Latest Research in Synthetic Biology

This is the second edition of Cell Crunch Index. Every Monday, notable research papers are compiled. Research explainers, Q&As and other writing are sent out on other weekdays.

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Good morning.

This is the second edition of Cell Crunch Index. Every Monday, notable research papers are compiled. Research explainers, Q&As and other writing are sent out on other weekdays. Thanks for reading.

Notable Papers

( * = open access, † = review article)

*Sonogenetic control of mammalian cells using exogenous Transient Receptor Potential A1 channels. Duque M. et al. Nature Communications.

*Protein nanowires with tunable functionality and programmable self-assembly using sequence-controlled synthesis. Shapiro D.M. et al. Nature Communications.

Genome-edited powdery mildew resistance in wheat without growth penalties. Li S. et al. Nature.

Basic Research

Cleavage of viral DNA by restriction endonucleases stimulates the type II CRISPR-Cas immune response. Maguin P. et al. Molecular Cell.

*Prime editing efficiency and fidelity are enhanced in the absence of mismatch repair. Ferreira da Silva J. et al. Nature Communications.

Modulation of microbial community dynamics by spatial partitioning. Wu F. et al. Nature Chemical Biology.

*In vivo CRISPR screens reveal a HIF-1α-mTOR-network regulates T follicular helper versus Th1 cells. Huang B. et al. Nature Communications.

*Deficiency of ribosomal proteins reshapes the transcriptional and translational landscape in human cells. Luan Y. et al. Nucleic Acids Research.

*Transcription-replication coordination revealed in single live cells. Tsirkas I. et al. Nucleic Acids Research.

Comprehensive interrogation of the ADAR2 deaminase domain for engineering enhanced RNA editing activity and specificity. Katrekar D. et al. eLife.

Computation

*Data-informed discovery of hydrolytic nanozymes. Li S. et al. Nature Communications.

Enhancing computational enzyme design by a maximum entropy strategy. Xie W.J., Asadi M. & Warshel A. PNAS.

*Whole-cell modeling in yeast predicts compartment-specific proteome constraints that drive metabolic strategies. Elsemman I.E. et al. Nature Communications.

*Protein sequence design with a learned potential. Anand N. et al. Nature Communications.

Genetic Engineering

dCas9-VPR-mediated transcriptional activation of functionally equivalent genes for gene therapy. Riedmayr L.M. et al. Nature Protocols.

*In vivo mitochondrial base editing via adeno-associated viral delivery to mouse post-mitotic tissue. Silva-Pinheiro P. et al. Nature Communications.

Engineered circular ADAR-recruiting RNAs increase the efficiency and fidelity of RNA editing in vitro and in vivo. Yi Z. et al. Nature Biotechnology.

Efficient in vitro and in vivo RNA editing via recruitment of endogenous ADARs using circular guide RNAs. Katrekar D. et al. Nature Biotechnology.

Medicine & Diagnostics

*Induction of tier-2 neutralizing antibodies in mice with a DNA-encoded HIV envelope native like trimer. Xu Z. et al. Nature Communications.

GD2-CAR T cell therapy for H3K27M-mutated diffuse midline gliomas. Majzner R.G. et al. Nature.

*Development of a skin- and neuro-attenuated live vaccine for varicella. Wang W. et al. Nature Communications.

*An optogenetic approach for regulating human parathyroid hormone secretion. Liu Y. et al. Nature Communications.

*Glycosite-deleted mRNA of SARS-CoV-2 spike protein as a broad-spectrum vaccine. Wu C. et al. PNAS.

Reversal of RNA toxicity in myotonic dystrophy via a decoy RNA-binding protein with high affinity for expanded CUG repeats. Arandel L. et al. Nature Biomedical Engineering.

Metabolic Engineering

Modular, synthetic chromosomes as new tools for large scale engineering of metabolism. Postma E.D. et al. Metabolic Engineering.

*Reconstituting the complete biosynthesis of D-lysergic acid in yeast. Wong G. et al. Nature Communications.

Production of Caffeic Acid with Co-fermentation of Xylose and Glucose by Multi-modular Engineering in Candida glycerinogenes. Wang X. et al. ACS Synthetic Biology.

Regulatory Part Engineering for High-Yield Protein Synthesis in an All-Streptomyces-Based Cell-Free Expression System. Xu H. et al. ACS Synthetic Biology.

Harnessing electrical-to-biochemical conversion for microbial synthesis. Fang Z., Tang Y.J. & Koffas M.A.G. Current Opinion in Biotechnology.

Molecular Engineering

Tailored enzymes as next-generation food-packaging tools. Sharma V.K. et al. Trends in Biotechnology.

NTR 2.0: a rationally engineered prodrug-converting enzyme with substantially enhanced efficacy for targeted cell ablation. Sharrock A.V. et al. Nature Methods.

*†Hot spots-making directed evolution easier. Yu H. et al. Biotechnology Advances.

*Defining molecular glues with a dual-nanobody cannabidiol sensor. Cao S. et al. Nature Communications.

*Engineering and exploiting synthetic allostery of NanoLuc luciferase. Guo Z. et al. Nature Communications.

Building an RNA-Based Toggle Switch Using Inhibitory RNA Aptamers. Climent-Catala A. et al. ACS Synthetic Biology.

New opportunities for genetic code expansion in synthetic yeast. Sanders J. et al. Current Opinion in Biotechnology.

Tools & Technology

*Versioning biological cells for trustworthy cell engineering. Tellechea-Luzardo J. et al. Nature Communications.

*A genetically encoded sensor for in vivo imaging of orexin neuropeptides. Duffet L. et al. Nature Methods.

*A programmable high-expression yeast platform responsive to user-defined signals. Liu Q. et al. Science Advances.

*†How to train your cell - Towards controlling phenotypes by harnessing the epigenome of Chinese hamster ovary production cell lines. Marx N. et al. Biotechnology Advances.

*Barcode fusion genetics-protein-fragment complementation assay (BFG-PCA): tools and resources that expand the potential for binary protein interaction discovery. Evans-Yamamoto D. et al. Nucleic Acids Research.

A scalable pipeline for SARS-CoV-2 replicon construction based on de-novo synthesis. Berkyurek A.C. et al. bioRxiv (preprint).

*Micro-mechanical blood clot testing using smartphones. Chan J. et al. Nature Communications.

Miscellaneous

An autonomously swimming biohybrid fish designed with human cardiac biophysics. Lee K.Y. et al. Science.

*Nonenzymatic assembly of active chimeric ribozymes from aminoacylated RNA oligonucleotides. Radakovic A. et al. PNAS.

*†Peptides before and during the nucleotide world: an origins story emphasizing cooperation between proteins and nucleic acids. Fried S.D. et al. Journal of the Royal Society Interface.

*Origin of life: protoribosome forms peptide bonds and links RNA and protein dominated worlds. Bose T. et al. Nucleic Acids Research.

Spotting-based differentiation of functional dopaminergic progenitors from human pluripotent stem cells. Kim J. et al. Nature Protocols.

Long-Lasting and Responsive DNA/Enzyme-Based Programs in Serum-Supplemented Extracellular Media. Galas J. et al. ACS Synthetic Biology.

Until next time,

Niko