- Methodology article
- Open Access
Development of a Premature Stop Codon-detection method based on a bacterial two-hybrid system
© Real et al; licensee BioMed Central Ltd. 2006
Received: 03 March 2006
Accepted: 02 September 2006
Published: 02 September 2006
The detection of Premature Stop Codons (PSCs) in human genes is very useful for the genetic diagnosis of different hereditary cancers, e.g. Familial Breast Cancer and Hereditary Non-Polyposis Colorectal Cancer (HNPCC). The products of these PSCs are truncated proteins, detectable in vitro by the Protein Truncation Test and in vivo by using the living translation machinery of yeast or bacteria. These living strategies are based on the construction of recombinant plasmids where the human sequence of interest is inserted upstream of a reporter gene. Although simple, these assays have their limitations. The yeast system requires extensive work to enhance its specificity, and the bacterial systems yield many false results due to translation re-initiation events occurring post PSCs. Our aim was to design a recombinant plasmid useful for detecting PSCs in human genes and resistant to bacterial translation re-initiation interferences.
A functional recombinant plasmid (pREAL) was designed based on a bacterial two-hybrid system. In our design, the in vivo translation of fused fragments of the Bordetella pertussis adenylate cyclase triggers the production of cAMP giving rise to a selectable bacterial phenotype. When a gene of interest is inserted between the two fragments, any PSC inhibits the enzymatic activity of the product, and translation re-initiation events post-PSC yield separated inactive fragments. We demonstrated that the system can accurately detect PSCs in human genes by inserting mutated fragments of the brca1 and msh2 gene. Western Blot assays revealed translation re-initiation events in all the tested colonies, implying that a simpler plasmid would not be resistant to this source of false negative results. The application of the system to a HNPCC family with a nonsense mutation in the msh2 gene correctly diagnosed wild type homozygous and heterozygous patients.
The developed pREAL is applicable to the detection of PSCs in human genes related to different diseases and is resistant to translation re-initiation events. The diagnosis steps are easy, have a low cost, detect only pathologic mutations, and allow the analysis of separated alleles.
The presence of Premature Stop Codons (PSCs) in tumorsupressor and Mismatch Repair genes are a very frequent cause of hereditary cancer that account for 50%-90% of the reported pathogenic mutations [1–3]. PSCs are observed in the apc gene related to Familial Adenomatous Polyposis (FAP) [4, 5], the brca1 and 2 genes related to Familial Breast Cancer [6–8] and the Mismatch Repair genes related to Hereditary Non-Polyposis Colorectal Cancer (HNPCC) [9, 10]. PSCs are produced by nonsense or frameshift mutations resulting in the premature termination of proteins [11, 12]. These truncated proteins can either loose completely their function producing haploinsufficiency in the cell or acquire a dominant negative effect on the full-length protein produced by the wild type allele [13, 14]. In most cases, both consequences are pathologic. The mentioned genes related to hereditary cancers show an extremely heterogeneous mutation spectrum, but although the alterations are scattered throughout the complete coding sequence, most of the identified mutations produce premature termination of protein translation [15, 16].
The detection of mutations in genomic DNA is one of the most common diagnosis methods used for these diseases – e.g. SSCP, DGGE, HA – [17, 18]. These techniques have the advantage of using only DNA -an easy to handle molecule- and have widely proved their usefulness. Still, they have their limitations. They reveal all sequence changes, including silent mutations and polymorphisms without pinpointing the type of mutation. Therefore, subsequent analyses are sometimes needed to distinguish between pathologic mutations and polymorphisms .
The other major diagnosis methods are based on the detection of the protein product, and they have the advantage of detecting exclusively pathologic mutations. The translation machinery is exquisitely sensitive to PSCs that terminate the process of protein elongation. The analysis of the truncated proteins can be done in vitro – e.g. Protein Truncation Test (PTT) – by starting from either genomic DNA or RNA, amplifying the sequence to be analyzed, and using these products as templates for in vitro transcription and translation [20, 21]. The shorter products of the mutated alleles are then distinguished from the full-length protein products of normal alleles. A disadvantage of the conventional PTT is the involvement of SDS-PAGE followed by autoradiography or Western blotting. As it relies on visual inspection to detect the mobility of shifted bands, it may also be subject to evaluator error. Another limitation of the method is the lack of sensitivity to diagnose mutations near the translation end that produce too small mobility shifts to be detected .
The PTT test is based on cell-free transcription and translation. However, the same machinery is present and functional in living cells. Therefore, in principle, it would be possible to carry out the diagnosis by using the translation machinery of cells. Several models have been developed in the past that use living-system strategies. For these methods, PCR amplifications of consecutive fragments of the gene are introduced in a reporter-plasmid, which is then transformed into yeast or bacteria . The DNA to be tested is ligated upstream an easily detectable protein. The presence of a PSC in the sequence will stop translation prematurely and prevent the expression of the reporter protein.
The so called "yeast-based stop codon assay" has been reported for the detection of chain-terminating mutations in some specific genes. The PCR-amplified coding sequence is inserted by homologous recombination into a yeast expression vector system, and transformants are assayed for growing in a nutrition-deficient medium. To allow the insertion of the DNA sequence by homologous recombination, a gap-vector must be previously generated to introduce homologous flanking sequences for the posterior recombination insertion step. Therefore, this method requires the construction of an expression vector that is specific for each tested sequence (e.g. exon), and hence is not applicable to a new candidate gene. A modification made by Kataoka et al , consists of the development of a universal gap-vector to permit the automatic integration of any gene fragment. Each primer used to amplify the sequence of interest carries a 24bp recombination tail. However, this method requires performing a nested PCR to reduce nonspecific amplification products; hence, it has many steps for a routine diagnosis.
Bacteria have the advantage of being easier to manipulate than yeast. However, even though some authors have reported the development of bacterial systems based on the cloning of relevant segments in-frame with a colorimetric marker gene , no data was found reporting their application in routine diagnosis. A problem with this strategy is the capability of bacteria to re-initiate translation downstream of the STOP, causing expression of the reporter even in the presence of a PSC (false negative diagnosis) .
The aim of this work was to develop an alternative methodology to detect PSCs in human genes using the transcription and translation machinery of bacteria while avoiding the translation re-initiation interference. The strategy was to introduce the DNA to be tested in a linker between the two fragments of the catalytic domain of adenylate cyclase (cya) of Bordetella pertussis, used for the bacterial two-hybrid system developed by Karimova et al . Re-initiation events will render two separate cya domains catalytically inactive. Our results show that the plasmid is a sensitive, specific, efficient and low-cost tool for the detection of PSCs and that it is insensitive to re-initiation artifacts.
Development of the recombinant pREAL plasmid
We reasoned that if we constructed a unique plasmid containing both complementary fragments of the reporter enzyme linked by a subcloned human gene of interest, the adenylate cyclase would be functional only in absence of any PSC in the subcloned DNA fragment. In the absence of PSC in the linker, the two domains would be synthesized as a single polypeptide with adenylate cyclase activity (Figure 1Ba). A PSC in the DNA fragment would stop translation and the second domain required for adenylate cyclase activity would not be present. Any possible translation re-initiation event downstream the PSCs would yield physically unattached fragments that should not be able to re-associate, and hence would not result in a false negative result (Figure 1Bb).
The two cya domains expressed as a single polypeptide are catalytically active
The system can accurately detect PSC in human DNA fragments
To test whether pREAL could be used to detect PSCs in human genes, three different fragments of exon 11 of the brca1 gene were amplified from a healthy donor. Reported pathogenic stop mutations related to breast and ovarian cancer were introduced by a mutagenic PCR strategy using the wild type DNA as template . A nonsense (NS) and a frameshift (FS) mutation were generated introducing the alterations with two different forward primers. A wild type (WT) version was used as control. All forward primers had BamHI site overhangs and the reverse primer had a 5' EcoRI site to facilitate insertion in the MCS of pREAL. The annealing site of the reverse primer was carefully selected to include ATG and GTG codons post PSC and in-frame with T18, in order to detect translation re-initiation events.
To confirm that the inserts of the white colonies had different sequences from those of the red colonies, we amplified DNA directly from the colonies (primers are represented with gray arrows in Figure 4B) touching with a single pipette tip a red and a white colony. The resulting mixed PCR product was heat denatured, and allowed to re-hybridize at low temperature. Finally, the mixed DNA product was ran in a non-denaturing PAGE. We expected the formation of homoduplexes (double-strand DNA composed by two complementary strands) in case of a mix with identical sequences, and the detection of heteroduplexes (double-strand DNA composed by two not completely complementary strands) in case of a mix with different sequences. The heteroduplexes are easily detectable by their delayed mobility on an electrophoresis assay. The PAGE showed the formation of heteroduplexes only in the mixed product, confirming that it contained different sequences (Figure 4C). In conclusion, these experiments indicate that insertion of a PSC-containing DNA in pREAL is easily detected by bacterial colony phenotype and that the assay is suitable for analyzing heterozygous samples.
PSCs were accurately detected even in the presence of re-initiation events
We speculated that the developed diagnosis system would be resistant to translation re-initiation, a common event in bacteria. To detect whether translation re-initiation events were occurring in our system, we used a murine anti-adenylate cyclase monoclonal antibody that binds to the distal portion – amino acids 373–399 – of fragment T18 (C-terminus domain of the protein). Our hypothesis was that, in the absence of PSC, a large product (59 kDa) would be detected by the antibody, whereas in the presence of PSC, if translation re-initiations occurred, smaller products recognized by the antibody should appear.
The system correctly detects a truncating mutation in a HNPCC patient
The pREAL plasmid has proved to be very efficient to detect stop codons introduced in exon 11 of the brca1 gene of a wild type DNA, even in heterozygous samples. We wanted to test the system with another gene and in a more realistic situation. For this propose, exon 13 of the msh2 gene was amplified from DNA obtained from peripheral blood of a patient from a HNPCC family. This family presents a mutation (TGA>TAA) on codon 711 of this gene. The PCR product was inserted in frame in the MCS of pREAL. Note that the patient was heterozygous; hence, the PCR product contained both, the mutated and the wild type alleles. DNA of an unaffected member of the HNPCC family was used as control.
In the assay with the brca1 exon, the reverse primer was designed in order to include ATG and GTG sequences on purpose to test the robustness of the method to translation re-initiation problems. We assessed the occurrence of re-initiation in this more realistic assay with the DNA amplified from a patient. Western Blot assays revealed the presence of re-initiation events in red and white colonies (Figure 6C, lanes 3 and 4), proving that a simpler plasmid, based on the expression of a single reporter would have strong limitations due to re-initiation events. Notice that, as expected, white colonies do not express the full-length (active) adenylate cyclase (Figure 6C, lane 4). These observations show that the pREAL strategy can be used in a relatively simple diagnostic scheme: PCR amplification from genomic DNA from patients, ligation into pREAL, transformation with the ligation product into BTH102, and bacterial phenotype screening in MacConkey or LB-Xgal media.
The diagnosis of hereditary diseases by molecular biology methods has proved to be a powerful tool for the managing of affected families and, in many cases, for the treatment of affected members. With a growing number of genes identified as related to specific syndromes, these methods are of great interest to the medical community. Although feasible, the complete sequencing of the suspected gene is still not efficient. Moreover, many mutations may be normal polymorphisms without pathological significance. Morbid mutations are frequently related to inactivation of the gene product by the conversion of wild type triplets to stop codons, or changes in the reading frame that usually introduce stop codons. Therefore, the detection of PSCs in disease-related genes is usually of great importance for the diagnosis of hereditary diseases.
We describe here a bacterial system that allows the detection of PSCs in human genes by a simple colony phenotype screening. The idea was originated in the two-hybrid system based on a reconstituted signal transduction pathway in bacteria, developed by Karimova et al  in the Pasteur Institute. In our design, the in vivo translation of Bordetella pertussis adenylate cyclase fragments linked by a PSC-free inserted DNA triggers the expression of cAMP-dependent genes. We took advantage of the fact that the T25 and T18 fragments are unable to recognize each other and cannot reconstitute a functional enzyme when expressed as separate entities. However, if they are attached by a polypeptide chain, the protein is active and cAMP is synthesized. Ultimately, cAMP, upon binding to CAP, activates the transcription of catabolic operons, allowing the bacteria to ferment carbohydrates such as maltose or lactose. We show here that any PSC in the DNA inserted between the adenylate cyclase fragments inhibits the activity of the translation product. We also show that translation re-initiation events do occur and that the pREAL system is resistant to this source of false negative results. Indeed, re-initiation was a very common event observed even in sequences lacking PSCs. We showed by Western blot that most of the possible initiation codons in the inserted fragment were used and generated a detectable polypeptide in the assay.
Patients with hereditary mutations in tumor suppressor genes are always heterozygous, because homozygous individuals are unviable. Hence, a mixed PCR product is obtained when DNA from these patients is amplified. However, a single PCR product is inserted per copy of the pREAL plasmid; in turn, only one pREAL copy transforms a cya- bacterium that expands in a clone on the plate. Therefore, each colony represents one allele. In conclusion, this method allows the analysis of separated alleles of heterozygous patients, avoiding possible allele-interfering events affecting other mutation detection systems .
For the application of the pREAL plasmid, we propose a diagnosis algorithm starting from genomic DNA extracted from peripheral blood of index patients suspected of FAP, HNPCC, Familial Breast Cancer, or any other disease related to PSCs. Each exon should be amplified with specific primers carrying endonuclease cleavage sequences. The amplification products should be subsequently inserted into pREAL, and BTH102 cells transformed directly with the ligation product. After plating on MacConkey for 20 hours, heterozygous exons with a PSC in one allele would be detected by a 50/50 red/white phenotype. To test the rest of the family members, only the affected exon should be amplified and inserted into pREAL to detect the presence or absence of the PSC.
The more complex step in this algorithm is the ligation of the PCR product into pREAL because it involves incubation with restriction enzymes and purification of the cleaved insert. Some strategies for directional in frame ligation have been developed by commercial companies (TOPO TA Cloning kits, Invitrogen Life Technologies). In addition, mRNA could be used as template, allowing the amplification by RT-PCR of consecutive exons and therefore reducing the cleavage/ligation steps. However, one of the disadvantages of the RNA-based approaches is the requirement for abundantly expressed and stable transcripts. In particular, mRNAs carrying PSCs are degraded by a specific mechanism (Nonsense Mediated Decay system) that prevents the translation of truncated proteins . Hence, the amount of mRNA carrying PSCs is highly reduced. Therefore, mRNA might not be a recommendable starting material for routine diagnosis.
Another predicted problem with the pREAL strategy is the possibility that the three-dimensional structure of the polypeptide chain linking the adenylate cyclase fragments may interfere with the functional interaction between the domains yielding an inactive enzyme. This false positive result would be easily detected because white colonies will be observed with control wild type inserts. If this problem is detected for an exon of a gene, Western blot analysis should be required to test the presence of full-length protein in the colonies. Alternatively, a different mutation detection system should be used for this exon. All in all, adenylate cyclase activity was detected with the three different linkers tested in the present report (i.e., empty vector, and pREAL carrying wildtype fragments of exon 13 of the msh2 gene and exon 11 of the brca1 gene). In conclusion, before using for clinical diagnosis, this method should be tested for each exon of the gene of interest in control and PTC containing samples. Moreover, the accuracy and efficiency of the system to detect PTCs should be confirmed by future prospective studies.
The pREAL plasmid is applicable for the detection of PSCs in human genes related to different diseases and is resistant to translation re-initiation events. The diagnosis steps are easy and have a low cost. They require only a laboratory equipped for DNA extraction, PCR amplification, ligation, and bacterial culture. The most relevant biological advantages of the method are the detection of only pathologic mutations, thus avoiding subsequent analysis for possible polymorphisms, and the analysis of separated alleles in heterozygous patients.
For human genes with a high frequency of PSCs, this tool can be applied as a first screening method in an exon by exon strategy. In developing countries, where present methods of molecular diagnoses of hereditary cancers are still expensive and unaffordable for many families, this mutation detection system may become a useful and applicable tool.
Strains and growth media
DMH1 (F-, cya-854, recA1, endA1, gyrA96, thi1, hsdR17, spoT1, rfbD1, glnV44), BTH101 (F-, cya-99, araD139, galE15, galK16, rpsL1, hsdR2, mcrA1, mcrB1), and BTH102 (F-, cya-99, recA1, sr1A::Tn10) are adenylate cyclase deficient strains (cya-) and were used for the bacterial phenotype screening setup. XL1-B strain (F- lac, proAB+ lacIq lacZΔM15 Tn10 Tetr, cya+, recA1 endA1 gyrA96 thi-1 relA1hsdR17 supE44) was used to clone the original plasmids of the two hybrid system and the recombinant plasmid pREAL. Frozen competent cells were thawed and transformed using a CaCl2 protocol. The growth medium used was rich Luria-Bertani (LB) supplemented when required with 100 μg/ml ampicillin or 50 μg/ml kanamycin. Screening for the ability to ferment lactose was performed either on MacConkey agar plates without additional maltose or on LB plates containing 40 mg/ml X-gal (5-bromo-4-chloro-3-indolyl-β-D-galatopyranoside).
Development of the pREAL plasmid
Two plasmids from the bacterial two-hybrid system were used: pKT25 (coding for the T25 fragment – aminoacids 1–224 – of the catalytic domain of adenylate cyclase) and pUT18 (coding for the T18 fragment – aminoacids 225–399 – of the catalytic domain of adenylate cyclase). To generate pREAL, we inserted the T25 sequence in pUT18, upstream and in frame with the T18 fragment. Cloning attempts with pREAL in cya- strains (DMH1, BTH101) were not successful and surprisingly the best cloning results were obtained in XL1-B bacteria (cya+) that seemed to resist the hypothetical excess of cAMP. The effect of pREAL on bacterial phenotype was better observed in BTH102, a rapid growing, cya-, endA, but also recA1 strain. Competent BTH102 (50 μl) were transformed with 2 μl of pREAL and after an expansion at 37°C for 45 min, 15 μl were plated on MacConkey medium with 100 μg/ml ampicillin. Addition of 1% maltose or 0.1 mM IPTG to the medium did not significantly improve the colony number or growth rate.
Generation of human DNA fragments with PSCs by mutagenic PCR and insertion in the pREAL
Three versions of the exon 11 of the human brca1 gene were generated with three different forward primers: i) "nonsense product"(NS), with a TAA nonsense codon at position 672 of the gene (5' GG GAT CCT TAACCT GCA ACT GGA), ii) "frame-shift product"(FS), with an insertion of two base pairs, which provoked a frame shift and a PSC at position 698, 25 codons downstream of the insertion site (5' GG GAT CCA CTG CAA CTG GAG CCA A), and iii) "wild type product"(WT) (5'GG GAT CCT GCA ACT GGA GCC AA). Each of the forward primers was combined with the same reverse primer (5' GGAATTCCTTGCCTTCCCTAGAG) to generate PCR products of 383, 379, and 377 bp, respectively. The annealing site for the reverse primer was selected to include translation initiation codons (ATG and GTG) downstream of the PSCs. The three different amplified products were cut with EcoRI and BamHI (1 h at 37°C), purified from an agarose gel, and inserted in the MCS of pREAL. After transforming XL1-B, the plasmids were isolated using the Wizard Plus Miniprep Purification system (Promega Corporation, Biodynamics, Buenos Aires, Argentina). BTH102 were transformed with pREAL/WT, pREAL/FS, pREAL/NS, and with a 1:1 mix of pREAL/WT and pREAL/NS. After 45 minutes of expansion, cultures were 1:3 diluted with LB and 15 μl were plated on MacConkey medium. Without this dilution, we observed a few Lac+ colonies in BTH102/PSC plates. A possible source of these false negative results is bacterial phenotype reversion due to endogenous mutations. The informed frequency of this events is 10-7 – 10-8 ; however we observed a higher reversion rate (3–6%), likely because of natural selection acting on the cya- bacteria. Notice that this reversion percentage would not disturb the diagnosis. Reverted colonies were seldom found when the total number of bacteria per plate was reduced by a 1:3 dilution with LB.
Heteroduplex analysis from red and white colonies
To confirm that the different colored colonies had different inserts, white and red clones from the plate were touched with a pipette tip. Both tips were added to a same PCR mix to perform a single amplification from both colonies using the forward primer (5' GGTCCAAGCTTGGCTATGACCATGCAG) previously used to amplify fragment T25, and the reverse primer used for brca1 exon 11. Then, the PCR products were boiled 5 min at 95°C and renatured at RT for 30 min to allow the formation of heteroduplexes. The samples were run on a non-denaturing 8% PAGE for 3 h at 120 Volts. As control, separately PCR products from white and red colonies were used. PCR products were visualized by ethidium bromide staining and UV light exposure of the gel.
Western blot of T18 to detect re-initiation events
50 μl of bacterial cultures were centrifuged at 10,000 rpm. The bacterial pellets were resuspended in sample buffer (10 μl), boiled for 5 min, and resolved on 10% SDS-PAGE at 15mA. The gels were electroblotted onto nitrocellulose. Membranes with transferred proteins were incubated with murine anti-adenylate cyclase toxin monoclonal antibody (3D1, List Biological Laboratories, INC, Campbell, California, USA) (0.16 μg/ml) as primary antibody, followed by incubation with anti-mouse IgG coupled to HRP (Sigma-Aldrich, St Louis, MO, USA) (0.25 μg/ml) as secondary antibody. Chemiluminescence reaction using the ECL kit (Amersham Bioscience, Buenos Aires, Argentina) was carried out for 1 min followed by exposure to Kodak XAR Radiograph film (Eastman Kodak, Rochester, NY, USA) for 15 and 60 sec.
Application for the detection of a truncating mutation in a HNPCC patient
DNA of a previously diagnosed HNPCC patient , heterozygous for a PSC, was used as template. This patient has a CGA>TGA nonsense mutation in codon 711 of gene msh2. Primers were designed to include the PSC with 5' overhangs for EcoRI and BamHI sites. The sequences of the primers were: forward 5' AGGACTAAGGATCCATTTAT and reverse 5' TATGGAATTCCAAGCAGTTTCCAACAT. A 277 bp PCR product was obtained, incubated with EcoRI and BamHI for 1 h at 37°C, purified from an agarose gel and inserted in the MCS of pREAL. To avoid the subsequent miniprep purification step and carry out directly the diagnosis screening, it was necessary to increase the concentration of transformants before plating. Adding glucose during the expansion step and removing it before plating did not give a different number of colonies on MacConkey or LB-Xgal. However, a three-fold longer expansion time of the transformants before plating produced enough colonies (80–100/plate) for a heterozygous diagnosis. Hence, 50 μl of BTH102 were transformed with 2 μl of recombinant plasmid, expanded in LB in a shaker at 37°C for 3 hours. The culture was centrifuged and the pellet was plated on MacConkey medium and incubated for 20 hours at 37°C.
To evaluate the different bacterial phenotypes on the plate of the heterozygous patient, Western Blot assays were performed as described on white and red colonies. To confirm the presence of the PSC in white colonies and its absence in red colonies, a previously engineered PCR-based diagnosis method was used . The strategy is to introduce a mutation that abuts the PSC site with the forward primer. This mutation creates a restriction site for the HaeIII enzyme only in the wild type allele, but not in the allele carrying the PSC. Sequences of the diagnosis primers were: forward, 5'TTGTGGACTGCATCTTAGGC and reverse, 5' CAGTTTCCAACATTTCAGCCA. White and red colonies from the plate were touched with a pipette tip, and each tip was separately added to a PCR mix with the mentioned primers to run the amplification. PCR products were then incubated with the restriction enzyme HaeIII for 1 h at 37°C, and run on non-denaturing 10% PAGE.
We thank Gouzel Karimova and Daniel Ladant of the Department de Biologie Structurale et Chimie, Institut Pasteur, Paris for the plasmids and cya- strains of the bacterial two hybrid system. We also thank Claudia Tomes for her advice and guidance in Western Blots and cya- strains handling. This work was supported by a grant from the Secretaria de Ciencia, Tecnica y Posgrado de la Universidad Nacional de Cuyo (SeCTyP), Mendoza, Argentina.
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