Development and Characterization of Flavin-Binding Fluorescent Proteins, Part I: Basic Characterization.
Flavin
Flavin-binding fluorescent protein
Fluorescence microscopy
Genome mining
LOV domain
Journal
Methods in molecular biology (Clifton, N.J.)
ISSN: 1940-6029
Titre abrégé: Methods Mol Biol
Pays: United States
ID NLM: 9214969
Informations de publication
Date de publication:
2023
2023
Historique:
entrez:
15
9
2022
pubmed:
16
9
2022
medline:
20
9
2022
Statut:
ppublish
Résumé
Flavin-based fluorescent proteins (FbFPs) are small fluorescent proteins derived from light-oxygen-voltage (LOV) domains. The proteins bind ubiquitous endogenous flavins as chromophores and can be used as versatile in vivo reporter proteins under aerobic and anaerobic conditions. This chapter presents the methodology to identify LOV domain sequences in genomic databases; design new FbFPs; characterize their biochemical, spectroscopic, photophysical, and photochemical properties; and conduct basic fluorescence microscopy experiments.
Identifiants
pubmed: 36107340
doi: 10.1007/978-1-0716-2667-2_6
doi:
Substances chimiques
Dinitrocresols
0
Flavins
0
Proteins
0
4,6-dinitro-o-cresol
1604ZJR09T
Oxygen
S88TT14065
Types de publication
Journal Article
Research Support, Non-U.S. Gov't
Langues
eng
Sous-ensembles de citation
IM
Pagination
121-141Informations de copyright
© 2023. The Author(s), under exclusive license to Springer Science+Business Media, LLC, part of Springer Nature.
Références
Chalfie M, Kain SR (eds) (2005) Green fluorescent protein: properties, applications and protocols. Wiley-Liss, Hoboken
Craggs TD (2009) Green fluorescent protein: structure, folding and chromophore maturation. Chem Soc Rev 38:2865–2875
doi: 10.1039/b903641p
Drepper T, Eggert T, Circolone F et al (2007) Reporter proteins for in vivo fluorescence without oxygen. Nat Biotechnol 25:443–445
doi: 10.1038/nbt1293
Lobo LA, Smith CJ, Rocha ER (2011) Flavin mononucleotide (FMN)-based fluorescent protein (FbFP) as reporter for gene expression in the anaerobe Bacteroides fragilis. FEMS Microbiol Lett 317:67–74
doi: 10.1111/j.1574-6968.2011.02212.x
Potzkei J, Kunze M, Drepper T et al (2012) Real-time determination of intracellular oxygen in bacteria using a genetically encoded FRET-based biosensor. BMC Biol 10:28
doi: 10.1186/1741-7007-10-28
Walter J, Hausmann S, Drepper T et al (2012) Flavinmononucleotide-based fluorescent proteins function in mammalian cells without oxygen requirement. PLoS One 7:e43921
doi: 10.1371/journal.pone.0043921
Wingen M, Potzkei J, Endres S et al (2014) The photophysics of LOV-based fluorescent proteins – new tools for cell biology. Photochem Photobiol Sci 13:875–883
doi: 10.1039/C3PP50414J
Buckley AM, Petersen J, Roe AJ et al (2015) LOV-based reporters for fluorescence imaging. Curr Opin Chem Biol 27:39–45
doi: 10.1016/j.cbpa.2015.05.011
Mukherjee A, Schroeder CM (2015) Flavin-based fluorescent proteins: emerging paradigms in biological imaging. Curr Opin Biotechnol 31:16–23
doi: 10.1016/j.copbio.2014.07.010
Buckley AM, Jukes C, Candlish D et al (2016) Lighting up Clostridium difficile: reporting gene expression using fluorescent LOV domains. Sci Rep 6:23463
doi: 10.1038/srep23463
Rupprecht C, Wingen M, Potzkei J et al (2017) A novel FbFP-based biosensor toolbox for sensitive in vivo determination of intracellular pH. J Biotechnol 258:25–32
doi: 10.1016/j.jbiotec.2017.05.006
Yudenko A, Smolentseva A, Maslov I et al (2021) Rational design of a split flavin-based fluorescent reporter. ACS Synth Biol 10:72–83
doi: 10.1021/acssynbio.0c00454
Chapman S, Faulkner C, Kaiserli E et al (2008) The photoreversible fluorescent protein iLOV outperforms GFP as a reporter of plant virus infection. Proc Natl Acad Sci U S A 105:20038–20043
doi: 10.1073/pnas.0807551105
Glantz ST, Carpenter EJ, Melkonian M et al (2016) Functional and topological diversity of LOV domain photoreceptors. Proc Natl Acad Sci U S A 113:E1442–E1451
doi: 10.1073/pnas.1509428113
Wingen M, Jaeger K-E, Gensch T et al (2017) Novel thermostable Flavin-binding fluorescent proteins from thermophilic organisms. Photochem Photobiol 93:849–856
doi: 10.1111/php.12740
Nazarenko VV, Remeeva A, Yudenko A et al (2019) A thermostable flavin-based fluorescent protein from Chloroflexus aggregans: a framework for ultra-high resolution structural studies. Photochem Photobiol Sci 18:1793–1805
doi: 10.1039/C9PP00067D
Goncharov IM, Smolentseva A, Semenov O et al (2021) High-resolution structure of a naturally red-shifted LOV domain. Biochem Biophys Res Commun 567:143–147
doi: 10.1016/j.bbrc.2021.06.046
Losi A, Gardner KH, Möglich A (2018) Blue-light receptors for Optogenetics. Chem Rev 118:10659–10709
doi: 10.1021/acs.chemrev.8b00163
Studier FW (2005) Protein production by auto-induction in high-density shaking cultures. Protein Expr Purif 41:207–234
doi: 10.1016/j.pep.2005.01.016
Sayers EW, Cavanaugh M, Clark K et al (2022) GenBank. Nucleic Acids Res 50:D161–D164
doi: 10.1093/nar/gkab1135
Johnson M, Zaretskaya I, Raytselis Y et al (2008) NCBI BLAST: a better web interface. Nucleic Acids Res 36:W5–W9
doi: 10.1093/nar/gkn201
Blum M, Chang H-Y, Chuguransky S et al (2021) The InterPro protein families and domains database: 20 years on. Nucleic Acids Res 49:D344–D354
doi: 10.1093/nar/gkaa977
Waterhouse A, Bertoni M, Bienert S et al (2018) SWISS-MODEL: homology modelling of protein structures and complexes. Nucleic Acids Res 46:W296–W303
doi: 10.1093/nar/gky427
Verma M, Choi J, Cottrell KA et al (2019) A short translational ramp determines the efficiency of protein synthesis. Nat Commun 10:5774
doi: 10.1038/s41467-019-13810-1
Weber M, Burgos R, Yus E et al (2020) Impact of C-terminal amino acid composition on protein expression in bacteria. Mol Syst Biol 16:e9208
doi: 10.15252/msb.20199208
Smolentseva A, Goncharov IM, Yudenko A et al (2021) Extreme dependence of Chloroflexus aggregans LOV domain thermo- and photostability on the bound flavin species. Photochem Photobiol Sci 20:1645–1656
doi: 10.1007/s43630-021-00138-3
Duvaud S, Gabella C, Lisacek F et al (2021) Expasy, the Swiss bioinformatics resource portal, as designed by its users. Nucleic Acids Res 49:W216–W227
doi: 10.1093/nar/gkab225
Cubitt AB, Woollenweber LA, Heim R (1998) Chapter 2: understanding structure—function relationships in the Aequorea victoria green fluorescent protein. In: Sullivan KF, Kay SA, Sullivan KF, Kay SA (eds) Methods in cell biology. Elsevier, pp 19–30
Jiménez-Banzo A, Nonell S, Hofkens J et al (2008) Singlet oxygen photosensitization by EGFP and its chromophore HBDI. Biophys J 94:168–172
doi: 10.1529/biophysj.107.107128
Endres S, Wingen M, Torra J et al (2018) An optogenetic toolbox of LOV-based photosensitizers for light-driven killing of bacteria. Sci Rep 8:1–14
doi: 10.1038/s41598-018-33291-4
Siliprandi N, Bianchi P (1955) A new method for preparing flavin-adenine-dinucleotide. Biochim Biophys Acta 16:424–428
doi: 10.1016/0006-3002(55)90248-1
Kataoka M, Shimizu S, Yamada H (1992) Purification and characterization of a novel FMN-dependent enzyme. Membrane-bound L-(+)-pantoyl lactone dehydrogenase from Nocardia asteroides. Eur J Biochem 204:799–806
doi: 10.1111/j.1432-1033.1992.tb16698.x
Röllen K, Granzin J, Remeeva A et al (2021) The molecular basis of spectral tuning in blue- and red-shifted flavin-binding fluorescent proteins. J Biol Chem 296:100662
doi: 10.1016/j.jbc.2021.100662