Rational Design of the β-Bulge Gate in a Green Fluorescent Protein Accelerates the Kinetics of Sulfate Sensing

Directed Evolution of a Genetically Encoded Indicator for Chloride

Inarguably, the green fluorescent protein (GFP) family is an exemplary model for protein engineering, accessing a range of unparalleled functions and utility in biology. The first variant to recognize and provide an optical output of chloride in living cells was serendipitously uncovered more than 25 years ago. Since then, researchers have actively expanded the potential of GFP indicators for chloride through site-directed and combinatorial site-saturation mutagenesis, along with chimeragenesis. However, to date, the power of directed evolution has yet to be unleashed. As a proof-of-concept, here, we use random mutagenesis paired with anion walking to engineer a chloride-insensitive fluorescent protein named OFPxm into a functional indicator named ChlorOFF. The sampled mutational landscape unveils an evolutionary convergent solution at one position in the anion binding pocket and nine other mutations across eight positions, of which only one has been previously linked to chloride sensing potential in the GFP family.

NitrOFF: An engineered fluorescent biosensor to illuminate nitrate transport in living cells

The duality of nitrate is nowhere best exemplified than in human physiology - a detrimental pollutant but also a protective nutrient and signaling ion - particularly as connected to reactive nitrogen oxides. Aside from limited insights into nitrate uptake and storage, foundational nitrate biology has lagged. Genetically encoded fluorescent biosensors can address this gap with real-time imaging. However, imaging technologies for mammalian cell applications remain rare. Here, we set out to design and engineer a two-domain chimera fusing the split green fluorescent protein EGFP and the nitrate recognition domain NreA from Staphylococcus carnosus . Over 7 rounds of directed evolution, 15 mutations were accumulated resulting in the functional biosensor NitrOFF. NitrOFF has a high degree of allosteric communication between the domains reflected in a turn-off intensiometric response ( K d ≈ 9 µM). This was further reinforced by X-ray crystal structures of apo and nitrate bound NitrOFF, which revealed that the two domains undergo a large-scale conformational rearrangement that changes the relative positioning of the EGFP and NreA domains by 68.4°. Such a dramatic difference was triggered by the formation of a long helix at the engineered linker connecting the two domains, peeling the β7 strand off the EGFP and thus extinguishing the fluorescence upon nitrate binding. Finally, as a proof-of-concept, we highlighted the utility of this first-generation biosensor to monitor exogenous nitrate uptake and modulation in a human embryonic kidney (HEK) 293 cell line.

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A chemigenetic indicator based on a synthetic chelator and a green fluorescent protein for imaging of intracellular sodium ions

A chemigenetic indicator with an affinity suitable for imaging of intracellular sodium ions (Na+) in mammalian cells was developed. The indicator, based on a chimera of green fluorescent protein (GFP) and HaloTag labeled with a synthetic crown ether chelator, was produced by a combination of rational design and directed evolution. In mammalian cells the indicator exhibited an approximately 100% increase in excitation ratio when the cells were treated with 20 mM Na+ and an ionophore.

Illuminating anions in biology with genetically encoded fluorescent biosensors

Anions are critical to all life forms. Anions can be absorbed as nutrients or biosynthesized. Anions shape a spectrum of fundamental biological processes at the organismal, cellular, and subcellular scales. Genetically encoded fluorescent biosensors can capture anions in action across time and space dimensions with microscopy. The firsts of such technologies were reported more than 20 years for monoatomic chloride and polyatomic cAMP anions. However, the recent boom of anion biosensors illuminates the unknowns and opportunities that remain for toolmakers and end users to meet across the aisle to spur innovations in biosensor designs and applications for discovery anion biology. In this review, we will canvas progress made over the last three years for biologically relevant anions that are classified as halides, oxyanions, carboxylates, and nucleotides.

Directed Evolution of a Genetically Encoded Indicator for Chloride

Inarguably, the green fluorescent protein (GFP) family is an exemplary model for protein engineering, accessing a range of unparalleled functions and utility in biology. The first variant to recognize and provide an optical output of chloride in living cells was serendipitously uncovered more than 25 years ago. Since then, researchers have actively expanded the potential of GFP indicators for chloride through site-directed and combinatorial site-saturation mutagenesis, along with chimeragenesis. However, to date, the power of directed evolution has yet to be unleashed. As a proof-of-concept, here, we use random mutagenesis paired with anion walking to engineer a chloride-insensitive fluorescent protein named OFPxm into a functional indicator named ChlorOFF. The sampled mutational landscape unveils an evolutionary convergent solution at one position in the anion binding pocket and nine other mutations across eight positions, of which only one has been previously linked to chloride sensing potential in the GFP family.

Genetically encoded green fluorescent sensor for probing sulfate transport activity of solute carrier family 26 member a2 (Slc26a2) protein

Genetically encoded fluorescent biosensors became indispensable tools for biological research, enabling real-time observation of physiological processes in live cells. Recent protein engineering efforts have resulted in the generation of a large variety of fluorescent biosensors for a wide range of biologically relevant processes, from small ions to enzymatic activity and signaling pathways. However, biosensors for imaging sulfate ions, the fourth most abundant physiological anion, in mammalian cells are still lacking. Here, we report the development and characterization of a green fluorescent biosensor for sulfate named Thyone. Thyone, derived through structure-guided design from bright green fluorescent protein mNeonGreen, exhibited a large negative fluorescence response upon subsecond association with sulfate anion with an affinity of 11 mM in mammalian cells. By integrating mutagenesis analyses with molecular dynamics simulations, we elucidated the molecular mechanism of sulfate binding and revealed key amino acid residues responsible for sulfate sensitivity. High anion selectivity and sensitivity of Thyone allowed for imaging of sulfate anion transients mediated by sulfate transporter heterologously expressed in cultured mammalian cells. We believe that Thyone will find a broad application for assaying the sulfate transport in mammalian cells via anion transporters and exchangers.

Engineering the ChlorON Series: Turn-On Fluorescent Protein Sensors for Imaging Labile Chloride in Living Cells

Beyond its role as the "queen of electrolytes", chloride can also serve as an allosteric regulator or even a signaling ion. To illuminate this essential anion across such a spectrum of biological processes, researchers have relied on fluorescence imaging with genetically encoded sensors. In large part, these have been derived from the green fluorescent protein found in the jellyfish Aequorea victoria. However, a standalone sensor with a turn-on intensiometric response at physiological pH has yet to be reported. Here, we address this technology gap by building on our discovery of the anion-sensitive fluorescent protein mNeonGreen (mNG). The targeted engineering of two non-coordinating residues, namely K143 and R195, in the chloride binding pocket of mNG coupled with an anion walking screening and selection strategy resulted in the ChlorON sensors: ChlorON-1 (K143W/R195L), ChlorON-2 (K143R/R195I), and ChlorON-3 (K143R/R195L). In vitro spectroscopy revealed that all three sensors display a robust turn-on fluorescence response to chloride (20- to 45-fold) across a wide range of affinities (Kd ≈ 30-285 mM). We further showcase how this unique sensing mechanism can be exploited to directly image labile chloride transport with spatial and temporal resolution in a cell model overexpressing the cystic fibrosis transmembrane conductance regulator. Building from this initial demonstration, we anticipate that the ChlorON technology will have broad utility, accelerating the path forward for fundamental and translational aspects of chloride biology.