of promoters and 5' and 3' untranslated regions (UTRs) in higher plant chloroplast gene expression, we analyze a collection of 23 5'UTRs, 10 3'UTRs, and 6 chloroplast promoters, assessed their expression in spinach and wheat extracts, and found consistency in expression patterns, suggesting cross-species compatibility. Looking forward, our chloroplast CFE systems open new avenues for plant synthetic biology, offering prototyping tools for both understanding gene expression and developing engineered plants, which could help meet the demands of a changing global climate.
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Affiliation(s)
- Clemens V Böhm
- Max-Planck Institute for Terrestrial Microbiology, 35043 Marburg, Germany
- Center for Synthetic Microbiology, Philipps-Universität Marburg, 35032 Marburg, Germany
| | - René Inckemann
- Max-Planck Institute for Terrestrial Microbiology, 35043 Marburg, Germany
- Center for Synthetic Microbiology, Philipps-Universität Marburg, 35032 Marburg, Germany
| | - Michael Burgis
- Center for Synthetic Microbiology, Philipps-Universität Marburg, 35032 Marburg, Germany
| | - Jessica Baumann
- Molecular Plant Physiology, Philipps-Universität Marburg, 35043 Marburg, Germany
| | - Cedric K Brinkmann
- Max-Planck Institute for Terrestrial Microbiology, 35043 Marburg, Germany
| | - Katarzyna E Lipinska
- Max-Planck Institute for Terrestrial Microbiology, 35043 Marburg, Germany
- Center for Synthetic Microbiology, Philipps-Universität Marburg, 35032 Marburg, Germany
| | - Sara Gilles
- Max-Planck Institute for Terrestrial Microbiology, 35043 Marburg, Germany
- Center for Synthetic Microbiology, Philipps-Universität Marburg, 35032 Marburg, Germany
| | - Jonas Freudigmann
- Molecular Plant Physiology, Philipps-Universität Marburg, 35043 Marburg, Germany
| | - Vinca N Seiler
- Molecular Plant Physiology, Philipps-Universität Marburg, 35043 Marburg, Germany
| | - Lauren G Clark
- Department of Chemical and Biological Engineering, Northwestern University, Evanston, Illinois 60208, United States
| | - Michael C Jewett
- Department of Chemical and Biological Engineering, Northwestern University, Evanston, Illinois 60208, United States
| | - Lars M Voll
- Center for Synthetic Microbiology, Philipps-Universität Marburg, 35032 Marburg, Germany
- Molecular Plant Physiology, Philipps-Universität Marburg, 35043 Marburg, Germany
| | - Henrike Niederholtmeyer
- Max-Planck Institute for Terrestrial Microbiology, 35043 Marburg, Germany
- Center for Synthetic Microbiology, Philipps-Universität Marburg, 35032 Marburg, Germany
- Technical University of Munich, Campus Straubing for Biotechnology and Sustainability, 94315 Straubing, Germany
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3
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Navarrete A, Pollak B. Context-dependent antisense transcription from a neighboring gene interferes with the expression of mNeonGreen as a functional in vivo fluorescent reporter in the chloroplast of Chlamydomonas reinhardtii. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2024. [PMID: 39015950 DOI: 10.1111/tpj.16915] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/04/2023] [Revised: 03/18/2024] [Accepted: 06/18/2024] [Indexed: 07/18/2024]
Abstract
Advancing chloroplast genetic engineering in Chlamydomonas reinhardtii remains challenging, decades after its first successful transformation. This study introduces the development of a chloroplast-optimized mNeonGreen fluorescent reporter, enabling in vivo observation through a sixfold increase in fluorescence via context-aware construct engineering. Our research highlights the influence of transcriptional readthrough and antisense mRNA pairing on post-transcriptional regulation, pointing to novel strategies for optimizing heterologous gene expression. We further demonstrate the applicability of these insights using an accessible experimentation system using glass-bead transformation and reestablishment of photosynthesis using psbH mutants, focusing on the mitigation of transcriptional readthrough effects. By characterizing heterologous expression using regulatory elements such as PrrnS, 5'atpA, and 3' rbcL in a sense-transcriptional context, we further documented up to twofold improvement in fluorescence levels. Our findings contribute new tools for molecular biology research in the chloroplast and evidence fundamental gene regulation processes that could enable the development of more effective chloroplast engineering strategies. This work not only paves the way for more efficient genetic engineering of chloroplasts but also deepens our understanding of the regulatory mechanisms at play.
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Affiliation(s)
- Axel Navarrete
- Instituto Milenio de Biología Integrativa (iBio), Santiago, Chile
| | - Bernardo Pollak
- Instituto Milenio de Biología Integrativa (iBio), Santiago, Chile
- Fundación Ciencia y Vida, Santiago, Chile
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4
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Ferreira SS, Antunes MS. Genetically encoded Boolean logic operators to sense and integrate phenylpropanoid metabolite levels in plants. THE NEW PHYTOLOGIST 2024; 243:674-687. [PMID: 38752334 DOI: 10.1111/nph.19823] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/05/2023] [Accepted: 04/30/2024] [Indexed: 06/21/2024]
Abstract
Synthetic biology has the potential to revolutionize biotechnology, public health, and agriculture. Recent studies have shown the enormous potential of plants as chassis for synthetic biology applications. However, tools to precisely manipulate metabolic pathways for bioproduction in plants are still needed. We used bacterial allosteric transcription factors (aTFs) that control gene expression in a ligand-specific manner and tested their ability to repress semi-synthetic promoters in plants. We also tested the modulation of their repression activity in response to specific plant metabolites, especially phenylpropanoid-related molecules. Using these aTFs, we also designed synthetic genetic circuits capable of computing Boolean logic operations. Three aTFs, CouR, FapR, and TtgR, achieved c. 95% repression of their respective target promoters. For TtgR, a sixfold de-repression could be triggered by inducing its ligand accumulation, showing its use as biosensor. Moreover, we designed synthetic genetic circuits that use AND, NAND, IMPLY, and NIMPLY Boolean logic operations and integrate metabolite levels as input to the circuit. We showed that biosensors can be implemented in plants to detect phenylpropanoid-related metabolites and activate a genetic circuit that follows a predefined logic, demonstrating their potential as tools for exerting control over plant metabolic pathways and facilitating the bioproduction of natural products.
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Affiliation(s)
- Savio S Ferreira
- Department of Biological Sciences, University of North Texas, Denton, TX, 76203, USA
- BioDiscovery Institute, University of North Texas, Denton, TX, 76203, USA
| | - Mauricio S Antunes
- Department of Biological Sciences, University of North Texas, Denton, TX, 76203, USA
- BioDiscovery Institute, University of North Texas, Denton, TX, 76203, USA
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5
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Deng JL, Zhao L, Wei H, Ye HX, Yang L, Sun L, Zhao Z, Murray JD, Liu CW. A deeply conserved amino acid required for VAPYRIN localization and function during legume-rhizobial symbiosis. THE NEW PHYTOLOGIST 2024; 243:14-22. [PMID: 38703001 DOI: 10.1111/nph.19779] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/22/2024] [Accepted: 04/10/2024] [Indexed: 05/06/2024]
Affiliation(s)
- Jin-Li Deng
- MOE Key Laboratory for Cellular Dynamics, School of Life Sciences, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, 230027, China
| | - Li Zhao
- MOE Key Laboratory for Cellular Dynamics, School of Life Sciences, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, 230027, China
| | - Hong Wei
- The First Affiliated Hospital of USTC, MOE Key Laboratory for Membraneless Organelles and Cellular Dynamics, Hefei National Research Center for Interdisciplinary Sciences at the Microscale, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, 230027, China
| | - Han-Xiao Ye
- MOE Key Laboratory for Cellular Dynamics, School of Life Sciences, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, 230027, China
| | - Li Yang
- MOE Key Laboratory for Cellular Dynamics, School of Life Sciences, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, 230027, China
| | - Linfeng Sun
- The First Affiliated Hospital of USTC, MOE Key Laboratory for Membraneless Organelles and Cellular Dynamics, Hefei National Research Center for Interdisciplinary Sciences at the Microscale, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, 230027, China
| | - Zhong Zhao
- Chinese Academy of Sciences Center for Excellence in Molecular Plant Sciences, MOE Key Laboratory for Cellular Dynamics, School of Life Sciences, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, 230027, China
| | - Jeremy D Murray
- National Key Laboratory of Plant Molecular Genetics, CAS-JIC Centre of Excellence for Plant and Microbial Science (CEPAMS), Center for Excellence in Molecular Plant Sciences, Chinese Academy of Sciences, Shanghai, 200032, China
- John Innes Centre, Norwich Research Park, Norwich, NR4 7UH, UK
| | - Cheng-Wu Liu
- MOE Key Laboratory for Cellular Dynamics, School of Life Sciences, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, 230027, China
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6
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Fernandez‐Moreno J, Yaschenko AE, Neubauer M, Marchi AJ, Zhao C, Ascencio‐Ibanez JT, Alonso JM, Stepanova AN. A rapid and scalable approach to build synthetic repetitive hormone-responsive promoters. PLANT BIOTECHNOLOGY JOURNAL 2024; 22:1942-1956. [PMID: 38379432 PMCID: PMC11182585 DOI: 10.1111/pbi.14313] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/21/2023] [Revised: 02/04/2024] [Accepted: 02/06/2024] [Indexed: 02/22/2024]
Abstract
Advancement of DNA-synthesis technologies has greatly facilitated the development of synthetic biology tools. However, high-complexity DNA sequences containing tandems of short repeats are still notoriously difficult to produce synthetically, with commercial DNA synthesis companies usually rejecting orders that exceed specific sequence complexity thresholds. To overcome this limitation, we developed a simple, single-tube reaction method that enables the generation of DNA sequences containing multiple repetitive elements. Our strategy involves commercial synthesis and PCR amplification of padded sequences that contain the repeats of interest, along with random intervening sequence stuffers that include type IIS restriction enzyme sites. GoldenBraid molecular cloning technology is then employed to remove the stuffers, rejoin the repeats together in a predefined order, and subclone the tandem(s) in a vector using a single-tube digestion-ligation reaction. In our hands, this new approach is much simpler, more versatile and efficient than previously developed solutions to this problem. As a proof of concept, two different phytohormone-responsive, synthetic, repetitive proximal promoters were generated and tested in planta in the context of transcriptional reporters. Analysis of transgenic lines carrying the synthetic ethylene-responsive promoter 10x2EBS-S10 fused to the GUS reporter gene uncovered several developmentally regulated ethylene response maxima, indicating the utility of this reporter for monitoring the involvement of ethylene in a variety of physiologically relevant processes. These encouraging results suggest that this reporter system can be leveraged to investigate the ethylene response to biotic and abiotic factors with high spatial and temporal resolution.
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Affiliation(s)
| | - Anna E. Yaschenko
- Department of Plant and Microbial BiologyNorth Carolina State UniversityRaleighNCUSA
| | - Matthew Neubauer
- Department of Plant and Microbial BiologyNorth Carolina State UniversityRaleighNCUSA
| | - Alex J. Marchi
- Department of Plant and Microbial BiologyNorth Carolina State UniversityRaleighNCUSA
| | - Chengsong Zhao
- Department of Plant and Microbial BiologyNorth Carolina State UniversityRaleighNCUSA
| | - José T. Ascencio‐Ibanez
- Department of Molecular and Structural BiochemistryNorth Carolina State UniversityRaleighNCUSA
| | - Jose M. Alonso
- Department of Plant and Microbial BiologyNorth Carolina State UniversityRaleighNCUSA
| | - Anna N. Stepanova
- Department of Plant and Microbial BiologyNorth Carolina State UniversityRaleighNCUSA
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7
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D’Alessandro S, Velay F, Lebrun R, Zafirov D, Mehrez M, Romand S, Saadouni R, Forzani C, Citerne S, Montané MH, Robaglia C, Menand B, Meyer C, Field B. Posttranslational regulation of photosynthetic activity via the TOR kinase in plants. SCIENCE ADVANCES 2024; 10:eadj3268. [PMID: 38896607 PMCID: PMC11186500 DOI: 10.1126/sciadv.adj3268] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/20/2023] [Accepted: 05/13/2024] [Indexed: 06/21/2024]
Abstract
Chloroplasts are the powerhouse of the plant cell, and their activity must be matched to plant growth to avoid photooxidative damage. We have identified a posttranslational mechanism linking the eukaryotic target of rapamycin (TOR) kinase that promotes growth and the guanosine tetraphosphate (ppGpp) signaling pathway of prokaryotic origins that regulates chloroplast activity and photosynthesis in particular. We find that RelA SpoT homolog 3 (RSH3), a nuclear-encoded enzyme responsible for ppGpp biosynthesis, interacts directly with the TOR complex via a plant-specific amino-terminal region which is phosphorylated in a TOR-dependent manner. Down-regulating TOR activity causes a rapid increase in ppGpp synthesis in RSH3 overexpressors and reduces photosynthetic capacity in an RSH-dependent manner in wild-type plants. The TOR-RSH3 signaling axis therefore regulates the equilibrium between chloroplast activity and plant growth, setting a precedent for the regulation of organellar function by TOR.
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Affiliation(s)
- Stefano D’Alessandro
- Aix Marseille Univ, CEA, CNRS, BIAM, LGBP Team, 13009 Marseille, France
- Università di Torino, Dipartimento di Scienze della vita e Biologia dei Sistemi, 10135 Torino, Italy
| | - Florent Velay
- Aix Marseille Univ, CEA, CNRS, BIAM, LGBP Team, 13009 Marseille, France
| | - Régine Lebrun
- Aix Marseille Univ, CNRS, Plate-forme Protéomique, Marseille Protéomique (MaP), IMM FR 3479, 31 Chemin Joseph Aiguier, 13009 Marseille, France
| | - Delyan Zafirov
- Aix Marseille Univ, CEA, CNRS, BIAM, LGBP Team, 13009 Marseille, France
| | - Marwa Mehrez
- Aix Marseille Univ, CEA, CNRS, BIAM, LGBP Team, 13009 Marseille, France
- Faculty of Sciences of Tunis, University of Tunis El Manar, 2092 Tunis, Tunisia
| | - Shanna Romand
- Aix Marseille Univ, CEA, CNRS, BIAM, LGBP Team, 13009 Marseille, France
| | - Rim Saadouni
- Aix Marseille Univ, CEA, CNRS, BIAM, LGBP Team, 13009 Marseille, France
- Aix Marseille Univ, CNRS, Plate-forme Protéomique, Marseille Protéomique (MaP), IMM FR 3479, 31 Chemin Joseph Aiguier, 13009 Marseille, France
| | - Céline Forzani
- Institut Jean-Pierre Bourgin, INRAE, AgroParisTech, CNRS, Université Paris-Saclay, 78000 Versailles, France
| | - Sylvie Citerne
- Institut Jean-Pierre Bourgin, INRAE, AgroParisTech, CNRS, Université Paris-Saclay, 78000 Versailles, France
| | | | | | - Benoît Menand
- Aix Marseille Univ, CEA, CNRS, BIAM, LGBP Team, 13009 Marseille, France
| | - Christian Meyer
- Institut Jean-Pierre Bourgin, INRAE, AgroParisTech, CNRS, Université Paris-Saclay, 78000 Versailles, France
| | - Ben Field
- Aix Marseille Univ, CEA, CNRS, BIAM, LGBP Team, 13009 Marseille, France
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8
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Romani F, Sauret-Güeto S, Rebmann M, Annese D, Bonter I, Tomaselli M, Dierschke T, Delmans M, Frangedakis E, Silvestri L, Rever J, Bowman JL, Romani I, Haseloff J. The landscape of transcription factor promoter activity during vegetative development in Marchantia. THE PLANT CELL 2024; 36:2140-2159. [PMID: 38391349 PMCID: PMC11132968 DOI: 10.1093/plcell/koae053] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/13/2023] [Revised: 12/08/2023] [Accepted: 12/22/2023] [Indexed: 02/24/2024]
Abstract
Transcription factors (TFs) are essential for the regulation of gene expression and cell fate determination. Characterizing the transcriptional activity of TF genes in space and time is a critical step toward understanding complex biological systems. The vegetative gametophyte meristems of bryophytes share some characteristics with the shoot apical meristems of flowering plants. However, the identity and expression profiles of TFs associated with gametophyte organization are largely unknown. With only ∼450 putative TF genes, Marchantia (Marchantia polymorpha) is an outstanding model system for plant systems biology. We have generated a near-complete collection of promoter elements derived from Marchantia TF genes. We experimentally tested reporter fusions for all the TF promoters in the collection and systematically analyzed expression patterns in Marchantia gemmae. This allowed us to build a map of expression domains in early vegetative development and identify a set of TF-derived promoters that are active in the stem-cell zone. The cell markers provide additional tools and insight into the dynamic regulation of the gametophytic meristem and its evolution. In addition, we provide an online database of expression patterns for all promoters in the collection. We expect that these promoter elements will be useful for cell-type-specific expression, synthetic biology applications, and functional genomics.
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Affiliation(s)
- Facundo Romani
- Department of Plant Sciences, University of Cambridge, Cambridge CB3 EA, UK
| | | | - Marius Rebmann
- Department of Plant Sciences, University of Cambridge, Cambridge CB3 EA, UK
| | - Davide Annese
- Department of Plant Sciences, University of Cambridge, Cambridge CB3 EA, UK
| | - Ignacy Bonter
- Department of Plant Sciences, University of Cambridge, Cambridge CB3 EA, UK
| | - Marta Tomaselli
- Department of Plant Sciences, University of Cambridge, Cambridge CB3 EA, UK
| | - Tom Dierschke
- School of Biological Sciences, Monash University, Clayton, Melbourne, VIC 3800, Australia
- ARC Centre of Excellence for Plant Success in Nature and Agriculture, Monash University, Clayton, Melbourne, VIC 3800, Australia
| | - Mihails Delmans
- Department of Plant Sciences, University of Cambridge, Cambridge CB3 EA, UK
| | | | - Linda Silvestri
- Department of Plant Sciences, University of Cambridge, Cambridge CB3 EA, UK
| | - Jenna Rever
- Department of Plant Sciences, University of Cambridge, Cambridge CB3 EA, UK
| | - John L Bowman
- School of Biological Sciences, Monash University, Clayton, Melbourne, VIC 3800, Australia
- ARC Centre of Excellence for Plant Success in Nature and Agriculture, Monash University, Clayton, Melbourne, VIC 3800, Australia
| | - Ignacio Romani
- Departamento de Ciencias Sociales, Universidad Nacional de Quilmes, Bernal, Buenos Aires 1876, Argentina
| | - Jim Haseloff
- Department of Plant Sciences, University of Cambridge, Cambridge CB3 EA, UK
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9
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Salesse-Smith CE, Lochocki EB, Doran L, Haas BE, Stutz SS, Long SP. Greater mesophyll conductance and leaf photosynthesis in the field through modified cell wall porosity and thickness via AtCGR3 expression in tobacco. PLANT BIOTECHNOLOGY JOURNAL 2024. [PMID: 38687118 DOI: 10.1111/pbi.14364] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/16/2024] [Revised: 04/02/2024] [Accepted: 04/11/2024] [Indexed: 05/02/2024]
Abstract
Mesophyll conductance (gm) describes the ease with which CO2 passes from the sub-stomatal cavities of the leaf to the primary carboxylase of photosynthesis, Rubisco. Increasing gm is suggested as a means to engineer increases in photosynthesis by increasing [CO2] at Rubisco, inhibiting oxygenation and accelerating carboxylation. Here, tobacco was transgenically up-regulated with Arabidopsis Cotton Golgi-related 3 (CGR3), a gene controlling methylesterification of pectin, as a strategy to increase CO2 diffusion across the cell wall and thereby increase gm. Across three independent events in tobacco strongly expressing AtCGR3, mesophyll cell wall thickness was decreased by 7%-13%, wall porosity increased by 75% and gm measured by carbon isotope discrimination increased by 28%. Importantly, field-grown plants showed an average 8% increase in leaf photosynthetic CO2 uptake. Up-regulating CGR3 provides a new strategy for increasing gm in dicotyledonous crops, leading to higher CO2 assimilation and a potential means to sustainable crop yield improvement.
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Affiliation(s)
- Coralie E Salesse-Smith
- Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, IL, USA
| | - Edward B Lochocki
- Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, IL, USA
| | - Lynn Doran
- Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, IL, USA
| | - Benjamin E Haas
- Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, IL, USA
| | - Samantha S Stutz
- Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, IL, USA
| | - Stephen P Long
- Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, IL, USA
- Departments of Plant Biology and of Crop Sciences, University of Illinois at Urbana-Champaign, Urbana, IL, USA
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10
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Hieronimus K, Donauer T, Klein J, Hinkel B, Spänle JV, Probst A, Niemeyer J, Kibrom S, Kiefer AM, Schneider L, Husemann B, Bischoff E, Möhring S, Bayer N, Klein D, Engels A, Ziehmer BG, Stieβ J, Moroka P, Schroda M, Deponte M. A Modular Cloning Toolkit for the production of recombinant proteins in Leishmania tarentolae. MICROBIAL CELL (GRAZ, AUSTRIA) 2024; 11:128-142. [PMID: 38799406 PMCID: PMC11121976 DOI: 10.15698/mic2024.04.821] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 01/05/2024] [Revised: 03/20/2024] [Accepted: 03/28/2024] [Indexed: 05/29/2024]
Abstract
Modular Cloning (MoClo) is based on libraries of standardized genetic parts that can be directionally assembled via Golden Gate cloning in one-pot reactions into transcription units and multigene constructs. Here, a team of bachelor students established a MoClo toolkit for the protist Leishmania tarentolae in the frame of the international Genetically Engineered Machine (iGEM) competition. Our modular toolkit is based on a domesticated version of a commercial LEXSY expression vector and comprises 34 genetic parts encoding various affinity tags, targeting signals as well as fluorescent and luminescent proteins. We demonstrated the utility of our kit by the successful production of 16 different tagged versions of the receptor binding domain (RBD) of the SARS-CoV-2 spike protein in L. tarentolae liquid cultures. While highest yields of secreted recombinant RBD were obtained for GST-tagged fusion proteins 48 h post induction, C-terminal peptide tags were often degraded and resulted in lower yields of secreted RBD. Fusing secreted RBD to a synthetic O-glycosylation SP20 module resulted in an apparent molecular mass shift around 10 kDa. No disadvantage regarding the production of RBD was detected when the three antibiotics of the LEXSY system were omitted during the 48-h induction phase. Furthermore, the successful purification of secreted RBD from the supernatant of L. tarentolae liquid cultures was demonstrated in pilot experiments. In summary, we established a MoClo toolkit and exemplified its application for the production of recombinant proteins in L. tarentolae.
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Affiliation(s)
- Katrin Hieronimus
- Faculty of Biology, Molecular Biotechnology & Systems
Biology, RPTU Kaiserslautern, D-67663 Kaiserslautern, Germany
- Faculty of Chemistry, Comparative Biochemistry, RPTU
Kaiserslautern, D-67663 Kaiserslautern, Germany
| | - Tabea Donauer
- Faculty of Biology, Molecular Biotechnology & Systems
Biology, RPTU Kaiserslautern, D-67663 Kaiserslautern, Germany
- Faculty of Chemistry, Comparative Biochemistry, RPTU
Kaiserslautern, D-67663 Kaiserslautern, Germany
| | - Jonas Klein
- Faculty of Biology, Molecular Biotechnology & Systems
Biology, RPTU Kaiserslautern, D-67663 Kaiserslautern, Germany
| | - Bastian Hinkel
- Faculty of Biology, Molecular Biotechnology & Systems
Biology, RPTU Kaiserslautern, D-67663 Kaiserslautern, Germany
| | - Julia Vanessa Spänle
- Faculty of Biology, Molecular Biotechnology & Systems
Biology, RPTU Kaiserslautern, D-67663 Kaiserslautern, Germany
| | - Anna Probst
- Faculty of Biology, Molecular Biotechnology & Systems
Biology, RPTU Kaiserslautern, D-67663 Kaiserslautern, Germany
| | - Justus Niemeyer
- Faculty of Biology, Molecular Biotechnology & Systems
Biology, RPTU Kaiserslautern, D-67663 Kaiserslautern, Germany
| | - Salina Kibrom
- Faculty of Biology, Molecular Biotechnology & Systems
Biology, RPTU Kaiserslautern, D-67663 Kaiserslautern, Germany
| | - Anna Maria Kiefer
- Faculty of Biology, Molecular Biotechnology & Systems
Biology, RPTU Kaiserslautern, D-67663 Kaiserslautern, Germany
| | - Luzia Schneider
- Faculty of Chemistry, Comparative Biochemistry, RPTU
Kaiserslautern, D-67663 Kaiserslautern, Germany
| | - Britta Husemann
- Faculty of Chemistry, Comparative Biochemistry, RPTU
Kaiserslautern, D-67663 Kaiserslautern, Germany
| | - Eileen Bischoff
- Faculty of Chemistry, Comparative Biochemistry, RPTU
Kaiserslautern, D-67663 Kaiserslautern, Germany
| | - Sophie Möhring
- Faculty of Chemistry, Comparative Biochemistry, RPTU
Kaiserslautern, D-67663 Kaiserslautern, Germany
| | - Nicolas Bayer
- Faculty of Biology, Molecular Biotechnology & Systems
Biology, RPTU Kaiserslautern, D-67663 Kaiserslautern, Germany
| | - Dorothée Klein
- Faculty of Biology, Molecular Biotechnology & Systems
Biology, RPTU Kaiserslautern, D-67663 Kaiserslautern, Germany
| | - Adrian Engels
- Faculty of Biology, Molecular Biotechnology & Systems
Biology, RPTU Kaiserslautern, D-67663 Kaiserslautern, Germany
| | - Benjamin Gustav Ziehmer
- Faculty of Chemistry, Comparative Biochemistry, RPTU
Kaiserslautern, D-67663 Kaiserslautern, Germany
| | - Julian Stieβ
- Faculty of Computer Science, RPTU Kaiserslautern, D-67663
Kaiserslautern, Germany
| | - Pavlo Moroka
- Faculty of Biology, Molecular Biotechnology & Systems
Biology, RPTU Kaiserslautern, D-67663 Kaiserslautern, Germany
| | - Michael Schroda
- Faculty of Biology, Molecular Biotechnology & Systems
Biology, RPTU Kaiserslautern, D-67663 Kaiserslautern, Germany
| | - Marcel Deponte
- Faculty of Chemistry, Comparative Biochemistry, RPTU
Kaiserslautern, D-67663 Kaiserslautern, Germany
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11
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Webster LJ, Villa-Gomez D, Brown R, Clarke W, Schenk PM. A synthetic biology approach for the treatment of pollutants with microalgae. Front Bioeng Biotechnol 2024; 12:1379301. [PMID: 38646010 PMCID: PMC11032018 DOI: 10.3389/fbioe.2024.1379301] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2024] [Accepted: 03/11/2024] [Indexed: 04/23/2024] Open
Abstract
The increase in global population and industrial development has led to a significant release of organic and inorganic pollutants into water streams, threatening human health and ecosystems. Microalgae, encompassing eukaryotic protists and prokaryotic cyanobacteria, have emerged as a sustainable and cost-effective solution for removing these pollutants and mitigating carbon emissions. Various microalgae species, such as C. vulgaris, P. tricornutum, N. oceanica, A. platensis, and C. reinhardtii, have demonstrated their ability to eliminate heavy metals, salinity, plastics, and pesticides. Synthetic biology holds the potential to enhance microalgae-based technologies by broadening the scope of treatment targets and improving pollutant removal rates. This review provides an overview of the recent advances in the synthetic biology of microalgae, focusing on genetic engineering tools to facilitate the removal of inorganic (heavy metals and salinity) and organic (pesticides and plastics) compounds. The development of these tools is crucial for enhancing pollutant removal mechanisms through gene expression manipulation, DNA introduction into cells, and the generation of mutants with altered phenotypes. Additionally, the review discusses the principles of synthetic biology tools, emphasizing the significance of genetic engineering in targeting specific metabolic pathways and creating phenotypic changes. It also explores the use of precise engineering tools, such as CRISPR/Cas9 and TALENs, to adapt genetic engineering to various microalgae species. The review concludes that there is much potential for synthetic biology based approaches for pollutant removal using microalgae, but there is a need for expansion of the tools involved, including the development of universal cloning toolkits for the efficient and rapid assembly of mutants and transgenic expression strains, and the need for adaptation of genetic engineering tools to a wider range of microalgae species.
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Affiliation(s)
- Luke J. Webster
- Australian Institute for Bioengineering and Nanotechnology, The University of Queensland, Brisbane, QLD, Australia
| | - Denys Villa-Gomez
- Australian Institute for Bioengineering and Nanotechnology, The University of Queensland, Brisbane, QLD, Australia
- School of Civil Engineering, The University of Queensland, Brisbane, QLD, Australia
| | - Reuben Brown
- Algae Biotechnology Laboratory, School of Agriculture and Food Sustainability, The University of Queensland, Brisbane, QLD, Australia
| | - William Clarke
- School of Civil Engineering, The University of Queensland, Brisbane, QLD, Australia
| | - Peer M. Schenk
- Algae Biotechnology Laboratory, School of Agriculture and Food Sustainability, The University of Queensland, Brisbane, QLD, Australia
- Algae Biotechnology, Sustainable Solutions Hub, Global Sustainable Solutions Pty Ltd, Brisbane, QLD, Australia
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12
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Lambert L, de Carpentier F, André P, Marchand CH, Danon A. Type II metacaspase mediates light-dependent programmed cell death in Chlamydomonas reinhardtii. PLANT PHYSIOLOGY 2024; 194:2648-2662. [PMID: 37971939 PMCID: PMC10980519 DOI: 10.1093/plphys/kiad618] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/01/2023] [Revised: 10/12/2023] [Accepted: 10/22/2023] [Indexed: 11/19/2023]
Abstract
Among the crucial processes that preside over the destiny of cells from any type of organism are those involving their self-destruction. This process is well characterized and conceptually logical to understand in multicellular organisms; however, the levels of knowledge and comprehension of its existence are still quite enigmatic in unicellular organisms. We use Chlamydomonas (Chlamydomonas reinhardtii) to lay the foundation for understanding the mechanisms of programmed cell death (PCD) in a unicellular photosynthetic organism. In this paper, we show that while PCD induces the death of a proportion of cells, it allows the survival of the remaining population. A quantitative proteomic analysis aiming at unveiling the proteome of PCD in Chlamydomonas allowed us to identify key proteins that led to the discovery of essential mechanisms. We show that in Chlamydomonas, PCD relies on the light dependence of a photosynthetic organism to generate reactive oxygen species and induce cell death. Finally, we obtained and characterized mutants for the 2 metacaspase genes in Chlamydomonas and showed that a type II metacaspase is essential for PCD execution.
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Affiliation(s)
- Lou Lambert
- Institut de Biologie Paris Seine, UMR 7238, CNRS, Sorbonne Université, Paris 75005, France
| | - Félix de Carpentier
- Institut de Biologie Paris Seine, UMR 7238, CNRS, Sorbonne Université, Paris 75005, France
- Doctoral School of Plant Sciences, Université Paris-Saclay, Saint-Aubin 91190, France
| | - Phuc André
- Institut de Biologie Paris Seine, UMR 7238, CNRS, Sorbonne Université, Paris 75005, France
| | - Christophe H Marchand
- Institut de Biologie Paris Seine, UMR 7238, CNRS, Sorbonne Université, Paris 75005, France
- Institut de Biologie Physico-Chimique, Centre National de la Recherche Scientifique (CNRS), Paris F-75005, France
| | - Antoine Danon
- Institut de Biologie Paris Seine, UMR 7238, CNRS, Sorbonne Université, Paris 75005, France
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13
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Gallinari RH, Lyczakowski JJ, Llerena JPP, Mayer JLS, Rabelo SC, Menossi Teixeira M, Dupree P, Araujo P. Silencing ScGUX2 reduces xylan glucuronidation and improves biomass saccharification in sugarcane. PLANT BIOTECHNOLOGY JOURNAL 2024; 22:587-601. [PMID: 38146142 PMCID: PMC10893953 DOI: 10.1111/pbi.14207] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/27/2023] [Revised: 10/02/2023] [Accepted: 10/06/2023] [Indexed: 12/27/2023]
Abstract
There is an increasing need for renewable energy sources to replace part of our fossil fuel-based economy and reduce greenhouse gas emission. Sugarcane bagasse is a prominent feedstock to produce cellulosic bioethanol, but strategies are still needed to improve the cost-effective exploitation of this potential energy source. In model plants, it has been shown that GUX genes are involved in cell wall hemicellulose decoration, adding glucuronic acid substitutions on the xylan backbone. Mutation of GUX genes increases enzyme access to cell wall polysaccharides, reducing biomass recalcitrance in Arabidopsis thaliana. Here, we characterized the sugarcane GUX genes and silenced GUX2 in commercial hybrid sugarcane. The transgenic lines had no penalty in development under greenhouse conditions. The sugarcane GUX1 and GUX2 enzymes generated different patterns of xylan glucuronidation, suggesting they may differently influence the molecular interaction of xylan with cellulose and lignin. Studies using biomass without chemical or steam pretreatment showed that the cell wall polysaccharides, particularly xylan, were less recalcitrant in sugarcane with GUX2 silenced than in WT plants. Our findings suggest that manipulation of GUX in sugarcane can reduce the costs of second-generation ethanol production and enhance the contribution of biofuels to lowering the emission of greenhouse gases.
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Affiliation(s)
- Rafael Henrique Gallinari
- Department of Genetic, Evolution, Microbiology and Immunology, Institute of BiologyUniversity of Campinas—UNICAMPSão PauloBrazil
- Department of BiochemistryUniversity of CambridgeCambridgeUK
| | - Jan J. Lyczakowski
- Department of BiochemistryUniversity of CambridgeCambridgeUK
- Department of Plant Biotechnology, Faculty of Biochemistry, Biophysics and BiotechnologyJagiellonian UniversityKrakowPoland
| | - Juan Pablo Portilla Llerena
- Department of Genetic, Evolution, Microbiology and Immunology, Institute of BiologyUniversity of Campinas—UNICAMPSão PauloBrazil
- Department of Plant Biology, Institute of BiologyUniversity of Campinas—UNICAMPSão PauloBrazil
| | | | - Sarita Cândida Rabelo
- Department of Bioprocess and Biotechnology, School of AgricultureSão Paulo State University—UNESPBotucatuBrazil
| | - Marcelo Menossi Teixeira
- Department of Genetic, Evolution, Microbiology and Immunology, Institute of BiologyUniversity of Campinas—UNICAMPSão PauloBrazil
| | - Paul Dupree
- Department of BiochemistryUniversity of CambridgeCambridgeUK
| | - Pedro Araujo
- Department of Genetic, Evolution, Microbiology and Immunology, Institute of BiologyUniversity of Campinas—UNICAMPSão PauloBrazil
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14
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Weerasooriya HN, Longstreth DJ, DiMario RJ, Rosati VC, Cassel BA, Moroney JV. Carbonic anhydrases in the cell wall and plasma membrane of Arabidopsis thaliana are required for optimal plant growth on low CO 2. Front Mol Biosci 2024; 11:1267046. [PMID: 38455761 PMCID: PMC10917985 DOI: 10.3389/fmolb.2024.1267046] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2023] [Accepted: 01/15/2024] [Indexed: 03/09/2024] Open
Abstract
Introduction: Plants have many genes encoding both alpha and beta type carbonic anhydrases. Arabidopsis has eight alpha type and six beta type carbonic anhydrase genes. Individual carbonic anhydrases are localized to specific compartments within the plant cell. In this study, we investigate the roles of αCA2 and βCA4.1 in the growth of the plant Arabidopsis thaliana under different CO2 regimes. Methods: Here, we identified the intracellular location of αCA2 and βCA4.1 by linking the coding region of each gene to a fluorescent tag. Tissue expression was determined by investigating GUS expression driven by the αCA2 and βCA4.1 promoters. Finally, the role of these proteins in plant growth and photosynthesis was tested in plants with T-DNA insertions in the αCA2 and βCA4 genes. Results: Fluorescently tagged proteins showed that αCA2 is localized to the cell wall and βCA4.1 to the plasma membrane in plant leaves. Both proteins were expressed in roots and shoots. Plants missing either αCA2 or βCA4 did not show any growth defects under the conditions tested in this study. However, if both αCA2 and βCA4 were disrupted, plants had a significantly smaller above- ground fresh weight and rosette area than Wild Type (WT) plants when grown at 200 μL L-1 CO2 but not at 400 and 1,000 μL L-1 CO2. Growth of the double mutant plants at 200 μL L-1 CO2 was restoredif either αCA2 or βCA4.1 was transformed back into the double mutant plants. Discussion: Both the cell wall and plasma membrane CAs, αCA2 and βCA4.1 had to be knocked down to produce an effect on Arabidopsis growth and only when grown in a CO2 concentration that was significantly below ambient. This indicates that αCA2 and βCA4.1 have overlapping functions since the growth of lines where only one of these CAs was knocked down was indistinguishable from WT growth. The growth results and cellular locations of the two CAs suggest that together, αCA2 and βCA4.1 play an important role in the delivery of CO2 and HCO3 - to the plant cell.
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Affiliation(s)
| | | | | | | | | | - James V. Moroney
- Department of Biological Sciences, Louisiana State University, Baton Rouge, LA, United States
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15
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Bibik JD, Hamberger B. Plant Engineering to Enable Platforms for Sustainable Bioproduction of Terpenoids. Methods Mol Biol 2024; 2760:3-20. [PMID: 38468079 DOI: 10.1007/978-1-0716-3658-9_1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/13/2024]
Abstract
Terpenoids represent the most diverse class of natural products, with a broad spectrum of industrial relevance including applications in green solvents, flavors and fragrances, nutraceuticals, colorants, and therapeutics. They are typically challenging to extract from their natural sources, where they occur in small amounts and mixtures of related but unwanted byproducts. Formal chemical synthesis, where established, is reliant on petrochemistry. Hence, there is great interest in developing sustainable solutions to assemble biosynthetic pathways in engineered host organisms. Metabolic engineering for chemical production has largely focused on microbial hosts, yet plants offer a sustainable production platform. In addition to containing the precursor pathways that generate the terpenoid building blocks as well as the cell structures and compartments required, or tractable localization for the enzymes involved, plants may provide a low input system to produce these chemicals using carbon dioxide and sunlight only. There have been significant recent advancements in the discovery of pathways to terpenoids of interest as well as strategies to boost yields in host plants. While part of the phytochemical field is focusing on the discovery of biosynthetic pathways, this review will focus on advancements using the pathway toolbox and toward engineering plants for the production of terpenoids. We will highlight strategies currently used to produce target products, optimization of known pathways to improve yields, compartmentalization of pathways within cells, and genetic tools developed to facilitate complex engineering of biosynthetic pathways. These advancements in Synthetic Biology are bringing engineered plant systems closer to commercially relevant hosts for the bioproduction of terpenoids.
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Affiliation(s)
- Jacob D Bibik
- Department of Biochemistry, Michigan State University, East Lansing, MI, USA
- MelaTech, LLC, Baltimore, MD, USA
| | - Björn Hamberger
- Department of Biochemistry, Michigan State University, East Lansing, MI, USA.
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16
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Russo MT, Rogato A, Jaubert M, Karas BJ, Falciatore A. Phaeodactylum tricornutum: An established model species for diatom molecular research and an emerging chassis for algal synthetic biology. JOURNAL OF PHYCOLOGY 2023; 59:1114-1122. [PMID: 37975560 DOI: 10.1111/jpy.13400] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/05/2023] [Accepted: 10/05/2023] [Indexed: 11/19/2023]
Abstract
Diatoms are prominent and highly diverse microalgae in aquatic environments. Compared with other diatom species, Phaeodactylum tricornutum is an "atypical diatom" displaying three different morphotypes and lacking the usual silica shell. Despite being of limited ecological relevance, its ease of growth in the laboratory and well-known physiology, alongside the steady increase in genome-enabled information coupled with effective tools for manipulating gene expression, have meant it has gained increased recognition as a powerful experimental model for molecular research on diatoms. We here present a brief overview of how over the last 25 years P. tricornutum has contributed to the unveiling of fundamental aspects of diatom biology, while also emerging as a new tool for algal process engineering and synthetic biology.
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Affiliation(s)
- Monia T Russo
- Department of Ecosustainable Marine Biotechnology, Stazione Zoologica Anton Dohrn, Naples, Italy
| | - Alessandra Rogato
- Institute of Biosciences and Bioresources, National Research Council, IBBR-CNR, Naples, Italy
- Department of Integrative Marine Ecology, Stazione Zoologica Anton Dohrn, Naples, Italy
| | - Marianne Jaubert
- UMR7141 Laboratoire de Biologie du chloroplaste et perception de la lumière chez les micro-algues, Institut de Biologie Physico-Chimique, Paris, France
| | - Bogumil J Karas
- Department of Biochemistry, Schulich School of Medicine and Dentistry, The University of Western Ontario, London, Ontario, Canada
| | - Angela Falciatore
- UMR7141 Laboratoire de Biologie du chloroplaste et perception de la lumière chez les micro-algues, Institut de Biologie Physico-Chimique, Paris, France
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17
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Wilson LFL, Neun S, Yu L, Tryfona T, Stott K, Hollfelder F, Dupree P. The biosynthesis, degradation, and function of cell wall β-xylosylated xyloglucan mirrors that of arabinoxyloglucan. THE NEW PHYTOLOGIST 2023; 240:2353-2371. [PMID: 37823344 PMCID: PMC10952531 DOI: 10.1111/nph.19305] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/12/2023] [Accepted: 09/02/2023] [Indexed: 10/13/2023]
Abstract
Xyloglucan is an abundant polysaccharide in many primary cell walls and in the human diet. Decoration of its α-xylosyl sidechains with further sugars is critical for plant growth, even though the sugars themselves vary considerably between species. Plants in the Ericales order - prevalent in human diets - exhibit β1,2-linked xylosyl decorations. The biosynthetic enzymes responsible for adding these xylosyl decorations, as well as the hydrolases that remove them in the human gut, are unidentified. GT47 xyloglucan glycosyltransferase candidates were expressed in Arabidopsis and endo-xyloglucanase products from transgenic wall material were analysed by electrophoresis, mass spectrometry, and nuclear magnetic resonance (NMR) spectroscopy. The activities of gut bacterial hydrolases BoGH43A and BoGH43B on synthetic glycosides and xyloglucan oligosaccharides were measured by colorimetry and electrophoresis. CcXBT1 is a xyloglucan β-xylosyltransferase from coffee that can modify Arabidopsis xyloglucan and restore the growth of galactosyltransferase mutants. Related VmXST1 is a weakly active xyloglucan α-arabinofuranosyltransferase from cranberry. BoGH43A hydrolyses both α-arabinofuranosylated and β-xylosylated oligosaccharides. CcXBT1's presence in coffee and BoGH43A's promiscuity suggest that β-xylosylated xyloglucan is not only more widespread than thought, but might also nourish beneficial gut bacteria. The evolutionary instability of transferase specificity and lack of hydrolase specificity hint that, to enzymes, xylosides and arabinofuranosides are closely resemblant.
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Affiliation(s)
- Louis F. L. Wilson
- Department of BiochemistryUniversity of CambridgeHopkins Building, Tennis Court RoadCambridgeCB2 1QWUK
| | - Stefanie Neun
- Department of BiochemistryUniversity of CambridgeSanger Building, Tennis Court RoadCambridgeCB2 1GAUK
| | - Li Yu
- Department of BiochemistryUniversity of CambridgeHopkins Building, Tennis Court RoadCambridgeCB2 1QWUK
| | - Theodora Tryfona
- Department of BiochemistryUniversity of CambridgeHopkins Building, Tennis Court RoadCambridgeCB2 1QWUK
| | - Katherine Stott
- Department of BiochemistryUniversity of CambridgeSanger Building, Tennis Court RoadCambridgeCB2 1GAUK
| | - Florian Hollfelder
- Department of BiochemistryUniversity of CambridgeSanger Building, Tennis Court RoadCambridgeCB2 1GAUK
| | - Paul Dupree
- Department of BiochemistryUniversity of CambridgeHopkins Building, Tennis Court RoadCambridgeCB2 1QWUK
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18
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Blázquez B, León DS, Torres-Bacete J, Gómez-Luengo Á, Kniewel R, Martínez I, Sordon S, Wilczak A, Salgado S, Huszcza E, Popłoński J, Prieto A, Nogales J. Golden Standard: a complete standard, portable, and interoperative MoClo tool for model and non-model proteobacteria. Nucleic Acids Res 2023; 51:e98. [PMID: 37718823 PMCID: PMC10602866 DOI: 10.1093/nar/gkad758] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2022] [Accepted: 09/06/2023] [Indexed: 09/19/2023] Open
Abstract
Modular cloning has become a benchmark technology in synthetic biology. However, a notable disparity exists between its remarkable development and the need for standardization to facilitate seamless interoperability among systems. The field is thus impeded by an overwhelming proliferation of organism-specific systems that frequently lack compatibility. To overcome these issues, we present Golden Standard (GS), a Type IIS assembly method underpinned by the Standard European Vector Architecture. GS unlocks modular cloning applications for most bacteria, and delivers combinatorial multi-part assembly to create genetic circuits of up to twenty transcription units (TUs). Reliance on MoClo syntax renders GS fully compatible with many existing tools and it sets the path towards efficient reusability of available part libraries and assembled TUs. GS was validated in terms of DNA assembly, portability, interoperability and phenotype engineering in α-, β-, γ- and δ-proteobacteria. Furthermore, we provide a computational pipeline for parts characterization that was used to assess the performance of GS parts. To promote community-driven development of GS, we provide a dedicated web-portal including a repository of parts, vectors, and Wizard and Setup tools that guide users in designing constructs. Overall, GS establishes an open, standardized framework propelling the progress of synthetic biology as a whole.
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Affiliation(s)
- Blas Blázquez
- Department of Systems Biology, Centro Nacional de Biotecnología, CSIC, Madrid, Spain
- Interdisciplinary Platform for Sustainable Plastics towards a Circular Economy-Spanish National Research Council (SusPlast-CSIC), Madrid, Spain
| | - David San León
- Department of Systems Biology, Centro Nacional de Biotecnología, CSIC, Madrid, Spain
- Interdisciplinary Platform for Sustainable Plastics towards a Circular Economy-Spanish National Research Council (SusPlast-CSIC), Madrid, Spain
| | - Jesús Torres-Bacete
- Department of Systems Biology, Centro Nacional de Biotecnología, CSIC, Madrid, Spain
| | - Álvaro Gómez-Luengo
- Department of Systems Biology, Centro Nacional de Biotecnología, CSIC, Madrid, Spain
- Interdisciplinary Platform for Sustainable Plastics towards a Circular Economy-Spanish National Research Council (SusPlast-CSIC), Madrid, Spain
| | - Ryan Kniewel
- Microbial and Plant Biotechnology Department, Biological Research Center-Margarita Salas, CSIC, Madrid, Spain
| | - Igor Martínez
- Department of Systems Biology, Centro Nacional de Biotecnología, CSIC, Madrid, Spain
| | - Sandra Sordon
- Wrocław University of Environmental and Life Sciences, Department of Food Chemistry and Biocatalysis, Norwida 25, 50-375, Wrocław, Poland
| | - Aleksandra Wilczak
- Wrocław University of Environmental and Life Sciences, Department of Food Chemistry and Biocatalysis, Norwida 25, 50-375, Wrocław, Poland
| | - Sergio Salgado
- Interdisciplinary Platform for Sustainable Plastics towards a Circular Economy-Spanish National Research Council (SusPlast-CSIC), Madrid, Spain
- Microbial and Plant Biotechnology Department, Biological Research Center-Margarita Salas, CSIC, Madrid, Spain
| | - Ewa Huszcza
- Wrocław University of Environmental and Life Sciences, Department of Food Chemistry and Biocatalysis, Norwida 25, 50-375, Wrocław, Poland
| | - Jarosław Popłoński
- Wrocław University of Environmental and Life Sciences, Department of Food Chemistry and Biocatalysis, Norwida 25, 50-375, Wrocław, Poland
| | - Auxiliadora Prieto
- Interdisciplinary Platform for Sustainable Plastics towards a Circular Economy-Spanish National Research Council (SusPlast-CSIC), Madrid, Spain
- Microbial and Plant Biotechnology Department, Biological Research Center-Margarita Salas, CSIC, Madrid, Spain
| | - Juan Nogales
- Department of Systems Biology, Centro Nacional de Biotecnología, CSIC, Madrid, Spain
- Interdisciplinary Platform for Sustainable Plastics towards a Circular Economy-Spanish National Research Council (SusPlast-CSIC), Madrid, Spain
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19
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Kreis E, König K, Misir M, Niemeyer J, Sommer F, Schroda M. TurboID reveals the proxiomes of Chlamydomonas proteins involved in thylakoid biogenesis and stress response. PLANT PHYSIOLOGY 2023; 193:1772-1796. [PMID: 37310689 PMCID: PMC10602608 DOI: 10.1093/plphys/kiad335] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/03/2023] [Revised: 04/24/2023] [Accepted: 05/04/2023] [Indexed: 06/14/2023]
Abstract
In Chlamydomonas (Chlamydomonas reinhardtii), the VESICLE-INDUCING PROTEIN IN PLASTIDS 1 and 2 (VIPP1 and VIPP2) play roles in the sensing and coping with membrane stress and in thylakoid membrane biogenesis. To gain more insight into these processes, we aimed to identify proteins interacting with VIPP1/2 in the chloroplast and chose proximity labeling (PL) for this purpose. We used the transient interaction between the nucleotide exchange factor CHLOROPLAST GRPE HOMOLOG 1 (CGE1) and the stromal HEAT SHOCK PROTEIN 70B (HSP70B) as test system. While PL with APEX2 and BioID proved to be inefficient, TurboID resulted in substantial biotinylation in vivo. TurboID-mediated PL with VIPP1/2 as baits under ambient and H2O2 stress conditions confirmed known interactions of VIPP1 with VIPP2, HSP70B, and the CHLOROPLAST DNAJ HOMOLOG 2 (CDJ2). Proteins identified in the VIPP1/2 proxiomes can be grouped into proteins involved in the biogenesis of thylakoid membrane complexes and the regulation of photosynthetic electron transport, including PROTON GRADIENT REGULATION 5-LIKE 1 (PGRL1). A third group comprises 11 proteins of unknown function whose genes are upregulated under chloroplast stress conditions. We named them VIPP PROXIMITY LABELING (VPL). In reciprocal experiments, we confirmed VIPP1 in the proxiomes of VPL2 and PGRL1. Our results demonstrate the robustness of TurboID-mediated PL for studying protein interaction networks in the chloroplast of Chlamydomonas and pave the way for analyzing functions of VIPPs in thylakoid biogenesis and stress responses.
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Affiliation(s)
- Elena Kreis
- Molekulare Biotechnologie & Systembiologie, RPTU Kaiserslautern-Landau, Paul-Ehrlich Straße 23, D-67663 Kaiserslautern, Germany
| | - Katharina König
- Molekulare Biotechnologie & Systembiologie, RPTU Kaiserslautern-Landau, Paul-Ehrlich Straße 23, D-67663 Kaiserslautern, Germany
| | - Melissa Misir
- Molekulare Biotechnologie & Systembiologie, RPTU Kaiserslautern-Landau, Paul-Ehrlich Straße 23, D-67663 Kaiserslautern, Germany
| | - Justus Niemeyer
- Molekulare Biotechnologie & Systembiologie, RPTU Kaiserslautern-Landau, Paul-Ehrlich Straße 23, D-67663 Kaiserslautern, Germany
| | - Frederik Sommer
- Molekulare Biotechnologie & Systembiologie, RPTU Kaiserslautern-Landau, Paul-Ehrlich Straße 23, D-67663 Kaiserslautern, Germany
| | - Michael Schroda
- Molekulare Biotechnologie & Systembiologie, RPTU Kaiserslautern-Landau, Paul-Ehrlich Straße 23, D-67663 Kaiserslautern, Germany
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20
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Piepers M, Erbstein K, Reyes-Hernandez J, Song C, Tessi T, Petrasiunaite V, Faerber N, Distel K, Maizel A. GreenGate 2.0: Backwards compatible addons for assembly of complex transcriptional units and their stacking with GreenGate. PLoS One 2023; 18:e0290097. [PMID: 37682951 PMCID: PMC10490876 DOI: 10.1371/journal.pone.0290097] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2023] [Accepted: 08/27/2023] [Indexed: 09/10/2023] Open
Abstract
Molecular cloning is a crucial technique in genetic engineering that enables the precise design of synthetic transcriptional units (TUs) and the manipulation of genomes. GreenGate and several other modular molecular cloning systems were developed about ten years ago and are widely used in plant research. All these systems define grammars for assembling transcriptional units from building blocks, cloned as Level 0 modules flanked by four-base pair overhangs and recognition sites for a particular Type IIs endonuclease. Modules are efficiently assembled into Level 1 TUs in a hierarchical assembly process, and Level 2 multigene constructs are assembled by stacking Level 1 TUs. GreenGate is highly popular but has three main limitations. First, using ad-hoc overhangs added by PCR and classical restriction/ligation prevents the efficient use of a one-pot, one-step reaction to generate entry clones and domesticate internal sites; second, a Level 1 TU is assembled from a maximum of six modules, which may be limiting for applications such as multiplex genome editing; third, the generation of Level 2 assemblies is sequential and inefficient. GreenGate 2.0 (GG2.0) expands GreenGate features. It introduces additional overhangs, allowing for the combination of up to 12 Level 0 modules in a Level 1 TU. It includes a Universal Entry Generator plasmid (pUEG) to streamline the generation of Level 0 modules. GG2.0 introduces GreenBraid, a convenient method for stacking transcriptional units iteratively for multigene assemblies. Importantly, GG2.0 is backwards compatible with most existing GreenGate modules. Additionally, GG2.0 includes Level 0 modules for multiplex expression of guide RNAs for CRISPR/Cas9 genome editing and pre-assembled Level 1 vectors for dexamethasone-inducible gene expression and ubiquitous expression of plasma membrane and nuclear fluorescent markers. GG2.0 streamlines and increases the versatility of assembling complex transcriptional units and their combination.
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Affiliation(s)
- Marcel Piepers
- Center for Organismal Studies (COS), University of Heidelberg, Heidelberg, Germany
| | - Katarina Erbstein
- Center for Organismal Studies (COS), University of Heidelberg, Heidelberg, Germany
| | | | - Changzheng Song
- Center for Organismal Studies (COS), University of Heidelberg, Heidelberg, Germany
| | - Tomas Tessi
- Center for Organismal Studies (COS), University of Heidelberg, Heidelberg, Germany
| | - Vesta Petrasiunaite
- Center for Organismal Studies (COS), University of Heidelberg, Heidelberg, Germany
| | - Naja Faerber
- Center for Organismal Studies (COS), University of Heidelberg, Heidelberg, Germany
| | - Kathrin Distel
- Center for Organismal Studies (COS), University of Heidelberg, Heidelberg, Germany
| | - Alexis Maizel
- Center for Organismal Studies (COS), University of Heidelberg, Heidelberg, Germany
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21
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Wang Y, Demirer GS. Synthetic biology for plant genetic engineering and molecular farming. Trends Biotechnol 2023; 41:1182-1198. [PMID: 37012119 DOI: 10.1016/j.tibtech.2023.03.007] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2023] [Revised: 03/03/2023] [Accepted: 03/09/2023] [Indexed: 04/03/2023]
Abstract
Many efforts have been put into engineering plants to improve crop yields and stress tolerance and boost the bioproduction of valuable molecules. Yet, our capabilities are still limited due to the lack of well-characterized genetic building blocks and resources for precise manipulation and given the inherently challenging properties of plant tissues. Advancements in plant synthetic biology can overcome these bottlenecks and release the full potential of engineered plants. In this review, we first discuss the recently developed plant synthetic elements from single parts to advanced circuits, software, and hardware tools expediting the engineering cycle. Next, we survey the advancements in plant biotechnology enabled by these recent resources. We conclude the review with outstanding challenges and future directions of plant synthetic biology.
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Affiliation(s)
- Yunqing Wang
- Department of Bioengineering, California Institute of Technology, Pasadena, CA 91125, USA
| | - Gozde S Demirer
- Department of Chemical Engineering, California Institute of Technology, Pasadena, CA 91125, USA.
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22
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Boisset ND, Favoino G, Meloni M, Jomat L, Cassier-Chauvat C, Zaffagnini M, Lemaire SD, Crozet P. Phosphoribulokinase abundance is not limiting the Calvin-Benson-Bassham cycle in Chlamydomonas reinhardtii. FRONTIERS IN PLANT SCIENCE 2023; 14:1230723. [PMID: 37719215 PMCID: PMC10501310 DOI: 10.3389/fpls.2023.1230723] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 05/29/2023] [Accepted: 07/21/2023] [Indexed: 09/19/2023]
Abstract
Improving photosynthetic efficiency in plants and microalgae is of utmost importance to support the growing world population and to enable the bioproduction of energy and chemicals. Limitations in photosynthetic light conversion efficiency can be directly attributed to kinetic bottlenecks within the Calvin-Benson-Bassham cycle (CBBC) responsible for carbon fixation. A better understanding of these bottlenecks in vivo is crucial to overcome these limiting factors through bio-engineering. The present study is focused on the analysis of phosphoribulokinase (PRK) in the unicellular green alga Chlamydomonas reinhardtii. We have characterized a PRK knock-out mutant strain and showed that in the absence of PRK, Chlamydomonas cannot grow photoautotrophically while functional complementation with a synthetic construct allowed restoration of photoautotrophy. Nevertheless, using standard genetic elements, the expression of PRK was limited to 40% of the reference level in complemented strains and could not restore normal growth in photoautotrophic conditions suggesting that the CBBC is limited. We were subsequently able to overcome this initial limitation by improving the design of the transcriptional unit expressing PRK using diverse combinations of DNA parts including PRK endogenous promoter and introns. This enabled us to obtain strains with PRK levels comparable to the reference strain and even overexpressing strains. A collection of strains with PRK levels between 16% and 250% of WT PRK levels was generated and characterized. Immunoblot and growth assays revealed that a PRK content of ≈86% is sufficient to fully restore photoautotrophic growth. This result suggests that PRK is present in moderate excess in Chlamydomonas. Consistently, the overexpression of PRK did not increase photosynthetic growth indicating that that the endogenous level of PRK in Chlamydomonas is not limiting the Calvin-Benson-Bassham cycle under optimal conditions.
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Affiliation(s)
- Nicolas D. Boisset
- Laboratoire de Biologie Computationnelle et Quantitative, Institut de Biologie Parie-Seine, Sorbonne Université, CNRS, UMR 7238, Paris, France
- Laboratoire de Biologie Moléculaire et Cellulaire des Eucaryotes, Institut de Biologie Physico-Chimique, Sorbonne Université, CNRS, UMR 8226, Paris, France
- Doctoral School of Plant Sciences, Université Paris-Saclay, Saint-Aubin, France
| | - Giusi Favoino
- Laboratoire de Biologie Computationnelle et Quantitative, Institut de Biologie Parie-Seine, Sorbonne Université, CNRS, UMR 7238, Paris, France
| | - Maria Meloni
- Department of Pharmacy and Biotechnologies, University of Bologna, Bologna, Italy
| | - Lucile Jomat
- Laboratoire de Biologie Computationnelle et Quantitative, Institut de Biologie Parie-Seine, Sorbonne Université, CNRS, UMR 7238, Paris, France
| | - Corinne Cassier-Chauvat
- Université Paris-Saclay, CEA, CNRS, Institute for Integrative Biology of the Cell (I2BC), UMR 9198, Gif-sur-Yvette, France
| | - Mirko Zaffagnini
- Department of Pharmacy and Biotechnologies, University of Bologna, Bologna, Italy
| | - Stéphane D. Lemaire
- Laboratoire de Biologie Computationnelle et Quantitative, Institut de Biologie Parie-Seine, Sorbonne Université, CNRS, UMR 7238, Paris, France
- Laboratoire de Biologie Moléculaire et Cellulaire des Eucaryotes, Institut de Biologie Physico-Chimique, Sorbonne Université, CNRS, UMR 8226, Paris, France
| | - Pierre Crozet
- Laboratoire de Biologie Computationnelle et Quantitative, Institut de Biologie Parie-Seine, Sorbonne Université, CNRS, UMR 7238, Paris, France
- Laboratoire de Biologie Moléculaire et Cellulaire des Eucaryotes, Institut de Biologie Physico-Chimique, Sorbonne Université, CNRS, UMR 8226, Paris, France
- Polytech-Sorbonne, Sorbonne Université, Paris, France
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23
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Yang JS, Reyna-Llorens I. Plant synthetic biology: exploring the frontiers of sustainable agriculture and fundamental plant biology. JOURNAL OF EXPERIMENTAL BOTANY 2023; 74:3787-3790. [PMID: 37462736 DOI: 10.1093/jxb/erad220] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/21/2023]
Affiliation(s)
- Jae-Seong Yang
- Centre for Research in Agricultural Genomics (CRAG), CSIC-IRTA-UAB-UB, Campus UAB, Bellaterra, Barcelona, Spain
| | - Ivan Reyna-Llorens
- Centre for Research in Agricultural Genomics (CRAG), CSIC-IRTA-UAB-UB, Campus UAB, Bellaterra, Barcelona, Spain
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24
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Kocaoglan EG, Radhakrishnan D, Nakayama N. Synthetic developmental biology: molecular tools to re-design plant shoots and roots. JOURNAL OF EXPERIMENTAL BOTANY 2023; 74:3864-3876. [PMID: 37155965 PMCID: PMC10826796 DOI: 10.1093/jxb/erad169] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/18/2023] [Accepted: 05/04/2023] [Indexed: 05/10/2023]
Abstract
Plant morphology and anatomy strongly influence agricultural yield. Crop domestication has strived for desirable growth and developmental traits, such as larger and more fruits and semi-dwarf architecture. Genetic engineering has accelerated rational, purpose-driven engineering of plant development, but it can be unpredictable. Developmental pathways are complex and riddled with environmental and hormonal inputs, as well as feedback and feedforward interactions, which occur at specific times and places in a growing multicellular organism. Rational modification of plant development would probably benefit from precision engineering based on synthetic biology approaches. This review outlines recently developed synthetic biology technologies for plant systems and highlights their potential for engineering plant growth and development. Streamlined and high-capacity genetic construction methods (Golden Gate DNA Assembly frameworks and toolkits) allow fast and variation-series cloning of multigene transgene constructs. This, together with a suite of gene regulation tools (e.g. cell type-specific promoters, logic gates, and multiplex regulation systems), is starting to enable developmental pathway engineering with predictable outcomes in model plant and crop species.
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Affiliation(s)
- Elif Gediz Kocaoglan
- Department of Bioengineering, Centre for Synthetic Biology, Imperial College London, London SW7 2AZ, UK
| | - Dhanya Radhakrishnan
- Department of Bioengineering, Centre for Synthetic Biology, Imperial College London, London SW7 2AZ, UK
| | - Naomi Nakayama
- Department of Bioengineering, Centre for Synthetic Biology, Imperial College London, London SW7 2AZ, UK
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25
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Zhou A, Kirkpatrick LD, Ornelas IJ, Washington LJ, Hummel NFC, Gee CW, Tang SN, Barnum CR, Scheller HV, Shih PM. A Suite of Constitutive Promoters for Tuning Gene Expression in Plants. ACS Synth Biol 2023; 12:1533-1545. [PMID: 37083366 DOI: 10.1021/acssynbio.3c00075] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/22/2023]
Abstract
The need for convenient tools to express transgenes over a large dynamic range is pervasive throughout plant synthetic biology; however, current efforts are largely limited by the heavy reliance on a small set of strong promoters, precluding more nuanced and refined engineering endeavors in planta. To address this technical gap, we characterize a suite of constitutive promoters that span a wide range of transcriptional levels and develop a GoldenGate-based plasmid toolkit named PCONS, optimized for versatile cloning and rapid testing of transgene expression at varying strengths. We demonstrate how easy access to a stepwise gradient of expression levels can be used for optimizing synthetic transcriptional systems and the production of small molecules in planta. We also systematically investigate the potential of using PCONS as an internal standard in plant biology experimental design, establishing the best practices for signal normalization in experiments. Although our library has primarily been developed for optimizing expression in N. benthamiana, we demonstrate the translatability of our promoters across distantly related species using a multiplexed reporter assay with barcoded transcripts. Our findings showcase the advantages of the PCONS library as an invaluable toolkit for plant synthetic biology.
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Affiliation(s)
- Andy Zhou
- Department of Plant and Microbial Biology, University of California, Berkeley, Berkeley, California 94720, United States
- Feedstocks Division, Joint BioEnergy Institute, Emeryville, California 94608, United States
- Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, California 94705, United States
| | - Liam D Kirkpatrick
- Department of Plant and Microbial Biology, University of California, Berkeley, Berkeley, California 94720, United States
- Feedstocks Division, Joint BioEnergy Institute, Emeryville, California 94608, United States
- Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, California 94705, United States
| | - Izaiah J Ornelas
- Feedstocks Division, Joint BioEnergy Institute, Emeryville, California 94608, United States
- Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, California 94705, United States
- Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, California 94720, United States
| | - Lorenzo J Washington
- Department of Plant and Microbial Biology, University of California, Berkeley, Berkeley, California 94720, United States
- Feedstocks Division, Joint BioEnergy Institute, Emeryville, California 94608, United States
- Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, California 94705, United States
| | - Niklas F C Hummel
- Feedstocks Division, Joint BioEnergy Institute, Emeryville, California 94608, United States
- Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, California 94705, United States
| | - Christopher W Gee
- Feedstocks Division, Joint BioEnergy Institute, Emeryville, California 94608, United States
- Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, California 94705, United States
| | - Sophia N Tang
- Feedstocks Division, Joint BioEnergy Institute, Emeryville, California 94608, United States
- Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, California 94705, United States
- Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, California 94720, United States
| | - Collin R Barnum
- Biochemistry, Molecular, Cellular and Developmental Biology Graduate Group, University of California, Davis, California 95616, United States
| | - Henrik V Scheller
- Department of Plant and Microbial Biology, University of California, Berkeley, Berkeley, California 94720, United States
- Feedstocks Division, Joint BioEnergy Institute, Emeryville, California 94608, United States
- Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, California 94705, United States
| | - Patrick M Shih
- Department of Plant and Microbial Biology, University of California, Berkeley, Berkeley, California 94720, United States
- Feedstocks Division, Joint BioEnergy Institute, Emeryville, California 94608, United States
- Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, California 94705, United States
- Innovative Genomics Institute, University of California, Berkeley, California 94720, United States
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26
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Singh P, Stevenson SR, Dickinson PJ, Reyna-Llorens I, Tripathi A, Reeves G, Schreier TB, Hibberd JM. C 4 gene induction during de-etiolation evolved through changes in cis to allow integration with ancestral C 3 gene regulatory networks. SCIENCE ADVANCES 2023; 9:eade9756. [PMID: 36989352 PMCID: PMC10058240 DOI: 10.1126/sciadv.ade9756] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/23/2022] [Accepted: 03/01/2023] [Indexed: 06/19/2023]
Abstract
C4 photosynthesis has evolved by repurposing enzymes found in C3 plants. Compared with the ancestral C3 state, accumulation of C4 cycle proteins is enhanced. We used de-etiolation of C4 Gynandropsis gynandra and C3 Arabidopsis thaliana to understand this process. C4 gene expression and chloroplast biogenesis in G. gynandra were tightly coordinated. Although C3 and C4 photosynthesis genes showed similar induction patterns, in G. gynandra, C4 genes were more strongly induced than orthologs from A. thaliana. In vivo binding of TGA and homeodomain as well as light-responsive elements such as G- and I-box motifs were associated with the rapid increase in transcripts of C4 genes. Deletion analysis confirmed that regions containing G- and I-boxes were necessary for high expression. The data support a model in which accumulation of transcripts derived from C4 photosynthesis genes in C4 leaves is enhanced because modifications in cis allowed integration into ancestral transcriptional networks.
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27
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Förster B, Rourke LM, Weerasooriya HN, Pabuayon ICM, Rolland V, Au EK, Bala S, Bajsa-Hirschel J, Kaines S, Kasili R, LaPlace L, Machingura MC, Massey B, Rosati VC, Stuart-Williams H, Badger MR, Price GD, Moroney JV. The Chlamydomonas reinhardtii chloroplast envelope protein LCIA transports bicarbonate in planta. JOURNAL OF EXPERIMENTAL BOTANY 2023:erad116. [PMID: 36987927 DOI: 10.1093/jxb/erad116] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/10/2023] [Indexed: 06/19/2023]
Abstract
LCIA is a chloroplast envelope protein associated with the CO2 concentrating mechanism of the green alga Chlamydomonas reinhardtii. LCIA is postulated to be a HCO3- channel, but previous studies were unable to show that LCIA was actively transporting bicarbonate in planta. Therefore, LCIA activity was investigated more directly in two heterologous systems: an E. coli mutant (DCAKO) lacking both native carbonic anhydrases and an Arabidopsis mutant (βca5) missing the plastid carbonic anhydrase βCA5. Both DCAKO and βca5 cannot grow in ambient CO2 conditions, as they lack carbonic anhydrase-catalyzed production of the necessary HCO3- concentration for lipid and nucleic acid biosynthesis. Expression of LCIA restored growth in both systems in ambient CO2 conditions, which strongly suggests that LCIA is facilitating HCO3- uptake in each system. To our knowledge, this is the first direct evidence that LCIA moves HCO3- across membranes in bacteria and plants. Furthermore, the βca5 plant bioassay used in this study is the first system for testing HCO3- transport activity in planta, an experimental breakthrough that will be valuable for future studies aimed at improving the photosynthetic efficiency of crop plants using components from algal CO2 concentrating mechanisms.
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Affiliation(s)
- Britta Förster
- The Australian National University, Canberra, ACT 2600, Australia
| | - Loraine M Rourke
- The Australian National University, Canberra, ACT 2600, Australia
| | - Hiruni N Weerasooriya
- Department of Biological Sciences, Louisiana State University, Baton Rouge, LA 70803, USA
| | - Isaiah C M Pabuayon
- Department of Biological Sciences, Louisiana State University, Baton Rouge, LA 70803, USA
| | - Vivien Rolland
- CSIRO Agriculture and Food, Canberra, ACT 2601, Australia
| | - Eng Kee Au
- The Australian National University, Canberra, ACT 2600, Australia
| | - Soumi Bala
- The Australian National University, Canberra, ACT 2600, Australia
| | - Joanna Bajsa-Hirschel
- Natural Products Utilization Research Unit, United States Department of Agriculture, University, MS 38677, USA
| | - Sarah Kaines
- The Australian National University, Canberra, ACT 2600, Australia
| | - Remmy Kasili
- Department of Biological Sciences, Louisiana State University, Baton Rouge, LA 70803, USA
| | - Lillian LaPlace
- Department of Biological Sciences, Louisiana State University, Baton Rouge, LA 70803, USA
| | | | - Baxter Massey
- The Australian National University, Canberra, ACT 2600, Australia
| | - Viviana C Rosati
- Department of Biology, Centre for Novel Agricultural Products (CNAP), University of York, Wentworth Way, York YO10 5DD, UK
| | | | - Murray R Badger
- The Australian National University, Canberra, ACT 2600, Australia
| | - G Dean Price
- The Australian National University, Canberra, ACT 2600, Australia
| | - James V Moroney
- Department of Biological Sciences, Louisiana State University, Baton Rouge, LA 70803, USA
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28
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Chamness JC, Kumar J, Cruz AJ, Rhuby E, Holum MJ, Cody JP, Tibebu R, Gamo ME, Starker CG, Zhang F, Voytas DF. An extensible vector toolkit and parts library for advanced engineering of plant genomes. THE PLANT GENOME 2023:e20312. [PMID: 36896468 DOI: 10.1002/tpg2.20312] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/04/2022] [Accepted: 01/15/2023] [Indexed: 06/18/2023]
Abstract
Plant biotechnology is rife with new advances in transformation and genome engineering techniques. A common requirement for delivery and coordinated expression in plant cells, however, places the design and assembly of transformation constructs at a crucial juncture as desired reagent suites grow more complex. Modular cloning principles have simplified some aspects of vector design, yet many important components remain unavailable or poorly adapted for rapid implementation in biotechnology research. Here, we describe a universal Golden Gate cloning toolkit for vector construction. The toolkit chassis is compatible with the widely accepted Phytobrick standard for genetic parts, and supports assembly of arbitrarily complex T-DNAs through improved capacity, positional flexibility, and extensibility in comparison to extant kits. We also provision a substantial library of newly adapted Phytobricks, including regulatory elements for monocot and dicot gene expression, and coding sequences for genes of interest such as reporters, developmental regulators, and site-specific recombinases. Finally, we use a series of dual-luciferase assays to measure contributions to expression from promoters, terminators, and from cross-cassette interactions attributable to enhancer elements in certain promoters. Taken together, these publicly available cloning resources can greatly accelerate the testing and deployment of new tools for plant engineering.
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Affiliation(s)
- James C Chamness
- Department of Genetics, Cell Biology and Development, College of Biological Sciences, University of Minnesota, Minneapolis, MN, USA
- Center for Precision Plant Genomics, University of Minnesota, Minneapolis, MN, USA
- Center for Genome Engineering, University of Minnesota, Minneapolis, MN, USA
| | - Jitesh Kumar
- Center for Precision Plant Genomics, University of Minnesota, Minneapolis, MN, USA
- Department of Plant and Microbial Biology, College of Biological Sciences, University of Minnesota, Minneapolis, MN, USA
| | - Anna J Cruz
- Department of Genetics, Cell Biology and Development, College of Biological Sciences, University of Minnesota, Minneapolis, MN, USA
- Center for Precision Plant Genomics, University of Minnesota, Minneapolis, MN, USA
| | - Elissa Rhuby
- Department of Genetics, Cell Biology and Development, College of Biological Sciences, University of Minnesota, Minneapolis, MN, USA
- Center for Precision Plant Genomics, University of Minnesota, Minneapolis, MN, USA
| | - Mason J Holum
- Department of Genetics, Cell Biology and Development, College of Biological Sciences, University of Minnesota, Minneapolis, MN, USA
- Center for Precision Plant Genomics, University of Minnesota, Minneapolis, MN, USA
| | - Jon P Cody
- Department of Genetics, Cell Biology and Development, College of Biological Sciences, University of Minnesota, Minneapolis, MN, USA
- Center for Precision Plant Genomics, University of Minnesota, Minneapolis, MN, USA
- Center for Genome Engineering, University of Minnesota, Minneapolis, MN, USA
| | - Redeat Tibebu
- Center for Precision Plant Genomics, University of Minnesota, Minneapolis, MN, USA
- Department of Plant and Microbial Biology, College of Biological Sciences, University of Minnesota, Minneapolis, MN, USA
| | - Maria Elena Gamo
- Department of Genetics, Cell Biology and Development, College of Biological Sciences, University of Minnesota, Minneapolis, MN, USA
- Center for Precision Plant Genomics, University of Minnesota, Minneapolis, MN, USA
- Center for Genome Engineering, University of Minnesota, Minneapolis, MN, USA
| | - Colby G Starker
- Department of Genetics, Cell Biology and Development, College of Biological Sciences, University of Minnesota, Minneapolis, MN, USA
- Center for Precision Plant Genomics, University of Minnesota, Minneapolis, MN, USA
- Center for Genome Engineering, University of Minnesota, Minneapolis, MN, USA
| | - Feng Zhang
- Center for Precision Plant Genomics, University of Minnesota, Minneapolis, MN, USA
- Center for Genome Engineering, University of Minnesota, Minneapolis, MN, USA
- Department of Plant and Microbial Biology, College of Biological Sciences, University of Minnesota, Minneapolis, MN, USA
| | - Daniel F Voytas
- Department of Genetics, Cell Biology and Development, College of Biological Sciences, University of Minnesota, Minneapolis, MN, USA
- Center for Precision Plant Genomics, University of Minnesota, Minneapolis, MN, USA
- Center for Genome Engineering, University of Minnesota, Minneapolis, MN, USA
- Department of Plant and Microbial Biology, College of Biological Sciences, University of Minnesota, Minneapolis, MN, USA
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29
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Synthetic memory circuits for stable cell reprogramming in plants. Nat Biotechnol 2022; 40:1862-1872. [PMID: 35788565 DOI: 10.1038/s41587-022-01383-2] [Citation(s) in RCA: 33] [Impact Index Per Article: 16.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2022] [Accepted: 06/01/2022] [Indexed: 01/14/2023]
Abstract
Plant biotechnology predominantly relies on a restricted set of genetic parts with limited capability to customize spatiotemporal and conditional expression patterns. Synthetic gene circuits have the potential to integrate multiple customizable input signals through a processing unit constructed from biological parts to produce a predictable and programmable output. Here we present a suite of functional recombinase-based gene circuits for use in plants. We first established a range of key gene circuit components compatible with plant cell functionality. We then used these to develop a range of operational logic gates using the identify function (activation) and negation function (repression) in Arabidopsis protoplasts and in vivo, demonstrating their utility for programmable manipulation of transcriptional activity in a complex multicellular organism. Specifically, using recombinases and plant control elements, we activated transgenes in YES, OR and AND gates and repressed them in NOT, NOR and NAND gates; we also implemented the A NIMPLY B gate that combines activation and repression. Through use of genetic recombination, these circuits create stable long-term changes in expression and recording of past stimuli. This highly compact programmable gene circuit platform provides new capabilities for engineering sophisticated transcriptional programs and previously unrealized traits into plants.
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30
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Weerasooriya HN, DiMario RJ, Rosati VC, Rai AK, LaPlace LM, Filloon VD, Longstreth DJ, Moroney JV. Arabidopsis plastid carbonic anhydrase βCA5 is important for normal plant growth. PLANT PHYSIOLOGY 2022; 190:2173-2186. [PMID: 36149291 PMCID: PMC9706431 DOI: 10.1093/plphys/kiac451] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/05/2022] [Accepted: 09/07/2022] [Indexed: 05/19/2023]
Abstract
Carbonic anhydrases (CAs) are zinc-metalloenzymes that catalyze the interconversion of CO2 and HCO3-. In heterotrophic organisms, CAs provide HCO3- for metabolic pathways requiring a carboxylation step. Arabidopsis (Arabidopsis thaliana) has 14 α- and β-type CAs, two of which are plastid CAs designated as βCA1 and βCA5. To study their physiological properties, we obtained knock-out (KO) lines for βCA1 (SALK_106570) and βCA5 (SALK_121932). These mutant lines were confirmed by genomic PCR, RT-PCR, and immunoblotting. While βca1 KO plants grew normally, growth of βca5 KO plants was stunted under ambient CO2 conditions of 400 µL L-1; high CO2 conditions (30,000 µL L-1) partially rescued their growth. These results were surprising, as βCA1 is more abundant than βCA5 in leaves. However, tissue expression patterns of these genes indicated that βCA1 is expressed only in shoot tissue, while βCA5 is expressed throughout the plant. We hypothesize that βCA5 compensates for loss of βCA1 but, owing to its expression being limited to leaves, βCA1 cannot compensate for loss of βCA5. We also demonstrate that βCA5 supplies HCO3- required for anaplerotic pathways that take place in plastids, such as fatty acid biosynthesis.
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Affiliation(s)
- Hiruni N Weerasooriya
- Department of Biological Sciences, Louisiana State University, Baton Rouge, Louisiana 70803, USA
| | - Robert J DiMario
- School of Biological Sciences, Washington State University, Pullman, Washington 99164, USA
| | - Viviana C Rosati
- Department of Biology, Centre for Novel Agricultural Products (CNAP), University of York, York YO10 5DD, UK
| | - Ashwani K Rai
- Department of Biological Sciences, Louisiana State University, Baton Rouge, Louisiana 70803, USA
| | - Lillian M LaPlace
- Department of Biological Sciences, Louisiana State University, Baton Rouge, Louisiana 70803, USA
| | - Victoria D Filloon
- Department of Biological Sciences, Louisiana State University, Baton Rouge, Louisiana 70803, USA
| | - David J Longstreth
- Department of Biological Sciences, Louisiana State University, Baton Rouge, Louisiana 70803, USA
| | - James V Moroney
- Department of Biological Sciences, Louisiana State University, Baton Rouge, Louisiana 70803, USA
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31
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Abstract
The continual demand for specialized molecular cloning techniques that suit a broad range of applications has driven the development of many different cloning strategies. One method that has gained significant traction is Golden Gate assembly, which achieves hierarchical assembly of DNA parts by utilizing Type IIS restriction enzymes to produce user-specified sticky ends on cut DNA fragments. This technique has been modularized and standardized, and includes different subfamilies of methods, the most widely adopted of which are the MoClo and Golden Braid standards. Moreover, specialized toolboxes tailored to specific applications or organisms are also available. Still, the quantity and range of assembly methods can constitute a barrier to adoption for new users, and even experienced scientists might find it difficult to discern which tools are best suited toward their goals. In this review, we provide a beginner-friendly guide to Golden Gate assembly, compare the different available standards, and detail the specific features and quirks of commonly used toolboxes. We also provide an update on the state-of-the-art in Golden Gate technology, discussing recent advances and challenges to inform existing users and promote standard practices.
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Affiliation(s)
- Jasmine
E. Bird
- School
of Computing, Faculty of Science Agriculture and Engineering, Newcastle University, Newcastle upon Tyne, NE1 7RU, United Kingdom
| | - Jon Marles-Wright
- Biosciences
Institute, Faculty of Medical Sciences, Newcastle University, Newcastle
upon Tyne, NE2 4HH, United
Kingdom,
| | - Andrea Giachino
- Biosciences
Institute, Faculty of Medical Sciences, Newcastle University, Newcastle
upon Tyne, NE2 4HH, United
Kingdom,School
of Science, Engineering & Environment, University of Salford, Salford, M5 4NT, United Kingdom
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32
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Li XR, Sun J, Albinsky D, Zarrabian D, Hull R, Lee T, Jarratt-Barnham E, Chiu CH, Jacobsen A, Soumpourou E, Albanese A, Kohlen W, Luginbuehl LH, Guillotin B, Lawrensen T, Lin H, Murray J, Wallington E, Harwood W, Choi J, Paszkowski U, Oldroyd GED. Nutrient regulation of lipochitooligosaccharide recognition in plants via NSP1 and NSP2. Nat Commun 2022; 13:6421. [PMID: 36307431 PMCID: PMC9616857 DOI: 10.1038/s41467-022-33908-3] [Citation(s) in RCA: 17] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2022] [Accepted: 10/07/2022] [Indexed: 12/25/2022] Open
Abstract
Many plants associate with arbuscular mycorrhizal fungi for nutrient acquisition, while legumes also associate with nitrogen-fixing rhizobial bacteria. Both associations rely on symbiosis signaling and here we show that cereals can perceive lipochitooligosaccharides (LCOs) for activation of symbiosis signaling, surprisingly including Nod factors produced by nitrogen-fixing bacteria. However, legumes show stringent perception of specifically decorated LCOs, that is absent in cereals. LCO perception in plants is activated by nutrient starvation, through transcriptional regulation of Nodulation Signaling Pathway (NSP)1 and NSP2. These transcription factors induce expression of an LCO receptor and act through the control of strigolactone biosynthesis and the karrikin-like receptor DWARF14-LIKE. We conclude that LCO production and perception is coordinately regulated by nutrient starvation to promote engagement with mycorrhizal fungi. Our work has implications for the use of both mycorrhizal and rhizobial associations for sustainable productivity in cereals.
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Affiliation(s)
- Xin-Ran Li
- grid.5335.00000000121885934Sainsbury Laboratory, University of Cambridge, 47 Bateman Street, Cambridge, CB2 1LR UK
| | - Jongho Sun
- grid.5335.00000000121885934Sainsbury Laboratory, University of Cambridge, 47 Bateman Street, Cambridge, CB2 1LR UK
| | - Doris Albinsky
- grid.5335.00000000121885934Crop Science Centre, University of Cambridge, 93 Lawrence Weaver Road, Cambridge, CB3 0LE UK
| | - Darius Zarrabian
- grid.5335.00000000121885934Crop Science Centre, University of Cambridge, 93 Lawrence Weaver Road, Cambridge, CB3 0LE UK
| | - Raphaella Hull
- grid.5335.00000000121885934Crop Science Centre, University of Cambridge, 93 Lawrence Weaver Road, Cambridge, CB3 0LE UK
| | - Tak Lee
- grid.5335.00000000121885934Sainsbury Laboratory, University of Cambridge, 47 Bateman Street, Cambridge, CB2 1LR UK ,grid.5335.00000000121885934Crop Science Centre, University of Cambridge, 93 Lawrence Weaver Road, Cambridge, CB3 0LE UK
| | - Edwin Jarratt-Barnham
- grid.5335.00000000121885934Crop Science Centre, University of Cambridge, 93 Lawrence Weaver Road, Cambridge, CB3 0LE UK
| | - Chai Hao Chiu
- grid.5335.00000000121885934Crop Science Centre, University of Cambridge, 93 Lawrence Weaver Road, Cambridge, CB3 0LE UK
| | - Amy Jacobsen
- grid.5335.00000000121885934Crop Science Centre, University of Cambridge, 93 Lawrence Weaver Road, Cambridge, CB3 0LE UK
| | - Eleni Soumpourou
- grid.5335.00000000121885934Crop Science Centre, University of Cambridge, 93 Lawrence Weaver Road, Cambridge, CB3 0LE UK
| | - Alessio Albanese
- grid.5335.00000000121885934Crop Science Centre, University of Cambridge, 93 Lawrence Weaver Road, Cambridge, CB3 0LE UK
| | - Wouter Kohlen
- grid.4818.50000 0001 0791 5666Laboratory for Molecular Biology, Wageningen University & Research, Droevendaalsesteeg 1, 6708 PB Wageningen, the Netherlands
| | - Leonie H. Luginbuehl
- grid.14830.3e0000 0001 2175 7246John Innes Centre, Norwich Research Park, Norwich, NR4 7UH UK
| | - Bruno Guillotin
- grid.503344.50000 0004 0445 6769Laboratoire de Recherche en Sciences Végétales, Université de Toulouse, CNRS, UPS, Castanet-Tolosan, France ,grid.137628.90000 0004 1936 8753Present Address: NYU-Center of Genomic and System Biology, 12 Waverly Place, New York, NY USA
| | - Tom Lawrensen
- grid.14830.3e0000 0001 2175 7246John Innes Centre, Norwich Research Park, Norwich, NR4 7UH UK
| | - Hui Lin
- grid.14830.3e0000 0001 2175 7246John Innes Centre, Norwich Research Park, Norwich, NR4 7UH UK
| | - Jeremy Murray
- grid.14830.3e0000 0001 2175 7246John Innes Centre, Norwich Research Park, Norwich, NR4 7UH UK
| | - Emma Wallington
- grid.17595.3f0000 0004 0383 6532NIAB, 93 Lawrence Weaver Road, Cambridge, CB3 0LE UK
| | - Wendy Harwood
- grid.14830.3e0000 0001 2175 7246John Innes Centre, Norwich Research Park, Norwich, NR4 7UH UK
| | - Jeongmin Choi
- grid.5335.00000000121885934Crop Science Centre, University of Cambridge, 93 Lawrence Weaver Road, Cambridge, CB3 0LE UK
| | - Uta Paszkowski
- grid.5335.00000000121885934Crop Science Centre, University of Cambridge, 93 Lawrence Weaver Road, Cambridge, CB3 0LE UK
| | - Giles E. D. Oldroyd
- grid.5335.00000000121885934Sainsbury Laboratory, University of Cambridge, 47 Bateman Street, Cambridge, CB2 1LR UK ,grid.5335.00000000121885934Crop Science Centre, University of Cambridge, 93 Lawrence Weaver Road, Cambridge, CB3 0LE UK
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33
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Bowman JL, Arteaga-Vazquez M, Berger F, Briginshaw LN, Carella P, Aguilar-Cruz A, Davies KM, Dierschke T, Dolan L, Dorantes-Acosta AE, Fisher TJ, Flores-Sandoval E, Futagami K, Ishizaki K, Jibran R, Kanazawa T, Kato H, Kohchi T, Levins J, Lin SS, Nakagami H, Nishihama R, Romani F, Schornack S, Tanizawa Y, Tsuzuki M, Ueda T, Watanabe Y, Yamato KT, Zachgo S. The renaissance and enlightenment of Marchantia as a model system. THE PLANT CELL 2022; 34:3512-3542. [PMID: 35976122 PMCID: PMC9516144 DOI: 10.1093/plcell/koac219] [Citation(s) in RCA: 26] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/08/2021] [Accepted: 06/21/2022] [Indexed: 05/07/2023]
Abstract
The liverwort Marchantia polymorpha has been utilized as a model for biological studies since the 18th century. In the past few decades, there has been a Renaissance in its utilization in genomic and genetic approaches to investigating physiological, developmental, and evolutionary aspects of land plant biology. The reasons for its adoption are similar to those of other genetic models, e.g. simple cultivation, ready access via its worldwide distribution, ease of crossing, facile genetics, and more recently, efficient transformation, genome editing, and genomic resources. The haploid gametophyte dominant life cycle of M. polymorpha is conducive to forward genetic approaches. The lack of ancient whole-genome duplications within liverworts facilitates reverse genetic approaches, and possibly related to this genomic stability, liverworts possess sex chromosomes that evolved in the ancestral liverwort. As a representative of one of the three bryophyte lineages, its phylogenetic position allows comparative approaches to provide insights into ancestral land plants. Given the karyotype and genome stability within liverworts, the resources developed for M. polymorpha have facilitated the development of related species as models for biological processes lacking in M. polymorpha.
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Affiliation(s)
| | - Mario Arteaga-Vazquez
- Instituto de Biotecnología y Ecología Aplicada, Universidad Veracruzana, Xalapa VER 91090, México
| | - Frederic Berger
- Gregor Mendel Institute (GMI), Austrian Academy of Sciences, Vienna Biocenter (VBC), Vienna 1030, Austria
| | - Liam N Briginshaw
- School of Biological Sciences, Monash University, Melbourne VIC 3800, Australia
- ARC Centre of Excellence for Plant Success in Nature and Agriculture, Monash University, Melbourne VIC 3800, Australia
| | - Philip Carella
- Department of Cell and Developmental Biology, John Innes Centre, Norwich NR4 7UH, UK
| | - Adolfo Aguilar-Cruz
- Instituto de Biotecnología y Ecología Aplicada, Universidad Veracruzana, Xalapa VER 91090, México
| | - Kevin M Davies
- The New Zealand Institute for Plant and Food Research Limited, Palmerston North 4442, New Zealand
| | - Tom Dierschke
- School of Biological Sciences, Monash University, Melbourne VIC 3800, Australia
| | - Liam Dolan
- Gregor Mendel Institute (GMI), Austrian Academy of Sciences, Vienna Biocenter (VBC), Vienna 1030, Austria
| | - Ana E Dorantes-Acosta
- Instituto de Biotecnología y Ecología Aplicada, Universidad Veracruzana, Xalapa VER 91090, México
| | - Tom J Fisher
- School of Biological Sciences, Monash University, Melbourne VIC 3800, Australia
- ARC Centre of Excellence for Plant Success in Nature and Agriculture, Monash University, Melbourne VIC 3800, Australia
| | - Eduardo Flores-Sandoval
- School of Biological Sciences, Monash University, Melbourne VIC 3800, Australia
- ARC Centre of Excellence for Plant Success in Nature and Agriculture, Monash University, Melbourne VIC 3800, Australia
| | - Kazutaka Futagami
- Department of Life Sciences, Graduate School of Arts and Sciences, The University of Tokyo, Tokyo 153-8902, Japan
| | | | - Rubina Jibran
- The New Zealand Institute for Plant & Food Research Limited, Auckland 1142, New Zealand
| | - Takehiko Kanazawa
- Division of Cellular Dynamics, National Institute for Basic Biology, Myodaiji, Okazaki, Aichi 444-8585, Japan
- The Department of Basic Biology, SOKENDAI (The Graduate University for Advanced Studies), Okazaki, Aichi 444-8585, Japan
| | - Hirotaka Kato
- Graduate School of Science, Kobe University, Kobe 657-8501, Japan
- Graduate School of Science and Engineering, Ehime University, Matsuyama, Ehime 790-8577, Japan
| | - Takayuki Kohchi
- Graduate School of Biostudies, Kyoto University, Kyoto 606-8502, Japan
| | - Jonathan Levins
- School of Biological Sciences, Monash University, Melbourne VIC 3800, Australia
| | - Shih-Shun Lin
- Institute of Biotechnology, National Taiwan University, Taipei 106, Taiwan
| | - Hirofumi Nakagami
- Basic Immune System of Plants, Max-Planck Institute for Plant Breeding Research, 50829 Cologne, Germany
| | - Ryuichi Nishihama
- Department of Applied Biological Science, Tokyo University of Science, Noda, Chiba 278-8510, Japan
| | - Facundo Romani
- Department of Plant Sciences, University of Cambridge, Cambridge CB2 3EA, UK
| | | | - Yasuhiro Tanizawa
- Department of Informatics, National Institute of Genetics, Mishima, Shizuoka 411-8540, Japan
| | - Masayuki Tsuzuki
- Department of Life Sciences, Graduate School of Arts and Sciences, The University of Tokyo, Tokyo 153-8902, Japan
| | - Takashi Ueda
- Division of Cellular Dynamics, National Institute for Basic Biology, Myodaiji, Okazaki, Aichi 444-8585, Japan
- The Department of Basic Biology, SOKENDAI (The Graduate University for Advanced Studies), Okazaki, Aichi 444-8585, Japan
| | - Yuichiro Watanabe
- Department of Life Sciences, Graduate School of Arts and Sciences, The University of Tokyo, Tokyo 153-8902, Japan
| | - Katsuyuki T Yamato
- Faculty of Biology-Oriented Science and Technology, Kindai University, Kinokawa, Wakayama 649-6493, Japan
| | - Sabine Zachgo
- Division of Botany, School of Biology and Chemistry, Osnabrück University, Osnabrück 49076, Germany
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34
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Gomide MDS, Leitão MDC, Coelho CM. Biocircuits in plants and eukaryotic algae. FRONTIERS IN PLANT SCIENCE 2022; 13:982959. [PMID: 36212277 PMCID: PMC9545776 DOI: 10.3389/fpls.2022.982959] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 06/30/2022] [Accepted: 08/22/2022] [Indexed: 06/16/2023]
Abstract
As one of synthetic biology's foundations, biocircuits are a strategy of genetic parts assembling to recognize a signal and to produce a desirable output to interfere with a biological function. In this review, we revisited the progress in the biocircuits technology basis and its mandatory elements, such as the characterization and assembly of functional parts. Furthermore, for a successful implementation, the transcriptional control systems are a relevant point, and the computational tools help to predict the best combinations among the biological parts planned to be used to achieve the desirable phenotype. However, many challenges are involved in delivering and stabilizing the synthetic structures. Some research experiences, such as the golden crops, biosensors, and artificial photosynthetic structures, can indicate the positive and limiting aspects of the practice. Finally, we envision that the modulatory structural feature and the possibility of finer gene regulation through biocircuits can contribute to the complex design of synthetic chromosomes aiming to develop plants and algae with new or improved functions.
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Affiliation(s)
- Mayna da Silveira Gomide
- Laboratory of Synthetic Biology, Department of Genetics and Morphology, Institute of Biological Science, University of Brasília (UnB), Brasília, Distrito Federal, Brazil
- School of Medicine, Federal University of Juiz de Fora (UFJF), Juiz de Fora, Minas Gerais, Brazil
| | - Matheus de Castro Leitão
- Laboratory of Synthetic Biology, Department of Genetics and Morphology, Institute of Biological Science, University of Brasília (UnB), Brasília, Distrito Federal, Brazil
| | - Cíntia Marques Coelho
- Laboratory of Synthetic Biology, Department of Genetics and Morphology, Institute of Biological Science, University of Brasília (UnB), Brasília, Distrito Federal, Brazil
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35
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Moreno-Giménez E, Selma S, Calvache C, Orzáez D. GB_SynP: A Modular dCas9-Regulated Synthetic Promoter Collection for Fine-Tuned Recombinant Gene Expression in Plants. ACS Synth Biol 2022; 11:3037-3048. [PMID: 36044643 PMCID: PMC9486966 DOI: 10.1021/acssynbio.2c00238] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2022] [Indexed: 01/24/2023]
Abstract
Programmable transcriptional factors based on the CRISPR architecture are becoming commonly used in plants for endogenous gene regulation. In plants, a potent CRISPR tool for gene induction is the so-called dCasEV2.1 activation system, which has shown remarkable genome-wide specificity combined with a strong activation capacity. To explore the ability of dCasEV2.1 to act as a transactivator for orthogonal synthetic promoters, a collection of DNA parts was created (GB_SynP) for combinatorial synthetic promoter building. The collection includes (i) minimal promoter parts with the TATA box and 5'UTR regions, (ii) proximal parts containing single or multiple copies of the target sequence for the gRNA, thus functioning as regulatory cis boxes, and (iii) sequence-randomized distal parts that ensure the adequate length of the resulting promoter. A total of 35 promoters were assembled using the GB_SynP collection, showing in all cases minimal background and predictable activation levels depending on the proximal parts used. GB_SynP was also employed in a combinatorial expression analysis of an autoluminescence pathway in Nicotiana benthamiana, showing the value of this tool in extracting important biological information such as the determination of the limiting steps in an enzymatic pathway.
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Affiliation(s)
- Elena Moreno-Giménez
- Instituto
de Biología Molecular y Celular de Plantas (IBMCP), Consejo
Superior de Investigaciones Científicas, Universidad Politécnica de Valencia, Camino de Vera s/n, Valencia 46022, Spain
| | - Sara Selma
- Instituto
de Biología Molecular y Celular de Plantas (IBMCP), Consejo
Superior de Investigaciones Científicas, Universidad Politécnica de Valencia, Camino de Vera s/n, Valencia 46022, Spain
| | - Camilo Calvache
- Instituto
de Biología Molecular y Celular de Plantas (IBMCP), Consejo
Superior de Investigaciones Científicas, Universidad Politécnica de Valencia, Camino de Vera s/n, Valencia 46022, Spain
| | - Diego Orzáez
- Instituto
de Biología Molecular y Celular de Plantas (IBMCP), Consejo
Superior de Investigaciones Científicas, Universidad Politécnica de Valencia, Camino de Vera s/n, Valencia 46022, Spain
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36
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Reconstitution of monoterpene indole alkaloid biosynthesis in genome engineered Nicotiana benthamiana. Commun Biol 2022; 5:949. [PMID: 36088516 PMCID: PMC9464250 DOI: 10.1038/s42003-022-03904-w] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2022] [Accepted: 08/25/2022] [Indexed: 12/17/2022] Open
Abstract
Monoterpene indole alkaloids (MIAs) are a diverse class of plant natural products that include a number of medicinally important compounds. We set out to reconstitute the pathway for strictosidine, a key intermediate of all MIAs, from central metabolism in Nicotiana benthamiana. A disadvantage of this host is that its rich background metabolism results in the derivatization of some heterologously produced molecules. Here we use transcriptomic analysis to identify glycosyltransferases that are upregulated in response to biosynthetic intermediates and produce plant lines with targeted mutations in the genes encoding them. Expression of the early MIA pathway in these lines produces a more favorable product profile. Strictosidine biosynthesis was successfully reconstituted, with the best yields obtained by the co-expression of 14 enzymes, of which a major latex protein-like enzyme (MLPL) from Nepeta (catmint) is critical for improving flux through the iridoid pathway. The removal of endogenous glycosyltransferases does not impact the yields of strictosidine, highlighting that the metabolic flux of the pathway enzymes to a stable biosynthetic intermediate minimizes the need to engineer the endogenous metabolism of the host. The production of strictosidine in planta expands the range of MIA products amenable to biological synthesis. The biosynthesis of strictosidine, a key intermediate of monoterpene indole alkaloids, was successfully reconstructed in Nicotiana benthamiana, demonstrating the potential of Nicotiana benthamiana as a bioproduction chassis for small molecules.
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37
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Peter J, Huleux M, Spaniol B, Sommer F, Neunzig J, Schroda M, Li-Beisson Y, Philippar K. Fatty acid export (FAX) proteins contribute to oil production in the green microalga Chlamydomonas reinhardtii. Front Mol Biosci 2022; 9:939834. [PMID: 36120551 PMCID: PMC9470853 DOI: 10.3389/fmolb.2022.939834] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2022] [Accepted: 07/11/2022] [Indexed: 11/24/2022] Open
Abstract
In algae and land plants, transport of fatty acids (FAs) from their site of synthesis in the plastid stroma to the endoplasmic reticulum (ER) for assembly into acyl lipids is crucial for cellular lipid homeostasis, including the biosynthesis of triacylglycerol (TAG) for energy storage. In the unicellular green alga Chlamydomonas reinhardtii, understanding and engineering of these processes is of particular interest for microalga-based biofuel and biomaterial production. Whereas in the model plant Arabidopsis thaliana, FAX (fatty acid export) proteins have been associated with a function in plastid FA-export and hence TAG synthesis in the ER, the knowledge on the function and subcellular localization of this protein family in Chlamydomonas is still scarce. Among the four FAX proteins encoded in the Chlamydomonas genome, we found Cr-FAX1 and Cr-FAX5 to be involved in TAG production by functioning in chloroplast and ER membranes, respectively. By in situ immunolocalization, we show that Cr-FAX1 inserts into the chloroplast envelope, while Cr-FAX5 is located in ER membranes. Severe reduction of Cr-FAX1 or Cr-FAX5 proteins by an artificial microRNA approach results in a strong decrease of the TAG content in the mutant strains. Further, overexpression of chloroplast Cr-FAX1, but not of ER-intrinsic Cr-FAX5, doubled the content of TAG in Chlamydomonas cells. We therefore propose that Cr-FAX1 in chloroplast envelopes and Cr-FAX5 in ER membranes represent a basic set of FAX proteins to ensure shuttling of FAs from chloroplasts to the ER and are crucial for oil production in Chlamydomonas.
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Affiliation(s)
- Janick Peter
- Plant Biology, Center for Human- and Molecular Biology (ZHMB), Saarland University, Saarbrücken, Germany
| | - Marie Huleux
- Aix Marseille Univ, CEA, CNRS, Institute of Bioscience and Biotechnology of Aix Marseille, BIAM, Saint Paul-Lez-Durance, France
| | - Benjamin Spaniol
- Molecular Biotechnology and Systems Biology, TU Kaiserslautern, Kaiserslautern, Germany
| | - Frederik Sommer
- Molecular Biotechnology and Systems Biology, TU Kaiserslautern, Kaiserslautern, Germany
| | - Jens Neunzig
- Plant Biology, Center for Human- and Molecular Biology (ZHMB), Saarland University, Saarbrücken, Germany
| | - Michael Schroda
- Molecular Biotechnology and Systems Biology, TU Kaiserslautern, Kaiserslautern, Germany
| | - Yonghua Li-Beisson
- Aix Marseille Univ, CEA, CNRS, Institute of Bioscience and Biotechnology of Aix Marseille, BIAM, Saint Paul-Lez-Durance, France
| | - Katrin Philippar
- Plant Biology, Center for Human- and Molecular Biology (ZHMB), Saarland University, Saarbrücken, Germany
- *Correspondence: Katrin Philippar,
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38
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De Saeger J, Vermeersch M, Gaillochet C, Jacobs TB. Simple and Efficient Modification of Golden Gate Design Standards and Parts Using Oligo Stitching. ACS Synth Biol 2022; 11:2214-2220. [PMID: 35675166 DOI: 10.1021/acssynbio.2c00072] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The assembly of DNA parts is a critical aspect of contemporary biological research. Gibson assembly and Golden Gate cloning are two popular options. Here, we explore the use of single stranded DNA oligos with Gibson assembly to augment Golden Gate cloning workflows in a process called "oligo stitching". Our results show that oligo stitching can efficiently convert Golden Gate parts between different assembly standards and directly assemble incompatible Golden Gate parts without PCR amplification. Building on previous reports, we show that it can also be used to assemble de novo sequences. As a final application, we show that restriction enzyme recognition sites can be removed from plasmids and utilize the same concept to perform saturation mutagenesis. Given oligo stitching's versatility and high efficiency, we expect that it will be a useful addition to the molecular biologist's toolbox.
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Affiliation(s)
- Jonas De Saeger
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Technologiepark 71, 9052 Ghent, Belgium.,VIB Center for Plant Systems Biology, Technologiepark 71, 9052 Ghent, Belgium
| | - Mattias Vermeersch
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Technologiepark 71, 9052 Ghent, Belgium.,VIB Center for Plant Systems Biology, Technologiepark 71, 9052 Ghent, Belgium
| | - Christophe Gaillochet
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Technologiepark 71, 9052 Ghent, Belgium.,VIB Center for Plant Systems Biology, Technologiepark 71, 9052 Ghent, Belgium
| | - Thomas B Jacobs
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Technologiepark 71, 9052 Ghent, Belgium.,VIB Center for Plant Systems Biology, Technologiepark 71, 9052 Ghent, Belgium
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39
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Fuchs LK, Holland AH, Ludlow RA, Coates RJ, Armstrong H, Pickett JA, Harwood JL, Scofield S. Genetic Manipulation of Biosynthetic Pathways in Mint. FRONTIERS IN PLANT SCIENCE 2022; 13:928178. [PMID: 35774811 PMCID: PMC9237610 DOI: 10.3389/fpls.2022.928178] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 04/25/2022] [Accepted: 05/24/2022] [Indexed: 06/15/2023]
Abstract
In recent years, the study of aromatic plants has seen an increase, with great interest from industrial, academic, and pharmaceutical industries. Among plants attracting increased attention are the Mentha spp. (mint), members of the Lamiaceae family. Mint essential oils comprise a diverse class of molecules known as terpenoids/isoprenoids, organic chemicals that are among the most diverse class of naturally plant derived compounds. The terpenoid profile of several Mentha spp. is dominated by menthol, a cyclic monoterpene with some remarkable biological properties that make it useful in the pharmaceutical, medical, cosmetic, and cleaning product industries. As the global market for Mentha essential oils increases, the desire to improve oil composition and yield follows. The monoterpenoid biosynthesis pathway is well characterised so metabolic engineering attempts have been made to facilitate this improvement. This review focuses on the Mentha spp. and attempts at altering the carbon flux through the biosynthetic pathways to increase the yield and enhance the composition of the essential oil. This includes manipulation of endogenous and heterologous biosynthetic enzymes through overexpression and RNAi suppression. Genes involved in the MEP pathway, the menthol and carvone biosynthetic pathways and transcription factors known to affect secondary metabolism will be discussed along with non-metabolic engineering approaches including environmental factors and the use of plant growth regulators.
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Affiliation(s)
- Lorenz K. Fuchs
- School of Biosciences, Cardiff University, Cardiff, United Kingdom
| | | | | | - Ryan J. Coates
- School of Biosciences, Cardiff University, Cardiff, United Kingdom
| | - Harvey Armstrong
- School of Biosciences, Cardiff University, Cardiff, United Kingdom
| | - John A. Pickett
- School of Chemistry, Cardiff University, Cardiff, United Kingdom
| | - John L. Harwood
- School of Biosciences, Cardiff University, Cardiff, United Kingdom
| | - Simon Scofield
- School of Biosciences, Cardiff University, Cardiff, United Kingdom
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40
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Temple H, Phyo P, Yang W, Lyczakowski JJ, Echevarría-Poza A, Yakunin I, Parra-Rojas JP, Terrett OM, Saez-Aguayo S, Dupree R, Orellana A, Hong M, Dupree P. Golgi-localized putative S-adenosyl methionine transporters required for plant cell wall polysaccharide methylation. NATURE PLANTS 2022; 8:656-669. [PMID: 35681018 DOI: 10.1038/s41477-022-01156-4] [Citation(s) in RCA: 21] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/09/2021] [Accepted: 04/20/2022] [Indexed: 06/15/2023]
Abstract
Polysaccharide methylation, especially that of pectin, is a common and important feature of land plant cell walls. Polysaccharide methylation takes place in the Golgi apparatus and therefore relies on the import of S-adenosyl methionine (SAM) from the cytosol into the Golgi. However, so far, no Golgi SAM transporter has been identified in plants. Here we studied major facilitator superfamily members in Arabidopsis that we identified as putative Golgi SAM transporters (GoSAMTs). Knockout of the two most highly expressed GoSAMTs led to a strong reduction in Golgi-synthesized polysaccharide methylation. Furthermore, solid-state NMR experiments revealed that reduced methylation changed cell wall polysaccharide conformations, interactions and mobilities. Notably, NMR revealed the existence of pectin 'egg-box' structures in intact cell walls and showed that their formation is enhanced by reduced methyl esterification. These changes in wall architecture were linked to substantial growth and developmental phenotypes. In particular, anisotropic growth was strongly impaired in the double mutant. The identification of putative transporters involved in import of SAM into the Golgi lumen in plants provides new insights into the paramount importance of polysaccharide methylation for plant cell wall structure and function.
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Affiliation(s)
- Henry Temple
- Department of Biochemistry, University of Cambridge, Cambridge, UK
| | - Pyae Phyo
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Weibing Yang
- Sainsbury Laboratory, University of Cambridge, Cambridge, UK
- National Key Laboratory of Plant Molecular Genetics, CAS Center for Excellence in Molecular Plant Sciences, Chinese Academy of Sciences (CAS) and CAS-JIC Center of Excellence for Plant and Microbial Sciences (CEPAMS), Shanghai, China
| | - Jan J Lyczakowski
- Department of Biochemistry, University of Cambridge, Cambridge, UK
- Department of Plant Biotechnology, Faculty of Biochemistry, Biophysics and Biotechnology, Jagiellonian University, Krakow, Poland
| | | | - Igor Yakunin
- Department of Biochemistry, University of Cambridge, Cambridge, UK
| | - Juan Pablo Parra-Rojas
- Centro de Biotecnología Vegetal, FONDAP Center for Genome Regulation, Facultad de Ciencias de la Vida, Universidad Andrés Bello, Santiago, Chile
| | - Oliver M Terrett
- Department of Biochemistry, University of Cambridge, Cambridge, UK
| | - Susana Saez-Aguayo
- Centro de Biotecnología Vegetal, FONDAP Center for Genome Regulation, Facultad de Ciencias de la Vida, Universidad Andrés Bello, Santiago, Chile
| | - Ray Dupree
- Department of Physics, University of Warwick, Coventry, UK
| | - Ariel Orellana
- Centro de Biotecnología Vegetal, FONDAP Center for Genome Regulation, Facultad de Ciencias de la Vida, Universidad Andrés Bello, Santiago, Chile
| | - Mei Hong
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge, MA, USA.
| | - Paul Dupree
- Department of Biochemistry, University of Cambridge, Cambridge, UK.
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Velay F, Soula M, Mehrez M, Belbachir C, D'Alessandro S, Laloi C, Crete P, Field B. MoBiFC: development of a modular bimolecular fluorescence complementation toolkit for the analysis of chloroplast protein-protein interactions. PLANT METHODS 2022; 18:69. [PMID: 35619173 PMCID: PMC9134606 DOI: 10.1186/s13007-022-00902-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/17/2021] [Accepted: 05/06/2022] [Indexed: 06/15/2023]
Abstract
BACKGROUND The bimolecular fluorescence complementation (BiFC) assay has emerged as one of the most popular methods for analysing protein-protein interactions (PPIs) in plant biology. This includes its increasing use as a tool for dissecting the molecular mechanisms of chloroplast function. However, the construction of chloroplast fusion proteins for BiFC can be difficult, and the availability and selection of appropriate controls is not trivial. Furthermore, the challenges of performing BiFC in restricted cellular compartments has not been specifically addressed. RESULTS Here we describe the development of a flexible modular cloning-based toolkit for BiFC (MoBiFC) and proximity labelling in the chloroplast and other cellular compartments using synthetic biology principles. We used pairs of chloroplast proteins previously shown to interact (HSP21/HSP21 and HSP21/PTAC5) and a negative control (HSP21/ΔPTAC5) to develop standardised Goldengate-compatible modules for the assembly of protein fusions with fluorescent protein (FP) fragments for BiFC expressed from a single multigenic T-DNA. Using synthetic biology principles and transient expression in Nicotiana benthamiana, we iteratively improved the approach by testing different FP fragments, promoters, reference FPs for ratiometric quantification, and cell types. A generic negative control (mCHERRY) was also tested, and modules for the identification of proximal proteins by Turbo-ID labelling were developed and validated. CONCLUSIONS MoBiFC facilitates the cloning process for organelle-targeted proteins, allows robust ratiometric quantification, and makes available model positive and negative controls. Development of MoBiFC underlines how Goldengate cloning approaches accelerate the development and enrichment of new toolsets, and highlights several potential pitfalls in designing BiFC experiments including the choice of FP split, negative controls, cell type, and reference FP. We discuss how MoBiFC could be further improved and extended to other compartments of the plant cell and to high throughput cloning approaches.
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Affiliation(s)
- Florent Velay
- Aix-Marseille Univ, CEA, CNRS, BIAM, UMR7265, 13009, Marseille, France
| | - Mélanie Soula
- Aix-Marseille Univ, CEA, CNRS, BIAM, UMR7265, 13009, Marseille, France
| | - Marwa Mehrez
- Aix-Marseille Univ, CEA, CNRS, BIAM, UMR7265, 13009, Marseille, France
- Laboratory of Molecular Genetics, Immunology and Biotechnology, Faculty of Sciences of Tunis, University of Tunis El Manar, 2092, Tunis, Tunisia
| | - Clément Belbachir
- Aix-Marseille Univ, CEA, CNRS, BIAM, UMR7265, 13009, Marseille, France
| | - Stefano D'Alessandro
- Aix-Marseille Univ, CEA, CNRS, BIAM, UMR7265, 13009, Marseille, France
- Dipartimento Scienze della Vita e Biologia dei Sistemi, Università degli Studi di Torino, 10135, Torino, Italy
| | - Christophe Laloi
- Aix-Marseille Univ, CEA, CNRS, BIAM, UMR7265, 13009, Marseille, France
| | - Patrice Crete
- Aix-Marseille Univ, CEA, CNRS, BIAM, UMR7265, 13009, Marseille, France.
| | - Ben Field
- Aix-Marseille Univ, CEA, CNRS, BIAM, UMR7265, 13009, Marseille, France.
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Plchová H, Moravec T, Čeřovská N, Pobořilová Z, Dušek J, Kratochvílová K, Navrátil O, Kundu JK. A GoldenBraid-Compatible Virus-Based Vector System for Transient Expression of Heterologous Proteins in Plants. Viruses 2022; 14:1099. [PMID: 35632840 PMCID: PMC9146717 DOI: 10.3390/v14051099] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2022] [Revised: 05/09/2022] [Accepted: 05/19/2022] [Indexed: 12/10/2022] Open
Abstract
We have developed a Potato virus X (PVX)-based vector system compatible with the GoldenBraid 2.0 (GB) cloning strategy to transiently express heterologous proteins or peptides in plants for biotechnological purposes. This vector system consists of three domestication vectors carrying three GB parts-the cauliflower mosaic virus (CaMV) 35S promoter with PVX upstream of the second subgenomic promoter of the PVX coat protein (PVX CP SGP), nopaline synthase (NOS) terminator with PVX downstream of the first PVX CP SGP and the gene of interest (GOI). The full-length PVX clone carrying the sequence encoding a green fluorescent protein (GFP) as GOI was incorporated into the binary GB vector in a one-step reaction of three GB parts using the four-nucleotide GB standard syntax. We investigated whether the obtained vector named GFP/pGBX enables systemic PVX infection and expression of GFP in Nicotiana benthamiana plants. We show that this GB-compatible vector system can be used for simple and efficient assembly of PVX-based expression constructs and that it meets the current need for interchange of standard biological parts used in different expression systems.
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Affiliation(s)
- Helena Plchová
- Laboratory of Virology, Centre for Plant Virus Research, Institute of Experimental Botany of the Czech Academy of Sciences, 16500 Prague, Czech Republic; (H.P.); (N.Č.); (Z.P.); (J.D.); (K.K.); (O.N.)
| | - Tomáš Moravec
- Laboratory of Virology, Centre for Plant Virus Research, Institute of Experimental Botany of the Czech Academy of Sciences, 16500 Prague, Czech Republic; (H.P.); (N.Č.); (Z.P.); (J.D.); (K.K.); (O.N.)
| | - Noemi Čeřovská
- Laboratory of Virology, Centre for Plant Virus Research, Institute of Experimental Botany of the Czech Academy of Sciences, 16500 Prague, Czech Republic; (H.P.); (N.Č.); (Z.P.); (J.D.); (K.K.); (O.N.)
| | - Zuzana Pobořilová
- Laboratory of Virology, Centre for Plant Virus Research, Institute of Experimental Botany of the Czech Academy of Sciences, 16500 Prague, Czech Republic; (H.P.); (N.Č.); (Z.P.); (J.D.); (K.K.); (O.N.)
| | - Jakub Dušek
- Laboratory of Virology, Centre for Plant Virus Research, Institute of Experimental Botany of the Czech Academy of Sciences, 16500 Prague, Czech Republic; (H.P.); (N.Č.); (Z.P.); (J.D.); (K.K.); (O.N.)
- Department of Plant Protection, Czech University of Life Sciences, 16500 Prague, Czech Republic
| | - Kateřina Kratochvílová
- Laboratory of Virology, Centre for Plant Virus Research, Institute of Experimental Botany of the Czech Academy of Sciences, 16500 Prague, Czech Republic; (H.P.); (N.Č.); (Z.P.); (J.D.); (K.K.); (O.N.)
- Department of Experimental Plant Biology, Faculty of Science, Charles University in Prague, 12843 Prague, Czech Republic
| | - Oldřich Navrátil
- Laboratory of Virology, Centre for Plant Virus Research, Institute of Experimental Botany of the Czech Academy of Sciences, 16500 Prague, Czech Republic; (H.P.); (N.Č.); (Z.P.); (J.D.); (K.K.); (O.N.)
| | - Jiban Kumar Kundu
- Laboratory of Virology, Centre for Plant Virus Research, Institute of Experimental Botany of the Czech Academy of Sciences, 16500 Prague, Czech Republic; (H.P.); (N.Č.); (Z.P.); (J.D.); (K.K.); (O.N.)
- Plant Virus and Vector Interactions, Centre for Plant Virus Research, Crop Research Institute, 16106 Prague, Czech Republic
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43
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New destination vectors facilitate Modular Cloning for Chlamydomonas. Curr Genet 2022; 68:531-536. [PMID: 35429260 PMCID: PMC9279246 DOI: 10.1007/s00294-022-01239-x] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2022] [Revised: 03/04/2022] [Accepted: 03/24/2022] [Indexed: 11/30/2022]
Abstract
Synthetic Biology is revolutionizing biological research by introducing principles of mechanical engineering, including the standardization of genetic parts and standardized part assembly routes. Both are realized in the Modular Cloning (MoClo) strategy. MoClo allows for the rapid and robust assembly of individual genes and multigene clusters, enabling iterative cycles of gene design, construction, testing, and learning in short time. This is particularly true if generation times of target organisms are short, as is the case for the unicellular green alga Chlamydomonas reinhardtii. Testing a gene of interest in Chlamydomonas with MoClo requires two assembly steps, one for the gene of interest itself and another to combine it with a selection marker. To reduce this to a single assembly step, we constructed five new destination vectors. They contain genes conferring resistance to commonly used antibiotics in Chlamydomonas and a site for the direct assembly of basic genetic parts. The vectors employ red/white color selection and, therefore, do not require costly compounds like X-gal and IPTG. mCherry expression is used to demonstrate the functionality of these vectors.
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44
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Ferigolo LF, Vicente MH, Nogueira FT. Brick into the Gateway (BiG): A novel approach for faster cloning combining Golden Gate and Gateway methods. Plasmid 2022; 121:102630. [DOI: 10.1016/j.plasmid.2022.102630] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2021] [Revised: 03/29/2022] [Accepted: 04/05/2022] [Indexed: 11/26/2022]
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Abstract
Genome engineering technologies enable targeted mutations to be induced at almost any location in plant genomes. In particular, Cas9 nucleases use easily recoded RNA guides to target user-defined sequences and generate double-stranded breaks (DSB) that are then repaired by the cell's endogenous repair mechanisms. Incorrect repair results in mutations at the target. When the targets are in coding sequences, this often results in loss-of-function mutations. In this chapter, we describe a method to rapidly design and assemble RNA-guided Cas9 constructs for plants and test their ability to induce mutations at their intended targets in rapid assays using both Agrobacterium-mediated transient expression and PEG-mediated DNA delivery to protoplasts, the latter of which can be adapted to a wide range of plant species. We describe a PCR-based method for detecting mutagenesis and outline the steps required to segregate the Cas9 transgene from the targeted mutation to enable the production of transgene-free mutated plants. These techniques are amenable to a range of plant species and should accelerate the application of Cas-9-mediated genome engineering for basic plant science as well as crop development.
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46
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Basu D, South PF. Design and Analysis of Native Photorespiration Gene Motifs of Promoter Untranslated Region Combinations Under Short Term Abiotic Stress Conditions. FRONTIERS IN PLANT SCIENCE 2022; 13:828729. [PMID: 35251099 PMCID: PMC8888687 DOI: 10.3389/fpls.2022.828729] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/03/2021] [Accepted: 01/18/2022] [Indexed: 05/09/2023]
Abstract
Quantitative traits are rarely controlled by a single gene, thereby making multi-gene transformation an indispensable component of modern synthetic biology approaches. However, the shortage of unique gene regulatory elements (GREs) for the robust simultaneous expression of multiple nuclear transgenes is a major bottleneck that impedes the engineering of complex pathways in plants. In this study, we compared the transcriptional efficacies of a comprehensive list of well-documented promoter and untranslated region (UTR) sequences side by side. The strength of GREs was examined by a dual-luciferase assay in conjunction with transient expression in tobacco. In addition, we created suites of new GREs with higher transcriptional efficacies by combining the best performing promoter-UTR sequences. We also tested the impact of elevated temperature and high irradiance on the effectiveness of these GREs. While constitutive promoters ensure robust expression of transgenes, they lack spatiotemporal regulations exhibited by native promoters. Here, we present a proof-of-principle study on the characterization of synthetic promoters based on cis-regulatory elements of three key photorespiratory genes. This conserved biochemical process normally increases under elevated temperature, low CO2, and high irradiance stress conditions and results in ∼25% loss in fixed CO2. To select stress-responsive cis-regulatory elements involved in photorespiration, we analyzed promoters of two chloroplast transporters (AtPLGG1 and AtBASS6) and a key plastidial enzyme, AtPGLP using PlantPAN3.0 and AthaMap. Our results suggest that these motifs play a critical role for PLGG1, BASS6, and PGLP in mediating response to elevated temperature and high-intensity light stress. These findings will not only enable the advancement of metabolic and genetic engineering of photorespiration but will also be instrumental in related synthetic biology approaches.
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Affiliation(s)
| | - Paul F. South
- Department of Biological Sciences, Louisiana State University, Baton Rouge, LA, United States
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47
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Lohani N, Singh MB, Bhalla PL. Biological Parts for Engineering Abiotic Stress Tolerance in Plants. BIODESIGN RESEARCH 2022; 2022:9819314. [PMID: 37850130 PMCID: PMC10521667 DOI: 10.34133/2022/9819314] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2021] [Accepted: 12/17/2021] [Indexed: 10/19/2023] Open
Abstract
It is vital to ramp up crop production dramatically by 2050 due to the increasing global population and demand for food. However, with the climate change projections showing that droughts and heatwaves becoming common in much of the globe, there is a severe threat of a sharp decline in crop yields. Thus, developing crop varieties with inbuilt genetic tolerance to environmental stresses is urgently needed. Selective breeding based on genetic diversity is not keeping up with the growing demand for food and feed. However, the emergence of contemporary plant genetic engineering, genome-editing, and synthetic biology offer precise tools for developing crops that can sustain productivity under stress conditions. Here, we summarize the systems biology-level understanding of regulatory pathways involved in perception, signalling, and protective processes activated in response to unfavourable environmental conditions. The potential role of noncoding RNAs in the regulation of abiotic stress responses has also been highlighted. Further, examples of imparting abiotic stress tolerance by genetic engineering are discussed. Additionally, we provide perspectives on the rational design of abiotic stress tolerance through synthetic biology and list various bioparts that can be used to design synthetic gene circuits whose stress-protective functions can be switched on/off in response to environmental cues.
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Affiliation(s)
- Neeta Lohani
- Plant Molecular Biology and Biotechnology Laboratory, Faculty of Veterinary and Agricultural Sciences, The University of Melbourne, Parkville, VIC 3010, Australia
| | - Mohan B. Singh
- Plant Molecular Biology and Biotechnology Laboratory, Faculty of Veterinary and Agricultural Sciences, The University of Melbourne, Parkville, VIC 3010, Australia
| | - Prem L. Bhalla
- Plant Molecular Biology and Biotechnology Laboratory, Faculty of Veterinary and Agricultural Sciences, The University of Melbourne, Parkville, VIC 3010, Australia
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48
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Harant A, Pai H, Sakai T, Kamoun S, Adachi H. A vector system for fast-forward studies of the HOPZ-ACTIVATED RESISTANCE1 (ZAR1) resistosome in the model plant Nicotiana benthamiana. PLANT PHYSIOLOGY 2022; 188:70-80. [PMID: 34633454 PMCID: PMC8774824 DOI: 10.1093/plphys/kiab471] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/07/2021] [Accepted: 09/08/2021] [Indexed: 05/25/2023]
Abstract
Nicotiana benthamiana has emerged as a complementary experimental system to Arabidopsis thaliana. It enables fast-forward in vivo analyses primarily through transient gene expression and is particularly popular in the study of plant immunity. Recently, our understanding of nucleotide-binding leucine-rich repeat (NLR) plant immune receptors has greatly advanced following the discovery of the Arabidopsis HOPZ-ACTIVATED RESISTANCE1 (ZAR1) resistosome. Here, we describe a vector system of 72 plasmids that enables functional studies of the ZAR1 resistosome in N. benthamiana. We showed that ZAR1 stands out among the coiled coil class of NLRs (CC-NLRs) for being highly conserved across distantly related dicot plant species and confirmed NbZAR1 as the N. benthamiana ortholog of Arabidopsis ZAR1. Effector-activated and autoactive NbZAR1 triggers the cell death response in N. benthamiana and this activity is dependent on a functional N-terminal α1 helix. C-terminally tagged NbZAR1 remains functional in N. benthamiana, thus enabling cell biology and biochemical studies in this plant system. We conclude that the NbZAR1 open source pZA plasmid collection forms an additional experimental system to Arabidopsis for in planta resistosome studies.
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Affiliation(s)
- Adeline Harant
- The Sainsbury Laboratory, University of East Anglia, Norwich Research Park, Norwich NR4 7UH, UK
| | - Hsuan Pai
- The Sainsbury Laboratory, University of East Anglia, Norwich Research Park, Norwich NR4 7UH, UK
| | - Toshiyuki Sakai
- The Sainsbury Laboratory, University of East Anglia, Norwich Research Park, Norwich NR4 7UH, UK
- Laboratory of Crop Evolution, Graduate School of Agriculture, Kyoto University, Mozume, Muko, Kyoto 617-0001, Japan
| | - Sophien Kamoun
- The Sainsbury Laboratory, University of East Anglia, Norwich Research Park, Norwich NR4 7UH, UK
| | - Hiroaki Adachi
- The Sainsbury Laboratory, University of East Anglia, Norwich Research Park, Norwich NR4 7UH, UK
- Graduate School of Biological Sciences, Nara Institute of Science and Technology, Ikoma 630-0192, Japan
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49
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Vazquez-Vilar M, Juarez P, Bernabé-Orts JM, Orzaez D. Design of Multiplexing CRISPR/Cas9 Constructs for Plant Genome Engineering Using the GoldenBraid DNA Assembly Standard. Methods Mol Biol 2022; 2379:27-44. [PMID: 35188654 DOI: 10.1007/978-1-0716-1791-5_2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/14/2023]
Abstract
Due to the huge potential of CRISPR/Cas9 for synthetic biology and genome engineering, many plant researchers are adopting this technology in their laboratories. CRISPR/Cas9 allows multiplexing of guide RNAs (gRNAs), therefore targeting several loci in the genome simultaneously. However, making DNA constructs for this purpose is not always straightforward for first-time users. Here we show how to make multiplex CRISPR/Cas9 constructs using the GoldenBraid (GB) DNA assembly system. As an example, we create a polycistronic gRNA construct that guides a dead version of Cas9 to three different positions of the nopaline synthase promoter, leading to transcriptional repression. After a description of the reagents, the protocol describes step-by-step the considerations for DNA target selection and the molecular cloning process of the final T-DNA construct as well as its testing by transient expression in Nicotiana benthamiana leaves along with a reporter construct for luciferase expression.
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Affiliation(s)
- M Vazquez-Vilar
- Instituto de Biología Molecular y Celular de Plantas (IBMCP), Consejo Superior de Investigaciones Científicas (CSIC), Universidad Politécnica de Valencia, Valencia, Spain
| | - P Juarez
- Instituto de Biología Molecular y Celular de Plantas (IBMCP), Consejo Superior de Investigaciones Científicas (CSIC), Universidad Politécnica de Valencia, Valencia, Spain
| | - J M Bernabé-Orts
- Instituto de Biología Molecular y Celular de Plantas (IBMCP), Consejo Superior de Investigaciones Científicas (CSIC), Universidad Politécnica de Valencia, Valencia, Spain
| | - D Orzaez
- Instituto de Biología Molecular y Celular de Plantas (IBMCP), Consejo Superior de Investigaciones Científicas (CSIC), Universidad Politécnica de Valencia, Valencia, Spain.
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50
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Schroda M, Remacle C. Molecular Advancements Establishing Chlamydomonas as a Host for Biotechnological Exploitation. FRONTIERS IN PLANT SCIENCE 2022; 13:911483. [PMID: 35845675 PMCID: PMC9277225 DOI: 10.3389/fpls.2022.911483] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/02/2022] [Accepted: 06/07/2022] [Indexed: 05/13/2023]
Abstract
Chlamydomonas reinhardtii is emerging as a production platform for biotechnological purposes thanks to recent achievements, which we briefly summarize in this review. Firstly, robust nuclear transgene expression is now possible because several impressive improvements have been made in recent years. Strains allowing efficient and stable nuclear transgene expression are available and were recently made more amenable to rational biotechnological approaches by enabling genetic crosses and identifying their causative mutation. The MoClo synthetic biology strategy, based on Golden Gate cloning, was developed for Chlamydomonas and includes a growing toolkit of more than 100 genetic parts that can be robustly and rapidly assembled in a predefined order. This allows for rapid iterative cycles of transgene design, building, testing, and learning. Another major advancement came from various findings improving transgene design and expression such as the systematic addition of introns into codon-optimized coding sequences. Lastly, the CRISPR/Cas9 technology for genome editing has undergone several improvements since its first successful report in 2016, which opens the possibility of optimizing biosynthetic pathways by switching off competing ones. We provide a few examples demonstrating that all these recent developments firmly establish Chlamydomonas as a chassis for synthetic biology and allow the rewiring of its metabolism to new capabilities.
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Affiliation(s)
- Michael Schroda
- Molecular Biotechnology and Systems Biology, TU Kaiserslautern, Kaiserslautern, Germany
| | - Claire Remacle
- Genetics and Physiology of Microalgae, InBios/Phytosystems Research Unit, University of Liege, Liege, Belgium
- *Correspondence: Claire Remacle,
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