1
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Magner ET, Freund Saxhaug K, Zambre A, Bruns K, Carroll P, Snell-Rood EC, Hegeman AD, Carter CJ. A multifunctional role for riboflavin in the yellow nectar of Capsicum baccatum and Capsicum pubescens. THE NEW PHYTOLOGIST 2024. [PMID: 38874372 DOI: 10.1111/nph.19886] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/16/2023] [Accepted: 05/14/2024] [Indexed: 06/15/2024]
Abstract
A few Capsicum (pepper) species produce yellow-colored floral nectar, but the chemical identity and biological function of the yellow pigment are unknown. A combination of analytical biochemistry techniques was used to identify the pigment that gives Capsicum baccatum and Capsicum pubescens nectars their yellow color. Microbial growth assays, visual modeling, and honey bee preference tests for artificial nectars containing riboflavin were used to assess potential biological roles for the nectar pigment. High concentrations of riboflavin (vitamin B2) give the nectars their intense yellow color. Nectars containing riboflavin generate reactive oxygen species when exposed to light and reduce microbial growth. Visual modeling also indicates that the yellow color is highly conspicuous to bees within the context of the flower. Lastly, field experiments demonstrate that honey bees prefer artificial nectars containing riboflavin. Some Capsicum nectars contain a yellow-colored vitamin that appears to play roles in (1) limiting microbial growth, (2) the visual attraction of bees, and (3) as a reward to nectar-feeding flower visitors (potential pollinators), which is especially interesting since riboflavin is an essential nutrient for brood rearing in insects. These results cumulatively suggest that the riboflavin found in some Capsicum nectars has several functions.
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Affiliation(s)
- Evin T Magner
- Department of Plant & Microbial Biology, University of Minnesota, 1479 Gortner Avenue, St. Paul, MN, 55108, USA
| | | | - Amod Zambre
- Department of Ecology, Evolution, and Behavior, University of Minnesota, St. Paul, MN, 55108, USA
| | - Kaitlyn Bruns
- Department of Plant & Microbial Biology, University of Minnesota, 1479 Gortner Avenue, St. Paul, MN, 55108, USA
| | - Patrick Carroll
- Department of Plant & Microbial Biology, University of Minnesota, 1479 Gortner Avenue, St. Paul, MN, 55108, USA
| | - Emilie C Snell-Rood
- Department of Ecology, Evolution, and Behavior, University of Minnesota, St. Paul, MN, 55108, USA
| | - Adrian D Hegeman
- Department of Plant & Microbial Biology, University of Minnesota, 1479 Gortner Avenue, St. Paul, MN, 55108, USA
- Department of Horticultural Science, University of Minnesota, St. Paul, MN, 55108, USA
| | - Clay J Carter
- Department of Plant & Microbial Biology, University of Minnesota, 1479 Gortner Avenue, St. Paul, MN, 55108, USA
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2
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Naradasu D, Miran W, Okamoto A. Electrochemical Characterization of Two Gut Microbial Strains Cooperatively Promoting Multiple Sclerosis Pathogenesis. Microorganisms 2024; 12:257. [PMID: 38399661 PMCID: PMC10892914 DOI: 10.3390/microorganisms12020257] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2023] [Revised: 01/13/2024] [Accepted: 01/16/2024] [Indexed: 02/25/2024] Open
Abstract
In this study, we explored the extracellular electron transfer (EET) capabilities of two bacterial strains, OTU0001 and OTU0002, which are demonstrated in biofilm formation in mouse gut and the induction of autoimmune diseases like multiple sclerosis. OTU0002 displayed significant electrogenic behaviour, producing microbial current on an indium tin-doped oxide electrode surface, particularly in the presence of glucose, with a current density of 60 nA/cm2. The presence of cell-surface redox substrate potentially mediating EET was revealed by the redox-based staining method and electrochemical voltammetry assay. However, medium swapping analyses and the addition of flavins, a model redox mediator, suggest that the current production is dominated by soluble endogenous redox substrates in OTU0002. Given redox substrates were detected at the cell surface, the secreted redox molecule may interact with the cellular surface of OTU0002. In contrast to OTU0002, OTU0001 did not exhibit notable electrochemical activity, lacking cell-surface redox molecules. Further, the mixture of the two strains did not increase the current production from OTU0001, suggesting that OTU0001 does not support the EET mechanism of OTU0002. The present work revealed the coexistence of EET and non-EET capable pathogens in multi-species biofilm.
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Affiliation(s)
- Divya Naradasu
- Oral Microbiology, Bristol Dental School, University of Bristol, Dorothy Hodgkin Building, Whitson Street, Bristol BS1 3NY, UK;
- International Center for Materials Nanoarchitectonics, National Institute for Materials Science, 1-1 Namiki, Tsukuba 305-0044, Ibaraki, Japan;
| | - Waheed Miran
- International Center for Materials Nanoarchitectonics, National Institute for Materials Science, 1-1 Namiki, Tsukuba 305-0044, Ibaraki, Japan;
- School of Chemical and Materials Engineering, National University of Sciences and Technology, Islamabad 44000, Pakistan
| | - Akihiro Okamoto
- International Center for Materials Nanoarchitectonics, National Institute for Materials Science, 1-1 Namiki, Tsukuba 305-0044, Ibaraki, Japan;
- Research Center for Macromolecules and Biomaterials, National Institute for Materials Science, Tsukuba 305-0044, Ibaraki, Japan
- Graduate School of Chemical Sciences and Engineering, Hokkaido University, North 13 West 8, Kita-ku, Sapporo 060-8628, Hokkaido, Japan
- Graduate School of Science and Engineering, College of Science and Engineering, University of Tsukuba, 1-1-1 Tennodai, Tsukuba 305-8573, Ibaraki, Japan
- Living Systems Materialogy (LiSM) Research Group, International Research Frontiers Initiative (IRFI), Tokyo Institute of Technology, 4259 Nagatsuta-cho, Midori-ku, Yokohama 226-8501, Kanagawa, Japan
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3
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Plavskii VY, Sobchuk AN, Mikulich AV, Dudinova ON, Plavskaya LG, Tretyakova AI, Nahorny RK, Ananich TS, Svechko AD, Yakimchuk SV, Leusenka IA. Identification by methods of steady-state and kinetic spectrofluorimetry of endogenous porphyrins and flavins sensitizing the formation of reactive oxygen species in cancer cells. Photochem Photobiol 2024. [PMID: 38258972 DOI: 10.1111/php.13911] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2023] [Revised: 12/20/2023] [Accepted: 01/09/2024] [Indexed: 01/24/2024]
Abstract
The question about acceptor molecules of optical radiation that determine the effects of photobiomodulation in relation to various types of cells still remains the focus of attention of researchers. This issue is most relevant for cancer cells, since, depending on the parameters of optical radiation, light can either stimulate their growth or inhibit them and lead to death. This study shows that endogenous porphyrins, which have sensitizing properties, may play an important role in the implementation of the effects of photobiomodulation, along with flavins. For the first time, using steady-state and kinetic spectrofluorimetry, free-base porphyrins and their zinc complexes were discovered and identified in living human cervical epithelial carcinoma (HeLa) cells, as well as in their extracts. It has been shown that reliable detection of porphyrin fluorescence in cells is hampered by the intense fluorescence of flavins due to their high concentration (micromolar range) and higher (compared to tetrapyrroles) fluorescence quantum yield. Optimization of the spectral range of excitation and the use of extractants that provide multiple quenching of the flavin component while increasing the emission efficiency of tetrapyrroles makes it possible to weaken the contribution of the flavin component to the recorded fluorescence spectra.
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Affiliation(s)
- Vitaly Yu Plavskii
- State Scientific Institution "B.I. Stepanov Institute of Physics of the National Academy of Sciences of Belarus", Minsk, Belarus
| | - Andrei N Sobchuk
- State Scientific Institution "B.I. Stepanov Institute of Physics of the National Academy of Sciences of Belarus", Minsk, Belarus
| | - Aliaksandr V Mikulich
- State Scientific Institution "B.I. Stepanov Institute of Physics of the National Academy of Sciences of Belarus", Minsk, Belarus
| | - Olga N Dudinova
- State Scientific Institution "B.I. Stepanov Institute of Physics of the National Academy of Sciences of Belarus", Minsk, Belarus
| | - Ludmila G Plavskaya
- State Scientific Institution "B.I. Stepanov Institute of Physics of the National Academy of Sciences of Belarus", Minsk, Belarus
| | - Antonina I Tretyakova
- State Scientific Institution "B.I. Stepanov Institute of Physics of the National Academy of Sciences of Belarus", Minsk, Belarus
| | - Raman K Nahorny
- State Scientific Institution "B.I. Stepanov Institute of Physics of the National Academy of Sciences of Belarus", Minsk, Belarus
| | - Tatsiana S Ananich
- State Scientific Institution "B.I. Stepanov Institute of Physics of the National Academy of Sciences of Belarus", Minsk, Belarus
| | - Alexei D Svechko
- State Scientific Institution "B.I. Stepanov Institute of Physics of the National Academy of Sciences of Belarus", Minsk, Belarus
| | - Sergey V Yakimchuk
- State Scientific Institution "B.I. Stepanov Institute of Physics of the National Academy of Sciences of Belarus", Minsk, Belarus
| | - Ihar A Leusenka
- State Scientific Institution "B.I. Stepanov Institute of Physics of the National Academy of Sciences of Belarus", Minsk, Belarus
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4
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Hu L, Wang N, Bryant JD, Liu L, Xie L, West AP, Walsh AJ. Label-free spatially maintained measurements of metabolic phenotypes in cells. Front Bioeng Biotechnol 2023; 11:1293268. [PMID: 38090715 PMCID: PMC10715269 DOI: 10.3389/fbioe.2023.1293268] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2023] [Accepted: 11/14/2023] [Indexed: 02/01/2024] Open
Abstract
Metabolic reprogramming at a cellular level contributes to many diseases including cancer, yet few assays are capable of measuring metabolic pathway usage by individual cells within living samples. Here, autofluorescence lifetime imaging is combined with single-cell segmentation and machine-learning models to predict the metabolic pathway usage of cancer cells. The metabolic activities of MCF7 breast cancer cells and HepG2 liver cancer cells were controlled by growing the cells in culture media with specific substrates and metabolic inhibitors. Fluorescence lifetime images of two endogenous metabolic coenzymes, reduced nicotinamide adenine dinucleotide (NADH) and oxidized flavin adenine dinucleotide (FAD), were acquired by a multi-photon fluorescence lifetime microscope and analyzed at the cellular level. Quantitative changes of NADH and FAD lifetime components were observed for cells using glycolysis, oxidative phosphorylation, and glutaminolysis. Conventional machine learning models trained with the autofluorescence features classified cells as dependent on glycolytic or oxidative metabolism with 90%-92% accuracy. Furthermore, adapting convolutional neural networks to predict cancer cell metabolic perturbations from the autofluorescence lifetime images provided improved performance, 95% accuracy, over traditional models trained via extracted features. Additionally, the model trained with the lifetime features of cancer cells could be transferred to autofluorescence lifetime images of T cells, with a prediction that 80% of activated T cells were glycolytic, and 97% of quiescent T cells were oxidative. In summary, autofluorescence lifetime imaging combined with machine learning models can detect metabolic perturbations between glycolysis and oxidative metabolism of living samples at a cellular level, providing a label-free technology to study cellular metabolism and metabolic heterogeneity.
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Affiliation(s)
- Linghao Hu
- Department of Biomedical Engineering, Texas A&M University, College Station, TX, United States
| | - Nianchao Wang
- Department of Biomedical Engineering, Texas A&M University, College Station, TX, United States
| | - Joshua D. Bryant
- Microbial Pathogenesis and Immunology, Health Science Center, Texas A&M University, College Station, TX, United States
| | - Lin Liu
- Department of Nutrition, Texas A&M University, College Station, TX, United States
- Department of Integrative Physiology, Baylor College of Medicine, Houston, TX, United States
| | - Linglin Xie
- Department of Nutrition, Texas A&M University, College Station, TX, United States
| | - A. Phillip West
- Microbial Pathogenesis and Immunology, Health Science Center, Texas A&M University, College Station, TX, United States
| | - Alex J. Walsh
- Department of Biomedical Engineering, Texas A&M University, College Station, TX, United States
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5
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Zhang L, Malkemper EP. Cryptochromes in mammals: a magnetoreception misconception? Front Physiol 2023; 14:1250798. [PMID: 37670767 PMCID: PMC10475740 DOI: 10.3389/fphys.2023.1250798] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2023] [Accepted: 08/01/2023] [Indexed: 09/07/2023] Open
Abstract
Cryptochromes are flavoproteins related to photolyases that are widespread throughout the plant and animal kingdom. They govern blue light-dependent growth in plants, control circadian rhythms in a light-dependent manner in invertebrates, and play a central part in the circadian clock in vertebrates. In addition, cryptochromes might function as receptors that allow animals to sense the Earth's magnetic field. As cryptochromes are also present in mammals including humans, the possibility of a magnetosensitive protein is exciting. Here we attempt to provide a concise overview of cryptochromes in mammals. We briefly review their canonical role in the circadian rhythm from the molecular level to physiology, behaviour and diseases. We then discuss their disputed light sensitivity and proposed role in the magnetic sense in mammals, providing three mechanistic hypotheses. Specifically, mammalian cryptochromes could form light-induced radical pairs in particular cellular milieus, act as magnetoreceptors in darkness, or as secondary players in a magnetoreception signalling cascade. Future research can test these hypotheses to investigate if the role of mammalian cryptochromes extends beyond the circadian clock.
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Affiliation(s)
| | - E. Pascal Malkemper
- Max Planck Research Group Neurobiology of Magnetoreception, Max Planck Institute for Neurobiology of Behavior—caesar, Bonn, Germany
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6
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Foroutannejad S, Good LL, Lin C, Carter ZI, Tadesse MG, Lucius AL, Crane BR, Maillard RA. The cofactor-dependent folding mechanism of Drosophila cryptochrome revealed by single-molecule pulling experiments. Nat Commun 2023; 14:1057. [PMID: 36828841 PMCID: PMC9958137 DOI: 10.1038/s41467-023-36701-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2022] [Accepted: 02/10/2023] [Indexed: 02/26/2023] Open
Abstract
The link between cofactor binding and protein activity is well-established. However, how cofactor interactions modulate folding of large proteins remains unknown. We use optical tweezers, clustering and global fitting to dissect the folding mechanism of Drosophila cryptochrome (dCRY), a 542-residue protein that binds FAD, one of the most chemically and structurally complex cofactors in nature. We show that the first dCRY parts to fold are independent of FAD, but later steps are FAD-driven as the remaining polypeptide folds around the cofactor. FAD binds to largely unfolded intermediates, yet with association kinetics above the diffusion-limit. Interestingly, not all FAD moieties are required for folding: whereas the isoalloxazine ring linked to ribitol and one phosphate is sufficient to drive complete folding, the adenosine ring with phosphates only leads to partial folding. Lastly, we propose a dCRY folding model where regions that undergo conformational transitions during signal transduction are the last to fold.
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Affiliation(s)
| | - Lydia L Good
- Department of Chemistry, Georgetown University, Washington, DC, USA
| | - Changfan Lin
- Department of Chemistry & Chemical Biology, Cornell University, Ithaca, NY, USA
| | - Zachariah I Carter
- Department of Chemistry, University of Alabama at Birmingham, Birmingham, AL, USA
| | - Mahlet G Tadesse
- Department of Mathematics and Statistics, Georgetown University, Washington, DC, USA
| | - Aaron L Lucius
- Department of Chemistry, University of Alabama at Birmingham, Birmingham, AL, USA
| | - Brian R Crane
- Department of Chemistry & Chemical Biology, Cornell University, Ithaca, NY, USA
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7
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Calloni G, Vabulas RM. The structural and functional roles of the flavin cofactor FAD in mammalian cryptochromes. Front Mol Biosci 2023; 9:1081661. [PMID: 36660433 PMCID: PMC9845712 DOI: 10.3389/fmolb.2022.1081661] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2022] [Accepted: 12/19/2022] [Indexed: 01/06/2023] Open
Abstract
The importance of circadian rhythms in human health and disease calls for a thorough understanding of the underlying molecular machinery, including its key components, the flavin adenine dinucleotide (FAD)-containing flavoproteins cryptochrome 1 and 2. Contrary to their Drosophila counterparts, mammalian cryptochromes are direct suppressors of circadian transcription and act independently of light. Light-independence poses the question regarding the role of the cofactor FAD in mammalian cryptochromes. The weak binding of the cofactor in vitro argues against its relevance and might be a functionless evolutionary remnant. From the other side, the FAD-binding pocket constitutes the part of mammalian cryptochromes directly related to their ubiquitylation by the ubiquitin ligase Fbxl3 and is the target for protein-stabilizing small molecules. Increased supplies of FAD stabilize cryptochromes in cell culture, and the depletion of the FAD precursor riboflavin with simultaneous knock-down of riboflavin kinase affects the expression of circadian genes in mice. This review presents the classical and more recent studies in the field, which help to comprehend the role of FAD for the stability and function of mammalian cryptochromes.
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Affiliation(s)
| | - R. Martin Vabulas
- Institute of Biochemistry, Charité-Universitätsmedizin Berlin, Berlin, Germany,*Correspondence: R. Martin Vabulas,
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8
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Liang GT, Lai C, Yue Z, Zhang H, Li D, Chen Z, Lu X, Tao L, Subach FV, Piatkevich KD. Enhanced small green fluorescent proteins as a multisensing platform for biosensor development. Front Bioeng Biotechnol 2022; 10:1039317. [PMID: 36324888 PMCID: PMC9618808 DOI: 10.3389/fbioe.2022.1039317] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2022] [Accepted: 09/30/2022] [Indexed: 12/02/2022] Open
Abstract
Engineered light, oxygen, and voltage (LOV)-based proteins are able to fluoresce without oxygen requirement due to the autocatalytic incorporation of exogenous flavin as a chromophore thus allowing for live cell imaging under hypoxic and anaerobic conditions. They were also discovered to have high sensitivity to transition metal ions and physiological flavin derivatives. These properties make flavin-binding fluorescent proteins (FPs) a perspective platform for biosensor development. However, brightness of currently available flavin-binding FPs is limited compared to GFP-like FPs creating a need for their further enhancement and optimization. In this study, we applied a directed molecular evolution approach to develop a pair of flavin-binding FPs, named miniGFP1 and miniGFP2. The miniGFP proteins are characterized by cyan-green fluorescence with excitation/emission maxima at 450/499 nm and a molecular size of ∼13 kDa. We carried out systematic benchmarking of miniGFPs in Escherichia coli and cultured mammalian cells against spectrally similar FPs including GFP-like FP, bilirubin-binding FP, and bright flavin-binding FPs. The miniGFPs proteins exhibited improved photochemical properties compared to other flavin-binding FPs enabling long-term live cell imaging. We demonstrated the utility of miniGFPs for live cell imaging in bacterial culture under anaerobic conditions and in CHO cells under hypoxia. The miniGFPs’ fluorescence was highly sensitive to Cu(II) ions in solution with Kd values of 67 and 68 nM for miniGFP1 and miniGFP2, respectively. We also observed fluorescence quenching of miniGFPs by the reduced form of Cu(I) suggesting its potential application as an optical indicator for Cu(I) and Cu(II). In addition, miniGFPs showed the ability to selectively bind exogenous flavin mononucleotide demonstrating a potential for utilization as a selective fluorescent flavin indicator. Altogether, miniGFPs can serve as a multisensing platform for fluorescence biosensor development for in vitro and in-cell applications.
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Affiliation(s)
- Guo-Teng Liang
- School of Life Sciences, Westlake University, Hangzhou, Zhejiang, China
- Westlake Laboratory of Life Sciences and Biomedicine, Hangzhou, Zhejiang, China
- Institute of Basic Medical Sciences, Westlake Institute for Advanced Study, Hangzhou, Zhejiang, China
- Department of Applied Biology and Chemical Technology, The Hong Kong Polytechnic University, Kowloon, Hong Kong SAR, China
| | - Cuixin Lai
- School of Life Sciences, Westlake University, Hangzhou, Zhejiang, China
- Westlake Laboratory of Life Sciences and Biomedicine, Hangzhou, Zhejiang, China
- Institute of Basic Medical Sciences, Westlake Institute for Advanced Study, Hangzhou, Zhejiang, China
| | - Zejun Yue
- School of Life Sciences, Westlake University, Hangzhou, Zhejiang, China
- Westlake Laboratory of Life Sciences and Biomedicine, Hangzhou, Zhejiang, China
- Institute of Basic Medical Sciences, Westlake Institute for Advanced Study, Hangzhou, Zhejiang, China
- School of Basic Medical Sciences, Xi’an Jiao Tong University, Xi’an, Shaanxi, China
| | - Hanbin Zhang
- School of Life Sciences, Westlake University, Hangzhou, Zhejiang, China
- Westlake Laboratory of Life Sciences and Biomedicine, Hangzhou, Zhejiang, China
- Institute of Basic Medical Sciences, Westlake Institute for Advanced Study, Hangzhou, Zhejiang, China
| | - Danyang Li
- School of Life Sciences, Westlake University, Hangzhou, Zhejiang, China
- Westlake Laboratory of Life Sciences and Biomedicine, Hangzhou, Zhejiang, China
- Institute of Basic Medical Sciences, Westlake Institute for Advanced Study, Hangzhou, Zhejiang, China
| | - Zhong Chen
- Key Laboratory of Precise Synthesis of Functional Molecules of Zhejiang Province, School of Science, Instrumentation and Service Center for Molecular Sciences, Westlake University, Hangzhou, Zhejiang, China
| | - Xingyu Lu
- Key Laboratory of Precise Synthesis of Functional Molecules of Zhejiang Province, School of Science, Instrumentation and Service Center for Molecular Sciences, Westlake University, Hangzhou, Zhejiang, China
| | - Liang Tao
- School of Life Sciences, Westlake University, Hangzhou, Zhejiang, China
- Westlake Laboratory of Life Sciences and Biomedicine, Hangzhou, Zhejiang, China
- Institute of Basic Medical Sciences, Westlake Institute for Advanced Study, Hangzhou, Zhejiang, China
| | - Fedor V. Subach
- Complex of NBICS Technologies, National Research Center “Kurchatov Institute”, Moscow, Russia
| | - Kiryl D. Piatkevich
- School of Life Sciences, Westlake University, Hangzhou, Zhejiang, China
- Westlake Laboratory of Life Sciences and Biomedicine, Hangzhou, Zhejiang, China
- Institute of Basic Medical Sciences, Westlake Institute for Advanced Study, Hangzhou, Zhejiang, China
- *Correspondence: Kiryl D. Piatkevich,
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9
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Sharma S, Yang J, Doamekpor SK, Grudizen-Nogalska E, Tong L, Kiledjian M. Identification of a novel deFADding activity in human, yeast and bacterial 5' to 3' exoribonucleases. Nucleic Acids Res 2022; 50:8807-8817. [PMID: 35904778 PMCID: PMC9410882 DOI: 10.1093/nar/gkac617] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2022] [Revised: 06/18/2022] [Accepted: 07/21/2022] [Indexed: 11/19/2022] Open
Abstract
Identification of metabolite caps including FAD on the 5' end of RNA has uncovered a previously unforeseen intersection between cellular metabolism and gene expression. To understand the function of FAD caps in cellular physiology, we characterised the proteins interacting with FAD caps in budding yeast. Here we demonstrate that highly conserved 5'-3' exoribonucleases, Xrn1 and Rat1, physically interact with the RNA 5' FAD cap and both possess FAD cap decapping (deFADding) activity and subsequently degrade the resulting RNA. Xrn1 deFADding activity was also evident in human cells indicating its evolutionary conservation. Furthermore, we report that the recently identified bacterial 5'-3' exoribonuclease RNase AM also possesses deFADding activity that can degrade FAD-capped RNAs in vitro and in Escherichia coli cells. To gain a molecular understanding of the deFADding reaction, an RNase AM crystal structure with three manganese ions coordinated by a sulfate molecule and the active site amino acids was generated that provided details underlying hydrolysis of the FAD cap. Our findings reveal a general propensity for 5'-3' exoribonucleases to hydrolyse and degrade RNAs with 5' end noncanonical caps in addition to their well characterized 5' monophosphate RNA substrates indicating an intrinsic property of 5'-3' exoribonucleases.
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Affiliation(s)
- Sunny Sharma
- Department of Cell Biology and Neurosciences, Rutgers, University, Piscataway, NJ 08854, USA
| | - Jun Yang
- Department of Cell Biology and Neurosciences, Rutgers, University, Piscataway, NJ 08854, USA
| | - Selom K Doamekpor
- Department Biological Sciences, Columbia University, New York, NY 10027, USA
| | - Ewa Grudizen-Nogalska
- Department of Cell Biology and Neurosciences, Rutgers, University, Piscataway, NJ 08854, USA
| | - Liang Tong
- Department Biological Sciences, Columbia University, New York, NY 10027, USA
| | - Megerditch Kiledjian
- Department of Cell Biology and Neurosciences, Rutgers, University, Piscataway, NJ 08854, USA
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10
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Abstract
Optogenetic actuators enable highly precise spatiotemporal interrogation of biological processes at levels ranging from the subcellular to cells, circuits and behaving organisms. Although their application in neuroscience has traditionally focused on the control of spiking activity at the somatodendritic level, the scope of optogenetic modulators for direct manipulation of presynaptic functions is growing. Presynaptically localized opsins combined with light stimulation at the terminals allow light-mediated neurotransmitter release, presynaptic inhibition, induction of synaptic plasticity and specific manipulation of individual components of the presynaptic machinery. Here, we describe presynaptic applications of optogenetic tools in the context of the unique cell biology of axonal terminals, discuss their potential shortcomings and outline future directions for this rapidly developing research area.
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11
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Baumschlager A. Engineering Light-Control in Biology. Front Bioeng Biotechnol 2022; 10:901300. [PMID: 35573251 PMCID: PMC9096073 DOI: 10.3389/fbioe.2022.901300] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2022] [Accepted: 04/14/2022] [Indexed: 11/13/2022] Open
Abstract
Unraveling the transformative power of optogenetics in biology requires sophisticated engineering for the creation and optimization of light-regulatable proteins. In addition, diverse strategies have been used for the tuning of these light-sensitive regulators. This review highlights different protein engineering and synthetic biology approaches, which might aid in the development and optimization of novel optogenetic proteins (Opto-proteins). Focusing on non-neuronal optogenetics, chromophore availability, general strategies for creating light-controllable functions, modification of the photosensitive domains and their fusion to effector domains, as well as tuning concepts for Opto-proteins are discussed. Thus, this review shall not serve as an encyclopedic summary of light-sensitive regulators but aims at discussing important aspects for the engineering of light-controllable proteins through selected examples.
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Affiliation(s)
- Armin Baumschlager
- Department of Biosystems Science and Engineering (D-BSSE), ETH Zürich, Basel, Switzerland
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12
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Mukunda DC, Rodrigues J, Joshi VK, Raghushaker CR, Mahato KK. A comprehensive review on LED-induced fluorescence in diagnostic pathology. Biosens Bioelectron 2022; 209:114230. [PMID: 35421670 DOI: 10.1016/j.bios.2022.114230] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2021] [Revised: 03/19/2022] [Accepted: 03/25/2022] [Indexed: 11/02/2022]
Abstract
Sensitivity, specificity, mobility, and affordability are important criteria to consider for developing diagnostic instruments in common use. Fluorescence spectroscopy has been demonstrating substantial potential in the clinical diagnosis of diseases and evaluating the underlying causes of pathogenesis. A higher degree of device integration with appropriate sensitivity and reasonable cost would further boost the value of the fluorescence techniques in clinical diagnosis and aid in the reduction of healthcare expenses, which is a key economic concern in emerging markets. Light-emitting diodes (LEDs), which are inexpensive and smaller are attractive alternatives to conventional excitation sources in fluorescence spectroscopy, are gaining a lot of momentum in the development of affordable, compact analytical instruments of clinical relevance. The commercial availability of a broad range of LED wavelengths (255-4600 nm) has opened up new avenues for targeting a wide range of clinically significant molecules (both endogenous and exogenous), thereby diagnosing a range of clinical illnesses. As a result, we have specifically examined the uses of LED-induced fluorescence (LED-IF) in preclinical and clinical evaluations of pathological conditions, considering the present advancements in the field.
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Affiliation(s)
| | - Jackson Rodrigues
- Department of Biophysics, Manipal School of Life Sciences, Manipal Academy of Higher Education, Manipal, Karnataka-576104, India
| | - Vijay Kumar Joshi
- Department of Biophysics, Manipal School of Life Sciences, Manipal Academy of Higher Education, Manipal, Karnataka-576104, India
| | - Chandavalli Ramappa Raghushaker
- Department of Biophysics, Manipal School of Life Sciences, Manipal Academy of Higher Education, Manipal, Karnataka-576104, India
| | - Krishna Kishore Mahato
- Department of Biophysics, Manipal School of Life Sciences, Manipal Academy of Higher Education, Manipal, Karnataka-576104, India.
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13
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Waldeck-Weiermair M, Yadav S, Spyropoulos F, Krüger C, Pandey AK, Michel T. Dissecting in vivo and in vitro redox responses using chemogenetics. Free Radic Biol Med 2021; 177:360-369. [PMID: 34752919 PMCID: PMC8639655 DOI: 10.1016/j.freeradbiomed.2021.11.006] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/13/2021] [Revised: 10/08/2021] [Accepted: 11/04/2021] [Indexed: 02/03/2023]
Abstract
Hydrogen peroxide (H2O2) is the most abundant reactive oxygen species (ROS) within mammalian cells. At low concentrations, H2O2 serves as a versatile cell signaling molecule that mediates vital physiological functions. Yet at higher concentrations, H2O2 can be a toxic molecule by promoting pathological oxidative stress in cells and tissues. Within normal cells, H2O2 is differentially distributed in a variety of subcellular locales. Moreover, many redox-active enzymes and their substrates are themselves differentially distributed within cells. Numerous reports have described the biological and biochemical consequences of adding exogenous H2O2 to cultured cells and tissues, but many of these observations are difficult to interpret: the effects of exogenous H2O2 do not necessarily replicate the cellular responses to endogenous H2O2. In recent years, chemogenetic approaches have been developed to dynamically regulate the abundance of H2O2 in specific subcellular locales. Chemogenetic approaches have been applied in multiple experimental systems, ranging from in vitro studies on the intracellular transport and metabolism of H2O2, all the way to in vivo studies that generate oxidative stress in specific organs in living animals. These chemogenetic approaches have exploited a yeast-derived d-amino acid oxidase (DAAO) that synthesizes H2O2 only in the presence of its d-amino acid substrate. DAAO can be targeted to various subcellular locales, and can be dynamically activated by the addition or withdrawal of its d-amino acid substrate. In addition, recent advances in the development of highly sensitive genetically encoded H2O2 biosensors are providing a better understanding of both physiological and pathological oxidative pathways. This review highlights several applications of DAAO as a chemogenetic tool across a wide range of biological systems, from analyses of subcellular H2O2 metabolism in cells to the development of new disease models caused by oxidative stress in vivo.
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Affiliation(s)
- Markus Waldeck-Weiermair
- Division of Cardiovascular Medicine, Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, 75 Francis Street, Boston, MA, 02115, USA; Molecular Biology and Biochemistry, Gottfried Schatz Research Center, Medical University of Graz, Neue Stiftingtalstraße 6/6, 8010, Graz, Austria
| | - Shambhu Yadav
- Division of Cardiovascular Medicine, Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, 75 Francis Street, Boston, MA, 02115, USA
| | - Fotios Spyropoulos
- Division of Cardiovascular Medicine, Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, 75 Francis Street, Boston, MA, 02115, USA; Department of Pediatric Newborn Medicine, Harvard Medical School, Brigham and Women's Hospital, 75 Francis Street, Boston, MA, USA
| | - Christina Krüger
- Division of Cardiovascular Medicine, Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, 75 Francis Street, Boston, MA, 02115, USA
| | - Arvind K Pandey
- Division of Cardiovascular Medicine, Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, 75 Francis Street, Boston, MA, 02115, USA
| | - Thomas Michel
- Division of Cardiovascular Medicine, Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, 75 Francis Street, Boston, MA, 02115, USA.
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14
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Recent analytical methodologies and analytical trends for riboflavin (vitamin B2) analysis in food, biological and pharmaceutical samples. Trends Analyt Chem 2021. [DOI: 10.1016/j.trac.2021.116412] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
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15
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Kalinina S, Freymueller C, Naskar N, von Einem B, Reess K, Sroka R, Rueck A. Bioenergetic Alterations of Metabolic Redox Coenzymes as NADH, FAD and FMN by Means of Fluorescence Lifetime Imaging Techniques. Int J Mol Sci 2021; 22:5952. [PMID: 34073057 PMCID: PMC8199032 DOI: 10.3390/ijms22115952] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2021] [Revised: 05/26/2021] [Accepted: 05/28/2021] [Indexed: 12/15/2022] Open
Abstract
Metabolic FLIM (fluorescence lifetime imaging) is used to image bioenergetic status in cells and tissue. Whereas an attribution of the fluorescence lifetime of coenzymes as an indicator for cell metabolism is mainly accepted, it is debated whether this is valid for the redox state of cells. In this regard, an innovative algorithm using the lifetime characteristics of nicotinamide adenine dinucleotide (phosphate) (NAD(P)H) and flavin adenine dinucleotide (FAD) to calculate the fluorescence lifetime induced redox ratio (FLIRR) has been reported so far. We extended the FLIRR approach and present new results, which includes FLIM data of the various enzymes, such as NAD(P)H, FAD, as well as flavin mononucleotide (FMN). Our algorithm uses a two-exponential fitting procedure for the NAD(P)H autofluorescence and a three-exponential fit of the flavin signal. By extending the FLIRR approach, we introduced FLIRR1 as protein-bound NAD(P)H related to protein-bound FAD, FLIRR2 as protein-bound NAD(P)H related to free (unbound) FAD and FLIRR3 as protein-bound NAD(P)H related to protein-bound FMN. We compared the significance of extended FLIRR to the metabolic index, defined as the ratio of protein-bound NAD(P)H to free NAD(P)H. The statistically significant difference for tumor and normal cells was found to be highest for FLIRR1.
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Affiliation(s)
- Sviatlana Kalinina
- Core Facility Confocal and Multiphoton Microscopy, Ulm University, Albert-Einstein-Allee 11, 89081 Ulm, Germany; (N.N.); (K.R.)
| | - Christian Freymueller
- Laser-Forschungslabor, LIFE Center, University Hospital, LMU Munich, Fraunhoferstrasse 20, 82152 Planegg, Germany; (C.F.); (R.S.)
- Department of Urology, University Hospital, LMU Munich, Marchioninistraße 15, 81377 Munich, Germany
| | - Nilanjon Naskar
- Core Facility Confocal and Multiphoton Microscopy, Ulm University, Albert-Einstein-Allee 11, 89081 Ulm, Germany; (N.N.); (K.R.)
| | - Bjoern von Einem
- Zentrum Biomedizinische Forschung (ZBMF), Department of Neurology, Ulm University, Helmholtzstrasse, 8/1, 89081 Ulm, Germany;
| | - Kirsten Reess
- Core Facility Confocal and Multiphoton Microscopy, Ulm University, Albert-Einstein-Allee 11, 89081 Ulm, Germany; (N.N.); (K.R.)
| | - Ronald Sroka
- Laser-Forschungslabor, LIFE Center, University Hospital, LMU Munich, Fraunhoferstrasse 20, 82152 Planegg, Germany; (C.F.); (R.S.)
- Department of Urology, University Hospital, LMU Munich, Marchioninistraße 15, 81377 Munich, Germany
| | - Angelika Rueck
- Core Facility Confocal and Multiphoton Microscopy, Ulm University, Albert-Einstein-Allee 11, 89081 Ulm, Germany; (N.N.); (K.R.)
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16
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Schmitz R, Tweed K, Walsh C, Walsh AJ, Skala MC. Extracellular pH affects the fluorescence lifetimes of metabolic co-factors. JOURNAL OF BIOMEDICAL OPTICS 2021; 26:JBO-210047LR. [PMID: 34032035 PMCID: PMC8144436 DOI: 10.1117/1.jbo.26.5.056502] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 02/10/2021] [Accepted: 05/11/2021] [Indexed: 06/12/2023]
Abstract
SIGNIFICANCE Autofluorescence measurements of the metabolic cofactors NADH and flavin adenine dinucleotide (FAD) provide a label-free method to quantify cellular metabolism. However, the effect of extracellular pH on flavin lifetimes is currently unknown. AIM To quantify the relationship between extracellular pH and the fluorescence lifetimes of FAD, flavin mononucleotide (FMN), and reduced nicotinamide adenine dinucleotide (phosphate) [NAD(P)H]. APPROACH Human breast cancer (BT474) and HeLa cells were placed in pH-adjusted media. Images of an intracellular pH indicator or endogenous fluorescence were acquired using two-photon fluorescence lifetime imaging. Fluorescence lifetimes of FAD and FMN in solutions were quantified over the same pH range. RESULTS The relationship between intracellular and extracellular pH was linear in both cell lines. Between extracellular pH 4 to 9, FAD mean lifetimes increased with increasing pH. NAD(P)H mean lifetimes decreased with increasing pH between extracellular pH 5 to 9. The relationship between NAD(P)H lifetime and extracellular pH differed between the two cell lines. Fluorescence lifetimes of FAD, FAD-cholesterol oxidase, and FMN solutions decreased, showed no trend, and showed no trend, respectively, with increasing pH. CONCLUSIONS Changes in endogenous fluorescence lifetimes with extracellular pH are mostly due to indirect changes within the cell rather than direct pH quenching of the endogenous molecules.
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Affiliation(s)
- Rebecca Schmitz
- Morgridge Institute for Research, Madison, Wisconsin, United States
- University of Wisconsin-Madison, Department of Biomedical Engineering, Madison, Wisconsin, United States
| | - Kelsey Tweed
- Morgridge Institute for Research, Madison, Wisconsin, United States
- University of Wisconsin-Madison, Department of Biomedical Engineering, Madison, Wisconsin, United States
| | - Christine Walsh
- Morgridge Institute for Research, Madison, Wisconsin, United States
| | - Alex J. Walsh
- Morgridge Institute for Research, Madison, Wisconsin, United States
- Texas A&M University, Department of Biomedical Engineering, College Station, Texas, United States
| | - Melissa C. Skala
- Morgridge Institute for Research, Madison, Wisconsin, United States
- University of Wisconsin-Madison, Department of Biomedical Engineering, Madison, Wisconsin, United States
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17
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Hu L, Wang N, Cardona E, Walsh AJ. Fluorescence intensity and lifetime redox ratios detect metabolic perturbations in T cells. BIOMEDICAL OPTICS EXPRESS 2020; 11:5674-5688. [PMID: 33149978 PMCID: PMC7587263 DOI: 10.1364/boe.401935] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/07/2020] [Revised: 08/21/2020] [Accepted: 09/08/2020] [Indexed: 05/17/2023]
Abstract
The auto-fluorescent coenzymes reduced nicotinamide dinucleotide (NADH) and oxidized flavin adenine dinucleotide (FAD) allow label-free detection of cellular metabolism. The optical redox ratio, which is traditionally computed as the ratio of NADH and FAD intensities, allows quantification of cell redox state. In addition to multiple formulations of the optical redox ratio from NADH and FAD intensity measurements, a fluorescence lifetime redox ratio (FLIRR) based on the fractions of protein-bound NADH and FAD was developed to overcome the limitations of experimental factors that influence fluorescence intensity measurements. In this paper, we compare fluorescence-intensity computations of the optical redox ratio with the fluorescence lifetime redox ratio for quiescent and activated T cells. Fluorescence lifetime images of NAD(P)H and FAD of T cells were acquired with a two-photon fluorescence lifetime microscope. Metabolic perturbation experiments, including inhibition of glycolysis, oxidative phosphorylation, glutaminolysis, and fatty acid synthesis revealed differences between the intensity and lifetime redox ratios. Statistical analysis reveals that the FLIRR has a lower standard deviation and skewness (two-tail T-test, P value = 0.05) than the intensity redox ratio. Correlation analysis revealed a weak relationship between FLIRR and intensity redox ratio for individual cells, with a stronger correlation identified for activated T cells (Linear regression, R-value = 0.450) than quiescent T cells (R-value = 0.172). Altogether, the results demonstrate that while both the fluorescence lifetime and intensity redox ratios resolve metabolic perturbations in T cells, the endpoints are influenced by different metabolic processes.
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18
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Ozbakir HF, Anderson NT, Fan KC, Mukherjee A. Beyond the Green Fluorescent Protein: Biomolecular Reporters for Anaerobic and Deep-Tissue Imaging. Bioconjug Chem 2020; 31:293-302. [PMID: 31794658 PMCID: PMC7033020 DOI: 10.1021/acs.bioconjchem.9b00688] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
Fluorescence imaging represents cornerstone technology for studying biological function at the cellular and molecular levels. The technology's centerpiece is a prolific collection of genetic reporters based on the green fluorescent protein (GFP) and related analogs. More than two decades of protein engineering have endowed the GFP repertoire with an incredible assortment of fluorescent proteins, allowing scientists immense latitude in choosing reporters tailored to various cellular and environmental contexts. Nevertheless, GFP and derivative reporters have specific limitations that hinder their unrestricted use for molecular imaging. These challenges have inspired the development of new reporter proteins and imaging mechanisms. Here, we review how these developments are expanding the frontiers of reporter gene techniques to enable nondestructive studies of cell function in anaerobic environments and deep inside intact animals-two important biological contexts that are fundamentally incompatible with the use of GFP-based reporters.
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Affiliation(s)
- Harun F. Ozbakir
- Department of Chemical Engineering, University of California, Santa Barbara, California 93106, United States
| | - Nolan T. Anderson
- Department of Chemical Engineering, University of California, Santa Barbara, California 93106, United States
| | - Kang-Ching Fan
- Department of Chemical Engineering, University of California, Santa Barbara, California 93106, United States
| | - Arnab Mukherjee
- Department of Chemical Engineering, University of California, Santa Barbara, California 93106, United States
- Department of Chemistry, University of California, Santa Barbara, California 93106, United States
- Neuroscience Research Institute, University of California, Santa Barbara, California 93106, United States
- Center for Bioengineering, University of California, Santa Barbara, California 93106, United States
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19
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Huo F, Wan T, Wang Y, Liu Y, Karmaker PG, Yang X. Enhanced light-emitting diode induced fluorescence detection system with capillary electrophoresis. J Chromatogr A 2020; 1619:460935. [PMID: 32067761 DOI: 10.1016/j.chroma.2020.460935] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2019] [Revised: 12/11/2019] [Accepted: 01/29/2020] [Indexed: 11/26/2022]
Abstract
An enhanced fluorescence detection system of capillary electrophoresis (CE) was equipped with a concave silver mirror, by which the detection sensitivity of light-emitting diode induced fluorescence (LEDIF) can be increased greatly. The silver concave mirror and the cathode window in photomultiplier tube (PMT) were accurately set face to face at the same axis. When the two labeled tumor markers exactly moved to the center of detection window, the emission from analytes are excitated by LED source. Currently, the analytes may be regarded as a luminescent source point. When the source point exactly moves to the focus of the concave mirror, the emission of the labeled sample was collected effectively, enhanced by convergence and reflected by the concave mirror. Then it was sensitively detected by the PMT. The optical mechanism of enhancing detection sensitivity was explored. A simple comparative test on sensitivity was carried out, which aimed to compare sensitivity of the new detection system with concave mirror to that without concave mirror but the other conditions were kept the same. Two tumor markers labeled with FITC were selected for the test, using the simple LEDIF detect system. The results (LOD, 150 nM for L-Leu and L-Val) showed that the detection sensitivity matched with concave mirror reached more 16 times than the detection method without concave mirror.
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Affiliation(s)
- Feng Huo
- School of Chemistry and Chemical Engineering, Analytical Testing Center, Institute of Micro&Nano Intelligent Sensing, Neijiang Normal University, Neijiang, 641100, PR China; Chemical Synthesis and Pollution Control Key Laboratory of Sichuan Province, China West Normal University, Nanchong, 637000, PR China
| | - Ting Wan
- School of Chemistry and Chemical Engineering, Analytical Testing Center, Institute of Micro&Nano Intelligent Sensing, Neijiang Normal University, Neijiang, 641100, PR China; Chemical Synthesis and Pollution Control Key Laboratory of Sichuan Province, China West Normal University, Nanchong, 637000, PR China
| | - Yaohui Wang
- School of Chemistry and Chemical Engineering, Analytical Testing Center, Institute of Micro&Nano Intelligent Sensing, Neijiang Normal University, Neijiang, 641100, PR China
| | - Yuhang Liu
- School of Chemistry and Chemical Engineering, Analytical Testing Center, Institute of Micro&Nano Intelligent Sensing, Neijiang Normal University, Neijiang, 641100, PR China; Chemical Synthesis and Pollution Control Key Laboratory of Sichuan Province, China West Normal University, Nanchong, 637000, PR China
| | - Pran Gopal Karmaker
- School of Chemistry and Chemical Engineering, Analytical Testing Center, Institute of Micro&Nano Intelligent Sensing, Neijiang Normal University, Neijiang, 641100, PR China
| | - Xiupei Yang
- Chemical Synthesis and Pollution Control Key Laboratory of Sichuan Province, China West Normal University, Nanchong, 637000, PR China.
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20
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Zhang L, Li S, Sun Y, Xiao K, Song G, Lu P, Yin S, Huang K, Yao Z. Self-assembly of flavin mononucleotide and a cationic polythiophene in aqueous media: spectroscopic studies and sensing applications. Polym Chem 2020. [DOI: 10.1039/d0py00403k] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023]
Abstract
Self-assembly of flavin mononucleotide and a cationic polythiophene in 100% aqueous media with colorimetric and fluorescence dual responses.
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Affiliation(s)
- Li Zhang
- College of Food Science and Nutritional Engineering
- China Agricultural University and Key Laboratory of Safety Assessment of Genetically Modified Organism (Food Safety)
- Ministry of Agriculture
- Beijing 100083
- China
| | - Shuanghong Li
- College of Food Science and Nutritional Engineering
- China Agricultural University and Key Laboratory of Safety Assessment of Genetically Modified Organism (Food Safety)
- Ministry of Agriculture
- Beijing 100083
- China
| | - Yanan Sun
- College of Food Science and Nutritional Engineering
- China Agricultural University and Key Laboratory of Safety Assessment of Genetically Modified Organism (Food Safety)
- Ministry of Agriculture
- Beijing 100083
- China
| | - Keren Xiao
- College of Food Science and Nutritional Engineering
- China Agricultural University and Key Laboratory of Safety Assessment of Genetically Modified Organism (Food Safety)
- Ministry of Agriculture
- Beijing 100083
- China
| | - Gang Song
- Guangdong Provincial Key Laboratory of Radionuclides Pollution Control and Resources
- Guangzhou University
- Guangzhou 510006
- P. R. China
| | - Pingan Lu
- College of Health and Environment
- Beijing Union University
- China
| | - Shutao Yin
- College of Food Science and Nutritional Engineering
- China Agricultural University and Key Laboratory of Safety Assessment of Genetically Modified Organism (Food Safety)
- Ministry of Agriculture
- Beijing 100083
- China
| | - Kunlun Huang
- College of Food Science and Nutritional Engineering
- China Agricultural University and Key Laboratory of Safety Assessment of Genetically Modified Organism (Food Safety)
- Ministry of Agriculture
- Beijing 100083
- China
| | - Zhiyi Yao
- College of Food Science and Nutritional Engineering
- China Agricultural University and Key Laboratory of Safety Assessment of Genetically Modified Organism (Food Safety)
- Ministry of Agriculture
- Beijing 100083
- China
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21
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Application of Capillary Electrophoresis with Laser-Induced Fluorescence to Immunoassays and Enzyme Assays. Molecules 2019; 24:molecules24101977. [PMID: 31121978 PMCID: PMC6571882 DOI: 10.3390/molecules24101977] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2019] [Revised: 05/20/2019] [Accepted: 05/21/2019] [Indexed: 02/07/2023] Open
Abstract
Capillary electrophoresis using laser-induced fluorescence detection (CE-LIF) is one of the most sensitive separation tools among electrical separation methods. The use of CE-LIF in immunoassays and enzyme assays has gained a reputation in recent years for its high detection sensitivity, short analysis time, and accurate quantification. Immunoassays are bioassay platforms that rely on binding reactions between an antigen (analyte) and a specific antibody. Enzyme assays measure enzymatic activity through quantitative analysis of substrates and products by the reaction of enzymes in purified enzyme or cell systems. These two category analyses play an important role in the context of biopharmaceutical analysis, clinical therapy, drug discovery, and diagnosis analysis. This review discusses the expanding portfolio of immune and enzyme assays using CE-LIF and focuses on the advantages and disadvantages of these methods over the ten years of existing technology since 2008.
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22
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Serer MI, Carrica MDC, Trappe J, López Romero S, Bonomi HR, Klinke S, Cerutti ML, Goldbaum FA. A high-throughput screening for inhibitors of riboflavin synthase identifies novel antimicrobial compounds to treat brucellosis. FEBS J 2019; 286:2522-2535. [PMID: 30927485 DOI: 10.1111/febs.14829] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2019] [Revised: 02/26/2019] [Accepted: 03/29/2019] [Indexed: 10/27/2022]
Abstract
Brucella spp. are pathogenic intracellular Gram-negative bacteria adapted to life within cells of several mammals, including humans. These bacteria are the causative agent of brucellosis, one of the zoonotic infections with the highest incidence in the world and for which a human vaccine is still unavailable. Current therapeutic treatments against brucellosis are based on the combination of two or more antibiotics for prolonged periods, which may lead to antibiotic resistance in the population. Riboflavin (vitamin B2) is biosynthesized by microorganisms and plants but mammals, including humans, must obtain it from dietary sources. Owing to the absence of the riboflavin biosynthetic enzymes in animals, this pathway is nowadays regarded as a rich resource of targets for the development of new antimicrobial agents. In this work, we describe a high-throughput screening approach to identify inhibitors of the enzymatic activity of riboflavin synthase, the last enzyme in this pathway. We also provide evidence for their subsequent validation as potential drug candidates in an in vitro brucellosis infection model. From an initial set of 44 000 highly diverse low molecular weight compounds with drug-like properties, we were able to identify ten molecules with 50% inhibitory concentrations in the low micromolar range. Further Brucella culture and intramacrophagic replication experiments showed that the most effective bactericidal compounds share a 2-Phenylamidazo[2,1-b][1,3]benzothiazole chemical scaffold. Altogether, these findings set up the basis for the subsequent lead optimization process and represent a promising advancement in the pursuit of novel and effective antimicrobial compounds against brucellosis.
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Affiliation(s)
- María Inés Serer
- Fundación Instituto Leloir, IIBBA-CONICET, Buenos Aires, Argentina
| | | | - Jörg Trappe
- Novartis Institutes for BioMedical Research, Basel, Switzerland
| | | | | | - Sebastián Klinke
- Fundación Instituto Leloir, IIBBA-CONICET, Buenos Aires, Argentina.,Plataforma Argentina de Biología Estructural y Metabolómica PLABEM, Buenos Aires, Argentina
| | - María Laura Cerutti
- Fundación Instituto Leloir, IIBBA-CONICET, Buenos Aires, Argentina.,Plataforma Argentina de Biología Estructural y Metabolómica PLABEM, Buenos Aires, Argentina
| | - Fernando Alberto Goldbaum
- Fundación Instituto Leloir, IIBBA-CONICET, Buenos Aires, Argentina.,Plataforma Argentina de Biología Estructural y Metabolómica PLABEM, Buenos Aires, Argentina
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23
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Graf A, Claßen J, Solle D, Hitzmann B, Rebner K, Hoehse M. A novel LED-based 2D-fluorescence spectroscopy system for in-line monitoring of Chinese hamster ovary cell cultivations - Part I. Eng Life Sci 2019; 19:352-362. [PMID: 32625014 DOI: 10.1002/elsc.201800149] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2018] [Revised: 03/01/2019] [Accepted: 03/13/2019] [Indexed: 11/07/2022] Open
Abstract
A new two-dimensional fluorescence sensor system was developed for in-line monitoring of mammalian cell cultures. Fluorescence spectroscopy allows for the detection and quantification of naturally occurring intra- and extracellular fluorophores in the cell broth. The fluorescence signals correlate to the cells' current redox state and other relevant process parameters. Cell culture pretests with twelve different excitation wavelengths showed that only three wavelengths account for a vast majority of spectral variation. Accordingly, the newly developed device utilizes three high-power LEDs as excitation sources in combination with a back-thinned CCD-spectrometer for fluorescence detection. This setup was first tested in a lab design of experiments study with process relevant fluorophores proving its suitability for cell culture monitoring with LOD in the μg/L range. The sensor was then integrated into a CHO-K1 cell culture process. The acquired fluorescence spectra of several batches were evaluated using multivariate methods. The resulting batch evolution models were challenged in deviating and "golden batch" validation runs. These first tests showed that the new sensor can trace the cells' metabolic state in a fast and reliable manner. Cellular distress is quickly detected as a deviation from the "golden batch".
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Affiliation(s)
- Alexander Graf
- R&D Spectroscopy & Chemometrics Sartorius Stedim Biotech GmbH Göttingen Germany
- Process Analysis and Technology (PA&T) Faculty Applied Chemistry Reutlingen University Reutlingen Germany
| | - Jens Claßen
- Institute of Technical Chemistry Gottfried Wilhelm Leibnitz University of Hanover Hanover Germany
| | - Dörte Solle
- Institute of Technical Chemistry Gottfried Wilhelm Leibnitz University of Hanover Hanover Germany
| | - Bernd Hitzmann
- Process Analytics and Cereal Science Institute of Food Science and Biotechnology University Hohenheim Stuttgart Germany
| | - Karsten Rebner
- Process Analysis and Technology (PA&T) Faculty Applied Chemistry Reutlingen University Reutlingen Germany
| | - Marek Hoehse
- R&D Spectroscopy & Chemometrics Sartorius Stedim Biotech GmbH Göttingen Germany
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24
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Identification of Flavin Mononucleotide as a Cell‐Active Artificial
N
6
‐Methyladenosine RNA Demethylase. Angew Chem Int Ed Engl 2019. [DOI: 10.1002/ange.201900901] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
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25
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Xie LJ, Yang XT, Wang RL, Cheng HP, Li ZY, Liu L, Mao L, Wang M, Cheng L. Identification of Flavin Mononucleotide as a Cell-Active Artificial N 6 -Methyladenosine RNA Demethylase. Angew Chem Int Ed Engl 2019; 58:5028-5032. [PMID: 30756480 DOI: 10.1002/anie.201900901] [Citation(s) in RCA: 23] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2019] [Indexed: 01/05/2023]
Abstract
N6 -Methyladenosine (m6 A) represents a common and highly dynamic modification in eukaryotic RNA that affects various cellular pathways. Natural dioxygenases such as FTO and ALKBH5 are enzymes that demethylate m6 A residues in mRNA. Herein, the first identification of a small-molecule modulator that functions as an artificial m6 A demethylase is reported. Flavin mononucleotide (FMN), the metabolite produced by riboflavin kinase, mediates substantial photochemical demethylation of m6 A residues of RNA in live cells. This study provides a new perspective to the understanding of demethylation of m6 A residues in mRNA and sheds light on the development of powerful small molecules as RNA demethylases and new probes for use in RNA biology.
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Affiliation(s)
- Li-Jun Xie
- Beijing National Laboratory for Molecular Sciences (BNLMS), CAS Key Laboratory of Molecular Recognition and Function, CAS Research/Education Center for Excellence in Molecular Sciences, Institute of Chemistry, Chinese Academy of Sciences, Beijing, 100190, China.,University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Xiao-Ti Yang
- BNLMS, CAS Key Laboratory of Analytical Chemistry for Living Biosystems, Institute of Chemistry, Chinese Academy of Sciences, China.,University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Rui-Li Wang
- Beijing National Laboratory for Molecular Sciences (BNLMS), CAS Key Laboratory of Molecular Recognition and Function, CAS Research/Education Center for Excellence in Molecular Sciences, Institute of Chemistry, Chinese Academy of Sciences, Beijing, 100190, China.,University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Hou-Ping Cheng
- Beijing National Laboratory for Molecular Sciences (BNLMS), CAS Key Laboratory of Molecular Recognition and Function, CAS Research/Education Center for Excellence in Molecular Sciences, Institute of Chemistry, Chinese Academy of Sciences, Beijing, 100190, China.,University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Zhi-Yan Li
- Beijing National Laboratory for Molecular Sciences (BNLMS), CAS Key Laboratory of Molecular Recognition and Function, CAS Research/Education Center for Excellence in Molecular Sciences, Institute of Chemistry, Chinese Academy of Sciences, Beijing, 100190, China
| | - Li Liu
- Beijing National Laboratory for Molecular Sciences (BNLMS), CAS Key Laboratory of Molecular Recognition and Function, CAS Research/Education Center for Excellence in Molecular Sciences, Institute of Chemistry, Chinese Academy of Sciences, Beijing, 100190, China.,University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Lanqun Mao
- BNLMS, CAS Key Laboratory of Analytical Chemistry for Living Biosystems, Institute of Chemistry, Chinese Academy of Sciences, China.,University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Ming Wang
- BNLMS, CAS Key Laboratory of Analytical Chemistry for Living Biosystems, Institute of Chemistry, Chinese Academy of Sciences, China.,University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Liang Cheng
- Beijing National Laboratory for Molecular Sciences (BNLMS), CAS Key Laboratory of Molecular Recognition and Function, CAS Research/Education Center for Excellence in Molecular Sciences, Institute of Chemistry, Chinese Academy of Sciences, Beijing, 100190, China.,Key Lab of Functional Molecular Engineering of Guangdong Province, South China University of Technology), Guangzhou, 510640, China.,University of Chinese Academy of Sciences, Beijing, 100049, China
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26
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Light SH, Su L, Rivera-Lugo R, Cornejo JA, Louie A, Iavarone AT, Ajo-Franklin CM, Portnoy DA. A flavin-based extracellular electron transfer mechanism in diverse Gram-positive bacteria. Nature 2018; 562:140-144. [PMID: 30209391 PMCID: PMC6221200 DOI: 10.1038/s41586-018-0498-z] [Citation(s) in RCA: 291] [Impact Index Per Article: 48.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/02/2018] [Accepted: 08/03/2018] [Indexed: 11/10/2022]
Abstract
Extracellular electron transfer (EET) describes microbial bioelectrochemical processes in which electrons are transferred from the cytosol to the exterior of the cell1. Mineral-respiring bacteria use elaborate haem-based electron transfer mechanisms2-4 but the existence and mechanistic basis of other EETs remain largely unknown. Here we show that the food-borne pathogen Listeria monocytogenes uses a distinctive flavin-based EET mechanism to deliver electrons to iron or an electrode. By performing a forward genetic screen to identify L. monocytogenes mutants with diminished extracellular ferric iron reductase activity, we identified an eight-gene locus that is responsible for EET. This locus encodes a specialized NADH dehydrogenase that segregates EET from aerobic respiration by channelling electrons to a discrete membrane-localized quinone pool. Other proteins facilitate the assembly of an abundant extracellular flavoprotein that, in conjunction with free-molecule flavin shuttles, mediates electron transfer to extracellular acceptors. This system thus establishes a simple electron conduit that is compatible with the single-membrane structure of the Gram-positive cell. Activation of EET supports growth on non-fermentable carbon sources, and an EET mutant exhibited a competitive defect within the mouse gastrointestinal tract. Orthologues of the genes responsible for EET are present in hundreds of species across the Firmicutes phylum, including multiple pathogens and commensal members of the intestinal microbiota, and correlate with EET activity in assayed strains. These findings suggest a greater prevalence of EET-based growth capabilities and establish a previously underappreciated relevance for electrogenic bacteria across diverse environments, including host-associated microbial communities and infectious disease.
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Affiliation(s)
- Samuel H Light
- Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, CA, USA
| | - Lin Su
- Molecular Foundry, Molecular Biophysics and Integrated Bioimaging, and Synthetic Biology Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
- State Key Laboratory of Bioelectronics, School of Biological Science and Medical Engineering, Southeast University, Nanjing, 210018, China
| | - Rafael Rivera-Lugo
- Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, CA, USA
| | - Jose A Cornejo
- Molecular Foundry, Molecular Biophysics and Integrated Bioimaging, and Synthetic Biology Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Alexander Louie
- Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, CA, USA
| | - Anthony T Iavarone
- QB3/Chemistry Mass Spectrometry Facility, University of California, Berkeley, Berkeley, CA, USA
| | - Caroline M Ajo-Franklin
- Molecular Foundry, Molecular Biophysics and Integrated Bioimaging, and Synthetic Biology Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Daniel A Portnoy
- Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, CA, USA.
- Plant and Microbial Biology, University of California, Berkeley, Berkeley, CA, USA.
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27
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Abstract
Sensory photoreceptors underpin light-dependent adaptations of organismal physiology, development, and behavior in nature. Adapted for optogenetics, sensory photoreceptors become genetically encoded actuators and reporters to enable the noninvasive, spatiotemporally accurate and reversible control by light of cellular processes. Rooted in a mechanistic understanding of natural photoreceptors, artificial photoreceptors with customized light-gated function have been engineered that greatly expand the scope of optogenetics beyond the original application of light-controlled ion flow. As we survey presently, UV/blue-light-sensitive photoreceptors have particularly allowed optogenetics to transcend its initial neuroscience applications by unlocking numerous additional cellular processes and parameters for optogenetic intervention, including gene expression, DNA recombination, subcellular localization, cytoskeleton dynamics, intracellular protein stability, signal transduction cascades, apoptosis, and enzyme activity. The engineering of novel photoreceptors benefits from powerful and reusable design strategies, most importantly light-dependent protein association and (un)folding reactions. Additionally, modified versions of these same sensory photoreceptors serve as fluorescent proteins and generators of singlet oxygen, thereby further enriching the optogenetic toolkit. The available and upcoming UV/blue-light-sensitive actuators and reporters enable the detailed and quantitative interrogation of cellular signal networks and processes in increasingly more precise and illuminating manners.
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Affiliation(s)
- Aba Losi
- Department of Mathematical, Physical and Computer Sciences , University of Parma , Parco Area delle Scienze 7/A-43124 Parma , Italy
| | - Kevin H Gardner
- Structural Biology Initiative, CUNY Advanced Science Research Center , New York , New York 10031 , United States.,Department of Chemistry and Biochemistry, City College of New York , New York , New York 10031 , United States.,Ph.D. Programs in Biochemistry, Chemistry, and Biology , The Graduate Center of the City University of New York , New York , New York 10016 , United States
| | - Andreas Möglich
- Lehrstuhl für Biochemie , Universität Bayreuth , 95447 Bayreuth , Germany.,Research Center for Bio-Macromolecules , Universität Bayreuth , 95447 Bayreuth , Germany.,Bayreuth Center for Biochemistry & Molecular Biology , Universität Bayreuth , 95447 Bayreuth , Germany
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28
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Antill LM, Woodward JR. Flavin Adenine Dinucleotide Photochemistry Is Magnetic Field Sensitive at Physiological pH. J Phys Chem Lett 2018; 9:2691-2696. [PMID: 29724094 DOI: 10.1021/acs.jpclett.8b01088] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/08/2023]
Abstract
We present time-resolved optical absorption and magnetic field effect data on the photochemistry following blue light excitation of flavin adenine dinucleotide (FAD) in aqueous solution in the pH range 2.3 to 8.0. Effects of closed form conformations of FAD in ground, excited singlet, and radical pair states exhibit significant influence on the observed kinetics and magnetic field dependence and remarkably, magnetic field effects are observed even at physiological pH where the FAD radical pairs are only 75% less magnetic field sensitive than at pH 2.3.
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Affiliation(s)
- Lewis M Antill
- Graduate School of Arts and Sciences , The University of Tokyo , 3-8-1 Komaba , Meguro-ku , Tokyo 153-8902 , Japan
| | - Jonathan R Woodward
- Graduate School of Arts and Sciences , The University of Tokyo , 3-8-1 Komaba , Meguro-ku , Tokyo 153-8902 , Japan
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29
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Kubota T, Tani O, Yamaguchi T, Namatame I, Sakashita H, Furukawa K, Yamasaki K. Crystal structures of FMN-bound and FMN-free forms of dihydroorotate dehydrogenase from Trypanosoma brucei. FEBS Open Bio 2018; 8:680-691. [PMID: 29632820 PMCID: PMC5881531 DOI: 10.1002/2211-5463.12403] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2018] [Revised: 02/08/2018] [Accepted: 02/08/2018] [Indexed: 01/29/2023] Open
Abstract
Dihydroorotate dehydrogenase (DHODH) is a flavin‐binding enzyme essential for pyrimidine biosynthesis, which converts dihydroorotate to orotate. Three‐dimensional structures of cytosolic DHODH of parasitic protozoa are of interest in drug discovery for neglected tropical diseases, especially because these enzymes possess significantly different structural and functional properties from the membrane‐associated human enzyme. The existing crystal structures of the flavin mononucleotide (FMN)‐bound DHODHs reveal a number of interactions stabilizing FMN. However, to understand the binding mechanism correctly, it is necessary to compare the structures of the FMN‐bound and FMN‐free forms, because the protein moiety of the former is not necessarily the same as the latter. Here, we prepared the FMN‐free DHODH of Trypanosoma brucei using an Escherichia coli overexpression system. Although this apoform lacks enzymatic activity, simple incubation with FMN activated the enzyme. It was stable enough to be crystallized, enabling us to determine its structure by X‐ray crystallography at 1.6 Å resolution. We also determined the FMN‐bound form at 1.8 Å resolution. Although the two structures have essentially the same scaffold, we observed flipping of a peptide‐bond plane in the vicinity of the FMN‐binding site, accompanied by an alternative hydrogen‐bonding pattern. Comparisons of B factors of the protein main chain revealed that binding of FMN decreased flexibility of most of the residues at the FMN‐binding site, but increased flexibility of a lid‐like loop structure over the active center. This increase was ascribed to a conformational change in an FMN‐contacting residue, Asn195, which induced a rearrangement of a hydrogen‐bond network of the residues comprising the lid.
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Affiliation(s)
- Tomomi Kubota
- Biomedical Research Institute National Institute of Advanced Industrial Science and Technology (AIST) Tsukuba Japan
| | - Osamu Tani
- Biomedical Research Institute National Institute of Advanced Industrial Science and Technology (AIST) Tsukuba Japan
| | | | | | - Hitoshi Sakashita
- Biomedical Research Institute National Institute of Advanced Industrial Science and Technology (AIST) Tsukuba Japan
| | - Koji Furukawa
- Biomedical Research Institute National Institute of Advanced Industrial Science and Technology (AIST) Tsukuba Japan
| | - Kazuhiko Yamasaki
- Biomedical Research Institute National Institute of Advanced Industrial Science and Technology (AIST) Tsukuba Japan
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30
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Tycova A, Gerhardt RF, Belder D. Surface enhanced Raman spectroscopy in microchip electrophoresis. J Chromatogr A 2018; 1541:39-46. [DOI: 10.1016/j.chroma.2018.02.014] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2017] [Revised: 02/01/2018] [Accepted: 02/06/2018] [Indexed: 11/27/2022]
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31
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Yong D, Ding D. Lasing with cell-endogenous fluorophores: parameters and conditions. Sci Rep 2017; 7:13569. [PMID: 29051508 PMCID: PMC5648766 DOI: 10.1038/s41598-017-12711-x] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2017] [Accepted: 09/18/2017] [Indexed: 01/05/2023] Open
Abstract
The notion of lasing with biologics has recently been realized and has rapidly developed with the collective objective of creating lasers in vivo. One major limitation of achieving this is the requirement of exogenous dyes and fluorescent materials. We thus investigate for the first time the possibility of lasing unlabelled cells, using just cell-endogenous fluorophores - the source of cell autofluorescence. In this work, we theoretically studied the lasing potential and efficiency of flavins and reduced nicotinamide adenine dinucleotide (phosphate) (NAD(P)H) using a dye lasing model based on coupled rate equations. Analytical solutions for one- and two-photon pumped system were used in multi-parameter studies. We found that at physiological conditions, the more abundant NAD(P)H can be lased with a cavity quality factor of 105. We then recommended the tuning of intersystem crossing to make the lasing of flavins feasible even at their low physiological concentrations. Under conditions of reduced intersystem crossing, we concluded that it is more practical to lase unlabelled cells using flavins, because lasing thresholds and cavity quality factors were both at least an order lower. We also note the higher threshold requirements and lower efficiencies of two-photon pumping, but recognize its potential for realizing lasing in vivo.
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Affiliation(s)
- Derrick Yong
- Precision Measurements Group, Singapore Institute of Manufacturing Technology, 2 Fusionopolis Way, Innovis #08-04, 138634, Singapore, Singapore.
| | - Ding Ding
- Precision Measurements Group, Singapore Institute of Manufacturing Technology, 2 Fusionopolis Way, Innovis #08-04, 138634, Singapore, Singapore
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32
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Wang Y, Landry AP, Ding H. The mitochondrial outer membrane protein mitoNEET is a redox enzyme catalyzing electron transfer from FMNH 2 to oxygen or ubiquinone. J Biol Chem 2017; 292:10061-10067. [PMID: 28461337 DOI: 10.1074/jbc.m117.789800] [Citation(s) in RCA: 41] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2017] [Revised: 04/29/2017] [Indexed: 01/20/2023] Open
Abstract
Increasing evidence suggests that mitoNEET, a target of the type II diabetes drug pioglitazone, is a key regulator of energy metabolism in mitochondria. MitoNEET is anchored to the mitochondrial outer membrane via its N-terminal α helix domain and hosts a redox-active [2Fe-2S] cluster in its C-terminal cytosolic region. The mechanism by which mitoNEET regulates energy metabolism in mitochondria, however, is not fully understood. Previous studies have shown that mitoNEET specifically interacts with the reduced flavin mononucleotide (FMNH2) and that FMNH2 can quickly reduce the mitoNEET [2Fe-2S] clusters. Here we report that the reduced mitoNEET [2Fe-2S] clusters can be readily oxidized by oxygen. In the presence of FMN, NADH, and flavin reductase, which reduces FMN to FMNH2 using NADH as the electron donor, mitoNEET mediates oxidation of NADH with a concomitant reduction of oxygen. Ubiquinone-2, an analog of ubiquinone-10, can also oxidize the reduced mitoNEET [2Fe-2S] clusters under anaerobic or aerobic conditions. Compared with oxygen, ubiquinone-2 is more efficient in oxidizing the mitoNEET [2Fe-2S] clusters, suggesting that ubiquinone could be an intrinsic electron acceptor of the reduced mitoNEET [2Fe-2S] clusters in mitochondria. Pioglitazone or its analog NL-1 appears to inhibit the electron transfer activity of mitoNEET by forming a unique complex with mitoNEET and FMNH2 The results suggest that mitoNEET is a redox enzyme that may promote oxidation of NADH to facilitate enhanced glycolysis in the cytosol and that pioglitazone may regulate energy metabolism in mitochondria by inhibiting the electron transfer activity of mitoNEET.
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Affiliation(s)
- Yiming Wang
- From the Department of Biological Sciences, Louisiana State University, Baton Rouge, Louisiana 70803
| | - Aaron P Landry
- From the Department of Biological Sciences, Louisiana State University, Baton Rouge, Louisiana 70803
| | - Huangen Ding
- From the Department of Biological Sciences, Louisiana State University, Baton Rouge, Louisiana 70803
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33
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Zhao C, Liu L, Ge J, He Y. Ultrasensitive determination for flavin coenzyme by using a ZnO nanorod photoelectrode in a four-electrode system. Mikrochim Acta 2017. [DOI: 10.1007/s00604-017-2230-3] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
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34
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The superfamily keeps growing: Identification in trypanosomatids of RibJ, the first riboflavin transporter family in protists. PLoS Negl Trop Dis 2017; 11:e0005513. [PMID: 28406895 PMCID: PMC5404878 DOI: 10.1371/journal.pntd.0005513] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2017] [Revised: 04/25/2017] [Accepted: 03/21/2017] [Indexed: 01/07/2023] Open
Abstract
Background Trypanosomatid parasites represent a major health issue affecting hundreds of million people worldwide, with clinical treatments that are partially effective and/or very toxic. They are responsible for serious human and plant diseases including Trypanosoma cruzi (Chagas disease), Trypanosoma brucei (Sleeping sickness), Leishmania spp. (Leishmaniasis), and Phytomonas spp. (phytoparasites). Both, animals and trypanosomatids lack the biosynthetic riboflavin (vitamin B2) pathway, the vital precursor of flavin mononucleotide (FMN) and flavin adenine dinucleotide (FAD) cofactors. While metazoans obtain riboflavin from the diet through RFVT/SLC52 transporters, the riboflavin transport mechanisms in trypanosomatids still remain unknown. Methodology/Principal findings Here, we show that riboflavin is imported with high affinity in Trypanosoma cruzi, Trypanosoma brucei, Leishmania (Leishmania) mexicana, Crithidia fasciculata and Phytomonas Jma using radiolabeled riboflavin transport assays. The vitamin is incorporated through a saturable carrier-mediated process. Effective competitive uptake occurs with riboflavin analogs roseoflavin, lumiflavin and lumichrome, and co-factor derivatives FMN and FAD. Moreover, important biological processes evaluated in T. cruzi (i.e. proliferation, metacyclogenesis and amastigote replication) are dependent on riboflavin availability. In addition, the riboflavin competitive analogs were found to interfere with parasite physiology on riboflavin-dependent processes. By means of bioinformatics analyses we identified a novel family of riboflavin transporters (RibJ) in trypanosomatids. Two RibJ members, TcRibJ and TbRibJ from T. cruzi and T. brucei respectively, were functionally characterized using homologous and/or heterologous expression systems. Conclusions/Significance The RibJ family represents the first riboflavin transporters found in protists and the third eukaryotic family known to date. The essentiality of riboflavin for trypanosomatids, and the structural/biochemical differences that RFVT/SLC52 and RibJ present, make the riboflavin transporter -and its downstream metabolism- a potential trypanocidal drug target. In this work, we show that riboflavin plays a key role in the trypanosomatid life cycles and describe a novel family of riboflavin transporters (RibJ) with uptake function. Despite the vital importance of riboflavin for all living cells, RibJ are the first transporters described in protists. We functionally characterized the T. cruzi and T. brucei RibJ members and the effect of riboflavin analogs on parasite physiology. The structural and biochemical differences presented between human transporters and RibJ members make riboflavin transport and downstream metabolism, attractive and potential trypanosomatid targets.
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35
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Landry AP, Wang Y, Cheng Z, Crochet RB, Lee YH, Ding H. Flavin nucleotides act as electron shuttles mediating reduction of the [2Fe-2S] clusters in mitochondrial outer membrane protein mitoNEET. Free Radic Biol Med 2017; 102:240-247. [PMID: 27923678 PMCID: PMC5209285 DOI: 10.1016/j.freeradbiomed.2016.12.001] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/03/2016] [Revised: 10/18/2016] [Accepted: 12/01/2016] [Indexed: 10/20/2022]
Abstract
MitoNEET, a primary target of type II diabetes drug pioglitazone, has an essential role in regulating energy metabolism, iron homeostasis, and production of reactive oxygen species in mitochondria. Structurally, mitoNEET is anchored to the mitochondrial outer membrane via its N-terminal transmembrane α-helix. The C-terminal cytosolic domain of mitoNEET hosts a redox active [2Fe-2S] cluster via three cysteine and one histidine residues. Here we report that the reduced flavin nucleotides can rapidly reduce the mitoNEET [2Fe-2S] clusters under anaerobic or aerobic conditions. In the presence of NADH and flavin reductase, 1 molecule of flavin nucleotide is sufficient to reduce about 100 molecules of the mitoNEET [2Fe-2S] clusters in 4min under aerobic conditions. The electron paramagnetic resonance (EPR) measurements show that flavin mononucleotide (FMN), but not flavin adenine dinucleotide (FAD), has a specific interaction with mitoNEET. Molecular docking models further reveal that flavin mononucleotide binds mitoNEET at the region between the N-terminal transmembrane α-helix and the [2Fe-2S] cluster binding domain. The closest distance between the [2Fe-2S] cluster and the bound flavin mononucleotide in mitoNEET is about 10Å, which could facilitate rapid electron transfer from the reduced flavin nucleotide to the [2Fe-2S] cluster in mitoNEET. The results suggest that flavin nucleotides may act as electron shuttles to reduce the mitoNEET [2Fe-2S] clusters and regulate mitochondrial functions in human cells.
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Affiliation(s)
- Aaron P Landry
- Department of Biological Sciences, Louisiana State University, Baton Rouge, LA 70803, USA
| | - Yiming Wang
- Department of Biological Sciences, Louisiana State University, Baton Rouge, LA 70803, USA
| | - Zishuo Cheng
- Department of Biological Sciences, Louisiana State University, Baton Rouge, LA 70803, USA
| | - Robert B Crochet
- Department of Biological Sciences, Louisiana State University, Baton Rouge, LA 70803, USA
| | - Yong-Hwan Lee
- Department of Biological Sciences, Louisiana State University, Baton Rouge, LA 70803, USA
| | - Huangen Ding
- Department of Biological Sciences, Louisiana State University, Baton Rouge, LA 70803, USA.
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36
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Ota Y, Itoh Y, Kaise A, Ohta K, Endo Y, Masuda M, Sowa Y, Sakai T, Suzuki T. Targeting Cancer with PCPA-Drug Conjugates: LSD1 Inhibition-Triggered Release of 4-Hydroxytamoxifen. Angew Chem Int Ed Engl 2016. [DOI: 10.1002/ange.201608711] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023]
Affiliation(s)
- Yosuke Ota
- Graduate School of Medical Science; Kyoto Prefectural University of Medicine; 1-5 Shimogamohangi-Cho Sakyo-Ku Kyoto 606-0823 Japan
| | - Yukihiro Itoh
- Graduate School of Medical Science; Kyoto Prefectural University of Medicine; 1-5 Shimogamohangi-Cho Sakyo-Ku Kyoto 606-0823 Japan
| | - Asako Kaise
- Faculty of Pharmaceutical Sciences; Tohoku Medical and Pharmaceutical University; 4-4-1 Komatsushima Aoba-ku Sendai 981-8558 Japan
| | - Kiminori Ohta
- Faculty of Pharmaceutical Sciences; Tohoku Medical and Pharmaceutical University; 4-4-1 Komatsushima Aoba-ku Sendai 981-8558 Japan
| | - Yasuyuki Endo
- Faculty of Pharmaceutical Sciences; Tohoku Medical and Pharmaceutical University; 4-4-1 Komatsushima Aoba-ku Sendai 981-8558 Japan
| | - Mitsuharu Masuda
- Graduate School of Medical Science; Kyoto Prefectural University of Medicine; 1-5 Shimogamohangi-Cho Sakyo-Ku Kyoto 606-0823 Japan
| | - Yoshihiro Sowa
- Graduate School of Medical Science; Kyoto Prefectural University of Medicine; 1-5 Shimogamohangi-Cho Sakyo-Ku Kyoto 606-0823 Japan
| | - Toshiyuki Sakai
- Graduate School of Medical Science; Kyoto Prefectural University of Medicine; 1-5 Shimogamohangi-Cho Sakyo-Ku Kyoto 606-0823 Japan
| | - Takayoshi Suzuki
- Graduate School of Medical Science; Kyoto Prefectural University of Medicine; 1-5 Shimogamohangi-Cho Sakyo-Ku Kyoto 606-0823 Japan
- CREST Japan Science and Technology Agency (JST); 4-1-8 Honcho Kawaguchi Saitama 332-0012 Japan
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37
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Ota Y, Itoh Y, Kaise A, Ohta K, Endo Y, Masuda M, Sowa Y, Sakai T, Suzuki T. Targeting Cancer with PCPA-Drug Conjugates: LSD1 Inhibition-Triggered Release of 4-Hydroxytamoxifen. Angew Chem Int Ed Engl 2016; 55:16115-16118. [DOI: 10.1002/anie.201608711] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2016] [Revised: 10/19/2016] [Indexed: 11/12/2022]
Affiliation(s)
- Yosuke Ota
- Graduate School of Medical Science; Kyoto Prefectural University of Medicine; 1-5 Shimogamohangi-Cho Sakyo-Ku Kyoto 606-0823 Japan
| | - Yukihiro Itoh
- Graduate School of Medical Science; Kyoto Prefectural University of Medicine; 1-5 Shimogamohangi-Cho Sakyo-Ku Kyoto 606-0823 Japan
| | - Asako Kaise
- Faculty of Pharmaceutical Sciences; Tohoku Medical and Pharmaceutical University; 4-4-1 Komatsushima Aoba-ku Sendai 981-8558 Japan
| | - Kiminori Ohta
- Faculty of Pharmaceutical Sciences; Tohoku Medical and Pharmaceutical University; 4-4-1 Komatsushima Aoba-ku Sendai 981-8558 Japan
| | - Yasuyuki Endo
- Faculty of Pharmaceutical Sciences; Tohoku Medical and Pharmaceutical University; 4-4-1 Komatsushima Aoba-ku Sendai 981-8558 Japan
| | - Mitsuharu Masuda
- Graduate School of Medical Science; Kyoto Prefectural University of Medicine; 1-5 Shimogamohangi-Cho Sakyo-Ku Kyoto 606-0823 Japan
| | - Yoshihiro Sowa
- Graduate School of Medical Science; Kyoto Prefectural University of Medicine; 1-5 Shimogamohangi-Cho Sakyo-Ku Kyoto 606-0823 Japan
| | - Toshiyuki Sakai
- Graduate School of Medical Science; Kyoto Prefectural University of Medicine; 1-5 Shimogamohangi-Cho Sakyo-Ku Kyoto 606-0823 Japan
| | - Takayoshi Suzuki
- Graduate School of Medical Science; Kyoto Prefectural University of Medicine; 1-5 Shimogamohangi-Cho Sakyo-Ku Kyoto 606-0823 Japan
- CREST Japan Science and Technology Agency (JST); 4-1-8 Honcho Kawaguchi Saitama 332-0012 Japan
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38
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Recognition of enzymes lacking bound cofactor by protein quality control. Proc Natl Acad Sci U S A 2016; 113:12156-12161. [PMID: 27733512 DOI: 10.1073/pnas.1611994113] [Citation(s) in RCA: 49] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023] Open
Abstract
Protein biogenesis is tightly linked to protein quality control (PQC). The role of PQC machinery in recognizing faulty polypeptides is becoming increasingly understood. Molecular chaperones and cytosolic and vacuolar degradation systems collaborate to detect, repair, or hydrolyze mutant, damaged, and mislocalized proteins. On the other hand, the contribution of PQC to cofactor binding-related enzyme maturation remains largely unexplored, although the loading of a cofactor represents an all-or-nothing transition in regard to the enzymatic function and thus must be surveyed carefully. Combining proteomics and biochemical analysis, we demonstrate here that cells are able to detect functionally immature wild-type enzymes. We show that PQC-dedicated ubiquitin ligase C-terminal Hsp70-interacting protein (CHIP) recognizes and marks for degradation not only a mutant protein but also its wild-type variant as long as the latter remains cofactor free. A distinct structural feature, the protruding C-terminal tail, which appears in both the mutant and wild-type polypeptides, contributes to recognition by CHIP. Our data suggest that relative insufficiency of apoprotein degradation caused by cofactor shortage can increase amyloidogenesis and aggravate protein aggregation disorders.
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39
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LOV2-Controlled Photoactivation of Protein Trans-Splicing. Methods Mol Biol 2016. [PMID: 27714620 DOI: 10.1007/978-1-4939-6451-2_15] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register]
Abstract
Protein trans-splicing is a posttranslational modification that joins two protein fragments together via a peptide a bond in a process that does not require exogenous cofactors. Towards achieving cellular control, synthetically engineered systems have used a variety of stimuli such as small molecules and light. Recently, split inteins have been engineered to be photoactive by the LOV2 domain (named LOVInC). Herein, we discuss (1) designing of LOV2-activated target proteins (e.g., inteins), (2) selecting feasible splice sites for the extein, and (3) imaging cells that express LOVInC-based target exteins.
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40
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Galievsky VA, Stasheuski AS, Krylov SN. "Getting the best sensitivity from on-capillary fluorescence detection in capillary electrophoresis" - A tutorial. Anal Chim Acta 2016; 935:58-81. [PMID: 27543015 DOI: 10.1016/j.aca.2016.06.015] [Citation(s) in RCA: 38] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2016] [Revised: 06/09/2016] [Accepted: 06/11/2016] [Indexed: 01/09/2023]
Abstract
Capillary electrophoresis with Laser-Induced Fluorescence (CE-LIF) detection is being applied to new analytical problems which challenge both the power of CE separation and the sensitivity of LIF detection. On-capillary LIF detection is much more practical than post-capillary detection in a sheath-flow cell. Therefore, commercial CE instruments utilize solely on-capillary CE-LIF detection with a Limit of Detection (LOD) in the nM range, while there are multiple applications of CE-LIF that require pM or lower LODs. This tutorial analyzes all aspects of on-capillary LIF detection in CE in an attempt to identify means for improving LOD of CE-LIF with on-capillary detection. We consider principles of signal enhancement and noise reduction, as well as relevant areas of fluorophore photochemistry and fluorescent microscopy.
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Affiliation(s)
- Victor A Galievsky
- Department of Chemistry and Centre for Research on Biomolecular Interactions, York University, Toronto, Ontario M3J 1P3, Canada
| | - Alexander S Stasheuski
- Department of Chemistry and Centre for Research on Biomolecular Interactions, York University, Toronto, Ontario M3J 1P3, Canada
| | - Sergey N Krylov
- Department of Chemistry and Centre for Research on Biomolecular Interactions, York University, Toronto, Ontario M3J 1P3, Canada.
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41
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Hopkins SL, Siewert B, Askes SHC, Veldhuizen P, Zwier R, Heger M, Bonnet S. An in vitro cell irradiation protocol for testing photopharmaceuticals and the effect of blue, green, and red light on human cancer cell lines. Photochem Photobiol Sci 2016; 15:644-53. [PMID: 27098927 PMCID: PMC5044800 DOI: 10.1039/c5pp00424a] [Citation(s) in RCA: 73] [Impact Index Per Article: 9.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2015] [Accepted: 03/30/2016] [Indexed: 12/21/2022]
Abstract
Traditionally, ultraviolet light (100-400 nm) is considered an exogenous carcinogen while visible light (400-780 nm) is deemed harmless. In this work, a LED irradiation system for in vitro photocytotoxicity testing is described. The LED irradiation system was developed for testing photopharmaceutical drugs, but was used here to determine the basal level response of human cancer cell lines to visible light of different wavelengths, without any photo(chemo)therapeutic. The effects of blue (455 nm, 10.5 mW cm(-2)), green (520 nm, 20.9 mW cm(-2)), and red light (630 nm, 34.4 mW cm(-2)) irradiation was measured for A375 (human malignant melanoma), A431 (human epidermoid carcinoma), A549 (human lung carcinoma), MCF7 (human mammary gland adenocarcinoma), MDA-MB-231 (human mammary gland adenocarcinoma), and U-87 MG (human glioblastoma-grade IV) cell lines. In response to a blue light dose of 19 J cm(-2), three cell lines exhibited a minimal (20%, MDA-MB-231) to moderate (30%, A549 and 60%, A375) reduction in cell viability, compared to dark controls. The other cell lines were not affected. Effective blue light doses that produce a therapeutic response in 50% of the cell population (ED50) compared to dark conditions were found to be 10.9 and 30.5 J cm(-2) for A375 and A549 cells, respectively. No adverse effects were observed in any of the six cell lines irradiated with a 19 J cm(-2) dose of 520 nm (green) or 630 nm (red) light. The results demonstrate that blue light irradiation can have an effect on the viability of certain human cancer cell types and controls should be used in photopharmaceutical testing, which uses high-energy (blue or violet) visible light activation.
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Affiliation(s)
- S. L. Hopkins
- Leiden Institute of Chemistry , Leiden University , Einsteinweg 55 , 2300RA Leiden , The Netherlands .
| | - B. Siewert
- Leiden Institute of Chemistry , Leiden University , Einsteinweg 55 , 2300RA Leiden , The Netherlands .
| | - S. H. C. Askes
- Leiden Institute of Chemistry , Leiden University , Einsteinweg 55 , 2300RA Leiden , The Netherlands .
| | - P. Veldhuizen
- Leiden Institute of Physics , Leiden University , Niels Bohrweg 2 , 2333CA Leiden , The Netherlands
| | - R. Zwier
- Leiden Institute of Physics , Leiden University , Niels Bohrweg 2 , 2333CA Leiden , The Netherlands
| | - Michal Heger
- Department of Experimental Surgery , Academic Medical Center , University of Amsterdam , Meibergdreef 9 , 1105 AZ Amsterdam , The Netherlands
| | - Sylvestre Bonnet
- Leiden Institute of Chemistry , Leiden University , Einsteinweg 55 , 2300RA Leiden , The Netherlands .
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