Physiological roles of antisense RNAs in prokaryotes

Bacterial RNase III: Targets and physiology

Bacteria can rapidly adapt to changes in their environment thanks to the innate flexibility of their genetic expression. The high turnover rate of RNAs, in particular messenger and regulatory RNAs, provides an important contribution to this dynamic adjustment. Recycling of RNAs is ensured by ribonucleases, among which RNase III is the focus of this review. RNase III enzymes are highly conserved from prokaryotes to eukaryotes and have the specific ability to cleave double-stranded RNAs. The role of RNase III in bacterial physiology has remained poorly explored for a long time. However, transcriptomic approaches recently uncovered a large impact of RNase III in gene expression in a wide range of bacteria, generating renewed interest in the physiological role of RNase III. In this review, we first describe the RNase III targets identified from global approaches in 8 bacterial species within 4 Phyla. We then present the conserved and unique functions of bacterial RNase III focusing on growth, resistance to stress, biofilm formation, motility and virulence. Altogether, this review highlights the underestimated impact of RNase III in bacterial adaptation.

Nitrogen-regulated antisense transcription in the adaptation to nitrogen deficiency in Nostoc sp. PCC 7120

Transcriptomic analyses using high-throughput methods have revealed abundant antisense transcription in bacteria. Antisense transcription is often due to the overlap of mRNAs with long 5' or 3' regions that extend beyond the coding sequence. In addition, antisense RNAs that do not contain any coding sequence are also observed. Nostoc sp. PCC 7120 is a filamentous cyanobacterium that, under nitrogen limitation, behaves as a multicellular organism with division of labor among two different cell types that depend on each other, the vegetative CO₂-fixing cells and the nitrogen-fixing heterocysts. The differentiation of heterocysts depends on the global nitrogen regulator NtcA and requires the specific regulator HetR. To identify antisense RNAs potentially involved in heterocyst differentiation, we assembled the Nostoc transcriptome using RNA-seq analysis of cells subjected to nitrogen limitation (9 or 24 h after nitrogen removal) in combination with a genome-wide set of transcriptional start sites and a prediction of transcriptional terminators. Our analysis resulted in the definition of a transcriptional map that includes >4,000 transcripts, 65% of which contain regions in antisense orientation to other transcripts. In addition to overlapping mRNAs, we identified nitrogen-regulated noncoding antisense RNAs transcribed from NtcA- or HetR-dependent promoters. As an example of this last category, we further analyzed an antisense (as_gltA) of the gene-encoding citrate synthase and showed that transcription of as_gltA takes place specifically in heterocysts. Since the overexpression of as_gltA reduces citrate synthase activity, this antisense RNA could eventually contribute to the metabolic remodeling that occurs during the differentiation of vegetative cells into heterocysts.

Using a whole genome co-expression network to inform the functional characterisation of predicted genomic elements from Mycobacterium tuberculosis transcriptomic data

A whole genome co-expression network was created using Mycobacterium tuberculosis transcriptomic data from publicly available RNA-sequencing experiments covering a wide variety of experimental conditions. The network includes expressed regions with no formal annotation, including putative short RNAs and untranslated regions of expressed transcripts, along with the protein-coding genes. These unannotated expressed transcripts were among the best-connected members of the module sub-networks, making up more than half of the 'hub' elements in modules that include protein-coding genes known to be part of regulatory systems involved in stress response and host adaptation. This data set provides a valuable resource for investigating the role of non-coding RNA, and conserved hypothetical proteins, in transcriptomic remodelling. Based on their connections to genes with known functional groupings and correlations with replicated host conditions, predicted expressed transcripts can be screened as suitable candidates for further experimental validation.

Three Novel Antisense Overlapping Genes in E. coli O157:H7 EDL933

The abundance of long overlapping genes in prokaryotic genomes is likely to be significantly underestimated. To date, only a few examples of such genes are fully established. Using RNA sequencing and ribosome profiling, we found expression of novel overlapping open reading frames in Escherichia coli O157:H7 EDL933 (EHEC). Indeed, the overlapping candidate genes are equipped with typical structural elements required for transcription and translation, i.e., promoters, transcription start sites, as well as terminators, all of which were experimentally verified. Translationally arrested mutants, unable to produce the overlapping encoded protein, were found to have a growth disadvantage when grown competitively against the wild type. Thus, the phenotypes found imply biological functionality of the genes at the level of proteins produced. The addition of 3 more examples of prokaryotic overlapping genes to the currently limited, yet constantly growing pool of such genes emphasizes the underestimated coding capacity of bacterial genomes. IMPORTANCE The abundance of long overlapping genes in prokaryotic genomes is likely to be significantly underestimated, since such genes are not allowed in genome annotations. However, ribosome profiling catches mRNA in the moment of being template for protein production. Using this technique and subsequent experiments, we verified 3 novel overlapping genes encoded in antisense of known genes. This adds more examples of prokaryotic overlapping genes to the currently limited, yet constantly growing pool of such genes.

Regulatory Interplay between RNase III and Antisense RNAs in E. coli: the Case of AsflhD and FlhD, Component of the Master Regulator of Motility

In order to respond to ever-changing environmental cues, bacteria display resilient regulatory mechanisms controlling gene expression. At the post-transcriptional level, this is achieved by a combination of RNA-binding proteins, such as ribonucleases (RNases), and regulatory RNAs, including antisense RNAs (asRNAs). Bound to their complementary mRNA, asRNAs are primary targets for the double-strand-specific endoribonuclease, RNase III. Taking advantage of our own and previously published transcriptomic data sets obtained in strains inactivated for RNase III, we selected several candidate asRNAs and confirmed the existence of RNase III-sensitive asRNAs for crp, ompR, phoP, and flhD genes, all encoding global regulators of gene expression in Escherichia coli. Using FlhD, a component of the master regulator of motility (FlhD₄C₂), as our model, we demonstrate that the asRNA AsflhD, transcribed from the coding sequence of flhD, is involved in the fine-tuning of flhD expression and thus participates in the control of motility.

The origin of RNA interference: Adaptive or neutral evolution?

The origin of RNA interference (RNAi) is usually explained by a defense-based hypothesis, in which RNAi evolved as a defense against transposable elements (TEs) and RNA viruses and was already present in the last eukaryotic common ancestor (LECA). However, since RNA antisense regulation and double-stranded RNAs (dsRNAs) are ancient and widespread phenomena, the origin of defensive RNAi should have occurred in parallel with its regulative functions to avoid imbalances in gene regulation. Thus, we propose a neutral evolutionary hypothesis for the origin of RNAi in which qualitative system drift from a prokaryotic antisense RNA gene regulation mechanism leads to the formation of RNAi through constructive neutral evolution (CNE). We argue that RNAi was already present in the ancestor of LECA before the need for a new defense system arose and that its presence helped to shape eukaryotic genomic architecture and stability.

Where does RNA interference come from? This Essay describes a new step-by-step evolutionary model of how RNA interference might have originated in early eukaryotes through neutral events from the molecular machinery present in prokaryotes.

A Novel Regulation of K-antigen Capsule Synthesis in Porphyromonas gingivalis Is Driven by the Response Regulator PG0720-Directed Antisense RNA

The periodontal pathogen Porphyromonas gingivalis strain W83 displays at least three different surface glycans, specifically two types of lipopolysaccharides (O-LPS and A-LPS) and K-antigen capsule. Despite the importance of K-antigen capsule to the virulence of P. gingivalis, little is known as to how expression of genes involved in the synthesis of this surface glycan is regulated. The genes required for K-antigen capsule synthesis are located in a locus that encodes a number of transcripts, including an operon (PG0104 to PG0121, generating ~19.4-kb transcript) which contains a non-coding 77-bp inverted repeat (77 bpIR) region near the 5'-end. Previously, we identified a 550-nucleotide antisense RNA molecule (designated asSuGR for antisense Surface Glycan Regulator) encoded within the 77-bpIR element that influences the synthesis of surface glycans. In this study, we demonstrate that the DNA-binding response regulator PG0720 can bind the promoter region of asSuGR and activate expression of asSuGR, indicating that PG0720 may indirectly influence transcript levels of the K-antigen capsule operon expressed from the sense strand. The data show that deletion of the PG0720 gene confers a defect in the presentation of surface polysaccharides compared with the parent strain and quantitative RT-PCR (qPCR) analysis determined that the overall expression of genes involved in K-antigen capsule synthesis were down-regulated in the PG0720 mutant. Furthermore, the defects of the PG0720 deletion mutant were restored by complementation. Importantly, the PG0720 deletion mutant showed reduced virulence. Altogether, our data show that the response regulator PG0720 regulates expression of asSuGR, a trans-acting antisense RNA molecule involved in modulating the production of surface polysaccharides in P. gingivalis strain W83. The data provide further evidence that surface glycans are key virulence determinants and significantly advances our understanding of the molecular mechanisms controlling the synthesis of P. gingivalis K-antigen capsule, a key virulence determinant.

Wolbachia Utilizes lncRNAs to Activate the Anti-Dengue Toll Pathway and Balance Reactive Oxygen Species Stress in Aedes aegypti Through a Competitive Endogenous RNA Network

Long non-coding RNAs (lncRNA), a class of RNA molecules without protein coding potential, are more than 200 nucleotides in length and widely present in a variety of species. Although increasing progress in regard to the determination of lncRNA function has been made in vertebrates, Aedes aegypti lncRNAs were only identified recently and the functions of few lncRNAs have been annotated so far. Herein, the genome-wide alteration of the lncRNA expression profile trigged by Wolbachia wAlbB infection was investigated by comparing A. aegypti Aag2 cells and W-Aag2 cells infected with Wolbachia wAlbB. Based on lncRNA sequencing, 3035 differentially expressed lncRNAs (DE lncRNAs) in total were identified upon Wolbachia infection, which were further validated by quantitative PCR. The constructed co-expression network of DE lncRNAs and mRNAs revealed that Wolbachia-induced DE lncRNAs were highly enriched in the oxidative phosphorylation pathway via trans-activity, according to the KEGG pathway enrichment analyses. In addition, the established competitive endogenous RNA (ceRNA) network identifies the DE lncRNAs enriched in cellular oxidant detoxification based on GO enrichment analysis. Furthermore, silencing of aae-lnc-7598, the significantly up-regulated lncRNA with the highest fold change induced by Wolbachia, caused a significant reduction of antioxidant catalase 1B (CAT1B) gene expression as well as the enhancement of mitochondrial reactive oxygen species (ROS) production in living cells. These findings indicate that Wolbachia manipulates lncRNA to balance intracellular ROS stress and ensure its endosymbiosis in host A. aegypti. Notably, the function assay demonstrated that aae-lnc-0165 suppressed by Wolbachia could induce expression of the REL1 gene, the key regulator of downstream Toll pathway, through the sequence-specific binding of aae-miR-980-5p, which contributes to the activation of Toll pathway. Moreover, the depletion of aae-lnc-0165 caused the suppression of mitochondrial ROS levels in living cells. Our data reveal that Wolbachia activates the anti-dengue Toll pathway through a lncRNA-ceRNA pattern. Taken together, our finding suggested that Wolbachia utilizes lncRNAs to activate host anti-dengue Toll pathway via a ceRNA network. Moreover, Wolbachia employs lncRNAs to ensure ROS homeostasis for ROS-based anti-dengue defense through either trans-regulation or the ceRNA network. This study identifies novel potential molecular biomarkers for prevention and control of epidemic dengue.

Modulation of Bacterial Fitness and Virulence Through Antisense RNAs

Regulatory RNAs contribute to gene expression control in bacteria. Antisense RNAs (asRNA) are a class of regulatory RNAs that are transcribed from opposite strands of their target genes. Typically, these untranslated transcripts bind to cognate mRNAs and rapidly regulate gene expression at the post-transcriptional level. In this article, we review asRNAs that modulate bacterial fitness and increase virulence. We chose examples that underscore the variety observed in nature including, plasmid- and chromosome-encoded asRNAs, a riboswitch-regulated asRNA, and asRNAs that require other RNAs or RNA-binding proteins for stability and activity. We explore how asRNAs improve bacterial fitness and virulence by modulating plasmid acquisition and maintenance, regulating transposon mobility, increasing resistance against bacteriophages, controlling flagellar production, and regulating nutrient acquisition. We conclude with a brief discussion on how this knowledge is helping to inform current efforts to develop new therapeutics.

Gene Regulation and Transcriptomics

Borrelia (Borreliella) burgdorferi, along with closely related species, is the etiologic agent of Lyme disease. The spirochete subsists in an enzootic cycle that encompasses acquisition from a vertebrate host to a tick vector and transmission from a tick vector to a vertebrate host. To adapt to its environment and persist in each phase of its enzootic cycle, B. burgdorferi wields three systems to regulate the expression of genes: the RpoN-RpoS alternative sigma factor cascade, the Hk1/Rrp1 two-component system and its product c-di-GMP, and the stringent response mediated by Rel_Bbu and DksA. These regulatory systems respond to enzootic phase-specific signals and are controlled or fine- tuned by transcription factors, including BosR and BadR, as well as small RNAs, including DsrABb and Bb6S RNA. In addition, several other DNA-binding and RNA-binding proteins have been identified, although their functions have not all been defined. Global changes in gene expression revealed by high-throughput transcriptomic studies have elucidated various regulons, albeit technical obstacles have mostly limited this experimental approach to cultivated spirochetes. Regardless, we know that the spirochete, which carries a relatively small genome, regulates the expression of a considerable number of genes required for the transitions between the tick vector and the vertebrate host as well as the adaptation to each.

Are Antisense Proteins in Prokaryotes Functional?

Many prokaryotic RNAs are transcribed from loci outside of annotated protein coding genes. Across bacterial species hundreds of short open reading frames antisense to annotated genes show evidence of both transcription and translation, for instance in ribosome profiling data. Determining the functional fraction of these protein products awaits further research, including insights from studies of molecular interactions and detailed evolutionary analysis. There are multiple lines of evidence, however, that many of these newly discovered proteins are of use to the organism. Condition-specific phenotypes have been characterized for a few. These proteins should be added to genome annotations, and the methods for predicting them standardized. Evolutionary analysis of these typically young sequences also may provide important insights into gene evolution. This research should be prioritized for its exciting potential to uncover large numbers of novel proteins with extremely diverse potential practical uses, including applications in synthetic biology and responding to pathogens.

Recommendations for bacterial ribosome profiling experiments based on bioinformatic evaluation of published data

Ribosome profiling (RIBO-Seq) has improved our understanding of bacterial translation, including finding many unannotated genes. However, protocols for RIBO-Seq and corresponding data analysis are not yet standardized. Here, we analyzed 48 RIBO-Seq samples from nine studies of Escherichia coli K12 grown in lysogeny broth medium and particularly focused on the size-selection step. We show that for conventional expression analysis, a size range between 22 and 30 nucleotides is sufficient to obtain protein-coding fragments, which has the advantage of removing many unwanted rRNA and tRNA reads. More specific analyses may require longer reads and a corresponding improvement in rRNA/tRNA depletion. There is no consensus about the appropriate sequencing depth for RIBO-Seq experiments in prokaryotes, and studies vary significantly in total read number. Our analysis suggests that 20 million reads that are not mapping to rRNA/tRNA are required for global detection of translated annotated genes. We also highlight the influence of drug-induced ribosome stalling, which causes bias at translation start sites. The resulting accumulation of reads at the start site may be especially useful for detecting weakly expressed genes. As different methods suit different questions, it may not be possible to produce a "one-size-fits-all" ribosome profiling data set. Therefore, experiments should be carefully designed in light of the scientific questions of interest. We propose some basic characteristics that should be reported with any new RIBO-Seq data sets. Careful attention to the factors discussed should improve prokaryotic gene detection and the comparability of ribosome profiling data sets.

Small RNAs as Fundamental Players in the Transference of Information During Bacterial Infectious Diseases

Communication shapes life on Earth. Transference of information has played a paramount role on the evolution of all living or extinct organisms since the appearance of life. Success or failure in this process will determine the prevalence or disappearance of a certain set of genes, the basis of Darwinian paradigm. Among different molecules used for transmission or reception of information, RNA plays a key role. For instance, the early precursors of life were information molecules based in primitive RNA forms. A growing field of research has focused on the contribution of small non-coding RNA forms due to its role on infectious diseases. These are short RNA species that carry out regulatory tasks in cis or trans. Small RNAs have shown their relevance in fine tuning the expression and activity of important regulators of essential genes for bacteria. Regulation of targets occurs through a plethora of mechanisms, including mRNA stabilization/destabilization, driving target mRNAs to degradation, or direct binding to regulatory proteins. Different studies have been conducted during the interplay of pathogenic bacteria with several hosts, including humans, animals, or plants. The sRNAs help the invader to quickly adapt to the change in environmental conditions when it enters in the host, or passes to a free state. The adaptation is achieved by direct targeting of the pathogen genes, or subversion of the host immune system. Pathogens trigger also an immune response in the host, which has been shown as well to be regulated by a wide range of sRNAs. This review focuses on the most recent host-pathogen interaction studies during bacterial infectious diseases, providing the perspective of the pathogen.

The world of asRNAs in Gram-negative and Gram-positive bacteria

Bacteria exhibit an amazing diversity of mechanisms controlling gene expression to both maintain essential functions and modulate accessory functions in response to environmental cues. Over the years, it has become clear that bacterial regulation of gene expression is still far from fully understood. This review focuses on antisense RNAs (asRNAs), a class of RNA regulators defined by their location in cis and their perfect complementarity with their targets, as opposed to small RNAs (sRNAs) which act in trans with only short regions of complementarity. For a long time, only few functional asRNAs in bacteria were known and were almost exclusively found on mobile genetic elements (MGEs), thus, their importance among the other regulators was underestimated. However, the extensive application of transcriptomic approaches has revealed the ubiquity of asRNAs in bacteria. This review aims to present the landscape of studied asRNAs in bacteria by comparing 67 characterized asRNAs from both Gram-positive and Gram-negative bacteria. First we describe the inherent ambiguity in the existence of asRNAs in bacteria, second, we highlight their diversity and their involvement in all aspects of bacterial life. Finally we compare their location and potential mode of action toward their target between Gram-negative and Gram-positive bacteria and present tendencies and exceptions that could lead to a better understanding of asRNA functions.