An integrative database and its application for plant synthetic biology research

Plant synthetic biology research requires diverse bioparts that facilitate the redesign and construction of new-to-nature biological devices or systems in plants.Limited by few well-characterized bioparts for plant chassis,the development of plant synthetic biology lags behind that of its microbial counterpart.Here,we constructed a web-based Plant Synthetic BioDatabase(PSBD),which currently categorizes 1677 catalytic bioparts and 384 regulatory elements and provides information on 309 species and 850 chemicals.Online bioinformatics tools including local BLAST,chem similarity,phylogenetic analysis,and visual strength are provided to assist with the rational design of genetic circuits for manipulation of gene expression in planta.We demonstrated the utility of the PSBD by functionally characterizing taxadiene synthase 2 and its quan-titative regulation in tobacco leaves.More powerful synthetic devices were then assembled to amplify the transcriptional signals,enabling enhanced expression offlavivirus non-structure 1 proteins in plants.The PSBD is expected to be an integrative and user-centered platform that provides a one-stop service for diverse applications in plant synthetic biology research.

From qualitative to quantitative:the state of the art and challenges for plant synthetic biology

Backgrounds:As an increasing number of synthetic switches and circuits have been created for plant systems and of synthetic products produced in plant chassis,plant synthetic biology is taking a strong foothold in agriculture and medicine.The ever-exploding data has also promoted the expansion of toolkits in this field.Genetic parts libraries and quantitative characterization approaches have been developed.However,plant synthetic biology is still in its infancy.The considerations for selecting biological parts to design and construct genetic circuits with predictable functions remain desired.Results:In this article,we review the current biotechnological progresses in field of plant synthetic biology.Assembly standardization and quantitative approaches of genetic parts and genetic circuits are discussed.We also highlight the main challenges in the iterative cycles of design-build-test-learn for introducing novel traits into plants.Conclusion:Plant synthetic biology promises to provide important solutions to many issues in agricultural production,human health care,and environmental sustainability.However,tremendous challenges exist in this field.For example,the quantitative characterization of genetic parts is limited;the orthogonality and the transfer functions of circuits are unpredictable;and also,the mathematical modeling-assisted circuits design still needs to improve predictability and reliability.These challenges are expected to be resolved in the near future as interests in this field are intensifying.

The CRISPR/Cas revolution continues: From efficient gene editing for crop breeding to plant synthetic biology

Since the discovery that nucleases of the bacterial CRISPR(clustered regularly interspaced palindromic repeat)-associated(Cas) system can be used as easily programmable tools for genome engineering,their application massively transformed different areas of plant biology. In this review, we assess the current state of their use for crop breeding to incorporate attractive new agronomical traits into specific cultivars of various crop plants. This can be achieved by the use of Cas9/12 nucleases for double-strand break induction,resulting in mutations by non-homologous recombinatr e-tion. Strategies for performing such experiments à from Rthe design of guide RNA to the use of different transformation technologies à are evaluated. Furtherweive-more, we sum up recent developments regarding the use of nuclease-deficient Cas9/12 proteins, as DNAbinding moieties for targeting different kinds of enzyme activities to specific sites within the genome. Progress in base deamination, transcriptional induction and transcriptional repression, as well as in imaging in plants, is also discussed. As different Cas9/12 enzymes are at hand, the simultaneous application of various enzyme activities, to multiple genomic sites, is now in reach to redirect plant metabolism in a multifunctional manner and pave the way for a new level of plant synthetic biology.

Plant synthetic biology: One answer to global challenges

In times of climate change, population growth and resource depletion, the future well-being of mankind will greatly depend on the ability to breed/engineer crop plants for high yield, low input and high quality.Based on the evaluation of historical yield increases, it seems that yield of major grain crops, such as rice or

Synthetic biology of plant natural products: From pathway elucidation to engineered biosynthesis in plant cells

Plant natural products(PNPs)are the main sources of drugs,food additives,and new biofuels and have become a hotspot in synthetic biology.In the past two decades,the engineered biosynthesis of many PNPs has been achieved through the construction of microbial cell factories.Alongside the rapid development of plant physiology,genetics,and plant genetic modification techniques,hosts have now expanded from single-celled microbes to complex plant systems.Plant synthetic biology is an emerging field that combines engineering principles with plant biology.In this review,we introduce recent advances in the biosynthetic pathway elucidation of PNPs and summarize the progress of engineered PNP biosynthesis in plant cells.Furthermore,a future vision of plant synthetic biology is proposed.Although we are still a long way from overcoming all the bottlenecks in plant synthetic biology,the ascent of this field is expected to provide a huge opportunity for future agriculture and industry.