1
|
Brandmair K, Dising D, Finkelmeier D, Schepky A, Kuehnl J, Ebmeyer J, Burger-Kentischer A. A novel three-dimensional Nrf2 reporter epidermis model for skin sensitization assessment. Toxicology 2024; 503:153743. [PMID: 38341018 DOI: 10.1016/j.tox.2024.153743] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2023] [Revised: 01/25/2024] [Accepted: 02/06/2024] [Indexed: 02/12/2024]
Abstract
Skin sensitization assessment has progressed from the use of animal models towards the application of New Approach Methodologies (NAMs). Several skin sensitization NAMs are accepted for regulatory use, but a majority relies on submerged in vitro cell cultures that limit their applicability domain, posing challenges for testing hydrophobic chemicals and mixtures. A newly developed three-dimensional (3D) Nrf2 reporter epidermis model for skin sensitization assessment is reported. This NAM may help to overcome these limitations. The NAM combines the in vivo-like biology and exposure conditions of 3D epidermis models with the reliability, convenience, and cost-effectiveness of secreted reporter gene technology. The Keap1-Nrf2-ARE pathway was chosen as the reporter gene read-out, as it is induced by most skin sensitizers and already adopted in OECD Test guideline 442D. Immortalized human primary keratinocytes (Ker-CT) were stably transfected with the pIGB-Nrf2-SEAP vector to construct a Nrf2 reporter cell line. Ker-CT Nrf2 reporter cells showed negligible basal expression of the Secreted Embryonic Alkaline Phosphatase (SEAP) reporter, which was induced 13.5-fold by exposure to the skin sensitizer cinnamic aldehyde (CA). Co-exposure to CA and the Nrf2 inhibitor glucocorticoid clobetasol propionate significantly suppressed the CA-induced SEAP expression, confirming dependance of the SEAP expression on Nrf2 activation. Using air-liquid interface and animal constituent free culture conditions, the Ker-CT Nrf2 reporter cells differentiated to stratified 3D epidermis models with an in vivo-like skin architecture and functional skin barrier. Evaluation of a Ker-CT Nrf2 reporter cell-based 2D assay by testing 10 conventional reference chemicals showed a predictive accuracy for skin sensitization potential of 80% and 70% compared to LLNA and human data in two independent laboratories and a high intra- and interlaboratory reproducibility. Moreover, the 3D epidermis models predicted 3 sensitizing and 2 non-sensitizing reference chemicals correctly in a first proof-of-concept study. Further investigations foresee the testing of additional chemicals, including hydrophobic compounds and mixtures to confirm the potential of the 3D epidermis models to broaden the applicability domain for NAM-based skin sensitization assessment.
Collapse
Affiliation(s)
- K Brandmair
- Beiersdorf AG, Beiersdorfstraße 1-9, Hamburg 20245, Germany
| | - D Dising
- Fraunhofer Institute for Interfacial Engineering and Biotechnology IGB, Cell and Tissue Technologies, Nobelstraße 12, Stuttgart 70569, Germany
| | - D Finkelmeier
- Fraunhofer Institute for Interfacial Engineering and Biotechnology IGB, Cell and Tissue Technologies, Nobelstraße 12, Stuttgart 70569, Germany
| | - A Schepky
- Beiersdorf AG, Beiersdorfstraße 1-9, Hamburg 20245, Germany
| | - J Kuehnl
- Beiersdorf AG, Beiersdorfstraße 1-9, Hamburg 20245, Germany
| | - J Ebmeyer
- Beiersdorf AG, Beiersdorfstraße 1-9, Hamburg 20245, Germany.
| | - A Burger-Kentischer
- Fraunhofer Institute for Interfacial Engineering and Biotechnology IGB, Cell and Tissue Technologies, Nobelstraße 12, Stuttgart 70569, Germany.
| |
Collapse
|
2
|
Niederau PA, Eglé P, Willig S, Parsons J, Hoernstein SNW, Decker EL, Reski R. Multifactorial analysis of terminator performance on heterologous gene expression in Physcomitrella. PLANT CELL REPORTS 2024; 43:43. [PMID: 38246952 PMCID: PMC10800305 DOI: 10.1007/s00299-023-03088-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/13/2023] [Accepted: 11/02/2023] [Indexed: 01/23/2024]
Abstract
KEY MESSAGE Characterization of Physcomitrella 3'UTRs across different promoters yields endogenous single and double terminators for usage in molecular pharming. The production of recombinant proteins for health applications accounts for a large share of the biopharmaceutical market. While many drugs are produced in microbial and mammalian systems, plants gain more attention as expression hosts to produce eukaryotic proteins. In particular, the good manufacturing practice (GMP)-compliant moss Physcomitrella (Physcomitrium patens) has outstanding features, such as excellent genetic amenability, reproducible bioreactor cultivation, and humanized protein glycosylation patterns. In this study, we selected and characterized novel terminators for their effects on heterologous gene expression. The Physcomitrella genome contains 53,346 unique 3'UTRs (untranslated regions) of which 7964 transcripts contain at least one intron. Over 91% of 3'UTRs exhibit more than one polyadenylation site, indicating the prevalence of alternative polyadenylation in Physcomitrella. Out of all 3'UTRs, 14 terminator candidates were selected and characterized via transient Dual-Luciferase assays, yielding a collection of endogenous terminators performing equally high as established heterologous terminators CaMV35S, AtHSP90, and NOS. High performing candidates were selected for testing as double terminators which impact reporter levels, dependent on terminator identity and positioning. Testing of 3'UTRs among the different promoters NOS, CaMV35S, and PpActin5 showed an increase of more than 1000-fold between promoters PpActin5 and NOS, whereas terminators increased reporter levels by less than tenfold, demonstrating the stronger effect promoters play as compared to terminators. Among selected terminator attributes, the number of polyadenylation sites as well as polyadenylation signals were found to influence terminator performance the most. Our results improve the biotechnology platform Physcomitrella and further our understanding of how terminators influence gene expression in plants in general.
Collapse
Affiliation(s)
| | - Pauline Eglé
- Plant Biotechnology, Faculty of Biology, University of Freiburg, Freiburg, Germany
| | - Sandro Willig
- Plant Biotechnology, Faculty of Biology, University of Freiburg, Freiburg, Germany
| | - Juliana Parsons
- Plant Biotechnology, Faculty of Biology, University of Freiburg, Freiburg, Germany
| | | | - Eva L Decker
- Plant Biotechnology, Faculty of Biology, University of Freiburg, Freiburg, Germany
| | - Ralf Reski
- Plant Biotechnology, Faculty of Biology, University of Freiburg, Freiburg, Germany.
- Signalling Research Centre BIOSS and CIBSS, University of Freiburg, Freiburg, Germany.
| |
Collapse
|
3
|
Cruz MGFDML, Santi AMM, de Morais-Teixeira E, Caldeira ASP, de Siqueira EP, Oliveira E, Alves TMDA, Murta SMF. Anti- Leishmania compounds can be screened using Leishmania spp. expressing red fluorescence ( tdTomato). Antimicrob Agents Chemother 2024; 68:e0050923. [PMID: 38063403 PMCID: PMC10777850 DOI: 10.1128/aac.00509-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2023] [Accepted: 10/30/2023] [Indexed: 01/11/2024] Open
Abstract
The main challenges associated with leishmaniasis chemotherapy are drug toxicity, the possible emergence of resistant parasites, and a limited choice of therapeutic agents. Therefore, new drugs and assays to screen and detect novel active compounds against leishmaniasis are urgently needed. We thus validated Leishmania braziliensis (Lb) and Leishmania infantum (Li) that constitutively express the tandem tomato red fluorescent protein (tdTomato) as a model for large-scale screens of anti-Leishmania compounds. Confocal microscopy of Lb and Li::tdTomato revealed red fluorescence distributed throughout the entire parasite, including the flagellum, and flow cytometry confirmed that the parasites emitted intense fluorescence. We evaluated the infectivity of cloned promastigotes and amastigotes constitutively expressing tdTomato, their growth profiles in THP-1 macrophages, and susceptibility to trivalent antimony, amphotericin, and miltefosine in vitro. The phenotypes of mutant and wild-type parasites were similar, indicating that the constitutive expression of tdTomato did not interfere with the evaluated parameters. We applied our validated model to a repositioning strategy and assessed the susceptibility of the parasites to eight commercially available drugs. We also screened 32 natural plant and fungal extracts and 10 pure substances to reveal new active compounds. The infectivity and Glucantime treatment efficacy of BALB/c mice and golden hamsters infected with Lb and Li::tdTomato mutant lines, respectively, were very similar compared to animals infected with wild-type parasites. Standardizing our methodology would offer more rapid, less expensive, and easier assays to screen of compounds against L. braziliensis and L. infantum in vitro and in vivo. Our method could also enhance the discovery of active compounds for treating leishmaniasis.
Collapse
Affiliation(s)
- Mariza Gabriela Faleiro de Moura Lodi Cruz
- Genômica Funcional de Parasitos, Instituto René Rachou, Fundação Oswaldo Cruz FIOCRUZ Minas, Belo Horizonte, Minas Gerais, Brazil
- Química de Produtos Naturais Bioativos, Instituto René Rachou, Fundação Oswaldo Cruz FIOCRUZ Minas, Belo Horizonte, Minas Gerais, Brazil
| | - Ana Maria Murta Santi
- Genômica Funcional de Parasitos, Instituto René Rachou, Fundação Oswaldo Cruz FIOCRUZ Minas, Belo Horizonte, Minas Gerais, Brazil
| | - Eliane de Morais-Teixeira
- Pesquisa Clínica e Políticas Públicas em Doenças Infecto-Parasitárias, Instituto René Rachou, Fundação Oswaldo Cruz FIOCRUZ Minas, Belo Horizonte, Minas Gerais, Brazil
| | - Alisson Samuel Portes Caldeira
- Química de Produtos Naturais Bioativos, Instituto René Rachou, Fundação Oswaldo Cruz FIOCRUZ Minas, Belo Horizonte, Minas Gerais, Brazil
| | - Ezequias Pessoa de Siqueira
- Química de Produtos Naturais Bioativos, Instituto René Rachou, Fundação Oswaldo Cruz FIOCRUZ Minas, Belo Horizonte, Minas Gerais, Brazil
| | - Edward Oliveira
- Genômica Funcional de Parasitos, Instituto René Rachou, Fundação Oswaldo Cruz FIOCRUZ Minas, Belo Horizonte, Minas Gerais, Brazil
| | - Tânia Maria de Almeida Alves
- Química de Produtos Naturais Bioativos, Instituto René Rachou, Fundação Oswaldo Cruz FIOCRUZ Minas, Belo Horizonte, Minas Gerais, Brazil
| | - Silvane Maria Fonseca Murta
- Genômica Funcional de Parasitos, Instituto René Rachou, Fundação Oswaldo Cruz FIOCRUZ Minas, Belo Horizonte, Minas Gerais, Brazil
| |
Collapse
|
4
|
Phonbuppha J, Tinikul R, Ohmiya Y, Chaiyen P. High Sensitivity and Low-Cost Flavin luciferase (FLUX Vc)-based Reporter Gene for Mammalian Cell Expression. J Biol Chem 2023; 299:104639. [PMID: 36965614 PMCID: PMC10164909 DOI: 10.1016/j.jbc.2023.104639] [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: 02/23/2023] [Revised: 03/12/2023] [Accepted: 03/13/2023] [Indexed: 03/27/2023] Open
Abstract
Luciferase-based gene reporters generating bioluminescence signals are important tools for biomedical research. Amongst the luciferases, flavin-dependent enzymes use the most economical chemicals. However, their applications in mammalian cells are limited due to their low signals compared to other systems. Here, we constructed Flavin Luciferase from Vibrio campbellii (Vc) for Mammalian Cell Expression (FLUXVc) by engineering luciferase from Vibrio campbellii (the most thermostable bacterial luciferase reported to date) and optimizing its expression and reporter assays in mammalian cells which can improve the bioluminescence light output by >400-fold as compared to the non-engineered version. We found that the FLUXVc reporter gene can be overexpressed in various cell lines and showed outstanding signal-to-background in HepG2 cells, significantly higher than that of firefly luciferase (Fluc). The combined use of FLUXVc/Fluc as target/control vectors gave the most stable signals, better than the standard set of Fluc(target)/Rluc(control). We also demonstrated that FLUXVc can be used for testing inhibitors of the NF-κB signaling pathway. Collectively, our results provide an optimized method for using the more economical flavin-dependent luciferase in mammalian cells.
Collapse
Affiliation(s)
- Jittima Phonbuppha
- School of Biomolecular Science & Engineering, Vidyasirimedhi Institute of Science and Technology (VISTEC), Wangchan valley, Rayong 21210 Thailand
| | - Ruchanok Tinikul
- Department of Biochemistry and Center for Excellence in Protein and Enzyme Technology, Faculty of Science, Mahidol University, Bangkok 10400 Thailand
| | - Yoshihiro Ohmiya
- School of Biomolecular Science & Engineering, Vidyasirimedhi Institute of Science and Technology (VISTEC), Wangchan valley, Rayong 21210 Thailand; National Institute of Advanced Industrial Science and Technology (AIST), Ikeda, Osaka 563-8577, Japan; Osaka Institute of Technology (OIT), Osaka, Osaka 535-8585, Japan
| | - Pimchai Chaiyen
- School of Biomolecular Science & Engineering, Vidyasirimedhi Institute of Science and Technology (VISTEC), Wangchan valley, Rayong 21210 Thailand.
| |
Collapse
|
5
|
Huang L, You L, Aziz N, Yu SH, Lee JS, Choung ES, Luong VD, Jeon MJ, Hur M, Lee S, Lee BH, Kim HG, Cho JY. Antiphotoaging and Skin-Protective Activities of Ardisia silvestris Ethanol Extract in Human Keratinocytes. PLANTS (BASEL, SWITZERLAND) 2023; 12:1167. [PMID: 36904025 PMCID: PMC10007040 DOI: 10.3390/plants12051167] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 01/20/2023] [Revised: 03/01/2023] [Accepted: 03/01/2023] [Indexed: 06/18/2023]
Abstract
Ardisia silvestris is a traditional medicinal herb used in Vietnam and several other countries. However, the skin-protective properties of A. silvestris ethanol extract (As-EE) have not been evaluated. Human keratinocytes form the outermost barrier of the skin and are the main target of ultraviolet (UV) radiation. UV exposure causes skin photoaging via the production of reactive oxygen species. Protection from photoaging is thus a key component of dermatological and cosmetic products. In this research, we found that As-EE can prevent UV-induced skin aging and cell death as well as enhance the barrier effect of the skin. First, the radical-scavenging ability of As-EE was checked using DPPH, ABTS, TPC, CUPRAC, and FRAP assays, and a 3-(4-5-dimethylthiazol-2-yl)-2-5-diphenyltetrazolium bromide assay was used to examine cytotoxicity. Reporter gene assays were used to determine the doses that affect skin-barrier-related genes. A luciferase assay was used to identify possible transcription factors. The anti-photoaging mechanism of As-EE was investigated by determining correlated signaling pathways using immunoblotting analyses. As-EE had no harmful effects on HaCaT cells, according to our findings, and As-EE revealed moderate radical-scavenging ability. With high-performance liquid chromatography (HPLC) analysis, rutin was found to be one of the major components. In addition, As-EE enhanced the expression levels of hyaluronic acid synthase-1 and occludin in HaCaT cells. Moreover, As-EE dose-dependently up-regulated the production of occludin and transglutaminase-1 after suppression caused by UVB blocking the activator protein-1 signaling pathway, in particular, the extracellular response kinase and c-Jun N-terminal kinase. Our findings suggest that As-EE may have anti-photoaging effects by regulating mitogen-activated protein kinase, which is good news for the cosmetics and dermatology sectors.
Collapse
Affiliation(s)
- Lei Huang
- Department of Biocosmetics, Sungkyunkwan University, Suwon 16419, Republic of Korea
| | - Long You
- Department of Integrative Biotechnology, Sungkyunkwan University, Suwon 16419, Republic of Korea
| | - Nur Aziz
- Pharmacy Program, Faculty of Science and Technology, Ma Chung University, Malang 65151, Indonesia
| | - Seung Hui Yu
- DanjoungBio, Co., Ltd., Wonju 26303, Republic of Korea
| | - Jong Sub Lee
- DanjoungBio, Co., Ltd., Wonju 26303, Republic of Korea
| | - Eui Su Choung
- DanjoungBio, Co., Ltd., Wonju 26303, Republic of Korea
| | - Van Dung Luong
- Department of Biology, Dalat University, 01 Phu Dong Thien Vuong, Dalat 66106, Vietnam
| | - Mi-Jeong Jeon
- National Institute of Biological Resources, Environmental Research Complex, Incheon 222689, Republic of Korea
| | - Moonsuk Hur
- National Institute of Biological Resources, Environmental Research Complex, Incheon 222689, Republic of Korea
| | - Sarah Lee
- National Institute of Biological Resources, Environmental Research Complex, Incheon 222689, Republic of Korea
| | - Byoung-Hee Lee
- National Institute of Biological Resources, Environmental Research Complex, Incheon 222689, Republic of Korea
| | - Han Gyung Kim
- Department of Integrative Biotechnology, Sungkyunkwan University, Suwon 16419, Republic of Korea
- Research Institute of Biomolecule Control and Biomedical Institute for Convergence at SKKU (BICS), Sungkyunkwan University, Suwon 16419, Republic of Korea
| | - Jae Youl Cho
- Department of Biocosmetics, Sungkyunkwan University, Suwon 16419, Republic of Korea
- Department of Integrative Biotechnology, Sungkyunkwan University, Suwon 16419, Republic of Korea
- Research Institute of Biomolecule Control and Biomedical Institute for Convergence at SKKU (BICS), Sungkyunkwan University, Suwon 16419, Republic of Korea
| |
Collapse
|
6
|
Kanungo B, Rufus ND, Gavini V. Efficient All-Electron Time-Dependent Density Functional Theory Calculations Using an Enriched Finite Element Basis. J Chem Theory Comput 2023; 19:978-991. [PMID: 36656153 DOI: 10.1021/acs.jctc.2c01052] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023]
Abstract
We present an efficient and systematically convergent approach to all-electron real-time time-dependent density functional theory (TDDFT) calculations using a mixed basis, termed as enriched finite element (EFE) basis. The EFE basis augments the classical finite element basis (CFE) with a compactly supported numerical atom-centered basis, obtained from atomic ground-state DFT calculations. Particularly, we orthogonalize the enrichment functions with respect to the classical finite element basis to ensure good conditioning of the resultant basis. We employ the second-order Magnus propagator in conjunction with an adaptive Krylov subspace method for efficient time evolution of the Kohn-Sham orbitals. We rely on a priori error estimates to guide our choice of an adaptive finite element mesh as well as the time step to be used in the TDDFT calculations. We observe close to optimal rates of convergence of the dipole moment with respect to spatial and temporal discretizations. Notably, we attain a 50-100 times speedup for the EFE basis over the CFE basis. We also demonstrate the efficacy of the EFE basis for both linear and nonlinear responses by studying the absorption spectra in sodium clusters, the linear to nonlinear response transition in the green fluorescence protein chromophore, and the higher harmonic generation in the magnesium dimer. Lastly, we attain good parallel scalability of our numerical implementation of the EFE basis for up to ∼1000 processors, using a benchmark system of a 50-atom sodium nanocluster.
Collapse
Affiliation(s)
- Bikash Kanungo
- Department of Mechanical Engineering, University of Michigan, Ann Arbor, Michigan48109, United States
| | - Nelson D Rufus
- Department of Mechanical Engineering, University of Michigan, Ann Arbor, Michigan48109, United States
| | - Vikram Gavini
- Department of Mechanical Engineering, University of Michigan, Ann Arbor, Michigan48109, United States.,Department of Materials Science and Engineering, University of Michigan, Ann Arbor, Michigan48109, United States
| |
Collapse
|
7
|
Comparison of Bioluminescent Substrates in Natural Infection Models of Neglected Parasitic Diseases. Int J Mol Sci 2022; 23:ijms232416074. [PMID: 36555716 PMCID: PMC9781651 DOI: 10.3390/ijms232416074] [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: 11/17/2022] [Revised: 12/08/2022] [Accepted: 12/09/2022] [Indexed: 12/23/2022] Open
Abstract
The application of in vivo bioluminescent imaging in infectious disease research has significantly increased over the past years. The detection of transgenic parasites expressing wildtype firefly luciferase is however hampered by a relatively low and heterogeneous tissue penetrating capacity of emitted light. Solutions are sought by using codon-optimized red-shifted luciferases that yield higher expression levels and produce relatively more red or near-infrared light, or by using modified bioluminescent substrates with enhanced cell permeability and improved luminogenic or pharmacokinetic properties. In this study, the in vitro and in vivo efficacy of two modified bioluminescent substrates, CycLuc1 and AkaLumine-HCl, were compared with that of D-luciferin as a gold standard. Comparisons were made in experimental and insect-transmitted animal models of leishmaniasis (caused by intracellular Leishmania species) and African trypanosomiasis (caused by extracellular Trypanosoma species), using parasite strains expressing the red-shifted firefly luciferase PpyRE9. Although the luminogenic properties of AkaLumine-HCl and D-luciferin for in vitro parasite detection were comparable at equal substrate concentrations, AkaLumine-HCl proved to be unsuitable for in vivo infection follow-up due to high background signals in the liver. CycLuc1 presented a higher in vitro luminescence compared to the other substrates and proved to be highly efficacious in vivo, even at a 20-fold lower dose than D-luciferin. This efficacy was consistent across infections with the herein included intracellular and extracellular parasitic organisms. It can be concluded that CycLuc1 is an excellent and broadly applicable alternative for D-luciferin, requiring significantly lower doses for in vivo bioluminescent imaging in rodent models of leishmaniasis and African trypanosomiasis.
Collapse
|
8
|
Zhang L. Machine learning for enumeration of cell colony forming units. Vis Comput Ind Biomed Art 2022; 5:26. [PMID: 36334176 PMCID: PMC9637067 DOI: 10.1186/s42492-022-00122-3] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2022] [Accepted: 10/08/2022] [Indexed: 11/08/2022] Open
Abstract
As one of the most widely used assays in biological research, an enumeration of the bacterial cell colonies is an important but time-consuming and labor-intensive process. To speed up the colony counting, a machine learning method is presented for counting the colony forming units (CFUs), which is referred to as CFUCounter. This cell-counting program processes digital images and segments bacterial colonies. The algorithm combines unsupervised machine learning, iterative adaptive thresholding, and local-minima-based watershed segmentation to enable an accurate and robust cell counting. Compared to a manual counting method, CFUCounter supports color-based CFU classification, allows plates containing heterologous colonies to be counted individually, and demonstrates overall performance (slope 0.996, SD 0.013, 95%CI: 0.97–1.02, p value < 1e-11, r = 0.999) indistinguishable from the gold standard of point-and-click counting. This CFUCounter application is open-source and easy to use as a unique addition to the arsenal of colony-counting tools.
Collapse
Affiliation(s)
- Louis Zhang
- grid.89336.370000 0004 1936 9924Department of Molecular Biosciences, College of Natural Sciences, University of Texas at Austin, Austin, TX 78713-8058 USA
| |
Collapse
|
9
|
Vidal G, Vitalis C, Muñoz Silva M, Castillo-Passi C, Yáñez Feliú G, Federici F, Rudge TJ. Accurate characterization of dynamic microbial gene expression and growth rate profiles. Synth Biol (Oxf) 2022; 7:ysac020. [PMID: 36267953 PMCID: PMC9569155 DOI: 10.1093/synbio/ysac020] [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: 12/09/2021] [Revised: 07/16/2022] [Accepted: 09/29/2022] [Indexed: 11/16/2022] Open
Abstract
Genetic circuits are subject to variability due to cellular and compositional contexts. Cells face changing internal states and environments, the cellular context, to which they sense and respond by changing their gene expression and growth rates. Furthermore, each gene in a genetic circuit operates in a compositional context of genes which may interact with each other and the host cell in complex ways. The context of genetic circuits can, therefore, change gene expression and growth rates, and measuring their dynamics is essential to understanding natural and synthetic regulatory networks that give rise to functional phenotypes. However, reconstruction of microbial gene expression and growth rate profiles from typical noisy measurements of cell populations is difficult due to the effects of noise at low cell densities among other factors. We present here a method for the estimation of dynamic microbial gene expression rates and growth rates from noisy measurement data. Compared to the current state-of-the-art, our method significantly reduced the mean squared error of reconstructions from simulated data of growth and gene expression rates, improving the estimation of timing and magnitude of relevant shapes of profiles. We applied our method to characterize a triple-reporter plasmid library combining multiple transcription units in different compositional and cellular contexts in Escherichia coli. Our analysis reveals cellular and compositional context effects on microbial growth and gene expression rate dynamics and suggests a method for the dynamic ratiometric characterization of constitutive promoters relative to an in vivo reference.
Collapse
Affiliation(s)
- Gonzalo Vidal
- Institute for Biological and Medical Engineering, Schools of Engineering, Biology and Medicine, Pontificia Universidad Católica de Chile, Santiago, Chile
- Interdisciplinary Computing and Complex BioSystems (ICOS) Research Group, School of Computing, Newcastle University, Newcastle Upon Tyne, UK
| | - Carolus Vitalis
- Institute for Biological and Medical Engineering, Schools of Engineering, Biology and Medicine, Pontificia Universidad Católica de Chile, Santiago, Chile
| | - Macarena Muñoz Silva
- Institute for Biological and Medical Engineering, Schools of Engineering, Biology and Medicine, Pontificia Universidad Católica de Chile, Santiago, Chile
| | - Carlos Castillo-Passi
- Institute for Biological and Medical Engineering, Schools of Engineering, Biology and Medicine, Pontificia Universidad Católica de Chile, Santiago, Chile
- School of Biomedical Engineering and Imaging Sciences, King’s College London, St Thomas’ Hospital, London, UK
- Millennium Institute for Intelligent Healthcare Engineering (iHEALTH), Santiago, Chile
| | - Guillermo Yáñez Feliú
- Interdisciplinary Computing and Complex BioSystems (ICOS) Research Group, School of Computing, Newcastle University, Newcastle Upon Tyne, UK
- Department of Chemical and Bioprocess Engineering, School of Engineering, Pontificia Universidad Católica de Chile, Santiago, Chile
| | - Fernán Federici
- Institute for Biological and Medical Engineering, Schools of Engineering, Biology and Medicine, Pontificia Universidad Católica de Chile, Santiago, Chile
- ANID – Millennium Science Initiative Program, Millennium Institute for Integrative Biology (iBio) & FONDAP Center for Genome Regulation, Santiago, Chile
| | - Timothy J Rudge
- Interdisciplinary Computing and Complex BioSystems (ICOS) Research Group, School of Computing, Newcastle University, Newcastle Upon Tyne, UK
| |
Collapse
|
10
|
Emerging biotechnology applications in natural product and synthetic pharmaceutical analyses. Acta Pharm Sin B 2022; 12:4075-4097. [DOI: 10.1016/j.apsb.2022.08.025] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2022] [Revised: 08/02/2022] [Accepted: 08/22/2022] [Indexed: 11/15/2022] Open
|
11
|
Li Y, Qin Z, Zhang F, Yang ST. Two-color fluorescent proteins reporting survivin regulation in breast cancer cells for high throughput drug screening. Biotechnol Bioeng 2021; 119:1004-1017. [PMID: 34914099 DOI: 10.1002/bit.28006] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2021] [Revised: 11/25/2021] [Accepted: 12/09/2021] [Indexed: 02/06/2023]
Abstract
Reporter gene assay is widely used for high throughput drug screening and drug action mechanism evaluation. In this study, we developed a robust dual-fluorescent reporter assay to detect drugs repressing the transcription of survivin, a cancer biomarker from the inhibitor of apoptosis family, in breast cancer cells cultured in three-dimensional (3D) microbioreactors. Survivin is overexpressed in numerous malignancies but almost silent in normal tissue cells and is considered a lead target for cancer therapy. Breast cancer MCF-7 cells were engineered to express enhanced green fluorescent protein driven by a survivin promoter and red fluorescent protein driven by a cytomegalovirus promoter as internal control to detect changes in survivin expression in cells as affected by drugs. This 3D dual-fluorescent reporter assay was validated with YM155 and doxorubicin, which were known to downregulate survivin in cancer cells, and further evaluated with two widely used anticancer compounds, cisplatin, and epigallocatechin gallate, to evaluate their effects on survivin expression. The results showed that the 3D dual-fluorescent reporter assay was robust for high throughput screening of drugs targeting survivin in breast cancer cells.
Collapse
Affiliation(s)
- You Li
- William G. Lowrie Department of Chemical and Biomolecular Engineering, The Ohio State University, Columbus, Ohio, USA
| | - Zhen Qin
- William G. Lowrie Department of Chemical and Biomolecular Engineering, The Ohio State University, Columbus, Ohio, USA
| | - Fengli Zhang
- William G. Lowrie Department of Chemical and Biomolecular Engineering, The Ohio State University, Columbus, Ohio, USA
| | - Shang-Tian Yang
- William G. Lowrie Department of Chemical and Biomolecular Engineering, The Ohio State University, Columbus, Ohio, USA
| |
Collapse
|
12
|
Jung H, Inaba Y, Banta S. Genetic engineering of the acidophilic chemolithoautotroph Acidithiobacillus ferrooxidans. Trends Biotechnol 2021; 40:677-692. [PMID: 34794837 DOI: 10.1016/j.tibtech.2021.10.004] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2021] [Revised: 10/05/2021] [Accepted: 10/06/2021] [Indexed: 12/21/2022]
Abstract
There are several natural and anthropomorphic environments where iron- and/or sulfur-oxidizing bacteria thrive in extremely acidic conditions. These acidophilic chemolithautotrophs play important roles in biogeochemical iron and sulfur cycles, are critical catalysts for industrial metal bioleaching operations, and have underexplored potential in future biotechnological applications. However, their unique growth conditions complicate the development of genetic techniques. Over the past few decades genetic tools have been successfully developed for Acidithiobacillus ferrooxidans, which serves as a model organism that exhibits both iron- and sulfur-oxidizing capabilities. Conjugal transfer of plasmids has enabled gene overexpression, gene knockouts, and some preliminary metabolic engineering. We highlight the development of genetic systems and recent genetic engineering of A. ferrooxidans, and discuss future perspectives.
Collapse
Affiliation(s)
- Heejung Jung
- Department of Chemical Engineering, Columbia University, 500 West 120th Street, New York, NY 10027, USA
| | - Yuta Inaba
- Department of Chemical Engineering, Columbia University, 500 West 120th Street, New York, NY 10027, USA
| | - Scott Banta
- Department of Chemical Engineering, Columbia University, 500 West 120th Street, New York, NY 10027, USA.
| |
Collapse
|
13
|
Abstract
Magnetosomes are complex membrane organelles synthesized by magnetotactic bacteria (MTB) for navigation in the Earth’s magnetic field. In the alphaproteobacterium Magnetospirillum gryphiswaldense, all steps of magnetosome formation are tightly controlled by >30 specific genes arranged in several gene clusters. However, the transcriptional organization of the magnetosome gene clusters has remained poorly understood. Here, by applying Cappable-seq and whole-transcriptome shotgun RNA sequencing, we show that mamGFDCop and feoAB1op are transcribed as single transcriptional units, whereas multiple transcription start sites (TSS) are present in mms6op, mamXYop, and the long (>16 kb) mamABop. Using a bioluminescence reporter assay and promoter knockouts, we demonstrate that most of the identified TSS originate from biologically meaningful promoters which mediate production of multiple transcripts and are functionally relevant for proper magnetosome biosynthesis. In addition, we identified a strong promoter in a large intergenic region within mamXYop, which likely drives transcription of a noncoding RNA important for gene expression in this operon. In summary, our data suggest a more complex transcriptional architecture of the magnetosome operons than previously recognized, which is largely conserved in other magnetotactic Magnetospirillum species and, thus, is likely fundamental for magnetosome biosynthesis in these organisms. IMPORTANCE Magnetosomes have emerged as a model system to study prokaryotic organelles and a source of biocompatible magnetic nanoparticles for various biomedical applications. However, the lack of knowledge about the transcriptional organization of magnetosome gene clusters has severely impeded the engineering, manipulation, and transfer of this highly complex biosynthetic pathway into other organisms. Here, we provide a high-resolution image of the previously unappreciated transcriptional landscape of the magnetosome operons. Our findings are important for further unraveling the complex genetic framework of magnetosome biosynthesis. In addition, they will facilitate the rational reengineering of magnetic bacteria for improved bioproduction of tunable magnetic nanoparticles, as well as transplantation of magnetosome biosynthesis into foreign hosts by synthetic biology approaches. Overall, our study exemplifies how a genetically complex pathway is orchestrated at the transcriptional level to ensure the balanced expression of the numerous constituents required for the proper assembly of one of the most intricate prokaryotic organelles.
Collapse
|
14
|
Engineering digitizer circuits for chemical and genetic screens in human cells. Nat Commun 2021; 12:6150. [PMID: 34686672 PMCID: PMC8536748 DOI: 10.1038/s41467-021-26359-9] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2021] [Accepted: 09/30/2021] [Indexed: 12/26/2022] Open
Abstract
Cell-based transcriptional reporters are invaluable in high-throughput compound and CRISPR screens for identifying compounds or genes that can impact a pathway of interest. However, many transcriptional reporters have weak activities and transient responses. This can result in overlooking therapeutic targets and compounds that are difficult to detect, necessitating the resource-consuming process of running multiple screens at various timepoints. Here, we present RADAR, a digitizer circuit for amplifying reporter activity and retaining memory of pathway activation. Reporting on the AP-1 pathway, our circuit identifies compounds with known activity against PKC-related pathways and shows an enhanced dynamic range with improved sensitivity compared to a classical reporter in compound screens. In the first genome-wide pooled CRISPR screen for the AP-1 pathway, RADAR identifies canonical genes from the MAPK and PKC pathways, as well as non-canonical regulators. Thus, our scalable system highlights the benefit and versatility of using genetic circuits in large-scale cell-based screening.
Collapse
|
15
|
Sheng T, Ho SWT, Ooi WF, Xu C, Xing M, Padmanabhan N, Huang KK, Ma L, Ray M, Guo YA, Sim NL, Anene-Nzelu CG, Chang MM, Razavi-Mohseni M, Beer MA, Foo RSY, Sundar R, Chan YH, Tan ALK, Ong X, Skanderup AJ, White KP, Jha S, Tan P. Integrative epigenomic and high-throughput functional enhancer profiling reveals determinants of enhancer heterogeneity in gastric cancer. Genome Med 2021; 13:158. [PMID: 34635154 PMCID: PMC8504099 DOI: 10.1186/s13073-021-00970-3] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2021] [Accepted: 09/15/2021] [Indexed: 12/21/2022] Open
Abstract
BACKGROUND Enhancers are distal cis-regulatory elements required for cell-specific gene expression and cell fate determination. In cancer, enhancer variation has been proposed as a major cause of inter-patient heterogeneity-however, most predicted enhancer regions remain to be functionally tested. METHODS We analyzed 132 epigenomic histone modification profiles of 18 primary gastric cancer (GC) samples, 18 normal gastric tissues, and 28 GC cell lines using Nano-ChIP-seq technology. We applied Capture-based Self-Transcribing Active Regulatory Region sequencing (CapSTARR-seq) to assess functional enhancer activity. An Activity-by-contact (ABC) model was employed to explore the effects of histone acetylation and CapSTARR-seq levels on enhancer-promoter interactions. RESULTS We report a comprehensive catalog of 75,730 recurrent predicted enhancers, the majority of which are GC-associated in vivo (> 50,000) and associated with lower somatic mutation rates inferred by whole-genome sequencing. Applying CapSTARR-seq to the enhancer catalog, we observed significant correlations between CapSTARR-seq functional activity and H3K27ac/H3K4me1 levels. Super-enhancer regions exhibited increased CapSTARR-seq signals compared to regular enhancers, even when decoupled from native chromatin contexture. We show that combining histone modification and CapSTARR-seq functional enhancer data improves the prediction of enhancer-promoter interactions and pinpointing of germline single nucleotide polymorphisms (SNPs), somatic copy number alterations (SCNAs), and trans-acting TFs involved in GC expression. We identified cancer-relevant genes (ING1, ARL4C) whose expression between patients is influenced by enhancer differences in genomic copy number and germline SNPs, and HNF4α as a master trans-acting factor associated with GC enhancer heterogeneity. CONCLUSIONS Our results indicate that combining histone modification and functional assay data may provide a more accurate metric to assess enhancer activity than either platform individually, providing insights into the relative contribution of genetic (cis) and regulatory (trans) mechanisms to GC enhancer functional heterogeneity.
Collapse
Affiliation(s)
- Taotao Sheng
- Department of Biochemistry, National University of Singapore, Singapore, 117596, Singapore
- Cancer and Stem Cell Biology Program, Duke-NUS Medical School, Singapore, 169857, Singapore
| | - Shamaine Wei Ting Ho
- Cancer and Stem Cell Biology Program, Duke-NUS Medical School, Singapore, 169857, Singapore
- Cancer Science Institute of Singapore, National University of Singapore, Singapore, 117599, Singapore
| | - Wen Fong Ooi
- Epigenetic and Epitranscriptomic Regulation, Genome Institute of Singapore, Singapore, 138672, Singapore
| | - Chang Xu
- Cancer and Stem Cell Biology Program, Duke-NUS Medical School, Singapore, 169857, Singapore
- Cancer Science Institute of Singapore, National University of Singapore, Singapore, 117599, Singapore
| | - Manjie Xing
- Cancer and Stem Cell Biology Program, Duke-NUS Medical School, Singapore, 169857, Singapore
- Epigenetic and Epitranscriptomic Regulation, Genome Institute of Singapore, Singapore, 138672, Singapore
| | - Nisha Padmanabhan
- Cancer and Stem Cell Biology Program, Duke-NUS Medical School, Singapore, 169857, Singapore
| | - Kie Kyon Huang
- Cancer and Stem Cell Biology Program, Duke-NUS Medical School, Singapore, 169857, Singapore
| | - Lijia Ma
- The Institute for Genomics and Systems Biology, The University of Chicago, Chicago, Illinois, USA
| | - Mohana Ray
- The Institute for Genomics and Systems Biology, The University of Chicago, Chicago, Illinois, USA
| | - Yu Amanda Guo
- Precision Medicine and Population Genomics (Somatic), Genome Institute of Singapore, Singapore, 138672, Singapore
| | - Ngak Leng Sim
- Precision Medicine and Population Genomics (Somatic), Genome Institute of Singapore, Singapore, 138672, Singapore
| | - Chukwuemeka George Anene-Nzelu
- Cardiovascular Research Institute, National University Health System, Singapore, 119074, Singapore
- Precision Medicine and Population Genomics (Germline), Genome Institute of Singapore, Singapore, Singapore
- Montreal Heart Institute, Montreal, Canada
- Department of Medicine, University of Montreal, Montreal, Canada
| | - Mei Mei Chang
- Precision Medicine and Population Genomics (Somatic), Genome Institute of Singapore, Singapore, 138672, Singapore
| | - Milad Razavi-Mohseni
- Department of Biomedical Engineering and McKusick-Nathans Department of Genetic Medicine, Johns Hopkins University, Baltimore, USA
| | - Michael A Beer
- Department of Biomedical Engineering and McKusick-Nathans Department of Genetic Medicine, Johns Hopkins University, Baltimore, USA
| | - Roger Sik Yin Foo
- Cardiovascular Research Institute, National University Health System, Singapore, 119074, Singapore
- Precision Medicine and Population Genomics (Germline), Genome Institute of Singapore, Singapore, Singapore
| | - Raghav Sundar
- Cancer and Stem Cell Biology Program, Duke-NUS Medical School, Singapore, 169857, Singapore
- Department of Haematology-Oncology, National University Cancer Institute Singapore, National University Hospital, Singapore, 119074, Singapore
| | - Yiong Huak Chan
- Biostatistics Unit, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, 119228, Singapore
| | - Angie Lay Keng Tan
- Cancer and Stem Cell Biology Program, Duke-NUS Medical School, Singapore, 169857, Singapore
| | - Xuewen Ong
- Cancer and Stem Cell Biology Program, Duke-NUS Medical School, Singapore, 169857, Singapore
| | - Anders Jacobsen Skanderup
- Precision Medicine and Population Genomics (Somatic), Genome Institute of Singapore, Singapore, 138672, Singapore
| | - Kevin P White
- The Institute for Genomics and Systems Biology, The University of Chicago, Chicago, Illinois, USA.
- Tempus Labs, Chicago, USA.
| | - Sudhakar Jha
- Department of Biochemistry, National University of Singapore, Singapore, 117596, Singapore.
- Cancer Science Institute of Singapore, National University of Singapore, Singapore, 117599, Singapore.
- NUS Center for Cancer Research, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, 117599, Singapore.
- Department of Physiological Sciences, College of Veterinary Medicine, Oklahoma State University, Stillwater, OK, USA.
| | - Patrick Tan
- Cancer and Stem Cell Biology Program, Duke-NUS Medical School, Singapore, 169857, Singapore.
- Cancer Science Institute of Singapore, National University of Singapore, Singapore, 117599, Singapore.
- Epigenetic and Epitranscriptomic Regulation, Genome Institute of Singapore, Singapore, 138672, Singapore.
- SingHealth/Duke-NUS Institute of Precision Medicine, National Heart Centre Singapore, Singapore, 168752, Singapore.
- Department of Physiology, National University of Singapore, Singapore, 117593, Singapore.
- Singapore Gastric Cancer Consortium, Singapore, 119228, Singapore.
| |
Collapse
|
16
|
Davies-Bolorunduro O, Osuolale O, Saibu S, Adeleye I, Aminah N. Bioprospecting marine actinomycetes for antileishmanial drugs: current perspectives and future prospects. Heliyon 2021; 7:e07710. [PMID: 34409179 PMCID: PMC8361068 DOI: 10.1016/j.heliyon.2021.e07710] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2021] [Revised: 07/25/2021] [Accepted: 07/30/2021] [Indexed: 01/01/2023] Open
Abstract
Revived analysis interests in natural products in the hope of discovering new and novel antileishmanial drug leads have been driven partially by the increasing incidence of drug resistance. However, the search for novel chemotherapeutics to combat drug resistance had previously concentrated on the terrestrial environment. As a result, the marine environment was often overlooked. For example, actinomycetes are an immensely important group of bacteria for antibiotic production, producing two-thirds of the known antibiotics. However, these bacteria have been isolated primarily from terrestrial sources. Consequently, there have been revived efforts to discover new compounds from uncharted or uncommon environments like the marine ecosystem. Isolation, purification and structure elucidation of target compounds from complex metabolic extract are major challenges in natural products chemistry. As a result, marine-derived natural products from actinomycetes that have antileishmanial bioactivity potentials have been understudied. This review highlights metagenomic and bioassay approaches which could help streamline the drug discovery process thereby greatly reducing time and cost of dereplication to identify suitable antileishmanial drug candidates.
Collapse
Affiliation(s)
- O.F. Davies-Bolorunduro
- Microbiology Department, Nigerian Institute of Medical Research, Lagos, Nigeria
- Postdoc Fellow Department of Chemistry, Faculty of Science and Technology, Universitas Airlangga, Komplek Kampus C, Jl. Mulyorejo, Surabaya, 60115, Indonesia
| | - O. Osuolale
- Applied Environmental Metagenomics and Infectious Diseases Research Group (AEMIDR), Department of Biological Sciences, Elizade University, Ilara Mokin, Nigeria
| | - S. Saibu
- Department of Microbiology, University of Lagos, Akoka, Lagos, Nigeria
| | - I.A. Adeleye
- Department of Microbiology, University of Lagos, Akoka, Lagos, Nigeria
| | - N.S. Aminah
- Department of Chemistry, Faculty of Science and Technology, Universitas Airlangga, Komplek Kampus C UNAIR, Jl. Mulyorejo, Surabaya, 60115, Indonesia
- Biotechnology of Tropical Medicinal Plants Research Group, Universitas Airlangga, Indonesia
| |
Collapse
|
17
|
Hassan RM, Aboutabl ME, Bozzi M, El-Behairy MF, El Kerdawy AM, Sampaolese B, Desiderio C, Vincenzoni F, Sciandra F, Ghannam IAY. Discovery of 4-benzyloxy and 4-(2-phenylethoxy) chalcone fibrate hybrids as novel PPARα agonists with anti-hyperlipidemic and antioxidant activities: Design, synthesis and in vitro/in vivo biological evaluation. Bioorg Chem 2021; 115:105170. [PMID: 34332233 DOI: 10.1016/j.bioorg.2021.105170] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2021] [Revised: 07/07/2021] [Accepted: 07/09/2021] [Indexed: 10/20/2022]
Abstract
In the current work, a series of novel 4-benzyloxy and 4-(2-phenylethoxy) chalcone fibrate hybrids (10a-o) and (11a-e) were synthesized and evaluated as new PPARα agonists in order to find new agents with higher activity and fewer side effects. The 2-propanoic acid derivative 10a and the 2-butanoic acid congener 10i showed the best overall PPARα agonistic activity showing Emax% values of 50.80 and 90.55%, respectively, and EC50 values of 8.9 and 25.0 μM, respectively, compared to fenofibric acid with Emax = 100% and EC50 = 23.22 μM, respectively. These two compounds also stimulated carnitine palmitoyltransferase 1A gene transcription in HepG2 cells and PPARα protein expression. Molecular docking simulations were performed for the newly synthesized compounds to study their predicted binding pattern and energies in PPARα active site to rationalize their promising activity. In vivo, compounds 10a and 10i elicited a significant hypolipidemic activity improving the lipid profile in triton WR-1339-induced hyperlipidemic rats, including serum triglycerides, total cholesterol, LDL, HDL and VLDL levels. Compound 10i possessed better anti-hyperlipidemic activity than 10a. At a dose of 200 mg/kg, it demonstrated significantly lower TC, TG, LDL and VLDL levels than that of fenofibrate at the same dose with similar HDL levels. Compounds 10i and 10a possessed atherogenic indices (CRR, AC, AI, CRI-II) like that of fenofibrate. Additionally, a promising antioxidant activity indicated by the increased tissue reduced glutathione and plasma total antioxidant capacity with decreased plasma malondialdehyde levels was demonstrated by compounds 10a and 10i. No histopathological alterations were recorded in the hepatic tissue of compound 10i (200 mg/kg).
Collapse
Affiliation(s)
- Rasha M Hassan
- Medicinal and Pharmaceutical Chemistry Department, Pharmaceutical and Drug Industries Research Division, National Research Centre (ID: 60014618), P.O. 12622, Dokki, Giza, Egypt
| | - Mona E Aboutabl
- Medicinal and Pharmaceutical Chemistry Department (Pharmacology Group), Pharmaceutical and Drug Industries Research Division, National Research Centre (ID: 60014618), 33 El Bohouth St., P.O. 12622, Dokki, Giza, Egypt
| | - Manuela Bozzi
- Dipartimento Universitario di Scienze Biotecnologiche di Base, Cliniche Intensivologiche e Perioperatorie, Sezione di Biochimica e Biochimica Clinica, Università Cattolica del Sacro Cuore di Roma, Largo F. Vito 1, 00168 Roma, Italy; Istituto di Scienze e Tecnologie Chimiche "Giulio Natta"- SCITEC (CNR) Sede di Roma, Largo F. Vito 1, 00168 Roma, Italy.
| | - Mohammed F El-Behairy
- Department of Organic and Medicinal Chemistry, Faculty of Pharmacy, University of Sadat City, Sadat City 32897, Egypt
| | - Ahmed M El Kerdawy
- Department of Pharmaceutical Chemistry, Faculty of Pharmacy, Cairo University, Cairo 11562, Egypt; Department of Pharmaceutical Chemistry, School of Pharmacy, New Giza University, Newgiza, km 22 Cairo-Alexandria Desert Road, Cairo, Egypt
| | - Beatrice Sampaolese
- Istituto di Scienze e Tecnologie Chimiche "Giulio Natta"- SCITEC (CNR) Sede di Roma, Largo F. Vito 1, 00168 Roma, Italy
| | - Claudia Desiderio
- Istituto di Scienze e Tecnologie Chimiche "Giulio Natta"- SCITEC (CNR) Sede di Roma, Largo F. Vito 1, 00168 Roma, Italy
| | - Federica Vincenzoni
- Dipartimento Universitario di Scienze Biotecnologiche di Base, Cliniche Intensivologiche e Perioperatorie, Sezione di Biochimica e Biochimica Clinica, Università Cattolica del Sacro Cuore di Roma, Largo F. Vito 1, 00168 Roma, Italy; Fondazione Policlinico Universitario "A. Gemelli", IRCCS, Largo A. Gemelli 8, 00168 Roma, Italy
| | - Francesca Sciandra
- Istituto di Scienze e Tecnologie Chimiche "Giulio Natta"- SCITEC (CNR) Sede di Roma, Largo F. Vito 1, 00168 Roma, Italy.
| | - Iman A Y Ghannam
- Chemistry of Natural and Microbial Products Department, Pharmaceutical and Drug Industries Research Division, National Research Centre, Dokki, Cairo 12622, Egypt.
| |
Collapse
|
18
|
Nath A, Kumer A, Zaben F, Khan MW. Investigating the binding affinity, molecular dynamics, and ADMET properties of 2,3-dihydrobenzofuran derivatives as an inhibitor of fungi, bacteria, and virus protein. BENI-SUEF UNIVERSITY JOURNAL OF BASIC AND APPLIED SCIENCES 2021. [DOI: 10.1186/s43088-021-00117-8] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
Abstract
Background
2,3-Dihydrobenzofurans (DHB) have proposed as advantages structures, and used as chemical entresol to design small compound libraries. The present study illustrates to explore 2,3-dihydrobenzofurans(DHB) in comparison to selected some derivatives drugs by using molecular docking and molecular dynamics, as well as ADMET studies. The online database “Molinspiration online server” was used to detect the physicochemical pharmacokinetics and drug likeness score of DHB drugs. For estimation of molecular docking, six pathogens, such as Aspergillus niger (PDB id: 1kum), Candida albicans (3dra), Escherichia coli (6og7), Salmonella typhi (4k6l), Influenza (1ru7), and Hepatitis C (4tyd), were chosen due to close biological studies.
Results
From Molinspiration online server has showed that DHB did not violate the “Lipinski five rule” as drugs, leading compound for molecular docking exhibited the potential interaction to the active residue. The binding affinity of DHB2 (−7.00 kcal/mol) against 3dra was higher than DHB8 (−6.40 kcal/mol) and DHB (5.70 kcal/mol) for compounds. The results of molecular docking show that the compounds mentioned in this study are not equally effective against pathogens, such as fungi, viruses, and bacteria. However, DHB2, DHB3, and DHB 8 compounds can work against almost given pathogens which results are derived from auto dock vina in terms of binding affinity around 6.00 kcal/mol, and Fire Dock has values from about 38.0 to 42.0 kcal/mol. To explore the dynamic nature of the interaction, 50 ns molecular dynamics (MD) simulation was performed on the selected protein-DHB complexes. Thus, DHB 8 has greater potential to interact for further for fungi.
Conclusion
Finding from this study can play an effective role as a drug in any biological system. This study as well recommends to researchers to synthesize these DHBs for evaluation of its biological activity.
Graphical abstract
Collapse
|
19
|
Zhou B, Takahashi S, Takemura T, Tanaka K, Imamura S. Establishment of a firefly luciferase reporter assay system in the unicellular red alga Cyanidioschyzon merolae. J GEN APPL MICROBIOL 2021; 67:42-46. [PMID: 32938840 DOI: 10.2323/jgam.2020.02.003] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
Abstract
The firefly luciferase (Luc) reporter assay is a powerful tool used to analyze promoter activities in living cells. In this report, we established a firefly Luc reporter assay system in the unicellular model red alga Cyanidioschyzon merolae. A nitrite reductase (NIR) promoter-Luc fusion gene was integrated into the URA5.3 genomic region to construct the C. merolae NIR-Luc strain. Luc activities in the NIR-Luc strain were increased, correlating with the accumulation of endogenous NIR transcripts in response to nitrogen depletion. Luc activity was also significantly increased by the overexpression of the MYB1 gene, which encodes a transcription factor responsible for NIR promoter activation. Thus, our results demonstrate the utility of the Luc reporter system in C. merolae.
Collapse
Affiliation(s)
- Baifeng Zhou
- Laboratory for Chemistry and Life Science, Institute of Innovative Research, Tokyo Institute of Technology.,School of Life Science and Technology, Tokyo Institute of Technology
| | - Sota Takahashi
- Laboratory for Chemistry and Life Science, Institute of Innovative Research, Tokyo Institute of Technology.,Interdisciplinary Graduate School of Science and Engineering, Tokyo Institute of Technology
| | - Tokiaki Takemura
- Laboratory for Chemistry and Life Science, Institute of Innovative Research, Tokyo Institute of Technology.,School of Life Science and Technology, Tokyo Institute of Technology
| | - Kan Tanaka
- Laboratory for Chemistry and Life Science, Institute of Innovative Research, Tokyo Institute of Technology
| | - Sousuke Imamura
- Laboratory for Chemistry and Life Science, Institute of Innovative Research, Tokyo Institute of Technology
| |
Collapse
|
20
|
Ito-Harashima S, Yagi T. Reporter gene assays for screening and identification of novel molting hormone- and juvenile hormone-like chemicals. JOURNAL OF PESTICIDE SCIENCE 2021; 46:29-42. [PMID: 33746544 PMCID: PMC7953021 DOI: 10.1584/jpestics.d20-079] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/18/2020] [Accepted: 12/23/2020] [Indexed: 06/12/2023]
Abstract
A reporter gene assay (RGA) is used to investigate the activity of synthetic chemicals mimicking the molting hormones (MHs) and juvenile hormones (JHs) of insects, so-called insect growth regulators (IGRs). The MH receptor, a heterodimer of the ecdysone receptor (EcR) and ultraspiracle (USP), and the JH receptor Methoprene-tolerant (Met) are ligand-dependent transcription factors. Ligand-bound EcR-USP and Met bind to specific cis-acting DNA elements, referred to as the ecdysone-responsive element (EcRE) and the JH-responsive element (JHRE), respectively, in order to transactivate target genes. Insect hormone-induced transactivation systems have been reconstituted by the introduction of reporter genes under the control of EcRE and JHRE, or two-hybrid reporter genes, into insect, mammalian, and yeast cells expressing receptor proteins. RGA is easy to use and convenient for examining the MH- and JH-like activities of synthetic chemicals and is suitable for the high-throughput screening of novel structural classes of chemicals targeting EcR-USP and Met.
Collapse
Affiliation(s)
- Sayoko Ito-Harashima
- Department of Biological Science, Graduate School of Science, Osaka Prefecture University, 1–1 Gakuen-cho, Naka-ku, Sakai city, Osaka 599–8531, Japan
| | - Takashi Yagi
- Department of Biological Science, Graduate School of Science, Osaka Prefecture University, 1–1 Gakuen-cho, Naka-ku, Sakai city, Osaka 599–8531, Japan
| |
Collapse
|
21
|
Phonbuppha J, Tinikul R, Chaiyen P. Use of Bacterial Luciferase as a Reporter Gene in Eukaryotic Systems. Methods Mol Biol 2021; 2274:53-65. [PMID: 34050462 DOI: 10.1007/978-1-0716-1258-3_6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/25/2023]
Abstract
Reporter gene assays are powerful tools for monitoring dynamic molecular changes and for evaluating the responses that occur at the genetic elements within cells in response to exogenous molecules. In general, various protein systems can be used as reporter genes, including luciferases. Here, the present protocol introduces a unique reporter gene system for monitoring molecular events in cells using bacterial luciferase (lux), which can generate blue-green light suitable for gene reporter applications with the highest cost performance. The protocol also guides the assay conditions and necessary components for using of lux gene (lux) as a eukaryotic reporter system. The lux system can be applied to monitor variety of molecular events inside mammalian cellular systems.
Collapse
Affiliation(s)
- Jittima Phonbuppha
- School of Biomolecular Science & Engineering, Vidyasirimedhi Institute of Science and Technology (VISTEC), Rayong, Thailand
| | - Ruchanok Tinikul
- Department of Biochemistry and Center for Excellence in Protein and Enzyme Technology, Faculty of Science, Mahidol University, Bangkok, Thailand
| | - Pimchai Chaiyen
- School of Biomolecular Science & Engineering, Vidyasirimedhi Institute of Science and Technology (VISTEC), Rayong, Thailand.
| |
Collapse
|
22
|
Kassotis CD, Harkness JS, Vo PH, Vu DC, Hoffman K, Cinnamon KM, Cornelius-Green JN, Vengosh A, Lin CH, Tillitt DE, Kruse RL, McElroy JA, Nagel SC. Endocrine disrupting activities and geochemistry of water resources associated with unconventional oil and gas activity. THE SCIENCE OF THE TOTAL ENVIRONMENT 2020; 748:142236. [PMID: 33039138 PMCID: PMC7772064 DOI: 10.1016/j.scitotenv.2020.142236] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/06/2020] [Revised: 09/01/2020] [Accepted: 09/03/2020] [Indexed: 05/12/2023]
Abstract
The rise of hydraulic fracturing and unconventional oil and gas (UOG) exploration in the United States has increased public concerns for water contamination induced from hydraulic fracturing fluids and associated wastewater spills. Herein, we collected surface and groundwater samples across Garfield County, Colorado, a drilling-dense region, and measured endocrine bioactivities, geochemical tracers of UOG wastewater, UOG-related organic contaminants in surface water, and evaluated UOG drilling production (weighted well scores, nearby well count, reported spills) surrounding sites. Elevated antagonist activities for the estrogen, androgen, progesterone, and glucocorticoid receptors were detected in surface water and associated with nearby shale gas well counts and density. The elevated endocrine activities were observed in surface water associated with medium and high UOG production (weighted UOG well score-based groups). These bioactivities were generally not associated with reported spills nearby, and often did not exhibit geochemical profiles associated with UOG wastewater from this region. Our results suggest the potential for releases of low-saline hydraulic fracturing fluids or chemicals used in other aspects of UOG production, similar to the chemistry of the local water, and dissimilar from defined spills of post-injection wastewater. Notably, water collected from certain medium and high UOG production sites exhibited bioactivities well above the levels known to impact the health of aquatic organisms, suggesting that further research to assess potential endocrine activities of UOG operations is warranted.
Collapse
Affiliation(s)
| | - Jennifer S Harkness
- U.S. Geological Survey, California Water Science Center, 6000 J Street, Placer Hall, Sacramento, CA 95819, USA
| | - Phuc H Vo
- Center for Agroforestry, School of Natural Resources, University of Missouri, Columbia, MO 65211, USA
| | - Danh C Vu
- Center for Agroforestry, School of Natural Resources, University of Missouri, Columbia, MO 65211, USA; Faculty of Technology, Van Lang University, Ho Chi Minh City, Viet Nam
| | - Kate Hoffman
- Nicholas School of the Environment, Duke University, Durham, NC 27708, USA
| | - Katelyn M Cinnamon
- Department of Obstetrics, Gynecology and Women's Health, University of Missouri, Columbia, MO 65211, USA
| | - Jennifer N Cornelius-Green
- Department of Obstetrics, Gynecology and Women's Health, University of Missouri, Columbia, MO 65211, USA
| | - Avner Vengosh
- Nicholas School of the Environment, Duke University, Durham, NC 27708, USA
| | - Chung-Ho Lin
- Center for Agroforestry, School of Natural Resources, University of Missouri, Columbia, MO 65211, USA
| | - Donald E Tillitt
- U.S. Geological Survey, Columbia Environmental Research Center, 4200 New Haven Road, Columbia, MO 65201, USA
| | - Robin L Kruse
- Department of Family and Community Medicine, University of Missouri, Columbia, MO 65211, USA
| | - Jane A McElroy
- Department of Family and Community Medicine, University of Missouri, Columbia, MO 65211, USA
| | - Susan C Nagel
- Department of Obstetrics, Gynecology and Women's Health, University of Missouri, Columbia, MO 65211, USA.
| |
Collapse
|
23
|
Huang CH, Huang TL, Liu YC, Chen TC, Lin SM, Shaw SY, Chang CC. Overexpression of a multifunctional β-glucosidase gene from thermophilic archaeon Sulfolobus solfataricus in transgenic tobacco could facilitate glucose release and its use as a reporter. Transgenic Res 2020; 29:511-527. [PMID: 32776308 DOI: 10.1007/s11248-020-00212-z] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2019] [Accepted: 07/25/2020] [Indexed: 11/25/2022]
Abstract
The β-glucosidase, which hydrolyzes the β(1-4) glucosidic linkage of disaccharides, oligosaccharides and glucose-substituted molecules, has been used in many biotechnological applications. The current commercial source of β-glucosidase is mainly microbial fermentation. Plants have been developed as bioreactors to produce various kinds of proteins including β-glucosidase because of the potential low cost. Sulfolobus solfataricus is a thermoacidophilic archaeon that can grow optimally at high temperature, around 80 °C, and pH 2-4. We overexpressed the β-glucosidase gene from S. solfataricus in transgenic tobacco via Agrobacteria-mediated transformation. Three transgenic tobacco lines with β-glucosidase gene expression driven by the rbcS promoter were obtained, and the recombinant proteins were accumulated in chloroplasts, endoplasmic reticulum and vacuoles up to 1%, 0.6% and 0.3% of total soluble protein, respectively. By stacking the transgenes via crossing distinct transgenic events, the level of β-glucosidase in plants could further increase. The plant-expressed β-glucosidase had optimal activity at 80 °C and pH 5-6. In addition, the plant-expressed β-glucosidase showed high thermostability; on heat pre-treatment at 80 °C for 2 h, approximately 70% residual activity remained. Furthermore, wind-dried leaf tissues of transgenic plants showed good stability in short-term storage at room temperature, with β-glucosidase activity of about 80% still remaining after 1 week of storage as compared with fresh leaf. Furthermore, we demonstrated the possibility of using the archaebacterial β-glucosidase gene as a reporter in plants based on alternative β-galactosidase activity.
Collapse
Affiliation(s)
- Chih-Hao Huang
- Department of Biotechnology and Bioindustry Sciences, National Cheng Kung University, Tainan, 701, Taiwan
| | - Tzu-Ling Huang
- Department of Biotechnology and Bioindustry Sciences, National Cheng Kung University, Tainan, 701, Taiwan
| | - Yu-Chang Liu
- Department of Biotechnology and Bioindustry Sciences, National Cheng Kung University, Tainan, 701, Taiwan
| | - Ting-Chieh Chen
- Department of Biotechnology and Bioindustry Sciences, National Cheng Kung University, Tainan, 701, Taiwan
| | - Shih-Ming Lin
- Department of Biotechnology and Bioindustry Sciences, National Cheng Kung University, Tainan, 701, Taiwan
| | - Shyh-Yu Shaw
- Department of Chemistry, National Cheng Kung University, Tainan, 701, Taiwan.
| | - Ching-Chun Chang
- Department of Biotechnology and Bioindustry Sciences, National Cheng Kung University, Tainan, 701, Taiwan.
| |
Collapse
|
24
|
Duong MM, Carmody CM, Nugen SR. Phage-based biosensors: in vivo analysis of native T4 phage promoters to enhance reporter enzyme expression. Analyst 2020; 145:6291-6297. [PMID: 32945826 DOI: 10.1039/d0an01413c] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Phage-based biosensors have shown significant promise in meeting the present needs of the food and agricultural industries due to a combination of sufficient portability, speed, ease of use, sensitivity, and low production cost. Although current phage-based methods do not meet the bacteria detection limit imposed by the EPA, FDA, and USDA, a better understanding of phage genetics can significantly increase their sensitivity as biosensors. In the current study, the signal sensitivity of a T4 phage-based detection system was improved via transcriptional upregulation of the reporter enzyme Nanoluc luciferase (Nluc). An efficient platform to evaluate the promoter activity of reporter T4 phages was developed. The ability to upregulate Nluc within T4 phages was evaluated using 15 native T4 promoters. Data indicates a six-fold increase in reporter enzyme signal from integration of the selected promoters. Collectively, this work demonstrates that fine tuning the expression of reporter enzymes such as Nluc through optimization of transcription can significantly reduce the limits of detection.
Collapse
Affiliation(s)
- Michelle M Duong
- Department of Food Science, Cornell University, Ithaca, NY 14853, USA.
| | | | | |
Collapse
|
25
|
Thiel Z, Nguyen J, Rivera‐Fuentes P. Genetically Encoded Activators of Small Molecules for Imaging and Drug Delivery. Angew Chem Int Ed Engl 2020; 59:7669-7677. [PMID: 31898373 PMCID: PMC7318188 DOI: 10.1002/anie.201915521] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2019] [Indexed: 12/30/2022]
Abstract
Chemical biologists have developed many tools based on genetically encoded macromolecules and small, synthetic compounds. The two different approaches are extremely useful, but they have inherent limitations. In this Minireview, we highlight examples of strategies that combine both concepts to tackle challenging problems in chemical biology. We discuss applications in imaging, with a focus on super-resolved techniques, and in probe and drug delivery. We propose future directions in this field, hoping to inspire chemical biologists to develop new combinations of synthetic and genetically encoded probes.
Collapse
Affiliation(s)
- Zacharias Thiel
- Institute of Chemical Sciences and EngineeringEPF LausanneCH C2 425, Station 61015LausanneSwitzerland
- Laboratory of Organic ChemistryETH ZurichVladimir-Prelog-Weg 38093ZurichSwitzerland
| | - Jade Nguyen
- Institute of Chemical Sciences and EngineeringEPF LausanneCH C2 425, Station 61015LausanneSwitzerland
- Laboratory of Organic ChemistryETH ZurichVladimir-Prelog-Weg 38093ZurichSwitzerland
| | - Pablo Rivera‐Fuentes
- Institute of Chemical Sciences and EngineeringEPF LausanneCH C2 425, Station 61015LausanneSwitzerland
| |
Collapse
|
26
|
Thiel Z, Nguyen J, Rivera‐Fuentes P. Genetically Encoded Activators of Small Molecules for Imaging and Drug Delivery. Angew Chem Int Ed Engl 2020. [DOI: 10.1002/ange.201915521] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Affiliation(s)
- Zacharias Thiel
- Institute of Chemical Sciences and Engineering EPF Lausanne CH C2 425, Station 6 1015 Lausanne Switzerland
- Laboratory of Organic Chemistry ETH Zurich Vladimir-Prelog-Weg 3 8093 Zurich Switzerland
| | - Jade Nguyen
- Institute of Chemical Sciences and Engineering EPF Lausanne CH C2 425, Station 6 1015 Lausanne Switzerland
- Laboratory of Organic Chemistry ETH Zurich Vladimir-Prelog-Weg 3 8093 Zurich Switzerland
| | - Pablo Rivera‐Fuentes
- Institute of Chemical Sciences and Engineering EPF Lausanne CH C2 425, Station 6 1015 Lausanne Switzerland
| |
Collapse
|
27
|
Soler-Bistué A, Aguilar-Pierlé S, Garcia-Garcerá M, Val ME, Sismeiro O, Varet H, Sieira R, Krin E, Skovgaard O, Comerci DJ, Rocha EPC, Mazel D. Macromolecular crowding links ribosomal protein gene dosage to growth rate in Vibrio cholerae. BMC Biol 2020; 18:43. [PMID: 32349767 PMCID: PMC7191768 DOI: 10.1186/s12915-020-00777-5] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2019] [Accepted: 03/31/2020] [Indexed: 12/15/2022] Open
Abstract
BACKGROUND In fast-growing bacteria, the genomic location of ribosomal protein (RP) genes is biased towards the replication origin (oriC). This trait allows optimizing their expression during exponential phase since oriC neighboring regions are in higher dose due to multifork replication. Relocation of s10-spc-α locus (S10), which codes for most of the RP, to ectopic genomic positions shows that its relative distance to the oriC correlates to a reduction on its dosage, its expression, and bacterial growth rate. However, a mechanism linking S10 dosage to cell physiology has still not been determined. RESULTS We hypothesized that S10 dosage perturbations impact protein synthesis capacity. Strikingly, we observed that in Vibrio cholerae, protein production capacity was independent of S10 position. Deep sequencing revealed that S10 relocation altered chromosomal replication dynamics and genome-wide transcription. Such changes increased as a function of oriC-S10 distance. Since RP constitutes a large proportion of cell mass, lower S10 dosage could lead to changes in macromolecular crowding, impacting cell physiology. Accordingly, cytoplasm fluidity was higher in mutants where S10 is most distant from oriC. In hyperosmotic conditions, when crowding differences are minimized, the growth rate and replication dynamics were highly alleviated in these strains. CONCLUSIONS The genomic location of RP genes ensures its optimal dosage. However, besides of its essential function in translation, their genomic position sustains an optimal macromolecular crowding essential for maximizing growth. Hence, this could be another mechanism coordinating DNA replication to bacterial growth.
Collapse
Affiliation(s)
- Alfonso Soler-Bistué
- Institut Pasteur, Unité Plasticité du Génome Bactérien, UMR3525, CNRS, Paris, France
- Instituto de Investigaciones Biotecnológicas "Dr. Rodolfo A. Ugalde," CONICET - Universidad Nacional de San Martín, San Martín, Buenos Aires, Argentina
| | | | - Marc Garcia-Garcerá
- Microbial Evolutionary Genomics, Département Génomes et Génétique, Institut Pasteur, Paris, France
- Centre National de la Recherche Scientifique UMR3525, Paris, France
- Department of Fundamental Microbiology, University of Lausanne, Quartier SORGE, 1003, Lausanne, Switzerland
| | - Marie-Eve Val
- Institut Pasteur, Unité Plasticité du Génome Bactérien, UMR3525, CNRS, Paris, France
| | - Odile Sismeiro
- Institut Pasteur, Plate-forme Transcriptome et Épigenome, Biomics, Centre d'Innovation et Recherche Technologique (Citech), Paris, France
| | - Hugo Varet
- Institut Pasteur, Plate-forme Transcriptome et Épigenome, Biomics, Centre d'Innovation et Recherche Technologique (Citech), Paris, France
| | - Rodrigo Sieira
- Fundación Instituto Leloir, IIBBA-CONICET, Buenos Aires, Argentina
| | - Evelyne Krin
- Institut Pasteur, Unité Plasticité du Génome Bactérien, UMR3525, CNRS, Paris, France
| | - Ole Skovgaard
- Department of Science and Environment, Roskilde University, Roskilde, Denmark
| | - Diego J Comerci
- Instituto de Investigaciones Biotecnológicas "Dr. Rodolfo A. Ugalde," CONICET - Universidad Nacional de San Martín, San Martín, Buenos Aires, Argentina
| | - Eduardo P C Rocha
- Microbial Evolutionary Genomics, Département Génomes et Génétique, Institut Pasteur, Paris, France
- Centre National de la Recherche Scientifique UMR3525, Paris, France
| | - Didier Mazel
- Institut Pasteur, Unité Plasticité du Génome Bactérien, UMR3525, CNRS, Paris, France.
| |
Collapse
|
28
|
Ogunlade O, Stowe C, Jathoul A, Kalber T, Lythgoe MF, Beard P, Pule M. In vivo photoacoustic imaging of a nonfluorescent E2 crimson genetic reporter in mammalian tissues. JOURNAL OF BIOMEDICAL OPTICS 2020; 25:1-12. [PMID: 32314561 PMCID: PMC7167598 DOI: 10.1117/1.jbo.25.4.046004] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/14/2019] [Accepted: 03/18/2020] [Indexed: 06/11/2023]
Abstract
SIGNIFICANCE Green-fluorescent protein (GFP)-like fluorescent proteins are used extensively as genetic reporters in fluorescence imaging due to their distinctive ability to form chromophores independent of external enzymes or cofactors. However, their use for photoacoustic (PA) imaging has not been demonstrated in mammalian tissues because they possess low PA signal generation efficiency in their native state. By engineering them to become nonfluorescent (NF), their PA generation efficiency was increased. This enabled the generation of in vivo contrast in mice, making it possible for GFP-like proteins to be used as PA genetic reporters in mammalian tissues. AIM The aim was to develop a darkened GFP-like protein reporter by modifying E2 crimson fluorescent protein (FP) in order to generate NF mutant proteins with high PA signal generation efficiency for in vivo imaging. APPROACH The absorbance, fluorescence, and PA amplitude spectra of purified protein solutions of the FP and engineered NF mutants were measured in order to identify the mutant with the highest PA signal generation efficiency. This mutant, referred to as NFA, and the native FP were then stably expressed in LS174T human colorectal tumor cells using a retroviral vector and tested for photostability under continuous pulsed illumination. To demonstrate the improvement in PA signal generation in vivo, cells expressing the FP and NFA mutant were injected subcutaneously in mice and imaged using a Fabry-Perot based PA scanner. RESULTS The NF mutants of E2 crimson exhibited fluorescence that was 2 orders of magnitude lower than the FP and a higher PA signal generation efficiency; the NFA-generated PA signal was approximately three times higher than the FP. Tumor cells expressing the NFA mutant provided sufficient image contrast to be visualized in vivo against a background of strong vascular contrast, whereas the FP-expressing cells did not generate visible contrast. CONCLUSION A GFP-like protein has been demonstrated as a genetic reporter for PA imaging in mammalian tissue for the first time. This was achieved by a mutation, which darkened the FP and increased the PA signal generation efficiency. The approach taken suggests that GFP-like proteins could be a promising addition to the current cohort of genetic reporters available for in vivo PA imaging.
Collapse
Affiliation(s)
- Olumide Ogunlade
- University College London, Department of Medical Physics and Biomedical Engineering, London, United Kingdom
| | - Cassandra Stowe
- University College London, UCL Centre for Advanced Biomedical Imaging, Division of Medicine, London, United Kingdom
- University College London, UCL Cancer Institute, Research Department of Haematology, London, United Kingdom
| | - Amit Jathoul
- University College London, UCL Cancer Institute, Research Department of Haematology, London, United Kingdom
| | - Tammy Kalber
- University College London, UCL Centre for Advanced Biomedical Imaging, Division of Medicine, London, United Kingdom
| | - Mark F Lythgoe
- University College London, UCL Centre for Advanced Biomedical Imaging, Division of Medicine, London, United Kingdom
| | - Paul Beard
- University College London, Department of Medical Physics and Biomedical Engineering, London, United Kingdom
| | - Martin Pule
- University College London, UCL Cancer Institute, Research Department of Haematology, London, United Kingdom
| |
Collapse
|
29
|
Development of reporter gene assays to determine the bioactivity of biopharmaceuticals. Biotechnol Adv 2020; 39:107466. [DOI: 10.1016/j.biotechadv.2019.107466] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2019] [Revised: 11/02/2019] [Accepted: 11/02/2019] [Indexed: 02/06/2023]
|
30
|
Yilmaz B, Terekeci H, Sandal S, Kelestimur F. Endocrine disrupting chemicals: exposure, effects on human health, mechanism of action, models for testing and strategies for prevention. Rev Endocr Metab Disord 2020; 21:127-147. [PMID: 31792807 DOI: 10.1007/s11154-019-09521-z] [Citation(s) in RCA: 254] [Impact Index Per Article: 63.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Endocrine Disrupting Chemicals (EDCs) are a global problem for environmental and human health. They are defined as "an exogenous chemical, or mixture of chemicals, that can interfere with any aspect of hormone action". It is estimated that there are about 1000 chemicals with endocrine-acting properties. EDCs comprise pesticides, fungicides, industrial chemicals, plasticizers, nonylphenols, metals, pharmaceutical agents and phytoestrogens. Human exposure to EDCs mainly occurs by ingestion and to some extent by inhalation and dermal uptake. Most EDCs are lipophilic and bioaccumulate in the adipose tissue, thus they have a very long half-life in the body. It is difficult to assess the full impact of human exposure to EDCs because adverse effects develop latently and manifest at later ages, and in some people do not present. Timing of exposure is of importance. Developing fetus and neonates are the most vulnerable to endocrine disruption. EDCs may interfere with synthesis, action and metabolism of sex steroid hormones that in turn cause developmental and fertility problems, infertility and hormone-sensitive cancers in women and men. Some EDCs exert obesogenic effects that result in disturbance in energy homeostasis. Interference with hypothalamo-pituitary-thyroid and adrenal axes has also been reported. In this review, potential EDCs, their effects and mechanisms of action, epidemiological studies to analyze their effects on human health, bio-detection and chemical identification methods, difficulties in extrapolating experimental findings and studying endocrine disruptors in humans and recommendations for endocrinologists, individuals and policy makers will be discussed in view of the relevant literature.
Collapse
Affiliation(s)
- Bayram Yilmaz
- Department of Physiology, Faculty of Medicine, Yeditepe University, Istanbul, Turkey
| | - Hakan Terekeci
- Department of Internal Medicine, Faculty of Medicine, Yeditepe University, Istanbul, Turkey
| | - Suleyman Sandal
- Department of Physiology, Faculty of Medicine, Inonu University, Malatya, Turkey
| | - Fahrettin Kelestimur
- Department of Endocrinology, Faculty of Medicine, Yeditepe University, Istanbul, Turkey.
| |
Collapse
|
31
|
Thavarajah W, Verosloff MS, Jung JK, Alam KK, Miller JD, Jewett MC, Young SL, Lucks JB. A Primer on Emerging Field-Deployable Synthetic Biology Tools for Global Water Quality Monitoring. NPJ CLEAN WATER 2020; 3:18. [PMID: 34267944 PMCID: PMC8279131 DOI: 10.1038/s41545-020-0064-8] [Citation(s) in RCA: 37] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/31/2019] [Accepted: 03/09/2020] [Indexed: 05/22/2023]
Abstract
Tracking progress towards Target 6.1 of the United Nations Sustainable Development Goals, "achieving universal and equitable access to safe and affordable drinking water for all", necessitates the development of simple, inexpensive tools to monitor water quality. The rapidly growing field of synthetic biology has the potential to address this need by taking DNA-encoded sensing elements from nature and reassembling them to create field-deployable 'biosensors' that can detect pathogenic or chemical water contaminants. Here we describe water quality monitoring strategies enabled by synthetic biology and compare them to previous approaches used to detect three priority water contaminants: fecal pathogens, arsenic, and fluoride in order to explain the potential for engineered biosensors to simplify and decentralize water quality monitoring. We also briefly discuss expanding biosensors to detect emerging contaminants including metals and pharmaceuticals. We conclude with an outlook on the future of biosensor development, in which we discuss adaptability to emerging contaminants, outline current limitations, and propose steps to overcome the field's outstanding challenges to facilitate global water quality monitoring.
Collapse
Affiliation(s)
- Walter Thavarajah
- Department of Chemical and Biological Engineering, Northwestern University, 2145, Sheridan Rd, Evanston, IL, 60208, USA
- Center for Synthetic Biology, Northwestern University, 2145 Sheridan Rd, Evanston, IL, 60208, USA
- Center for Water Research, Northwestern University, 2145 Sheridan Rd, Evanston, IL, 60208, USA
- Center for Engineering, Sustainability and Resilience, Northwestern University, 2145 Sheridan Rd, Evanston, IL, 60208, USA
| | - Matthew S. Verosloff
- Center for Synthetic Biology, Northwestern University, 2145 Sheridan Rd, Evanston, IL, 60208, USA
- Center for Water Research, Northwestern University, 2145 Sheridan Rd, Evanston, IL, 60208, USA
- Center for Engineering, Sustainability and Resilience, Northwestern University, 2145 Sheridan Rd, Evanston, IL, 60208, USA
- Interdisciplinary Biological Sciences Graduate Program, Northwestern University, 2204 Tech Drive, Evanston, IL, 60208, USA
| | - Jaeyoung K. Jung
- Department of Chemical and Biological Engineering, Northwestern University, 2145, Sheridan Rd, Evanston, IL, 60208, USA
- Center for Synthetic Biology, Northwestern University, 2145 Sheridan Rd, Evanston, IL, 60208, USA
- Center for Water Research, Northwestern University, 2145 Sheridan Rd, Evanston, IL, 60208, USA
- Center for Engineering, Sustainability and Resilience, Northwestern University, 2145 Sheridan Rd, Evanston, IL, 60208, USA
| | - Khalid K. Alam
- Department of Chemical and Biological Engineering, Northwestern University, 2145, Sheridan Rd, Evanston, IL, 60208, USA
- Center for Synthetic Biology, Northwestern University, 2145 Sheridan Rd, Evanston, IL, 60208, USA
- Center for Water Research, Northwestern University, 2145 Sheridan Rd, Evanston, IL, 60208, USA
- Center for Engineering, Sustainability and Resilience, Northwestern University, 2145 Sheridan Rd, Evanston, IL, 60208, USA
| | - Joshua D. Miller
- Center for Water Research, Northwestern University, 2145 Sheridan Rd, Evanston, IL, 60208, USA
- Department of Anthropology, Northwestern University, 1810 Hinman Ave., Evanston, IL, 60208, USA
| | - Michael C. Jewett
- Department of Chemical and Biological Engineering, Northwestern University, 2145, Sheridan Rd, Evanston, IL, 60208, USA
- Center for Synthetic Biology, Northwestern University, 2145 Sheridan Rd, Evanston, IL, 60208, USA
| | - Sera L. Young
- Center for Water Research, Northwestern University, 2145 Sheridan Rd, Evanston, IL, 60208, USA
- Department of Anthropology, Northwestern University, 1810 Hinman Ave., Evanston, IL, 60208, USA
- Institute for Policy Research, Northwestern University, 2040 Sheridan Rd, Evanston, IL, 60208 USA
- To whom correspondence should be addressed, ,
| | - Julius B. Lucks
- Department of Chemical and Biological Engineering, Northwestern University, 2145, Sheridan Rd, Evanston, IL, 60208, USA
- Center for Synthetic Biology, Northwestern University, 2145 Sheridan Rd, Evanston, IL, 60208, USA
- Center for Water Research, Northwestern University, 2145 Sheridan Rd, Evanston, IL, 60208, USA
- Center for Engineering, Sustainability and Resilience, Northwestern University, 2145 Sheridan Rd, Evanston, IL, 60208, USA
- To whom correspondence should be addressed, ,
| |
Collapse
|
32
|
In Vivo Dynamics of Reporter Flaviviridae Viruses. J Virol 2019; 93:JVI.01191-19. [PMID: 31462560 DOI: 10.1128/jvi.01191-19] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2019] [Accepted: 08/15/2019] [Indexed: 11/20/2022] Open
Abstract
Recombinant viruses possessing reporter proteins have been generated for virus research. In the case of the family Flaviviridae, we recently generated recombinant viruses, including the hepatitis C virus of the genus Hepacivirus, Japanese encephalitis virus (JEV) of the genus Flavivirus, and bovine viral diarrhea virus of the genus Pestivirus; all three viruses possess an 11-amino-acid subunit derived from NanoLuc luciferase (HiBiT). Here, we further developed the recombinant viruses and investigated their utility in vivo Recombinant viruses harboring HiBiT in the E, NS1, or NS3 protein constructed based on the predicted secondary structure, solvent-accessible surface area, and root mean square fluctuation of the proteins exhibited comparable replication to that of the wild-type virus in vitro The recombinant JEV carrying HiBiT in the NS1 protein exhibited propagation in mice comparable to that of the parental virus, and propagation of the recombinant was monitored by the luciferase activity. In addition, the recombinants of classical swine fever virus (CSFV) possessing HiBiT in the Erns or E2 protein also showed propagation comparable to that of the wild-type virus. The recombinant CSFV carrying HiBiT in Erns exhibited similar replication to the parental CSFV in pigs, and detection of viral propagation of this recombinant by luciferase activity was higher than that by quantitative PCR (qPCR). Taken together, these results demonstrated that the reporter Flaviviridae viruses generated herein are powerful tools for elucidating the viral life cycle and pathogeneses and provide a robust platform for the development of novel antivirals.IMPORTANCE In vivo applications of reporter viruses are necessary to understand viral pathogenesis and provide a robust platform for antiviral development. In developing such applications, determination of an ideal locus to accommodate foreign genes is important, because insertion of foreign genes into irrelevant loci can disrupt the protein functions required for viral replication. Here, we investigated the criteria to determine ideal insertion sites of foreign genes from the protein structure of viral proteins. The recombinant viruses generated by our criteria exhibited propagation comparable to that of parental viruses in vivo Our proteomic approach based on the flexibility profile of viral proteins may provide a useful tool for constructing reporter viruses, including Flaviviridae viruses.
Collapse
|
33
|
Salehi-Sedeh H, Ataei F, Jarchi S, Hamidi R, Hosseinkhani S. Effect of mutation at positively charged residues (K329 and R330) in a flexible region of firefly luciferase on structure and kinetic properties. Enzyme Microb Technol 2019; 131:109424. [PMID: 31615672 DOI: 10.1016/j.enzmictec.2019.109424] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2019] [Revised: 08/28/2019] [Accepted: 09/03/2019] [Indexed: 11/27/2022]
Abstract
Firefly luciferase as a bioluminescent enzyme has many applications in various fields from scientific research to commercial goals. This enzyme is relatively unstable with low functional capacity due to rapid inactivation in physiological temperature, low in vitro stability and high susceptibility to proteolytic degradation. Based on previous studies, two regions 206-220 and 329-341 on N-domain of Photinus pyralis luciferase are known accessible and flexible. Flexible regions may lead to protein instability. Here, the effect of mutation at positively charged residues Lys(K)329 and Arg(R)330 on the stability of luciferase was studied. Furthermore, the role of these mutations on the structure and function was evaluated. Introducing of these point mutations did not affect the orientation of critical residues in bioluminescence color determination. The kinetic studies showed that thermostability and Km value for luciferin in both mutants were decreased as compared to wild type. However, optimum pH and optimum temperature showed no significant changes in both mutants. Moreover, the structural data revealed an increase in tryptophan fluorescence intensity and secondary structure content for R330Q in compared with wild type, while intrinsic fluorescence and far-UV CD intensity in K329I mutant was decreased.
Collapse
Affiliation(s)
- Hossein Salehi-Sedeh
- Department of Biochemistry, Faculty of Biological Sciences, Tarbiat Modares University, Tehran, Iran
| | - Farangis Ataei
- Department of Biochemistry, Faculty of Biological Sciences, Tarbiat Modares University, Tehran, Iran.
| | - Samaneh Jarchi
- Department of Biochemistry, Faculty of Biological Sciences, Tarbiat Modares University, Tehran, Iran
| | - Roghaye Hamidi
- Department of Biochemistry, Faculty of Biological Sciences, Tarbiat Modares University, Tehran, Iran
| | - Saman Hosseinkhani
- Department of Biochemistry, Faculty of Biological Sciences, Tarbiat Modares University, Tehran, Iran
| |
Collapse
|
34
|
Branchini BR, Fontaine DM, Southworth TL, Huta BP, Racela A, Patel KD, Gulick AM. Mutagenesis and Structural Studies Reveal the Basis for the Activity and Stability Properties That Distinguish the Photinus Luciferases scintillans and pyralis. Biochemistry 2019; 58:4293-4303. [PMID: 31560532 DOI: 10.1021/acs.biochem.9b00719] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
Abstract
The dazzling yellow-green light emission of the common North American firefly Photinus pyralis and other bioluminescent organisms has provided a wide variety of prominent research applications like reporter gene assays and in vivo imaging methods. While the P. pyralis enzyme has been extensively studied, only recently has a second Photinus luciferase been cloned from the species scintillans. Even though the enzymes share very high sequence identity (89.8%), the color of the light they emit, their specific activity and their stability to heat, pH, and chemical denaturation are quite different with the scintillans luciferase being generally more resistant. Through the construction and evaluation of the properties of chimeric domain swapped, single point, and various combined variants, we have determined that only six amino acid changes are necessary to confer all of the properties of the scintillans enzyme to wild-type P. pyralis luciferase. Altered stability properties were attributed to four of the amino acid changes (T214N/S276T/H332N/E354N), and single mutations each predominantly changed emission color (Y255F) and specific activity (A222C). Results of a crystallographic study of the P. pyralis enzyme containing the six changes (Pps6) provide some insight into the structural basis for some of the documented property differences.
Collapse
Affiliation(s)
- Bruce R Branchini
- Department of Chemistry , Connecticut College , New London , Connecticut 06320 , United States
| | - Danielle M Fontaine
- Department of Chemistry , Connecticut College , New London , Connecticut 06320 , United States
| | - Tara L Southworth
- Department of Chemistry , Connecticut College , New London , Connecticut 06320 , United States
| | - Brian P Huta
- Department of Chemistry , Connecticut College , New London , Connecticut 06320 , United States
| | - Allison Racela
- Department of Chemistry , Connecticut College , New London , Connecticut 06320 , United States
| | - Ketan D Patel
- Department of Structural Biology, Jacobs School of Medicine and Biomedical Sciences , University at Buffalo , Buffalo , New York 14203 , United States
| | - Andrew M Gulick
- Department of Structural Biology, Jacobs School of Medicine and Biomedical Sciences , University at Buffalo , Buffalo , New York 14203 , United States
| |
Collapse
|
35
|
Morcillo-Parra MÁ, Beltran G, Mas A, Torija MJ. Determination of melatonin by a whole cell bioassay in fermented beverages. Sci Rep 2019; 9:9120. [PMID: 31235891 PMCID: PMC6591416 DOI: 10.1038/s41598-019-45645-7] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2019] [Accepted: 06/12/2019] [Indexed: 11/09/2022] Open
Abstract
Melatonin is a bioactive compound that is present in fermented beverages, such as wine and beer, at concentrations ranging from picograms to nanograms per mL of product. The purpose of this study was to optimize a novel fluorescent bioassay for detecting melatonin based on a cell line that contains the human melatonin receptor 1B gene and to compare these results with LC-MS/MS as a reference method. Conditions that could affect cell growth and detection (cell number per well, stimulation time, presence or absence of fetal bovine serum and adhesion of cells) were tested in the TANGO® cell line. Food matrices (wine and grape must) could not be directly used for the cell line due to low response. Therefore, for the determination of melatonin in food samples, an extraction procedure was required before conducting the assay. We demonstrated an improvement in melatonin determination by the cell-based bioassay due to increased sensitivity and specificity and improved quantification in complex matrices. Therefore, this method is a good alternative to determine melatonin content in some food samples, especially for those containing very low melatonin levels.
Collapse
Affiliation(s)
| | - Gemma Beltran
- Departament de Bioquimica i Biotecnologia, Facultat d'Enologia, Universitat Rovira i Virgili, Tarragona, Spain
| | - Albert Mas
- Departament de Bioquimica i Biotecnologia, Facultat d'Enologia, Universitat Rovira i Virgili, Tarragona, Spain
| | - María-Jesús Torija
- Departament de Bioquimica i Biotecnologia, Facultat d'Enologia, Universitat Rovira i Virgili, Tarragona, Spain.
| |
Collapse
|
36
|
Bilal M, Iqbal HM. Microbial-derived biosensors for monitoring environmental contaminants: Recent advances and future outlook. PROCESS SAFETY AND ENVIRONMENTAL PROTECTION 2019. [DOI: 10.1016/j.psep.2019.01.032] [Citation(s) in RCA: 31] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
|
37
|
Kassotis CD, Stapleton HM. Endocrine-Mediated Mechanisms of Metabolic Disruption and New Approaches to Examine the Public Health Threat. Front Endocrinol (Lausanne) 2019; 10:39. [PMID: 30792693 PMCID: PMC6374316 DOI: 10.3389/fendo.2019.00039] [Citation(s) in RCA: 32] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/28/2018] [Accepted: 01/17/2019] [Indexed: 01/29/2023] Open
Abstract
Obesity and metabolic disorders are of great societal concern and generate substantial human health care costs globally. Interventions have resulted in only minimal impacts on disrupting this worsening health trend, increasing attention on putative environmental contributors. Exposure to numerous environmental contaminants have, over decades, been demonstrated to result in increased metabolic dysfunction and/or weight gain in cell and animal models, and in some cases, even in humans. There are numerous mechanisms through which environmental contaminants may contribute to metabolic dysfunction, though certain mechanisms, such as activation of the peroxisome proliferator activated receptor gamma or the retinoid x receptor, have received considerably more attention than less-studied mechanisms such as antagonism of the thyroid receptor, androgen receptor, or mitochondrial toxicity. As such, research on putative metabolic disruptors is growing rapidly, as is our understanding of molecular mechanisms underlying these effects. Concurrent with these advances, new research has evaluated current models of adipogenesis, and new models have been proposed. Only in the last several years have studies really begun to address complex mixtures of contaminants and how these mixtures may disrupt metabolic health in environmentally relevant exposure scenarios. Several studies have begun to assess environmental mixtures from various environments and study the mechanisms underlying their putative metabolic dysfunction; these studies hold real promise in highlighting crucial mechanisms driving observed organismal effects. In addition, high-throughput toxicity databases (ToxCast, etc.) may provide future benefits in prioritizing chemicals for in vivo testing, particularly once the causative molecular mechanisms promoting dysfunction are better understood and expert critiques are used to hone the databases. In this review, we will review the available literature linking metabolic disruption to endocrine-mediated molecular mechanisms, discuss the novel application of environmental mixtures and implications for in vivo metabolic health, and discuss the putative utility of applying high-throughput toxicity databases to answering complex organismal health outcome questions.
Collapse
|
38
|
Gabriel GVDM, Yasuno R, Mitani Y, Ohmiya Y, Viviani VR. Novel application ofMacrolampissp2 firefly luciferase for intracellular pH-biosensing in mammalian cells. Photochem Photobiol Sci 2019; 18:1212-1217. [DOI: 10.1039/c8pp00573g] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Bioluminescence is widely used in biosensors.
Collapse
Affiliation(s)
| | - Rie Yasuno
- National Institute of Advanced Industrial Science and Technology (AIST)
- Biomedical Research Institute
- Tsukuba
- Japan
| | - Yasuo Mitani
- National Institute of Advanced Industrial Science and Technology (AIST)
- Bioproduction Research Institute
- Sapporo
- Japan
| | - Yoshihiro Ohmiya
- National Institute of Advanced Industrial Science and Technology (AIST)
- Biomedical Research Institute
- Tsukuba
- Japan
| | - Vadim Ravara Viviani
- Graduate School of Biotechnology and Environmental Monitoring
- Federal University of São Carlos (UFSCar)
- Sorocaba
- Brazil
- Graduate School of Evolutive Genetics and Molecular Biology
| |
Collapse
|
39
|
Zhang W, Takahara T, Achiha T, Shibata H, Maki M. Cellular Ca 2+-Responding Nanoluciferase Reporter Gene System Directed by Tandemly Repeated Pseudo-palindromic NFAT-Response Elements. Methods Mol Biol 2019; 1929:95-109. [PMID: 30710269 DOI: 10.1007/978-1-4939-9030-6_7] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Abstract
Luciferase reporter gene systems based on the NFAT-response element (RE) have been used to monitor intracellular Ca2+ elevation. However, Ca2+ mobilization agent (e.g., ionomycin) alone is not adequate to activate the currently often employed reporter gene that contains the NFAT-RE found in the IL2 promoter. In addition to activation of NFAT through the Ca2+-calmodulin/calcineurin pathway, activation of AP-1 as a partner transcription factor is essential for the IL2-based NFAT-RE system. Here, we describe a detailed method for the recently developed new reporter gene system containing the NFAT-RE from the IL8 promoter. This system enables us to monitor endpoint effects of Ca2+-mobilizing agonists independent of AP-1 activation.
Collapse
Affiliation(s)
- Wei Zhang
- Department of Applied Molecular Biosciences, Graduate School of Bioagricultural Sciences, Nagoya University, Nagoya, Japan
| | - Terunao Takahara
- Department of Applied Molecular Biosciences, Graduate School of Bioagricultural Sciences, Nagoya University, Nagoya, Japan.
| | - Takuya Achiha
- Department of Applied Molecular Biosciences, Graduate School of Bioagricultural Sciences, Nagoya University, Nagoya, Japan
| | - Hideki Shibata
- Department of Applied Molecular Biosciences, Graduate School of Bioagricultural Sciences, Nagoya University, Nagoya, Japan
| | - Masatoshi Maki
- Department of Applied Molecular Biosciences, Graduate School of Bioagricultural Sciences, Nagoya University, Nagoya, Japan.
| |
Collapse
|
40
|
Fan W, Deng H, Zhu L, Tu C, Su Y, Shi L, Yang J, Zhou L, Xu L, Zhu X. Site-dependent fluorescence enhanced polymers with a self-restricted GFP chromophore for living cell imaging. Biomater Sci 2019; 7:2421-2429. [DOI: 10.1039/c9bm00255c] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Amphipathic copolymers with a self-restricted GFP chromophore sited on different locations were successfully synthesized, characterized and applied in cell imaging.
Collapse
|
41
|
Alhaji SY, Ngai SC, Abdullah S. Silencing of transgene expression in mammalian cells by DNA methylation and histone modifications in gene therapy perspective. Biotechnol Genet Eng Rev 2018; 35:1-25. [PMID: 30514178 DOI: 10.1080/02648725.2018.1551594] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
DNA methylation and histone modifications are vital in maintaining genomic stability and modulating cellular functions in mammalian cells. These two epigenetic modifications are the most common gene regulatory systems known to spatially control gene expression. Transgene silencing by these two mechanisms is a major challenge to achieving effective gene therapy for many genetic conditions. The implications of transgene silencing caused by epigenetic modifications have been extensively studied and reported in numerous gene delivery studies. This review highlights instances of transgene silencing by DNA methylation and histone modification with specific focus on the role of these two epigenetic effects on the repression of transgene expression in mammalian cells from integrative and non-integrative based gene delivery systems in the context of gene therapy. It also discusses the prospects of achieving an effective and sustained transgene expression for future gene therapy applications.
Collapse
Affiliation(s)
- Suleiman Yusuf Alhaji
- a Medical Genetics Laboratory, Department of Biomedical Sciences, Faculty of Medicine and Health Sciences , Universiti Putra Malaysia, UPM , Serdang , Malaysia.,b Department of Human Anatomy , College of Medical Sciences, Abubakar Tafawa Balewa University Bauchi, ATBU , Bauchi , Nigeria
| | - Siew Ching Ngai
- c School of Biosciences, Faculty of Science , University of Nottingham Malaysia , Semenyih , Malaysia
| | - Syahril Abdullah
- a Medical Genetics Laboratory, Department of Biomedical Sciences, Faculty of Medicine and Health Sciences , Universiti Putra Malaysia, UPM , Serdang , Malaysia.,d UPM-MAKNA Cancer Research Laboratory, Institute of Bioscience , Universiti Putra Malaysia, UPM , Serdang , Malaysia
| |
Collapse
|
42
|
Serna S, Ercibengoa M, Marimón JM, Reichardt NC. Measuring Bacterial Glycosyl Hydrolase Activity with a Soluble Capture Probe by Mass Spectrometry. Anal Chem 2018; 90:12536-12543. [DOI: 10.1021/acs.analchem.8b02434] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2023]
Affiliation(s)
- Sonia Serna
- Glycotechnology Laboratory, CIC biomaGUNE, Paseo Miramón 182, San Sebastian 20014, Spain
| | - María Ercibengoa
- Hospital Universitario Donostia-Instituto de Investigación Sanitaria Biodonostia, Begiristain Doktorea Pasealekua 109, San Sebastián 20014, Spain
- Biomedical Research Center Network for Respiratory Diseases (CIBERES), ISCIII, Madrid 28029, Spain
| | - Jose María Marimón
- Hospital Universitario Donostia-Instituto de Investigación Sanitaria Biodonostia, Begiristain Doktorea Pasealekua 109, San Sebastián 20014, Spain
- Biomedical Research Center Network for Respiratory Diseases (CIBERES), ISCIII, Madrid 28029, Spain
| | - Niels-Christian Reichardt
- Glycotechnology Laboratory, CIC biomaGUNE, Paseo Miramón 182, San Sebastian 20014, Spain
- CIBER-BBN, Paseo Miramón 182, San Sebastian 20014, Spain
| |
Collapse
|
43
|
Pozzo T, Akter F, Nomura Y, Louie AY, Yokobayashi Y. Firefly Luciferase Mutant with Enhanced Activity and Thermostability. ACS OMEGA 2018; 3:2628-2633. [PMID: 30023842 PMCID: PMC6044891 DOI: 10.1021/acsomega.7b02068] [Citation(s) in RCA: 26] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/27/2017] [Accepted: 02/19/2018] [Indexed: 05/13/2023]
Abstract
The luciferase isolated from the firefly Photinus pyralis (Ppy) catalyzes a two-step reaction that results in the oxidation of d-luciferin accompanied by emission of yellow-green light with a peak at 560 nm. Among many applications, Ppy luciferase has been used extensively as a reporter gene in living cells and organisms. However, some biological applications are limited by the low stability of the luciferase and limited intracellular luciferin concentration. To address these challenges, efforts to protein engineer Ppy luciferase have resulted in a number of mutants with improved properties such as thermostability, pH tolerance, and catalytic turn over. In this work, we combined amino acid mutations that were shown to enhance the enzyme's thermostability (Mutant E) with those reported to enhance catalytic activity (LGR). The resulting mutant (YY5) contained eight amino acid changes from the wild-type luciferase and exhibited both improved thermostability and brighter luminescence at low luciferin concentrations. Therefore, YY5 may be useful for reporter gene applications.
Collapse
Affiliation(s)
- Tania Pozzo
- Department
of Biomedical Engineering, University of
California at Davis, One Shields Avenue, Davis, California 95616, United States
| | - Farhima Akter
- Department
of Biomedical Engineering, University of
California at Davis, One Shields Avenue, Davis, California 95616, United States
| | - Yoko Nomura
- Nucleic
Acid Chemistry and Engineering Unit, Okinawa
Institute of Science and Technology Graduate University, Onna, Okinawa 904 0495, Japan
| | - Angelique Y. Louie
- Department
of Biomedical Engineering, University of
California at Davis, One Shields Avenue, Davis, California 95616, United States
| | - Yohei Yokobayashi
- Nucleic
Acid Chemistry and Engineering Unit, Okinawa
Institute of Science and Technology Graduate University, Onna, Okinawa 904 0495, Japan
- E-mail:
| |
Collapse
|
44
|
Pseudomonas aeruginosa Biofilm Antibiotic Resistance Gene ndvB Expression Requires the RpoS Stationary-Phase Sigma Factor. Appl Environ Microbiol 2018; 84:AEM.02762-17. [PMID: 29352081 DOI: 10.1128/aem.02762-17] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2017] [Accepted: 01/11/2018] [Indexed: 01/21/2023] Open
Abstract
Chronic, biofilm-based bacterial infections are exceptionally difficult to eradicate due to the high degree of antibiotic recalcitrance exhibited by cells in biofilm communities. In the opportunistic pathogen Pseudomonas aeruginosa, biofilm recalcitrance is multifactorial and arises in part from the preferential expression of resistance genes in biofilms compared to exponential-phase planktonic cells. One such mechanism involves ndvB, which we have previously shown to be expressed specifically in biofilms. In this study, we investigated the regulatory basis of this lifestyle-specific expression by developing an unstable green fluorescent protein (GFP) transcriptional reporter to observe the expression pattern of ndvB We found that in addition to its expression in biofilms, ndvB was upregulated in planktonic cells as they enter stationary phase. The transcription of ndvB in both growth phases was shown to be dependent on the stationary-phase sigma factor RpoS, and mutation of a putative RpoS binding site in the ndvB promoter abolished the activity of the promoter in stationary-phase cells. Overall, we have expanded our understanding of the temporal expression of ndvB in P. aeruginosa and have uncovered a regulatory basis for its growth phase-dependent expression.IMPORTANCE Bacterial biofilms are more resistant to antibiotics than free-living planktonic cells, and understanding the mechanistic basis of this resistance can inform treatments of biofilm-based infections. In addition to chemical and structural barriers that can inhibit antibiotic entry, the upregulation of specific genes in biofilms contributes to the resistance. We investigated this biofilm-specific gene induction by examining expression patterns of ndvB, a gene involved in biofilm resistance of the opportunistic pathogen Pseudomonas aeruginosa We characterized ndvB expression in planktonic and biofilm growth conditions with an unstable green fluorescent protein (GFP) reporter and found that the expression of ndvB in biofilms is dependent on the stationary-phase sigma factor RpoS. Overall, our results support the physiological similarity between biofilms and stationary-phase cells and suggest that the induction of some stationary-phase genes in biofilms may contribute to their increased antibiotic resistance.
Collapse
|
45
|
Spring SA, Goggins S, Frost CG. Ratiometric electrochemical detection of β-galactosidase. Org Biomol Chem 2018; 15:7122-7126. [PMID: 28828425 DOI: 10.1039/c7ob01593c] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
Abstract
A novel ferrocene-based substrate for the ratiometric electrochemical detection of β-galactosidase was designed and synthesised. It was demonstrated to be an excellent electrochemical substrate for β-Gal detection with sensitivity as low as 0.1 U mL-1.
Collapse
Affiliation(s)
- Sam A Spring
- Department of Chemistry, University of Bath, Bath, BA2 7AY, UK.
| | | | | |
Collapse
|
46
|
Uno K, Murotomi K, Kazuki Y, Oshimura M, Nakajima Y. Bioluminescence-based cytotoxicity assay for simultaneous evaluation of cell viability and membrane damage in human hepatoma HepG2 cells. LUMINESCENCE 2018; 33:616-624. [PMID: 29424036 DOI: 10.1002/bio.3454] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2017] [Revised: 12/16/2017] [Accepted: 12/20/2017] [Indexed: 12/19/2022]
Abstract
We have developed a bioluminescence-based non-destructive cytotoxicity assay in which cell viability and membrane damage are simultaneously evaluated using Emerald luciferase (ELuc) and endoplasmic reticulum (ER)-targeted copepod luciferase (GLuc-KDEL), respectively, by using multi-integrase mouse artificial chromosome (MI-MAC) vector. We have demonstrated that the time-dependent concentration response curves of ELuc luminescence intensity and WST-1 assay, and GLuc-KDEL luminescence intensity and lactate dehydrogenase (LDH) activity in the culture medium accompanied by cytotoxicity show good agreement in toxicant-treated ELuc- and GLuc-KDEL-expressing HepG2 stable cell lines. We have clarified that the increase of GLuc-KDEL luminescence intensity in the culture medium reflects the type of cell death, including necrosis and late apoptosis, but not early apoptosis. We have also uncovered a strong correlation between GLuc-KDEL luminescence intensity in the culture medium and the extracellular release of high mobility group box 1 (HMGB1), a representative damage-associated molecular pattern (DAMP) molecule. The bioluminescence measurement assay using ELuc and GLuc-KDEL developed in this study can simultaneously monitor cell viability and membrane damage, respectively, and the increase of GLuc-KDEL luminescence intensity in the culture medium accompanied by the increase of cytotoxicity is an index of necrosis and late apoptosis associated with the extracellular release of DAMP molecules.
Collapse
Affiliation(s)
- Katsuhiro Uno
- Chromosome Engineering Research Center, Tottori University, Yonago, Tottori, Japan
| | - Kazutoshi Murotomi
- Health Research Institute, National Institute of Advanced Industrial Science and Technology (AIST), Takamatsu, Kagawa, Japan
| | - Yasuhiro Kazuki
- Chromosome Engineering Research Center, Tottori University, Yonago, Tottori, Japan
| | - Mitsuo Oshimura
- Chromosome Engineering Research Center, Tottori University, Yonago, Tottori, Japan
| | - Yoshihiro Nakajima
- Chromosome Engineering Research Center, Tottori University, Yonago, Tottori, Japan.,Health Research Institute, National Institute of Advanced Industrial Science and Technology (AIST), Takamatsu, Kagawa, Japan
| |
Collapse
|
47
|
Satoh D, Abe S, Kobayashi K, Nakajima Y, Oshimura M, Kazuki Y. Human and mouse artificial chromosome technologies for studies of pharmacokinetics and toxicokinetics. Drug Metab Pharmacokinet 2018; 33:17-30. [DOI: 10.1016/j.dmpk.2018.01.002] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2017] [Revised: 11/29/2017] [Accepted: 12/21/2017] [Indexed: 12/27/2022]
|
48
|
Zeng L, Wang YL, Wang F, Cui SQ, Hu L, Huang DN, Hou G. Construction of the POT1 promoter report gene vector, and the effect and underlying mechanism of the POT1 promoter in regulating telomerase and telomere length. Oncol Lett 2018; 14:7232-7240. [PMID: 29344158 PMCID: PMC5754914 DOI: 10.3892/ol.2017.7127] [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: 12/09/2015] [Accepted: 05/11/2017] [Indexed: 11/05/2022] Open
Abstract
By using human genomic DNA as a template to clone protection of telomere 1 (POT1) promoter gene segments and construct the POT1 promoter luciferase report gene vector (pGL3-Control-POT1-promoter), the association between POT1, and the regulation of telomerase and telomere length was investigated. In the present study, two recombinant luciferase report gene vectors were constructed, which included different regions of the POT1 promoter. The plasmids were transformed into DH5α and the positive clones were obtained. The two plasmids termed as pGL3-Control-POT1-promoter-1 and pGL3-Control-POT1-promoter-2, were confirmed using restriction enzyme analysis and sequencing. They were separately and transiently transfected into four types of human tumor cells (A549, H460, HepG2 and HeLa). The transcriptional activities of the POT1 promoter were verified using the dual-luciferase assay. The relative expression of POT1 and human telomerase reverse transcriptase (hTERT), and telomere length were analyzed using quantitative polymerase chain reaction in the four types of non-transfected tumor cells. Using SPSS software, correlations between POT1 promoter activity, and POT1 expression, hTERT expression and telomere length were analyzed. Two POT1 promoter fragments (POT1-promoter-1 and -2) were successfully constructed into the pGL3-Control luciferase report gene vector. POT1-promoter-1 exhibited significantly stronger transcription activity compared with POT1-promoter-2. The results of the partial correlation and linear regression analyses were similar: POT1 promoter activity was identified to be significantly and positively correlated with POT1 expression and telomere length (partial correlation coefficients, both P<0.05; linear regression, both P<0.01). However, POT1 promoter activity and hTERT expression were significantly negatively correlated (both P<0.05). The results obtained in the present study suggest that the POT1 promoter influences telomere length. Furthermore, these data indicated that POT1 promoter activity and POT1, as well as telomere length, may be a useful biomarker for tumor detection and future patient prognosis.
Collapse
Affiliation(s)
- Liang Zeng
- Department of Basic Medicine, Institute of Biochemistry and Molecular Biology, Guangdong Medical University, Zhanjiang, Guangdong 524023, P.R. China
| | - Yue-Li Wang
- Department of Basic Medicine, Institute of Biochemistry and Molecular Biology, Guangdong Medical University, Zhanjiang, Guangdong 524023, P.R. China
| | - Fa Wang
- Department of Basic Medicine, Institute of Biochemistry and Molecular Biology, Guangdong Medical University, Zhanjiang, Guangdong 524023, P.R. China
| | - Shi-Quan Cui
- Department of Basic Medicine, Institute of Biochemistry and Molecular Biology, Guangdong Medical University, Zhanjiang, Guangdong 524023, P.R. China
| | - Liang Hu
- Department of Basic Medicine, Institute of Biochemistry and Molecular Biology, Guangdong Medical University, Zhanjiang, Guangdong 524023, P.R. China
| | - Di-Nan Huang
- Department of Clinical Biochemistry, Guangdong Medical University, Dongguan, Guangdong 523808, P.R. China
| | - Gan Hou
- Department of Clinical Biochemistry, Guangdong Medical University, Dongguan, Guangdong 523808, P.R. China
| |
Collapse
|
49
|
Abstract
While luminescent reporter gene assays allow for a rapid and relatively interference free assessment of the activation state of a luminescent reporter, fluorescent reporters do not. They suffer from artifacts such as compound fluorescence and cellular debris which makes the assessment of whole well fluorescence signals difficult. However, the use of high-content screening allows for the isolation of individual cells, segmentation and thus enables the screener to utilize fluorescent reporters to assess the activation state of such a high-content reporter on a cell by cell level, thus minimizing artifacts. Here we discuss the use of such a high-content reporter that enables screening for compounds useful for HIV reactivation on Jurkat cells with high-content screening.
Collapse
Affiliation(s)
- Erica Cook
- Lead Discovery and Optimization, Bristol Myers Squibb, Pennington, NJ, USA
| | - Jeffrey Hermes
- Screening and Translational Enzymology, Roche, Basel, Canton of Basel-Stadt, Switzerland
| | - Jing Li
- Screening & Protein Sciences, Merck Research Labs, Merck & Co., Inc., North Wales, PA, USA
| | - Matthew Tudor
- Screening & Protein Sciences, Merck Research Labs, Merck & Co., Inc., North Wales, PA, USA.
| |
Collapse
|
50
|
Seo SO, Lu T, Jin YS, Blaschek HP. Development of an oxygen-independent flavin mononucleotide-based fluorescent reporter system in Clostridium beijerinckii and its potential applications. J Biotechnol 2017; 265:119-126. [PMID: 29158189 DOI: 10.1016/j.jbiotec.2017.11.003] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2017] [Revised: 11/02/2017] [Accepted: 11/06/2017] [Indexed: 12/21/2022]
Abstract
Clostridium beijerinckii is a predominant solventogenic clostridia with great attraction for renewable liquid biofuel and biochemical production. Metabolic engineering and synthetic biology can be employed to engineer the strain toward desirable phenotypes. However, current limited information such as promoter strength and gene regulation may hinder the efficient engineering of the strain. To investigate genetic information and complex cellular bioprocesses of C. beijerinckii, an in vivo fluorescence reporter system can be employed. In general, green fluorescence protein (GFP) and relative analogs have been widely used as real-time reporters. However, GFP-family proteins require molecular oxygen for fluorescence maturation. Considering the strict anaerobic growth requirement of the clostridia, an oxygen-independent fluorescence reporter such as a flavin mononucleotide-based fluorescent protein (FbFP) can be used as an alternative fluorescence reporter. In this study, we synthesized and expressed the codon-optimized FbFP gene for C. beijerinckii (CbFbFP) based on the nucleotide sequence of Bacillus subtilis YtvA variant EcFbFP in C. beijerinckii NCIMB 8052 wild-type. Protein expression and in vivo fluorescence of CbFbFP in C. beijeirnckii were confirmed under anaerobic growth conditions. Through fluorescence-activated cell sorting (FACS), we isolated the bright cells from the heterogenous population of C. beijerinckii cells expressing CbFbFP. Several mutations were found in the isolated plasmid which may be responsible for the high-level expression of CbFbFP in C. beijerinckii. The mutant plasmid and CbFbFP reporter were further utilized for strain selection, real-time fluorescence measurement, population analysis, and metabolic engineering in this study.
Collapse
Affiliation(s)
- Seung-Oh Seo
- Department of Food Science and Human Nutrition, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA; Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
| | - Ting Lu
- Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA; Department of Bioengineering and Department of Physics, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
| | - Yong-Su Jin
- Department of Food Science and Human Nutrition, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA; Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA.
| | - Hans P Blaschek
- Department of Food Science and Human Nutrition, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA.
| |
Collapse
|