Genetically encoded voltage indicator

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Genetically encoded voltage indicator (or GEVI) is a protein that can sense membrane potential in a cell and relate the change in voltage to a form of output, often fluorescent level. [1] It is a promising optogenetic recording tool that enables exporting electrophysiological signals from cultured cells, live animals, and ultimately human brain. Examples of notable GEVIs include ArcLight, [2] ASAP1, [3] ASAP3, [4] Archons, [5] SomArchon, [6] and Ace2N-mNeon. [7]

Contents

History

Despite that the idea of optical measurement of neuronal activity was proposed in the late 1960s, [8] the first successful GEVI that was convenient enough to put into actual use was not developed until technologies of genetic engineering had become mature in the late 1990s. The first GEVI, coined FlaSh, [9] was constructed by fusing a modified green fluorescent protein with a voltage-sensitive K+ channel (Shaker). Unlike fluorescent proteins, the discovery of new GEVIs were seldom inspired by the nature, for it is hard to find an organism which naturally has the ability to change its fluorescence based on voltage. Therefore, new GEVIs are mostly the products of genetic and protein engineering.

Two methods can be utilized to find novel GEVIs: rational design and directed evolution. The former method contributes to the most of new GEVI variants, but recent researches using directed evolution have shown promising results in GEVI optimization. [10] [11]

Structure

GEVI can have many configuration designs in order to realize voltage sensing function. [12] An essential feature of GEVI structure is that it must situate on the cell membrane. Conceptually, the structure of a GEVI should permit the function of sensing the voltage difference and reporting it by change in fluorescence. Usually, the voltage-sensing domain (VSD) of a GEVI spans across the membrane, and is connected to the fluorescent protein(s). However, it is not necessary that sensing and reporting should happen in different structures, e.g. Archons.

By structure, GEVIs can be classified into four categories based on the current findings: (1) GEVIs contain a fluorescent protein FRET pair, e.g. VSFP1, (2) Single opsin GEVIs, e.g. Arch, (3) Opsin-FP FRET pair GEVIs, e.g. MacQ-mCitrine, (4) single FP with special types of voltage sensing domains, e.g. ASAP1. A majority of GEVIs are based on the Ciona intestinalis voltage sensitive phosphatase (Ci-VSP or Ci-VSD (domain)), which was discovered in 2005 from the genomic survey of the organism. [13] Some GEVIs might have similar components, but with different positioning of them. For example, ASAP1 and ArcLight both use a VSD and one FP, but the FP of ASAP1 is on the outside of the cell whereas that of ArcLight is on the inside, and the two FPs of VSFP-Butterfly are separated by the VSD, while the two FPs of Mermaid are relatively close to each other.

Table of GEVIs and their structure
GEVI [A] YearSensingReportingPrecursor
FlaSh [9] 1997Shaker (K+ channel)GFP-
VSFP1 [14] 2001Rat Kv2.1 (K+ channel) FRET pair: CFP and YFP-
SPARC [15] 2002Rat Na+ channelGFP-
VSFP2's [16] 2007Ci-VSD FRET pair: CFP (Cerulean) and YFP (Citrine)VSFP1
Flare [17] 2007Kv1.4 (K+ channel)YFPFlaSh
VSFP3.1 [18] 2008Ci-VSDCFPVSFP2's
Mermaid [19] 2008Ci-VSD FRET pair: Marine GFP (mUKG) and OFP (mKOκ)VSFP2's
hVOS [20] 2008 Dipicrylamine GFP-
Red-shifted VSFP's [21] 2009Ci-VSDRFP/YFP (Citrine, mOrange2, TagRFP, or mKate2)VSFP3.1
PROPS [22] 2011Modified green-absorbing proteorhodopsin (GPR)Same as left-
Zahra, Zahra 2 [23] 2012Nv-VSD, Dr-VSD FRET pair: CFP (Cerulean) and YFP (Citrine)VSFP2's
ArcLight [24] 2012Ci-VSDModified super ecliptic pHluorin-
Arch [25] 2012 Archaerhodopsin 3 Same as left-
ElectricPk [26] 2012Ci-VSDCircularly permuted EGFPVSFP3.1
VSFP-Butterfly [27] 2012Ci-VSD FRET pair: YFP (mCitrine) and RFP (mKate2)VSFP2's
VSFP-CR [28] 2013Ci-VSD FRET pair: GFP (Clover) and RFP(mRuby2)VSFP2.3
Mermaid2 [29] 2013Ci-VSD FRET pair: CFP (seCFP2) and YFPMermaid
Mac GEVIs [30] 2014Mac rhodopsin (FRET acceptor)FRET doner: mCitrine, or mOrange2-
QuasAr1, QuasAr2 [31] 2014Modified Archaerhodopsin 3Same as leftArch
Archer [32] 2014Modified Archaerhodopsin 3Same as leftArch
ASAP1 [3] 2014Modified Gg-VSDCircularly permuted GFP-
Ace GEVIs [33] 2015Modified Ace rhodopsinFRET doner: mNeonGreenMac GEVIs
ArcLightning [34] 2015Ci-VSDModified super ecliptic pHluorinArcLight
Pado [35] 2016Voltage-gated proton channelSuper ecliptic pHluorin-
ASAP2f [36] 2016Modified Gg-VSDCircularly permuted GFPASAP1
FlicR1 [37] 2016Ci-VSDCircularly permuted RFP (mApple)VSFP3.1
Bongwoori [38] 2017Ci-VSDModified super ecliptic pHluorin ArcLight
ASAP2s [39] 2017Modified Gg-VSDCircularly permuted GFPASAP1
ASAP-Y [40] 2017Modified Gg-VSDCircularly permuted GFPASAP1
(pa)QuasAr3(-s) [41] 2019Modified Archaerhodopsin 3Same as leftQuasAr2
Voltron(-ST)2019Modified Ace rhodopsin (Ace2)FRET doner: Janelia Fluor (chemical)-
ASAP3 [4] 2019Modified Gg-VSDCircularly permuted GFPASAP2s
JEDI-2P [42] 2022Modified Gg-VSDCircularly permuted GFPASAP2s
  1. Names in italic denote GEVIs not named.

Characteristics

A GEVI can be evaluated by its many characteristics. These traits can be classified into two categories: performance and compatibility. The performance properties include brightness, photostability, sensitivity, kinetics (speed), linearity of response, etc., while the compatibility properties cover toxicity (phototoxicity), plasma membrane localization, adaptability of deep-tissue imaging, etc. [43] For now, no existing GEVI meets all the desired properties, so searching for a perfect GEVI is still a quite competitive research area.

Applications and advantages

Different types of GEVIs are being developed in many biological or physiological research areas. It is thought to be superior to conventional voltage detecting methods like electrode-based electrophysiological recordings, calcium imaging, or voltage sensitive dyes. It has subcellular spatial resolution [44] and temporal resolution as low as 0.2 milliseconds, about an order of magnitude faster than calcium imaging. This allows for spike detection fidelity comparable to electrode-based electrophysiology but without the invasiveness. [33] Researchers have used it to probe neural communications of an intact brain (of Drosophila [45] or mouse [46] ), electrical spiking of bacteria ( E. coli [22] ), and human stem-cell derived cardiomyocyte. [47] [48]

Future directions

For GEVI development, its future direction is highly coupled with the target applications. With newer generations of GEVIs overcome the poor performance of the first generation ones, we will see more routes open up for GEVIs to be used in more challenging and versatile applications. Like many other protein biosensors and actuators, once it passes the initial threshold of practicality, there will be more attempts to reshape the tool for its usage in different target applications, each with a different emphasis and requirement for a subset of performance metrics. For example, authors of JEDI-2P stated that the negative-going (bright-to-dim) sensor is good for detecting subthreshold depolarizations and hyperpolarizations but positive-going (dim-to-bright) sensors might be better for spike detection. [42] We may argue that it takes effort to engineer (screen) a perfect sensor, but often the more compelling reason is that simply there is not a unanimous definition of such perfection. For example, scientist might prefer sensors of different emission and excitation colors to be spectrally compatible with other optogenetic actuators. Recently, to compensate for the low signal-to-noise ratio (SNR) due to the poor brightness of GEVI, several denoising methods have been applied to increase SNR.

Related Research Articles

Channelrhodopsins are a subfamily of retinylidene proteins (rhodopsins) that function as light-gated ion channels. They serve as sensory photoreceptors in unicellular green algae, controlling phototaxis: movement in response to light. Expressed in cells of other organisms, they enable light to control electrical excitability, intracellular acidity, calcium influx, and other cellular processes. Channelrhodopsin-1 (ChR1) and Channelrhodopsin-2 (ChR2) from the model organism Chlamydomonas reinhardtii are the first discovered channelrhodopsins. Variants that are sensitive to different colors of light or selective for specific ions have been cloned from other species of algae and protists.

Cameleon is an engineered protein based on variant of green fluorescent protein used to visualize calcium levels in living cells. It is a genetically encoded calcium sensor created by Roger Y. Tsien and coworkers. The name is a conflation of CaM (the common abbreviation of calmodulin) and chameleon to indicate the fact that the sensor protein undergoes a conformation change and radiates at an altered wavelength upon calcium binding to the calmodulin element of the Cameleon. Cameleon was the first genetically encoded calcium sensor that could be used for ratiometric measurements and the first to be used in a transgenic animal to record activity in neurons and muscle cells. Cameleon and other genetically encoded calcium indicators (GECIs) have found many applications in neuroscience and other fields of biology, including understanding the mechanisms of cell signaling by conducting time-resolved Ca2+ activity measurement experiments with endoplasmic reticulum (ER) enzymes. It was created by fusing BFP, calmodulin, calmodulin-binding peptide M13 and EGFP.

<span class="mw-page-title-main">Hippocalcin</span> Protein-coding gene in the species Homo sapiens

Hippocalcin is a protein that in humans is encoded by the HPCA gene.

SCN2A Protein-coding gene in the species Homo sapiens

Sodium channel protein type 2 subunit alpha, is a protein that in humans is encoded by the SCN2A gene. Functional sodium channels contain an ion conductive alpha subunit and one or more regulatory beta subunits. Sodium channels which contain sodium channel protein type 2 subunit alpha are sometimes called Nav1.2 channels.

<span class="mw-page-title-main">Visinin-like protein 1</span> Protein-coding gene in the species Homo sapiens

Visinin-like protein 1 is a protein that in humans is encoded by the VSNL1 gene.

<span class="mw-page-title-main">NRCAM</span> Protein-coding gene in the species Homo sapiens

Neuronal cell adhesion molecule is a protein that in humans is encoded by the NRCAM gene.

<span class="mw-page-title-main">KCNIP1</span> Protein-coding gene in the species Homo sapiens

Kv channel-interacting protein 1 also known as KChIP1 is a protein that in humans is encoded by the KCNIP1 gene.

<span class="mw-page-title-main">KCNIP4</span> Protein-coding gene in the species Homo sapiens

Kv channel-interacting protein 4 is a protein that in humans is encoded by the KCNIP4 gene.

<span class="mw-page-title-main">Axon terminal</span> Nerve fiber part

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<span class="mw-page-title-main">RoGFP</span> Prodified GFP protein that exhibits different fluorescent properties when oxidized and reduced

The reduction-oxidation sensitive green fluorescent protein (roGFP) is a green fluorescent protein engineered to be sensitive to changes in the local redox environment. roGFPs are used as redox-sensitive biosensors.

Fluorescent chloride sensors are used for chemical analysis. The discoveries of chloride (Cl) participations in physiological processes stimulates the measurements of intracellular Cl in live cells and the development of fluorescent tools referred below.

<span class="mw-page-title-main">GCaMP</span> Genetically encoded calcium indicator

GCaMP is a genetically encoded calcium indicator (GECI) initially developed in 2001 by Junichi Nakai. It is a synthetic fusion of green fluorescent protein (GFP), calmodulin (CaM), and M13, a peptide sequence from myosin light-chain kinase. When bound to Ca2+, GCaMP fluoresces green with a peak excitation wavelength of 480 nm and a peak emission wavelength of 510 nm. It is used in biological research to measure intracellular Ca2+ levels both in vitro and in vivo using virally transfected or transgenic cell and animal lines. The genetic sequence encoding GCaMP can be inserted under the control of promoters exclusive to certain cell types, allowing for cell-type specific expression of GCaMP. Since Ca2+ is a second messenger that contributes to many cellular mechanisms and signaling pathways, GCaMP allows researchers to quantify the activity of Ca2+-based mechanisms and study the role of Ca2+ ions in biological processes of interest.

<span class="mw-page-title-main">HVCN1</span> Protein-coding gene in the species Homo sapiens

Voltage-gated hydrogen channel 1 is a protein that in humans is encoded by the HVCN1 gene.

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ArcLight is a genetically-encoded voltage indicator (GEVI) created from Ciona intestinalis voltage sensor and the fluorescent protein super ecliptic pHluorin that carries a critical point mutation (A227D).

<span class="mw-page-title-main">Archaerhodopsin</span> Family of archaea

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A genetically engineered fluorescent protein that changes its fluorescence when bound to the neurotransmitter glutamate. Glutamate-sensitive fluorescent reporters are used to monitor the activity of presynaptic terminals by fluorescence microscopy. GluSnFRs are a class of optogenetic sensors used in neuroscience research. In brain tissue, two-photon microscopy is typically used to monitor GluSnFR fluorescence.

Casper Hoogenraad is a Dutch Cell Biologist who specializes in molecular neuroscience. The focus of his research is the basic molecular and cellular mechanisms that regulate the development and function of the brain. As of January 2020, he serves as Vice President of Neuroscience at Genentech Research and Early Development.

Michael Z. Lin is a Taiwanese-American biochemist and bioengineer. He is an Associate Professor of Neurobiology and Bioengineering at Stanford University. He is best known for his work on engineering optically and chemically controllable proteins.

Optogenetics began with methods to alter neuronal activity with light, using e.g. channelrhodopsins. In a broader sense, optogenetic approaches also include the use of genetically encoded biosensors to monitor the activity of neurons or other cell types by measuring fluorescence or bioluminescence. Genetically encoded calcium indicators (GECIs) are used frequently to monitor neuronal activity, but other cellular parameters such as membrane voltage or second messenger activity can also be recorded optically. The use of optogenetic sensors is not restricted to neuroscience, but plays increasingly important roles in immunology, cardiology and cancer research.

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