Establishment of a system for conditional gene expression using an inducible tRNA suppressor gene

Regulating Expression of Mistranslating tRNAs by Readthrough RNA Polymerase II Transcription

Transfer RNA (tRNA) variants that alter the genetic code increase protein diversity and have many applications in synthetic biology. Since the tRNA variants can cause a loss of proteostasis, regulating their expression is necessary to achieve high levels of novel protein. Mechanisms to positively regulate transcription with exogenous activator proteins like those often used to regulate RNA polymerase II (RNAP II)-transcribed genes are not applicable to tRNAs as their expression by RNA polymerase III requires elements internal to the tRNA. Here, we show that tRNA expression is repressed by overlapping transcription from an adjacent RNAP II promoter. Regulating the expression of the RNAP II promoter allows inverse regulation of the tRNA. Placing either Gal4- or TetR–VP16-activated promoters downstream of a mistranslating tRNA^Ser variant that misincorporates serine at proline codons in Saccharomyces cerevisiae allows mistranslation at a level not otherwise possible because of the toxicity of the unregulated tRNA. Using this inducible tRNA system, we explore the proteotoxic effects of mistranslation on yeast cells. High levels of mistranslation cause cells to arrest in the G1 phase. These cells are impermeable to propidium iodide, yet growth is not restored upon repressing tRNA expression. High levels of mistranslation increase cell size and alter cell morphology. This regulatable tRNA expression system can be applied to study how native tRNAs and tRNA variants affect the proteome and other biological processes. Variations of this inducible tRNA system should be applicable to other eukaryotic cell types.

Translational Control using an Expanded Genetic Code

A bio-orthogonal and unnatural substance, such as an unnatural amino acid (Uaa), is an ideal regulator to control target gene expression in a synthetic gene circuit. Genetic code expansion technology has achieved Uaa incorporation into ribosomal synthesized proteins in vivo at specific sites designated by UAG stop codons. This site-specific Uaa incorporation can be used as a controller of target gene expression at the translational level by conditional read-through of internal UAG stop codons. Recent advances in optimization of site-specific Uaa incorporation for translational regulation have enabled more precise control over a wide range of novel important applications, such as Uaa-auxotrophy-based biological containment, live-attenuated vaccine, and high-yield zero-leakage expression systems, in which Uaa translational control is exclusively used as an essential genetic element. This review summarizes the history and recent advance of the translational control by conditional stop codon read-through, especially focusing on the methods using the site-specific Uaa incorporation.

Cellular dynamics of small RNAs

This review highlights the unexpectedly complicated nuclear egress and nuclear import of small RNAs. Although nucleus/cytoplasm trafficking was thought to be restricted to snRNAs of many, but not all, eukaryotes, recent data indicate that such traffic may be more common than previously appreciated. First, in conflict with numerous previous reports, new information indicates that Saccharomyces cerevisiae snRNAs may cycle between the nucleus and the cytoplasm. Second, recent studies also provide evidence that other small RNAs that function exclusively in the nucleus-the budding yeast telomerase RNA and possibly small nucleolar RNAs-may exit to the cytoplasm, only to return to the nucleus. Third, nucleus/cytoplasm cycling of RNAs also occurs for RNAs that function solely in the cytoplasm, as it has been discovered that cytoplasmic tRNAs of budding yeast travel "retrograde" to the nucleus and, perhaps, back again to the cytoplasm to function in protein synthesis. Fourth, there is at least one example in ciliates of small double-stranded RNAs traveling multiple cycles between the cytoplasm and distinct nuclei to direct genome structure. This report discusses data that support or argue against nucleus/cytoplasm bidirectional movement for each category of small RNA and the possible roles that such movement may serve.

Conditional inhibition of cancer cell proliferation by tetracycline-responsive, H1 promoter-driven silencing of PLK1

RNA interference (RNAi) is a powerful tool for studying gene function. We developed an inducible genetic element for short interfering RNA-mediated gene silencing. This system uses a tetracycline (Tet)-responsive derivative of the H1 promoter and the Tet repressor (TetR) for conditional expression of short hairpin RNA (shRNA) in HeLa cells. Promoter constructs were generated, which contain the Tet operator (TetO) derived from a prokaryotic Tet resistance transposon upstream and/or downstream of the TATA box. To quantify the response of controllable transcription units for shRNA expression, we examined the functional activity of polo-like kinase 1 (PLK1), a key component of mitotic progression, that is overexpressed in many human tumors. Cotransfection of plasmids for the expression of TetR and shRNA/PLK1 under the control of an H1 promoter-variant carrying TetO upstream of the TATA box did not alter PLK1 expression and proliferation properties of HeLa cells in the absence of doxycycline. Addition of the antibiotic led to marked downregulation of endogenous PLK1 accompanied by strong inhibition of cellular proliferation. Our data indicate that an inducible transcription system for shRNAs based on the human H1 promoter could be a versatile tool for controlled gene silencing in vitro.

Gene regulation by tetracyclines

Gene regulation by tetracyclines has become a widely-used tool to study gene functions in pro- and eukaryotes. This regulatory system originates from Gram-negative bacteria, in which it fine-tunes expression of a tetracycline-specific export protein mediating resistance against this antibiotic. This review attempts to describe briefly the selective pressures governing the evolution of tetracycline regulation, which have led to the unique regulatory properties underlying its success in manifold applications. After discussing the basic mechanisms we will present the large variety of designed alterations of activities which have contributed to the still growing tool-box of components available for adjusting the regulatory properties to study gene functions in different organisms or tissues. Finally, we provide an overview of the various experimental setups available for pro- and eukaryotes, and touch upon some highlights discovered by the use of tetracycline-dependent gene regulation.

Gene regulation by tetracyclines. Constraints of resistance regulation in bacteria shape TetR for application in eukaryotes

The Tet repressor protein (TetR) regulates transcription of a family of tetracycline (tc) resistance determinants in Gram-negative bacteria. The resistance protein TetA, a membrane-spanning H+-[tc.M]+ antiporter, must be sensitively regulated because its expression is harmful in the absence of tc, yet it has to be expressed before the drugs' concentration reaches cytoplasmic levels inhibitory for protein synthesis. Consequently, TetR shows highly specific tetO binding to reduce basal expression and high affinity to tc to ensure sensitive induction. Tc can cross biological membranes by diffusion enabling this inducer to penetrate the majority of cells. These regulatory and pharmacological properties are the basis for application of TetR to selectively control the expression of single genes in lower and higher eukaryotes. TetR can be used for that purpose in some organisms without further modifications. In mammals and in a large variety of other organisms, however, eukaryotic transcriptional activator or repressor domains are fused to TetR to turn it into an efficient regulator. Mechanistic understanding and the ability to engineer and screen for mutants with specific properties allow tailoring of the DNA recognition specificity, the response to inducer tc and the dimerization specificity of TetR-based eukaryotic regulators. This review provides an overview of the TetR properties as they evolved in bacteria, the functional modifications necessary to transform it into a convenient, specific and efficient regulator for use in eukaryotes and how the interplay between structure--function studies in bacteria and specific requirements of particular applications in eukaryotes have made it a versatile and highly adaptable regulatory system.

Gene replacement without selection: regulated suppression of amber mutations in Escherichia coli

We have developed a method called "gene gorging" to make precise mutations in the Escherichia coli genome at frequencies high enough (1-15%) to allow direct identification of mutants by PCR or other screen rather than by selection. Gene gorging begins by establishing a donor plasmid carrying the desired mutation in the target cell. This plasmid is linearized by in vivo expression of the meganuclease I-SceI, providing a DNA substrate for lambda Red mediated recombination. This results in efficient replacement of the wild type allele on the chromosome with the modified sequence. We demonstrate gene gorging by introducing amber stop codons into the genes xylA, melA, galK, fucI, citA, ybdO, and lacZ. To compliment this approach we developed an arabinose inducible amber suppressor tRNA. Controlled expression mediated by the suppressor was demonstrated for the lacZ and xylA amber mutants.

Regulated expression of myosin II heavy chain and RacB using an inducible tRNA suppressor gene

An inducible expression system that indirectly regulates gene expression through the use of an inducible suppressor tRNA has been used to express both endogenous and exogenous genes in Dictyostelium. The tetracycline repressor and tRNA suppressor (Glu) are expressed from a single G418 selectable vector, while a gene engineered to contain a stop codon is expressed from a separate hygromycin selectable vector. beta-Galactosidase could be induced over 300 fold with this system, and the extent of induction could be varied depending upon the amount of tetracycline added. It took 3 days to fully induce expression, and about 3 days for expression to decrease to baseline after removal of the tetracycline. Dictyostelium myosin II heavy chain could also be expressed in an inducible manner, although the induction ratio was not as high as beta-galactosidase and the maximum expression level was not as high as wild-type levels. A significant accumulation of the truncated peptide indicates that complete suppression of the stop codon was not achieved. Partial phenotypic reversion was observed in null mutants inducibly expressing myosin II. RacB could also be inducibly expressed, whereas the protein could not be expressed from a constitutive promoter, presumably because expression at high levels is lethal. Therefore, the inducible tRNA system can be used to control expression of endogenous Dictyostelium genes.

Trypanosoma cruzi: exogenously regulated gene expression

A regulated expression vector would provide a strong tool for the dissection of gene function in Trypanosoma cruzi. Herein, we establish a system in which genes in T. cruzi expression vectors can be exogenously regulated by tetracycline. We first generated strains of T. cruzi that stably express the repressor of the bacterial tetracycline resistance gene and T7 RNA polymerase. Based on these strains, we developed two T. cruzi expression systems regulated by tetracycline--the first by use of a regulated rRNA promoter and the second by use of a regulated T7 promoter. In the former, we constructed an expression vector in which tetracycline resistance gene operators flank the transcription start point of the T. cruzi rRNA gene promoter. Reporter gene activity from this modified promoter was regulated up to 20-fold in the presence of different concentrations of tetracycline. In the T7 system, tetracycline resistance gene operators flank the transcription start point of the T7 promoter. Reporter gene activity from this modified promoter was regulated up to 150-fold in the presence of different concentrations of tetracycline. Expression in these systems was repressed when tetracycline was removed even after full induction for extended periods in the presence of tetracycline. We are now using these two systems to test protein function in T. cruzi.

Gene function analysis by amber stop codon suppression: CMBF is a nuclear protein that supports growth and development of Dictyostelium amoebae

The C-module-binding factor, CMBF, is a nuclear DNA-binding protein which was originally identified through its specific binding to a promoter element within the retrotransposable element TRE5-A of Dictyostelium discoideum AX2 cells. In order to analyse putative physiological functions of CMBF for the TRE5-A-hosting D. discoideum cells, we used a novel strategy to create mutant cell lines which stably underexpressed functional CMBF. An amber (UAG) translation stop codon was introduced into the chromosomal copy of the CMBF-encoding gene (cbfA), and an amber suppressor tRNA gene was expressed in the same mutant cells. Due to the low efficiency of translation stop codon suppression in this system all recovered cell lines expressed <20 % of wild-type CMBF levels. The mutant cell lines displayed strong growth phenotypes when plated on their natural food source, bacteria. We show evidence that growth reduction was due to impaired phagocytosis of bacteria in the mutants. All obtained mutants showed a strong developmental defect which was defined by the formation of very small fruiting bodies. The strength of the developmental phenotype appeared to depend upon the residual CMBF levels maintained in the mutants. We propose that CMBF is a general transcription regulator which supports the normal expression of several genes required for the maintenance of high proliferation rates of D. discoideum amoebae as well as proper aggregation and development. Our results demonstrate that amber stop codon suppression may be a useful strategy to stably underexpress proteins whose coding genes cannot be successfully disrupted by homologous recombination.

Tetracycline regulated gene expression in Leishmania donovani

The prokaryotic tetracycline-responsive repressor/operator system has proven to be useful for studying the function of essential genes and the expression of toxic gene products in a number of organisms, including Trypanosoma brucei. We report here the adaptation of this system for use in Leishmania. The inducible promoter construct contains a bleomycin resistance-luciferase fusion (BLE-LUC) gene driven by an rRNA promoter with two copies of the TetO sequence inserted two nucleotides upstream of the transcriptional start site. This construct showed regulation of BLE-LUC expression by two orders of magnitude when targeted into the rDNA locus in the reverse orientation relative to transcription of the rRNA genes in a Leishmania donovani cell line expressing TETR. The luciferase expression level in the absence of tetracycline was approximately 50-fold lower than that in the tubulin locus (where it is transcribed by pol II), while the expression level in the presence of tetracycline was approximately five-fold higher than that from the tubulin locus. There was no linear relationship between the level of TETR expression and the regulation, and changing of positions of operator did not increase regulation.

Efficient control of gene expression by a tetracycline-dependent transactivator in single Dictyostelium discoideum cells

We established a tetracycline-regulated gene expression system that tightly controls expression of genes in Dictyostelium discoideum. The control elements are contained in two plasmid vectors, one being an integrated plasmid encoding a chimeric tetracycline-controlled transcriptional activator protein (tTA(s)(*)). The second component is an extrachromosomal plasmid harboring the gene of interest preceded by an inducible promoter. This promoter contains a tetracycline-responsive element, which is the binding site for tTA(s)(*). Tetracycline prevents tTA(s)(*) from binding to the tetracycline-responsive element, rendering the promoter virtually silent. In the absence of tetracycline, tTA(s)(*) binds to its target sequence and strongly induces gene expression. The kinetics of activation and repression of the system were monitored using luciferase as a reporter. The results reveal efficient inhibition of gene expression by low concentrations of tetracycline and an induction of gene expression by several orders of magnitude within a few hours after removal of tetracycline. Green fluorescent protein (GFP) provided information about the effects of modulation of the tetracycline concentration on gene expression, at the single cell level, using fluorescence activated cell sorting (FACS). We also report that not all cells in a clonal population express the reporter gene.

Control of the functional activity of an antisense RNA by a tetracycline-responsive derivative of the human U6 snRNA promoter

In an effort to develop a regulatable derivative of the promoter of the human gene for U6 snRNA, we generated several constructs composed of the human U6 snRNA promoter and sequences derived from the gene for the tetracycline operator of a prokaryotic tetracycline resistance transposon. One of the constructs had strong transcriptional activity in the presence of tetracycline that was equivalent to 80% of the activity of the wild-type promoter. Furthermore, the transcriptional activity was almost completely repressed in the absence of tetracycline. Transcriptional activity became detectable within 4 hr after the addition of tetracycline to the culture medium. We used this system to control the functional activity of an antisense RNA for a chimeric gene derived from genes for the epidermal growth factor receptor (EGFR) and green fluorescent protein (GFP). A plasmid that expressed the chimeric gene and a plasmid that expressed the antisense RNA under the control of the inducible U6 promoter were used to cotransfect HeLa cells that were producing the tetracycline repressor protein (Tet R). Addition of tetracycline to the culture medium 12 hr after transfection resulted in the almost complete disappearance of the fluorescent signal due to the chimeric protein within 24 hr. Our results suggest that this expression system might be a useful tool for controlling the expression of functional RNAs, such as aptamers and antisense RNAs, both in basic research and in gene therapy.

Tetracycline repressor, tetR, rather than the tetR-mammalian cell transcription factor fusion derivatives, regulates inducible gene expression in mammalian cells

This article describes the first (to our knowledge) tetracycline-inducible regulatory system that demonstrates that the tetracycline repressor (tetR) alone, rather than tetR-mammalian cell transcription factor fusion derivatives, can function as a potent trans-modulator to regulate gene expression in mammalian cells. With proper positioning of tetracycline operators downstream of the TATA element and of human epidermal growth factor (hEGF) as a reporter, we show that gene expression from the tetracycline operator-bearing hCMV major immediate-early enhancer-promoter (pcmvtetO) can be regulated by tetR over three orders of magnitude in response to tetracycline when (1) the reporter was cotransfected with tetR-expressing plasmid in transient expression assays, and (2) the reporter unit was stably integrated into the chromosome of a tetR-expressing cell line. This level of tetR-mediated inducible gene regulation is significantly higher than that of other repression-based mammalian cell transcription switch systems. In an in vivo porcine wound model, close to 60-fold tetR-mediated regulatory effects were detected and it was reversed when tetracycline was administered. Collectively, this study provides a direct implementation of this tetracycline-inducible regulatory switch for controlling gene expression in vitro, in vivo, and in gene therapy.

Regulated expression of plant tRNA genes by the prokaryotic tet and lac repressors

The prokaryotic tet operator (tetO) sequence was inserted at positions upstream and downstream of sequences encoding the Arabidopsis thaliana tRNA(Lys)AUC or tRNA(Trp)AUC suppressor tRNAs, and tRNA expression in carrot protoplasts was measured by translational suppression of a nonsense codon in a luciferase reporter gene. Regulation of tRNA expression by the tetracycline repressor (tetR) occurred from genes with the tetO inserted at position -1 (for the tRNA(Trp)AUC gene), or at positions -2, -6 and -10 (for the tRNA(Lys)AUC gene), and repression reached 90%. The inducer tetracycline (Tc) restored tRNA expression. Similarly, carrot protoplasts transfected with human tRNA(Ser)AUC genes containing the lac operator (lacO) in their 5'-flanking sequence with or without the lac repressor (lacI) gene, conditionally expressed tRNAs which suppressed the luciferase reporter. Up to 30-fold repression occurred by the lactose repressor when lacO was located at position -1 of the tRNA(Ser)AUC coding sequence. In the presence of the inducer isopropyl-beta-thiogalactoside (IPTG), repression was relieved. These results demonstrate that sequences flanking tRNA genes can strongly influence tRNA expression in plants, and in a conditional fashion when bound by inducible proteins.

Modulation of erythropoietin delivery from engineered muscles in mice

In most relevant diseases, the permanent systemic delivery of a therapeutic protein from engineered cells might be proposed only if secretion levels can be regulated. The tetracycline resistance operon of Escherichia coli provides a transcriptional regulatory system effective in mammalian cells, which could be used for that purpose. A chimeric transactivator (tTA) consisting of the tetracycline repressor fused to the transactivation domain of the herpes simplex virus VP16 protein stimulates transcription by binding a minimal cytomegalovirus (CMV) promoter containing repeats of the tetracycline operator (tetO-CMV). Binding is abolished by tetracycline, thus impairing promoter activation. We have transduced C2.7 myoblasts with two U3-deleted retroviral vectors containing these regulatory elements. The tetP-Epo vector expressed the murine erythropoietin (Epo) cDNA under the control of the tetO-CMV promoter. The D-De-tTA vector expressed tTA under the control of the muscle-specific human desmin enhancer-promoter. Northern blot analysis showed background Epo mRNA expression in myoblasts. Myotubes differentiation induced tTA expression, leading to a 28-fold increase of Epo mRNAs, which was suppressed by tetracycline. Basal Epo secretion in myoblasts increased 23- to 41-fold during the formation of multinucleated myotubes, and turned back close to myoblast level when tetracycline was added. Myoblasts transduced with both vectors and treated with mitomycin with the aim to prevent tumor formation were engrafted in skeletal muscles of syngeneic C3H mice. Hematocrit levels were significantly higher in animals bearing cells transduced with both vectors than in control animals grafted with cells transduced with the Epo vector only. This difference was abolished when tetracycline was given to mice. These data indicate that the tetracycline regulatory elements can modulate transcription in the context of retroviral vector genomes, and that this system can be used to control the in vivo delivery of a therapeutic protein from genetically modified muscles.

A tetracycline-inducible gene expression system in Entamoeba histolytica

We have developed an episomal inducible gene expression system in Entamoeba histolytica based on the TetR repressor. The tetR gene was placed under control of 5' and 3' ferredoxin (fdx) regulatory sequences on a plasmid encoding the hygromycin resistance gene directed by 5' and 3' hgl sequences. The reporter luciferase constructs were introduced on a second episome bearing the neomycin resistance gene controlled by 5' and 3' actin sequences. The reporter constructs were driven by the hgl5 promoter in which the tetO sequence was introduced. We found that the optimal tetO location for induction by tetracycline was +4 from the start of transcription. The efficiency of repression and the induction ratio could be improved by increasing hygromycin levels, presumably by increasing tetR plasmid levels. Under these conditions, maximal induction of reporter luciferase could be effected with 5 micrograms/ml tetracycline in 18 h. This system permits regulated expression of the reporter gene over two orders of magnitude and should be useful in the analysis of gene function.

Fast large-scale purification of tetracycline repressor variants from overproducing Escherichia coli strains

We constructed a plasmid for overexpression of Tn10 Tet repressor (TetR) by placing a synthetic tetR gene under control of the Pc promoter. Active TetR is expressed up to 30% of the total soluble cell protein. A protocol containing anion-exchange, cation-exchange, and size-exclusion chromatography steps is described for the large-scale purification of milligram amounts of TetR in three days. Cation-exchange chromatography already yields almost homogenous TetR. Purification of about fifty TetR mutants demonstrates that this protocol is generally applicable. No correlation between net charge of TetR variants and elution behaviour was detected for the anion-exchange column. On the other hand, TetR mutants with increased negative charge in their DNA binding domain eluted at lower NaCl concentration from the cation-exchange column. The applicability of this purification protocol to the wide variety of TetR variants suggests that it can be used for the rapid purification of other DNA binding proteins as well.

Analysis of gene function in Dictyostelium

Over the past ten years, powerful molecular genetic techniques have been developed to analyze gene function in Dictyostelium. DNA-mediated transformation using a variety of selections and vectors has allowed the introduction of wild-type or modified genes that are under various forms of transcriptional control. Homologous recombination is efficient and can be used to modify the genome in precise ways. In addition, it is now possible to clone genes based on their mutant phenotype alone, either by insertional mutagenesis, or by screening antisense expression cDNA libraries. Finally, a nearly complete physical map of the genome is available and so genes are easily mapped by physical techniques. We discuss many of these advances within the context of major research problems presently under study.

Suppression of single and double nonsense mutations introduced into the diphtheria toxin A-chain gene: a potential binary system for toxin gene therapy

We have previously shown that ablation of specific cells can be achieved through the transcriptionally regulated expression of the diphtheria toxin A-chain (DT-A) gene in both cell culture and transgenic mice. Such targeted toxin gene expression provides a novel approach to cancer and acquired immunodeficiency syndrome (AIDS) therapy. The use of mutants of DT-A with attenuated toxicity may allow targeting of cells for which only moderately selective gene regulatory elements are available. Alternatively, conditional mutants might be used to target cells in which conditions can be established for suppression of the mutation. We have investigated the effects of mutating selected serine codons to amber (TAG) nonsense codons in the DT-A coding sequence. In transient transfection of HeLa cells, DT-A activity was markedly reduced by the introduction of a single amber codon and was virtually eliminated by two amber mutations. Cotransfection of a serine inserting suppressor tRNA expression plasmid substantially restored DT-A expression from both single and double amber mutants. Expression of the same suppressor tRNA also suppressed a previously described amber mutation at the tyrosine codon 28 in DT-A. Thus, nonsense suppression can be used to control the expression of DT-A in mammalian cells, potentially allowing binary control over the targeting of tissues for selective ablation.

Inducible gene expression systems for higher eukaryotic cells

Of the wide variety of regulatory systems that have been developed to control gene expression in higher eukaryotes, those utilizing elements from prokaryotic systems presently achieve the highest specificity. In particular, systems based on the repressor/operator elements of an Escherichia coli tetracycline resistance operon appear broadly applicable. During the past year, the usefulness of these systems has been demonstrated not only at the cellular level, but also at the organismal level (i.e. in transgenic animals and plants).