HB tag modules for PCR-based gene tagging and tandem affinity purification in Saccharomyces cerevisiae

We have recently developed the HB tag as a useful tool for tandem-affinity purification under native as well as fully denaturing conditions. The HB tag and its derivatives consist of a hexahistidine tag and a bacterially-derived in vivo biotinylation signal peptide, which support sequential purification by Ni2+ -chelate chromatography and binding to immobilized streptavidin. To facilitate tagging of budding yeast proteins with HB tags, we have created a series of plasmids with various selectable markers. These plasmids allow single-step PCR-based tagging and expression under control of the endogenous promoters or the inducible GAL1 promoter. HB tagging of several budding yeast ORFs demonstrated efficient biotinylation of the HB tag in vivo by endogenous yeast biotin ligases. No adverse effects of the HB tag on protein function were observed. The HB tagging plasmids presented here are related to previously reported epitope-tagging plasmids, allowing PCR-based tagging with the same locus-specific primer sets that are used for other widely used epitope-tagging strategies. The Sequences for the described plasmids were submitted to GenBank under Accession Numbers DQ407918-pFA6a-HBH-kanMX6 DQ407927-pFA6a-RGS18H-kanMX6 DQ407919-pFA6a-HBH-hphMX4 DQ407928-pFA6a-RGS18H-hphMX4 DQ407920-pFA6a-HBH-TRP1 DQ407929-pFA6a-RGS18H-TRP1 DQ407921-pFA6a-HTB-kanMX6 DQ407930-pFA6a-kanMX6-PGAL1-HBH DQ407922-pFA6a-HTB-hphMX4 DQ407931-pFA6a-TRP1-PGAL1-HBH DQ407923-pFA6a-HTB-TRP1 DQ407924-pFA6a-BIO-kanMX6 DQ407925-pFA6a-BIO-hphMX4 DQ407926-pFA6a-BIO-TRP1.     

New modules for the repeated internal and N-terminal epitope tagging of genes in Saccharomyces cerevisiae

Epitope tagging is a powerful method for the rapid analysis of protein function. In Saccharomyces cerevisiae epitope tags are introduced easily into chromosomal loci by homologous recombination using a simple PCR-based strategy. Although quite a number of tools exist for C-terminal tagging as well as N-terminal tagging of proteins expressed by heterologous promoters, there are only very limited possibilities to tag proteins at the N-terminus and retain the endogenous expression level. Furthermore, no PCR-templates for internal tagging have been reported. Here we describe new modules that are suitable for both the repeated N-terminal and internal tagging of proteins, leaving their endogenous promoters intact. The tags include 6xHA, 9xMyc, yEGFP, TEV-GST-6xHIS, ProtA, TEV-ProtA and TEV-ProtA-7xHIS in conjunction with different heterologous selection markers.     

A vector system for efficient and economical switching of C-terminal epitope tags in Saccharomyces cerevisiae

In Saccharomyces cerevisiae, one-step PCR-mediated modification of chromosomal genes allows fast and efficient tagging of yeast proteins with various epitopes at the C- or N-terminus. For many purposes, C-terminal tagging is advantageous in that the expression pattern of epitope tag is comparable to that of the authentic protein and the possibility for the tag to affect normal folding of polypeptide chain during translation is minimized. As experiments are getting complicated, it is often necessary to construct several fusion proteins tagged with various kinds of epitopes. Here, we describe development of a series of plasmids that allow efficient and economical switching of C-terminally tagged epitopes, using just one set of universal oligonucleotide primers. Containing a variety of epitopes (GFP, TAP, GST, Myc, HA and FLAG tag) and Kluyveromyces lactis URA3 gene as a selectable marker, the plasmids can be used to replace any MX6 module-based C-terminal epitope tag with one of the six epitopes. Furthermore, the plasmids also allow additional C-terminal epitope tagging of proteins in yeast cells that already carry MX6 module-based gene deletion or C-terminal epitope tag.     

Functional analysis reports. Precise gene disruption in Saccharomyces cerevisiae by double fusion polymerase chain reaction

We adapted a fusion polymerase chain reaction (PCR) strategy to synthesize gene disruption alleles of any sequenced yeast gene of interest. The first step of the construction is to amplify sequences flanking the reading frame we want to disrupt and to amplify the selectable marker sequence. Then we fuse the upstream fragment to the marker sequence by fusion PCR, isolate this product and fuse it to the downstream sequence in a second fusion PCR reaction. The final PCR product can then be transformed directly into yeast. This method is rapid, relatively inexpensive, offers the freedom to choose from among a variety of selectable markers and allows one to construct precise disruptions of any sequenced open reading frame in Saccharomyces cerevisiae.     

Sticky-end polymerase chain reaction method for systematic gene disruption in Saccharomyces cerevisiae

We describe a new procedure for the generation of plasmids containing a large promoter and terminator region of a gene of interest, useful for gene disruption. In a two-step polymerase chain reaction (PCR), a fragment, corresponding to the terminator and promoter regions separated by a 16 bp sequence containing a rare restriction site (e.g. AscI), is synthesized (T-P fragment). This PCR fragment is cloned in vectors presenting a rare blunt-end cloning site and a yeast marker for selection in Saccharomyces cerevisiae (TRP1, HIS3 and KanMX). The final plasmids are used directly for gene disruption after linearization by the enzyme (e.g. AscI) specific for the rare restriction site. This approach was used to disrupt three open reading frames identified during the sequencing of COS14–1 from chromosome XIV of S. cerevisiae.     

A flexible protein linker improves the function of epitope-tagged proteins in Saccharomyces cerevisiae

Epitope tagging permits the detection of proteins when protein-specific antibodies are not available. However, the epitope tag can reduce the function of the tagged protein. Here we describe a cassette that can be used to introduce an eight amino acid flexible linker between multiple Myc epitopes and the open reading frame of a given gene. We show that inserting the linker improves the in vivo ability of the telomerase subunits Est2p and Est1p to maintain telomere length. The methods used here are generally applicable to improve the function of tagged proteins in both Saccharomyces cerevisiae and Schizosaccharomyces pombe.     

A suite of polymerase chain reaction-based peptide tagging plasmids for epitope-targeted enzymatic functionalization of yeast proteins

The budding yeast and model eukaryote Saccharomyces cerevisiae has been invaluable for purification and analysis of numerous evolutionarily conserved proteins and multisubunit complexes that cannot be readily reconstituted in Escherichia coli. For many studies, it is desirable to functionalize a particular protein or subunit of a complex with a ligand, fluorophore or other small molecule. Enzyme-catalysed site-specific modification of proteins bearing short peptide tags is a powerful strategy to overcome the limitations associated with traditional nonselective labelling chemistries. Towards this end, we developed a suite of template plasmids for C-terminal tagging with short peptide sequences that can be site-specifically functionalized with high efficiency and selectivity. We have also combined these sequences with the FLAG tag as a handle for purification or immunological detection of the modified protein. We demonstrate the utility of these plasmids by site-specifically labelling the 28-subunit core particle subcomplex of the 26S proteasome with the small molecule fluorophore Cy5. The full set of plasmids has been deposited in the non-profit plasmid repository Addgene ( http://www.addgene.org ).     

Optimized cassettes for fluorescent protein tagging in Saccharomyces cerevisiae

Green fluorescent protein (GFP) has become an increasingly popular protein tag for determining protein localization and abundance. With the availability of GFP variants with altered fluorescence spectra, as well as GFP homologues from other organisms, multi-colour fluorescence with protein tags is now possible, as is measuring protein interactions using fluorescence resonance energy transfer (FRET). We have created a set of yeast tagging vectors containing codon-optimized variants of GFP, CFP (cyan), YFP (yellow), and Sapphire (a UV-excitable GFP). These codon-optimized tags are twice as detectable as unoptimized tags. We have also created a tagging vector containing the monomeric DsRed construct tdimer2, which is up to 15-fold more detectable than tags currently in use. These tags significantly improve the detection limits for live-cell fluorescence imaging in yeast, and provide sufficient distinguishable fluorophores for four-colour imaging.     

Small epitope‐linker modules for PCR‐based C‐terminal tagging in Saccharomyces cerevisiae

PCR‐mediated gene modification is a powerful approach to the functional analysis of genes in Saccharomyces cerevisiae. One application of this method is epitope‐tagging of a gene to analyse the corresponding protein by immunological methods. However, the number of epitope tags available in a convenient format is still low, and interference with protein function by the epitope, particularly if it is large, is not uncommon. To address these limitations and broaden the utility of the method, we constructed a set of convenient template plasmids designed for PCR‐based C‐terminal tagging with 10 different, relatively short peptide sequences that are recognized by commercially available monoclonal antibodies. The encoded tags are FLAG, 3 × FLAG, T7, His‐tag, Strep‐tag II, S‐tag, Myc, HSV, VSV‐G and V5. The same pair of primers can be used to construct tagged alleles of a gene of interest with any of the 10 tags. In addition, a six‐glycine linker sequence is inserted upstream of these tags to minimize the influence of the tag on the target protein and maximize its accessibility for antibody binding. Three marker genes, HIS3MX6, kanMX6 and hphMX4, are available for each epitope. We demonstrate the utility of the new tags for both immunoblotting and one‐step affinity purification of the regulatory particle of the 26S proteasome. The set of plasmids has been deposited in the non‐profit plasmid repository Addgene ( http://www.addgene.org ). Copyright © 2009 John Wiley & Sons, Ltd.     

Additional vectors for PCR-based gene tagging in Saccharomyces cerevisiae and Schizosaccharomyces pombe using nourseothricin resistance

The one-step PCR-mediated technique used for modification of chromosomal loci is a powerful tool for functional analysis in yeast. Both Saccharomyces cerevisiae and Schizosaccharomyces pombe are amenable to this technique. However, the scarce availability of selectable markers for Sz. pombe hampers the easy use of this technique in this species. Here, we describe the construction of new vectors deriving from the pFA6a family, which are suitable for tagging in both yeasts owing to the presence of a nourseothricin-resistance cassette. These plasmids allow various gene manipulations at chromosomal loci, viz. N- and C-terminal tagging with 3HA (haemagglutinin) or 13Myc epitopes, GST (glutathione S-transferase), 4TAP (tandem affinity purification) and several GFP (green fluorescent protein) isoforms. For N-terminal modifications, the use of different promoters allows constitutive (PADH1) or regulatable (PGAL1) promoters for S. cerevisiae and derivatives of Pnmt1 for Sz. pombe expression.     

A vector for double epitope tagging with a recyclable marker

Multimeric protein complexes play diverse and vital roles in the cell, but following the composition of these complexes under varying growth conditions can be challenging. Toward that goal, we have designed a vector that permits the double epitope tagging of a protein at its carboxy terminus. One 'universal' tag, a triple repeat of the HA1 epitope, is fused with every protein to be studied, allowing the composition and stoichiometry of the proteins in a complex to be detected with a single antibody. Each protein also can be tagged with a second epitope specific for that protein. This 'specific' tag can be used to immunoprecipitate complexes containing that protein of interest. Any epitope to which a specific antibody is available can be used for this second tag. Because there are a limited number of selection markers for cloning in yeast, the kanamycin cassette, flanked by loxP sites, was incorporated into the vector to permit marker recycling using Cre-lox recombinase. This vector was used to tag 4 proteins involved in ribosome biogenesis-Ytm1, Cic1, Brx1 and Drs1. An anti-HA1 antibody could detect all four proteins in crude lysates and yielded the relative abundance of these four proteins, of which Drs1 is reproducibly less abundant than any of the others, which may have implications for the control of ribosome biogenesis. The Ytm1 protein was also tagged with the VSV epitope and can be specifically detected using an anti-VSV antibody. This vector may prove useful for exploring other protein complexes.     

Detection of peanut using real-time polymerase chain reaction

Preliminary results are presented on a sensitive and robust assay for the identification of peanut in commercial products using real-time PCR technology. Peanut specific primers and probe, designed using the Arah 2 gene, were optimised for real-time PCR using an ABI PRISM 7700. Commercial extraction kits employing different technological strategies were assessed for the extraction of PCR quality peanut DNA template. The specificity of the primer and probe set was determined using a wide range of food items and the limit of detection and quantification calculated using dilutions of peanut DNA. The assay was used to detect spiked or trace level of peanut in commercial samples and was finally used to detect peanut in a biscuit prepared with 2 ppm of lightly roasted peanut powder.An erratum to this article can be found at     

pMPY-ZAP: A reusable polymerase chain reaction-directed gene disruption cassette for Saccharomyces cerevisiae

Gene disruption is an important method for genetic analysis in Saccharomyces cerevisiae. We have designed a polymerase chain reaction-directed gene disruption cassette that allows rapid disruption of genes in S. cerevisiae without previously cloning them. In addition, this cassette allows recycling of URA3, generating gene disruptions without the permanent loss of the ura3 marker. An indefinite number of disruptions can therefore be made in the same strain.     

Expanding the repertoire of plasmids for PCR-mediated epitope tagging in yeast

Epitope tagging of yeast proteins provides a convenient means of tracking proteins of interest in Western blots and immunoprecipitation experiments without the need to raise and test specific antibodies. We have constructed four plasmids for use as templates in PCR-based epitope tagging in the yeast Saccharomyces cerevisiae. These plasmids expand the range of epitopes available in a tag-URA3-tag context to include the FLAG, HSV, V5 and VSV-G epitopes. The cloning strategy used would be easily applicable to the construction of a similar tag-URA3-tag molecule for essentially any desired epitope. Oligonucleotides designed for PCR from one plasmid may be used interchangeably with any of the other template molecules to allow tagging with different epitopes without the need for new primer synthesis. We have tagged Tfc6 with each of the triple epitope tags and assessed the efficiency of these epitopes for chromatin immunoprecipitation (ChIP). For all the tagged alleles, ChIP occupancy signals are easily detectable at known Tfc6 target genes. These new tags provide additional options in experimental schemes requiring multiple tagged proteins.     

实时荧光PCR快速筛选食品中鸭源性成分

基于鸭线粒体细胞色素Cyt b基因建立了肉制品中的鸭源性成分检测的real-time PCR方法,并对模拟样本和市售样本进行了检测分析,检出限低至1%,适用于实验室的鸭源性成分的鉴定分析。      

菠萝成分的实时荧光PCR检测方法的建立

目的本文研究建立食品中菠萝成分的实时荧光PCR检测方法。方法根据菠萝rbcL基因设计菠萝物种特异性检测引物和荧光探针,对样品中的靶标基因片段进行检测,并进行物种特异性检测、灵敏度测试和实际应用检测。结果通过对供试的58种动植物材料进行检测,只有菠萝出现特异性扩增,其他物种材料无扩增;对不同浓度菠萝DNA样品和不同含量的菠萝粉样品进行灵敏度测试,该检测方法对菠萝成分的检测灵敏度分别为0.01 ng/μL菠萝DNA和0.1%菠萝粉;对市场销售的实际样品进行检测,能够满足于检测需求。结论该方法简单、灵敏、快速、准确,能应用于食品中菠萝成分检测。     

实时荧光定量RT-PCR检测沙门氏菌活菌

沙门氏菌是引起食物中毒的最常见致病菌,而基于DNA水平的常规PCR(DNA-PCR)检测法虽然快速、灵敏,但在检测时无法区分死活菌,死亡的细菌会出现假阳性结果,严重影响日常检测结果的判断。提取沙门氏菌总RNA之后,采用一步法逆转录聚合酶链式反应(RT-PCR),以沙门氏菌invAmRNA为检测对象,发现只有活的沙门氏菌显阳性,死亡的沙门氏菌呈阴性。而且RT-PCR法的稳定性良好,能够准确定量活的沙门氏菌,在纯培养时,检出限可达1CFU/3mL。实验表明,建立的RT-PCR法是一种能够快速、精确检测沙门氏菌活菌的方法。     

实时荧光PCR技术快速检测食品中的牛源成分

目的:建立基于实时荧光PCR技术的食品中牛源性成分快速检测方法。方法:以牛线粒体细胞色素b为目的基因,设计特异性引物和探针,通过特异性、灵敏性实验,及模拟混合肉样和市售肉制品检测,对该体系进行验证。结果:该牛源荧光PCR检测体系具有很好的特异性及灵敏性,可检测1pg牛源DNA的存在,对于各模拟肉类样品中掺杂的牛源性成分,其检测限低至0.5%,且经市售加工食品验证具有较好的应用能力。结论:所建立的牛引物探针体系具有特异性好、灵敏度高,快速高效等优点,可用于对食品中牛源性成分的掺假鉴别检测。      

多重聚合酶链式反应技术在食源性致病菌检测上的应用研究进展

多重聚合酶链式反应(polymerase chain reaction,PCR)技术是在常规PCR技术基础上发展起来的,其反应原理、反应试剂和操作过程与常规PCR相同,区别在于多重PCR技术在同一个反应体系中加入2对或2对以上引物,分别扩增不同的模板,得到不同的目的片段.多重PCR技术在食源性致病菌检测中具有高通量、节...     

Plasmids with E2 epitope tags: tagging modules for N‐ and C‐terminal PCR‐based gene targeting in both budding and fission yeast,and inducible expression vectors for fission yeast

A single‐step PCR‐based epitope tagging enables fast and efficient gene targeting with various epitope tags. This report presents a series of plasmids for the E2 epitope tagging of proteins in Saccharomyces cerevisiae and Schizosaccharomyces pombe. E2Tags are 10‐amino acids (epitope E2a: SSTSSDFRDR)‐ and 12 amino acids (epitope E2b: GVSSTSSDFRDR)‐long peptides derived from the E2 protein of bovine papillomavirus type 1. The modules for C‐terminal tagging with E2a and E2b epitopes were constructed by the modification of the pYM‐series plasmid. The N‐terminal E2a and E2b tagging modules were based on pOM‐series plasmid. The pOM‐series plasmids were selected for this study because of their use of the Cre–loxP recombination system. The latter enables a marker cassette to be removed after integration into the loci of interest and, thereafter, the tagged protein is expressed under its endogenous promoter. Specifically for fission yeast, high copy pREP plasmids containing the E2a epitope tag as an N‐terminal or C‐terminal tag were constructed. The properties of E2a and E2b epitopes and the sensitivity of two anti‐E2 monoclonal antibodies (5E11 and 3F12) were tested using several S. cerevisiae and Sz. pombe E2‐tagged strains. Copyright © 2009 John Wiley & Sons, Ltd.