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Anderson NT, Xie JS, Chacko AN, Liu VL, Fan KC, Mukherjee A. Rational Design of a Circularly Permuted Flavin-Based Fluorescent Protein. Chembiochem 2024; 25:e202300814. [PMID: 38356332 PMCID: PMC11065581 DOI: 10.1002/cbic.202300814] [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: 12/01/2023] [Revised: 02/12/2024] [Accepted: 02/14/2024] [Indexed: 02/16/2024]
Abstract
Flavin-based fluorescent proteins are oxygen-independent reporters that hold great promise for imaging anaerobic and hypoxic biological systems. In this study, we explored the feasibility of applying circular permutation, a valuable method for the creation of fluorescent sensors, to flavin-based fluorescent proteins. We used rational design and structural data to identify a suitable location for circular permutation in iLOV, a flavin-based reporter derived from A. thaliana. However, relocating the N- and C-termini to this position resulted in a significant reduction in fluorescence. This loss of fluorescence was reversible, however, by fusing dimerizing coiled coils at the new N- and C-termini to compensate for the increase in local chain entropy. Additionally, by inserting protease cleavage sites in circularly permuted iLOV, we developed two protease sensors and demonstrated their application in mammalian cells. In summary, our work establishes the first approach to engineer circularly permuted FbFPs optimized for high fluorescence and further showcases the utility of circularly permuted FbFPs to serve as a scaffold for sensor engineering.
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Affiliation(s)
| | - Jason S. Xie
- Department of Molecular, Cellular, and Developmental Biology
| | | | - Vannie L. Liu
- Department of Molecular, Cellular, and Developmental Biology
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2
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Liang GT, Lai C, Yue Z, Zhang H, Li D, Chen Z, Lu X, Tao L, Subach FV, Piatkevich KD. Enhanced small green fluorescent proteins as a multisensing platform for biosensor development. Front Bioeng Biotechnol 2022; 10:1039317. [PMID: 36324888 PMCID: PMC9618808 DOI: 10.3389/fbioe.2022.1039317] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2022] [Accepted: 09/30/2022] [Indexed: 12/02/2022] Open
Abstract
Engineered light, oxygen, and voltage (LOV)-based proteins are able to fluoresce without oxygen requirement due to the autocatalytic incorporation of exogenous flavin as a chromophore thus allowing for live cell imaging under hypoxic and anaerobic conditions. They were also discovered to have high sensitivity to transition metal ions and physiological flavin derivatives. These properties make flavin-binding fluorescent proteins (FPs) a perspective platform for biosensor development. However, brightness of currently available flavin-binding FPs is limited compared to GFP-like FPs creating a need for their further enhancement and optimization. In this study, we applied a directed molecular evolution approach to develop a pair of flavin-binding FPs, named miniGFP1 and miniGFP2. The miniGFP proteins are characterized by cyan-green fluorescence with excitation/emission maxima at 450/499 nm and a molecular size of ∼13 kDa. We carried out systematic benchmarking of miniGFPs in Escherichia coli and cultured mammalian cells against spectrally similar FPs including GFP-like FP, bilirubin-binding FP, and bright flavin-binding FPs. The miniGFPs proteins exhibited improved photochemical properties compared to other flavin-binding FPs enabling long-term live cell imaging. We demonstrated the utility of miniGFPs for live cell imaging in bacterial culture under anaerobic conditions and in CHO cells under hypoxia. The miniGFPs’ fluorescence was highly sensitive to Cu(II) ions in solution with Kd values of 67 and 68 nM for miniGFP1 and miniGFP2, respectively. We also observed fluorescence quenching of miniGFPs by the reduced form of Cu(I) suggesting its potential application as an optical indicator for Cu(I) and Cu(II). In addition, miniGFPs showed the ability to selectively bind exogenous flavin mononucleotide demonstrating a potential for utilization as a selective fluorescent flavin indicator. Altogether, miniGFPs can serve as a multisensing platform for fluorescence biosensor development for in vitro and in-cell applications.
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Affiliation(s)
- Guo-Teng Liang
- School of Life Sciences, Westlake University, Hangzhou, Zhejiang, China
- Westlake Laboratory of Life Sciences and Biomedicine, Hangzhou, Zhejiang, China
- Institute of Basic Medical Sciences, Westlake Institute for Advanced Study, Hangzhou, Zhejiang, China
- Department of Applied Biology and Chemical Technology, The Hong Kong Polytechnic University, Kowloon, Hong Kong SAR, China
| | - Cuixin Lai
- School of Life Sciences, Westlake University, Hangzhou, Zhejiang, China
- Westlake Laboratory of Life Sciences and Biomedicine, Hangzhou, Zhejiang, China
- Institute of Basic Medical Sciences, Westlake Institute for Advanced Study, Hangzhou, Zhejiang, China
| | - Zejun Yue
- School of Life Sciences, Westlake University, Hangzhou, Zhejiang, China
- Westlake Laboratory of Life Sciences and Biomedicine, Hangzhou, Zhejiang, China
- Institute of Basic Medical Sciences, Westlake Institute for Advanced Study, Hangzhou, Zhejiang, China
- School of Basic Medical Sciences, Xi’an Jiao Tong University, Xi’an, Shaanxi, China
| | - Hanbin Zhang
- School of Life Sciences, Westlake University, Hangzhou, Zhejiang, China
- Westlake Laboratory of Life Sciences and Biomedicine, Hangzhou, Zhejiang, China
- Institute of Basic Medical Sciences, Westlake Institute for Advanced Study, Hangzhou, Zhejiang, China
| | - Danyang Li
- School of Life Sciences, Westlake University, Hangzhou, Zhejiang, China
- Westlake Laboratory of Life Sciences and Biomedicine, Hangzhou, Zhejiang, China
- Institute of Basic Medical Sciences, Westlake Institute for Advanced Study, Hangzhou, Zhejiang, China
| | - Zhong Chen
- Key Laboratory of Precise Synthesis of Functional Molecules of Zhejiang Province, School of Science, Instrumentation and Service Center for Molecular Sciences, Westlake University, Hangzhou, Zhejiang, China
| | - Xingyu Lu
- Key Laboratory of Precise Synthesis of Functional Molecules of Zhejiang Province, School of Science, Instrumentation and Service Center for Molecular Sciences, Westlake University, Hangzhou, Zhejiang, China
| | - Liang Tao
- School of Life Sciences, Westlake University, Hangzhou, Zhejiang, China
- Westlake Laboratory of Life Sciences and Biomedicine, Hangzhou, Zhejiang, China
- Institute of Basic Medical Sciences, Westlake Institute for Advanced Study, Hangzhou, Zhejiang, China
| | - Fedor V. Subach
- Complex of NBICS Technologies, National Research Center “Kurchatov Institute”, Moscow, Russia
| | - Kiryl D. Piatkevich
- School of Life Sciences, Westlake University, Hangzhou, Zhejiang, China
- Westlake Laboratory of Life Sciences and Biomedicine, Hangzhou, Zhejiang, China
- Institute of Basic Medical Sciences, Westlake Institute for Advanced Study, Hangzhou, Zhejiang, China
- *Correspondence: Kiryl D. Piatkevich,
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Abstract
Trichomonas vaginalis is an anaerobic/microaerophilic protist parasite which causes trichomoniasis, one of the most prevalent sexually transmitted diseases worldwide. T. vaginalis not only is important as a human pathogen but also is of great biological interest because of its peculiar cell biology and metabolism, in earlier times fostering the erroneous notion that this microorganism is at the root of eukaryotic evolution. This review summarizes the major advances in the last five years in the T. vaginalis field with regard to genetics, molecular biology, ecology, and pathogenicity of the parasite.
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Affiliation(s)
- David Leitsch
- Department of Specific Prophylaxis and Tropical Medicine, Medical University of Vienna, Vienna, Austria
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4
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Anderson NT, Weyant KB, Mukherjee A. Characterization of flavin binding in oxygen-independent fluorescent reporters. AIChE J 2020; 66. [PMID: 34305141 DOI: 10.1002/aic.17083] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Abstract
Fluorescent proteins based on light, oxygen, and voltage (LOV) sensing photoreceptors are among the few reporter gene technologies available for studying living systems in oxygen-free environments that render reporters based on the green fluorescent protein nonfluorescent. LOV reporters develop fluorescence by binding flavin mononucleotide (FMN), which they endogenously obtain from cells. As FMN is essential to cell physiology as well as for determining fluorescence in LOV proteins, it is important to be able to study and characterize flavin binding in LOV reporters. To this end, we report a method for reversibly separating FMN from two commonly used LOV reporters to prepare stable and soluble apoproteins. Using fluorescence titration, we measured the equilibrium dissociation constant for binding with all three cellular flavins: FMN, flavin adenine dinucleotide, and riboflavin. Finally, we exploit the riboflavin affinity of apo LOV reporters, identified in this work, to develop a fluorescence turn-on biosensor for vitamin B2.
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Affiliation(s)
- Nolan T. Anderson
- Department of Chemical Engineering University of California Santa Barbara California 93106 USA
| | - Kevin B. Weyant
- Smith School of Chemical & Biomolecular Engineering Cornell University Ithaca New York 14853 USA
| | - Arnab Mukherjee
- Department of Chemical Engineering University of California Santa Barbara California 93106 USA
- Department of Chemistry University of California Santa Barbara California 93106 USA
- Neuroscience Research Institute University of California Santa Barbara California 93106 USA
- Center for Bioengineering University of California Santa Barbara California 93106 USA
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5
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Synthetic Biology on Acetogenic Bacteria for Highly Efficient Conversion of C1 Gases to Biochemicals. Int J Mol Sci 2020; 21:ijms21207639. [PMID: 33076477 PMCID: PMC7589590 DOI: 10.3390/ijms21207639] [Citation(s) in RCA: 27] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2020] [Revised: 10/13/2020] [Accepted: 10/13/2020] [Indexed: 12/13/2022] Open
Abstract
Synthesis gas, which is mainly produced from fossil fuels or biomass gasification, consists of C1 gases such as carbon monoxide, carbon dioxide, and methane as well as hydrogen. Acetogenic bacteria (acetogens) have emerged as an alternative solution to recycle C1 gases by converting them into value-added biochemicals using the Wood-Ljungdahl pathway. Despite the advantage of utilizing acetogens as biocatalysts, it is difficult to develop industrial-scale bioprocesses because of their slow growth rates and low productivities. To solve these problems, conventional approaches to metabolic engineering have been applied; however, there are several limitations owing to the lack of required genetic bioparts for regulating their metabolic pathways. Recently, synthetic biology based on genetic parts, modules, and circuit design has been actively exploited to overcome the limitations in acetogen engineering. This review covers synthetic biology applications to design and build industrial platform acetogens.
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6
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Wang SE, Brooks AES, Poole AM, Simoes-Barbosa A. Determinants of translation efficiency in the evolutionarily-divergent protist Trichomonas vaginalis. BMC Mol Cell Biol 2020; 21:54. [PMID: 32689943 PMCID: PMC7370421 DOI: 10.1186/s12860-020-00297-8] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2020] [Accepted: 06/29/2020] [Indexed: 01/08/2023] Open
Abstract
BACKGROUND Trichomonas vaginalis, the causative agent of a prevalent urogenital infection in humans, is an evolutionarily divergent protozoan. Protein-coding genes in T. vaginalis are largely controlled by two core promoter elements, producing mRNAs with short 5' UTRs. The specific mechanisms adopted by T. vaginalis to fine-tune the translation efficiency (TE) of mRNAs remain largely unknown. RESULTS Using both computational and experimental approaches, this study investigated two key factors influencing TE in T. vaginalis: codon usage and mRNA secondary structure. Statistical dependence between TE and codon adaptation index (CAI) highlighted the impact of codon usage on mRNA translation in T. vaginalis. A genome-wide interrogation revealed that low structural complexity at the 5' end of mRNA followed closely by a highly structured downstream region correlates with TE variation in this organism. To validate these findings, a synthetic library of 15 synonymous iLOV genes was created, representing five mRNA folding profiles and three codon usage profiles. Fluorescence signals produced by the expression of these synonymous iLOV genes in T. vaginalis were consistent with and validated our in silico predictions. CONCLUSIONS This study demonstrates the role of codon usage bias and mRNA secondary structure in TE of T. vaginalis mRNAs, contributing to a better understanding of the factors that influence, and possibly regulate, gene expression in this human pathogen.
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Affiliation(s)
- Shuqi E Wang
- School of Biological Sciences, The University of Auckland, Auckland, New Zealand
- Department of Microbiology, Immunology, and Molecular Genetics, University of California, Los Angeles, Los Angeles, USA
| | - Anna E S Brooks
- School of Biological Sciences, The University of Auckland, Auckland, New Zealand
- Maurice Wilkins Centre, The University of Auckland, Auckland, New Zealand
| | - Anthony M Poole
- School of Biological Sciences, The University of Auckland, Auckland, New Zealand
- Bioinformatics Institute, The University of Auckland, Auckland, New Zealand
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7
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Ran X, Zhang Q, Zhang Y, Chen J, Wei Z, He Y, Guo L. Probing the Electron Transfer between iLOV Protein and Ag Nanoparticles. Molecules 2020; 25:molecules25112544. [PMID: 32486057 PMCID: PMC7321358 DOI: 10.3390/molecules25112544] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2020] [Revised: 05/18/2020] [Accepted: 05/25/2020] [Indexed: 01/10/2023] Open
Abstract
Nanomaterials have been widely used in biomedical sciences; however, the mechanism of interaction between nanoparticles and biomolecules is still not fully understood. In the present study, we report the interaction mechanism between differently sized Ag nanoparticles and the improved light-oxygen-voltage (iLOV) protein. The steady-state and time-resolved fluorescence results demonstrated that the fluorescence intensity and lifetime of the iLOV protein decreased upon its adsorption onto Ag nanoparticles, and this decrease was dependent upon nanoparticle size. Further, we showed that the decrease of fluorescence intensity and lifetime arose from electron transfer between iLOV and Ag nanoparticles. Moreover, through point mutation and controlled experimentation, we demonstrated for the first time that electron transfer between iLOV and Ag nanoparticles is mediated by the tryptophan residue in the iLOV protein. These results are of great importance in revealing the function of iLOV protein as it applies to biomolecular sensors, the field of nano-photonics, and the interaction mechanism between the protein and nanoparticles.
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Affiliation(s)
- Xia Ran
- Institute of Micro/Nano Photonic Materials and Application, School of Physics and Electronics, Henan University, Kaifeng 475004, China; (X.R.); (Q.Z.); (J.C.); (Z.W.)
- Key Laboratory of Plant Stress Biology, Henan University, Kaifeng 475001, China;
| | - Qianqian Zhang
- Institute of Micro/Nano Photonic Materials and Application, School of Physics and Electronics, Henan University, Kaifeng 475004, China; (X.R.); (Q.Z.); (J.C.); (Z.W.)
| | - Yu Zhang
- Key Laboratory of Plant Stress Biology, Henan University, Kaifeng 475001, China;
| | - Jin Chen
- Institute of Micro/Nano Photonic Materials and Application, School of Physics and Electronics, Henan University, Kaifeng 475004, China; (X.R.); (Q.Z.); (J.C.); (Z.W.)
| | - Zhongran Wei
- Institute of Micro/Nano Photonic Materials and Application, School of Physics and Electronics, Henan University, Kaifeng 475004, China; (X.R.); (Q.Z.); (J.C.); (Z.W.)
| | - Yulu He
- Institute of Micro/Nano Photonic Materials and Application, School of Physics and Electronics, Henan University, Kaifeng 475004, China; (X.R.); (Q.Z.); (J.C.); (Z.W.)
- Key Laboratory of Plant Stress Biology, Henan University, Kaifeng 475001, China;
- Correspondence: (Y.H.); (L.G.)
| | - Lijun Guo
- Institute of Micro/Nano Photonic Materials and Application, School of Physics and Electronics, Henan University, Kaifeng 475004, China; (X.R.); (Q.Z.); (J.C.); (Z.W.)
- Key Laboratory of Plant Stress Biology, Henan University, Kaifeng 475001, China;
- Correspondence: (Y.H.); (L.G.)
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8
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Ozbakir HF, Anderson NT, Fan KC, Mukherjee A. Beyond the Green Fluorescent Protein: Biomolecular Reporters for Anaerobic and Deep-Tissue Imaging. Bioconjug Chem 2020; 31:293-302. [PMID: 31794658 PMCID: PMC7033020 DOI: 10.1021/acs.bioconjchem.9b00688] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
Fluorescence imaging represents cornerstone technology for studying biological function at the cellular and molecular levels. The technology's centerpiece is a prolific collection of genetic reporters based on the green fluorescent protein (GFP) and related analogs. More than two decades of protein engineering have endowed the GFP repertoire with an incredible assortment of fluorescent proteins, allowing scientists immense latitude in choosing reporters tailored to various cellular and environmental contexts. Nevertheless, GFP and derivative reporters have specific limitations that hinder their unrestricted use for molecular imaging. These challenges have inspired the development of new reporter proteins and imaging mechanisms. Here, we review how these developments are expanding the frontiers of reporter gene techniques to enable nondestructive studies of cell function in anaerobic environments and deep inside intact animals-two important biological contexts that are fundamentally incompatible with the use of GFP-based reporters.
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Affiliation(s)
- Harun F. Ozbakir
- Department of Chemical Engineering, University of California, Santa Barbara, California 93106, United States
| | - Nolan T. Anderson
- Department of Chemical Engineering, University of California, Santa Barbara, California 93106, United States
| | - Kang-Ching Fan
- Department of Chemical Engineering, University of California, Santa Barbara, California 93106, United States
| | - Arnab Mukherjee
- Department of Chemical Engineering, University of California, Santa Barbara, California 93106, United States
- Department of Chemistry, University of California, Santa Barbara, California 93106, United States
- Neuroscience Research Institute, University of California, Santa Barbara, California 93106, United States
- Center for Bioengineering, University of California, Santa Barbara, California 93106, United States
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9
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Zhao H, Zhang Y, Pan M, Song Y, Bai L, Miao Y, Huang Y, Zhu X, Song CP. Dynamic imaging of cellular pH and redox homeostasis with a genetically encoded dual-functional biosensor, pHaROS, in yeast. J Biol Chem 2019; 294:15768-15780. [PMID: 31488545 PMCID: PMC6816096 DOI: 10.1074/jbc.ra119.007557] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2019] [Revised: 08/25/2019] [Indexed: 11/06/2022] Open
Abstract
Intracellular pH and redox states are critical for multiple processes and partly determine cell behavior. Here, we developed a genetically encoded dual-function probe, named p H and redox-sensitive fluorescent protein (pHaROS), for simultaneous real-time detection of changes in redox potential and pH in living cells. pHaROS consists of the Arabidopsis flavin mononucleotide-binding fluorescent protein iLOV and an mKATE variant, mBeRFP. Using pHaROS in Saccharomyces cerevisiae cells, we confirmed that H2O2 raises the overall redox potential of the cell and found that this increase is accompanied by a decrease in cytosolic pH. Furthermore, we observed spatiotemporal pH and redox homeostasis within the nucleus at various stages of the cell cycle in budding yeast (Saccharomyces cerevisiae) during cellular development and responses to oxidative stress. Importantly, we could tailor pHaROS to specific applications, including measurements in different organelles and cell types and the GSH/GSSG ratio, highlighting pHaROS's high flexibility and versatility. In summary, we have developed pHaROS as a dual-function probe that can be used for simultaneously measuring cellular pH and redox potential, representing a very promising tool for determining the cross-talk between intracellular redox- and pH-signaling processes in yeast and mammalian U87 cell.
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Affiliation(s)
- Hang Zhao
- Department of Biology, Institute of Plant Stress Biology, State Key Laboratory of Cotton Biology, Henan University, Kaifeng, China 475001
| | - Yu Zhang
- Department of Biology, Institute of Plant Stress Biology, State Key Laboratory of Cotton Biology, Henan University, Kaifeng, China 475001
| | - Mingming Pan
- Department of Biology, Institute of Plant Stress Biology, State Key Laboratory of Cotton Biology, Henan University, Kaifeng, China 475001
| | - Yichen Song
- Department of Biology, Institute of Plant Stress Biology, State Key Laboratory of Cotton Biology, Henan University, Kaifeng, China 475001
| | - Ling Bai
- Department of Biology, Institute of Plant Stress Biology, State Key Laboratory of Cotton Biology, Henan University, Kaifeng, China 475001
| | - Yuchen Miao
- Department of Biology, Institute of Plant Stress Biology, State Key Laboratory of Cotton Biology, Henan University, Kaifeng, China 475001
| | - Yanqin Huang
- Department of Biology, Institute of Plant Stress Biology, State Key Laboratory of Cotton Biology, Henan University, Kaifeng, China 475001
| | - Xiaohong Zhu
- Department of Biology, Institute of Plant Stress Biology, State Key Laboratory of Cotton Biology, Henan University, Kaifeng, China 475001
| | - Chun-Peng Song
- Department of Biology, Institute of Plant Stress Biology, State Key Laboratory of Cotton Biology, Henan University, Kaifeng, China 475001
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10
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Xin C, Li J, Gong P, Wu B, Zhang N, Yang J, Cai X, Zhang X. Viral RNA-based transfection and expression of enhanced green fluorescent protein in the parasitic protozoan Eimeria stiedae. Acta Biochim Biophys Sin (Shanghai) 2019; 51:216-218. [PMID: 30566566 DOI: 10.1093/abbs/gmy155] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2018] [Revised: 11/13/2018] [Accepted: 11/20/2018] [Indexed: 11/14/2022] Open
Affiliation(s)
- Caiyan Xin
- Key Laboratory of Zoonosis Research by Ministry of Education, Institute of Zoonosis, College of Veterinary Medicine, Jilin University, Changchun, China
- College of Basic Medicine, Southwest Medical University, Luzhou, China
| | - Jianhua Li
- Key Laboratory of Zoonosis Research by Ministry of Education, Institute of Zoonosis, College of Veterinary Medicine, Jilin University, Changchun, China
| | - Pengtao Gong
- Key Laboratory of Zoonosis Research by Ministry of Education, Institute of Zoonosis, College of Veterinary Medicine, Jilin University, Changchun, China
| | - Bin Wu
- Key Laboratory of Zoonosis Research by Ministry of Education, Institute of Zoonosis, College of Veterinary Medicine, Jilin University, Changchun, China
| | - Nan Zhang
- Key Laboratory of Zoonosis Research by Ministry of Education, Institute of Zoonosis, College of Veterinary Medicine, Jilin University, Changchun, China
| | - Ju Yang
- Key Laboratory of Zoonosis Research by Ministry of Education, Institute of Zoonosis, College of Veterinary Medicine, Jilin University, Changchun, China
| | - Xuepeng Cai
- Key Laboratory of Zoonosis Research by Ministry of Education, Institute of Zoonosis, College of Veterinary Medicine, Jilin University, Changchun, China
- State Key Laboratory of Veterinary Etiological Biology, Lanzhou Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Lanzhou, China
| | - Xichen Zhang
- Key Laboratory of Zoonosis Research by Ministry of Education, Institute of Zoonosis, College of Veterinary Medicine, Jilin University, Changchun, China
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11
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Di H, Morantz EK, Sadhwani H, Madden JC, Brinton MA. Insertion position as well as the inserted TRS and gene sequences differentially affect the retention of foreign gene expression by simian hemorrhagic fever virus (SHFV). Virology 2018; 525:150-160. [PMID: 30286427 DOI: 10.1016/j.virol.2018.09.014] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2018] [Revised: 09/18/2018] [Accepted: 09/19/2018] [Indexed: 12/26/2022]
Abstract
Recombinant SHFV infectious cDNA clones expressing a foreign gene from an additional sg mRNA were constructed. Two 3' genomic region sites, between ORF4' and ORF2b and between ORF4 and ORF5, were utilized for insertion of the myxoma M013 gene with a C-terminal V5 tag followed by one of the three inserted transcription regulatory sequences (TRS), TRS2', TRS4' or TRS7. M013 insertion at the ORF4'/ORF2b site but not the ORF4/ORF5 site generated progeny virus but only the recombinant virus with an inserted TRS2' retained the entire M013 gene through passage four. Insertion of an auto-fluorescent protein gene, iLOV, with an inserted TRS2' at the ORF4'/ORF2b site, generated viable progeny virus. iLOV expression was maintained through passage eight. Although regulation of SHFV subgenomic RNA synthesis is complex, the ORF4'/ORF2b site, which is located between the two sets of minor structural proteins, is able to tolerate foreign gene insertion.
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Affiliation(s)
- Han Di
- Department of Biology, Georgia State University, Atlanta, GA 30303, United States
| | - Esther K Morantz
- Department of Biology, Georgia State University, Atlanta, GA 30303, United States
| | - Heena Sadhwani
- Department of Biology, Georgia State University, Atlanta, GA 30303, United States
| | - Joseph C Madden
- Department of Biology, Georgia State University, Atlanta, GA 30303, United States
| | - Margo A Brinton
- Department of Biology, Georgia State University, Atlanta, GA 30303, United States.
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12
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Mercer F, Johnson PJ. Trichomonas vaginalis: Pathogenesis, Symbiont Interactions, and Host Cell Immune Responses. Trends Parasitol 2018; 34:683-693. [PMID: 30056833 PMCID: PMC11132421 DOI: 10.1016/j.pt.2018.05.006] [Citation(s) in RCA: 73] [Impact Index Per Article: 12.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2018] [Revised: 05/21/2018] [Accepted: 05/30/2018] [Indexed: 01/03/2023]
Abstract
The parasite Trichomonas vaginalis (Tv) causes a highly prevalent sexually transmitted infection. As an extracellular pathogen, the parasite mediates adherence to epithelial cells to colonize the human host. In addition, the parasite interfaces with the host immune system and the vaginal microbiota. Modes of Tv pathogenesis include damage to host tissue mediated by parasite killing of host cells, disruption of steady-state vaginal microbial ecology, and eliciting inflammation by activating the host immune response. Recent Tv research has uncovered new players that contribute to multifactorial mechanisms of host-parasite adherence and killing, and has examined the relationship between Tv and vaginal bacteria. Mechanisms that may lead to parasite recognition and killing, or the evasion of host immune cells, have also been revealed.
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Affiliation(s)
- Frances Mercer
- Department of Biological Sciences, California State Polytechnic University, 3801 West Temple Avenue, Pomona, CA 91768, USA.
| | - Patricia J Johnson
- Department of Microbiology, Immunology & Molecular Genetics, University of California, 1602 Molecular Sciences Building, 609 Charles E. Young Drive East, Los Angeles, CA 90095-1489, USA.
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13
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Abstract
Sensory photoreceptors underpin light-dependent adaptations of organismal physiology, development, and behavior in nature. Adapted for optogenetics, sensory photoreceptors become genetically encoded actuators and reporters to enable the noninvasive, spatiotemporally accurate and reversible control by light of cellular processes. Rooted in a mechanistic understanding of natural photoreceptors, artificial photoreceptors with customized light-gated function have been engineered that greatly expand the scope of optogenetics beyond the original application of light-controlled ion flow. As we survey presently, UV/blue-light-sensitive photoreceptors have particularly allowed optogenetics to transcend its initial neuroscience applications by unlocking numerous additional cellular processes and parameters for optogenetic intervention, including gene expression, DNA recombination, subcellular localization, cytoskeleton dynamics, intracellular protein stability, signal transduction cascades, apoptosis, and enzyme activity. The engineering of novel photoreceptors benefits from powerful and reusable design strategies, most importantly light-dependent protein association and (un)folding reactions. Additionally, modified versions of these same sensory photoreceptors serve as fluorescent proteins and generators of singlet oxygen, thereby further enriching the optogenetic toolkit. The available and upcoming UV/blue-light-sensitive actuators and reporters enable the detailed and quantitative interrogation of cellular signal networks and processes in increasingly more precise and illuminating manners.
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Affiliation(s)
- Aba Losi
- Department of Mathematical, Physical and Computer Sciences , University of Parma , Parco Area delle Scienze 7/A-43124 Parma , Italy
| | - Kevin H Gardner
- Structural Biology Initiative, CUNY Advanced Science Research Center , New York , New York 10031 , United States.,Department of Chemistry and Biochemistry, City College of New York , New York , New York 10031 , United States.,Ph.D. Programs in Biochemistry, Chemistry, and Biology , The Graduate Center of the City University of New York , New York , New York 10016 , United States
| | - Andreas Möglich
- Lehrstuhl für Biochemie , Universität Bayreuth , 95447 Bayreuth , Germany.,Research Center for Bio-Macromolecules , Universität Bayreuth , 95447 Bayreuth , Germany.,Bayreuth Center for Biochemistry & Molecular Biology , Universität Bayreuth , 95447 Bayreuth , Germany
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Janssen BD, Chen YP, Molgora BM, Wang SE, Simoes-Barbosa A, Johnson PJ. CRISPR/Cas9-mediated gene modification and gene knock out in the human-infective parasite Trichomonas vaginalis. Sci Rep 2018; 8:270. [PMID: 29321601 PMCID: PMC5762654 DOI: 10.1038/s41598-017-18442-3] [Citation(s) in RCA: 34] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2017] [Accepted: 12/11/2017] [Indexed: 12/20/2022] Open
Abstract
The sexually-transmitted parasite Trichomonas vaginalis infects ~1/4 billion people worldwide. Despite its prevalence and myriad adverse outcomes of infection, the mechanisms underlying T. vaginalis pathogenesis are poorly understood. Genetic manipulation of this single-celled eukaryote has been hindered by challenges presented by its complex, repetitive genome and inefficient methods for introducing DNA (i.e. transfection) into the parasite. Here, we have developed methods to increase transfection efficiency using nucleofection, with the goal of efficiently introducing multiple DNA elements into a single T. vaginalis cell. We then created DNA constructs required to express several components essential to drive CRISPR/Cas9-mediated DNA modification: guide RNA (gRNA), the Cas9 endonuclease, short oligonucleotides and large, linearized DNA templates. Using these technical advances, we have established CRISPR/Cas9-mediated repair of mutations in genes contained on circular DNA plasmids harbored by the parasite. We also engineered CRISPR/Cas9 directed homologous recombination to delete (i.e. knock out) two non-essential genes within the T. vaginalis genome. This first report of the use of the CRISPR/Cas9 system in T. vaginalis greatly expands the ability to manipulate the genome of this pathogen and sets the stage for testing of the role of specific genes in many biological processes.
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Affiliation(s)
- Brian D Janssen
- Department of Microbiology, Immunology & Molecular Genetics, University of California, Los Angeles, California, USA
| | - Yi-Pei Chen
- Department of Microbiology, Immunology & Molecular Genetics, University of California, Los Angeles, California, USA
- Molecular Biology Institute, University of California, Los Angeles, California, USA
| | - Brenda M Molgora
- Department of Microbiology, Immunology & Molecular Genetics, University of California, Los Angeles, California, USA
- Molecular Biology Institute, University of California, Los Angeles, California, USA
| | - Shuqi E Wang
- School of Biological Sciences, University of Auckland, Auckland, New Zealand
| | | | - Patricia J Johnson
- Department of Microbiology, Immunology & Molecular Genetics, University of California, Los Angeles, California, USA.
- Molecular Biology Institute, University of California, Los Angeles, California, USA.
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