Plant Engineering Lags A Decade Behind

This week, a Science paper reports how simple genetic circuits can be assembled in plants.

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Many of the world’s greatest artists — Jimi Hendrix, Janis Joplin, Jim Morrison, Jean-Michel Basquiat, Kurt Cobain, Amy Winehouse — died at the age of 27. Today, I turn 28.

Plant synthetic biology is at least a decade behind. We’ve been building complex genetic circuits in bacteria, yeast, and mammalian cells for ages. Plants? Not so much.

This week, a Science paper reports how simple genetic circuits can be assembled in plants. For those who say, “synthetic biology is a mature field,” read the paper and ask yourself: Can this field truly be called ‘mature’ if it has only recently implemented its most promising tools in, arguably, our planet’s most useful organisms?

Engineering plants is surely among the most important things that synthetic biologists can do. Nitrogen-fixing roots, larger crops, drought-resistant plants — all of these advances will help ameliorate climate change and feed 10 billion people by 2050, as I wrote about last week, in the face of water scarcity and record heat waves. Why, then, aren’t we devoting more resources to plant synthetic biology?

Just look at funding data from the National Science Foundation. The NSF has awarded roughly $13 million to explicitly plant-focused projects since 2015. That’s out of more than $238 million, total, for systems and synthetic biology grants.

The latest Science paper from Brophy et al. (and another paper, published last month in Nature Biotechnology) emphasize just how difficult it is to implement even simple genetic circuits in plants, compared with other organisms.

The Science study reports a collection of synthetic promoters — inducible and constitutive, activatable and repressible — and engineered transcription factors to control gene expression in plants. These genetic parts were used to construct genetic circuits capable of Boolean logic operations in N. benthamiana and Arabidopsis. The authors also built logic gates that could control gene expression levels in plant roots to control their lateral densities. This paper presents a basic, genetic toolkit for plants — and that was enough for Science.

Don’t get me wrong; this is a great paper. It really is the state-of-the-art for published work in plant engineering. And that’s the problem: Grant-making and academic incentives that prioritize rapid results have enabled the massive gap that now divides E. coli and plant synthetic biology.

Still, there is much to be excited about. Ongoing work from Chris Voigt, Mark Isalan and other groups will, I’m sure, continue to push the envelope in plant engineering. Lots of companies are also using microbes to replace environmentally-destructive nitrogen manufacturing processes (see Pivot Bio, Joyn Bio, and Kula Bio) because it’s easier to engineer commensal microbes than plant roots directly. I remain excited about efforts to engineer Rubisco and synthetic photosynthesis pathways to boost crop yields.

But our future needs are clear: More investments to develop robust tools for plant engineering and, perhaps, a greater emphasis on private-public partnerships to develop crops that can materially improve our planet.

This issue of Index also features on-demand vaccines and Himalayan microbial pigments. Plus, a paper from the Journal of Fish Diseases! Hurray.

Bio(tech) Index

(↑ = recommended article, * = open access, † = review, comment, etc. )

Basic Research

↑Prokaryotic innate immunity through pattern recognition of conserved viral proteins. Gao LA…Zhang F. Science. Link

Nested epistasis enhancer networks for robust genome regulation. Lin X…Qi LS. Science. Link

*4-bit adhesion logic enables universal multicellular interface patterning. Kim H…Riedel-Kruse IH. Nature. Link

↑*A systematic, complexity-reduction approach to dissect the kombucha tea microbiome. Huang X, Xin Y & Lu T. eLife. Link // News article

Rational engineering of a synthetic insect-bacterial mutualism. Su Y…Dale C. Current Biology. Link

*Connecting single-cell ATP dynamics to overflow metabolism, cell growth, and the cell cycle in Escherichia coli. Lin W-H & Jacobs-Wagner C. Current Biology. Link

*Rapid evolution of mutation rate and spectrum in response to environmental and population-genetic challenges. Wei W…Lynch M. Nature Communications. Link

Robustness of DNA looping across multiple cell divisions in individual bacteria. Chang C…Cluzel P. PNAS. Link

*Widespread repression of anti-CRISPR production by anti-CRISPR-associated proteins. Shehreen S…Brown CM. Nucleic Acids Research. Link

Biomanufacturing & Metabolic Engineering

↑*A low-cost, thermostable, cell-free protein synthesis platform for on demand production of conjugate vaccines. Warfel KF…Jewett MC. bioRxiv (preprint). Link

  • Adding maltodextrin to cell-free reactions enhances their thermostability — by a big margin. Cell-free extracts with added maltodextrin “produce conjugate vaccines for ~$0.50 per dose after storage at room temperature or 37 °C for up to 4 weeks and ~$1.00 per dose after storage at 50 °C for up to 4 weeks.” The vaccines were administered to mice and proved effective at preventing E. coli O78:H11 infections.

*Implementation of the β-hydroxyaspartate cycle increases growth performance of Pseudomonas putida on the PET monomer ethylene glycol. von Borzyskowski LS…Erb TJ. bioRxiv (preprint). Link

Biosynthesis of tetrahydropapaverine and semisynthesis of papaverine in yeast. Jamil OK…Smolke CD. PNAS. Link

*Biosynthesis of insect sex pheromone precursors via engineered β-oxidation in yeast. Petkevicius K…Borodina I. FEMS Yeast Research. Link

Escherichia coli minicells with targeted enzymes as bioreactors for producing toxic compounds. Kim S-J, Chang W & Oh M-K. Metabolic Engineering. Link

*Evaluating and mitigating clinical samples matrix effects on TX-TL cell-free performance. Voyvodic PL…Bonnet J. Scientific Reports. Link

Development of a nonauxotrophic L-homoserine hyperproducer in Escherichia coli by systems metabolic engineering. Cai M…Rao Z. Metabolic Engineering. Link

De novo production of versatile oxidized kaurene diterpenes in Escherichia coli. Sun Y…Wang Y. Metabolic Engineering. Link

*Directed Evolution of (R)-2-Hydroxyglutarate Dehydrogenase Improves 2-Oxoadipate Reduction by 2 Orders of Magnitude. Saez-Jimenez V…Olsson L. ACS Synthetic Biology. Link

Cell-Free Protein Synthesis from Exonuclease-Deficient Cellular Extracts Utilizing Linear DNA Templates. Azad MS…Kushwaha M. JoVE Journal. Link

*Effects of DNA Template Preparation on Variability in Cell-Free Protein Production. Romantseva E…Strychalski EA. Synthetic Biology. Link

Kluyveromyces marxianus as a microbial cell factory for lignocellulosic biomass valorisation. Baptista M & Domingues L. Biotechnology Advances. Link

Biosensors & Biomaterials

*Integrating CRISPR-Cas12a with a crRNA-Mediated Catalytic Network for the Development of a Modular and Sensitive Aptasensor. Shu X…Yan Y. ACS Synthetic Biology. Link

†*A Framework for the Systematic Selection of Biosensor Chassis for Environmental Synthetic Biology. Sridhar S, Ajo-Franklin CM & Masiello CA. ACS Synthetic Biology. Link

Computational Tools & Models

*Nonlinear manipulation and analysis of large DNA datasets. Cui M…Zhang Y. Nucleic Acids Research. Link

†An interactive metabolic map of bio-based chemicals. Jang WD, Kim GB & Lee SY. Trends in Biotechnology. Link

*A method for Boolean analysis of protein interactions at a molecular level. Raykova D…Söderberg O. Nature Communications. Link

*A resource for the comparison and integration of heterogeneous microbiome networks. Hu Z…Segrè D. bioRxiv (preprint). Link

CRISPR & Gene Editing

↑High-fidelity Cas13 variants for targeted RNA degradation with minimal collateral effects. Tong H…Yang H. Nature Biotechnology. Link

*Programmable RNA targeting by bacterial Argonaute nucleases with unconventional guide binding and cleavage specificity. Lisitskaya L…Kulbachinskiy A. Nature Communications. Link

*CRISPR-RNAa: targeted activation of translation using dCas13 fusions to translation initiation factors. Otoupal PB…Schoeniger JS. Nucleic Acids Research. Link

*Ultra-deep sequencing validates safety of CRISPR/Cas9 genome editing in human hematopoietic stem and progenitor cells. Cromer MK…Porteus MH. Nature Communications. Link

↑*Cytosine base editing systems with minimized off-target effect and molecular size. Li A…Nishida K. Nature Communications. Link

Designing and executing prime editing experiments in mammalian cells. Doman JL…Liu DR. Nature Protocols. Link

Gene Drives

↑*A multiplexed, confinable CRISPR/Cas9 gene drive propagates in caged Aedes aegypti populations. Anderson MAE…Alphey L. bioRxiv (preprint). Link

Medicine & Diagnostics

*An open-label pilot study of recombinant granulocyte-colony stimulating factor in Friedreich’s ataxia. Kemp KC…Wilkins A. Nature Communications. Link

↑*Rapid detection of SARS-CoV-2 RNA in saliva via Cas13. Chandrasekaran SS…Hsu PD. Nature Biomedical Engineering. Link

  • An assay detects SARS-CoV-2 with a fluorescent readout within 60 minutes. The assay has an acronym (of course) — it’s called DISCoVER (diagnostics with coronavirus enzymatic reporting), which is…a stretch. DISCoVER can detect the virus in saliva with a sensitivity of 40 copies per microliter. It is 94% sensitive and 100% specific, and was tested against 33 SARS-CoV-2-positive nasal swab samples. It works by extracting saliva —> lysing the sample —> isothermal RNA amplification and T7 transcription —> Cas13-mediated quenching of a fluorophore. The assay is bundled into a little microfluidics device. Besides being less labor-intensive and faster than qPCR, how is this an improvement over current tests? I’d assume that, like, 90% of countries on earth don’t have access to these technologies.

*Engineered IL13 variants direct specificity of IL13Rα2-targeted CAR T cell therapy. Stern LA…Brown CE. PNAS. Link

*Programmable DARPin-based receptors for the detection of thrombotic markers. Strittmatter T…Fussenegger M. Nature Chemical Biology. Link

Adenoviral-based vaccine promotes neoantigen-specific CD8+ T cell stemness and tumor rejection. D’Alise AM…Pace L. Science Translational Medicine. Link

Generation of T-cell-receptor-negative CD8αβ-positive CAR T cells from T-cell-derived induced pluripotent stem cells. van der Stegen SJC…Sadelain M. Nature Biomedical Engineering. Link

Differentiation of crescent-forming kidney progenitor cells into podocytes attenuates severe glomerulonephritis in mice. Melica ME…Romagnani P. Science Translational Medicine. Link

*Generation of a CRISPR activation mouse that enables modelling of aggressive lymphoma and interrogation of venetoclax resistance. Deng Y…Herold MJ. Nature Communications. Link

*A CRISPR-based ultrasensitive assay detects attomolar concentrations of SARS-CoV-2 antibodies in clinical samples. Tang Y…Li F. Nature Communications. Link

*Development of a pentavalent broadly protective nucleoside-modified mRNA vaccine against influenza B viruses. Pardi N…McMahon M. Nature Communications. Link

*A suite of PCR-LwCas13a assays for detection and genotyping of Treponema pallidum in clinical samples. Chen W…Zheng H. Nature Communications. Link

Plants

↑Synthetic genetic circuits as a means of reprogramming plant roots. Brophy JAN…Dinneny JR. Science. Link

Natural variation identifies new effectors of water-use efficiency in Arabidopsis. Bhaskara GB…Juenger TE. PNAS. Link

*FAR knockout significantly inhibits Chilo suppressalis survival and transgene expression of double-stranded FAR in rice exhibits strong pest resistance. Sun Y…Qiu L. Plant Biotechnology Journal. Link

Protein & Molecular Engineering

*A 33-residue peptide tag increases solubility and stability of Escherichia coli produced single-chain antibody fragments. Wang Y…Wang Y-X. Nature Communications. Link

Tools & Technology

*Optogenetic control of cell signaling with red/far-red light-responsive optogenetic tools in Caenorhabditis elegans. Oda S…Aoki K. bioRxiv (preprint). Link

From empirical to data-driven host selection: a broad-host-range expression platform to facilitate chassis screening. Mol V…Jensen SI. bioRxiv (preprint). Link

*Method for Reproducible Automated Bacterial Cell Culture and Measurement. Ross, D, Tonner PD & Vasilyeva OB. Synthetic Biology. Link

*Onepot-Seq: capturing single-cell transcriptomes simultaneously in a continuous medium via transient localization of mRNA. Shin D…bang D. Nucleic Acids Research. Link

*Mobile Translation Systems Generate Genomically Engineered Escherichia coli Cells with Improved Growth Phenotypes. Gowland S & Jewett MC. ACS Synthetic Biology. Link

†*Standardization of Synthetic Biology Tools and Assembly Methods for Saccharomyces cerevisiae and Emerging Yeast Species. Malcı K…Rios-Solis L. ACS Synthetic Biology. Link

Other…

↑†*Microbial pigments: Learning from Himalayan perspective to industrial applications. Kumar S…Singh D. Journal of Industrial Microbiology and Biotechnology. Link

  • A review about microbial pigments in remote, inaccessible regions of the Himalayas, written by scientists from the Himalayas. There are pinkish-reds, deep yellows, and prodgiosin reds from organisms like Serratia nematodiphila and Rhodonellum psychrophilium. The review even explains where the microbes can be found, including Pangong Tso Lake and the Himalayan glaciers of Uttarakhand, India.
File:Pangong Tso lake.jpg - Wikimedia Commons
Pangong Tso lake. Wikimedia photo by dipak123.

*Evaluating the Persistence and Stability of a DNA-Barcoded Microbial System in a Mock Home Environment. McDonald ND…Buckley PE. Synthetic Biology. Link

↑†*Synthetic biology landscape in the UK. Wachter GKA…Horsfall L. Biotechnology Notes. Link

Smartphone-compatible, CRISPR-based platforms for sensitive detection of acute hepatopancreatic necrosis disease in shrimp. Naranitus P…Chaijarasphong T. Journal of Fish Diseases. Link


More soon,

— Niko McCarty

Twitter: @NikoMcCarty