1
|
Luo Y, Pi S, Liu YJ. Mechanistic Insights into the Bacterial Luciferase-based Bioluminescence Resonance Energy Transfer Luminescence: The Role of Protein Complex Dimer. Chemphyschem 2024; 25:e202300973. [PMID: 38345139 DOI: 10.1002/cphc.202300973] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2024] [Revised: 02/11/2024] [Indexed: 02/29/2024]
Abstract
Bacterial bioluminescence holds significant potential in the realm of optical imaging due to the inherent advantages of bioluminescence and ease of operation. However, its practical utility is hindered by its low light intensity. The fusion of bacterial luciferase with a highly fluorescent protein has been demonstrated to significantly enhance autonomous luminescence. Nevertheless, the underlying mechanism behind this enhancement remains unclear, and there is a dearth of research investigating the mechanistic aspects of bioluminescence resonance energy transfer (BRET) luminescence, whether it occurs naturally or can be achieved through experimental means. In this study, we investigated the phenomenon of bacterial luciferase-based BRET luminescence employing a range of computational techniques, including structural modeling, molecular docking, molecular dynamics simulations, as well as combined quantum mechanics and molecular mechanics calculations. The theoretical findings suggest that the BRET luminescence occurs through resonance energy transfer between the excited bioluminophore and the ground chromophore within the protein complex dimer. The proposed mechanism of the protein complex dimer offers a microscopic understanding of the intriguing BRET phenomenon and has the potential to inspire further practical applications in the field of optical imaging.
Collapse
Affiliation(s)
- Yanling Luo
- School of Chinese Materia Medica, Tianjin University of Traditional Chinese Medicine, Tianjin, China
| | - Shuangqi Pi
- Key Laboratory of Theoretical and Computational Photochemistry, Ministry of Education, College of Chemistry, Beijing Normal University, Beijing, China
| | - Ya-Jun Liu
- Key Laboratory of Theoretical and Computational Photochemistry, Ministry of Education, College of Chemistry, Beijing Normal University, Beijing, China
- Center for Advanced Materials Research, Beijing Normal University, Zhuhai, China
| |
Collapse
|
2
|
Giuliani G, Melaccio F, Gozem S, Cappelli A, Olivucci M. QM/MM Investigation of the Spectroscopic Properties of the Fluorophore of Bacterial Luciferase. J Chem Theory Comput 2021; 17:605-613. [PMID: 33449693 PMCID: PMC9220819 DOI: 10.1021/acs.jctc.0c01078] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
We employ replica-exchange molecular dynamics (REMD) and a hybrid ab initio multiconfigurational quantum mechanics/molecular mechanics (QM/MM) approach to model the absorption and fluorescence properties of bacterial luciferin-luciferase. Specifically, we employ complete active space perturbation theory (CASPT2) and study the effect of active space, basis set, and IPEA shift on the computed energies. We discuss the effect of the protein environment on the fluorophore's excited-state potential energy surface and the role that the protein plays in enhancing the fluorescence quantum yield in bacterial bioluminescence.
Collapse
Affiliation(s)
- Germano Giuliani
- Department of Biotechnology, Chemistry and Pharmacy, University of Siena, Via A. Moro 2, 53100 Siena, Italy
| | - Federico Melaccio
- Department of Biotechnology, Chemistry and Pharmacy, University of Siena, Via A. Moro 2, 53100 Siena, Italy
| | - Samer Gozem
- Department of Chemistry, Georgia State University, Atlanta, Georgia 30302, United States
| | - Andrea Cappelli
- Department of Biotechnology, Chemistry and Pharmacy, University of Siena, Via A. Moro 2, 53100 Siena, Italy
| | - Massimo Olivucci
- Department of Biotechnology, Chemistry and Pharmacy, University of Siena, Via A. Moro 2, 53100 Siena, Italy
- Department of Chemistry, Bowling Green State University, Bowing Green, Ohio 43403, United States
| |
Collapse
|
3
|
Lee J, Müller F, Visser AJWG. The Sensitized Bioluminescence Mechanism of Bacterial Luciferase. Photochem Photobiol 2018; 95:679-704. [PMID: 30485901 DOI: 10.1111/php.13063] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2018] [Accepted: 11/17/2018] [Indexed: 11/27/2022]
Abstract
After more than one-half century of investigations, the mechanism of bioluminescence from the FMNH2 assisted oxygen oxidation of an aliphatic aldehyde on bacterial luciferase continues to resist elucidation. There are many types of luciferase from species of bioluminescent bacteria originating from both marine and terrestrial habitats. The luciferases all have close sequence homology, and in vitro, a highly efficient light generation is obtained from these natural metabolites as substrates. Sufficient exothermicity equivalent to the energy of a blue photon is available in the chemical oxidation of the aldehyde to the corresponding carboxylic acid, and a luciferase-bound FMNH-OOH is a key player. A high energy species, the source of the exothermicity, is unknown except that it is not a luciferin cyclic peroxide, a dioxetanone, as identified in the pathway of the firefly and the marine bioluminescence systems. Besides these natural substrates, variable bioluminescence properties are found using other reactants such as flavin analogs or aldehydes, but results also depend on the luciferase type. Some rationalization of the mechanism has resulted from spatial structure determination, NMR of intermediates and dynamic optical spectroscopy. The overall light path appears to fall into the sensitized class of chemiluminescence mechanism, distinct from the dioxetanone types.
Collapse
Affiliation(s)
- John Lee
- Department of Biochemistry and Molecular Biology, University of Georgia, Athens, GA
| | | | - Antonie J W G Visser
- Laboratory of Biochemistry Microspectroscopy Centre, Wageningen University, Wageningen, The Netherlands
| |
Collapse
|
4
|
Lee J. Perspectives on Bioluminescence Mechanisms. Photochem Photobiol 2016; 93:389-404. [PMID: 27748947 DOI: 10.1111/php.12650] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2016] [Accepted: 08/24/2016] [Indexed: 11/27/2022]
Abstract
The molecular mechanisms of the bioluminescence systems of the firefly, bacteria and those utilizing imidazopyrazinone luciferins such as coelenterazine are gradually being uncovered using modern biophysical methods such as dynamic (ns-ps) fluorescence spectroscopy, NMR, X-ray crystallography and computational chemistry. The chemical structures of all reactants are well defined, and the spatial structures of the luciferases are providing important insight into interactions within the active cavity. It is generally accepted that the firefly and coelenterazine systems, although proceeding by different chemistries, both generate a dioxetanone high-energy species that undergoes decarboxylation to form directly the product in its S1 state, the bioluminescence emitter. More work is still needed to establish the structure of the products completely. In spite of the bacterial system receiving the most research attention, the chemical pathway for excitation remains mysterious except that it is clearly not by a decarboxylation. Both the coelenterazine and bacterial systems have in common of being able to employ "antenna proteins," lumazine protein and the green-fluorescent protein, for tuning the color of the bioluminescence. Spatial structure information has been most valuable in informing the mechanism of the Ca2+ -regulated photoproteins and the antenna protein interactions.
Collapse
Affiliation(s)
- John Lee
- Department of Biochemistry and Molecular Biology, University of Georgia, Athens, GA
| |
Collapse
|
5
|
Titushin MS, Feng Y, Lee J, Vysotski ES, Liu ZJ. Protein-protein complexation in bioluminescence. Protein Cell 2012; 2:957-72. [PMID: 22231355 DOI: 10.1007/s13238-011-1118-y] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2011] [Accepted: 11/07/2011] [Indexed: 12/01/2022] Open
Abstract
In this review we summarize the progress made towards understanding the role of protein-protein interactions in the function of various bioluminescence systems of marine organisms, including bacteria, jellyfish and soft corals, with particular focus on methodology used to detect and characterize these interactions. In some bioluminescence systems, protein-protein interactions involve an "accessory protein" whereby a stored substrate is efficiently delivered to the bioluminescent enzyme luciferase. Other types of complexation mediate energy transfer to an "antenna protein" altering the color and quantum yield of a bioluminescence reaction. Spatial structures of the complexes reveal an important role of electrostatic forces in governing the corresponding weak interactions and define the nature of the interaction surfaces. The most reliable structural model is available for the protein-protein complex of the Ca(2+)-regulated photoprotein clytin and green-fluorescent protein (GFP) from the jellyfish Clytia gregaria, solved by means of Xray crystallography, NMR mapping and molecular docking. This provides an example of the potential strategies in studying the transient complexes involved in bioluminescence. It is emphasized that structural studies such as these can provide valuable insight into the detailed mechanism of bioluminescence.
Collapse
Affiliation(s)
- Maxim S Titushin
- National Laboratory of Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing, 100101, China
| | | | | | | | | |
Collapse
|
6
|
Sasaki S, Mori Y, Ogawa M, Funatsuka S. Spatio-Temporal Control of Bacterial-Suspension Luminescence Using a PDMS Cell. JOURNAL OF CHEMICAL ENGINEERING OF JAPAN 2010. [DOI: 10.1252/jcej.10we137] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Affiliation(s)
| | - Yusuke Mori
- Graduate School of Bionics, Tokyo University of Technology
| | | | | |
Collapse
|
7
|
Gerasimova M, Sizykh A, Slyusareva E. The role of energy transfer in bioluminescence quenching by xanthene dyes. JOURNAL OF PHOTOCHEMISTRY AND PHOTOBIOLOGY B-BIOLOGY 2009; 97:117-22. [DOI: 10.1016/j.jphotobiol.2009.08.007] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/11/2009] [Revised: 07/27/2009] [Accepted: 08/03/2009] [Indexed: 10/20/2022]
|
8
|
Kudryasheva NS. Bioluminescence and exogenous compounds: physico-chemical basis for bioluminescent assay. JOURNAL OF PHOTOCHEMISTRY AND PHOTOBIOLOGY B-BIOLOGY 2006; 83:77-86. [PMID: 16413195 DOI: 10.1016/j.jphotobiol.2005.10.003] [Citation(s) in RCA: 53] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/27/2005] [Revised: 07/28/2005] [Accepted: 10/27/2005] [Indexed: 11/28/2022]
Abstract
Bioluminescent systems are convenient objects to study mechanisms of influence of exogenous molecules on living organisms. Classification of physical and physico-chemical mechanisms of the effects of luminous bacteria Photobacterium leiognathi on bioluminescent reactions is suggested. Five mechanisms are discussed: (1) change of electron-excited states' population and energy transfer, (2) change of efficiency of S-T conversion in the presence of external heavy atom, (3) change of rates of coupled reactions, (4) interactions with enzymes and variation of enzymatic activity, (5) nonspecific effects of electron acceptors. Effects of various groups of chemical compounds are discussed according to the classification suggested. The compounds are: a series of fluorescent dyes, organic oxidizers, organic and inorganic heavy-atom containing compounds, and metallic salts. Applications of fluorescence time-resolved and steady-state techniques, as well as bioluminescence kinetics study, are discussed. The patterns of exogenous compounds' influence form a physico-chemical basis for bioluminescent ecological assay.
Collapse
|
9
|
Zmijewski MA, Kwiatkowska JM, Lipińska B. Complementation studies of the DnaK-DnaJ-GrpE chaperone machineries from Vibrio harveyi and Escherichia coli, both in vivo and in vitro. Arch Microbiol 2004; 182:436-49. [PMID: 15448982 DOI: 10.1007/s00203-004-0727-8] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2004] [Revised: 08/03/2004] [Accepted: 08/10/2004] [Indexed: 11/29/2022]
Abstract
The marine bacterium Vibrio harveyi is a potential indicator organism for evaluating marine environmental pollution. The DnaK-DnaJ-GrpE chaperone machinery of V. harveyi has been studied as a model of response to stress conditions and compared to the Escherichia coli DnaK system. The genes encoding DnaK, DnaJ and GrpE of V. harveyi were cloned into expression vectors and grpE was sequenced. It was found that V. harveyi possesses a unique organization of the hsp gene cluster (grpE-gltP-dnaK-dnaJ), which is present exclusively in marine Vibrio species. In vivo experiments showed that suppression of the E. coli dnaK mutation by V. harveyi DnaK protein was weak or absent, while suppression of the dnaJ and grpE mutations by V. harveyi DnaJ and GrpE proteins was efficient. These results suggest higher species-specificity of the DnaK chaperone than the GrpE and DnaJ cochaperones. Proteins of the DnaK chaperone machinery of V. harveyi were purified to homogeneity and their efficient cooperation with the E. coli chaperones in the luciferase refolding reaction and in stimulation of DnaK ATPase activity was demonstrated. Compared to the E. coli system, the purified DnaK-DnaJ-GrpE system of V. harveyi exhibited about 20% lower chaperoning activity in the luciferase reactivation assay. ATPase activity of V. harveyi DnaK protein was at least twofold higher than that of the E. coli model DnaK but its stimulation by the cochaperones DnaJ and GrpE was significantly (10 times) weaker. These results indicate that, despite their high structural identity (approximately 80%) and similar mechanisms of action, the DnaK chaperones of closely related V. harveyi and E.coli bacteria differ functionally.
Collapse
Affiliation(s)
- Michał A Zmijewski
- Department of Biochemistry, University of Gdansk, Kladki 24, 80-822 Gdansk, Poland
| | | | | |
Collapse
|
10
|
Kudryasheva NS, Nemtseva EV, Sizykh AG, Kratasyuk VA, Visser AJWG. Estimation of energy of the upper electron-excited states of the bacterial bioluminescent emitter. JOURNAL OF PHOTOCHEMISTRY AND PHOTOBIOLOGY. B, BIOLOGY 2002; 68:88-92. [PMID: 12468202 DOI: 10.1016/s1011-1344(02)00360-3] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
Abstract
The hypothesis of activity of the upper electron-excited states of the bacterial bioluminescent emitter was verified using dye molecules as foreign energy acceptors. Six compounds were selected having fluorescent state energies ranging from 25,700 to 32,000 cm(-1) (anthracene, pyrene, 1.4-bis(5-phenyloxasol-2-yl)benzene (POPOP), p-bis(o-methylstyryl)benzene (MSB), 2-methoxy-naphtalene, p-terphenyl), exceeding that of the bioluminescent emitter (22,000 cm(-1)). Their absorption spectra do not overlap with the bioluminescence spectrum; the trivial light absorption and the intermolecular resonance S-S energy transfer were excluded. Bacterial bioluminescent spectra of the coupled enzyme system NADH:FMN-oxidoreductase-luciferase in the presence of MSB were presented as an example. The weak sensitized fluorescence of MSB was registered. The results obtained have confirmed the activity of the energetic precursor in the bacterial bioluminescence. Its energy can be located in the interval of 26,000-27,000 cm(-1).
Collapse
Affiliation(s)
- N S Kudryasheva
- Institute of Biophysics, Siberian Branch of the Russian Academy of Sciences, Akademgorodok, Krasnoyarsk 660036, Russia.
| | | | | | | | | |
Collapse
|
11
|
Bacher A, Eberhardt S, Eisenreich W, Fischer M, Herz S, Illarionov B, Kis K, Richter G. Biosynthesis of riboflavin. VITAMINS AND HORMONES 2001; 61:1-49. [PMID: 11153262 DOI: 10.1016/s0083-6729(01)61001-x] [Citation(s) in RCA: 76] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
The biosynthesis of one riboflavin molecule requires one molecule of GTP and two molecules of ribulose 5-phosphate. The imidazole ring of GTP is hydrolytically opened, yielding a 4,5-diaminopyrimidine that is converted to 5-amino-6-ribitylamino-2,4(1H,3H)-pyrimidinedione by a sequence of deamination, side chain reduction, and dephosphorylation. Condensation of 5-amino-6-ribitylamino-2,4(1H,3H)-pyrimidinedione with 3,4-dihydroxy-2-butanone 4-phosphate obtained from ribulose 5-phosphate affords 6,7-dimethyl-8-ribityllumazine. Dismutation of the lumazine derivative yields riboflavin and 5-amino-6-ribitylamino-2,4(1H,3H)-pyrimidinedione, which is recycled in the biosynthetic pathway. Two reaction steps in the biosynthetic pathway catalyzed by 3,4-dihydroxy-2-butanone 4-phosphate synthase and riboflavin synthase are mechanistically very complex. The enzymes of the riboflavin pathway are potential targets for antibacterial agents.
Collapse
Affiliation(s)
- A Bacher
- Lehrstuhl für Organische Chemie und Biochemie, Technische Universität München, D-85747 Garching, Germany
| | | | | | | | | | | | | | | |
Collapse
|
12
|
Petushkov VN, Gibson BG, Lee J. Properties of recombinant fluorescent proteins from Photobacterium leiognathi and their interaction with luciferase intermediates. Biochemistry 1995; 34:3300-9. [PMID: 7880825 DOI: 10.1021/bi00010a020] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023]
Abstract
Ligand binding and luciferase interaction properties of the recombinant protein corresponding to the lumazine protein gene (EMBL X56534) of Photobacterium leiognathi have been determined by fluorescence dynamics, circular dichroism, gel filtration, and SDS-PAGE. Scatchard analysis of a fluorescence titration shows that the apoprotein possess one binding site, and at 30 degrees C the KdS (microM) are as follows: 6,7-dimethyl-8-ribityllumazine, 0.26; riboflavin, 0.53; and much more weakly bound FMN, 30. All holoproteins are highly fluorescent and have absorption spectra distinct from each other and from the free ligands. The longest wavelength absorption maxima are, respectively (nm, 2 degrees C), 420, 463, and 458. Ligand binding produces no change in the far-UV circular dichroism; all have mean residual ellipticity at 210 nm of -6500 deg cm2 dmol-1, the same as the native protein. However, in the bioluminescence reaction only the lumazine holoprotein shows a bioluminescence effect. Fluorescence emission anisotropy decay was used to establish that none of these holoproteins complexed with native luciferase and that the lumazine protein alone formed a 1:1 complex with the luciferase hydroxyflavin fluorescent transient and the luciferase peroxyflavin intermediates, revealed by a dominant channel of anisotropy loss, with rotational correlation time of 2.5 ns, and attributed to excitation transfer from the luciferase flavin donor to the acceptor, the lumazine ligand. The complex stability was sufficient to allow its isolation by FPLC gel filtration and verification by SDS-PAGE. These methods also confirmed the absence of interaction of the holoflavoproteins.
Collapse
Affiliation(s)
- V N Petushkov
- Department of Biochemistry and Molecular Biology, University of Georgia, Athens 30602
| | | | | |
Collapse
|
13
|
Abstract
The spectral properties of lumazine protein and mixtures with the intermediates of the bacterial luciferase reaction, are reviewed. Measurements of fluorescence dynamics in particular have been employed with the aim of elucidating the mechanism by which lumazine protein functions in the bioluminescence of the bacteria of the type Photobacterium. The reaction of bacterial luciferase with its substrates produces bioluminescence emission with a spectral maximum at 496 nm. This spectrum is the same as the fluorescence of a luciferase flavin intermediate in the reaction, called the Fluorescent Transient. When lumazine protein is also present in the reaction; however, the bioluminescence emission now corresponds to the fluorescence of lumazine protein, which has a maximum at 475 nm. From measurements of the decay of fluorescence anisotropy of lumazine protein alone and in mixtures with the luciferase fluorescent transient, it is shown that a protein-protein complex is formed and that there is rapid energy transfer between the flavin on the luciferase and the lumazine derivative bound to its protein. An approximate calculation estimates the rate of this energy transfer to be faster than 10(9) s-1, and this would account for the efficient transfer of excitation from the flavin on the associated luciferase in the mixed protein bioluminescence reaction.
Collapse
Affiliation(s)
- J Lee
- Department of Biochemistry, University of Georgia, Athens 30602
| |
Collapse
|
14
|
Meighen EA, Dunlap PV. Physiological, biochemical and genetic control of bacterial bioluminescence. Adv Microb Physiol 1993; 34:1-67. [PMID: 8452091 DOI: 10.1016/s0065-2911(08)60027-2] [Citation(s) in RCA: 114] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/30/2023]
Affiliation(s)
- E A Meighen
- Department of Biochemistry, McGill University, Montreal, Quebec, Canada
| | | |
Collapse
|
15
|
Abstract
In bacteria, most genes required for the bioluminescence phenotype are contained in lux operons. Sequence alignments of several lux gene products show the existence of at least two groups of paralogous products. The alpha- and beta-subunits of bacterial luciferase and the non-fluorescent flavoprotein are paralogous, and two antennae proteins (lumazine protein and yellow fluorescence protein) are paralogous with riboflavin synthetase. Models describing the evolution of these paralogous proteins are suggested, as well as a postulate for the identity of the gene encoding a protobioluminescent luciferase.
Collapse
Affiliation(s)
- D J O'Kane
- Department of Biochemistry, University of Georgia, Athens 30602
| | | |
Collapse
|