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Nine Epigenetic Editing Tools: Index #66
Plus: AlphaFold is bad at drug discovery (at least, for predicting antibiotic-protein interactions.)
Welcome to Codon. Each week, I highlight biotechnology advances. Sometimes I publish essays, too. Subscribe for free:
President Biden signed an Executive Order yesterday, outlining plans for a U.S. Biotechnology and Biomanufacturing Initiative. No budget details just yet — those will come on Wednesday. But it’s worth noting that the national semiconductor industry accounts for about 1% of the total economy — five times less than biomanufacturing and biotechnology — and the House recently approved a $52 billion bill to help their domestic manufacturing.
Also: If you live in the Boston area, there’s a free event, “A Celebration of Synthetic Biology,” at Harvard Medical School on October 25. Great speaker lineup, and you can learn more or register here.
This newsletter features new epigenome editing tools, a semi-automated way to evolve proteins with new abilities, and explains why AlphaFold is (probably) bad at drug discovery. Thanks for reading.
(↑ = recommended article, * = open access, † = review, comment, etc. )
↑*Systematic Epigenome Editing Captures the Context-dependent Instructive Function of Chromatin Modifications. Policarpi C…Hackett JA. bioRxiv (preprint). Link
A beautiful paper that reports a suite of epigenetic editing tools to add nine different types of chromatin modifications to specific sites in DNA. The authors fused catalytically inactivated Cas9 protein to a slew of different “effector” proteins. Each of these fusion proteins can add a different type of epigenetic modification, including methyl groups, H3K4me3, and many others. The Cas9 fusion proteins only modify the epigenome after they are switched on with doxycycline, a chemical.
Towards the end of the paper, the authors demonstrate that adding H3K4me3 groups to promoters, in mouse cells, “causally instructs transcription activation by hierarchically remodeling the chromatin landscape.” This study is a gem, and you should check it out.
↑Biosynthesis of selenium-containing small molecules in diverse microorganisms. Kayrouz CM…Seyedsayamdost MR. Nature. Link
↑*Microbial biofilms as living photoconductors due to ultrafast electron transfer in cytochrome OmcS nanowires. Neu J…Malvankar NS. Nature Communications. Link
*Biosignature stability in space enables their use for life detection on Mars. Baqué M…De Vera J-P.P. Science Advances. Link
*Systematic analysis of low-affinity transcription factor binding site clusters in vitro and in vivo establishes their functional relevance. Shahein A…Maerkl SJ. Nature Communications. Link
*Aging is associated with increased chromatin accessibility and reduced polymerase pausing in liver. Bozukova M…Tessarz P. Molecular Systems Biology. Link
Delayed In Vivo Encapsulation of Enzymes Alters the Catalytic Activity of Virus-Like Particle Nanoreactors. Patterson DP…Bird J. ACS Synthetic Biology. Link
*Loss-of-function mutation survey revealed that genes with background-dependent fitness are rare and functionally related in yeast. Caudal E…Schacherer J. PNAS. Link
Biomanufacturing & Metabolic Engineering
↑*Generation of an Escherichia coli strain growing on methanol via the ribulose monophosphate cycle. Keller P…Vorholt JA. Nature Communications. Link
↑*Expanding the terpene biosynthetic code with non-canonical 16 carbon atom building blocks. Ignea C…Kampranis SC. Nature Communications. Link
*Production and secretion of recombinant proteins using the endotoxin-free, Gram-negative bacterium Sphingobium japonicum. Shahar E…Yadid I. bioRxiv (preprint). Link
*Engineering diverse fatty acid compositions of phospholipids in Escherichia coli. Bai W…Zhang F. Metabolic Engineering. Link
Metabolic engineering of E. coli for β-alanine production using a multi-biosensor enabled approach. Yuan S-F…Alper HS. Metabolic Engineering. Link
*Production of surfactant-stable keratinase from Bacillus cereus YQ15 and its application as detergent additive. Zhang R-X…Yang T-Y. BMC Biotechnology. Link
Computational Tools & Models
↑*Benchmarking AlphaFold-enabled molecular docking predictions for antibiotic discovery. Wong F…Collins JJ. Molecular Systems Biology. Link
AlphaFold2 and molecular simulations were combined to ask a simple question: Can we predict whether various antibacterial compounds bind to specific bacterial proteins? The answer, alas, is no.
Jim Collins’ team at MIT tested predictions for “protein-ligand interactions between 296 proteins spanning Escherichia coli's essential proteome, and 218 active antibacterial compounds and 100 inactive compounds.” But they found that computational tools and AI models were no better than chance at predicting the interactions.
AlphaFold2 is certainly an impressive tool, but we still need to train it on the sorts of datasets that are relevant to drug discovery. That means we need to solve more structures for interacting proteins or for mutated proteins or for proteins with disordered regions. Protein structures slip and morph in the presence of small molecules; AlphaFold cannot predict these changes.
Also, “it is very, very rare for knowledge of a protein’s structure to be any sort of rate-limiting step in a drug discovery project! That’s because you’re almost always running the project based on assays using the pure protein or with living cells,” writes Derek Lowe in Chemistry World. “Those numbers are supposed to answer the key questions: are these compounds doing what we want, and are they getting better as we make new ones? The protein’s structure might help generate ideas about what compounds to make next, but then again, it might not. In the end the real numbers from the real biological system are what matter.”
*Co-substrate pools can constrain and regulate pathway fluxes in cell metabolism. West R…Soyer OS. bioRxiv (preprint). Link
*MVsim is a toolset for quantifying and designing multivalent interactions. Bruncsics B, Errington WJ & Sarkar CA. Nature Communications. Link
*Accounting for small variations in the tracrRNA sequence improves sgRNA activity predictions for CRISPR screening. DeWeirdt PC…Doench JG. Nature Communications. Link
*devCellPy is a machine learning-enabled pipeline for automated annotation of complex multilayered single-cell transcriptomic data. Galdos FX…Wu SM. Nature Communications. Link
*Automated reconstruction of whole-embryo cell lineages by learning from sparse annotations. Malin-Mayor C…Funke J. Nature Biotechnology. Link
*Integrating and formatting biomedical data as pre-calculated knowledge graph embeddings in the Bioteque. Fernández-Torras A…Aloy P. Nature Communications. Link
CRISPR & Gene Editing
*High-throughput continuous evolution of compact Cas9 variants targeting single-nucleotide-pyrimidine PAMs. Huang TP…Liu DR. Nature Biotechnology. Link
Two labs in Boston — Ahmad Khalil and David Liu — teamed up to evolve small Cas9 proteins with a wider PAM targeting range. They succeeded, ultimately creating four new Cas9 variants for gene editing. Some of these variants have less restrictive PAM requirements, higher activity in human cells, and lower off-target activity at specific DNA sequences.
One of the new variants is derived from Nme2Cas9, which is a small Cas9 protein that edits mammalian genomes with little or no off-target effects. Normally, this protein can only recognize NNNNCC sequences (where N is any nucleotide in the DNA sequence). After the experiments, though, the protein could recognize most NNNNYN sequences, where Y is C or T. That’s a huge improvement, and it matters because PAM sequences are not always available near the genes we want to correct; whether or not the ‘right’ sequence exists can determine the whole scope of a precision gene editing project.
The Cas9 proteins were evolved by combining two systems: PANCE (a technique that uses phages to select for proteins with desired functions) and the Khalil lab’s eVOLVER, a DIY, continuous cell culture system.
Development of Base Editors for Simultaneously Editing Multiple Loci in Lactococcus lactis. Tian K…Qiao J. ACS Synthetic Biology. Link
*Base Editing for Reprogramming Cyanobacterium Synechococcus elongatus. Wang S-Y…Xia P-F. bioRxiv (preprint). Link
Gene Synthesis & Assembly
*Synthesis of point-modified mRNA. Hertler J…Helm M. Nucleic Acids Research. Link
Medicine & Diagnostics
↑*CRISPR-Cas12a-based detection of monkeypox virus. Sui Y…Liu J. Journal of Infection. Link
↑*In vivo adenine base editing reverts C282Y and improves iron metabolism in hemochromatosis mice. Rovai A…Ott M. Nature Communications. Link
*In vitro modeling and rescue of ciliopathy associated with IQCB1/NPHP5 mutations using patient-derived cells. Kruczek K…Swaroop A. Stem Cell Reports. Link
*Simple, low-cost production of DNA MS2 virus-like particles as molecular diagnostic controls. Crone MA & Freemont PS. bioRxiv (preprint). Link
Multiplexed, single-molecule, epigenetic analysis of plasma-isolated nucleosomes for cancer diagnostics. Fedyuk V…Shema E. Nature Biotechnology. Link
*Targeted immunotherapy against distinct cancer-associated fibroblasts overcomes treatment resistance in refractory HER2+ breast tumors. Rivas EI…Calon A. Nature Communications. Link
*Combination of T cell-redirecting bispecific antibody ERY974 and chemotherapy reciprocally enhances efficacy against non-inflamed tumours. Sano Y…Endo M. Nature Communications. Link
*Arsenal of nanobodies shows broad-spectrum neutralization against SARS-CoV-2 variants of concern in vitro and in vivo in hamster models. Rossotti MA…Tanha J. Communications Biology. Link
*Heat selection enables highly scalable methylome profiling in cell-free DNA for noninvasive monitoring of cancer patients. Cheruba E…Cheow LF. Science Advances. Link
↑↑↑Design, construction, and in vivo augmentation of a complex gut microbiome. Cheng AG…Fischbach MA. Cell. Link
†A pathway to improve seaweed aquaculture through microbiota manipulation. Li J…Egan S. Trends in Biotechnology. Link
*CRISPR/Cas12a-based biosensing platform for the on-site detection of single-base mutants in gene-edited rice. Wang M…Wang X. Frontiers in Plant Science. Link
*A CRISPR-based lateral flow assay for plant genotyping and pathogen diagnostics. Sánchez E…Mahfouz M. Plant Biotechnology Journal. Link
*Accurate flux predictions using tissue-specific gene expression in plant metabolic modeling. Kaste JAM & Shachar-Hill Y. bioRxiv (preprint). Link
Tissue, Protein & Molecular Engineering
A modular XNAzyme cleaves long, structured RNAs under physiological conditions and enables allele-specific gene silencing. Taylor AI…Holliger P. Nature Chemistry. Link
*Engineered marble-like bovine fat tissue for cultured meat. Zagury Y…Levenberg S. Communications Biology. Link
De novo construction of T cell compartment in humanized mice engrafted with iPSC-derived thymus organoids. Zeleniak A…Fan Y. Nature Methods. Link
*Pseudotyping Bacteriophage P2 Tail Fibers to Extend the Host Range for Biomedical Applications. Cunliffe TG, Parker AL & Jaramillo A. ACS Synthetic Biology. Link
*Signal processing and generation of bioactive nitric oxide in a model prototissue. Liu S…Liu J. Nature Communications. Link
*Converting non-neutralizing SARS-CoV-2 antibodies into broad-spectrum inhibitors. Weidenbacher P.A-B…Kim PS. Nature Chemical Biology. Link
*Development of a red fluorescent protein-based cGMP indicator applicable for live-cell imaging. Takizawa M…Tsuboi T. Communications Biology. Link
Tools & Technology
↑*Multiplexed mobilization and expression of biosynthetic gene clusters. Libis V…Brady SF. Nature Communications. Link
*Gas modulating microcapsules for spatiotemporal control of hypoxia. Molley TG…Kilian KA. bioRxiv (preprint). Link
*Single molecule co-occupancy of RNA-binding proteins with an evolved RNA deaminase. Lin Y…Floor SN. bioRxiv (preprint). Link
*Single-molecule identification of the target RNAs of different RNA binding proteins simultaneously in cells. Flamand MN…Meyer KD. bioRxiv (preprint). Link
S1-END-seq reveals DNA secondary structures in human cells. Matos-Rodrigues G…Nussenzweig A. Molecular Cell. Link
*A visualization reporter system for characterizing antibiotic biosynthetic gene clusters expression with high-sensitivity. Liu X…Tan H. Communications Biology. Link
A genetic platform to investigate the functions of bacterial drug efflux pumps. Teelucksingh T…Cox G. Nature Chemical Biology. Link
†Biotechnological approaches for controlling postharvest fruit softening. Brummell DA, Bowen JK & Gapper NE. Current Opinion in Biotechnology. Link