Ribosomes Make Ribosomes Outside a Cell: Index #65
And how I make this newsletter.
People often ask about my ‘process’ in making this newsletter. So here it is:
I’ve made a list of all the journals that a) seem reasonably reputable and b) publish synthetic biology research.
I run a Python script to ‘visit’ each journal, each week, and retrieve potential papers for this newsletter. This was harder to figure out than it sounds and required some classification algorithms to differentiate between e.g. biopharma and synthetic biology.
I manually screen the papers and read the abstracts. I (try to) add good ones to this email.
This newsletter features ribosomes making ribosomes in vitro … yeast engineered with the largest biosynthetic pathway to-date … Jay Keasling’s Twitter habits … and a slew of computational tools to design DNA with predictable expression levels. Thanks for reading.
Bio(tech) Index
(↑ = recommended article, * = open access, † = review, comment, etc. )
Basic Research
↑Horizontal gene transfer enables programmable gene stability in synthetic microbiota. Wang T…You L. Nature Chemical Biology. Link
↑*Reconstitution of ribosome self-replication outside a living cell. Kosaka Y…Aoki W. bioRxiv (preprint). Link
Building a ribosome — that megalithic protein that makes other proteins — is very complicated. The ribosome itself is built from 54 protein pieces, and its jigsaw-like assembly is orchestrated by about 100 “accessory factors.”
Many people have dreamt of making ribosomes that can make more ribosomes in vitro, because it’d help us build synthetic cells, or make longer-lasting cell-free systems to manufacture medicines. And by building ribosomes in a test tube, we could easily engineer them to manufacture other types of polymers — not just proteins. Indeed, this is a driving mission of Jason Chin’s group at the MRC LMB, and I’ve previously outlined one option for doing this in a technical report (which I used in a PhD application to work with — you guessed it — Jason Chin).
Now a Japanese group has done it; they’ve reconstituted ribosome biogenesis outside of a living cell. This paper was so good, I woke up at like 8 A.M. on Saturday to tweet about it. The team started with a cell-free extract from E. coli (which already has the accessory factors) and then used polymerase and ribosomes to transcribe and translate the 54 genes that encode the various ribosome pieces. They also transcribed the three rRNAs that comprise a ribosome’s catalytic activity. With some molecular tweaks, their approach actually worked — the myriad pieces came together to build functional ribosomes. This paper thus solves “ one of the largest long-standing challenges in synthetic biology.”
*Dynamic mechanisms of CRISPR interference by Escherichia coli CRISPR-Cas3. Yoshimi K…Mashimo T. Nature Communications. Link
*A gene cluster in Ginkgo biloba encodes unique multifunctional cytochrome P450s that initiate ginkgolide biosynthesis. Forman V…Pateraki I. Nature Communications. Link
*The pathway for coenzyme M biosynthesis in bacteria. Wu H-H…Peters JW. PNAS. Link
Biomanufacturing & Metabolic Engineering
↑*A microbial supply chain for production of the anti-cancer drug vinblastine. Zhang J…Keasling JD. Nature. Link
Vinblastine is a chemotherapy drug. It’s injected directly into the veins and is used to treat specific cancers, often with devastating side effects. The drug itself is isolated from the Madagascar Periwinkle plant, or Catharanthus roseus, in a low-yield extraction process.
Now, yeast have been engineered to produce not vinblastine, but a precursor molecule, using a 30-step biosynthetic pathway. This is the longest biosynthetic pathway ever engineered into yeast. It required 56 genetic edits, the expression of 34 genes from plants, and the over- or underexpression of 10 yeast genes. The result: Yeast can build monoterpene indole alkaloids and “a virtually infinite number of new-to-nature analogues.”
Also, Jay Keasling tweets like three times a year (and didn’t tweet at all in 2020). So when he does, you know the paper’s gonna be a banger.
*Carbon Catabolite Repression Relaxation: Approaches for Sugar Co-Utilization in Escherichia coli. Fox KJ & Prather KJ. MIT Thesis. Link
Pushing and pulling proteins into the yeast secretory pathway enhances recombinant protein secretion. Zahrl RJ…Gasser B. Metabolic Engineering. Link
*Base editor enables rational genome-scale functional screening for enhanced industrial phenotypes in Corynebacterium glutamicum. Liu Y…Wang M. Science Advances. Link
Engineering diverse fatty acid compositions of phospholipids in Escherichia coli. Bai W…Zhang F. Metabolic Engineering. Link
†Killing two birds with one stone: chemical and biological upcycling of polyethylene terephthalate plastics into food. Schaerer LG…Techtmann SM. Trends in Biotechnology. Link
*Engineered nickel bioaccumulation in Escherichia coli by NikABCDE transporter and metallothionein overexpression. Diep P…Mahadevan R. bioRxiv (preprint). Link
Build-A-Cell
*Spatiotemporal control of signal-driven enzymatic reaction in artificial cell-like polymersomes. Seo H & Lee H. Nature Communications. Link
Computational Tools & Models
↑*Automated model-predictive design of synthetic promoters to control transcriptional profiles in bacteria. LaFleur TL, Hossain A & Salis HM. Nature Communications. Link
A new Promoter Calculator “predicts sigma70 transcription rates at every site across an arbitrary DNA sequence,” according to a worthwhile Twitter thread from Howard Salis. The tool can accurately predict transcription rates, too, and uses 346 different “interaction energies” to quantify interactions between RNA polymerase protein and sigma70 sequences. It was used to design promoters with transcription levels that range 1525-fold. (The paper below also looks useful; it reports a GAN that can generate “regulatory DNA with prespecified target mRNA levels.”)
↑*Controlling gene expression with deep generative design of regulatory DNA. Zrimec J…Zelezniak A. Nature Communications. Link
↑*The automated Galaxy-SynBioCAD pipeline for synthetic biology design and engineering. Hérisson J…Faulon J-L. Nature Communications. Link
*CoRa—A general approach for quantifying biological feedback control. Gómez-Schiavon M & El-Samad H. PNAS. Link
*Environment-specificity and universality of the microbial growth law. Wang Q & Lin J. Communications Biology. Link
*The interplay between metabolic stochasticity and regulation in single E. coli cells. Wehrens M…Tans SJ. bioRxiv (preprint). Link
CRISPR & Gene Editing
*Programmable RNA base editing with a single gRNA-free enzyme. Han W…Wang Z. Nucleic Acids Research. Link
*Small-molecule activators specific to adenine base editors through blocking the canonical TGF-β pathway. Yang Y…Zhang M. Nucleic Acids Research. Link
*Chemically synthesized guide RNAs can direct CRISPR-CasRx cleavage of circRNAs with high efficiency and specificity. Rahimi K…Kjems J. bioRxiv (preprint). Link
Gene Editing in Random Organisms
Genome Editing by CRISPR/Cas12 Recognizing AT-Rich PAMs in Shewanella oneidensis MR-1. Chen Y…Cao Y. ACS Synthetic Biology. Link
*Gene editing in the nematode parasite Nippostrongylus brasiliensis using extracellular vesicles to deliver active Cas9/guide RNA complexes. Hagen J…Selkirk ME. bioRxiv (preprint). Link
*Polycomb response elements reduce leaky expression of Cas9 under temperature-inducible Hsp70Bb promoter in Drosophila melanogaster. Warsinger-Pepe N…Akbari OS. bioRxiv (preprint). Link
*Efficient gene delivery into the embryonic chicken brain using neuron-specific promoters and in ovo electroporation. Jung KM…Han JY. BMC Biotechnology. Link
Genetic Circuits
*A Network Approach to Genetic Circuit Designs. Crowther M, Wipat A & Goñi-Moreno Á. ACS Synthetic Biology. Link
Gene Synthesis & Assembly
*DeepConsensus improves the accuracy of sequences with a gap-aware sequence transformer. Baid G…Carroll A. Nature Biotechnology. Link
Medicine & Diagnostics
*Non-viral, specifically targeted CAR-T cells achieve high safety and efficacy in B-NHL. Zhang J…Huang H. Nature. Link
Quantitative immunopeptidomics reveals a tumor stroma–specific target for T cell therapy. Kim GB…Riley JL. Science Translational Medicine. Link
Cardioprotective factors against myocardial infarction selected in vivo from an AAV secretome library. Ruozi G…Giacca M. Science Translational Medicine. Link
Prebiotics-Controlled Disposable Engineered Bacteria for Intestinal Diseases. Fang T-T…Ye B-C. ACS Synthetic Biology. Link
Plants
*GB_SynP: A Modular dCas9-Regulated Synthetic Promoter Collection for Fine-Tuned Recombinant Gene Expression in Plants. Moreno-Giménez E…Orzáez D. ACS Synthetic Biology. Link
CRISPR/Cas-based precision gene replacement in plants via homologous recombination-independent approaches. Vu TV…Kim J-Y. bioRxiv (preprint). Link
*Engineering plant immune circuit: walking to the bright future with a novel toolbox. Vuong UT…Kim SH. Plant Biotechnology Journal. Link
*Metabolic engineering of energycane to hyperaccumulate lipids in vegetative biomass. Luo G…Altpeter F. BMC Biotechnology. Link
Protein & Molecular Engineering
↑*Accurate de novo design of membrane-traversing macrocycles. Bhardwaj G…Baker D. Cell. Link
↑Affinity-matured DLL4 ligands as broad-spectrum modulators of Notch signaling. Gonzalez-Perez D…Luca VC. Nature Chemical Biology. Link
*Rational engineering of a β-glucosidase (H0HC94) from glycosyl family I (GH1) to improve catalytic performance on cellobiose. Sengupta S…Datta S. bioRxiv (preprint). Link
*Directed evolution of phosphite dehydrogenase to cycle noncanonical redox cofactors via universal growth selection platform. Zhang L…Li H. Nature Communications. Link
†Design and engineering of genetically encoded protein biosensors for small molecules. Leonard AC & Whitehead TA. Current Opinion in Biotechnology. Link
Tools & Technology
↑helixCAM: A platform for programmable cellular assembly in bacteria and human cells. Chao G…Church GM. Cell. Link
*A method for targeting a specified segment of DNA to a bacterial microorganelle. Otoničar J…Butala M. Nucleic Acids Research. Link
*Manipulating complex chromatin folding via CRISPR-guided bioorthogonal chemistry. Qin G…Qu X. PNAS. Link
†Two-photon calcium imaging of neuronal activity. Grienberger C…Portera-Cailliau C. Nature Reviews Methods Primers. Link
*An Easy-to-Use Plasmid Toolset for Efficient Generation and Benchmarking of Synthetic Small RNAs in Bacteria. Köbel TS…Schindler D. ACS Synthetic Biology. Link
*A visualization reporter system for characterizing antibiotic biosynthetic gene clusters expression with high-sensitivity. Liu X…Tan H. Communications Biology. Link
Rapid screening of antimicrobial probiotics using CRISPR cascade. Lu Y…Deng R. Biosensors and Bioelectronics. Link
Other…
*Engineered endosymbionts that alter mammalian cell surface marker, cytokine and chemokine expression. Madsen CS…Contag CH. Communications Biology. Link
↑*A confinable female-lethal population suppression system in the malaria vector, Anopheles gambiae. Smidler AL…Akbari OS. bioRxiv (preprint). Link
*Beyond the Brick: Collaborations with a Sensing Microbial System in the Built Environment. Maria Gonzalez L. MIT Thesis. Link
More soon,
— Niko McCarty
Twitter: @NikoMcCarty // Email: niko@newscience.org