Molecular engineering articles within Nature Communications

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  • Comment
    | Open Access

    Biofoundries provide an integrated infrastructure to enable the rapid design, construction, and testing of genetically reprogrammed organisms for biotechnology applications and research. Many biofoundries are being built and a Global Biofoundry Alliance has recently been established to coordinate activities worldwide.

    • Nathan Hillson
    • , Mark Caddick
    •  & Paul S. Freemont

  • Article
    | Open Access

    Plastic polymer PET degrading enzymes are of great interest for achieving sustainable plastics recycling. Here, the authors present the crystal structures of the plastic degrading bacterial enzymes PETase, MHETase in its apo-form and MHETase bound to a non-hydrolyzable substrate analog.

    • Gottfried J. Palm
    • , Lukas Reisky
    •  & Gert Weber

  • Article
    | Open Access

    Gene-drives use CRISPR-Cas9 to be transmitted in a super-Mendelian fashion. Here the authors develop an allelic-drive for selective inheritance of a desired allele.

    • Annabel Guichard
    • , Tisha Haque
    •  & Ethan Bier

  • Article
    | Open Access

    Genome editing often requires cleavage within a narrow sequence window. Here the authors develop an expanded set of zinc finger nuclease architectures that increase the available configurations by a factor of 64 and can target almost every base at loci of therapeutic significance.

    • David E. Paschon
    • , Stephanie Lussier
    •  & Edward J. Rebar

  • Article
    | Open Access

    Optical control over receptor tyrosine kinase (RTK) activity can find application in both basic biology and synthetic biology. Here the authors combine the photosensory module of DrBphP bacterial phytochrome with the Trk family of RTKs to obtain Trks that are reversibly switchable with near-infrared and far-red light.

    • Anna V. Leopold
    • , Konstantin G. Chernov
    •  & Vladislav V. Verkhusha

  • Article
    | Open Access

    Metabolic engineering usually focuses on manipulating enzyme(s) within a single pathway. Here, the authors show that a promiscuous enzymatic activity-based multiple-pathway design can minimize cell metabolic burden and allow carbon flow rearrangement, leading to efficient hydroxytyrosol biosynthesis.

    • Wei Chen
    • , Jun Yao
    •  & Shuang-Yan Tang

  • Article
    | Open Access

    The genomic locations that can be targeted for editing by CRISPR are limited by the presence of the nuclease-specific PAM sequence. Here, the authors show PAM recognition can be expanded by replacing the key region in the PAM interaction domain of SaCas9 with the corresponding region of SaCas9 orthologs.

    • Dacheng Ma
    • , Zhimeng Xu
    •  & Zhen Xie

  • Article
    | Open Access

    Genetic logic devices allow the host cell to incorporate multiple inputs to determine output behaviour. Here the authors provide a framework for engineering reliable recombinase-based devices and demonstrate 4-input logic in a multicellular system.

    • Sarah Guiziou
    • , Pauline Mayonove
    •  & Jerome Bonnet

  • Article
    | Open Access

    The Cas12b family of CRISPR nucleases has been underutilized in mammalian cells due to the high temperature requirement of known members. Here the authors engineer BhCas12b to overcome this limitation for robust and specific genome editing applications in human cells.

    • Jonathan Strecker
    • , Sara Jones
    •  & Feng Zhang

  • Article
    | Open Access

    Near-infrared (NIR) fluorescent proteins (FPs) offer advantages for spectral multiplexing and deep-tissue imaging. Here the authors engineer a smaller NIR FP based on the unexplored cyanobacteriochrome photoreceptor and demonstrate its use in various applications in cell culture as well as whole-body imaging in vivo in mice.

    • Olena S. Oliinyk
    • , Anton A. Shemetov
    •  & Vladislav V. Verkhusha

  • Article
    | Open Access

    The use of enzymes as drugs requires that they persist within target tissues over therapeutically relevant time frames. Here the authors use a galectin-3 fusion to anchor enzymes at injection sites for up to 14 days.

    • Shaheen A. Farhadi
    • , Evelyn Bracho-Sanchez
    •  & Gregory A. Hudalla

  • Article
    | Open Access

    The construction of complex RNA-delivered genetic circuits in mammalian cells is challenging, though offers advantages over DNA circuits in clinical use. Here the authors construct a set of logic gates that respond to multiple miRNAs and demonstrate an apoptosis-regulatory AND gate.

    • Satoshi Matsuura
    • , Hiroki Ono
    •  & Hirohide Saito

  • Article
    | Open Access

    Cancer therapy using systemically administrated 4-1BB-targeting antibodies is often associated with severe toxicity due to the nonspecific activation of autoreactive T cells. Here, the authors have developed a trimeric antibody targeting both 4-1BB and EGFR, which activates T cells effectively and shows negligible cytotoxicity.

    • Marta Compte
    • , Seandean Lykke Harwood
    •  & Luis Alvarez-Vallina

  • Article
    | Open Access

    Mutating natural enzymes is effective in broadening the substrate or product range, but generally leads to reduced titers. Here the authors engineer hybrid polyketide synthases for efficient production of short-chain ketones from plant biomass hydrolysates in Streptomyces, which can increase the octane of gasoline.

    • Satoshi Yuzawa
    • , Mona Mirsiaghi
    •  & Jay D. Keasling

  • Article
    | Open Access

    Methods to directly label active neurons are still lacking. Here the authors develop CaMPARI2, a photoconvertible fluorescent protein sensor for neuronal activity with improved brightness and calcium binding kinetics, as well as an antibody to amplify the activated sensor signal in fixed samples.

    • Benjamien Moeyaert
    • , Graham Holt
    •  & Eric R. Schreiter

  • Article
    | Open Access

    Gene synthesis has expanded the ability to modify and create DNA sequences, with implications for biosurveillance. The authors use machine learning and codon theory to identify synthetic genes in Addgene data, and show that synthesis accelerates human-directed gene transfer across the tree of life.

    • Aditya M. Kunjapur
    • , Philipp Pfingstag
    •  & Neil C. Thompson

  • Article
    | Open Access

    RNA-encoded regulatory circuits are desirable because they do not integrate in the host and are less immunogenic, but the availability of regulatory devices is limited. Here the authors develop viral protease RNA-binding proteins and protease–protease genetic circuits that ultimately regulate mRNA translation.

    • Federica Cella
    • , Liliana Wroblewska
    •  & Velia Siciliano

  • Article
    | Open Access

    Designing split protein approaches is time consuming and often results in high background activity due to spontaneous assembly. Here the authors present an automated approach which uses a split energy scoring function to identify optimal protein split sites and reduces spontaneous assembly.

    • Onur Dagliyan
    • , Andrey Krokhotin
    •  & Nikolay V. Dokholyan

  • Article
    | Open Access

    Characterizing the binding selectivity landscape of interacting proteins is crucial in protein engineering. Here the authors use multi-target selective library screening and in silico next-generation sequencing to map the binding landscape of proteins and produce improved proteases inhibitors.

    • Si Naftaly
    • , Itay Cohen
    •  & Niv Papo

  • Article
    | Open Access

    Tightly regulated promoters with strong inducibility and scalability are highly desirable for biological applications. Here the authors describe ‘Jungle Express’, a EilR repressor-based broad host system activated by cationic dyes.

    • Thomas L. Ruegg
    • , Jose H. Pereira
    •  & Michael P. Thelen

  • Article
    | Open Access

    Previous efforts to assemble Rubisco within a cyanobacterial carboxysome-derived protein shell in plant chloroplasts to concentrate CO2 have been unsuccessful. Here, Long et al. produce carboxysomes in tobacco chloroplasts that encapsulate the introduced Rubisco and enable autotrophic growth at elevated CO2.

    • Benedict M. Long
    • , Wei Yih Hee
    •  & G. Dean Price

  • Article
    | Open Access

    Bacterial microcompartments (BMCs) are protein-bound organelles encapsulating segments of metabolic pathways. Here the authors utilize specific de novo coiled-coil protein-protein interactions to display proteins on the outer or inner surface of BMCs.

    • Matthew J. Lee
    • , Judith Mantell
    •  & Martin J. Warren

  • Article
    | Open Access

    Current approaches to conditionally deplete target proteins require site-specific genetic engineering or have poor temporal control. Here the authors overcome these limitations by combining the AID system with nanobodies to reversibly degrade GFP-tagged proteins in living cells and zebrafish.

    • Katrin Daniel
    • , Jaroslav Icha
    •  & Jörg Mansfeld

  • Article
    | Open Access

    Designer organelles with new biochemical functionalities are of great interest in synthetic biology and cellular engineering. Here the authors present a single-protein-based platform for generating synthetic membraneless compartments that is capable of enzymatically-triggered alterations to phase behavior and of recruiting and concentrating cargo proteins.

    • Benjamin S. Schuster
    • , Ellen H. Reed
    •  & Daniel A. Hammer

  • Perspective
    | Open Access

    Synthetic biology often views the organism as a chassis into which a circuit can be inserted. Here the authors explore the idea of the organism as a core aspect of design, aiding researchers in navigating the genetic space opened up by SCRaMbLE.

    • Erika Szymanski
    •  & Jane Calvert

  • Article
    | Open Access

    The engineering of synthetic microbial communities necessitates the use of synthetic, orthogonal cell-to-cell communication channels. Here the authors present a library of characterised AHL-receiver devices and a software tool for the automatic identification of non-interfering chemical communication channels.

    • Nicolas Kylilis
    • , Zoltan A. Tuza
    •  & Karen M. Polizzi

  • Article
    | Open Access

    The absence of effective gene activators in bacteria limits regulated expression programs. Here the authors design synthetic bacterial CRISPR-Cas transcriptional activators that can be used to construct multi-gene programs of activation and repression.

    • Chen Dong
    • , Jason Fontana
    •  & Jesse G. Zalatan

  • Article
    | Open Access

    MicroRNAs (miRNAs) are important post-transcriptional regulators of gene expression but many quantitative aspects of miRNA biology remain to be elucidated. Based on a library of miRNA sensors, the authors quantify miRNA regulation at single cell level and develop a model to predict miRNA target interactions.

    • Jeremy J. Gam
    • , Jonathan Babb
    •  & Ron Weiss

  • Article
    | Open Access

    Pentatricopeptide repeat proteins bind single-stranded RNA and have been used to study ssRNA biology. Here the authors co-opt these proteins to target ssDNA and demonstrate specific binding of telomere sequences, the structural basis for ssDNA wrapping, and use them as potent telomerase inhibitors.

    • Henrik Spåhr
    • , Tiongsun Chia
    •  & Oliver Rackham

  • Article
    | Open Access

    The use of synthetic chromosomes and the recombinase-based SCRaMbLE system could enable rapid strain evolution through massive chromosome rearrangements. Here the authors present ReSCuES, which uses auxotrophic markers to rapidly identify yeast with rearrangements for strain engineering.

    • Zhouqing Luo
    • , Lihui Wang
    •  & Junbiao Dai

  • Article
    | Open Access

    SCRaMbLE allows for the rapid and large scale rearrangement of genetic data in yeast carrying synthetic chromosomes. Here the authors demonstrate an in vitro use of the method to generate DNA libraries for optimization of biochemical reactions.

    • Yi Wu
    • , Rui-Ying Zhu
    •  & Jef D. Boeke

  • Article
    | Open Access

    SCRaMbLE has been used to rearrange synthetic chromosomes that have been introduced into host yeast. Here the authors produce semi-synthetic heterozygous diploid strains for rapid selection of phenotypes and map the rearrangements underlying selected phenotypes such as thermoresistance and caffeine resistance.

    • Michael J. Shen
    • , Yi Wu
    •  & Jef D. Boeke

  • Article
    | Open Access

    The SCRaMbLE system integrated into Sc2.0’s synthetic yeast chromosome project allows rapid strain evolution. Here the authors use a genetic logic gate to control induction of recombination in a haploid and diploid yeast carrying synthetic chromosomes.

    • Bin Jia
    • , Yi Wu
    •  & Ying-Jin Yuan

  • Article
    | Open Access

    CXCR2 antagonism has been shown to be anti-arthritic, but anti-chemokine therapies usually fail in the clinic owing to redundancy in chemokine-receptor interactions. Here the authors develop single-chain antibodies with multiple chemokine specificities to achieve high affinity and broad specificity to mouse and human CXC chemokines with efficacy in a K/BxN serum transfer model of arthritis.

    • Alessandro Angelini
    • , Yoshishige Miyabe
    •  & K. Dane Wittrup

  • Article
    | Open Access

    Two-component systems are a major family of signal transduction pathways and a rich source of sensors for biotechnology. Here, the authors develop a general method for rationally tuning two-component system input detection thresholds via specific point mutations in sensor histidine kinase proteins.

    • Brian P. Landry
    • , Rohan Palanki
    •  & Jeffrey J. Tabor

  • Article
    | Open Access

    Compartmentalization of proteins can potentially increase the productivity of engineered metabolic pathways. Here the authors use encapsulins to build non-endogenous organelles in Saccharomyces cerevisiae.

    • Yu Heng Lau
    • , Tobias W. Giessen
    •  & Pamela A. Silver

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