Short Peptides Act as Inducers, Anti-Inducers and Corepressors of Tet Repressor

Status quo of tet regulation in bacteria

The tetracycline repressor (TetR) belongs to the most popular, versatile and efficient transcriptional regulators used in bacterial genetics. In the tetracycline (Tc) resistance determinant tet(B) of transposon Tn10, tetR regulates the expression of a divergently oriented tetA gene that encodes a Tc antiporter. These components of Tn10 and of other natural or synthetic origins have been used for tetracycline‐dependent gene regulation (tet regulation) in at least 40 bacterial genera. Tet regulation serves several purposes such as conditional complementation, depletion of essential genes, modulation of artificial genetic networks, protein overexpression or the control of gene expression within cell culture or animal infection models. Adaptations of the promoters employed have increased tet regulation efficiency and have made this system accessible to taxonomically distant bacteria. Variations of TetR, different effector molecules and mutated DNA binding sites have enabled new modes of gene expression control. This article provides a current overview of tet regulation in bacteria.

Procaspase activating compound 1 controls tetracycline repressor-regulated gene expression system

The tetracycline repressor (TetR)-regulated system is a widely used tool to study gene functions through control of its expression. Various effectors such as tetracycline (Tc) and doxycycline (Dox) quickly induce or shut down gene expression, but reversing gene expression has not been eligible due to long half-lives of such effectors. Here, we found that procaspase activating compound 1 (PAC-1) rapidly reduces transient expression of TetR-regulated green fluorescent protein (GFP) in mammalian cells. Next, we applied PAC-1 to control of expression of transient receptor potential melastatin 7 (TRPM7) protein, whose downstream cellular events can be monitored by cell morphological changes. We observed that PAC-1 quickly reduces TRPM7 expression, consequently affecting cell morphology regulated by TRPM7. The present study demonstrates the first small molecule that efficiently turns off the TetR-regulated gene expression in mammalian cells, thereby precisely regulating the expression level of target gene.

Synthetic circuits that process multiple light and chemical signal inputs

Background

Multi-signal processing circuits are essential for rational design of sophisticated synthetic systems with good controllability and modularity, therefore, enable construction of high-level networks. Moreover, light-inducible systems provide fast and reversible means for spatiotemporal control of gene expression.

Results

Here, in HEK 293 cells, we present combinatory genetic circuits responding to light and chemical signals, simultaneously. We first constructed a dual input circuit converting different light intensities into varying of the sensitivity of the promoter to a chemical inducer (doxycycline). Next, we generated a ternary input circuit, which responded to light, doxycycline and cumate. This circuit allowed us to use different combinations of blue light and the two chemical inducers to generate gradual output values over two orders of magnitude.

Conclusions

Overall, in this study, we devise genetic circuits sensing and processing light and chemical inducers. Our work may provide insights into bio-computation and fine-tuning expression of the transgene.

Electronic supplementary material

The online version of this article (doi:10.1186/s12918-016-0384-y) contains supplementary material, which is available to authorized users.

Label-Free, In-Solution Screening of Peptide Libraries for Binding to Protein Targets Using Hydrogen Exchange Mass Spectrometry

There is considerable interest in the discovery of peptide ligands that bind to protein targets. Discovery of such ligands is usually approached by screening large peptide libraries. However, the individual peptides must be tethered to a tag that preserves their individual identities (e.g., phage display or one-bead one-compound). To overcome this limitation, we have developed a method for screening libraries of label-free peptides for binding to a protein target in solution as a single batch. The screening is based on decreased amide hydrogen exchange by peptides that bind to the target. Hydrogen exchange is measured by mass spectrometry. We demonstrate the approach using a peptide library derived from the Escherichia coli proteome that contained 6664 identifiable features. The library was spiked separately with a peptide spanning the calmodulin binding domain of endothelial nitric oxide synthase (eNOS, 494-513) and a peptide spanning the N-terminal 20 residues of bovine ribonuclease A (S peptide). Human calmodulin and bovine ribonuclease S (RNase S) were screened against the library. Using a novel data analysis workflow, we identified the eNOS peptide as the only calmodulin binding peptide and S peptide as the only ribonuclease S binding peptide in the library.

Global analyses of TetR family transcriptional regulators in mycobacteria indicates conservation across species and diversity in regulated functions

BACKGROUND

Mycobacteria inhabit diverse niches and display high metabolic versatility. They can colonise both humans and animals and are also able to survive in the environment. In order to succeed, response to environmental cues via transcriptional regulation is required. In this study we focused on the TetR family of transcriptional regulators (TFTRs) in mycobacteria.

RESULTS

We used InterPro to classify the entire complement of transcriptional regulators in 10 mycobacterial species and these analyses showed that TFTRs are the most abundant family of regulators in all species. We identified those TFTRs that are conserved across all species analysed and those that are unique to the pathogens included in the analysis. We examined genomic contexts of 663 of the conserved TFTRs and observed that the majority of TFTRs are separated by 200 bp or less from divergently oriented genes. Analyses of divergent genes indicated that the TFTRs control diverse biochemical functions not limited to efflux pumps. TFTRs typically bind to palindromic motifs and we identified 11 highly significant novel motifs in the upstream regions of divergently oriented TFTRs. The C-terminal ligand binding domain from the TFTR complement in M. tuberculosis showed great diversity in amino acid sequence but with an overall architecture common to other TFTRs.

CONCLUSION

This study suggests that mycobacteria depend on TFTRs for the transcriptional control of a number of metabolic functions yet the physiological role of the majority of these regulators remain unknown.

Tet-Trap, a genetic approach to the identification of bacterial RNA thermometers: application to Pseudomonas aeruginosa

Modulation of mRNA translatability either by trans-acting factors (proteins or sRNAs) or by in cis-acting riboregulators is widespread in bacteria and controls relevant phenotypic traits. Unfortunately, global identification of post-transcriptionally regulated genes is complicated by poor structural and functional conservation of regulatory elements and by the limitations of proteomic approaches in protein quantification. We devised a genetic system for the identification of post-transcriptionally regulated genes and we applied this system to search for Pseudomonas aeruginosa RNA thermometers, a class of regulatory RNA that modulates gene translation in response to temperature changes. As P. aeruginosa is able to thrive in a broad range of environmental conditions, genes differentially expressed at 37 °C versus lower temperatures may be involved in infection and survival in the human host. We prepared a plasmid vector library with translational fusions of P. aeruginosa DNA fragments (PaDNA) inserted upstream of TIP2, a short peptide able to inactivate the Tet repressor (TetR) upon expression. The library was assayed in a streptomycin-resistant merodiploid rpsL(+)/rpsL31 Escherichia coli strain in which the dominant rpsL(+) allele, which confers streptomycin sensitivity, was repressed by TetR. PaDNA fragments conferring thermosensitive streptomycin resistance (i.e., expressing PaDNA-TIP2 fusions at 37°C, but not at 28°C) were sequenced. We identified four new putative thermosensors. Two of them were validated with conventional reporter systems in E. coli and P. aeruginosa. Interestingly, one regulates the expression of ptxS, a gene implicated in P. aeruginosa pathogenesis.

A novel TetR-regulating peptide turns off rtTA-mediated activation of gene expression

Conditional regulation of gene expression is a powerful and indispensable method for analyzing gene function. The “Tet-On” system is a tool widely used for that purpose. Here, the transregulator rtTA mediates expression of a gene of interest after addition of the small molecule effector doxycycline. Although very effective in rapidly turning on gene expression, the system is hampered by the long half-life of doxycycline which makes shutting down gene expression rapidly very difficult to achieve. We isolated an rtTA-binding peptide by in vivo selection that acts as a doxycycline antagonist and leads to rapid and efficient shut down of rtTA-mediated reporter gene expression in a human cell line. This peptide represents the basis for novel effector molecules which complement the “Tet-system” by enabling the investigator to rapidly turn gene expression not just on at will, but now also off.

Wide-dynamic-range promoters engineered for cyanobacteria

BACKGROUND

Cyanobacteria, prokaryotic cells with oxygenic photosynthesis, are excellent bioengineering targets to convert solar energy into solar fuels. Tremendous genetic engineering approaches and tools have been and still are being developed for prokaryotes. However, the progress for cyanobacteria is far behind with a specific lack of non-native inducible promoters.

RESULTS

We report the development of engineered TetR-regulated promoters with a wide dynamic range of transcriptional regulation. An optimal 239 (±16) fold induction in darkness (white-light-activated heterotrophic growth, 24 h) and an optimal 290 (±93) fold induction in red light (photoautotrophic growth, 48 h) were observed with the L03 promoter in cells of the unicellular cyanobacterium Synechocystis sp. strain ATCC27184 (i.e. glucose-tolerant Synechocystis sp. strain PCC 6803). By altering only few bases of the promoter in the narrow region between the -10 element and transcription start site significant changes in the promoter strengths, and consequently in the range of regulations, were observed.

CONCLUSIONS

The non-native inducible promoters developed in the present study are ready to be used to further explore the notion of custom designed cyanobacterial cells in the complementary frameworks of metabolic engineering and synthetic biology.

A novel method to analyze nucleocytoplasmic transport in vivo by using short peptide tags

Regulated nucleocytoplasmic transport is of vital importance for maintaining the physiology of the cell, and disturbed nucleocytoplasmic shuttling of certain proteins has been found in a variety of diseases including cancer. The most frequently used procedure to analyze those processes is to fuse the protein of interest to a fluorescent protein such as GFP (green fluorescent protein)--a technique that is prone to impair normal protein function and subcellular localization. We report a novel approach to monitor nucleocytoplasmic transport processes in vivo by combining short TetR inducing peptide tags (TIP) with a TetR-controlled reporter gene in a human cell line. The technology is exemplified by demonstrating nucleocytoplasmic shuttling of the glucocorticoid receptor and activity of two further TIP fusions to cancer-related proteins. The technology presented provides the basis for efficient screening systems to isolate compounds altering the nucleocytoplasmic distribution of a protein of interest.

Protein expression can be monitored in yeast by peptide-mediated induction of TetR-controlled gene expression

The rapidly increasing number of completed genome sequences urgently calls for convenient and efficient methods for analysis of gene function and expression. TetR-inducing peptides (TIP) can induce reporter gene expression controlled by Tet repressor (TetR) when fused to a protein of choice which makes them a highly valuable tool for monitoring expression in vivo. However, TIP functionality has only been demonstrated in bacteria so far. Here, we report that TIP is also functional in yeast. An mCherry-TIP fusion that locates to the nucleus induces TetR-controlled gfp+ expression in a dose-dependent manner. This opens up potential applications in proteome research in which the expression of proteins can be analyzed in vivo by fusing TIP to proteins of choice in conjunction with a Tet-controlled reporter system.

Promoter strength driving TetR determines the regulatory properties of Tet-controlled expression systems

Bacteria frequently rely on transcription repressors and activators to alter gene expression patterns in response to changes in the surrounding environment. Tet repressor (TetR) is a paradigm transcription factor that senses the environmental state by binding small molecule effectors, the tetracyclines. However, recently isolated peptides that act as inducers of TetR after having been fused to the C-terminus of a carrier protein, suggest that TetR can also regulate gene expression in a signal-transduction pathway. For this shift in regulatory mechanism to be successful, induction of TetR must be sensitive enough to respond to an inducing protein expressed at its endogenous level. To determine this regulatory parameter, a synthetic Tet-regulated system was introduced into the human pathogen Salmonella enterica serovar Typhimurium and tested for inducibility by a peptide. Reporter gene expression was detected if the peptide-containing carrier protein Thioredoxin 1 was strongly overproduced, but not if it was expressed at a level similar to the physiological level of Thioredoxin 1. This was attributed to high steady-state amounts of TetR which was expressed by the promoter of the chloramphenicol acetyl transferase gene (P(cat)). Reducing P(cat) strength either by directed or by random mutagenesis of its -10 element concomitantly reduced the intracellular amounts of TetR. Sensitive and quantitative induction of TetR by an inducing peptide, when it was fused to Thioredoxin 1 at its native locus in the genome, was only obtained with weak P(cat) promoter variants containing GC-rich -10 elements. A second important observation was that reducing the TetR steady-state level did not impair repression. This permits flexible adjustment of an inducible system's sensitivity simply by altering the expression level of the transcription factor. These two new layers of expression control will improve the quality and, thus, the applicability of the Tet and other regulatory systems.