A trans-acting riboswitch controls expression of the virulence regulator PrfA in Listeria monocytogenes

Blue and red light modulates SigB-dependent gene transcription, swimming motility and invasiveness in Listeria monocytogenes

BACKGROUND

In a number of gram-positive bacteria, including Listeria, the general stress response is regulated by the alternative sigma factor B (SigB). Common stressors which lead to the activation of SigB and the SigB-dependent regulon are high osmolarity, acid and several more. Recently is has been shown that also blue and red light activates SigB in Bacillus subtilis.

METHODOLOGY/PRINCIPAL FINDINGS

By qRT-PCR we analyzed the transcriptional response of the pathogen L. monocytogenes to blue and red light in wild type bacteria and in isogenic deletion mutants for the putative blue-light receptor Lmo0799 and the stress sigma factor SigB. It was found that both blue (455 nm) and red (625 nm) light induced the transcription of sigB and SigB-dependent genes, this induction was completely abolished in the SigB mutant. The blue-light effect was largely dependent on Lmo0799, proving that this protein is a genuine blue-light receptor. The deletion of lmo0799 enhanced the red-light effect, the underlying mechanism as well as that of SigB activation by red light remains unknown. Blue light led to an increased transcription of the internalin A/B genes and of bacterial invasiveness for Caco-2 enterocytes. Exposure to blue light also strongly inhibited swimming motility of the bacteria in a Lmo0799- and SigB-dependent manner, red light had no effect there.

CONCLUSIONS/SIGNIFICANCE

Our data established that visible, in particular blue light is an important environmental signal with an impact on gene expression and physiology of the non-phototrophic bacterium L. monocytogenes. In natural environments these effects will result in sometimes random but potentially also cyclic fluctuations of gene activity, depending on the light conditions prevailing in the respective habitat.

Thiamin (vitamin B1) biosynthesis and regulation: a rich source of antimicrobial drug targets?

Drug resistance of pathogens has necessitated the identification of novel targets for antibiotics. Thiamin (vitamin B1) is an essential cofactor for all organisms in its active form thiamin diphosphate (ThDP). Therefore, its metabolic pathways might be one largely untapped source of antibiotics targets. This review describes bacterial thiamin biosynthetic, salvage, and transport pathways. Essential thiamin synthetic enzymes such as Dxs and ThiE are proposed as promising drug targets. The regulation mechanism of thiamin biosynthesis by ThDP riboswitch is also discussed. As drug targets of existing antimicrobial compound pyrithiamin, the ThDP riboswitch might serves as alternative targets for more antibiotics.

Bacterial aptamers that selectively bind glutamine

The continued expansion of microbial sequence data has allowed for the detection of an increasing number of conserved RNA motifs by using comparative sequence analysis. Recently, we reported the discovery of two structured non-coding RNA motifs, called glnA and Downstream-peptide, that have similarity in sequence and secondary structure. In this report, we describe data demonstrating that representatives of both RNA motifs selectively bind the amino acid L-glutamine. These glutamine aptamers are found exclusively in cyanobacteria and marine metagenomic sequences, wherein several glnA RNA representatives reside upstream of genes involved in nitrogen metabolism. These motifs have genomic distributions that are consistent with a gene regulation function, suggesting they are components of glutamine-responsive riboswitches. Thus, our findings implicate glutamine as a regulator of cyanobacterial nitrogen metabolism pathways. Furthermore, our findings expand the collection of natural aptamer classes that bind amino acids to include glycine, lysine and glutamine.

RNAs: regulators of bacterial virulence

RNA-based pathways that regulate protein expression are much more widespread than previously thought. Regulatory RNAs, including 5' and 3' untranslated regions next to the coding sequence, cis-acting antisense RNAs and trans-acting small non-coding RNAs, are effective regulatory molecules that can influence protein expression and function in response to external cues such as temperature, pH and levels of metabolites. This Review discusses the mechanisms by which these regulatory RNAs, together with accessory proteins such as RNases, control the fate of mRNAs and proteins and how this regulation influences virulence in pathogenic bacteria.

Ribozymes and riboswitches: modulation of RNA function by small molecules

Diverse small molecules interact with catalytic RNAs (ribozymes) as substrates and cofactors, and their intracellular concentrations are sensed by gene-regulatory mRNA domains (riboswitches) that modulate transcription, splicing, translation, or RNA stability. Although recognition mechanisms vary from RNA to RNA, structural analyses reveal recurring strategies that arise from the intrinsic properties of RNA such as base pairing and stacking with conjugated heterocycles, and cation-dependent recognition of anionic functional groups. These studies also suggest that, to a first approximation, the magnitude of ligand-induced reorganization of an RNA is inversely proportional to the complexity of the riboswitch or ribozyme. How these small molecule binding-induced changes in RNA lead to alteration in gene expression is less well understood. While different riboswitches have been proposed to be under either kinetic or thermodynamic control, the biochemical and structural mechanisms that give rise to regulatory consequences downstream of small molecule recognition by RNAs mostly remain to be elucidated.

Listeria monocytogenes: at the coalface of host-pathogen research

Listeria monocytogenes is a highly adaptable food-borne pathogen that causes the life threatening illness listeriosis in infected individuals. Within the host this bacterium invades cells, escapes into the host cell cytosol and replicates intracellularly. To achieve this L. monocytogenes has evolved a sophisticated set of molecular weaponry that allows it to interact with and manipulate the cell biology of the host to its own advantage. Many of these interactions are well understood, putting this pathogen at the forefront of host-pathogen research, but fascinating new interactions are still emerging. The seventeenth International Symposium on Problems of Listeriosis (ISOPOL) was held in Portugal (Porto) in May of this year and this report describes some of the exciting developments that were presented at the meeting. The report focuses on developments in understanding the molecular interactions between L. monocytogenes and the host; it describes novel uses for L. monocytogenes as an anti-cancer treatment; and it describes some innovative uses of transcriptional profiling and reporter gene fusions that are helping illuminate our understanding of the basic biology of this important pathogen.

A eubacterial riboswitch class that senses the coenzyme tetrahydrofolate

Comparative sequence analyses of bacterial genomes are revealing many structured RNA motifs that function as metabolite-binding riboswitches. We have identified an RNA motif frequently positioned in the 5' UTRs of folate transport and biosynthesis genes in Firmicute genomes. Biochemical experiments confirm that representatives of this new-found RNA class selectively bind derivatives of the vitamin folate, including di- and tetrahydrofolate coenzymes. In addition, representatives of this aptamer class occasionally reside upstream of RNA structures that are predicted to control translation initiation in response to ligand binding. These findings expand the number of coenzymes that are directly sensed by RNA and reveal possible riboswitch-controlled regulons that respond to changes in single-carbon metabolism.

Genetic characterization of plasmid-associated benzalkonium chloride resistance determinants in a Listeria monocytogenes strain from the 1998-1999 outbreak

Quaternary ammonium compounds such as benzalkonium chloride (BC) are widely used as disinfectants in both food processing and medical environments. BC-resistant strains of Listeria monocytogenes have been implicated in multistate outbreaks of listeriosis and have been frequently isolated from food processing plants. However, the genetic basis for BC resistance in L. monocytogenes remains poorly understood. In this study, we have characterized a plasmid (pLM80)-associated BC resistance cassette in L. monocytogenes H7550, a strain implicated in the 1998-1999 multistate outbreak involving contaminated hot dogs. The BC resistance cassette (bcrABC) restored resistance to BC (MIC, 40 μg/ml) in a plasmid-cured derivative of H7550. All three genes of the cassette were essential for imparting BC resistance. The transcription of H7550 BC resistance genes was increased under sublethal (10 μg/ml) BC exposure and was higher at reduced temperatures (4, 8, or 25°C) than at 37°C. The level of transcription was higher at 10 μg/ml than at 20 or 40 μg/ml. In silico analysis suggested that the BC resistance cassette was harbored by an IS1216 composite transposon along with other genes whose functions are yet to be determined. The findings from this study will further our understanding of the adaptations of this organism to disinfectants such as BC and may contribute to the elucidation of possible BC resistance dissemination in L. monocytogenes.

Regulatory RNA in bacterial pathogens

Bacteria constitute a large and diverse class of infectious agents, causing devastating diseases in humans, animals, and plants. Our understanding of gene expression control, which forms the basis for successful prevention and treatment strategies, has until recently neglected the many roles that regulatory RNAs might have in bacteria. In recent years, several such regulators have been found to facilitate host-microbe interactions and act as key switches between saprophytic and pathogenic lifestyles. This review covers the versatile regulatory RNA mechanisms employed by bacterial pathogens and highlights the dynamic interplay between riboregulation and virulence factor expression.

Characterization of a novel riboswitch-regulated lysine transporter in Aggregatibacter actinomycetemcomitans

Aggregatibacter actinomycetemcomitans is an opportunistic pathogen that resides primarily in the mammalian oral cavity. In this environment, A. actinomycetemcomitans faces numerous host- and microbe-derived stresses, including intense competition for nutrients and exposure to the host immune system. While it is clear that A. actinomycetemcomitans responds to precise cues that allow it to adapt and proliferate in the presence of these stresses, little is currently known about the regulatory mechanisms that underlie these responses. Many bacteria use noncoding regulatory RNAs (ncRNAs) to rapidly alter gene expression in response to environmental stresses. Although no ncRNAs have been reported in A. actinomycetemcomitans, we propose that they are likely important for colonization and persistence in the oral cavity. Using a bioinformatic and experimental approach, we identified three putative metabolite-sensing riboswitches and nine small regulatory RNAs (sRNAs) in A. actinomycetemcomitans during planktonic and biofilm growth. Molecular characterization of one of the riboswitches revealed that it is a lysine riboswitch and that its target gene, lysT, encodes a novel lysine-specific transporter. Finally, we demonstrated that lysT and the lysT lysine riboswitch are conserved in over 40 bacterial species, including the phylogenetically related pathogen Haemophilus influenzae.

Premature terminator analysis sheds light on a hidden world of bacterial transcriptional attenuation

BACKGROUND

Bacterial transcription attenuation occurs through a variety of cis-regulatory elements that control gene expression in response to a wide range of signals. The signal-sensing structures in attenuators are so diverse and rapidly evolving that only a small fraction have been properly annotated and characterized to date. Here we apply a broad-spectrum detection tool in order to achieve a more complete view of the transcriptional attenuation complement of key bacterial species.

RESULTS

Our protocol seeks gene families with an unusual frequency of 5' terminators found across multiple species. Many of the detected attenuators are part of annotated elements, such as riboswitches or T-boxes, which often operate through transcriptional attenuation. However, a significant fraction of candidates were not previously characterized in spite of their unmistakable footprint. We further characterized some of these new elements using sequence and secondary structure analysis. We also present elements that may control the expression of several non-homologous genes, suggesting co-transcription and response to common signals. An important class of such elements, which we called mobile attenuators, is provided by 3' terminators of insertion sequences or prophages that may be exapted as 5' regulators when inserted directly upstream of a cellular gene.

CONCLUSIONS

We show here that attenuators involve a complex landscape of signal-detection structures spanning the entire bacterial domain. We discuss possible scenarios through which these diverse 5' regulatory structures may arise or evolve.

A bacterial mRNA leader that employs different mechanisms to sense disparate intracellular signals

Bacterial mRNAs often contain leader sequences that respond to specific metabolites or ions by altering expression of the associated downstream protein-coding sequences. Here we report that the leader RNA of the Mg(2+) transporter gene mgtA of Salmonella enterica, which was previously known to function as a Mg(2+)-sensing riboswitch, harbors an 18 codon proline-rich open reading frame-termed mgtL-that permits intracellular proline to regulate mgtA expression. Interfering with mgtL translation by genetic, pharmacological, or environmental means was observed to increase the mRNA levels from the mgtA coding region. Substitution of the mgtL proline codons by other codons abolished the response to proline and to hyperosmotic stress but not to Mg(2+). Our findings show that mRNA leader sequences can consist of complex regulatory elements that utilize different mechanisms to sense separate signals and mediate an appropriate cellular response.

Deciphering the physiological blueprint of a bacterial cell: revelations of unanticipated complexity in transcriptome and proteome

During the last few months, several pioneer genome-wide transcriptomic, proteomic and metabolomic studies have revolutionised the understanding of bacterial biological processes, leading to a picture that resembles eukaryotic complexity. Technological advances such as next-generation high-throughput sequencing and high-density oligonucleotide microarrays have allowed the determination, in several bacteria, of the entire boundaries of all expressed transcripts. Consequently, novel RNA-mediated regulatory mechanisms have been discovered including multifunctional RNAs. Moreover, resolution of bacterial proteome organisation (interactome) and global protein localisation (localizome) have unveiled an unanticipated complexity that highlights the significance of protein multifunctionality and localisation in the cell. Also, analysis of a complete bacterial metabolic network has again revealed a high fraction of multifunctional enzymes and an unexpectedly high level of metabolic responses and adaptation. Altogether, these novel approaches have permitted the deciphering of the entire physiological landscape of one of the smallest bacteria, Mycoplasma pneumoniae. Here, we summarise and discuss recent findings aimed at defining the blueprint of any prokaryote.

Free state conformational sampling of the SAM-I riboswitch aptamer domain

Riboswitches are highly structured elements residing in the 5' untranslated region of messenger RNAs that specifically bind cellular metabolites to alter gene expression. While there are many structures of ligand-bound riboswitches that reveal details of bimolecular recognition, their unliganded structures remain poorly characterized. Characterizing the molecular details of the unliganded state is crucial for understanding the riboswitch's mechanism of action because it is this state that actively interrogates the cellular environment and helps direct the regulatory outcome. To develop a detailed description of the ligand-free form of an S-adenosylmethionine binding riboswitch at the local and global levels, we have employed a series of biochemical, biophysical, and computational methods. Our data reveal that the ligand binding domain adopts an ensemble of states that minimizes the energy barrier between the free and bound states to establish an efficient decision making branchpoint in the regulatory process.

Riboswitch function: flipping the switch or tuning the dimmer?

Riboswitches are structured mRNA elements involved in gene regulation that respond to the intracellular concentration of specific small molecules. Binding of their cognate ligand is thought to elicit a global conformational change of the riboswitch, in addition to modulating the fine structure of the binding site. X-ray crystallography has produced detailed descriptions of the three-dimensional structures of the ligand-bound conformations of several riboswitches. We have employed small-angle X-ray scattering (SAXS) to generate low-resolution reconstructions of the ligand-free states of the ligand-binding domains of riboswitches that respond to thiamine pyrophosphate (TPP), and cyclic diguanylate (c-di-GMP), a bacterial second messenger. Comparison of the SAXS reconstructions with the crystal structures of these two riboswitches demonstrates that the RNAs undergo dramatic ligand-induced global conformational changes. However, this is not an universal feature of riboswitches. SAXS analysis of the solution behavior of several other riboswitch ligand-binding domains demonstrates a broad spectrum of conformational switching behaviors, ranging from the unambiguous switching of the TPP and c-di-GMP riboswitches to complete lack of switching for the flavin mononucleotide (FMN) riboswitch. Moreover, the switching behavior varies between examples of the same riboswitch from different organisms. The range of observed behaviors suggests that in response to the evolutionary need for precise genetic regulation, riboswitches may be tuned to function more as dimmers or rheostats than binary on/off switches.

Transcriptomic and phenotypic responses of Listeria monocytogenes strains possessing different growth efficiencies under acidic conditions

In an experiment delineating aciduric strains, food and clinical Listeria monocytogenes isolates tended to produce the most biomass whereas ovine and avian strains produced comparatively less biomass when exposed to high levels of sodium diacetate (SD) and potassium sorbate. Compared to reference strains that exhibited greater acid sensitivity, representative food isolates with comparatively good growth capacities in the presence of 21 mM SD at pH 5.0 accumulated reduced levels of acetate anion and K(+) ion. The aciduric nature of SD-resistant strains was also reflected by comparatively high tolerance to pH 2.4 (HCl) acid challenges, a property boosted by the presence of SD. Exposure to elevated levels of SD (21 mM SD at pH 5.0) was found to have broad effects on gene expression, as differentiated from effects caused by mildly acidic conditions (pH 5.0). SD-resistant strain FW04/0025 was more responsive to elevated SD, increasing the expression of 222 genes (>2-fold change [P < 0.05]), compared to the more sensitive EGD reference strain, which exhibited increases in expression of 112 genes. Key differences between the strains in relation to SD-enhanced transcripts were notably associated with the cell envelope, oxidative stress management, and intermediary metabolism. SD thus appears to differentially influence growth efficiency and survival of strains, under conditions relevant to acidic foods, that could be due to altered cell wall and metabolic phenotypes.

Probing adenine rings and backbone linkages using base specific isotope-edited Raman spectroscopy: application to group II intron ribozyme domain V

Raman difference spectroscopy is used to probe the properties of a 36-nt RNA molecule, "D5", which lies at the heart of the catalytic apparatus in group II introns. For D5 that has all of its adenine residues labeled with (13)C and (15)N and utilizing Raman difference spectroscopy, we identify the conformationally sensitive -C-O-P-O-C- stretching modes of the unlabeled bonds adjacent to adenine bases, as well as the adenine ring modes themselves. The phosphodiester modes can be assigned to individual adenine residues based on earlier NMR data. The effect of Mg(2+) binding was explored by analyzing the Raman difference spectra for [D5 + Mg(2+)] minus [D5 no Mg(2+)], for D5 unlabeled, or D5 labeled with (13)C/(15)N-enriched adenine. In both sets of data we assign differential features to G ring modes perturbed by Mg(2+) binding at the N7 position. In the A-labeled spectra we attribute a Raman differential near 1450 cm(-1) and changes of intensity at 1296 cm(-1) to Mg binding at the N7 position of adenine bases. The A and G bases involved in Mg(2+) binding again can be identified using earlier NMR results. For the unlabeled D5, a change in the C-O-P-O-C stretch profile at 811 cm(-1) upon magnesium binding is due to a "tightening up" (in the sense of a more rigid molecule with less dynamic interchange among competing ribose conformers) of the D5 structure. For adenine-labeled D5, small changes in the adenine backbone bond signatures in the 810-830 cm(-1) region suggest that small conformational changes occur in the tetraloop and bulge regions upon binding of Mg(2+). The PO(2)(-) stretching vibration, near 1100 cm(-1), from the nonbridging phosphate groups, probes the effect of Mg(2+)-hydrate inner-sphere interactions that cause an upshift. In turn, the upshift is modulated by the presence of monovalent cations since in the presence of Na(+) and Li(+) the upshift is 23 +/- 2 cm(-1) while in the presence of K(+) and Cs(+) it is 13 +/- 3 cm(-1), a finding that correlates with the differences in hydration radii. These subtle differences in electrostatic interactions may be related to observed variations in catalytic activity. For a reconstructed ribozyme comprising domains 1-3 (D123) connected in cis plus domain 5 (D5) supplied in trans, cleavage of spliced exon substrates in the presence of magnesium and K(+) or Cs(+) is more efficient than that in the presence of magnesium with Na(+) or Li(+).

Experimental discovery of small RNAs in Staphylococcus aureus reveals a riboregulator of central metabolism

Using an experimental approach, we investigated the RNome of the pathogen Staphylococcus aureus to identify 30 small RNAs (sRNAs) including 14 that are newly confirmed. Among the latter, 10 are encoded in intergenic regions, three are generated by premature transcription termination associated with riboswitch activities, and one is expressed from the complementary strand of a transposase gene. The expression of four sRNAs increases during the transition from exponential to stationary phase. We focused our study on RsaE, an sRNA that is highly conserved in the bacillales order and is deleterious when over-expressed. We show that RsaE interacts in vitro with the 5' region of opp3A mRNA, encoding an ABC transporter component, to prevent formation of the ribosomal initiation complex. A previous report showed that RsaE targets opp3B which is co-transcribed with opp3A. Thus, our results identify an unusual case of riboregulation where the same sRNA controls an operon mRNA by targeting two of its cistrons. A combination of biocomputational and transcriptional analyses revealed a remarkably coordinated RsaE-dependent downregulation of numerous metabolic enzymes involved in the citrate cycle and the folate-dependent one-carbon metabolism. As we observed that RsaE accumulates transiently in late exponential growth, we propose that RsaE functions to ensure a coordinate downregulation of the central metabolism when carbon sources become scarce.

Evidence for widespread gene control function by the ydaO riboswitch candidate

Nearly all representatives of experimentally validated riboswitch classes in bacteria control the expression of genes for the transport or synthesis of key metabolic compounds. Recent findings have revealed that some riboswitches also regulate genes involved in physiological changes, virulence, and stress responses. Many novel RNA motifs are being identified by using bioinformatics algorithms that search for conserved sequence and structural features located in intergenic regions. Some of these RNAs are likely to function as riboswitches for metabolites or signaling compounds, and confirmation of this function would reveal the basis of the genetic control of new regulons. Herein we describe the analysis of the ydaO riboswitch candidate, which represents one of the most widespread candidates remaining to be validated. These RNAs are common in Gram-positive bacteria, and their genomic associations with diverse genes suggest that they sense a compound that signals broader physiological changes. We determined that the ydaO motif exhibits sequence- and structure-dependent gene control, and reporter assays indicate that its natural ligand is present even when cells are grown in defined media. A transposon-mediated knockout screen resulted in mutants with a dysregulated expression of genes controlled by the RNA motif. The mutations disrupt genes that drastically modulate energy-generating pathways, suggesting that the intracellular concentration of the ligand sensed by the ydaO motif is altered under these stress conditions.

Cartography of methicillin-resistant S. aureus transcripts: detection, orientation and temporal expression during growth phase and stress conditions

BACKGROUND

Staphylococcus aureus is a versatile bacterial opportunist responsible for a wide spectrum of infections. The severity of these infections is highly variable and depends on multiple parameters including the genome content of the bacterium as well as the condition of the infected host. Clinically and epidemiologically, S. aureus shows a particular capacity to survive and adapt to drastic environmental changes including the presence of numerous antimicrobial agents. Mechanisms triggering this adaptation remain largely unknown despite important research efforts. Most studies evaluating gene content have so far neglected to analyze the so-called intergenic regions as well as potential antisense RNA molecules.

PRINCIPAL FINDINGS

Using high-throughput sequencing technology, we performed an inventory of the whole transcriptome of S. aureus strain N315. In addition to the annotated transcription units, we identified more than 195 small transcribed regions, in the chromosome and the plasmid of S. aureus strain N315. The coding strand of each transcript was identified and structural analysis enabled classification of all discovered transcripts. RNA purified at four time-points during the growth phase of the bacterium allowed us to define the temporal expression of such transcripts. A selection of 26 transcripts of interest dispersed along the intergenic regions was assessed for expression changes in the presence of various stress conditions including pH, temperature, oxidative shocks and growth in a stringent medium. Most of these transcripts showed expression patterns specific for the defined stress conditions that we tested.

CONCLUSIONS

These RNA molecules potentially represent important effectors of S. aureus adaptation and more generally could support some of the epidemiological characteristics of the bacterium.

A processive riboantiterminator seeks a switch to make biofilms

Since the discovery of the first signal-sensing RNA structure by Grundy and Henkin in 1993, the list of cis-acting riboregulators has grown dramatically. Riboswitches fold into elaborate structures and respond to binding of small metabolites by altering the folding pattern of the surrounding transcript, thereby altering the gene expression programme. Riboswitches that use short-range mechanisms to control transcription attenuation and translation initiation and mediate mRNA cleavage have been characterized in many Gram-positive bacteria. Their action typically relies on alternative RNA structures that are differentially stabilized by the ligand binding. In this issue of Molecular Microbiology, Irnov and Winkler describe a novel Bacillus subtilis riboregulator called EAR that shares structural complexity with riboswitches but possesses a unique mechanism of action. EAR increases expression of exopolysaccharide genes and biofilm formation, and appears to act as a processive, long-range antiterminator, the first such example outside of Escherichia coli. While it is unclear whether EAR senses a biofilm-inducing signal, the results suggest that its action depends on yet unidentified auxiliary factors. Interestingly, efficient capsule biogenesis in E. coli and Bacteroides fragilis also depends on processive antiterminators but utilizes the protein-based mechanisms instead.

Regulatory crosstalk of the metabolic network

The metabolic network has a modular architecture, is robust to perturbations, and responds to biological stimuli and environmental conditions. Through monitoring by metabolite responsive macromolecules, metabolic pathways interact with the transcriptome and proteome. Whereas pathway interconnecting cofactors and substrates report on the overall state of the network, specialised intermediates measure the activity of individual functional units. Transitions in the network affect many of these regulatory metabolites, facilitating the parallel regulation of the timing and control of diverse biological processes. The metabolic network controls its own balance, chromatin structure and the biosynthesis of molecular cofactors; moreover, metabolic shifts are crucial in the response to oxidative stress and play a regulatory role in cancer.

Prokaryotic transcriptomics: a new view on regulation, physiology and pathogenicity

Transcriptome-wide studies in eukaryotes have been instrumental in the characterization of fundamental regulatory mechanisms for more than a decade. By contrast, in prokaryotes (bacteria and archaea) whole-transcriptome studies have not been performed until recently owing to the general view that microbial gene structures are simple, as well as technical difficulties in enriching for mRNAs that lack poly(A) tails. Deep RNA sequencing and tiling array studies are now revolutionizing our understanding of the complexity, plasticity and regulation of microbial transcriptomes.