Exploring sRNA-mediated gene silencing mechanisms using artificial small RNAs derived from a natural RNA scaffold in Escherichia coli

Post-transcriptional control of bacterial nitrogen metabolism by regulatory noncoding RNAs

Nitrogen metabolism is the most basic process of material and energy metabolism in living organisms, and processes involving the uptake and use of different nitrogen sources are usually tightly regulated at the transcriptional and post-transcriptional levels. Bacterial regulatory noncoding RNAs are novel post-transcriptional regulators that repress or activate the expression of target genes through complementarily pairing with target mRNAs; therefore, these noncoding RNAs play an important regulatory role in many physiological processes, such as bacterial substance metabolism and stress response. In recent years, a study found that noncoding RNAs play a vital role in the post-transcriptional regulation of nitrogen metabolism, which is currently a hot topic in the study of bacterial nitrogen metabolism regulation. In this review, we present an overview of recent advances that increase our understanding on the regulatory roles of bacterial noncoding RNAs and describe in detail how noncoding RNAs regulate biological nitrogen fixation and nitrogen metabolic engineering. Furthermore, our goal is to lay a theoretical foundation for better understanding the molecular mechanisms in bacteria that are involved in environmental adaptations and metabolically-engineered genetic modifications.

Development of multiplexing gene silencing system using conditionally induced polycistronic synthetic antisense RNAs in Escherichia coli

Although efficient methods of gene silencing have been established in eukaryotes, many different techniques are still used in bacteria due to the lack of a standardized tool. Here, we developed a convenient and efficient method to downregulate the expression of a specific gene using ∼140 nucleotide RNA with a 24-nucleotide antisense region from an arabinose-inducible expression plasmid by taking Escherichia coli lacZ and phoA genes encoding β-galactosidase and alkaline phosphatase, respectively, as target genes to evaluate the model. We examined the antisense RNA (asRNA) design, including targeting position, uORF stability elements at the 5'-end, and Hfq-binding module at the 3'-end, and inducer amount required to obtain effective experimental conditions for gene silencing. Furthermore, we constructed multiplexed dual-acting asRNA genes in the plasmid, which were transcribed as polycistronic RNA and were able to knockdown multiple target genes simultaneously. We observed the highest inhibition level of 98.6% when lacZ was targeted using the pMKN104 asRNA expression plasmid, containing a five times stronger P_BAD -10 promoter sequence with no requirement of the Hfq protein for repression. These features allow the system to be utilized as an asRNA expression platform in many bacteria, besides E. coli, for gene regulation.

Orchestration of virulence factor expression and modulation of biofilm dispersal in Erwinia amylovora through activation of the Hfq-dependent small RNA RprA

Erwinia amylovora is the causative agent of the devastating disease fire blight of pome fruit trees. After infection of host plant leaves at apple shoot tips, E. amylovora cells form biofilms in xylem vessels, restrict water flow, and cause wilting symptoms. Although E. amylovora is well known to be able to cause systemic infection, how biofilm cells of E. amylovora transit from the sessile mode of growth in xylem to the planktonic mode of growth in cortical parenchyma remains unknown. Increasing evidence has suggested the important modulatory roles of Hfq-dependent small RNAs (sRNAs) in the pathogenesis of E. amylovora. Here, we demonstrate that the sRNA RprA acts as a positive regulator of amylovoran exopolysaccharide production, the type III secretion system (T3SS), and flagellar-dependent motility, and as a negative regulator of levansucrase activity and cellulose production. We also show that RprA affects the promoter activity of multiple virulence factor genes and regulates hrpS, a critical T3SS regulator, at the posttranscriptional level. We determined that rprA expression can be activated by the Rcs phosphorelay, and that expression is active during T3SS-mediated host infection in an immature pear fruit infection model. We further showed that overexpression of rprA activated the in vitro dispersal of E. amylovora cells from biofilms. Thus, our investigation of the varied role of RprA in affecting E. amylovora virulence provides important insights into the functions of this sRNA in biofilm control and systemic infection.

An Effective Method for Specific Gene Silencing in Escherichia coli Using Artificial Small RNA

Knockdown or silencing of a specific gene presents a powerful strategy for elucidating gene function in a variety of organisms. To date, efficient silencing methods have been established in eukaryotes, but not bacteria. In this chapter, an efficient and versatile gene silencing method using artificial small RNA (afsRNA) is described. For this purpose, target-recognizing sequences were introduced in specially designed RNA scaffolds to exist as single-stranded stretches in afsRNA. The translation initiation region of target genes was used as the sequence for afsRNA recognition, based on the theory that this site is usually highly accessible to ribosomes, and therefore, possibly, afsRNA. Two genes transcribed as monocistrons were tested with our protocol. Both genes were effectively silenced by their cognate afsRNAs.

Synthetic small regulatory RNAs in microbial metabolic engineering

Small regulatory RNAs (sRNAs) finely control gene expression in prokaryotes and synthetic sRNA has become a useful high-throughput approach to tackle current challenges in metabolic engineering because of its many advantages compared to conventional gene knockouts. In this review, we first focus on the modular structures of sRNAs and rational design strategies of synthetic sRNAs on the basis of their modular structures. The wide applications of synthetic sRNAs in bacterial metabolic engineering, with or without the aid of heterogeneously expressed Hfq protein, were also covered. In addition, we give attention to the improvements in implementing synthetic sRNAs, which make the synthetic sRNA strategy universally applicable in metabolic engineering and synthetic biology. KEY POINTS: • Synthetic sRNAs can be rationally designed based on modular structures of natural sRNAs. • Synthetic sRNAs were widely used for metabolic engineering in various microorganisms. • Several technological improvements made the synthetic sRNA strategy more applicable.

Effect of periostin silencing on Runx2, RANKL and OPG expression in osteoblasts

OBJECTIVE

Normal tooth eruption is closely related to relevant genes and the dynamic balance between osteoblasts and osteoclasts. If secretion of RANKL and OPG by osteoblasts is disordered, relevant gene deficiencies or mutations will result in serious tooth eruption disturbances, e.g., cleidocranial dysplasia (CCD). Thus, we examined changes in Runx2, RANKL, and OPG protein expression in MC3T3-E1 cells after silencing the periostin gene, thus, providing an experimental basis to study tooth eruption mechanisms.

METHODS

Based on previous research, cells were divided into two groups according to the virus number: the contrast group (NC group; pFU-GW-016 PSC53349-1) and the experimental group (KD group; LVpFU-GW-016PSC66473-1). Cells were infected with the lentiviral vector (multiplicity of infection = 100) and assessed by image cytometry 72 h after infection. After screening cells for the strongest gene silencing effect, Runx2, RANKL and OPG protein expression were detected by western blotting.

RESULTS

Based on quantitative PCR, the periostin gene silencing efficiency in the KD group was over 90% (P < 0.01). After periostin gene silencing, compared with the control group, Runx2 and RANKL expression in the KD group was reduced (P < 0.01 and P < 0.05, respectively), but OPG protein expression showed no significant change (P > 0.05). The RANKL/OPG ratios in the KD group were lower than those in the NC group after periostin gene silencing (P < 0.05).

CONCLUSIONS

Silencing periostin may reduce the expression of Runx2, suggesting that there may be a synergistic relationship between periostin and Runx2 in their effects on osteoblast differentiation, while reducing RANKL expression obviously confirms that the NF-κB (nuclear factor κB) pathway plays an important role in this process and that periostin silencing changes the underlying tendency toward bone metabolism. This method could even provide an experimental basis for using exogenous periostin protein to treat some abnormal bone metabolism diseases, as it could be used as a supplement for the treatment of tooth eruption abnormalities caused by Runx2 gene deficiencies or mutations (CCD).

Global mRNA and microRNA expression dynamics in response to anthracnose infection in sorghum

BACKGROUND

Anthracnose is a damaging disease of sorghum caused by the fungal pathogen Colletotrichum sublineolum. Genome-wide mRNA and microRNA (miRNA) profiles of resistant and susceptible sorghum genotypes were studied to understand components of immune responses, and fungal induced miRNA and target gene networks.

RESULTS

A total of 18 mRNA and 12 miRNA libraries from resistant and susceptible sorghum lines were sequenced prior to and after inoculation with C. sublineolum. Significant differences in transcriptomes of the susceptible and resistant genotypes were observed with dispersion distance and hierarchical cluster tree analyses. Of the total 33,032 genes predicted in the sorghum genome, 19,593 were induced by C. sublineolum, and 15,512 were differentially expressed (DEGs) between the two genotypes. The resistant line was marked by significant reprogramming of the transcriptome at 24 h post inoculation (hpi), and a decrease at 48 hpi, whereas the susceptible line displayed continued changes in gene expression concordant with elevated fungal growth in the susceptible genotype. DEGs encode proteins implicated in diverse functions including photosynthesis, synthesis of tetrapyrrole, carbohydrate and secondary metabolism, immune signaling, and chitin binding. Genes encoding immune receptors, MAPKs, pentatricopeptide repeat proteins, and WRKY transcription factors were induced in the resistant genotype. In a parallel miRNA profiling, the susceptible line displayed greater number of differentially expressed miRNAs than the resistant line indicative of a widespread suppression of gene expression. Interestingly, we found 75 miRNAs, including 36 novel miRNAs, which were differentially expressed in response to fungal inoculation. The expression of 50 miRNAs was significantly different between resistant and susceptible lines. Subsequently, for 35 differentially expressed miRNAs, the corresponding 149 target genes were identified. Expression of 56 target genes were significantly altered after inoculation, showing inverse expression with the corresponding miRNAs.

CONCLUSIONS

We provide insights into genome wide dynamics of mRNA and miRNA profiles, biological and cellular processes underlying host responses to fungal infection in sorghum. Resistance is correlated with early transcriptional reprogramming of genes in various pathways. Fungal induced genes, miRNAs and their targets with a potential function in host responses to anthracnose were identified, opening avenues for genetic dissection of resistance mechanisms.

Antimicrobial antisense RNA delivery to F-pili producing multidrug-resistant bacteria via a genetically engineered bacteriophage

Multidrug-resistant bacteria are a growing issue worldwide. This study developed a convenient and effective method to downregulate the expression of a specific gene to produce a novel antimicrobial tool using a small (140 nucleotide) RNA with a 24-nucleotide antisense (as) region from an arabinose-inducible expression phagemid vector in Escherichia coli. Knockdown effects of rpoS encoding RNA polymerase sigma factor were observed using this inducible artificial asRNA approach. asRNAs targeting several essential E. coli genes produced significant growth defects, especially when targeted to acpP and ribosomal protein coding genes rplN, rplL, and rpsM. Growth inhibited phenotypes were facilitated in hfq^- conditions. Phage lysates were prepared from cells harboring phagemids as a lethal-agent delivery tool. Targeting the rpsM gene by phagemid-derived M13 phage infection of E. coli containing a carbapenem-producing F-plasmid and multidrug-resistant Klebsiella pneumoniae containing an F-plasmid resulted in the death of over 99.99% of infected bacteria. This study provides a possible strategy for treating bacterial infection and can be applied to any F-pilus producing bacterial species.

Effect of Periostin Silencing on the Autophagy of Osteoblasts

The objective of the present work was to investigate the effect of Periostin (POSTN) silencing on autophagy in osteoblasts, and provide an experimental basis for studying the mechanism of dental eruption. The cells were divided into the following four groups according to their viral number: the NC group, pFU-GW-016PSC53349-1; group KD1, LVpFU-GW-016PSC66471-1; group KD2, LVpFU-GW-016PSC66472-1; and group KD3, LVpFU-GW-016PSC66473-1. The lentiviral vector was infected at MOI = 100 in the ENi.S medium containing 5 g/mL Polybrene. The target gene expression was observed by a Celigo^® Image Cytometer at 72 hours after infection, and the positive rate of fluorescence was noted. A two-step method of quantitative real-time PCR (qRT-PCR) was used to detect the silencing effect of POSTN. Western blotting was then performed to assess the expression of autophagy-related proteins Beclin-1 and LC3 in the group showing the best gene silencing effects. The experimental results showed that there was strong green fluorescence in group KD3. As confirmed via qRT-PCR analysis, the POSTN silencing efficiency in group KD3 reached 92.1%. The Western blotting revealed that the expression of Beclin-1 protein in group KD3 was significantly higher than that in the NC group. However, the LC3 protein expression was not significantly different from that of the control group. The lentiviral vector targeting POSTN in osteoblasts was constructed successfully. In addition, the expression of autophagy protein in mouse osteoblasts increased after POSTN silencing. This finding may provide new approaches for understanding the molecular signal transduction of POSTN during the tooth eruption process.

Mechanism for coordinate regulation of rpoS by sRNA-sRNA interaction in Escherichia coli

RpoS is a key regulator of general stress responses in Escherichia coli. Its expression is post-transcriptionally up-regulated by the small RNAs (sRNAs), ArcZ, DsrA and RprA, through sRNA-rpoS mRNA interactions. Although overexpression of the sRNA, CyaR, was reported to down-regulate rpoS expression, how CyaR regulates rpoS has not been determined. Here, we report that CyaR represses rpoS expression by base-pairing with a region next to the ArcZ binding site in the 5' UTR of rpoS mRNA and that CyaR expression itself is down-regulated by ArcZ through sRNA-sRNA interaction. The short form of ArcZ, but not the full-length form, can base-pair with CyaR. This ArcZ-CyaR interaction triggers degradation of CyaR by RNase E, alleviating the CyaR-mediated rpoS repression. These results suggest that ArcZ not only participates in rpoS translation as an activator, but also acts as a regulator of the reciprocally acting CyaR, maximizing its rpoS-activating effect.

Coordinate regulation of the expression of SdsR toxin and its downstream pphA gene by RyeA antitoxin in Escherichia coli

In Escherichia coli, SdsR and RyeA, a unique pair of mutually cis-encoded small RNAs (sRNAs), act as toxin and antitoxin, respectively. SdsR and RyeA expression are reciprocally regulated; however, how each regulates the synthesis of the other remains unclear. Here, we characterized the biosynthesis of the two sRNAs during growth and investigated their coordinate regulation using sdsR and ryeA promoter mutant strains. We found that RyeA transcription occurred even upon entry of cells into the stationary phase, but its apparent expression was restricted to exponentially growing cells because of its degradation by SdsR. Likewise, the appearance of SdsR was delayed owing to its RyeA-mediated degradation. We also found that the sdsR promoter was primarily responsible for transcription of the downstream pphA gene encoding a phosphatase and that pphA mRNA was synthesized by transcriptional read-through over the sdsR terminator. Transcription from the σ⁷⁰-dependent ryeA promoter inhibited transcription from the σ^S-dependent sdsR promoter through transcriptional interference. This transcriptional inhibition also downregulated pphA expression, but RyeA itself did not downregulate pphA expression.

Mechanisms for Hfq-Independent Activation of rpoS by DsrA, a Small RNA, in Escherichia coli

Many small RNAs (sRNAs) regulate gene expression by base pairing to their target messenger RNAs (mRNAs) with the help of Hfq in Escherichia coli. The sRNA DsrA activates translation of the rpoS mRNA in an Hfq-dependent manner, but this activation ability was found to partially bypass Hfq when DsrA is overproduced. The precise mechanism by which DsrA bypasses Hfq is unknown. In this study, we constructed strains lacking all three rpoS-activating sRNAs (i.e., ArcZ, DsrA, and RprA) in hfq+ and Hfq- backgrounds, and then artificially regulated the cellular DsrA concentration in these strains by controlling its ectopic expression. We then examined how the expression level of rpoS was altered by a change in the concentration of DsrA. We found that the translation and stability of the rpoS mRNA are both enhanced by physiological concentrations of DsrA regardless of Hfq, but that depletion of Hfq causes a rapid degradation of DsrA and thereby decreases rpoS mRNA stability. These results suggest that the observed Hfq dependency of DsrA-mediated rpoS activation mainly results from the destabilization of DsrA in the absence of Hfq, and that DsrA itself contributes to the translational activation and stability of the rpoS mRNA in an Hfq-independent manner.

The small RNA, SdsR, acts as a novel type of toxin in Escherichia coli

Most small noncoding RNAs (sRNAs) are known to base pair with target mRNAs and regulate mRNA stability or translation to trigger various changes in the cell metabolism of Escherichia coli. The SdsR sRNA is expressed specifically during the stationary phase and represses tolC and mutS expression. However, it was not previously known whether the growth-phase-dependent regulation of SdsR is important for cell growth. Here, we ectopically expressed SdsR during the exponential phase and examined cell growth and survival. We found that ectopic expression of SdsR led to a significant and Hfq-dependent cell death with accompanying cell filamentation. This SdsR-driven cell death was alleviated by overexpression of RyeA, an sRNA transcribed on the opposite DNA strand, suggesting that SdsR/RyeA is a novel type of toxin-antitoxin (T/A) system in which both the toxin and the antitoxin are sRNAs. We defined the minimal region required for the SdsR-driven cell death. We also performed RNA-seq analysis and identified 209 genes whose expression levels were altered by more than two-fold following pulse expression of ectopic SdsR at exponential phase. Finally, we found that that the observed SdsR-driven cell death was mainly caused by the SdsR-mediated repression of yhcB, which encodes an inner membrane protein.

Design rules of synthetic non-coding RNAs in bacteria

One of the long-term goals of synthetic biology is to develop designable genetic parts with predictable behaviors that can be utilized to implement diverse cellular functions. The discovery of non-coding RNAs and their importance in cellular processing have rapidly attracted researchers' attention towards designing functional non-coding RNA molecules. These synthetic non-coding RNAs have simple design principles governed by Watson-Crick base pairing, but exhibit increasingly complex functions. Importantly, due to their specific and modular behaviors, synthetic non-coding RNAs have been widely adopted to modulate transcription and translation of target genes. In this review, we summarize various design rules and strategies employed to engineer synthetic non-coding RNAs. Specifically, we discuss how RNA molecules can be transformed into powerful regulators and utilized to control target gene expression. With the establishment of generalizable non-coding RNA design rules, the research community will shift its focus to RNA regulators from protein regulators.

Balancing gene expression without library construction via a reusable sRNA pool

Balancing protein expression is critical when optimizing genetic systems. Typically, this requires library construction to vary the genetic parts controlling each gene, which can be expensive and time-consuming. Here, we develop sRNAs corresponding to 15nt ‘target’ sequences that can be inserted upstream of a gene. The targeted gene can be repressed from 1.6- to 87-fold by controlling sRNA expression using promoters of different strength. A pool is built where six sRNAs are placed under the control of 16 promoters that span a ∼10³-fold range of strengths, yielding ∼10⁷ combinations. This pool can simultaneously optimize up to six genes in a system. This requires building only a single system-specific construct by placing a target sequence upstream of each gene and transforming it with the pre-built sRNA pool. The resulting library is screened and the top clone is sequenced to determine the promoter controlling each sRNA, from which the fold-repression of the genes can be inferred. The system is then rebuilt by rationally selecting parts that implement the optimal expression of each gene. We demonstrate the versatility of this approach by using the same pool to optimize a metabolic pathway (β-carotene) and genetic circuit (XNOR logic gate).

Retargeting a Dual-Acting sRNA for Multiple mRNA Transcript Regulation

Multitargeting small regulatory RNAs (sRNAs) represent a potentially useful tool for metabolic engineering applications. Natural multitargeting sRNAs govern bacterial gene expression by binding to the translation initiation regions of protein-coding mRNAs through base pairing. We designed an Escherichia coli based genetic system to create and assay dual-acting retargeted-sRNA variants. The variants can be assayed for coordinate translational regulation of two alternate mRNA leaders fused to independent reporter genes. Accordingly, we began with the well-characterized E. coli native DsrA sRNA. The merits of using DsrA include its well-characterized separation of function into two independently folded stem-loop domains, wherein alterations at one stem do not necessarily abolish activity at the other stem. Expression of the sRNA and each reporter mRNA was independently controlled by small inducer molecules, allowing precise quantification of the regulatory effects of each sRNA:mRNA interaction in vivo with a microtiter plate assay. Using this system, we semirationally designed DsrA variants screened in E. coli for their ability to regulate key mRNA leader sequences from the Clostridium acetobutylicum n-butanol synthesis pathway. To coordinate intervention at two points in a metabolic pathway, we created bifunctional sRNA prototypes by combining sequences from two singly retargeted DsrA variants. This approach constitutes a platform for designing sRNAs to specifically target arbitrary mRNA transcript sequences, and thus provides a generalizable tool for retargeting and characterizing multitarget sRNAs for metabolic engineering.

MicroRNAs in Serum Exosomes as Potential Biomarkers in Clear-cell Renal Cell Carcinoma

BACKGROUND

Circulating microRNAs (miRNAs) in exosomes are emerging as clinically useful tools for cancer detection. However, little is known about their diagnostic impact in clear-cell renal cell carcinoma (ccRCC).

OBJECTIVE

To investigate whether miRNAs in serum exosomes can serve as biomarkers in ccRCC.

DESIGN, SETTING, AND PARTICIPANTS

Serum samples were obtained from 82 patients with ccRCC and 80 healthy volunteers. Exosomes were extracted and purified to selectively capture exosomes positive for tumor-associated epithelial cell adhesion molecule (EpCAM) via a magnetic bead technique. Total RNA was extracted and expression levels of miR-210, miR-1233, and miR-15a miRNAs were quantified and normalized to U6 levels.

OUTCOME MEASUREMENTS AND STATISTICAL ANALYSIS

Expression levels were compared using a Mann-Whitney U-test, Friedman test, or Wilcoxon test. Receiver operating characteristic (ROC) curves were plotted to assess the diagnostic value of exosomal miRNAs for differentiation between ccRCC patients and controls.

RESULTS AND LIMITATIONS

Expression levels of exosomal miR-210 and miR-1233 were significantly higher in ccRCC patients than in healthy individuals (both p<0.01). No significant difference was observed for exosomal miR-15a. Exosomal miR-210 and miR-1233 expression levels in different TNM stages were significantly higher than in the controls (all p<0.01). Exosomal miR-210 and miR-1233 expression levels were significantly lower in postoperative than in preoperative samples (both p<0.01). ROC analysis demonstrated that exosomal expression levels distinguished ccRCC patients from healthy individuals with 70% sensitivity and 62.2% specificity for miR-210, and 81% sensitivity and 76% specificity for miR-1233. The retrospective design and lack of other tumor subtypes are limitations of the study.

CONCLUSIONS

Serum exosomal miRNAs might represent potential diagnostic biomarkers in ccRCC in the future.

PATIENT SUMMARY

Circulating levels of exosomal microRNAs miR-210 and miR-1233 have potential as biomarkers for diagnostic and monitoring purposes in renal cancer in the future. These molecules can be measured in serum in so-called liquid biopsy.

Visualized and precise design of artificial small RNAs for regulating T7 RNA polymerase and enhancing recombinant protein folding in Escherichia coli

Small non-coding RNAs (sRNAs) have received much attention in recent years due to their unique biological properties, which can efficiently and specifically tune target gene expressions in bacteria. Inspired by natural sRNAs, recent works have proposed the use of artificial sRNAs (asRNAs) as genetic tools to regulate desired gene that has been applied in several fields, such as metabolic engineering and bacterial physiology studies. However, the rational design of asRNAs is still a challenge. In this study, we proposed structure and length as two criteria to implement rational visualized and precise design of asRNAs. T7 expression system was one of the most useful recombinant protein expression systems. However, it was deeply limited by the formation of inclusion body. To settle this problem, we designed a series of asRNAs to inhibit the T7 RNA polymerase (Gene1) expression to balance the rate between transcription and folding of recombinant protein. Based on the heterologous expression of Aspergillus oryzae Li-3 glucuronidase in E. coli, the asRNA-antigene1-17bp can effectively decrease the inclusion body and increase the enzyme activity by 169.9%.

Identification of novel sRNAs involved in biofilm formation, motility, and fimbriae formation in Escherichia coli

Bacterial small RNAs (sRNAs) are known regulators in many physiological processes. In Escherichia coli, a large number of sRNAs have been predicted, among which only about a hundred are experimentally validated. Despite considerable research, the majority of their functions remain uncovered. Therefore, collective analysis of the roles of sRNAs in specific cellular processes may provide an effective approach to identify their functions. Here, we constructed a collection of plasmids overexpressing 99 individual sRNAs, and analyzed their effects on biofilm formation and related phenotypes. Thirty-three sRNAs significantly affecting these cellular processes were identified. No consistent correlations were observed, except that all five sRNAs suppressing type I fimbriae inhibited biofilm formation. Interestingly, IS118, yet to be characterized, suppressed all the processes. Our data not only reveal potentially critical functions of individual sRNAs in biofilm formation and other phenotypes but also highlight the unexpected complexity of sRNA-mediated metabolic pathways leading to these processes.

Effects of different target sites on antisense RNA-mediated regulation of gene expression

Antisense RNA is a type of noncoding RNA (ncRNA) that binds to complementary mRNA sequences and induces gene repression by inhibiting translation or degrading mRNA. Recently, several small ncRNAs (sRNAs) have been identified in Escherichia coli that act as antisense RNA mainly via base pairing with mRNA. The base pairing predominantly leads to gene repression, and in some cases, gene activation. In the current study, we examined how the location of target sites affects sRNA-mediated gene regulation. An efficient antisense RNA expression system was developed, and the effects of antisense RNAs on various target sites in a model mRNA were examined. The target sites of antisense RNAs suppressing gene expression were identified, not only in the translation initiation region (TIR) of mRNA, but also at the junction between the coding region and 3' untranslated region. Surprisingly, an antisense RNA recognizing the upstream region of TIR enhanced gene expression through increasing mRNA stability.

Rapid and high-throughput construction of microbial cell-factories with regulatory noncoding RNAs

Due to global crises such as pollution and depletion of fossil fuels, sustainable technologies based on microbial cell-factories have been garnering great interest as an alternative to chemical factories. The development of microbial cell-factories is imperative in cutting down the overall manufacturing cost. Thus, diverse metabolic engineering strategies and engineering tools have been established to obtain a preferred genotype and phenotype displaying superior productivity. However, these tools are limited to only a handful of genes with permanent modification of a genome and significant labor costs, and this is one of the bottlenecks associated with biofactory construction. Therefore, a groundbreaking rapid and high-throughput engineering tool is needed for efficient construction of microbial cell-factories. During the last decade, copious small noncoding RNAs (ncRNAs) have been discovered in bacteria. These are involved in substantial regulatory roles like transcriptional and post-transcriptional gene regulation by modulating mRNA elongation, stability, or translational efficiency. Because of their vulnerability, ncRNAs can be used as another layer of conditional control over gene expression without modifying chromosomal sequences, and hence would be a promising high-throughput tool for metabolic engineering. Here, we review successful design principles and applications of ncRNAs for high-throughput metabolic engineering or physiological studies of diverse industrially important microorganisms.

An Effective Method for Specific Gene Silencing in Escherichia coli Using Artificial Small RNA

Knockdown or silencing of a specific gene presents a powerful strategy for elucidating gene function in a variety of organisms. To date, efficient silencing methods have been established in eukaryotes, but not bacteria. In this chapter, an efficient and versatile gene silencing method using artificial small RNA (afsRNA) is described. For this purpose, target-recognizing sequences were introduced in specially designed RNA scaffolds to exist as single-stranded stretches in afsRNA. The translation initiation region of target genes was used as the sequence for afsRNA recognition, based on the theory that this site is usually highly accessible to ribosomes, and therefore, possibly, afsRNA. Two genes transcribed as monocistrons were tested with our protocol. Both genes were effectively silenced by their cognate afsRNAs.

Large-scale mapping of sequence-function relations in small regulatory RNAs reveals plasticity and modularity

Two decades into the genomics era the question of mapping sequence to function has evolved from identifying functional elements to characterizing their quantitative properties including, in particular, their specificity and efficiency. Here, we use a large-scale approach to establish a quantitative map between the sequence of a bacterial regulatory RNA and its efficiency in modulating the expression of its targets. Our approach generalizes the sort-seq method, introduced recently to analyze promoter sequences, in order to accurately quantify the efficiency of a large library of sequence variants. We focus on two small RNAs (sRNAs) in E. coli, DsrA and RyhB, and their regulation of both repressed and activated targets. In addition to precisely identifying functional elements in the sRNAs, our data establish quantitative relationships between structural and energetic features of the sRNAs and their regulatory activity, and characterize a large set of direct and indirect interactions between nucleotides. A core of these interactions supports a model where specificity can be enhanced by a rigid molecular structure. Both sRNAs exhibit a modular design with limited cross-interactions, dividing the requirements for structural stability and target binding among modules.

A new method for simultaneous gene deletion and down-regulation in Brucella melitensis Rev.1

In this study, our aim was to integrate an antisense expression cassette in bacterial chromosome for providing a long-term expression down-regulation in a bid to develop a new approach for simultaneous deletion and down-regulation of target genes in bacterial system. Therefore, we were used this approach for simultaneous deletion of the perosamine synthetase (per) gene and down-regulation of the virB1 expression in Brucella melitensis Rev.1. The per gene, which is one of the LPS O-chain coding genes, was replaced by homologous recombination with an antisense virB1 expression cassette together with kanamycin resistance cassette (kan(R)). Deletion of the per gene was characterized by PCR analysis and DNA sequencing. The expression of antisense virB1 cassette was confirmed by RT-PCR. Down-regulation of the virB1 mRNA expression was quantified by real-time RT-PCR using virB1 specific primers relative to the groEL reference gene. The survival rate of mutant strain was evaluated by CFU count in the BALB/c mice. The virB1 mRNA expression was down-regulated on average 10-fold in mutant strain as compared to parental strain. The loss of per gene function and decrease of the virB1 mRNA expression resulted in reduced entry and survival of the mutant Rev.1 strain in BALB/c mice splenocytes. We propose that this method can be used for simultaneous regulation of multiple genes expression.

Small RNAs in mycobacteria: an unfolding story

Mycobacteria represent a class of powerful pathogens, including those causing tuberculosis and leprosy, which continue to be worldwide health challenges. In the last 20 years, an abundance of non-coding, small RNAs (sRNAs) have been discovered in model bacteria and gained significant attention as regulators of cellular responses, including pathogenesis. Naturally, a search in mycobacteria followed, revealing over 200 sRNAs thus far. Characterization of these sRNAs is only beginning, but differential expression under environmental stresses suggests relevance to mycobacterial pathogenesis. This review provides a comprehensive overview of the current knowledge of sRNAs in mycobacteria, including historical perspective and techniques used for identification and characterization.

Regulatory RNAs: charming gene management styles for synthetic biology applications

RNAs have many important functional properties, including that they are independently controllable and highly tunable. As a result of these advantageous properties, their use in a myriad of sophisticated devices has been widely explored. Yet, the exploitation of RNAs for synthetic applications is highly dependent on the ability to characterize the many new molecules that continue to be discovered by large-scale sequencing and high-throughput screening techniques. In this review, we present an exhaustive survey of the most recent synthetic bacterial riboswitches and small RNAs while emphasizing their virtues in gene expression management. We also explore the use of these RNA components as building blocks in the RNA synthetic biology toolbox and discuss examples of synthetic RNA components used to rewire bacterial regulatory circuitry. We anticipate that this field will expand its catalog of smart devices by mimicking and manipulating natural RNA mechanisms and functions.

(Non-)translational medicine: targeting bacterial RNA

The rise and spread of antibiotic resistance is among the most severe challenges facing modern medicine. Despite this fact, attempts to develop novel classes of antibiotic have been largely unsuccessful. The traditional mechanisms by which antibiotics work are subject to relatively rapid bacterial resistance via mutation, and hence have a limited period of efficacy. One promising strategy to ameliorate this problem is to shift from the use of chemical compounds targeting protein structures and processes to a new era of RNA-based therapeutics. RNA-mediated regulation (riboregulation) has evolved naturally in bacteria and is therefore a highly efficient means by which gene expression can be manipulated. Here, we describe recent advances toward the development of effective anti-bacterial therapies, which operate through various strategies centered on RNA.