Sucrose-driven carbon redox rebalancing eliminates the Crabtree effect and boosts energy metabolism in yeast - Nature Communications The Crabtree effect affects yeast-based bioproduction. Here, the authors report the development of a Crabtree-negative yeast through introducing the sucrose phosphorolysis pathway, deletion of the pho...

Sucrose-driven carbon redox rebalancing eliminates the Crabtree effect and boosts energy metabolism in yeast

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Spatially blocked split CRISPR-Cas12a system for ultra-sensitive and versatile small molecule activation and detection - Nature Communications Detecting small molecules is pivotal across many fields. Here, authors leverage a split crRNA mode to construct spatially blocked split CRISPR-Cas12a system. This approach establishes a low-background...

Spatially blocked split CRISPR-Cas12a system for ultra-sensitive and versatile small molecule activation and detection

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Precision multiplexed base editing in human cells using Cas12a-derived base editors - Nature Communications Current base editors cannot simultaneously edit multiple loci with base-pair level precision, hindering complex genotype generation. Here the authors describe optimized Cas12a gRNA array designs, enab...

Precision multiplexed base editing in human cells using Cas12a-derived base editors

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Circular RNA-mediated inverse prime editing in human cells - Nature Communications Prime editors are restricted to performing precise edits downstream of cleavage sites. Here, authors develop helicase-assisted circular RNA-mediated inverse PEs (ciPEs) to increase editing efficiencie...

Circular RNA-mediated inverse prime editing in human cells

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Prime editor with rational design and AI-driven optimization for reverse editing window and enhanced fidelity - Nature Communications Expanding editing scope while reducing byproducts is now possible for prime editing. Here, authors develop reverse prime editing (rPE), a SpCas9-based tool enabling editing in reverse window with high...

Prime editor with rational design and AI-driven optimization for reverse editing window and enhanced fidelity

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Feedback-responsive cell factories for dynamic modulation of the unfolded protein response - Nature Communications Engineering cell factories that support the production of large quantities of protein therapeutics remains a significant biomanufacturing challenge. Here the authors engineered cells to sense an early...

Feedback-responsive cell factories for dynamic modulation of the unfolded protein response

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Generative and predictive neural networks for the design of functional RNA molecules - Nature Communications Designing high performance RNA molecules is a unifying challenge across many areas of biotechnology research. Here, authors develop GARDN and SANDSTORM, a data-efficient generative AI framework for de...

Generative and predictive neural networks for the design of functional RNA molecules

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A chimeric viral platform for directed evolution in mammalian cells - Nature Communications Directed evolution is a process of mutation and artificial selection to breed biomolecules with new or improved activity. Here the authors develop a directed evolution platform (PROTein Evolution Usin...

A chimeric viral platform for directed evolution in mammalian cells

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Designer artificial environments for membrane protein synthesis - Nature Communications Membrane proteins are notoriously difficult to synthesize. Here, authors introduce MEMPLEX, a high-throughput experimentation platform guided by machine learning that designs artificial cell-free envi...

Designer artificial environments for membrane protein synthesis

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A generalizable approach for programming protease-responsive conformationally inhibited artificial transcriptional factors - Nature Communications Artificial transcription factors (ATFs) are core elements of customized circuits responsible for signal output and event transformation. Here, the authors report the design of a protease-responsive co...

A generalizable approach for programming protease-responsive conformationally inhibited artificial transcriptional factors

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Directed evolution of aminoacyl-tRNA synthetases through in vivo hypermutation - Nature Communications Genetic code expansion (GCE) enables the incorporation of new amino acids into proteins. Here, authors demonstrate the rapid OrthoRep-driven evolution of aminoacyl-tRNA synthetases for GCE, increasing...

Directed evolution of aminoacyl-tRNA synthetases through in vivo hypermutation

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Expanded ribosomal synthesis of non-standard cyclic backbones in vitro - Nature Communications The ribosome has evolved to link standard amino acids into proteins via peptide bonds. Here, authors expand its chemistry to directly synthesize novel 5- and 6- membered cyclic backbones from noncanon...

Expanded ribosomal synthesis of non-standard cyclic backbones in vitro

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Construction of multi-targeted CRISPR libraries in tomato to overcome functional redundancy at genome-scale level - Nature Communications Genetic variance is vital for breeding programs and mutant screening, yet traditional mutagenesis methods wrestle with genetic redundancy and a lack of specificity in gene targeting. Here the authors ...

Construction of multi-targeted CRISPR libraries in tomato to overcome functional redundancy at genome-scale level

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Dual inhibition of DNA-PK and Polϴ boosts precision of diverse prime editing systems - Nature Communications Prime editing can generate undesired editing outcomes. Here, authors describe a method for reducing both on-target and off-target imprecise editing outcomes of diverse prime editing modalities in diff...

Dual inhibition of DNA-PK and Polϴ boosts precision of diverse prime editing systems

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A CRISPR/Cas9-based enhancement of high-throughput single-cell transcriptomics - Nature Communications Single-cell RNAseq can struggle to capture cellular heterogeneity due to the relatively low expression of biologically meaningful transcripts. Here the authors present an approach called scCLEAN, whic...

A CRISPR/Cas9-based enhancement of high-throughput single-cell transcriptomics

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Elucidating the genetic mechanisms governing cytosine base editing outcomes through CRISPRi screens - Nature Communications Cytosine base editors use an uracil-containing intermediate to introduce C•G to T•A and C•G to G•C point mutations. Here, the authors couple gene knockdown with reporters of these two cytosine base ed...

Elucidating the genetic mechanisms governing cytosine base editing outcomes through CRISPRi screens

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Genetically encoded fluorescent reporter for polyamines - Nature Communications Polyamines are essential metabolites linked to aging, cancer, and Parkinson’s disease. Here, authors develop a live-cell polyamine reporter and use a genome-wide CRISPR screen to uncover a link betwee...

Genetically encoded fluorescent reporter for polyamines

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Design of diverse, functional mitochondrial targeting sequences across eukaryotic organisms using variational autoencoder - Nature Communications Mitochondria play a key role in cellular metabolism. Here, authors develop a Variational Autoencoder to design novel mitochondrial targeting sequences, validating them across several eukaryotic organi...

Design of diverse, functional mitochondrial targeting sequences across eukaryotic organisms using variational autoencoder

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Cost-effective urine recycling enabled by a synthetic osteoyeast platform for production of hydroxyapatite - Nature Communications Upcycling urine in wastewater for nitrogen and phosphorus production has gained attention, but their low market values hamper the application. Here, the authors develop a yeast platform that mimics os...

Cost-effective urine recycling enabled by a synthetic osteoyeast platform for production of hydroxyapatite

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A megatransposon drives the adaptation of Thermoanaerobacter kivui to carbon monoxide - Nature Communications Carbon monoxide (CO) present in syngas severely inhibits growth of many acetogens. Here, the authors adapt, characterize, and engineer utilization of CO as sole carbon and energy source by the thermop...

A megatransposon drives the adaptation of Thermoanaerobacter kivui to carbon monoxide

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Regulating triacylglycerol cycling for high-efficiency production of polyunsaturated fatty acids and derivatives - Nature Communications The authors demonstrate the role and mechanism of triacylglycerol (TAG) cycling in polyunsaturated fatty acid biosynthesis and develop a strategy of decoupling the TAG biosynthesis and degradation to ...

Regulating triacylglycerol cycling for high-efficiency production of polyunsaturated fatty acids and derivatives

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Microbial synthesis of branched-chain β,γ-diols from amino acid metabolism - Nature Communications The position of hydroxyl groups, the carbon number of the alkyl chain, and the modification of the side chain are key factors determining the function of diols. Here, the authors report a biosynthetic...

Microbial synthesis of branched-chain β,γ-diols from amino acid metabolism

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Modular deregulation of central carbon metabolism for efficient xylose utilization in Saccharomyces cerevisiae - Nature Communications Here, the authors show that a modular deregulation strategy in Saccharomyces cerevisiae boosts xylose conversion to 3-HP by engineering central carbon metabolism with five strategies, achieving a 4.7-...

Modular deregulation of central carbon metabolism for efficient xylose utilization in Saccharomyces cerevisiae

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Designing pathways for bioproducing complex chemicals by combining tools for pathway extraction and ranking - Nature Communications Synthesis of complex molecules requires reactions from multiple pathways operating in balanced subnetworks. Here, the authors report a computational algorithm that combines the strength of constraint-...

Designing pathways for bioproducing complex chemicals by combining tools for pathway extraction and ranking

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Engineered microbial platform confers resistance against heavy metals via phosphomelanin biosynthesis - Nature Communications Heavy metals and plastics are two major environmental pollutants. Here, the authors engineer microbial platforms capable of endogenously biosynthesizing phosphomelanin for simultaneously heavy metals ...

Economic and sustainable revolution to facilitate one-carbon biomanufacturing

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Economic and sustainable revolution to facilitate one-carbon biomanufacturing - Nature Communications The implementation of one-carbon (C1) biomanufacturing is limited to laboratory or pilot scales. Here, the authors highlight the economic and technical challenges associated with scaling up C1 biomanu...

Economic and sustainable revolution to facilitate one-carbon biomanufacturing

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Quite a lot of science today, let's dive right in

Dihydroartemisinic acid dehydrogenase-mediated alternative route for artemisinin biosynthesis - Nature Communications Semi-synthesis of artemisinin has been achieved by autooxidation of dihydroartemisinic acid (DHAA), but DHAA supply relies on chemical synthesis from artemisinic acid. Here, authors report the identif...

Dihydroartemisinic acid dehydrogenase-mediated alternative route for artemisinin biosynthesis

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Electron transfer engineering of artificially designed cell factory for complete biosynthesis of steroids - Nature Communications Bioproduction of steroids involves NADPH-dependent enzymes that mediate electron transfer reactions. Here, the author reveal the electron transfer mechanisms of NADPH-dependent enzymes and demonstrate...

Electron transfer engineering of artificially designed cell factory for complete biosynthesis of steroids

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Design and implementation of aerobic and ambient CO2-reduction as an entry-point for enhanced carbon fixation - Nature Communications Available enzymatic CO2 reduction strategies are not suitable for aerobic microorganisms and many industrial settings. Here, the authors design a new metabolic pathway that can operate under fully aer...

Design and implementation of aerobic and ambient CO2-reduction as an entry-point for enhanced carbon fixation

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