Design of orthogonal regulatory systems for modulating gene expression in plants

Belcher, Michael S.; Vuu, Khanh M.; Zhou, Andy; Mansoori, Nasim; Ramos, Amanda Agosto; Thompson, Mitchell G.; Scheller, Henrik Vibe; Loqué, Dominique; Shih, Patrick M.

doi:10.1038/s41589-020-0547-4

Cited by 65 publications

(81 citation statements)

References 54 publications

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“…Therefore, introducing an engineered photorespiratory bypass pathway into biofuel crops has the potential to increase the en- ergy conversion efficiency of the plant (Shih et al, 2014;South et al, 2019). Eventually, many of these traits can be stacked into individual biofuel crops to increase plant productivity and maximize biomass production as technologies for advanced plant engineering and gene regulation are developed (Belcher et al, 2020).…”

Section: Reviewmentioning

confidence: 99%

Biofuels for a sustainable future

Liu

Cruz-Morales

Zargar

et al. 2021

Cell

Self Cite

182

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Rapid increases of energy consumption and human dependency on fossil fuels have led to the accumulation of greenhouse gases and consequently, climate change. As such, major efforts have been taken to develop, test, and adopt clean renewable fuel alternatives. Production of bioethanol and biodiesel from crops is well developed, while other feedstock resources and processes have also shown high potential to provide efficient and cost-effective alternatives, such as landfill and plastic waste conversion, algal photosynthesis, as well as electrochemical carbon fixation. In addition, the downstream microbial fermentation can be further engineered to not only increase the product yield but also expand the chemical space of biofuels through the rational design and fine-tuning of biosynthetic pathways toward the realization of ''designer fuels'' and diverse future applications.

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Section: Reviewmentioning

confidence: 99%

Biofuels for a sustainable future

Liu

Cruz-Morales

Zargar

et al. 2021

Cell

Self Cite

182

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“…We recognize that our knowledge of biochemical pathways in plants are often not sufficiently complete that we can reasonably predict the consequences of changing the expression of targeted genes. Here, open-ended forward genetics approaches through genome editing may be useful as a complement to rational design (Zsögön et al, 2017;Andres et al, 2019;Belcher et al, 2020).…”

Section: Without Jeopardizing Yieldmentioning

confidence: 99%

Crops for Carbon Farming

et al. 2021

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Agricultural cropping systems and pasture comprise one third of the world’s arable land and have the potential to draw down a considerable amount of atmospheric CO2 for storage as soil organic carbon (SOC) and improving the soil carbon budget. An improved soil carbon budget serves the dual purpose of promoting soil health, which supports crop productivity, and constituting a pool from which carbon can be converted to recalcitrant forms for long-term storage as a mitigation measure for global warming. In this perspective, we propose the design of crop ideotypes with the dual functionality of being highly productive for the purposes of food, feed, and fuel, while at the same time being able to facilitate higher contribution to soil carbon and improve the below ground ecology. We advocate a holistic approach of the integrated plant-microbe-soil system and suggest that significant improvements in soil carbon storage can be achieved by a three-pronged approach: (1) design plants with an increased root strength to further allocation of carbon belowground; (2) balance the increase in belowground carbon allocation with increased source strength for enhanced photosynthesis and biomass accumulation; and (3) design soil microbial consortia for increased rhizosphere sink strength and plant growth-promoting (PGP) properties.

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“…For example, the strength of regulation implemented by a delivered synthetic transcription factor could be altered by tuning replication speed of the vector, to study the relationship between gene expression and developmental phenotypes ( Khakhar et al, 2018 ). This same approach could be used to titrate the levels of a delivered enzyme and study its impact on metabolic flux ( Belcher et al, 2020 ), a crucial aspect to metabolic engineering.…”

Section: Engineering Viral Vector Replicationmentioning

confidence: 99%

“…Synthetic biology approaches have been used to elucidate mechanistic rules behind core developmental and stress response pathways, such as auxin regulated development ( Pierre-Jerome et al, 2014 ; Moss et al, 2015 ) and abscisic acid triggered drought responses ( Park et al, 2015 ). Another major area of focus has been uncovering the rules governing promoter architecture utilizing synthetic biology both to study a diversity of elements in a massively parallel fashion ( Cai et al, 2020 ), and to study how targeted variation in promoter architectures affect gene transcription ( Antunes et al, 2009 ; Belcher et al, 2020 ) and associated phenotypes. Some of these insights coupled with innovations in modular plasmid assembly and synthetic transcription factors have enabled a new era of metabolic engineering with applications as diverse as enhancing photosynthesis ( South et al, 2019 ), producing valuable small molecules ( Moses et al, 2013 ), and providing auto luminescence ( Khakhar et al, 2020 ).…”

Section: Introductionmentioning

confidence: 99%

RNA Viral Vectors for Accelerating Plant Synthetic Biology

Khakhar

Voytas

2021

Front. Plant Sci.

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The tools of synthetic biology have enormous potential to help us uncover the fundamental mechanisms controlling development and metabolism in plants. However, their effective utilization typically requires transgenesis, which is plagued by long timescales and high costs. In this review we explore how transgenesis can be minimized by delivering foreign genetic material to plants with systemically mobile and persistent vectors based on RNA viruses. We examine the progress that has been made thus far and highlight the hurdles that need to be overcome and some potential strategies to do so. We conclude with a discussion of biocontainment mechanisms to ensure these vectors can be used safely as well as how these vectors might expand the accessibility of plant synthetic biology techniques. RNA vectors stand poised to revolutionize plant synthetic biology by making genetic manipulation of plants cheaper and easier to deploy, as well as by accelerating experimental timescales from years to weeks.

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Design of orthogonal regulatory systems for modulating gene expression in plants

Cited by 65 publications

References 54 publications

Biofuels for a sustainable future

Biofuels for a sustainable future

Crops for Carbon Farming

RNA Viral Vectors for Accelerating Plant Synthetic Biology

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