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Life
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Plant Synthetic Biology
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Plant Synthetic Biology

A special issue of Life (ISSN 2075-1729). This special issue belongs to the section "Synthetic Biology and Systems Biology".

Deadline for manuscript submissions: closed (30 June 2021) | Viewed by 26220

Special Issue Editors

Dr. Stéphane D. Lemaire

E-Mail Website
Guest Editor
Institut de Biologie Physico-Chimique, Sorbonne Université, CNRS, 75005 Paris, France
Interests: synthetic biology; systems biology, microalgae; photosynthesis
Dr. Paul F. South

E-Mail Website
Guest Editor
Biological Sciences, Louisiana State University, Baton Rouge, LA 70803, USA
Interests: plant physiology; synthetic biology

Special Issue Information

Dear Colleagues,

Biology is currently facing a revolution through its transition from analytic to synthetic approaches. Synthesis is a powerful methodology to understand by building rather than by deconstruction. Synthetic biology is a forward biological engineering discipline offering new possibilities to answer fundamental questions using new approaches and concepts or to create artificial systems that have potential biotechnological applications.

The field of plant synthetic biology encompasses many different types of photosynthetic chassis such as cyanobacteria, green algae, diatoms, bryophytes or land plants. These chassis with complex genomes and biochemical plasticity have become popular as the ability to synthesize, insert, delete, and modify genetic material has improved. The design–build–test–learn cycle coupled to standardization enables an engineering approach to plant biology. Synthetic biology is a wonderful opportunity to tackle the most important and unprecedented agricultural, environmental, scientific, industrial, and economic challenges of our time. Plants have been used as a food and fiber source throughout human history, and with current technological advances, the ability to redesign plant structure, metabolism, and physiology has become a reality.

The objective of the present Special Issue of Life is to highlight original research and review articles dealing with all aspects of plant synthetic biology.

Dr. Stéphane D. Lemaire
Dr. Paul F. South
Guest Editors

Manuscript Submission Information

Manuscripts should be submitted online at www.mdpi.com by registering and logging in to this website. Once you are registered, click here to go to the submission form. Manuscripts can be submitted until the deadline. All submissions that pass pre-check are peer-reviewed. Accepted papers will be published continuously in the journal (as soon as accepted) and will be listed together on the special issue website. Research articles, review articles as well as short communications are invited. For planned papers, a title and short abstract (about 100 words) can be sent to the Editorial Office for announcement on this website.

Submitted manuscripts should not have been published previously, nor be under consideration for publication elsewhere (except conference proceedings papers). All manuscripts are thoroughly refereed through a single-blind peer-review process. A guide for authors and other relevant information for submission of manuscripts is available on the Instructions for Authors page. Life is an international peer-reviewed open access monthly journal published by MDPI.

Please visit the Instructions for Authors page before submitting a manuscript. The Article Processing Charge (APC) for publication in this open access journal is 2600 CHF (Swiss Francs). Submitted papers should be well formatted and use good English. Authors may use MDPI's English editing service prior to publication or during author revisions.

Keywords

  • Genome editing
  • Metabolic modeling and metabolic engineering
  • Directed evolution and pathway design
  • Systems biology, molecular biology, biochemistry, and structural biology
  • Engineering primary productivity and photosynthesis
  • Novel bioproducts
  • New tools and technologies in plant synthetic biology
  • Biotic interactions, plant development, and morphology

Published Papers (5 papers)

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Research

Jump to: Review

20 pages, 6851 KiB  
Article
Exploring the Impact of Terminators on Transgene Expression in Chlamydomonas reinhardtii with a Synthetic Biology Approach
by Katrin Geisler, Mark A. Scaife, Paweł M. Mordaka, Andre Holzer, Eleanor V. Tomsett, Payam Mehrshahi, Gonzalo I. Mendoza Ochoa and Alison G. Smith
Life 2021, 11(9), 964; https://doi.org/10.3390/life11090964 - 14 Sep 2021
Cited by 6 | Viewed by 3214
Abstract
Chlamydomonas reinhardtii has many attractive features for use as a model organism for both fundamental studies and as a biotechnological platform. Nonetheless, despite the many molecular tools and resources that have been developed, there are challenges for its successful engineering, in particular to [...] Read more.
Chlamydomonas reinhardtii has many attractive features for use as a model organism for both fundamental studies and as a biotechnological platform. Nonetheless, despite the many molecular tools and resources that have been developed, there are challenges for its successful engineering, in particular to obtain reproducible and high levels of transgene expression. Here we describe a synthetic biology approach to screen several hundred independent transformants using standardised parts to explore different parameters that might affect transgene expression. We focused on terminators and, using a standardised workflow and quantitative outputs, tested 9 different elements representing three different size classes of native terminators to determine their ability to support high level expression of a GFP reporter gene. We found that the optimal size reflected the median size of element found in the C. reinhardtii genome. The behaviour of the terminator parts was similar with different promoters, in different host strains and with different transgenes. This approach is applicable to the systematic testing of other genetic elements, facilitating comparison to determine optimal transgene design. Full article
(This article belongs to the Special Issue Plant Synthetic Biology)
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13 pages, 2706 KiB  
Article
Rapid and Efficient Colony-PCR for High Throughput Screening of Genetically Transformed Chlamydomonas reinhardtii
by Serge Basile Nouemssi, Manel Ghribi, Rémy Beauchemin, Fatma Meddeb-Mouelhi, Hugo Germain and Isabel Desgagné-Penix
Life 2020, 10(9), 186; https://doi.org/10.3390/life10090186 - 10 Sep 2020
Cited by 10 | Viewed by 6445
Abstract
Microalgae biotechnologies are rapidly developing into new commercial settings. Several high value products already exist on the market, and biotechnological development is focused on genetic engineering of microalgae to open up future economic opportunities for food, fuel and pharmacological production. Colony-polymerase chain reaction [...] Read more.
Microalgae biotechnologies are rapidly developing into new commercial settings. Several high value products already exist on the market, and biotechnological development is focused on genetic engineering of microalgae to open up future economic opportunities for food, fuel and pharmacological production. Colony-polymerase chain reaction (colony-PCR or cPCR) is a critical method for screening genetically transformed microalgae cells. However, the ability to rapidly screen thousands of transformants using the current colony-PCR method, becomes a very laborious and time-consuming process. Herein, the non-homologous transformation of Chlamydomonas reinhardtii using the electroporation and glass beads methods generated more than seven thousand transformants. In order to manage this impressive number of clones efficiently, we developed a high-throughput screening (HTS) cPCR method to rapidly maximize the detection and selection of positively transformed clones. For this, we optimized the Chlamydomonas transformed cell layout on the culture media to improve genomic DNA extraction and cPCR in 96-well plate. The application of this optimized HTS cPCR method offers a rapid, less expensive and reliable method for the detection and selection of microalgae transformants. Our method, which saves up to 80% of the experimental time, holds promise for evaluating genetically transformed cells and selection for microalgae-based biotechnological applications such as synthetic biology and metabolic engineering. Full article
(This article belongs to the Special Issue Plant Synthetic Biology)
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16 pages, 2743 KiB  
Article
Potential for Applying Continuous Directed Evolution to Plant Enzymes: An Exploratory Study
by Jorge D. García-García, Jaya Joshi, Jenelle A. Patterson, Lidimarie Trujillo-Rodriguez, Christopher R. Reisch, Alex A. Javanpour, Chang C. Liu and Andrew D. Hanson
Life 2020, 10(9), 179; https://doi.org/10.3390/life10090179 - 5 Sep 2020
Cited by 16 | Viewed by 5653
Abstract
Plant evolution has produced enzymes that may not be optimal for maximizing yield and quality in today’s agricultural environments and plant biotechnology applications. By improving enzyme performance, it should be possible to alleviate constraints on yield and quality currently imposed by kinetic properties [...] Read more.
Plant evolution has produced enzymes that may not be optimal for maximizing yield and quality in today’s agricultural environments and plant biotechnology applications. By improving enzyme performance, it should be possible to alleviate constraints on yield and quality currently imposed by kinetic properties or enzyme instability. Enzymes can be optimized more quickly than naturally possible by applying directed evolution, which entails mutating a target gene in vitro and screening or selecting the mutated gene products for the desired characteristics. Continuous directed evolution is a more efficient and scalable version that accomplishes the mutagenesis and selection steps simultaneously in vivo via error-prone replication of the target gene and coupling of the host cell’s growth rate to the target gene’s function. However, published continuous systems require custom plasmid assembly, and convenient multipurpose platforms are not available. We discuss two systems suitable for continuous directed evolution of enzymes, OrthoRep in Saccharomyces cerevisiae and EvolvR in Escherichia coli, and our pilot efforts to adapt each system for high-throughput plant enzyme engineering. To test our modified systems, we used the thiamin synthesis enzyme THI4, previously identified as a prime candidate for improvement. Our adapted OrthoRep system shows promise for efficient plant enzyme engineering. Full article
(This article belongs to the Special Issue Plant Synthetic Biology)
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Review

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18 pages, 1796 KiB  
Review
Biosensors: A Sneak Peek into Plant Cell’s Immunity
by Valentina Levak, Tjaša Lukan, Kristina Gruden and Anna Coll
Life 2021, 11(3), 209; https://doi.org/10.3390/life11030209 - 7 Mar 2021
Cited by 3 | Viewed by 3439
Abstract
Biosensors are indispensable tools to understand a plant’s immunity as its spatiotemporal dimension is key in withstanding complex plant immune signaling. The diversity of genetically encoded biosensors in plants is expanding, covering new analytes with ever higher sensitivity and robustness, but their assortment [...] Read more.
Biosensors are indispensable tools to understand a plant’s immunity as its spatiotemporal dimension is key in withstanding complex plant immune signaling. The diversity of genetically encoded biosensors in plants is expanding, covering new analytes with ever higher sensitivity and robustness, but their assortment is limited in some respects, such as their use in following biotic stress response, employing more than one biosensor in the same chassis, and their implementation into crops. In this review, we focused on the available biosensors that encompass these aspects. We show that in vivo imaging of calcium and reactive oxygen species is satisfactorily covered with the available genetically encoded biosensors, while on the other hand they are still underrepresented when it comes to imaging of the main three hormonal players in the immune response: salicylic acid, ethylene and jasmonic acid. Following more than one analyte in the same chassis, upon one or more conditions, has so far been possible by using the most advanced genetically encoded biosensors in plants which allow the monitoring of calcium and the two main hormonal pathways involved in plant development, auxin and cytokinin. These kinds of biosensor are also the most evolved in crops. In the last section, we examine the challenges in the use of biosensors and demonstrate some strategies to overcome them. Full article
(This article belongs to the Special Issue Plant Synthetic Biology)
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21 pages, 1274 KiB  
Review
Genome Editing by CRISPR-Cas: A Game Change in the Genetic Manipulation of Chlamydomonas
by Manel Ghribi, Serge Basile Nouemssi, Fatma Meddeb-Mouelhi and Isabel Desgagné-Penix
Life 2020, 10(11), 295; https://doi.org/10.3390/life10110295 - 20 Nov 2020
Cited by 29 | Viewed by 5980
Abstract
Microalgae are promising photosynthetic unicellular eukaryotes among the most abundant on the planet and are considered as alternative sustainable resources for various industrial applications. Chlamydomonas is an emerging model for microalgae to be manipulated by multiple biotechnological tools in order to produce high-value [...] Read more.
Microalgae are promising photosynthetic unicellular eukaryotes among the most abundant on the planet and are considered as alternative sustainable resources for various industrial applications. Chlamydomonas is an emerging model for microalgae to be manipulated by multiple biotechnological tools in order to produce high-value bioproducts such as biofuels, bioactive peptides, pigments, nutraceuticals, and medicines. Specifically, Chlamydomonas reinhardtii has become a subject of different genetic-editing techniques adapted to modulate the production of microalgal metabolites. The main nuclear genome-editing tools available today include zinc finger nucleases (ZFNs), transcriptional activator-like effector nucleases (TALENs), and more recently discovered the clustered regularly interspaced short palindromic repeats (CRISPR)-CRISPR associated protein (Cas) nuclease system. The latter, shown to have an interesting editing capacity, has become an essential tool for genome editing. In this review, we highlight the available literature on the methods and the applications of CRISPR-Cas for C. reinhardtii genetic engineering, including recent transformation methods, most used bioinformatic tools, best strategies for the expression of Cas protein and sgRNA, the CRISPR-Cas mediated gene knock-in/knock-out strategies, and finally the literature related to CRISPR expression and modification approaches. Full article
(This article belongs to the Special Issue Plant Synthetic Biology)
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