1
|
Lautenschläger N, Schmidt K, Schiffer C, Wulff TF, Hahnke K, Finstermeier K, Mansour M, Elsholz AKW, Charpentier E. Expanding the genetic toolbox for the obligate human pathogen Streptococcus pyogenes. Front Bioeng Biotechnol 2024; 12:1395659. [PMID: 38911550 PMCID: PMC11190166 DOI: 10.3389/fbioe.2024.1395659] [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: 03/04/2024] [Accepted: 05/06/2024] [Indexed: 06/25/2024] Open
Abstract
Genetic tools form the basis for the study of molecular mechanisms. Despite many recent advances in the field of genetic engineering in bacteria, genetic toolsets remain scarce for non-model organisms, such as the obligatory human pathogen Streptococcus pyogenes. To overcome this limitation and enable the straightforward investigation of gene functions in S. pyogenes, we have developed a comprehensive genetic toolset. By adapting and combining different tools previously applied in other Gram-positive bacteria, we have created new replicative and integrative plasmids for gene expression and genetic manipulation, constitutive and inducible promoters as well as fluorescence reporters for S. pyogenes. The new replicative plasmids feature low- and high-copy replicons combined with different resistance cassettes and a standardized multiple cloning site for rapid cloning procedures. We designed site-specific integrative plasmids and verified their integration by nanopore sequencing. To minimize the effect of plasmid integration on bacterial physiology, we screened publicly available RNA-sequencing datasets for transcriptionally silent sites. We validated this approach by designing the integrative plasmid pSpy0K6 targeting the transcriptionally silent gene SPy_1078. Analysis of the activity of different constitutive promoters indicated a wide variety of strengths, with the lactococcal promoter P 23 showing the strongest activity and the synthetic promoter P xylS2 showing the weakest activity. Further, we assessed the functionality of three inducible regulatory elements including a zinc- and an IPTG-inducible promoter as well as an erythromycin-inducible riboswitch that showed low-to-no background expression and high inducibility. Additionally, we demonstrated the applicability of two codon-optimized fluorescent proteins, mNeongreen and mKate2, as reporters in S. pyogenes. We therefore adapted the chemically defined medium called RPMI4Spy that showed reduced autofluorescence and enabled efficient signal detection in plate reader assays and fluorescence microscopy. Finally, we developed a plasmid-based system for genome engineering in S. pyogenes featuring the counterselection marker pheS*, which enabled the scarless deletion of the sagB gene. This new toolbox simplifies previously laborious genetic manipulation procedures and lays the foundation for new methodologies to study gene functions in S. pyogenes, leading to a better understanding of its virulence mechanisms and physiology.
Collapse
Affiliation(s)
| | - Katja Schmidt
- Max Planck Unit for the Science of Pathogens, Berlin, Germany
| | | | - Thomas F. Wulff
- Max Planck Unit for the Science of Pathogens, Berlin, Germany
| | - Karin Hahnke
- Max Planck Unit for the Science of Pathogens, Berlin, Germany
| | | | - Moïse Mansour
- Max Planck Unit for the Science of Pathogens, Berlin, Germany
| | | | - Emmanuelle Charpentier
- Max Planck Unit for the Science of Pathogens, Berlin, Germany
- Institut für Biologie, Humboldt-Universität zu Berlin, Berlin, Germany
| |
Collapse
|
2
|
Yang W, Wang W, Jing L, Chen SL. Label-free photoacoustic microscopy: a potential tool for the live imaging of blood disorders in zebrafish. BIOMEDICAL OPTICS EXPRESS 2021; 12:3643-3657. [PMID: 34221685 PMCID: PMC8221952 DOI: 10.1364/boe.425994] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/25/2021] [Revised: 05/17/2021] [Accepted: 05/18/2021] [Indexed: 05/29/2023]
Abstract
The zebrafish has emerged as a useful model for human hematological disorders. Transgenic zebrafish that express green fluorescence protein (GFP) in red blood cells (RBCs) visualized by fluorescence microscopy (FLM) is a fundamental approach in such studies to understand the cellular processes and biological functions. However, additional and cumbersome efforts are required to breed a transgenic zebrafish line with reliable GFP expression. Further, the yolk autofluorescence and finite GFP fluorescence lifetimes also have an adverse impact on the observation of target signals. Here, we investigate the identification of intracerebral hemorrhage (ICH) and hemolytic anemia (HA) in zebrafish embryos using label-free photoacoustic microscopy (PAM) for imaging. First, ICH and HA in transgenic LCR-EGFP zebrafish are mainly studied by PAM and FLM. The results show that PAM is comparable to FLM in good identification of ICH and HA. Besides, PAM is more advantageous in circumventing the issue of autofluorescence. Secondly, ICH and HA in the transparent casper zebrafish without fluorescent labeling are imaged by PAM and bright-field microscopy (BFM). Because of the high contrast to reveal RBCs, PAM obviously outperforms BFM in the identification of both ICH and HA. Note that FLM cannot observe casper zebrafish due to its lack of fluorescent labeling. Our work proves that PAM can be a useful tool to study blood disorders in zebrafish, which has advantages: (i) Reliable results enabled by intrinsic absorption of RBCs; (ii) wide applicability to zebrafish strains (no requirement of a transgene); (iii) high sensitivity in identification of ICH and HA compared with BFM.
Collapse
Affiliation(s)
- Wenzhao Yang
- University of Michigan-Shanghai Jiao Tong University Joint Institute, Shanghai Jiao Tong University, Shanghai 200240, China
- These authors contributed equally to this work
| | - Wei Wang
- Engineering Research Center of Cell & Therapeutic Antibody, Ministry of Education, School of Pharmacy, Shanghai Jiao Tong University, Shanghai 200240, China
- These authors contributed equally to this work
| | - Lili Jing
- Engineering Research Center of Cell & Therapeutic Antibody, Ministry of Education, School of Pharmacy, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Sung-Liang Chen
- University of Michigan-Shanghai Jiao Tong University Joint Institute, Shanghai Jiao Tong University, Shanghai 200240, China
- Engineering Research Center of Digital Medicine and Clinical Translation, Ministry of Education, Shanghai 200030, China
- State Key Laboratory of Advanced Optical Communication Systems and Networks, Shanghai Jiao Tong University, Shanghai 200240, China
| |
Collapse
|
3
|
Capturing and Understanding the Dynamics and Heterogeneity of Gene Expression in the Living Cell. Int J Mol Sci 2020; 21:ijms21218278. [PMID: 33167354 PMCID: PMC7663833 DOI: 10.3390/ijms21218278] [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: 09/23/2020] [Revised: 10/29/2020] [Accepted: 11/03/2020] [Indexed: 11/21/2022] Open
Abstract
The regulation of gene expression is a fundamental process enabling cells to respond to internal and external stimuli or to execute developmental programs. Changes in gene expression are highly dynamic and depend on many intrinsic and extrinsic factors. In this review, we highlight the dynamic nature of transient gene expression changes to better understand cell physiology and development in general. We will start by comparing recent in vivo procedures to capture gene expression in real time. Intrinsic factors modulating gene expression dynamics will then be discussed, focusing on chromatin modifications. Furthermore, we will dissect how cell physiology or age impacts on dynamic gene regulation and especially discuss molecular insights into acquired transcriptional memory. Finally, this review will give an update on the mechanisms of heterogeneous gene expression among genetically identical individual cells. We will mainly focus on state-of-the-art developments in the yeast model but also cover higher eukaryotic systems.
Collapse
|
4
|
Evaluation of in vitro and in vivo antibiotic efficacy against a novel bioluminescent Shigella flexneri. Sci Rep 2019; 9:13567. [PMID: 31537849 PMCID: PMC6753072 DOI: 10.1038/s41598-019-49729-2] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2018] [Accepted: 08/30/2019] [Indexed: 12/13/2022] Open
Abstract
Shigella spp., the bacteria responsible for shigellosis, are one of the leading causes of diarrheal morbidity and mortality amongst children. There is a pressing need for the development of novel therapeutics, as resistance of Shigella to many currently used antibiotics is rapidly emerging. This paper describes the development of robust in vitro and in vivo tools to study antibiotic efficacy against Shigella flexneri. A novel bioluminescent S. flexneri strain (S. flexneri lux1) was generated, which can be used in a mammalian epithelial cell co-culture assay to evaluate antibiotic intracellular and extracellular efficacy. In addition, the S. flexneri lux1 strain was used with an intraperitoneal (IP) murine model of shigellosis to test the efficacy of ciprofloxacin and ampicillin. Both antibiotics significantly reduced the observed radiance from the gastrointestinal tissue of infected mice compared to vehicle control. Furthermore, plated gastrointestinal tissue homogenate confirmed antibiotic treatment significantly reduced the S. flexneri infection. However, in contrast to the results generated with tissue homogenate, the radiance data was not able to distinguish between the efficacy of ampicillin and ciprofloxacin. Compared to traditional methods, these models can be utilized for efficient screening of novel antibiotics aiding in the discovery of new treatments against shigellosis.
Collapse
|
5
|
Quitzke V, Fersch J, Seyhan D, Rother M. Selenium-dependent gene expression in Methanococcus maripaludis: Involvement of the transcriptional regulator HrsM. Biochim Biophys Acta Gen Subj 2018; 1862:2441-2450. [DOI: 10.1016/j.bbagen.2018.03.030] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2018] [Revised: 03/28/2018] [Accepted: 03/29/2018] [Indexed: 01/23/2023]
|
6
|
A set of synthetic versatile genetic control elements for the efficient expression of genes in Actinobacteria. Sci Rep 2018; 8:491. [PMID: 29323285 PMCID: PMC5765039 DOI: 10.1038/s41598-017-18846-1] [Citation(s) in RCA: 39] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2017] [Accepted: 12/18/2017] [Indexed: 12/22/2022] Open
Abstract
The design and engineering of secondary metabolite gene clusters that are characterized by complicated genetic organization, require the development of collections of well-characterized genetic control elements that can be reused reliably. Although a few intrinsic terminators and RBSs are used routinely, their translation and termination efficiencies have not been systematically studied in Actinobacteria. Here, we analyzed the influence of the regions surrounding RBSs on gene expression in these bacteria. We demonstrated that inappropriate RBSs can reduce the expression efficiency of a gene to zero. We developed a genetic device – an in vivo RBS-selector – that allows selection of an optimal RBS for any gene of interest, enabling rational control of the protein expression level. In addition, a genetic tool that provides the opportunity for measurement of termination efficiency was developed. Using this tool, we found strong terminators that lead to a 17–100-fold reduction in downstream expression and are characterized by sufficient sequence diversity to reduce homologous recombination when used with other elements. For the first time, a C-terminal degradation tag was employed for the control of protein stability in Streptomyces. Finally, we describe a collection of regulatory elements that can be used to control metabolic pathways in Actinobacteria.
Collapse
|
7
|
The Bacillus BioBrick Box 2.0: expanding the genetic toolbox for the standardized work with Bacillus subtilis. Sci Rep 2017; 7:15058. [PMID: 29118374 PMCID: PMC5678133 DOI: 10.1038/s41598-017-15107-z] [Citation(s) in RCA: 67] [Impact Index Per Article: 9.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2017] [Accepted: 10/20/2017] [Indexed: 12/03/2022] Open
Abstract
Standardized and well-characterized genetic building blocks allow the convenient assembly of novel genetic modules and devices, ensuring reusability of parts and reproducibility of experiments. In the first Bacillus subtilis-specific toolbox using the BioBrick standard, we presented integrative vectors, promoters, reporter genes and epitope tags for this Gram-positive model bacterium. With the Bacillus BioBrick Box 2.0, we significantly expand the range of our toolbox by providing new integrative vectors, introducing novel tools for fine-tuning protein expression, and carefully evaluating codon-adapted fluorescence proteins in B. subtilis, which cover the whole spectrum of visible light. Moreover, we developed new reporter systems to allow evaluating the strength of promoters and ribosome binding sites. This well-evaluated extension of our BioBrick-based toolbox increases the accessibility of B. subtilis and will therefore promote the use of this model bacterium and biotechnological workhorse as a host for fundamental and applied Synthetic Biology projects.
Collapse
|
8
|
Iqbal M, Doherty N, Page AML, Qazi SNA, Ajmera I, Lund PA, Kypraios T, Scott DJ, Hill PJ, Stekel DJ. Reconstructing promoter activity from Lux bioluminescent reporters. PLoS Comput Biol 2017; 13:e1005731. [PMID: 28922354 PMCID: PMC5619816 DOI: 10.1371/journal.pcbi.1005731] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2017] [Revised: 09/28/2017] [Accepted: 08/19/2017] [Indexed: 11/19/2022] Open
Abstract
The bacterial Lux system is used as a gene expression reporter. It is fast, sensitive and non-destructive, enabling high frequency measurements. Originally developed for bacterial cells, it has also been adapted for eukaryotic cells, and can be used for whole cell biosensors, or in real time with live animals without the need for euthanasia. However, correct interpretation of bioluminescent data is limited: the bioluminescence is different from gene expression because of nonlinear molecular and enzyme dynamics of the Lux system. We have developed a computational approach that, for the first time, allows users of Lux assays to infer gene transcription levels from the light output. This approach is based upon a new mathematical model for Lux activity, that includes the actions of LuxAB, LuxEC and Fre, with improved mechanisms for all reactions, as well as synthesis and turn-over of Lux proteins. The model is calibrated with new experimental data for the LuxAB and Fre reactions from Photorhabdus luminescens—the source of modern Lux reporters—while literature data has been used for LuxEC. Importantly, the data show clear evidence for previously unreported product inhibition for the LuxAB reaction. Model simulations show that predicted bioluminescent profiles can be very different from changes in gene expression, with transient peaks of light output, very similar to light output seen in some experimental data sets. By incorporating the calibrated model into a Bayesian inference scheme, we can reverse engineer promoter activity from the bioluminescence. We show examples where a decrease in bioluminescence would be better interpreted as a switching off of the promoter, or where an increase in bioluminescence would be better interpreted as a longer period of gene expression. This approach could benefit all users of Lux technology. Bioluminescent reporters are used in many areas of biology as fast, sensitive and non-destructive measures of gene expression. They have been developed for bacteria, adapted now for other kinds of organisms, and recently been used for whole cell biosensors, and for real-time live animal models for infection without the need for euthanasia. However, users of Lux technologies rely on the light output being similar to the gene expression they wish to measure. We show that this is not the case. Rather, there is a nonlinear relationship between the two: light output can be misleading and so limits the way that such data can be interpreted. We have developed a new computational method that, for the first time, allows users of Lux reporters to infer accurate gene transcription levels from bioluminescent data. We show examples where a small decrease in light would be better interpreted as promoter being switched off, or where an increase in light would be better interpreted as promoter activity for a longer time.
Collapse
Affiliation(s)
- Mudassar Iqbal
- Agricultural and Environmental Sciences, School of Biosciences, University of Nottingham, Sutton Bonington Campus, Loughborough, United Kingdom
| | - Neil Doherty
- Food Sciences, School of Biosciences, University of Nottingham, Sutton Bonington Campus, Loughborough, United Kingdom
| | - Anna M. L. Page
- Food Sciences, School of Biosciences, University of Nottingham, Sutton Bonington Campus, Loughborough, United Kingdom
| | - Saara N. A. Qazi
- Food Sciences, School of Biosciences, University of Nottingham, Sutton Bonington Campus, Loughborough, United Kingdom
| | - Ishan Ajmera
- Plant and Crop Sciences, School of Biosciences, University of Nottingham, Sutton Bonington Campus, Loughborough, United Kingdom
| | - Peter A. Lund
- School of Biosciences, University of Birmingham, Birmingham, United Kingdom
| | - Theodore Kypraios
- School of Mathematical Sciences, University of Nottingham, Nottingham, United Kingdom
| | - David J. Scott
- Food Sciences, School of Biosciences, University of Nottingham, Sutton Bonington Campus, Loughborough, United Kingdom
| | - Philip J. Hill
- Food Sciences, School of Biosciences, University of Nottingham, Sutton Bonington Campus, Loughborough, United Kingdom
| | - Dov J. Stekel
- Agricultural and Environmental Sciences, School of Biosciences, University of Nottingham, Sutton Bonington Campus, Loughborough, United Kingdom
- * E-mail:
| |
Collapse
|
9
|
Reporter Gene Assays in Ecotoxicology. ADVANCES IN BIOCHEMICAL ENGINEERING/BIOTECHNOLOGY 2017; 157:135-157. [PMID: 27928578 DOI: 10.1007/10_2016_47] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
Abstract
The need for simple and rapid means for evaluating the potential toxic effects of environmental samples has prompted the development of reporter gene assays, based on tester cells (bioreporters) genetically engineered to report on sample toxicity by producing a readily quantifiable signal. Bacteria are especially suitable to serve as bioreporters owing to their fast responses, low cost, convenient preservation, ease of handling, and amenability to genetic manipulations. Various bacterial bioreporters have been introduced for general toxicity and genotoxicity assessment, and the monitoring of endocrine disrupting and dioxin-like compounds has been mostly covered by similarly engineered eukaryotic cells. Some reporter gene assays have been validated, standardized, and accredited, and many others are under constant development. Efforts are aimed at broadening detection spectra, lowering detection thresholds, and combining toxicity identification capabilities with characterization of the toxic effects. Taking advantage of bacterial robustness, attempts are also being made to incorporate bacterial bioreporters into field instrumentation for online continuous monitoring or on-site spot checks. However, key hurdles concerning test validation, cell preservation, and regulatory issues related to the use of genetically modified organisms still remain to be overcome.
Collapse
|
10
|
Sharifian S, Homaei A, Hemmati R, Khajeh K. Light emission miracle in the sea and preeminent applications of bioluminescence in recent new biotechnology. JOURNAL OF PHOTOCHEMISTRY AND PHOTOBIOLOGY B-BIOLOGY 2017; 172:115-128. [DOI: 10.1016/j.jphotobiol.2017.05.021] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/23/2017] [Accepted: 05/16/2017] [Indexed: 02/08/2023]
|
11
|
Hecker JG. Non-Viral, Lipid-Mediated DNA and mRNA Gene Therapy of the Central Nervous System (CNS): Chemical-Based Transfection. Methods Mol Biol 2016; 1382:307-24. [PMID: 26611597 DOI: 10.1007/978-1-4939-3271-9_23] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
Appropriate gene delivery systems are essential for successful gene therapy in clinical medicine. Cationic lipid-mediated delivery is an alternative to viral vector-mediated gene delivery. Lipid-mediated delivery of DNA or mRNA is usually more rapid than viral-mediated delivery, offers a larger payload, and has a nearly zero risk of incorporation. Lipid-mediated delivery of DNA or RNA is therefore preferable to viral DNA delivery in those clinical applications that do not require long-term expression for chronic conditions. Delivery of RNA may be preferable to non-viral DNA delivery in some clinical applications, because transit across the nuclear membrane is not necessary and onset of expression with RNA is therefore even faster than with DNA, although both are faster than most viral vectors. Here, we describe techniques for cationic lipid-mediated delivery of nucleic acids encoding reporter genes in a variety of cell lines. We describe optimized formulations and transfection procedures that we previously assessed by bioluminescence and flow cytometry. RNA transfection demonstrates increased efficiency relative to DNA transfection in non-dividing cells. Delivery of mRNA results in onset of expression within 1 h after transfection and a peak in expression 5-7 h after transfection. Duration of expression in eukaryotic cells after mRNA transcript delivery depends on multiple factors, including transcript stability, protein turnover, and cell type. Delivery of DNA results in onset of expression within 5 h after transfection, a peak in expression 24-48 h after transfection, and a return to baseline that can be as long as several weeks after transfection. In vitro results are consistent with our in vivo delivery results, techniques for which are described as well. RNA delivery is suitable for short-term transient gene expression due to its rapid onset, short duration of expression and greater efficiency, particularly in non-dividing cells, while the longer duration and the higher mean levels of expression per cell that are ultimately obtained following DNA delivery confirm a continuing role for DNA gene delivery in clinical applications that require longer term transient gene expression.
Collapse
Affiliation(s)
- James G Hecker
- Department of Anesthesiology and Pain Medicine, Harborview Medical Center, University of Washington School of Medicine, Box 359724, 329 Ninth Ave., Seattle, WA, 98104, USA.
| |
Collapse
|
12
|
Molecular manipulations for enhancing luminescent bioreporters performance in the detection of toxic chemicals. ADVANCES IN BIOCHEMICAL ENGINEERING/BIOTECHNOLOGY 2014; 145:137-49. [PMID: 25216954 DOI: 10.1007/978-3-662-43619-6_4] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Abstract
Microbial whole-cell bioreporters are genetically modified microorganisms that produce a quantifiable output in response to the presence of toxic chemicals or other stress factors. These bioreporters harbor a genetic fusion between a sensing element (usually a gene regulatory element responsive to the target) and a reporter element, the product of which may be quantitatively monitored either by its presence or by its activity. In this chapter we review genetic manipulations undertaken in order to improve bioluminescent bioreporter performance by increasing luminescent output, lowering the limit of detection, and shortening the response time. We describe molecular manipulations applied to all aspects of whole-cell bioreporters: the host strain, the expression system, the sensing element, and the reporter element. The molecular construction of whole-cell luminescent bioreporters, harboring fusions of gene promoter elements to reporter genes, has been around for over three decades; in most cases, these two genetic elements are combined "as is." This chapter outlines diverse molecular manipulations for enhancing the performance of such sensors.
Collapse
|
13
|
Kassem II, Splitter GA, Miller S, Rajashekara G. Let There Be Light! Bioluminescent Imaging to Study Bacterial Pathogenesis in Live Animals and Plants. ADVANCES IN BIOCHEMICAL ENGINEERING/BIOTECHNOLOGY 2014; 154:119-45. [DOI: 10.1007/10_2014_280] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
|
14
|
Abstract
Appropriate gene delivery systems are essential for successful gene therapy in clinical medicine. Cationic lipid-mediated delivery is an alternative to viral vector-mediated gene delivery where transient gene expression is desirable. However, cationic lipid-mediated delivery of DNA to post-mitotic cells is often of low efficiency, due to the difficulty of DNA translocation to the nucleus. Rapid lipid-mediated delivery of RNA is preferable to nonviral DNA delivery in some clinical applications, because transit across the nuclear membrane is not necessary. Here we describe techniques for cationic lipid-mediated delivery of RNA encoding reporter genes in a variety of in vitro cell lines and in vivo. We describe optimized formulations and transfection procedures that we have previously assessed by flow cytometry. RNA transfection demonstrates increased efficiency relative to DNA transfection in nondividing cells. Delivery of mRNA results in onset of expression within 1 h after transfection and a peak in expression 5-7 h after transfection. These results are consistent with our in vivo delivery results, techniques for which are shown as well. Longer duration and the higher mean levels of expression per cell that are ultimately obtained following DNA delivery confirm a continuing role for DNA gene delivery in clinical applications that require long term transient gene expression. RNA delivery is suitable for short-term transient gene expression due to its rapid onset, short duration of expression, and greater efficiency, particularly in nondividing cells.
Collapse
Affiliation(s)
- James G Hecker
- Department of Anesthesiology and Pain Medicine, University of Washington School of Medicine, Seattle, WA, USA.
| |
Collapse
|
15
|
The fusion Vibrio campbellii luciferase as a eukaryotic gene reporter. J Biotechnol 2012; 162:346-53. [PMID: 23000378 DOI: 10.1016/j.jbiotec.2012.08.018] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2012] [Revised: 08/27/2012] [Accepted: 08/30/2012] [Indexed: 11/21/2022]
Abstract
Bacterial luciferase from Vibrio campbellii is a thermostable enzyme with an in vitro thermal inactivation half-life of ~1020 min at 37°C. The enzyme also binds tightly to reduced FMN. In this study, a V. campbellii fusion luciferase construct in which the α and β subunits are linked with a decapeptide was made and characterized. In general, the overall enzymatic properties of the two enzymes are similar. Expression of the enzymes in Escherichia coli demonstrated that the V. campbellii fusion luciferase emits less light than the native luciferase, but still emits a much greater amount of light than native luciferase from Vibrio harveyi and Photobacterium leiognathi TH1. The intensity of light emitted by the V. campbellii fusion luciferase was more than 80-fold greater than that from the V. harveyi native luciferase when expressed at 37°C. Biochemical characterization has shown that the V. campbellii fusion luciferase also retains a high binding affinity for reduced flavin mononucleotide and high thermostability. The levels of bioluminescence emitted by the V. campbellii fusion luciferase expressed in HEK293T cells reached ~1×10(6) Relative Light Units/mg total protein. These findings suggest that the V. campbellii fusion luciferase is a promising candidate for further development as a luciferase-based reporter for eukaryotic systems.
Collapse
|
16
|
Hentschel E, Will C, Mustafi N, Burkovski A, Rehm N, Frunzke J. Destabilized eYFP variants for dynamic gene expression studies in Corynebacterium glutamicum. Microb Biotechnol 2012; 6:196-201. [PMID: 22938655 PMCID: PMC3917462 DOI: 10.1111/j.1751-7915.2012.00360.x] [Citation(s) in RCA: 34] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2012] [Revised: 08/01/2012] [Accepted: 08/03/2012] [Indexed: 11/30/2022] Open
Abstract
Fluorescent reporter proteins are widely used for the non-invasive monitoring of gene expression patterns, but dynamic measurements are hampered by the extremely high stability of GFP and homologue proteins. In this study, we used SsrA-mediated peptide tagging for the construction of unstable variants of the GFP derivative eYFP (enhanced yellow fluorescent protein) and applied those for transient gene expression analysis in the industrial platform organism Corynebacterium glutamicum.
Collapse
Affiliation(s)
- Eva Hentschel
- Institut für Bio- und Geowissenschaften, IBG-1: Biotechnologie, Forschungszentrum Jülich, Germany
| | | | | | | | | | | |
Collapse
|
17
|
Ghim CM, Lee SK, Takayama S, Mitchell RJ. The art of reporter proteins in science: past, present and future applications. BMB Rep 2010; 43:451-60. [PMID: 20663405 DOI: 10.5483/bmbrep.2010.43.7.451] [Citation(s) in RCA: 62] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Starting with the first publication of lacZ gene fusion in 1980, reporter genes have just entered their fourth decade. Initial studies relied on the simple fusion of a promoter or gene with a particular reporter gene of interest. Such constructs were then used to determine the promoter activity under specific conditions or within a given cell or organ. Although this protocol was, and still is, very effective, current research shows a paradigm shift has occurred in the use of reporter systems. With the advent of innovative cloning and synthetic biology techniques and microfluidic/nanodroplet systems, reporter genes and their proteins are now finding themselves used in increasingly intricate and novel applications. For example, researchers have used fluorescent proteins to study biofilm formation and discovered that microchannels develop within the biofilm. Furthermore, there has recently been a "fusion" of art and science; through the construction of genetic circuits and regulatory systems, researchers are using bacteria to "paint" pictures based upon external stimuli. As such, this review will discuss the past and current trends in reporter gene applications as well as some exciting potential applications and models that are being developed based upon these remarkable proteins.
Collapse
Affiliation(s)
- Cheol-Min Ghim
- Ulsan National Institute of Science and Technology, Korea
| | | | | | | |
Collapse
|
18
|
Upgrading bioluminescent bacterial bioreporter performance by splitting the lux operon. Anal Bioanal Chem 2010; 400:1071-82. [DOI: 10.1007/s00216-010-4266-7] [Citation(s) in RCA: 41] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2010] [Revised: 09/28/2010] [Accepted: 09/28/2010] [Indexed: 11/25/2022]
|
19
|
Zou S, Scarfo K, Nantz MH, Hecker JG. Lipid-mediated delivery of RNA is more efficient than delivery of DNA in non-dividing cells. Int J Pharm 2010; 389:232-43. [PMID: 20080162 DOI: 10.1016/j.ijpharm.2010.01.019] [Citation(s) in RCA: 113] [Impact Index Per Article: 8.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2009] [Revised: 01/04/2010] [Accepted: 01/10/2010] [Indexed: 12/13/2022]
Abstract
The design of appropriate gene delivery systems is essential for the successful application of gene therapy to clinical medicine. Cationic lipid-mediated delivery is a viable alternative to viral vector-mediated gene delivery in applications where transient gene expression is desirable. However, cationic lipid-mediated delivery of DNA to post-mitotic cells such as neurons is often reported to be of low efficiency, due to the presumed inability of the DNA to translocate to the nucleus. Lipid-mediated delivery of RNA is an attractive alternative to non-viral DNA delivery in some clinical applications, because transit across the nuclear membrane is not necessary. Here we report a comparative investigation of cationic lipid-mediated delivery of RNA versus DNA vectors encoding the reporter gene green fluorescent protein (GFP) in Chinese Hamster Ovary (CHO) and NIH3T3 cells following chemical inhibition of proliferation, and in primary mixed neuronal cell cultures. Using optimized formulations and transfection procedures, we assess gene expression by flow cytometry to specifically address some of the advantages and disadvantages of lipid-mediated RNA and DNA gene transfer. Despite inhibition of cell proliferation, over 45% of CHO cells express GFP after lipid-mediated transfection with RNA vectors. Transfection efficiency of DNA encoding GFP in proliferation-inhibited CHO cells was less than 5%. Detectable expression after RNA transfection occurs at least 3h earlier than after DNA transfection, but DNA transfection eventually produces a mean level of per cell GFP expression (as assayed by flow cytometry) that is higher than after RNA transfection. Transfection of proliferation-inhibited NIH3T3 cells and primary mixed neuronal cultures produced similar results, with RNA encoded GFP expression in 2-4 times the number of cells as after DNA encoded GFP expression. These results demonstrate the increased efficiency of RNA transfection relative to DNA transfection in non-dividing cells. We used firefly luciferase encoded by RNA and DNA vectors to investigate the time course of gene expression after delivery of RNA or DNA to primary neuronal cortical cells. Delivery of mRNA resulted in rapid onset (within 1h) of luciferase expression after transfection, a peak in expression 5-7h after transfection, and a return to baseline within 12h after transfection. After DNA delivery significant luciferase activity did not appear until 7h after transfection, but peak luciferase expression was always at least one order of magnitude higher than after RNA delivery. The peak expression after luciferase-expressing DNA delivery occurred 36-48 h after transfection and remained at a significant level for at least one week before dropping to baseline. This observation is consistent with our in vivo delivery results, which are shown as well. RNA delivery may therefore be more suitable for short-term transient gene expression due to rapid onset, shorter duration of expression and greater efficiency, particularly in non-dividing cells. Higher mean levels of expression per cell obtained following DNA delivery and the longer duration of expression confirm a continuing role for DNA gene delivery in clinical applications that require longer term transient gene expression.
Collapse
Affiliation(s)
- S Zou
- Department of Anesthesiology and Critical Care, University of Pennsylvania School of Medicine, Morgan 305, 3620 Hamilton Walk, Philadelphia, PA 19104-6112, USA
| | | | | | | |
Collapse
|
20
|
Close DM, Ripp S, Sayler GS. Reporter proteins in whole-cell optical bioreporter detection systems, biosensor integrations, and biosensing applications. SENSORS (BASEL, SWITZERLAND) 2009; 9:9147-74. [PMID: 22291559 PMCID: PMC3260636 DOI: 10.3390/s91109147] [Citation(s) in RCA: 55] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/18/2009] [Revised: 10/14/2009] [Accepted: 10/23/2009] [Indexed: 11/19/2022]
Abstract
Whole-cell, genetically modified bioreporters are designed to emit detectable signals in response to a target analyte or related group of analytes. When integrated with a transducer capable of measuring those signals, a biosensor results that acts as a self-contained analytical system useful in basic and applied environmental, medical, pharmacological, and agricultural sciences. Historically, these devices have focused on signaling proteins such as green fluorescent protein, aequorin, firefly luciferase, and/or bacterial luciferase. The biochemistry and genetic development of these sensor systems as well as the advantages, challenges, and common applications of each one will be discussed.
Collapse
Affiliation(s)
- Dan M. Close
- The University of Tennessee, The Center for Environmental Biotechnology, 676 Dabney Hall, Knoxville, Tennessee, 37996, USA; E-Mails: (D.C.); (S.R.)
| | - Steven Ripp
- The University of Tennessee, The Center for Environmental Biotechnology, 676 Dabney Hall, Knoxville, Tennessee, 37996, USA; E-Mails: (D.C.); (S.R.)
| | - Gary S. Sayler
- The University of Tennessee, The Center for Environmental Biotechnology, 676 Dabney Hall, Knoxville, Tennessee, 37996, USA; E-Mails: (D.C.); (S.R.)
| |
Collapse
|