Fluorescent proteins articles within Nature Communications

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  • Article
    | Open Access

    Trait correlations impact evolvability as selection on one trait can influence others. Here, the authors examine trait correlation in two proteins, a fluorescent protein & an antibiotic resistance enzyme, observing rapid evolution of trait correlations through changes in the biophysical properties of these proteins.

    • Pouria Dasmeh
    • , Jia Zheng
    •  & Andreas Wagner

  • Article
    | Open Access

    Aberrant stem cell-like activity and impaired differentiation are central to the development of colorectal cancer. Here, authors develop a dual endogenous reporter system to identify functional regulators of aberrant stem cell and differentiation programs, showing that SMARCB1 restricts differentiation, and nominating other regulators with therapeutic potential.

    • Sandor Spisak
    • , David Chen
    •  & Nilay S. Sethi

  • Article
    | Open Access

    G protein responses mediated by GPCRs may differ depending on their environment. Here, using highly sensitive Gi/o sensors, the authors reveal the specific pharmacological and Gi/o protein responses of some native GPCRs in neurons, and the influence of G protein composition.

    • Chanjuan Xu
    • , Yiwei Zhou
    •  & Jianfeng Liu

  • Article
    | Open Access

    Photolabeling of intracellular molecules is an invaluable approach to study multiple cellular processes. Here, the authors report on the near-infrared to far-red photoconversion in the miRFP family of fluorescent proteins, which enables photolabeling entirely performed in the near-infrared range.

    • Francesca Pennacchietti
    • , Jonatan Alvelid
    •  & Ilaria Testa

  • Article
    | Open Access

    l-Lactate is increasingly recognized as a key metabolite and signalling molecule in mammals, but the methods to investigate it in vivo have been limited. Here, authors report a pair of improved biosensors—one green and one red—for visualizing l-lactate both inside and outside of cells.

    • Yusuke Nasu
    • , Abhi Aggarwal
    •  & Robert E. Campbell

  • 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

    Leukotriene B4 (LTB4) is a potent lipid chemoattractant driving leukocyte migration and neutrophil swarming, but methods for its real-time detection are lacking. Here, the authors develop GEM-LTB4, a genetically encoded fluorescent biosensor, and use it to visualize leukocyte-derived LTB4 gradients.

    • Szimonetta Xénia Tamás
    • , Benoit Thomas Roux
    •  & Balázs Enyedi

  • Article
    | Open Access

    MAM Ca2+ dynamics play an important role in diverse biological processes, but directly and specifically measuring Ca2+ concentrations in this region is technically challenging. Here the authors report a MAM-specific BRET-based Ca2+ indicator called MAM-Calflux, which works as both a Ca2+ indicator and a structural marker due to its ratiometric nature.

    • Eunbyul Cho
    • , Youngsik Woo
    •  & Sang Ki Park

  • 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

    Recombinant proteins in complex solutions are typically detected with tag-specific antibodies in Western blots. Here, the author describes an antibody-free alternative in which tagged proteins are detected directly in polyacrylamide gels via fluorophore-labelling of the tagged protein using a ligase.

    • Adrian C. D. Fuchs

  • Article
    | Open Access

    Itaconate has been identified as an immunomodulatory metabolite produced by activated macrophages, but methods for detecting itaconate in live cells are lacking. Here, the authors develop a fluorescent biosensor named BioITA for detecting itaconate in subcellular compartments of living macrophages.

    • Pengkai Sun
    • , Zhenxing Zhang
    •  & Xinjian Li

  • Article
    | Open Access

    β-TrCP plays an important role in diverse cellular processes such as the cell cycle and inflammation. Here the authors develop a biosensor for β-TrCP activity and use it to investigate β-TrCP dynamics during the cell cycle, and to screen a small-molecule library for β-TrCP activators and inhibitors.

    • Debasish Paul
    • , Stephen C. Kales
    •  & Steven D. Cappell

  • Article
    | Open Access

    Measuring sub-cellular pH with high accuracy and spatiotemporal resolution remains challenging. Here, Johnston and co-workers develop a pH biosensor that combines the pH dependant fluorescent lifetime of mApple with deep learning to accurately determine sub-cellular pH in individual vesicles.

    • Joshua J. Rennick
    • , Cameron J. Nowell
    •  & Angus P. R. Johnston

  • Article
    | Open Access

    Subcellular signaling is critical to generating cellular responses that modulate inflammatory pathways at the chemokine receptor CXCR3. Eiger et al. determine that agonist-biased CXCR3 signaling at endosomes differs from that at the plasma membrane, proposing location bias as an important phenomenon in signal transduction.

    • Dylan Scott Eiger
    • , Noelia Boldizsar
    •  & Sudarshan Rajagopal

  • Article
    | Open Access

    AMP activated protein kinase (AMPK) is a master regulator of cellular metabolism, but how AMPK activity is spatiotemporally regulated remains unclear. Here, Schmitt et al develop a sensitive biosensor for AMPK, which they use to uncover mechanisms for AMPK activity in the lysosome and nucleus.

    • Danielle L. Schmitt
    • , Stephanie D. Curtis
    •  & Jin Zhang

  • Article
    | Open Access

    Fluorescent biosensors are important tools for studying cellular metabolism, but development and optimization are challenging. Koveal et al. present a high-throughput multiparameter screen for sensor performance, and used it to generate LiLac, a high-performance, quantitative lactate sensor.

    • Dorothy Koveal
    • , Paul C. Rosen
    •  & Gary Yellen

  • Article
    | Open Access

    Biosensors often report relative rather than absolute values. Here the authors report a method that utilises the photochromic properties of biosensors to provide an absolute measure of the analyte concentration or activity: photochromism-enabled absolute quantification (PEAQ) biosensing.

    • Franziska Bierbuesse
    • , Anaïs C. Bourges
    •  & Peter Dedecker

  • Article
    | Open Access

    Currently, genetically encoded calcium indicators are not suitable for direct quantification. Here the authors engineer a fluorescence lifetime imaging calcium biosensor, Turquoise Calcium Fluorescence LIfeTime Sensor (Tq-Ca-FLITS), and measure intracellular calcium concentrations in human-derived organoids.

    • Franka H. van der Linden
    • , Eike K. Mahlandt
    •  & Joachim Goedhart

  • Article
    | Open Access

    l-lactate is an important intercellular energy currency. Here the authors report a genetically encoded biosensor eLACCO1.1 to monitor extracellular l-lactate; they use eLACCO1.1 to image extracellular l-lactate in cultured mammalian cells and brain tissue.

    • Yusuke Nasu
    • , Ciaran Murphy-Royal
    •  & Robert E. Campbell

  • Article
    | Open Access

    Many current immunoassays require multiple washing, incubation and optimization steps. Here the authors present Ratiometric Plug-and-Play Immunodiagnostics (RAPPID), a generic assay platform that uses ratiometric bioluminescent detection to allow sandwich immunoassays to be performed directly in solution.

    • Yan Ni
    • , Bas J. H. M. Rosier
    •  & Maarten Merkx

  • Article
    | Open Access

    Performing multiple FRET measurements at once can be challenging. Here the authors report a method to discriminate between overlapping FRET pairs, even if the fluorophores display almost identical absorption and emission spectra, based on the photochromism of the donor fluorophores.

    • Thijs Roebroek
    • , Wim Vandenberg
    •  & Peter Dedecker

  • Article
    | Open Access

    Fluorescent protein reporters based on GFP exist, but have intrinsic disadvantages. Here the authors incorporate pH, Ca2+ and protein–protein interaction sensing modalities into de novo designed mini-fluorescence-activating proteins (mFAPs), with increased photostability and smaller size, which bind a range of DFHBI chromophore variants.

    • Jason C. Klima
    • , Lindsey A. Doyle
    •  & David Baker

  • Article
    | Open Access

    Membrane-less organelles or compartments are considered to be dynamic reaction centers for spatiotemporal control of diverse cellular processes. Here authors report quantitative measurements of changes in protein interactions for the proteins recruited into membrane-less compartments (termed client proteins) in living cells.

    • Daesun Song
    • , Yongsang Jo
    •  & Yongwon Jung

  • Article
    | Open Access

    Existing fluorescent protein-based sensor measurements are limited to 4 or fewer simultaneously recorded modalities due to spectral overlap. Here the authors introduce Multiplexed Optical Sensors in Arrayed Islands of Cells (MOSAIC), which enables parallel recording of tens of physiological parameters using dense arrays of cell islands, each expressing a different fluorescent sensor.

    • Christopher A. Werley
    • , Stefano Boccardo
    •  & Adam E. Cohen

  • Article
    | Open Access

    Fiber optic implantation in deep areas of the rodent’s brain for MRI combined with optogenetics is challenging. Here the authors use an MRI-guided robotic arm as the navigation method for accurate fiber optic placement and precise microinjection during multi-modal fMRI, optogenetics and calcium recordings.

    • Yi Chen
    • , Patricia Pais-Roldan
    •  & Xin Yu

  • Article
    | Open Access

    FRET sensors hardly achieve visualization of spatiotemporal dynamics of protein activity in vivo. Here the authors present intensiometric small GTPase biosensors based on dimerization-dependent fluorescent proteins that enable monitoring of activity of small GTPases in the brains of behaving mice at a single spine resolution.

    • Jihoon Kim
    • , Sangkyu Lee
    •  & Won Do Heo

  • Article
    | Open Access

    Poly ADP-ribosylation (PARylation) is a highly dynamic post-translation protein modification, but most methods only detect stable PARylation events. Here the authors develop a split-GFP-based sensor for PARylation detection in live cells and use it to identify a new centrosomal PARylation target.

    • Dragomir B. Krastev
    • , Stephen J. Pettitt
    •  & Christopher J. Lord

  • Article
    | Open Access

    Visualization of synaptic activity in the living brain is challenging. This study devises a simple and efficient scheme that reports synaptic vesicle recycling in vivo using SynaptoZip, a genetically encoded sensor of past synaptic activities.

    • Mattia Ferro
    • , Jacopo Lamanna
    •  & Antonio Malgaroli

  • Article
    | Open Access

    Generally, fluorescence imaging needs to be done in a dark environment using molecules with spectrally separated emissions. Here, Quérard et al. develop a protocol for high-speed imaging and remote sensing of spectrally overlapping reversible photoswitchable fluorophores in ambient light.

    • Jérôme Quérard
    • , Ruikang Zhang
    •  & Ludovic Jullien

  • Article
    | Open Access

    Single fluorescent protein biosensors are susceptible to expression and instrumental artifacts. Here Ast et al. describe a dual fluorescent protein design whereby a reference fluorescent protein is nested within a reporter fluorescent protein to control for such artifacts while preserving sensitivity and dynamic range.

    • Cindy Ast
    • , Jessica Foret
    •  & Wolf B. Frommer

  • Article
    | Open Access

    Split fluorescent proteins (FPs) have been widely used to visualise proteins in cells. Here the authors develop a screen for engineering new split FPs, and report a yellow-green split-mNeonGreen2 with reduced background, a red split-sfCherry2 for multicolour labeling, and its photoactivatable variant for super-resolution use.

    • Siyu Feng
    • , Sayaka Sekine
    •  & Bo Huang

  • Article
    | Open Access

    Cellular signalling is often facilitated by membrane protein clustering, but detection of protein clustering at high spatiotemporal resolution is challenging. Here the authors develop a single-chain FRET sensor they name CliF to look at intermolecular associations and dynamics of TCR-CD3 clusters on the T cell surface.

    • Yuanqing Ma
    • , Elvis Pandzic
    •  & Katharina Gaus

  • Article
    | Open Access

    The role of force in activating integrin cell adhesion receptors is not known. Here the authors develop fluorescent tension sensors for αL and β2 integrins and show that in migrating T cells force is transduced across the β2 integrin, and that this correlates with an active conformational state.

    • Pontus Nordenfelt
    • , Hunter L. Elliott
    •  & Timothy A. Springer

  • Article
    | Open Access

    In the construction of single fluorescent protein biosensors, selection of the insertion point of a fluorescent protein into a ligand-binding domain is a rate-limiting step. Here, the authors develop an unbiased, high-throughput approach, called domain insertion profiling with DNA sequencing (DIP-seq), to generate a novel trehalose biosensor.

    • Dana C. Nadler
    • , Stacy-Anne Morgan
    •  & David F. Savage

  • Article
    | Open Access

    Tagging proteins with fluorescent proteins is a powerful method for both imaging and non-imaging applications. Here the authors use the eleventh β-strand of sfGFP and sfCherry as epitope tags for multicolour imaging and amplified signals by tandem arrangement; shortness of the tag enabled introduction into genomic loci using CRISPR/Cas9.

    • Daichi Kamiyama
    • , Sayaka Sekine
    •  & Bo Huang

  • Article |

    Quantitative live cell imaging of protein trafficking suffers from misfolding and inappropriate disulphide bond formation of fluorescent proteins in the secretory pathway. Here, the authors present an optimized collection of fluorescent proteins suitable for use in oxidizing subcellular compartments.

    • Lindsey M. Costantini
    • , Mikhail Baloban
    •  & Erik L. Snapp

  • Article
    | Open Access

    Models for protein diffusion in cells assume a large macromolecular crowding effect. Here Di Rienzo et al.visualize GFP diffusion at the millisecond timescale to observe unobstructed Brownian motion in mammalian cells for distances up to 100 nm, revealing minimal influence of macromolecular crowding.

    • Carmine Di Rienzo
    • , Vincenzo Piazza
    •  & Francesco Cardarelli

  • Article |

    Infrared fluorescent proteins offer advantages for deep in vivo imaging thanks to the tissue-penetrating properties of infrared light. Here, Yu et al. design a monomeric infrared fluorescent protein that, when combined with expression of haeme oxygenase in cells, shows improved performance for in vivoimaging of neurons and brain tumours.

    • Dan Yu
    • , William Clay Gustafson
    •  & Xiaokun Shu

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