Far-Red Fluorescent Proteins: Tools for Advancing In Vivo Imaging

Overview

Journal Biosensors (Basel)

Specialty Biotechnology

Date 2024 Aug 28

PMID 39194588

Authors

Angyang Shang

Shuai Shao

Luming Zhao

Bo Liu

Affiliations

Soon will be listed here.

Abstract

Far-red fluorescent proteins (FPs) have emerged as indispensable tools in in vivo imaging, playing a pivotal role in elucidating fundamental mechanisms and addressing application issues in biotechnology and biomedical fields. Their ability for deep penetration, coupled with reduced light scattering and absorption, robust resistance to autofluorescence, and diminished phototoxicity, has positioned far-red biosensors at the forefront of non-invasive visualization techniques for observing intracellular activities and intercellular behaviors. In this review, far-red FPs and their applications in living systems are mainly discussed. Firstly, various far-red FPs, characterized by emission peaks spanning from 600 nm to 650 nm, are introduced. This is followed by a detailed presentation of the fundamental principles enabling far-red biosensors to detect biomolecules and environmental changes. Furthermore, the review accentuates the superiority of far-red FPs in multi-color imaging. In addition, significant emphasis is placed on the value of far-red FPs in improving imaging resolution, highlighting their great contribution to the advancement of in vivo imaging.

Citing Articles

Editorial on the Special Issue "Fluorescence Imaging and Analysis of Cellular Systems".

Sharma A J Imaging. 2024; 10(11).

PMID: 39590757 PMC: 11595843. DOI: 10.3390/jimaging10110293.

References

Shirmanova M, Gavrina A, Kovaleva T, Dudenkova V, Zelenova E, Shcheslavskiy V . Insight into redox regulation of apoptosis in cancer cells with multiparametric live-cell microscopy. Sci Rep. 2022; 12(1):4476. PMC: 8927414. DOI: 10.1038/s41598-022-08509-1. View

Shcherbo D, Murphy C, Ermakova G, Solovieva E, Chepurnykh T, Shcheglov A . Far-red fluorescent tags for protein imaging in living tissues. Biochem J. 2009; 418(3):567-74. PMC: 2893397. DOI: 10.1042/BJ20081949. View

Wiedenmann J, Vallone B, Renzi F, Nienhaus K, Ivanchenko S, Rocker C . Red fluorescent protein eqFP611 and its genetically engineered dimeric variants. J Biomed Opt. 2005; 10(1):14003. DOI: 10.1117/1.1854680. View

Su H, Liao Z, Yang C, Zhang Y, Su J . Grass Carp Reovirus VP56 Allies VP4, Recruits, Blocks, and Degrades RIG-I to More Effectively Attenuate IFN Responses and Facilitate Viral Evasion. Microbiol Spectr. 2021; 9(2):e0100021. PMC: 8557896. DOI: 10.1128/Spectrum.01000-21. View

Pletneva N, Pletnev V, Shemiakina I, Chudakov D, Artemyev I, Wlodawer A . Crystallographic study of red fluorescent protein eqFP578 and its far-red variant Katushka reveals opposite pH-induced isomerization of chromophore. Protein Sci. 2011; 20(7):1265-74. PMC: 3149199. DOI: 10.1002/pro.654. View

An H, Harper J . Systematic analysis of ribophagy in human cells reveals bystander flux during selective autophagy. Nat Cell Biol. 2017; 20(2):135-143. PMC: 5786475. DOI: 10.1038/s41556-017-0007-x. View

Nienhaus K, Nar H, Heilker R, Wiedenmann J, Nienhaus G . Trans-cis isomerization is responsible for the red-shifted fluorescence in variants of the red fluorescent protein eqFP611. J Am Chem Soc. 2008; 130(38):12578-9. DOI: 10.1021/ja8046443. View

Shemetov A, Monakhov M, Zhang Q, Canton-Josh J, Kumar M, Chen M . A near-infrared genetically encoded calcium indicator for in vivo imaging. Nat Biotechnol. 2020; 39(3):368-377. PMC: 7956128. DOI: 10.1038/s41587-020-0710-1. View

Sun F, Zhou J, Dai B, Qian T, Zeng J, Li X . Next-generation GRAB sensors for monitoring dopaminergic activity in vivo. Nat Methods. 2020; 17(11):1156-1166. PMC: 7648260. DOI: 10.1038/s41592-020-00981-9. View

10.

Orlov N, Ignatova A, Kryukova E, Yakimov S, Kirpichnikov M, Nekrasova O . Combining mKate2-Kv1.3 Channel and Atto488-Hongotoxin for the Studies of Peptide Pore Blockers on Living Eukaryotic Cells. Toxins (Basel). 2022; 14(12). PMC: 9780825. DOI: 10.3390/toxins14120858. View

11.

Lin M, McKeown M, Ng H, Aguilera T, Shaner N, Campbell R . Autofluorescent proteins with excitation in the optical window for intravital imaging in mammals. Chem Biol. 2009; 16(11):1169-79. PMC: 2814181. DOI: 10.1016/j.chembiol.2009.10.009. View

12.

Lyu T, Sohn S, Jimenez R, Joo T . Temperature-Dependent Fluorescence of mPlum Fluorescent Protein from 295 to 20 K. J Phys Chem B. 2022; 126(12):2337-2344. DOI: 10.1021/acs.jpcb.1c10516. View

13.

Strack R, Hein B, Bhattacharyya D, Hell S, Keenan R, Glick B . A rapidly maturing far-red derivative of DsRed-Express2 for whole-cell labeling. Biochemistry. 2009; 48(35):8279-81. PMC: 2861903. DOI: 10.1021/bi900870u. View

14.

Mudalige K, Habuchi S, Goodwin P, Pai R, De Schryver F, Cotlet M . Photophysics of the red chromophore of HcRed: evidence for cis-trans isomerization and protonation-state changes. J Phys Chem B. 2010; 114(13):4678-85. DOI: 10.1021/jp9102146. View

15.

Mino R, Chen Z, Mettlen M, Schmid S . An internally eGFP-tagged α-adaptin is a fully functional and improved fiduciary marker for clathrin-coated pit dynamics. Traffic. 2020; 21(9):603-616. PMC: 7495412. DOI: 10.1111/tra.12755. View

16.

Li C, Burdick R, Nagashima K, Hu W, Pathak V . HIV-1 cores retain their integrity until minutes before uncoating in the nucleus. Proc Natl Acad Sci U S A. 2021; 118(10). PMC: 7958386. DOI: 10.1073/pnas.2019467118. View

17.

Eapen V, Swarup S, Hoyer M, Paulo J, Harper J . Quantitative proteomics reveals the selectivity of ubiquitin-binding autophagy receptors in the turnover of damaged lysosomes by lysophagy. Elife. 2021; 10. PMC: 8523161. DOI: 10.7554/eLife.72328. View

18.

Han Y, Wang S, Zhang Z, Ma X, Li W, Zhang X . In vivo imaging of protein-protein and RNA-protein interactions using novel far-red fluorescence complementation systems. Nucleic Acids Res. 2014; 42(13):e103. PMC: 4117741. DOI: 10.1093/nar/gku408. View

19.

Wilmann P, Petersen J, Pettikiriarachchi A, Buckle A, Smith S, Olsen S . The 2.1A crystal structure of the far-red fluorescent protein HcRed: inherent conformational flexibility of the chromophore. J Mol Biol. 2005; 349(1):223-37. DOI: 10.1016/j.jmb.2005.03.020. View

20.

Evans S, Shi D, Chavarha M, Plitt M, Taxidis J, Madruga B . A positively tuned voltage indicator for extended electrical recordings in the brain. Nat Methods. 2023; 20(7):1104-1113. PMC: 10627146. DOI: 10.1038/s41592-023-01913-z. View