Creation of Circularly Permutated Yellow Fluorescent Proteins Using Fluorescence Screening and a Tandem Fusion Template

By experimenting with many different circularly permutated yellow fluorescent protein (cpYFP) variants as acceptors in fluorescence resonance energy transfer based biosensors, the optimal dynamic range can be discovered by sampling the possibilities of relative fluorophore orientations before and after bioactivity. Hence, to facilitate the sampling process, we introduced a new approach to construct a library of cpYFP variants using fluorescence screening and a tandem fusion template. This new approach is rapid because it does not require creating intermediate N- and C-terminal fragments and it allows quick screening for positive colonies by fluorescence. As a demonstration, eleven cpYFP variants were created and eight showed fluorescence. The emission and excitation spectra of these cpYFP variants showed strong similarity to YFP and therefore can be used in replacement. Revisions requested 27 October 2005; Revisions received 23 December 2005     

Fluorescent Labeling of COS-7 Expressing SNAP-tag Fusion Proteins for Live Cell Imaging

SNAP-tag and CLIP-tag protein labeling systems enable the specific, covalent attachment of molecules, including fluorescent dyes, to a protein of interest in live cells. These systems offer a broad selection of fluorescent substrates optimized for a range of imaging instrumentation. Once cloned and expressed, the tagged protein can be used with a variety of substrates for numerous downstream applications without having to clone again. There are two steps to using this system: cloning and expression of the protein of interest as a SNAP-tag fusion, and labeling of the fusion with the SNAP-tag substrate of choice. The SNAP-tag is a small protein based on human O⁶-alkylguanine-DNA-alkyltransferase (hAGT), a DNA repair protein. SNAP-tag labels are dyes conjugated to guanine or chloropyrimidine leaving groups via a benzyl linker. In the labeling reaction, the substituted benzyl group of the substrate is covalently attached to the SNAP-tag. CLIP-tag is a modified version of SNAP-tag, engineered to react with benzylcytosine rather than benzylguanine derivatives. When used in conjunction with SNAP-tag, CLIP-tag enables the orthogonal and complementary labeling of two proteins simultaneously in the same cells.Download video file.^{(47M, mov)}     

Characterization and Use of Green Fluorescent Proteins from Renilla mulleri and Ptilosarcus guernyi for the Human Cell Display of Functional Peptides

Green fluorescent protein (GFP) is useful as an intracellular scaffold for the display of random peptide libraries in yeast. GFPs with a different sequence from Aequorea victoria have recently been identified from Renilla mulleri and Ptilosarcus gurneyi. To examine these proteins as intracellular scaffolds for peptide display in human cells, we have determined the expression level of retrovirally delivered human codon-optimized versions in Jurkat-E acute lymphoblastic leukemia cells using fluorescence activated cell sorting and Western blots. Each wild type protein is expressed at 40% higher levels than A. victoria mutants optimized for maximum fluorescence. We have compared the secondary structure and stability of these GFPs with A. victoria GFP using circular dichroism (CD). All three GFPs essentially showed a perfect -strand conformation and their melting temperatures (T_m) are very similar, giving an experimental evidence of a similar overall structure. Folded Renilla GFP allows display of an influenza hemagglutinin epitope tag in several internal insertion sites, including one which is not permissive for such display in Aequorea GFP, giving greater flexibility in peptide display options. To test display of a functional peptide, we show that the SV-40 derived nuclear localization sequence PPKKKRKV, when inserted into two different potential loops, results in the complete localization of Renilla GFP to the nucleus of human A549 cells.     

Intravital Microscopy for Imaging Subcellular Structures in Live Mice Expressing Fluorescent Proteins

Here we describe a procedure to image subcellular structures in live rodents that is based on the use of confocal intravital microscopy. As a model organ, we use the salivary glands of live mice since they provide several advantages. First, they can be easily exposed to enable access to the optics, and stabilized to facilitate the reduction of the motion artifacts due to heartbeat and respiration. This significantly facilitates imaging and tracking small subcellular structures. Second, most of the cell populations of the salivary glands are accessible from the surface of the organ. This permits the use of confocal microscopy that has a higher spatial resolution than other techniques that have been used for in vivo imaging, such as two-photon microscopy. Finally, salivary glands can be easily manipulated pharmacologically and genetically, thus providing a robust system to investigate biological processes at a molecular level.In this study we focus on a protocol designed to follow the kinetics of the exocytosis of secretory granules in acinar cells and the dynamics of the apical plasma membrane where the secretory granules fuse upon stimulation of the beta-adrenergic receptors. Specifically, we used a transgenic mouse that co-expresses cytosolic GFP and a membrane-targeted peptide fused with the fluorescent protein tandem-Tomato. However, the procedures that we used to stabilize and image the salivary glands can be extended to other mouse models and coupled to other approaches to label in vivo cellular components, enabling the visualization of various subcellular structures, such as endosomes, lysosomes, mitochondria, and the actin cytoskeleton.     

Measuring and Sorting Cell Populations Expressing Isospectral Fluorescent Proteins with Different Fluorescence Lifetimes

Study of signal transduction in live cells benefits from the ability to visualize and quantify light emitted by fluorescent proteins (XFPs) fused to different signaling proteins. However, because cell signaling proteins are often present in small numbers, and because the XFPs themselves are poor fluorophores, the amount of emitted light, and the observable signal in these studies, is often small. An XFP''s fluorescence lifetime contains additional information about the immediate environment of the fluorophore that can augment the information from its weak light signal. Here, we constructed and expressed in Saccharomyces cerevisiae variants of Teal Fluorescent Protein (TFP) and Citrine that were isospectral but had shorter fluorescence lifetimes, ∼1.5 ns vs ∼3 ns. We modified microscopic and flow cytometric instruments to measure fluorescence lifetimes in live cells. We developed digital hardware and a measure of lifetime called a “pseudophasor” that we could compute quickly enough to permit sorting by lifetime in flow. We used these abilities to sort mixtures of cells expressing TFP and the short-lifetime TFP variant into subpopulations that were respectively 97% and 94% pure. This work demonstrates the feasibility of using information about fluorescence lifetime to help quantify cell signaling in living cells at the high throughput provided by flow cytometry. Moreover, it demonstrates the feasibility of isolating and recovering subpopulations of cells with different XFP lifetimes for subsequent experimentation.     

人类鸟苷酸结合蛋白抗病毒机制研究进展

人类鸟苷酸结合蛋白(Human guanylate binding proteins,hGBPs)是一种干扰素诱导型细胞因子,属于鸟苷酸结合蛋白家族(Guanosine triphosphatases,GTPases)。GBPs能够介导经典与非经典炎症激活途径,诱导先天性和适应性免疫应答,还可以诱导自噬和控制囊泡运输,在宿主抵御细菌、病毒和其他病原微生物时发挥重要作用。本文主要介绍了hGBPs的发现和结构,并对7种hGBPs的抗病毒机制进行概述。     

Green Fluorescent Protein-based Expression Screening of Membrane Proteins in Escherichia coli

The production of recombinant membrane proteins for structural and functional studies remains technically challenging due to low levels of expression and the inherent instability of many membrane proteins once solubilized in detergents. A protocol is described that combines ligation independent cloning of membrane proteins as GFP fusions with expression in Escherichia coli detected by GFP fluorescence. This enables the construction and expression screening of multiple membrane protein/variants to identify candidates suitable for further investment of time and effort. The GFP reporter is used in a primary screen of expression by visualizing GFP fluorescence following SDS polyacrylamide gel electrophoresis (SDS-PAGE). Membrane proteins that show both a high expression level with minimum degradation as indicated by the absence of free GFP, are selected for a secondary screen. These constructs are scaled and a total membrane fraction prepared and solubilized in four different detergents. Following ultracentrifugation to remove detergent-insoluble material, lysates are analyzed by fluorescence detection size exclusion chromatography (FSEC). Monitoring the size exclusion profile by GFP fluorescence provides information about the mono-dispersity and integrity of the membrane proteins in different detergents. Protein: detergent combinations that elute with a symmetrical peak with little or no free GFP and minimum aggregation are candidates for subsequent purification. Using the above methodology, the heterologous expression in E. coli of SED (shape, elongation, division, and sporulation) proteins from 47 different species of bacteria was analyzed. These proteins typically have ten transmembrane domains and are essential for cell division. The results show that the production of the SEDs orthologues in E. coli was highly variable with respect to the expression levels and integrity of the GFP fusion proteins. The experiment identified a subset for further investigation.     

表达绿色荧光蛋白的重组CVI988病毒的构建及特性

提取马立克氏病毒Ⅰ型疫苗毒株CVI988的总DNA为模板,利用PCR技术扩增出病毒生长非必需的US2基因并克隆入T—easy载体。将CMV启动子和增强子控制的含GFP基因表达盒克隆入US2基因中,成功构建了含GFP基因的转移质粒载体pGUS2GFP。用脂质体将其与CVI988株共转染CEF细胞,用96孔板稀释法得到纯化的表达绿色荧光蛋白的重组CVI988病毒株rCVIGFP,并分别测定其在体内和体外的生长情况。表达EGFP基因的重组病毒在细胞上生长曲线与亲本毒CVI988类似,体外实验表明,1日龄腹腔接种该重组毒后,可以从鸡体内分离到表达绿色荧光的病毒。     

表达绿色荧光蛋白的重组CVI988病毒的构建及特性

提取马立克氏病毒I型疫苗毒株CVI988的总DNA为模板,利用PCR技术扩增出病毒生长非必需的US2基因并克隆入T-easy载体.将CMV启动子和增强子控制的含GFP基因表达盒克隆入US2基因中,成功构建了含GFP基因的转移质粒载体pGUS2GFP.用脂质体将其与CVI988 株共转染CEF细胞,用96孔板稀释法得到纯化的表达绿色荧光蛋白的重组CVI988病毒株rCVIGFP,并分别测定其在体内和体外的生长情况.表达EGFP基因的重组病毒在细胞上生长曲线与亲本毒CVI988类似,体外实验表明,1日龄腹腔接种该重组毒后,可以从鸡体内分离到表达绿色荧光的病毒.     

Fluorescent Proteins and Their Use in Marine Biosciences,Biotechnology, and Proteomics

This review explores the field of fluorescent proteins (FPs) from the perspective of their marine origins and their applications in marine biotechnology and proteomics. FPs occur in hydrozoan, anthozoan, and copepodan species, and possibly in other metazoan niches as well. Many FPs exhibit unique photophysical and photochemical properties that are the source of exciting research opportunities and technological development. Wild-type FPs can be enhanced by mutagenetic modifications leading to variants with optimized fluorescence and new functionalities. Paradoxically, the benefits from ocean-derived FPs have been realized, first and foremost, for terrestrial organisms. In recent years, however, FPs have also made inroads into aquatic biosciences, primarily as genetically encoded fluorescent fusion tags for optical marking and tracking of proteins, organelles, and cells. Examples of FPs and applications summarized here testify to growing utilization of FP-based platform technologies in basic and applied biology of aquatic organisms. Hydra, sea squirt, zebrafish, striped bass, rainbow trout, salmonids, and various mussels are only a few of numerous instances where FPs have been used to address questions relevant to evolutionary and developmental research and aquaculture.     

Characterization of Disease-Associated Mutations in Human Transmembrane Proteins

Transmembrane protein coding genes are commonly associated with human diseases. We characterized disease causing mutations and natural polymorphisms in transmembrane proteins by mapping missense genetic variations from the UniProt database on the transmembrane protein topology listed in the Human Transmembrane Proteome database. We found characteristic differences in the spectrum of amino acid changes within transmembrane regions: in the case of disease associated mutations the non-polar to non-polar and non-polar to charged amino acid changes are equally frequent. In contrast, in the case of natural polymorphisms non-polar to charged amino acid changes are rare while non-polar to non-polar changes are common. The majority of disease associated mutations result in glycine to arginine and leucine to proline substitutions. Mutations to positively charged amino acids are more common in the center of the lipid bilayer, where they cause more severe structural and functional anomalies. Our analysis contributes to the better understanding of the effect of disease associated mutations in transmembrane proteins, which can help prioritize genetic variations in personal genomic investigations.     

融合标签技术在膜蛋白结构研究中的应用

膜蛋白高级结构的研究包括不同的层次,即膜蛋白拓扑学结构的研究、利用核磁共振技术和蛋白质晶体衍射技术对三维结构的研究,以及膜蛋白复合体的研究。在研究过程中,如果能够基于膜蛋白的拓扑学结构预测,选择合适的蛋白质或多肽融合标签,利用基因融合技术在基因水平上对膜蛋白进行改造,可以产生含有融合标签的重组膜蛋自,不仅具有原有膜蛋白的功能活性,还具有融合标签所特有的生理生化特性,将会极大地促进膜蛋白结构和功能的研究。我们就目前膜蛋白结构研究中所涉及的融合标签技术及其应用策略和所取得的进展做一简述。     

Characterization of Fluorescent Proteins for Three- and Four-Color Live-Cell Imaging in S. cerevisiae

Saccharomyces cerevisiae are widely used for imaging fluorescently tagged protein fusions. Fluorescent proteins can easily be inserted into yeast genes at their chromosomal locus, by homologous recombination, for expression of tagged proteins at endogenous levels. This is especially useful for incorporation of multiple fluorescent protein fusions into a single strain, which can be challenging in organisms where genetic manipulation is more complex. However, the availability of optimal fluorescent protein combinations for 3-color imaging is limited. Here, we have characterized a combination of fluorescent proteins, mTFP1/mCitrine/mCherry for multicolor live cell imaging in S. cerevisiae. This combination can be used with conventional blue dyes, such as DAPI, for potential four-color live cell imaging.     

Construction and Characterization of a Streptococcus suis Serotype 2 Recombinant Expressing Enhanced Green Fluorescent Protein

Streptococcus suis serotype 2 (S. suis 2) is an important pathogen, responsible for diverse diseases in swine and humans. To obtain a S. suis 2 strain that can be tracked in vitro and in vivo, we constructed the Egfp-HA9801 recombinant S. suis 2 strain with egfp and spc(r) genes inserted via homologous recombination. To assess the effects of the egfp and spc(r) genes in HA9801, the biochemical characteristics, growth features and virulence in Balb/C mice were compared between the recombinant and the parent HA9801 strain. We detected the EGFP expression from Egfp-HA9801 by epifluorescence microscopy. The results showed that the biochemical characterization and growth features of the Egfp-HA9801 recombinant were highly similar to that of the parent HA9801. We did not find significant differences in lethality (50% lethal dose), morbidity and mortality between the two strains. Furthermore, the bacterial counts in each various tissues of Egfp-HA9801-infected mice displayed similar dynamic compared with the HA9801-infected mice. Our results also showed that the Egfp-HA9801 cells grown at 37°C for 36 h displayed greater green fluorescence signals than the cells grown at 28°C for 36 h and 37°C for 24 h. The fluorescence in the tissue cryosections of Egfp-HA9801-injected mice was also stronger than that of the HA9801 group. Together, these results indicate that the egfp and spc(r) insertions into the Egfp-HA9801 recombinant did not significantly change the virulence when compared with HA980, and this EGFP labeled strain can be used for future S. suis 2 pathogenesis research.     

表达全人源抗人IgE单抗的细胞株构建及筛选

目的:构建及筛选高效表达原创性全人源抗人Ig E单克隆抗体的重组工程细胞株。方法:将采用核糖体展示技术筛选到的原创性全人源抗人Ig E单链抗体(sc Fv)基因改构设计为Ig G1κ型全长抗体,构建重组真核表达质粒并电转染CHO-S细胞,Dot-blot法选取多株高表达克隆进行40ml摇瓶批次培养,再据细胞生长特征及抗体表达量选取高表达克隆进行40ml摇瓶及3L摇瓶流加培养研究,选取候选细胞株并对改构前后抗体的生物学活性进行比较研究。结果:成功构建了p MH3-H、p MH3-L、p CApuro-H、p CApuro-L四种重组真核表达质粒并成功共转染CHO-S细胞。完成了4次电转染8轮细胞克隆筛选,获得两株表达量较高的候选克隆Mab1#和Mab2#,在3L摇瓶流加培养中抗体表达量分别达到470mg/L及499mg/L。生物膜光干涉技术(Bio-Layer Interferometry,BLI)亲和力结果显示Mab1#及Mab2#两株单抗亲和力均达到nmol/L级(10-9),与现有唯一上市的抗人Ig E单抗药物奥马珠单抗(Omalizumab)的亲和力相当。选取Mab1#全长抗体与其改构前的母本单链抗体的表面等离子共振技术(surface plasmon resonance,SPR)中和活性比较结果显示Mab1#抑制h Ig E与FcεRI结合的EC50为3nmol/L,EC90为9nmol/L,较改造前亲和力提高了4.3倍,中和活性(EC50)提高了23.7倍,中和活性(EC90)提高了41.3倍。结论:成功将表达原创性全人源抗人Ig E的单链抗体(约25k Da)改造为亲和力及中和活性均大幅提升的全长抗体(约150k Da),获得2个候选细胞株。     

A New Set of Reversibly Photoswitchable Fluorescent Proteins for Use in Transgenic Plants

Fluorescent reporter proteins that allow repeated switching between a fluorescent and a non-fluorescent state in response to specific wavelengths of light are novel tools for monitoring of protein trafficking and super-resolu- tion fluorescence microscopy in living organisms. Here, we describe variants of the reversibly photoswitchable fluores- cent proteins rsFastLime, bsDronpa, and Padron that have been codon-optimized for the use in transgenic Arabidopsis plants. The synthetic proteins, designated rsFastLIME-s, bsDRONPA-s, and PADRON C-s, showed photophysical properties and switching behavior comparable to those reported for the original proteins. By combining the ＇positively switchable＇ PADRON C-s with the ＇negatively switchable＇ rsFastLIME-s or bsDRONPA-s, two different fluorescent reporter proteins could be imaged at the same wavelength upon transient expression in Nicotiana benthamiana cells. Thus, co-localiza- tion analysis can be performed using only a single detection channel. Furthermore, the proteins were used to tag the RNA-binding protein AtGRP7 （Arabidopsis thaliana glycine-rich RNA-binding protein 7） in transgenic Arabidopsis plants. Because the new reversibly photoswitchable fluorescent proteins show an increase in signal strength during each pho- toactivation cycle, we were able to generate a large number of scans of the same region and reconstruct 3-D images of AtGRP7 expression in the root tip. Upon photoactivation of the AtGRP7：rsFastLIME-s fusion protein in a defined region of a transgenic Arabidopsis root, spreading of the fluorescence signal into adjacent regions was observed, indicating that movement from cell to cell can be monitored. Our results demonstrate that rsFastLIME-s, bsDRONPA-s, and PADRON C-s are versatile fluorescent markers in plants, Furthermore, the proteins also show strong fluorescence in mammalian cells including COS-7 and HeLa cells.     

Characterization of Ethanol-Sensitive and Insensitive Fibroblast Cell Lines Expressing Human L1

Abstract: Ethanol inhibits L1-mediated cell-cell adhesion in fibroblast cell lines stably transfected with human L1. Here we show that this action of ethanol is present in only a subset of transfected NIH/3T3 and L cell clonal cell lines. All L1-expressing cell lines had higher levels of cell adhesion than cell lines transfected with empty vector. In all ethanol-sensitive cell lines, L1-mediated adhesion was inhibited by ethanol (IC₅₀ 5–10 m M ), 2 m M butanol, but not 5 m M pentanol. In contrast, ethanol-insensitive cell lines were not inhibited by up to 200 m M ethanol, 2 m M butanol, or 5 m M pentanol. Ethanol sensitivity or insensitivity was a stable property of each cell line and was not associated with differences in electrophoretic mobility, abundance, or cell surface localization of L1. Fab fragments prepared from anti-L1 polyclonal antisera inhibited cell adhesion only in the ethanol-sensitive cell lines. These data suggest that L1 may exist in an alcohol-sensitive or an alcohol-insensitive state that may be governed by host cell factors.     

Characterization of Thermobifida fusca Cutinase-Carbohydrate-Binding Module Fusion Proteins and Their Potential Application in Bioscouring

Cutinase from Thermobifida fusca is thermally stable and has potential application in the bioscouring of cotton in the textile industry. In the present study, the carbohydrate-binding modules (CBMs) from T. fusca cellulase Cel6A (CBM_Cel6A) and Cellulomonas fimi cellulase CenA (CBM_CenA) were fused, separately, to the carboxyl terminus of T. fusca cutinase. Both fusion enzymes, cutinase-CBM_Cel6A and cutinase-CBM_CenA, were expressed in Escherichia coli and purified to homogeneity. Enzyme characterization showed that both displayed similar catalytic properties and pH stabilities in response to T. fusca cutinase. In addition, both fusion proteins displayed an activity half-life of 53 h at their optimal temperature of 50°C. Compared to T. fusca cutinase, in the absence of pectinase, the binding activity on cotton fiber was enhanced by 2% for cutinase-CBM_Cel6A and by 28% for cutinase-CBM_CenA, whereas in the presence of pectinase, the binding activity was enhanced by 40% for the former and 45% for the latter. Notably, a dramatic increase of up to 3-fold was observed in the amount of released fatty acids from cotton fiber by both cutinase-CBM fusion proteins when acting in concert with pectinase. This is the first report of improving the scouring efficiency of cutinase by fusing it with CBM. The improvement in activity and the strong synergistic effect between the fusion proteins and pectinase suggest that they may have better applications in textile bioscouring than the native cutinase.Cotton fiber has a multilayered structure, with its outermost surface being the cuticle that is cross-linked to the primary cell wall of cotton fiber by esterified pectin substances. The major component of the cuticle is cutin, an insoluble polyester composed mainly of saturated C₁₆ and C₁₈ hydroxy and epoxy fatty acids (14, 16, 27, 38). During the process of scouring in the textile industry, the cuticle layer has to be removed in order to improve the wettability of cotton fiber, which then facilitates uniform dyeing and finishing. Traditionally, this process is performed by hot hydrolysis in alkaline medium, which not only consumes large quantities of water and energy but also causes severe pollution and fiber damage (20, 21, 33). Therefore, environment-friendly scouring methods based on biocatalysts have been actively sought (2, 30, 36).Cutinase is a multifunctional esterase capable of degrading the cutin component of the cuticle. Earlier reports showed that the fungal cutinase from Fusarium solani pisi has potential use for cotton cuticle degradation and exhibits a good synergistic effect with pectinase, an enzyme utilized to degrade pectin, in the scouring of cotton fiber (1, 7, 8, 14). Moreover, site-directed mutagenesis has been performed to replace the specific amino acid residues near the active site of cutinase (3) to improve its hydrolytic activity toward polyesters. More recently, a cutinase from the thermophilic bacterium Thermobifida fusca has been identified and overexpressed in Escherichia coli in our laboratory (10). The good thermal stability and alkali resistance of this recombinant T. fusca cutinase make it potentially more amenable to textile bioscouring (10).To further improve the applicability and/or catalytic efficiency of T. fusca cutinase, the present study attempts to engineer a novel cutin-degrading enzyme, based on analysis of the surface structure of cotton fiber. It has been observed that, in addition to cutin, pectin, proteins and other components, there is also a large amount of cellulose on the surface layer of cotton fiber (23). Thus, it is tempting to hypothesize that if the enzyme can be engineered to specifically bind to cellulose through a “gain of function” modification, its concentration on the surface of cotton fiber could increase significantly. Subsequently, its catalytic efficiency for cutin breakdown could be improved due to a proximity effect. In order to design such an enzyme, a fusion protein strategy in which a cellulose-binding protein/module will be attached to cutinase is considered.It is well known that cellulase is capable of binding specifically to cellulose (25, 31). This enzyme has two separate modules: a catalytic module and a carbohydrate-binding module (CBM) (11). The two modules are discrete structural and functional units usually connected by a flexible linker (5, 17, 28). CBM has high specific capacities for cellulose binding. Previously, it has been reported that CBM is able to be fused to a chosen target protein by genetic manipulation (36), resulting in enhanced binding of this fusion protein to cellulose (6, 29). For example, fusion proteins were constructed by fusing CBM to β-glucose nucleotide enzyme (GUS) (13) or β-glycosidase (BglA) (19), which facilitates biochemical analysis of scouring efficiency for cotton fabrics.In the present study, the CBM from T. fusca cellulase Cel6A (CBM_Cel6A) and the CBM from Cellulomonas fimi cellulase CenA (CBM_CenA) were fused, separately, to the carboxyl terminus of T. fusca cutinase. The resulting fusion enzymes were compared to the native cutinase in terms of their biochemical properties, as well as the catalytic efficiency in cutin breakdown on cotton fiber. This is the first report of improving the scouring efficiency of cutinase by fusing it with CBM.