Evolution of the EF-hand calcium-binding protein family: Evidence for exon shuffling and intron insertion

Summary The evolutionary history of the intracellular calcium-binding protein superfamily is well documented. The members of this gene family are all believed to be derived from a common ancestor, which, itself, was the product of two successive gene duplications. In this study, we have compared and analyzed the structures of the recently described genes coding for these proteins. We propose a series of evolutionary events, which include exon shuffling and intron insertion, that could account for the evolutionary origin of all the members of this super-family. According to this hypothesis, the ancestral gene, a product of two successive duplications, consisted of at least four exons. Each exon coding for a peptide (a calcium-binding domain) was separated by an intron that had mediated the duplication. Each distinct lineage evolved from this ancestor by genomic rearrangement, with insertion of introns being a prominent feature.     

分段DNA shuffling: 一种大分子海藻糖合酶有效的定向进化方法

[目的]红色亚栖热菌(Meiothermus ruber)海藻糖合酶(Trehalose synthase,M-TreS)将麦芽糖转化生成海藻糖只需一步反应,且具有很好的热稳定性及pH耐受性,是潜在的工业生产海藻糖的酶源.为了提高该酶的性能,有必要对其进行定向进化.[方法]M-TreS基因(M-treS)大小为2 889bp.该蛋白质分子本身具有很大的进化空间,但是却不宜进行全长基因Shuffling.分段DNA shuffling是为大分子蛋白质(基因≥2 000 bp)的进化而设计的一种方法.该方法分为三步:(1)用两对引物分别扩增目的基因的上游片段和下游片段;(2)上下游片段各自进行Shuffling; (3)利用重叠延伸PCR连接上下游突变群,建立完整基因的突变文库.[结果]结合易错PCR,通过该方法经一轮进化获得一株酶活力是野生型1.6倍、催化效率是野生型2倍的突变株.序列分析表明,该突变株共有6个位点发生了氨基酸的替代,其中一个来自易错突变,2个来自同源重组,3个为随机突变.[结论]分段DNA shuffling是进化大分子蛋白质的有效方法.     

荧光蛋白在肿瘤分子影像研究中的应用

绿色荧光蛋白（green fluorescent protein,GFP）是在水母中发现的新型报告分子,该蛋白及其衍生物能在多种生物体内表达并发出荧光,是目前在生物学中研究和开发应用得最广泛的蛋白质之一。尤其是在肿瘤的研究中,荧光蛋白的分子影像可为深入揭示肿瘤发生发展的病理过程的机制,以及对其治疗进行实时、动态、细致、无创、靶向性的探测和跟踪提供有效手段。     

Prion protein with Y145STOP mutation induces mitochondria-mediated apoptosis and PrP-containing deposits in vitro

A pathogenic truncation of an amber mutation at codon 145 (Y145STOP) in Gerstmann-Straussler-Scheinker disease (GSS) was investigated through the real-time imaging in living cells, by utilizing GFP-PrP constructs. GFP-PrP(1-144) exhibited an aberrant localization to mitochondria in mouse neuroblastoma neuro2a (N2a) and HpL3-4 cells, a hippocampal cell line established from prnp gene-ablated mice, whereas full-length GFP-PrP did not. The aberrant mitochondrial localization was also confirmed by Western blot analysis. Since GFP-PrP(1-121), as previously reported, and full-length GFP-PrP do not exhibit such mitochondrial localization, the mitochondrial localization of GFP-PrP(1-144) requires not only PrP residues 121-144 (in human sequence) but also COOH-terminal truncation in the current experimental condition. Subsequently, the GFP-PrP(1-144) induced a change in the mitochondrial innermembrane potential (DeltaPsi(m)), release of cytochrome c from the intermembrane space into the cytosol, and DNA fragmentation in these cells. Non-fluorescent PrP(1-144) also induced the DNA fragmentation in N2a and HpL3-4 cells after the proteasomal inhibition. These data may provide clues as to the molecular mechanism of the neurotoxic property of Y145STOP mutation. Furthermore, immunoelectron microscopy revealed numerous electron-dense deposits in mitochondria clusters of GFP-PrP(1-144)-transfected N2a cells, whereas no deposit was detected in the cells transfected with full-length GFP-PrP. Co-localization of GFP/PrP-immunogold particles with porin-immunogold particles as a mitochondrial marker was observed in such electron-dense vesicular foci, resembling those found in autophagic vacuoles forming secondary lysosomes. Whether such electron-dense deposits may serve as a seed for the growth of amyloid plaques, a characteristic feature of GSS with Y145STOP, awaits further investigations.     

A large-scale validation of dosage analysis by robust dosage-polymerase chain reaction

Epidemiological and clinical diagnostic assays benefit from accurate detection of deletions and duplications commonly missed by the conventional strategy of polymerase chain reaction (PCR) amplification and sequencing of individual exons. Robust dosage-PCR (RD-PCR) is a quantitative duplex PCR method that coamplifies a target template and an endogenous internal control (an autosomal and an X-chromosomal segment) for detection of these mutations. In this study, 110 consecutive RD-PCR assays were developed and validated. The average linear regression coefficient between template copy number and product yield and the average coefficient of determination for linear correlation, R(2), were very high: 0.95 and 0.98, respectively. The accuracy of RD-PCR revealed somatic mosaicism for a deletion in the factor 9 gene. Advantages of RD-PCR include (1) high accuracy and consistency, (2) easy calibration of linearity using male and female samples, (3) use of an endogenous internal dosage control to eliminate preparation and manipulation errors, and (4) detection of gene dosage over a wide dynamic range. Deletions and duplications can be easily detected (a 2x decrease or a 1.5x increase in gene dosage). Thus, RD-PCR is a general and accurate method for detecting changes in gene dosage.     

Rectified photocurrent of molecular photodiode consisting of cytochrome c/GFP hetero thin films.

Photoinduced electron transfer in the molecular electronic device consisting of protein-adsorbed hetero Langmuir–Blodgett (LB) film was investigated. Three kinds of functional molecules, cytochrome c, viologen, and green fluorescent protein (GFP) were used as an electron acceptor, a mediator, and a sensitizer, respectively. The hetero-LB film was fabricated by subsequently depositing cytochrome c and viologen onto the pretreated ITO or quartz glass. GFP adsorbed hetero-LB films were prepared by soaking the hetero-LB films into the buffer solution containing GFP. The MIM (metal/insulator/metal) structured molecular device was constructed by depositing aluminum onto the surface of the GFP-adsorbed hetero LB films. Due to the excitation by irradiation with a 460 nm monochromic light source, the photoinduced unidirectional flow of electrons in the MIM device could be achieved and was detected as photocurrents. The photoswitching function was achieved and the rectifying characteristic was observed in the molecular device. Based on the measurement of transient photocurrent of molecular device, the unidirectional flow of electrons was verified.     

Fluorescence based assay of GAL system in yeast Saccharomyces cerevisiae

The GAL1 promoter is one of the strongest inducible promoters in the yeast Saccharomyces cerevisiae. In order to improve recombinant protein production we have developed a fluorescence based method for screening and evaluating the contribution of various gene deletions to protein expression from the GAL1 promoter. The level of protein synthesis was determined in 28 selected mutant strains simultaneously, by direct measurement of fluorescence in living cells using a microplate reader. The highest, 2.4-fold increase in GFP production was observed in a gal1 mutant strain. Deletion of GAL80 caused a 1.3-fold increase in fluorescence relative to the isogenic strain. GAL3, GAL4 and MTH1 gene deletion completely abrogated GFP synthesis. Growth of gal7, gal10 and gal3 also exhibited reduced fitness in galactose medium. Other genetic perturbations affected the GFP expression level only moderately. The fluorescence based method proved to be useful for screening genes involved in GAL1 promoter regulation and provides insight into more efficient manipulation of the GAL system.     

Green fluorescent protein (GFP) as a direct biosensor for mutation detection: elimination of false-negative errors in target gene expression

A new method was developed to determine the mutagenic efficacy of a suspected mutagen by employing green fluorescent protein (GFP) as a direct biosensor for mutation detection. Alterations in target gene (AcGFP1) expression after mutagen [(±)-7p,8a-dihydroxy-9a,10a-epoxy-7,8,9,10-tetrahydrobenzo[a]pyrene (BPDE)] treatment were measured to detect the mutagenic efficacy of the carcinogen. In contrast to mutagen treatment of the entire plasmid or cell culture, the target AcGFP1gene devoid of the plasmid backbone was exposed to BPDE (10–500 μM) to eliminate the need for an additional fusion gene. Shuttle vectors (pAcGFP-N1) were religated to the AcGFP1 gene with BPDE adducts (0–8.59 μM) and replicated in the eukaryotic host. This approach eliminated false-negative errors in target gene expression that arose from BPDE adduct formation in the residual plasmid backbone rather than in the AcGFP1 gene. Determination of the BPDE–AcGFP1 adducts allowed the quantitative mutagenic effect of the BPDE adducts on AcGFP1 gene expression to be monitored. The results obtained with flow cytometry and confocal microscopy validate our method and demonstrate efficient and direct use of GFP as a biosensor for mutation detection.     

Electron microscopic visualization of fluorescent signals in cellular compartments and organelles by means of DAB-photoconversion

In this work, we show the photoconversion of the fluorochromes enhanced green fluorescent protein (EGFP), yellow fluorescent protein (YFP), and BODIPY into electron dense diaminobenzidine (DAB)-deposits using the examples of five different target proteins, and the lipid ceramide. High spatial resolution and specificity in the localization of the converted protein-fluorochrome complexes and the fluorochrome-labelled lipid were achieved by methodical adaptations around the DAB-photooxidation step, such as fixation, illumination, controlled DAB-precipitation, and osmium postfixation. The DAB-deposits at the plasma membrane and membranous compartments, such as endoplasmic reticulum and Golgi apparatus in combination with the fine structural preservation and high membrane contrast enabled differential topographical analyses, and allowed three-dimensional reconstructions of complex cellular architectures, such as trans-Golgi–ER junctions. On semithin sections the quality, distribution and patterns of the signals were evaluated; defined areas of interest were used for electron microscopic analyses and correlative microscopy of consecutive ultrathin sections. The results obtained with the proteins golgin 84 (G-84), protein disulfide isomerase (PDI), scavenger receptor classB type1 (SR-BI), and γ-aminobutyric acid (GABA) transporter 1 (GAT1), on one hand closely matched with earlier immunocytochemical data and, on the other hand, led to new information about their subcellular localizations as exemplified by a completely novel sight on the subcellular distribution and kinetics of the SR-BI, and provided a major base for the forthcoming research.     

Proteolytic activity assayed by subcellular localization switching of a substrate

An approach to assay proteolytic activity in vivo by altering the subcellular localization of a labelled substrate was demonstrated. The assay included a protein shuttling between different cellular compartments and a site-specific recombinant protease. The shuttle protein used was the human immunodeficiency virus type 1 (HIV-1) Rev protein tandemly fused to the enhanced green fluorescent protein (EGFP) and the red fluorescent protein (RFP), while the protease was the site-specific protease VP24 from the herpes simplex virus type 1 (HSV-1). The fluorescent proteins in the Rev fusion protein were separated by a cleavage site specific for the VP24 protease. When co-expressed in COS-7 cells proteolysis was observed by fluorescence microscopy as a shift from a predominantly cytoplasmic localization of the fusion protein RevEGFP to a nuclear localization while the RFP part of the fusion protein remained in the cytoplasm. The cleavage of the fusion protein by VP24 was confirmed by Western blot analysis. The activity of VP24, when tagged N-terminally by the Myc-epitope, was found to be comparable to VP24. These results demonstrates that the activity and localization of a recombinantly expressed protease can be assessed by protease-mediated cleavage of fusion proteins containing a specific protease cleavage site.     

Development of transgenic fish for ornamental and bioreactor by strong expression of fluorescent proteins in the skeletal muscle

In the present study, new applications of the transgenic technology in developing novel varieties of ornamental fish and bioreactor fish were explored in a model fish, the zebrafish (Danio rerio). Three "living color" fluorescent proteins, green fluorescent protein (GFP), yellow fluorescent protein (YFP), and red fluorescent protein (RFP or dsRed), were expressed under a strong muscle-specific mylz2 promoter in stable lines of transgenic zebrafish. These transgenic zebrafish display vivid fluorescent colors (green, red, yellow, or orange) visible to unaided eyes under both daylight and ultraviolet light in the dark. The level of foreign protein expression is estimated between 3% and 17% of total muscle proteins, equivalent to 4.8-27.2mg/g wet muscle tissue. Thus, the fish muscle may be explored as another useful bioreactor system for production of recombinant proteins. In spite of the high level of foreign protein expression, the expression of endogenous mylz2 mRNAs was not negatively affected. Furthermore, compared to the wild-type fish, these fluorescent transgenic fish have no advantage in survival and reproduction.     

Disassembly of structurally modified viral nanoparticles: characterization by fluorescence correlation spectroscopy

Analysis of the breakdown products of engineered viral particles can give useful information on the particle structure. We used various methods to breakdown both a recombinant enveloped virus and virus-like particles (VLPs) from two non-enveloped viruses and analysed the resulting subunits by fluorescence correlation spectroscopy (FCS). Analysis of the enveloped baculovirus, Autographa californica multicapsid nucleopolyhedrovirus (AcMNPV), displaying the green fluorescent protein (GFP) fused to its envelope protein gp64 was performed in the presence and absence of 5 mM SDS and 25 mM DTT. Without treatment, the viral particle showed a diffusion time of 3.3 ms. In the presence of SDS, fluorescent subunits with diffusion times of 0.2 ms were observed. Additional treatment with DTT caused a drop in the diffusion time to 0.1 ms. Changes in the amplitude of the autocorrelation function suggested a 3-fold increase in fluorescent particle number when viral particles were treated with SDS, and a further 1.5-fold increase with additional treatment with DTT. Thus, the data showed that an average of 4.5 molecules of gp64-GFP was incorporated in the membrane of the modified baculovirus. Further, this suggests that each fluorescent gp64 trimer carries on average 1.5 fluorescent units. Similar experiments were carried out with two non-enveloped fluorescent virus-like particles (fVLPs) that displayed enhanced green fluorescent protein (EGFP). These, fVLPs of canine and human B19 parvoviruses were treated with 6 M urea and 5 mM SDS, respectively. Correspondingly, the original hydrodynamic radii of 17 and 14 nm were reduced to 9 and 5 nm after treatment. Here, the change in the amplitude of the autocorrelation curve suggested a 10-fold increase in particle number when viral particles of CPV were treated with 6 M urea at 50 degrees C for 10 min. For EGFP-B19, there was a decrease in the amplitude, accompanied by a 9-fold increase in the number of fluorescent units with SDS treatment. The results showed that approximately 10 and 9 fluorescent units were associated with the corresponding CPV and B19 VLPs. In summary, we were able to estimate the number of fluorescent subunits in a baculovirus containing a GFP-fusion with its gp64 envelope protein and in two different parvo-VLPs containing EGFP-fused with their VP2 capsid proteins.     

Direct detection of caspase-3 activation in single live cells by cross-correlation analysis

Dual color fluorescence cross-correlation spectroscopy (FCCS) provides information about the coincidence of spectrally well-defined two fluorescent molecules in a small observation area at the single-molecule level. To evaluate the activity of caspase-3 in vivo directly, FCCS was applied to single live cells. We constructed chimeric proteins that consisted of tandemly fused enhanced green FP (EGFP) and monomeric red FP (mRFP). In control experiments, the protease reaction was monitored in solution, where a decrease in cross-correlation amplitude was observed due to specific cleavage of the amino acid sequence between EGFP and mRFP. Moreover, a decrease in cross-correlation amplitude could be detected in a live cell, where caspase-3 activation was induced by apoptosis. This is the first report of FP-based in vivo cross-correlation analysis. FP-based FCCS may become the most versatile method for analysis of protein-protein interactions in live cells.     

Rectified photocurrent of molecular photodiode consisting of cytochrome c/GFP hetero thin films

Photoinduced electron transfer in the molecular electronic device consisting of protein-adsorbed hetero Langmuir–Blodgett (LB) film was investigated. Three kinds of functional molecules, cytochrome c, viologen, and green fluorescent protein (GFP) were used as an electron acceptor, a mediator, and a sensitizer, respectively. The hetero-LB film was fabricated by subsequently depositing cytochrome c and viologen onto the pretreated ITO or quartz glass. GFP adsorbed hetero-LB films were prepared by soaking the hetero-LB films into the buffer solution containing GFP. The MIM (metal/insulator/metal) structured molecular device was constructed by depositing aluminum onto the surface of the GFP-adsorbed hetero LB films. Due to the excitation by irradiation with a 460 nm monochromic light source, the photoinduced unidirectional flow of electrons in the MIM device could be achieved and was detected as photocurrents. The photoswitching function was achieved and the rectifying characteristic was observed in the molecular device. Based on the measurement of transient photocurrent of molecular device, the unidirectional flow of electrons was verified.     

Xfect介导重组质粒pEGFP-C2/LAT-ORF3高效转染Vero细胞的方法及其条件的优化

旨在用Xfect试剂介导重组质粒pEGFP-C2/LAT-ORF3转染Vero细胞,以期获得转染效率较高的方法,并检测目标片段的表达,从而为进一步研究HSV-2 LAT基因及其ORF3片段的生物学功能奠定基础。用Xfect试剂介导重组质粒pEGFP-C2/LAT-ORF3转染Vero细胞,48 h后观察荧光表达情况,并计算不同转染方法分别在有无血清及质粒与Xfect Polymer比例不同时的转染效率。用RT-PCR检测ORF3片段在Vero细胞中的表达。结果显示,采用贴壁转染法,在有血清及质粒与Xfect Polymer比例为5μg/2μL时转染效率较高;RT-PCR可以获得目的条带,证明ORF3片段在Vero细胞中得到表达。本试验获得的优化条件可以显著提高Xfect Polymer对Vero细胞的转染效率;以绿色荧光蛋白作为标签鉴定目的基因在细胞中表达的方法切实可行。     

In vitro selection of GTP-binding proteins by block shuffling of estrogen-receptor fragments

To what extent has alternative splicing contributed to the evolution of protein-function diversity? We previously constructed a pool of block-deletion mutants of the human estrogen receptor α ligand binding domain by random multi-recombinant PCR. Here we performed iterative in vitro selection of GTP-binding proteins by using the library of mRNA-displayed proteins and GTP-affinity chromatography combined with quantitative real-time PCR. We obtained a novel GTP-binding protein with moderate affinity and substrate-specificity. The results of our in vitro simulation imply that alternative splicing may have contributed substantially to the diversification of protein function during evolution.     

Thermostabilization of protein A-luciferase fusion protein by single amino acid mutation

A gene expression plasmid, pMALU7, for coding a fusion protein between protein A (SpA) and mutated firefly luciferase (Luc), was constructed. The fused gene was expressed in Escherichia coli and the resulting protein (SpA-LucTS) was purified with affinity chromatography. By changing a single amino acid, from Glu to Lys at the position 354 in the luciferase moiety, the thermostability of luciferase was improved.     

人结直肠癌细胞HCT116红色和绿色荧光标记肿瘤模型的建立

目的筛选表达绿色荧光蛋白和红色荧光蛋白基因的人的单克隆结直肠癌细胞系,为体内监测肿瘤的早期生长建立一种新的肿瘤动物模型。方法以脂质体2000介导chickenβ-actin-GFP-neo和chickenβ-actin-DsRed-neo转染人结直肠癌细胞HCT-116,经梯度浓度G418筛选获得稳定表达红色和绿色荧光蛋白的细胞克隆并扩大培养。BALB/CA-nu裸鼠皮下接种1×10^6个发光细胞使其成瘤,活体荧光成像系统观察肿瘤的生长情况。结果获得了稳定表达GFP、DsRed的人结肠癌细胞株,将其接种到裸鼠体内可成瘤,利用活体成像系统观察了肿瘤的生长过程,肿瘤的发光随着观察时间的延长而增加。结论红色和绿色荧光蛋白能够在人结直肠癌细胞HCT-116中长期稳定表达,用红色和绿色荧光蛋白标记的人结直肠癌细胞HCT-116建立的裸鼠肿瘤模型为进一步研究结肠肿瘤和相应的药物筛选提供了一种简便、可行的新方法。     

Monitoring receptor-mediated activation of heterotrimeric G-proteins by fluorescence resonance energy transfer

Green fluorescent protein (GFP)-centered fluorescence resonance energy transfer (FRET) relies on a distance-dependent transfer of energy from a donor fluorophore to an acceptor fluorophore and can be used to examine protein interactions in living cells. Here we describe a method to monitor the association and disassociation of heterotrimeric GTP-binding (G-proteins) from one another before and after stimulation of coupled receptors in living Dictyostelium discoideum cells. The Galpha(2)and Gbetagamma proteins were tagged with cyan and yellow fluorescent proteins and used to observe the state of the G-protein heterotrimer. Data from emission spectra were used to detect the FRET fluorescence and to determine kinetics and dose-response curves of bound ligand and analogs. Extending G-protein FRET to mammalian G-proteins should enable direct in situ mechanistic studies and applications such as drug screening and identifying ligands of new G-protein-coupled receptors.     

Quantification of plasmid loss in Escherichia coli cells by use of flow cytometry

A method was developed to study plasmid stability in Escherichia coli cells, which utilised the high speed analysis properties of flow cytometry. To discriminate between plasmid-harbouring cells and plasmid-free cells a plasmid-encoded Lac repressor protein was used to regulate the expression of a chromosomally inserted green fluorescent protein gene in the host cells. Flow cytometric analysis enabled detection and quantification of plasmid-free cells due to their green fluorescent phenotype. The reported system offers real-time analysis in combination with a very low detection level of plasmid loss in bacterial populations. This could be useful in future investigations of plasmid stability and population selection in bacterial communities.