Transcriptional Interference in Convergent Promoters as a Means for Tunable Gene Expression

Synonymous codon substitutions modulate transcription and translation of a divergent upstream gene by modulating antisense RNA production

Synonymous codons were originally viewed as interchangeable, with no phenotypic consequences. However, substantial evidence has now demonstrated that synonymous substitutions can perturb a variety of gene expression and protein homeostasis mechanisms, including translational efficiency, translational fidelity, and cotranslational folding of the encoded protein. To date, most studies of synonymous codon-derived perturbations have focused on effects within a single gene. Here, we show that synonymous codon substitutions made far within the coding sequence of Escherichia coli plasmid-encoded chloramphenicol acetyltransferase (cat) can significantly increase expression of the divergent upstream tetracycline resistance gene, tetR. In four out of nine synonymously recoded cat sequences tested, expression of the upstream tetR gene was significantly elevated due to transcription of a long antisense RNA (asRNA) originating from a transcription start site within cat. Surprisingly, transcription of this asRNA readily bypassed the native tet transcriptional repression mechanism. Even more surprisingly, accumulation of the TetR protein correlated with the level of asRNA, rather than total tetR RNA. These effects of synonymous codon substitutions on transcription and translation of a neighboring gene suggest that synonymous codon usage in bacteria may be under selection to both preserve the amino acid sequence of the encoded gene and avoid DNA sequence elements that can significantly perturb expression of neighboring genes. Avoiding such sequences may be especially important in plasmids and prokaryotic genomes, where genes and regulatory elements are often densely packed. Similar considerations may apply to the design of genetic circuits for synthetic biology applications.

RNAi-based Boolean gates in the yeast Saccharomyces cerevisiae

Boolean gates, the fundamental components of digital circuits, have been widely investigated in synthetic biology because they permit the fabrication of biosensors and facilitate biocomputing. This study was conducted to design and construct Boolean gates in the yeast Saccharomyces cerevisiae, the main component of which was the RNA interference pathway (RNAi) that is naturally absent from the budding yeast cells. We tested different expression cassettes for the siRNA precursor (a giant hairpin sequence, a DNA fragment-flanked by one or two introns-between convergent promoters or transcribed separately in the sense and antisense directions) and placed different components under the control of the circuit inputs (i.e., the siRNA precursor or proteins such as the Dicer and the Argonaute). We found that RNAi-based logic gates are highly sensitive to promoter leakage and, for this reason, challenging to implement in vivo. Convergent-promoter architecture turned out to be the most reliable solution, even though the overall best performance was achieved with the most difficult design based on the siRNA precursor as a giant hairpin.

Modeling Control of Supercoiling Dynamics and Transcription Using DNA-Binding Proteins

Nearly all natural and synthetic gene networks rely on the fundamental process of transcription to enact biological feedback, genetic programs, and living circuitry. In this work, we investigate the efficacy of controlling transcription using a new biophysical mechanism, control of localized supercoiling near a gene of interest. We postulate a basic reaction network model for describing the general phenomenon of transcription and introduce a separate set of equations to describe the dynamics of supercoiling. We show that supercoiling and transcription introduce a shared reaction flux term in the model dynamics and illustrate how the modulation of supercoiling can be used to control transcription rates. We show the supercoiling-transcription model can be written as a nonlinear state-space model, with a radial basis function nonlinearity to capture the empirical relationship between supercoiling and transcription rates. We show the system admits a single, globally exponentially stable equilibrium point. Notably, we show that mRNA steady-state levels can be controlled directly by increasing a length-scale parameter for genetic spacing. Finally, we build a mathematical model to explore the use of a DNA binding protein, to define programmable boundary conditions on supercoiling propagation, which we show can be used to control transcriptional bursting or pulsatile transcriptional response. We show there exists a stabilizing control law for mRNA tracking, using the method of control Lyapunov functions and illustrate these results with numerical simulations.

MetJ-Based Mutually Interfering SAM-ON/SAM-OFF Biosensors

SAM (S-adenosylmethionine) is an important metabolite that operates as a major donor of methyl groups and is a controller of various physiological processes. Its availability is also believed to be a major bottleneck in the biological production of numerous high-value metabolites. Here, we constructed SAM-sensing systems using MetJ, an SAM-dependent transcriptional regulator, as a core component. SAM is a corepressor of MetJ, which suppresses the MetJ promoter with an increasing cellular concentration of SAM (SAM-OFF sensor). The application of transcriptional interference and evolutionary tuning effectively inverted its response, yielding a SAM-ON sensor (signal increases with increasing SAM concentration). By linking two genes encoding fluorescent protein reporters in such a way that their transcription events interfere with each other's and by placing one of them under the control of MetJ, we could increase the effective signal-to-noise ratio of the SAM sensor while decreasing the batch-to-batch deviation in signal output, likely by canceling out the growth-associated fluctuation in translational resources. By taking the ratio of SAM-ON/SAM-OFF signals and by resetting the default pool size of SAM, we could rapidly identify SAM synthetase (MetK) mutants with increased cellular activity from a random library. The strategy described herein should be widely applicable for identifying activity mutants, which would be otherwise overlooked because of the strong homeostasis of metabolic networks.

Genetic context effects can override canonical cis regulatory elements in Escherichia coli

Recent experiments have shown that in addition to control by cis regulatory elements, the local chromosomal context of a gene also has a profound impact on its transcription. Although this chromosome-position dependent expression variation has been empirically mapped at high-resolution, the underlying causes of the variation have not been elucidated. Here, we demonstrate that 1 kb of flanking, non-coding synthetic sequences with a low frequency of guanosine and cytosine (GC) can dramatically reduce reporter expression compared to neutral and high GC-content flanks in Escherichia coli. Natural and artificial genetic context can have a similarly strong effect on reporter expression, regardless of cell growth phase or medium. Despite the strong reduction in the maximal expression level from the fully-induced reporter, low GC synthetic flanks do not affect the time required to reach the maximal expression level after induction. Overall, we demonstrate key determinants of transcriptional propensity that appear to act as tunable modulators of transcription, independent of regulatory sequences such as the promoter. These findings provide insight into the regulation of naturally occurring genes and an independent control for optimizing expression of synthetic biology constructs.

Synthetic neuromorphic computing in living cells

Computational properties of neuronal networks have been applied to computing systems using simplified models comprising repeated connected nodes, e.g., perceptrons, with decision-making capabilities and flexible weighted links. Analogously to their revolutionary impact on computing, neuro-inspired models can transform synthetic gene circuit design in a manner that is reliable, efficient in resource utilization, and readily reconfigurable for different tasks. To this end, we introduce the perceptgene, a perceptron that computes in the logarithmic domain, which enables efficient implementation of artificial neural networks in Escherichia coli cells. We successfully modify perceptgene parameters to create devices that encode a minimum, maximum, and average of analog inputs. With these devices, we create multi-layer perceptgene circuits that compute a soft majority function, perform an analog-to-digital conversion, and implement a ternary switch. We also create a programmable perceptgene circuit whose computation can be modified from OR to AND logic using small molecule induction. Finally, we show that our approach enables circuit optimization via artificial intelligence algorithms.

Transcriptional Interference in Toehold Switch-Based RNA Circuits

Gene regulation based on regulatory RNA is an important mechanism in cells and is increasingly used for regulatory circuits in synthetic biology. Toehold switches are rationally designed post-transcriptional riboregulators placed in the 5' untranslated region of mRNA molecules. In the inactive state of a toehold switch, the ribosome-binding site is inaccessible to the ribosome. In the presence of a trigger RNA molecule, protein production is turned on. Using antisense RNA against trigger molecules (antitrigger RNA), gene expression can also be switched off again. We here study the utility of antisense transcription in this context, which enables a particularly compact circuit design. Our circuits utilize two inducible promoters that separately regulate trigger and antitrigger transcription, whereas their cognate toehold switch, regulating the expression of a reporter protein, is transcribed from a constitutive promoter. We explore various design options for the arrangement of the promoters and demonstrate that the resulting dynamic behavior is influenced by transcriptional interference (TI) effects depending on the promoter distance. Our experimental results are consistent with previous findings that enhanced local RNA polymerase concentrations due to active promoters in close proximity lead to an increase in transcriptional activity of the strongest promoter in the circuits. We observed that the range of this effect is larger when the participating promoters are stronger. Based on this insight, we combined two promoter arrangements for the realization of a genetic circuit comprised of two toehold switches, two triggers, and two antitriggers that function as a two-input two-output logic gate.

An Antisense RNA Fine-Tunes Gene Expression of the Type II MazEF Toxin-Antitoxin System

Despite their ubiquitous nature, few antisense RNAs have been functionally characterized, and this class of RNAs is considered by some to be transcriptional noise. Here, we report that an antisense RNA (asRNA), aMEF (antisense mazEF), functions as a dual regulator for the type II toxin-antitoxin (TA) system mazEF. Unlike type I TA systems and many other regulatory asRNAs, aMEF stimulates the synthesis and translation of mazEF rather than inhibition and degradation. Our data indicate that a double-stranded RNA intermediate and RNase III are not necessary for aMEF-dependent regulation of mazEF expression. The lack of conservation of asRNA promoters has been used to support the hypothesis that asRNAs are spurious transcriptional noise and nonfunctional. We demonstrate that the aMEF promoter is active and functional in Escherichia coli despite poor sequence conservation, indicating that the lack of promoter sequence conservation should not be correlated with functionality. IMPORTANCE Next-generation RNA sequencing of numerous organisms has revealed that transcription is widespread across the genome, termed pervasive transcription, and does not adhere to annotated gene boundaries. The function of pervasive transcription is enigmatic and has generated considerable controversy as to whether it is transcriptional noise or biologically relevant. Antisense transcription is one class of pervasive transcription that occurs from the DNA strand opposite an annotated gene. Relatively few pervasively transcribed asRNAs have been functionally characterized, and their regulatory roles or lack thereof remains unknown. It is important to study examples of these asRNAs and determine if they are functional regulators. In this study, we elucidate the function of an asRNA (aMEF) demonstrating that pervasive transcripts can be functional.

Analytical kinetic model of native tandem promoters in E. coli

Closely spaced promoters in tandem formation are abundant in bacteria. We investigated the evolutionary conservation, biological functions, and the RNA and single-cell protein expression of genes regulated by tandem promoters in E. coli. We also studied the sequence (distance between transcription start sites ‘d_TSS’, pause sequences, and distances from oriC) and potential influence of the input transcription factors of these promoters. From this, we propose an analytical model of gene expression based on measured expression dynamics, where RNAP-promoter occupancy times and d_TSS are the key regulators of transcription interference due to TSS occlusion by RNAP at one of the promoters (when d_TSS ≤ 35 bp) and RNAP occupancy of the downstream promoter (when d_TSS > 35 bp). Occlusion and downstream promoter occupancy are modeled as linear functions of occupancy time, while the influence of d_TSS is implemented by a continuous step function, fit to in vivo data on mean single-cell protein numbers of 30 natural genes controlled by tandem promoters. The best-fitting step is at 35 bp, matching the length of DNA occupied by RNAP in the open complex formation. This model accurately predicts the squared coefficient of variation and skewness of the natural single-cell protein numbers as a function of d_TSS. Additional predictions suggest that promoters in tandem formation can cover a wide range of transcription dynamics within realistic intervals of parameter values. By accurately capturing the dynamics of these promoters, this model can be helpful to predict the dynamics of new promoters and contribute to the expansion of the repertoire of expression dynamics available to synthetic genetic constructs.

Tandem promoters are common in nature, but investigations on their dynamics have so far largely relied on synthetic constructs. Thus, their regulation and potentially unique dynamics remain unexplored. We first performed a comprehensive exploration of the conservation of genes regulated by these promoters in E. coli and the properties of their input transcription factors. We then measured protein and RNA levels expressed by 30 Escherichia coli tandem promoters, to establish an analytical model of the expression dynamics of genes controlled by such promoters. We show that start site occlusion and downstream RNAP occupancy can be realistically captured by a model with RNAP binding affinity, the time length of open complex formation, and the nucleotide distance between transcription start sites. This study contributes to a better understanding of the unique dynamics tandem promoters can bring to the dynamics of gene networks and will assist in their use in synthetic genetic circuits.

Engineering Transcriptional Interference through RNA Polymerase Processivity Control

Antisense transcription is widespread in all kingdoms of life and has been shown to influence gene expression through transcriptional interference (TI), a phenomenon in which one transcriptional process negatively influences another in cis. The processivity, or uninterrupted transcription, of an RNA polymerase (RNAP) is closely tied to levels of antisense transcription in bacterial genomes, but its influence on TI, while likely important, is not well-characterized. Here, we show that TI can be tuned through processivity control via three distinct antitermination strategies: the antibiotic bicyclomycin, phage protein Psu, and ribosome-RNAP coupling. We apply these methods toward TI and tune ribosome-RNAP coupling to produce 38-fold transcription-level gene repression due to both RNAP collisions and antisense RNA interference. We then couple protein roadblock and TI to design minimal genetic NAND and NOR logic gates. Together, these results show the importance of processivity control for strong TI and demonstrate TI's potential for synthetic biology.

Analysis of the organization and expression patterns of the convergent Pseudomonas aeruginosa lasR/rsaL gene pair uncovers mutual influence

The two adjacent genes encoding the major Pseudomonas aeruginosa quorum-sensing regulator, LasR, and its opponent, RsaL, overlap in their coding 3' ends and produce mRNA transcripts with long untranslated 3' ends that overlap with the sense transcripts of the gene on the opposing DNA strand. In this study, we evaluated whether the overlapping genes are involved in mutual regulatory events and studied interference by natural antisense transcripts. We introduced various gene expression constructs into a P. aeruginosa PA14 lasR/rsaL double deletion mutant, and found that although complementary RNA is produced, this does not interfere with the sense gene expression levels of lasR and rsaL and does not have functional consequences on down-stream gene regulation. Nevertheless, expression of lasR, but not of rsaL, was shown to be enhanced if transcription was terminated at the end of the respective gene so that no overlapping transcription was allowed. Our data indicate that the natural organization with a partial overlap at the 3' ends of the lasR/rsaL genes gives rise to a system of checks and balances to prevent dominant and unilateral control by LasR over the RsaL transcriptional regulator of opposing function.

Genetic code expansion in mammalian cells: A plasmid system comparison

Genetic code expansion with unnatural amino acids (UAAs) has significantly broadened the chemical repertoire of proteins. Applications of this method in mammalian cells include probing of molecular interactions, conditional control of biological processes, and new strategies for therapeutics and vaccines. A number of methods have been developed for transient UAA mutagenesis in mammalian cells, each with unique features and advantages. All have in common a need to deliver genes encoding additional protein biosynthetic machinery (an orthogonal tRNA/tRNA synthetase pair) and a gene for the protein of interest. In this study, we present a comparative evaluation of select plasmid-based genetic code expansion systems and a detailed analysis of suppression efficiency with different UAAs and in different cell lines.

Natural antisense transcripts in the biological hallmarks of cancer: powerful regulators hidden in the dark

Natural antisense transcripts (NATs), which are transcribed from opposite strands of DNA with partial or complete overlap, affect multiple stages of gene expression, from epigenetic to post-translational modifications. NATs are dysregulated in various types of cancer, and an increasing number of studies focusing on NATs as pivotal regulators of the hallmarks of cancer and as promising candidates for cancer therapy are just beginning to unravel the mystery. Here, we summarize the existing knowledge on NATs to highlight their underlying mechanisms of functions in cancer biology, discuss their potential roles in therapeutic application, and explore future research directions.

Universal Actuator for Efficient Silencing of Escherichia coli Genes Based on Convergent Transcription Resistant to Rho-Dependent Termination

Dynamic control is a distinguished strategy in modern metabolic engineering, in which inducible convergent transcription is an attractive approach for conditional gene silencing. Instead of a simple strong "reverse" (r-) promoter, a three-component actuator has been developed for constitutive genes silencing. These actuators, consisting of r-promoters with different strengths, the ribosomal transcription antitermination-inducing sequence rrnG-AT, and the RNase III processing site, were inserted into the 3'-UTR of three E. coli metabolic genes. Second and third actuator components were important to improve the effectiveness and robustness of the approach. The maximal silencing folds achieved for gltA, pgi, and ppc were approximately 7, 11, and >100, respectively. Data were analyzed using a simple model that considered RNA polymerase (RNAP) head-on collisions as the unique reason for gene silencing and continued transcription after collision with only one of two molecules. It was previously established that forward (f-) RNAP with a trailing ribosome was approximately 13-times more likely to continue transcription after head-on collision than untrailed r-RNAP which is sensitive to Rho-dependent transcription termination (RhoTT). According to the current results, this bias in complex stabilities decreased to no more than (3.0-5.7)-fold if r-RNAP became resistant to RhoTT. Therefore, the developed constitutive actuator could be considered as an improved tool for controlled gene expression mainly due to the transfer of r-transcription into a state that is resistant to potential termination and used as the basis for the design of tightly regulated actuators for the achievement of conditional silencing.

Tunable Transcriptional Interference at the Endogenous Alcohol Dehydrogenase Gene Locus in Drosophila melanogaster

Neighboring sequences of a gene can influence its expression. In the phenomenon known as transcriptional interference, transcription at one region in the genome can repress transcription at a nearby region in cis. Transcriptional interference occurs at a number of eukaryotic loci, including the alcohol dehydrogenase (Adh) gene in Drosophila melanogaster. Adh is regulated by two promoters, which are distinct in their developmental timing of activation. It has been shown using transgene insertion that when the promoter distal from the Adh start codon is deleted, transcription from the proximal promoter becomes de-regulated. As a result, the Adh proximal promoter, which is normally active only during the early larval stages, becomes abnormally activated in adults. Whether this type of regulation occurs in the endogenous Adh context, however, remains unclear. Here, we employed the CRISPR/Cas9 system to edit the endogenous Adh locus and found that removal of the distal promoter also resulted in the untimely expression of the proximal promoter-driven mRNA isoform in adults, albeit at lower levels than previously reported. Importantly, transcription from the distal promoter was sufficient to repress proximal transcription in larvae, and the degree of this repression was dependent on the degree of distal promoter activity. Finally, upregulation of the distal Adh transcript led to the enrichment of histone 3 lysine 36 trimethylation over the Adh proximal promoter. We conclude that the endogenous Adh locus is developmentally regulated by transcriptional interference in a tunable manner.

A minimum set of regulators to thrive in the ocean

Marine cyanobacteria of the genus Prochlorococcus thrive in high cell numbers throughout the euphotic zones of the world's subtropical and tropical oligotrophic oceans, making them some of the most ecologically relevant photosynthetic microorganisms on Earth. The ecological success of these free-living phototrophs suggests that they are equipped with a regulatory system competent to address many different stress situations. However, Prochlorococcus genomes are compact and streamlined, with the majority encoding only five different sigma factors, five to six two-component systems and eight types of other transcriptional regulators. Here, we summarize the existing information about the functions of these protein regulators, about transcriptomic responses to defined stress conditions, and discuss the current knowledge about riboswitches, RNA-based regulation and the roles of certain metabolites as co-regulators. We focus on the best-studied isolate, Prochlorococcus MED4, but extend to other strains and ecotypes when appropriate, and we include some information gained from metagenomic and metatranscriptomic analyses.

A human somatic cell culture system for modelling gene silencing by transcriptional interference

Transcriptional interference and transcription through regulatory elements (transcriptional read-through) are implicated in gene silencing and the establishment of DNA methylation. Transcriptional read-through is needed to seed DNA methylation at imprinted genes in the germ line and can lead to aberrant gene silencing by DNA methylation in human disease. To enable the study of parameters and factors influencing transcriptional interference and transcriptional read-through at human promoters, we established a somatic cell culture system. At two promoters of imprinted genes (UBE3A and SNRPN) and two promoters shown to be silenced by aberrant transcriptional read-through in human disease (MSH2 and HBA2) we tested, if transcriptional read-through is sufficient for gene repression and the acquisition of DNA methylation. Induction of transcriptional read-through from the doxycycline-inducible CMV promoter resulted in consistent repression of all downstream promoters, independent of promoter type and orientation. Repression was dependent on ongoing transcription, since withdrawal of induction resulted in reactivation. DNA methylation was not acquired at any of the promoters. Overexpression of DNMT3A and DNMT3L, factors needed for DNA methylation establishment in oocytes, was still not sufficient for the induction of DNA methylation. This indicates that induction of DNA methylation has more complex requirements than transcriptional read-through and the presence of de novo DNA methyltransferases.

Construction of Two-Input Logic Gates Using Transcriptional Interference

Transcriptional interference (TI) has been shown to regulate gene expression at the DNA level via different molecular mechanisms. The obstacles present on the DNA that a transcribing RNA polymerase might encounter, for example, a DNA-bound protein or another RNA polymerase, can result in TI causing termination of transcription, thus reducing gene expression. However, the potential of TI as a new strategy to engineer complex gene expression modules has not been fully explored yet. Here we created a series of two-input genetic devices that use the presence of a roadblocking protein to control gene expression and analyzed their behaviors using both experimental and mathematical modeling approaches. We explored how multiple characteristics affect the response of genetic devices engineered to act like either AND, OR, or single input logic gates. We show that the dissociation constant of the roadblocking protein, inducer activation of promoter and operator sites, and distance between tandem promoters tune gate behavior. This work highlights the potential of rationally creating different types of genetic responses using the same transcription factors in subtly different genetic architectures.

Characterizing Transcriptional Interference between Converging Genes in Bacteria

Antisense transcription is common in naturally occurring genomes and is increasingly being used in synthetic genetic circuitry as a tool for gene expression control. Mutual influence on the expression of convergent genes can be mediated by antisense RNA effects and by transcriptional interference (TI). We aimed to quantitatively characterize long-range TI between convergent genes with untranslated intergenic spacers of increasing length. After controlling for antisense RNA-mediated effects, which contributed about half of the observed total expression inhibition, the TI effect was modeled. To achieve model convergence, RNA polymerase processivity and collision resistance were assumed to be modulated by ribosome trailing. The spontaneous transcription termination rate in regions of untranslated DNA was experimentally determined. Our modeling suggests that an elongating RNA polymerase with a trailing ribosome is about 13 times more likely to resume transcription than an opposing RNA polymerase without a trailing ribosome, upon head-on collision of the two.

Extracytoplasmic Function σ Factors Can Be Implemented as Robust Heterologous Genetic Switches in Bacillus subtilis

In bacteria, the promoter specificity of RNA polymerase is determined by interchangeable σ subunits. Extracytoplasmic function σ factors (ECFs) form the largest and most diverse family of alternative σ factors, and their suitability for constructing genetic switches and circuits was already demonstrated. However, a systematic study on how genetically determined perturbations affect the behavior of these switches is still lacking, which impairs our ability to predict their behavior in complex circuitry. Here, we implemented four ECF switches in Bacillus subtilis and comprehensively characterized their robustness toward genetic perturbations, including changes in copy number, protein stability, or antisense transcription. All switches show characteristic dose-response behavior that varies depending on the individual ECF-promoter pair. Most perturbations had performance costs. Although some general design rules could be derived, a detailed characterization of each ECF switch before implementation is recommended to understand and thereby accommodate its individual behavior.

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Four heterologous ECF-based genetic switches were implemented in Bacillus subtilis

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Each ECF switch was excessively modified and comprehensively evaluated

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The robustness to genetic perturbations differed significantly between switches

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B. subtilis has a narrow phylogenetic acceptance range for heterologous ECFs

Interactions between the transcription and replication machineries regulate the RNA and DNA synthesis in the herpesviruses

The temporal coordination of viral gene expression is imperative for the regulation of the herpesvirus replication cycle. While the main factors of this transcriptional coordination are known, the subtler control mechanisms of gene expression remain elusive. Recent long read sequencing-based approached have revealed an intricate meshwork of overlaps between the herpesvirus transcripts and the overlap of the replication origins with noncoding RNAs. It has been shown that the transcriptional apparatuses can physically interfere with one another while transcribing overlapping regions. We hypothesize that transcriptional interference regulates the global gene expression across the herpesvirus genome. Additionally, an overall decrease in transcriptional activity in individual viral genes has been observed following the onset of DNA replication. An overlap of the replication origins with specific transcripts has also been described in several herpesviruses. The genome-wide interactions between the transcriptional apparatuses and between the replication and transcriptional machineries suggest the existence of novel layers of genetic regulation.

CRISPR Gene Perturbations Provide Insights for Improving Bacterial Biofuel Tolerance

Economically-viable biofuel production is often limited by low levels of microbial tolerance to high biofuel concentrations. Here we demonstrate the first application of deactivated CRISPR perturbations of gene expression to improve Escherichia coli biofuel tolerance. We construct a library of 31 unique CRISPR inhibitions and activations of gene expression in E. coli and explore their impacts on growth during 10 days of exposure to n-butanol and n-hexane. We show that perturbation of metabolism and membrane-related genes induces the greatest impacts on growth in n-butanol, as does perturbation of redox-related genes in n-hexanes. We identify uncharacterized genes yjjZ and yehS with strong potential for improving tolerance to both biofuels. Perturbations demonstrated significant temporal dependencies, suggesting that rationally designing time-sensitive gene circuits can optimize tolerance. We also introduce a sgRNA-specific hyper-mutator phenotype (~2,600-fold increase) into our perturbation strains using error-prone Pol1. We show that despite this change, strains exhibited similar growth phenotypes in n-butanol as before, demonstrating the robustness of CRISPR perturbations during prolonged use. Collectively, these results demonstrate the potential of CRISPR manipulation of gene expression for improving biofuel tolerance and provide constructive starting points for optimization of biofuel producing microorganisms.

Widespread Antisense Transcription in Prokaryotes

Although bacterial genomes are usually densely protein-coding, genome-wide mapping approaches of transcriptional start sites revealed that a significant fraction of the identified promoters drive the transcription of noncoding RNAs. These can be trans-acting RNAs, mainly originating from intergenic regions and, in many studied examples, possessing regulatory functions. However, a significant fraction of these noncoding RNAs consist of natural antisense transcripts (asRNAs), which overlap other transcriptional units. Naturally occurring asRNAs were first observed to play a role in bacterial plasmid replication and in bacteriophage λ more than 30 years ago. Today's view is that asRNAs abound in all three domains of life. There are several examples of asRNAs in bacteria with clearly defined functions. Nevertheless, many asRNAs appear to result from pervasive initiation of transcription, and some data point toward global functions of such widespread transcriptional activity, explaining why the search for a specific regulatory role is sometimes futile. In this review, we give an overview about the occurrence of antisense transcription in bacteria, highlight particular examples of functionally characterized asRNAs, and discuss recent evidence pointing at global relevance in RNA processing and transcription-coupled DNA repair.

Investigation of specific interactions between T7 promoter and T7 RNA polymerase by force spectroscopy using atomic force microscope

The specific recognition and binding of promoter and RNA polymerase is the first step of transcription initiation in bacteria and largely determines transcription activity. Therefore, direct analysis of the interaction between promoter and RNA polymerase in vitro may be a new strategy for promoter characterization, to avoid interference due to the cell's biophysical condition and other regulatory elements. In the present study, the specific interaction between T7 promoter and T7 RNA polymerase was studied as a model system using force spectroscopy based on atomic force microscope (AFM). The specific interaction between T7 promoter and T7 RNA polymerase was verified by control experiments, and the rupture force in this system was measured as 307.2 ± 6.7 pN. The binding between T7 promoter mutants with various promoter activities and T7 RNA polymerase was analyzed. Interaction information including rupture force, rupture distance and binding percentage were obtained in vitro, and reporter gene expression regulated by these promoters was also measured according to a traditional promoter activity characterization method in vivo. Using correlation analysis, it was found that the promoter strength characterized by reporter gene expression was closely correlated with rupture force and the binding percentage by force spectroscopy. These results indicated that the analysis of the interaction between promoter and RNA polymerase using AFM-based force spectroscopy was an effective and valid approach for the quantitative characterization of promoters.

Transcription of a 5' extended mRNA isoform directs dynamic chromatin changes and interference of a downstream promoter

Cell differentiation programs require dynamic regulation of gene expression. During meiotic prophase in Saccharomyces cerevisiae, expression of the kinetochore complex subunit Ndc80 is downregulated by a 5' extended long undecoded NDC80 transcript isoform. Here we demonstrate a transcriptional interference mechanism that is responsible for inhibiting expression of the coding NDC80 mRNA isoform. Transcription from a distal NDC80 promoter directs Set1-dependent histone H3K4 dimethylation and Set2-dependent H3K36 trimethylation to establish a repressive chromatin state in the downstream canonical NDC80 promoter. As a consequence, NDC80 expression is repressed during meiotic prophase. The transcriptional mechanism described here is rapidly reversible, adaptable to fine-tune gene expression, and relies on Set2 and the Set3 histone deacetylase complex. Thus, expression of a 5' extended mRNA isoform causes transcriptional interference at the downstream promoter. We demonstrate that this is an effective mechanism to promote dynamic changes in gene expression during cell differentiation.