Molecular engineering articles within Nature Communications

Featured

  • Article
    | Open Access

    Synthetic auxotrophy in which cell viability depends on the presence of an unnatural amino acid provides a powerful strategy to restrict unwanted propagation of genetically modified organisms in open environments and potentially prevent industrial espionage. Here the authors establish a general framework for the creation and optimization of synthetic auxotrophs in yeast.

    • Tiantian Chang
    • , Weichao Ding
    •  & Xian Fu

  • Article
    | Open Access

    DNA is an alternative to data storage materials for its durability, density, and energetics. Here the authors demonstrate the storage of digital information on DNA molecules using base-editing.

    • Afsaneh Sadremomtaz
    • , Robert F. Glass
    •  & Reza Zadegan

  • Article
    | Open Access

    One method for reducing the impact of vector-borne diseases is through the use of CRISPR-based gene drives, which manipulate insect populations due to their ability to rapidly propagate desired genetic traits into a target population. Here the authors describe a Cas12a gene drive system whose activity can be finetuned in a temperature-dependent manner.

    • Sara Sanz Juste
    • , Emily M. Okamoto
    •  & Víctor López Del Amo

  • Article
    | Open Access

    Designing promoters with desired properties is crucial in synthetic biology. Here, authors introduce DeepSEED, an AI-aided flanking sequence optimisation framework which combines expert knowledge with deep learning techniques to efficiently design promoters in both eukaryotic and prokaryotic cells.

    • Pengcheng Zhang
    • , Haochen Wang
    •  & Xiaowo Wang

  • Article
    | Open Access

    Most current anti-coronavirus nanoparticle vaccines target epitopes within the RBD. Here, the authors developed nanoparticles displaying an array of spike fusion proteins derived from various coronaviruses and show that immunizing mice with these vaccines elicits broad and potent cross-reactive antibodies.

    • Geoffrey B. Hutchinson
    • , Olubukola M. Abiona
    •  & Kizzmekia S. Corbett-Helaire

  • Article
    | Open Access

    Archiving data in synthetic DNA offers unprecedented storage density and longevity. To understand how experimental choices affect the integrity of digital data stored in DNA, the authors study the evolution of errors and bias and with a digital twin they supply tools for experimental planning and design of error-correcing codes.

    • Andreas L. Gimpel
    • , Wendelin J. Stark
    •  & Robert N. Grass

  • Article
    | Open Access

    TadA deaminases widely used in many base editors lack post-translational control in cells. Here the authors report a split adenine base editor (sABE) using chemically induced dimerisation (CID) to control the catalytic activity of TadA8e and show this can be used for PCSK9 gene editing in the mouse liver.

    • Hongzhi Zeng
    • , Qichen Yuan
    •  & Xue Gao

  • Article
    | Open Access

    Cas12a is widely used in diagnostic platforms. Here the authors show that Cas12a can be programmed to directly detect RNA substrates, this is due to the 3’-end of the crRNA tolerating both RNA and DNA substrates: they use this to report a method, SAHARA, to detect RNA sequences.

    • Santosh R. Rananaware
    • , Emma K. Vesco
    •  & Piyush K. Jain

  • Article
    | Open Access

    Memory is a basic tenet of intelligent biological systems. Here the authors engineered a programmable and expandable iteration of recombinase-based synthetic memory (interception) that functions post-translation, resulting in faster recombination.

    • Andrew E. Short
    • , Dowan Kim
    •  & Corey J. Wilson

  • Article
    | Open Access

    New delivery platforms are needed to allow broader application of biotherapeutics for CNS diseases. Here, the authors show enhanced CNS delivery with a transport vehicle engineered to bind CD98hc, a highly expressed target at the blood-brain barrier.

    • Kylie S. Chew
    • , Robert C. Wells
    •  & Mihalis S. Kariolis

  • Article
    | Open Access

    Conformational cooperativity is a universal molecular effect mechanism and plays a critical role in signalling pathways. Here the authors present a programmable conformational cooperativity strategy to construct the oligo-protein signal transduction platform for logic operations and gene regulations which can be cooperatively regulated by conformational signals.

    • Yuan Liang
    • , Yunkai Qie
    •  & Cheng Zhang

  • Article
    | Open Access

    Engineered living materials (ELMs) are emerging as a field at the intersection of materials science and synthetic biology. Here, the authors describe a photosynthetic ELM composed of genetically engineered cyanobacteria in a hydrogel matrix, capable of bioremediation and inducible cell death.

    • Debika Datta
    • , Elliot L. Weiss
    •  & Jonathan K. Pokorski

  • Article
    | Open Access

    Protein-protein interactions (PPIs) are crucial for biological functions and have applications ranging from drug design to synthetic cell circuits. Here the authors develop an assay and computational methods to identify more orthogonal coiled-coil pairs, critical for biological processes and drug design.

    • W. Clifford Boldridge
    • , Ajasja Ljubetič
    •  & Sriram Kosuri

  • Article
    | Open Access

    Extensive research efforts have been directed towards the development of PET hydrolases with improved activity, but template enzymes used are limited. Here, the authors report a PET hydrolase from Cryptosporangium aurantiacum (CaPETase) that exhibits high thermostability and PET degradation activity at ambient temperatures and determine its crystal structure.

    • Hwaseok Hong
    • , Dongwoo Ki
    •  & Kyung-Jin Kim

  • Article
    | Open Access

    Although diagnosis of urinary tract infections has improved through the use of point-of-care molecular technologies, they are however limited by poor specificity and / or sensitivity, and requirement of laboratory resources. In this work, the authors develop a bacteriophage-based diagnostic assay for the detection of prevalent uropathogens.

    • Susanne Meile
    • , Jiemin Du
    •  & Samuel Kilcher

  • Article
    | Open Access

    Nonalcoholic steatohepatitis (NASH) starts with lipid droplet accumulation in the liver that eventually causes inflammation and fibrosis. Here, authors use lipophagy activators to limit the accumulation of lipids in the liver and show that this can prevent disease progression in a mouse model of nonalcoholic steatohepatitis.

    • Yoshito Minami
    • , Atsushi Hoshino
    •  & Satoaki Matoba

  • Article
    | Open Access

    Endonucleases play crucial roles in various biological processes but endonucleases that target small non-coding RNAs have not been reported. Here, the authors combined the metal binding non-canonical amino acid BpyAla and a high affinity binder to engineer a catalyst that degrades small non-coding RNAs.

    • Noreen Ahmed
    • , Nadine Ahmed
    •  & John Paul Pezacki

  • Article
    | Open Access

    Resource competition can be the cause of unintended coupling between co-expressed genetic constructs. Here the authors quantify the resource load imposed by different mammalian genetic components to identify construct designs with increased performance and reduced resource footprint.

    • Roberto Di Blasi
    • , Mara Pisani
    •  & Francesca Ceroni

  • Article
    | Open Access

    Natural proteins exhibit rich structural diversity based on the folds of an invariably linear chain. Here the authors design a single-domain GFP catenane as the counterpart of conventional linear GFP with enhanced thermal resilience and to provide a robust scaffold for making fusion protein catenanes.

    • Zhiyu Qu
    • , Jing Fang
    •  & Wen-Bin Zhang

  • Article
    | Open Access

    Here, the authors develop a protein engineering method that enables high-resolution structural biology study of human fatty acid synthase. Using this technique, they uncover unique structural features of the enzyme and the mechanism of its inhibition by an anticancer drug Denifanstat.

    • S. M. Naimul Hasan
    • , Jennifer W. Lou
    •  & Mohammad T. Mazhab-Jafari

  • Article
    | Open Access

    In vivo mutagenesis allows improving cell factories through directed evolution. Here, the authors present CoMuTER, a tool for targetable random mutagenesis of complete biosynthetic pathways using a Cas3 enzyme fused to a cytidine deaminase.

    • Anna Zimmermann
    • , Julian E. Prieto-Vivas
    •  & Kevin J. Verstrepen

  • Article
    | Open Access

    NADP(H) is a crucial cofactor, acting as a reducing agent in numerous pathways in living organisms. Here the authors report a ratiometric biosensor named NERNST, which can be used to estimate the NADP(H) redox status in bacterial, plant and animal cells and organelles.

    • Pamela E. Molinari
    • , Adriana R. Krapp
    •  & Matias D. Zurbriggen

  • Article
    | Open Access

    Safe delivery of genes is needed for gene therapy. Here the authors build “artificial viral vectors” (AVVs) by engineering the well-characterised structural components of bacteriophage T4: the large capacity, all-in-one, multiplex, programmable, and phage-based AVV nanomaterials have potential for gene therapy.

    • Jingen Zhu
    • , Himanshu Batra
    •  & Venigalla B. Rao

  • Article
    | Open Access

    Multi-enzymatic cascades benefit from precise nanometric organization but achieving this using available scaffolds is challenging. Here the authors present strategy for organizing multienzymatic systems using a protein scaffold based on TRAP domains, and demonstrate improved catalytic output.

    • Alba Ledesma-Fernandez
    • , Susana Velasco-Lozano
    •  & Aitziber L. Cortajarena

  • Article
    | Open Access

    Genetic modules are sensitive to changes in their context and to environmental perturbations. Here, the authors develop a genetic optimizer based on common synthetic biology parts to ensure optimal and robust cellular performance in diverse contexts.

    • Andras Gyorgy
    • , Amor Menezes
    •  & Murat Arcak

  • Article
    | Open Access

    Sustained drug delivery is critical for patient adherence to chronic disease treatments. Here the authors apply machine learning to engineer multifunctional peptides with high melanin binding, high cell-penetration, and low cytotoxicity, enhancing the duration and efficacy of peptide-drug conjugates for sustained ocular delivery.

    • Henry T. Hsueh
    • , Renee Ti Chou
    •  & Laura M. Ensign

  • Article
    | Open Access

    Omicron BA.1 is attenuated in infection models though the precise nature of this attenuation remains unknown as generating replication-competent viral genomes is challenging. Here the authors present pGLUE, a plasmid-based viral genome assembly and rescue strategy, to systematically characterize Omicron mutations and show that Omicron NSP6 has weakened lipid flow to replication organelles and reduced viral RNA replication.

    • Taha Y. Taha
    • , Irene P. Chen
    •  & Melanie Ott

  • Article
    | Open Access

    Biological computation is becoming a viable and fast-growing alternative to traditional electronic computing. Here the authors present Trumpet, which uses DNA and enzymes to build logic gate circuits with amplified fluorescent readout.

    • Judee A. Sharon
    • , Chelsea Dasrath
    •  & Katarzyna P. Adamala

  • Article
    | Open Access

    The scarcity of qualified RNA-binding proteins hinders the development of artificial translational regulators and synthetic gene circuits. Here, the authors repurposed CRISPR-Cas proteins as translational regulators to build synthetic circuits.

    • Shunsuke Kawasaki
    • , Hiroki Ono
    •  & Hirohide Saito

  • Article
    | Open Access

    Tools for the spatiotemporal control of protein abundance are valuable in studying diverse complex biological processes. Here, authors engineered a protein tag which is stabilized upon light induction but which quickly degrades the protein of interest in the dark, demonstrating control of protein stability in yeast and zebrafish.

    • Miaowei Mao
    • , Yajie Qian
    •  & Yi Yang

  • Article
    | Open Access

    New protein assemblies can be introduced through the fusion of selected proteins with di/oligomerization domains, which interact specifically with their partners but not with other cellular proteins. Here the authors demonstrate that a single four-helical bundle protein can be segmented into several different parts, defining up to four interacting molecules for enzyme reconstitution, gene expression, or CAR-T cell regulation.

    • Estera Merljak
    • , Benjamin Malovrh
    •  & Roman Jerala

  • Article
    | Open Access

    Synthetic circuits that can record in vivo signaling networks is critical in elucidating developmental process. Here, the authors describe the engineering and application of synthetic in vivo recorders with different promoters that can drive spatiotemporally-specific integrase switching during lateral root initiation.

    • Sarah Guiziou
    • , Cassandra J. Maranas
    •  & Jennifer L. Nemhauser

  • Article
    | Open Access

    Induced proximity can be used to control diverse cellular processes. Here, the authors develop nanobody-based proximity inducers called SNACIPs, which can be used to regulate either tagged or endogenous proteins, and demonstrate their use in blocking microtubule nucleation for tumour growth inhibition in vivo.

    • Xiaofeng Sun
    • , Chengjian Zhou
    •  & Xi Chen

  • Article
    | Open Access

    Nucleic acid sensing involving CRISPR technologies is powerful but has certain limitations, such as PAM sequence requirements and limited multiplexing. Here, authors report a CRISPR-based barcoding technology which enables multiple outputs from any target sequence, based on cis- and trans-cleavage.

    • Margot Karlikow
    • , Evan Amalfitano
    •  & Keith Pardee

  • Article
    | Open Access

    There is a low efficiency of A-to-G base conversion in at specific positions using base editors. Here the authors fuse ABE8e with the Rad51 DNA-binding domain to generate a hyperactive ABE allowing improved A-to-G editing efficiency at the region proximal to the PAM and improved simultaneous A/C conversion efficiency.

    • Niannian Xue
    • , Xu Liu
    •  & Xiaohui Zhang

  • Article
    | Open Access

    While the ribosome has been harnessed for synthetic biology, designing ribosomes has remained challenging. Here, the authors demonstrate a community science approach for rational design of ribosomes with beneficial properties.

    • Antje Krüger
    • , Andrew M. Watkins
    •  & Michael C. Jewett

  • Article
    | Open Access

    The treatment of snakebite envenoming is currently suboptimal. Existing antivenoms often lack efficacy and may cause adverse reactions. Here, the authors derive, develop, and demonstrate the utility of toxin-specific broadly-neutralizing human monoclonal antibodies with established reactivity across related venom toxins from different snake species and show efficacy in rodent models.

    • Line Ledsgaard
    • , Jack Wade
    •  & Aneesh Karatt-Vellatt

  • Article
    | Open Access

    Genome editing in bacteria normally requires efficient recombination and high transformation efficiencies, which often isn’t. Here the authors report that systematically attenuating DNA targeting activity enables RecA-mediated repair in different bacteria, allowing chromosomal cleavage to drive editing.

    • Daphne Collias
    • , Elena Vialetto
    •  & Chase L. Beisel

  • Article
    | Open Access

    The currently available transgenic T cell receptor (TCR) models represent high affinity antigen-TCR interactions. Authors here present an alternative approach to target an exogenous TCR into the physiological Trac locus in the germline of mice, which uncovers that the natural genomic context for TCRs can enhance the antigen sensitivity of lower affinity TCRs and enables the physiologic range of antigen-TCR interaction and a gene dosage dependent mechanism of central tolerance.

    • Meagan R. Rollins
    • , Jackson F. Raynor
    •  & Ingunn M. Stromnes

  • Article
    | Open Access

    RNA provides a unique readout of a cell’s identity, physiologic status, and phenotype. Here the authors deliver an RNA sensing system that can use the information contained within cellular RNA to selectively control the activity of genetic programs.

    • Lauren Gambill
    • , August Staubus
    •  & James Chappell

  • Article
    | Open Access

    Properties of cytidine and adenosine deaminases lead to off-target effects for cytosine base editors (CBEs) and adenine base editors (ABEs). Here the authors report that 25 TadA orthologs could be engineered to generate functional ABEs, CBEs or ACBEs via single/double mutations with minimised off-targets.

    • Shuqian Zhang
    • , Bo Yuan
    •  & Tian-Lin Cheng

  • Article
    | Open Access

    Hypercompact CRISPR-Cas12f systems have been engineered to generate miniABEs but these have limitations. Here the authors generate Cas12f-derived miniCBEs and develop miniABEs with improved editing and targeting scopes; they use these to correct pathogenic mutations in cell lines and introduce mutations in vivo.

    • Shuqian Zhang
    • , Liting Song
    •  & Tian-Lin Cheng

Browse broader subjects

Browse narrower subjects

Browse Molecular engineering across other nature.com journals