RNA-RNA Interactomes of ProQ and Hfq Reveal Overlapping and Competing Roles.

Base pairing RNAs modulate gene expression in all studied organisms. In many bacteria, the base pairing between most small regulatory RNAs (sRNAs) and their targets is mediated by the Hfq RNA chaperone. However, recent studies have shown FinO-domain proteins also bind sRNAs. To examine the global contribution of the FinO-domain ProQ protein in Escherichia coli, we carried out RIL-seq to identify RNA pairs bound to this protein. The RNA-RNA interactome for ProQ contains hundreds of pairs. Intriguingly, a significant fraction of the ProQ-bound RNA pairs are also found associated with Hfq, indicating overlapping, complementary, or competing roles for the two proteins. Characterization of one novel RNA pair bound by both chaperones revealed that while Hfq is required for RNA sponge-mediated downregulation of the sRNA, ProQ can inhibit this regulation. Overall, our results uncover increased complexity in RNA regulatory networks involving RNA chaperone proteins, RNases, sRNAs, and mRNAs.

Advancing Heteroanionicity in Zintl Phases: Crystal Structures, Thermoelectric and Magnetic Properties of Two Quaternary Semiconducting Arsenide Oxides, Eu8Zn2As6O and Eu14Zn5As12O.

Two novel quaternary oxyarsenides, Eu8Zn2As6O and Eu14Zn5As12O, were synthesized through metal flux reactions, and their crystal structures were established by single-crystal X-ray diffraction methods. Eu8Zn2As6O crystallizes in the orthorhombic space group Pbca, featuring polyanionic ribbons composed of corner-shared triangular [ZnAs3] units, running along the [100] direction. The structure of Eu14Zn5As12O crystallizes in the monoclinic space group P2/m and its anionic substructure can be described as an infinite "ribbonlike" chain comprised of [ZnAs3] trigonal-planar units, although the structural complexity here is greater and also amplified by disorder on multiple crystallographic positions. In both structures, the O2- anion occupies an octahedral void with six neighboring Eu2+ cations. Formal electron counting, electronic structure calculations, and transport properties reveal the charge-balanced semiconducting nature of these heteroanionic Zintl phases. High-temperature thermoelectric transport properties measurements on Eu14Zn5As12O reveal relatively high resistivity (ρ500K = 8 Ω·cm) and Seebeck coefficient values (S500K = 220 µV K-1), along with a low concentration and mobility of holes as the dominant charge-carriers (n500K = 8.0 × 1017 cm-3, µ500K = 6.4 cm2/V s). Magnetic studies indicate the presence of divalent Eu2+ species in Eu14Zn5As12O and complex magnetic ordering, with two transitions observed at T1 = 21.6 K and T2 = 9 K.

BB0562 is a nutritional virulence determinant with lipase activity important for Borrelia burgdorferi infection and survival in fatty acid deficient environments.

The Lyme disease spirochete Borrelia burgdorferi relies on uptake of essential nutrients from its host environments for survival and infection. Therefore, nutrient acquisition mechanisms constitute key virulence properties of the pathogen, yet these mechanisms remain largely unknown. In vivo expression technology applied to B. burgdorferi (BbIVET) during mammalian infection identified gene bb0562, which encodes a hypothetical protein comprised of a conserved domain of unknown function, DUF3996. DUF3996 is also found across adjacent encoded hypothetical proteins BB0563 and BB0564, suggesting the possibility that the three proteins could be functionally related. Deletion of bb0562, bb0563 and bb0564 individually and together demonstrated that bb0562 alone was important for optimal disseminated infection in immunocompetent and immunocompromised mice by needle inoculation and tick bite transmission. Moreover, bb0562 promoted spirochete survival during the blood dissemination phase of infection. Gene bb0562 was also found to be important for spirochete growth in low serum media and the growth defect of Δbb0562 B. burgdorferi was rescued with the addition of various long chain fatty acids, particularly oleic acid. In mammals, fatty acids are primarily stored in fat droplets in the form of triglycerides. Strikingly, addition of glyceryl trioleate, the triglyceride form of oleic acid, to the low serum media did not rescue the growth defect of the mutant, suggesting bb0562 may be important for the release of fatty acids from triglycerides. Therefore, we searched for and identified two canonical GXSXG lipase motifs within BB0562, despite the lack of homology to known bacterial lipases. Purified BB0562 demonstrated lipolytic activity dependent on the catalytic serine residues within the two motifs. In sum, we have established that bb0562 is a novel nutritional virulence determinant, encoding a lipase that contributes to fatty acid scavenge for spirochete survival in environments deficient in free fatty acids including the mammalian host.

Australia is 'free to choose' economic growth and falling environmental pressures.

Over two centuries of economic growth have put undeniable pressure on the ecological systems that underpin human well-being. While it is agreed that these pressures are increasing, views divide on how they may be alleviated. Some suggest technological advances will automatically keep us from transgressing key environmental thresholds; others that policy reform can reconcile economic and ecological goals; while a third school argues that only a fundamental shift in societal values can keep human demands within the Earth's ecological limits. Here we use novel integrated analysis of the energy-water-food nexus, rural land use (including biodiversity), material flows and climate change to explore whether mounting ecological pressures in Australia can be reversed, while the population grows and living standards improve. We show that, in the right circumstances, economic and environmental outcomes can be decoupled. Although economic growth is strong across all scenarios, environmental performance varies widely: pressures are projected to more than double, stabilize or fall markedly by 2050. However, we find no evidence that decoupling will occur automatically. Nor do we find that a shift in societal values is required. Rather, extensions of current policies that mobilize technology and incentivize reduced pressure account for the majority of differences in environmental performance. Our results show that Australia can make great progress towards sustainable prosperity, if it chooses to do so.

Borrelia burgdorferi bbk13 Is Critical for Spirochete Population Expansion in the Skin during Early Infection.

Lyme disease is caused by the spirochete Borrelia burgdorferi and is transmitted via the bite of an infected tick. B. burgdorferi enters the skin, disseminates via the bloodstream, and infects various distal tissues, leading to inflammatory sequelae, such as Lyme arthritis and Lyme carditis. B. burgdorferi linear plasmid 36 (lp36) is critical for mammalian infectivity; however, the full complement of genes on lp36 that contribute to this process remains unknown. Through a targeted mutagenesis screen of the genes on lp36, we identified a novel infectivity gene of unknown function, bbk13, which encodes an immunogenic, non-surface-exposed membrane protein that is important for efficient mammalian infection. Loss of bbk13 resulted in reduced spirochete loads in distal tissues in a mouse model of infection. Through a detailed analysis of B. burgdorferi infection kinetics, we discovered that bbk13 is important for promoting spirochete proliferation in the skin inoculation site. The attenuated ability of Δbbk13 spirochetes to proliferate in the inoculation site was followed by reduced numbers of B. burgdorferi spirochetes in the bloodstream and, ultimately, consistently reduced spirochete loads in distal tissues. Together, our data indicate that bbk13 contributes to disseminated infection by promoting spirochete proliferation in the early phase of infection in the skin. This work not only increases the understanding of the contribution of the genes on lp36 to B. burgdorferi infection but also begins to define the genetic basis for B. burgdorferi expansion in the skin during localized infection and highlights the influence of the early expansion of spirochetes in the skin on the outcome of infection.

In vivo expression technology and 5' end mapping of the Borrelia burgdorferi transcriptome identify novel RNAs expressed during mammalian infection.

Borrelia burgdorferi, the bacterial pathogen responsible for Lyme disease, modulates its gene expression profile in response to the environments encountered throughout its tick-mammal infectious cycle. To begin to characterize the B. burgdorferi transcriptome during murine infection, we previously employed an in vivo expression technology-based approach (BbIVET). This identified 233 putative promoters, many of which mapped to un-annotated regions of the complex, segmented genome. Herein, we globally identify the 5' end transcriptome of B. burgdorferi grown in culture as a means to validate non-ORF associated promoters discovered through BbIVET. We demonstrate that 119 BbIVET promoters are associated with transcription start sites (TSSs) and validate novel RNA transcripts using Northern blots and luciferase promoter fusions. Strikingly, 49% of BbIVET promoters were not found to associate with TSSs. This finding suggests that these sequences may be primarily active in the mammalian host. Furthermore, characterization of the 6042 B. burgdorferi TSSs reveals a variety of RNAs including numerous antisense and intragenic transcripts, leaderless RNAs, long untranslated regions and a unique nucleotide frequency for initiating intragenic transcription. Collectively, this is the first comprehensive map of TSSs in B. burgdorferi and characterization of previously un-annotated RNA transcripts expressed by the spirochete during murine infection.

Ultrathin two-dimensional superconductivity with strong spin-orbit coupling.

We report on a study of epitaxially grown ultrathin Pb films that are only a few atoms thick and have parallel critical magnetic fields much higher than the expected limit set by the interaction of electron spins with a magnetic field, that is, the Clogston-Chandrasekhar limit. The epitaxial thin films are classified as dirty-limit superconductors because their mean-free paths, which are limited by surface scattering, are smaller than their superconducting coherence lengths. The uniformity of superconductivity in these thin films is established by comparing scanning tunneling spectroscopy, scanning superconducting quantum interference device (SQUID) magnetometry, double-coil mutual inductance, and magneto-transport, data that provide average superfluid rigidity on length scales covering the range from microscopic to macroscopic. We argue that the survival of superconductivity at Zeeman energies much larger than the superconducting gap can be understood only as the consequence of strong spin-orbit coupling that, together with substrate-induced inversion-symmetry breaking, produces spin splitting in the normal-state energy bands that is much larger than the superconductor's energy gap.

Gene bb0318 Is Critical for the Oxidative Stress Response and Infectivity of Borrelia burgdorferi.

A greater understanding of the molecular mechanisms that Borrelia burgdorferi uses to survive during mammalian infection is critical for the development of novel diagnostic and therapeutic tools to improve the clinical management of Lyme disease. By use of an in vivo expression technology (IVET)-based approach to identify B. burgdorferi genes expressed in vivo, we discovered the bb0318 gene, which is thought to encode the ATPase component of a putative riboflavin ABC transport system. Riboflavin is a critical metabolite enabling all organisms to maintain redox homeostasis. B. burgdorferi appears to lack the metabolic capacity for de novo synthesis of riboflavin and so likely relies on scavenging riboflavin from the host environment. In this study, we sought to investigate the role of bb0318 in B. burgdorferi pathogenesis. No in vitro growth defect was observed for the Δbb0318 clone. However, the mutant spirochetes displayed reduced levels of survival when exposed to exogenous hydrogen peroxide or murine macrophages. Spirochetes lacking bb0318 were found to have a 100-fold-higher 50% infectious dose than spirochetes containing bb0318 In addition, at a high inoculum dose, bb0318 was found to be important for effective spirochete dissemination to deep tissues for as long as 3 weeks postinoculation and to be critical for B. burgdorferi infection of mouse hearts. Together, these data implicate bb0318 in the oxidative stress response of B. burgdorferi and indicate the contribution of bb0318 to B. burgdorferi mammalian infectivity.

Electrocardiographic reference values for a population of older adults in sub-Saharan Africa.

BACKGROUND/OBJECTIVES: Older adults in sub-Saharan Africa (SSA) are at greatest risk of an impending noncommunicable diseases epidemic, of which cardiac disease is the most prevalent contributor. Thus, it is essential to establish electrocardiographic reference values for a population that is likely to differ genetically and environmentally from others where reference values are established. METHODS: Two thousand two hundred thirty-two apparently healthy community-based participants without known cardiac disease aged 70+ in rural Tanzania underwent 12-lead electrocardiography. Electrocardiograms were digitally analyzed and gender-specific reference values for P duration (PD), P amplitude (PAMP), P area (PAREA), P terminal negative force (V1) (PTNF), PR interval, QRS duration (QRSD), QT/QTc, R amplitude (II, V5) (RAMP) LVH index (LVHI), R axis and R/S ratio (V1) reported, following univariate analysis of covariance using a multiple linear regression model, adjusting for age, systolic blood pressure (SBP), body mass index (BMI), and RR interval. RESULTS: Data from 1824 subjects were suitable for analysis. Adjusted mean values for men/women were: PD 115/110 ms, PAMP (avg) 123/114 µV, PAMP (II) 203/190 µV, PAREA (avg) 5.3/4.6 mV*s, PAREA (II) 9.3/8.1 mV*s, PTNF 1.7/1.4 mV*s, PR 158/152 ms, QRSD 89/84 ms, QT 370/375 ms, QTc 421/427 ms, RAMP (II) 805/854 µV, (V5) 2022/1742 µV, LVHI 3.0/2.8 mV (Sokolow-Lyon), 1.293/1.146 mV (Cornell), R axis 51/49°, R/S 0.2/0.2. Excluding PTNF , R axis and R/S ratio, all gender differences were significant (P < 0.001 apart from LVHI [Sokolow-Lyon; P < 0.005)] and RAMP (II) [P < 0.05]) following adjustment for age, SBP, BMI, and RR interval. CONCLUSIONS: Our description of comprehensive electrocardiographic parameters establishes reference values in this genetically and environmentally diverse SSA population thereby allowing identification of "outliers" with potential cardiac disease.

Electrocardiographic assessment of coronary artery disease and stroke risk factors in rural and urban Tanzania: a case-control study.

BACKGROUND: Although the association between cerebrovascular and coronary artery disease (CAD) is well known in high-income countries, this association is not well documented in black Africans. AIMS: The aim of this study was to document electrocardiographic (ECG) evidence of CAD in stroke cases and controls and to identify other common ECG abnormalities related to known stroke risk factors in a community-based population of incident stroke cases in Tanzania, East Africa. METHODS: This was a case-control study. Incident stroke cases were identified by the Tanzanian Stroke Incidence Project. Age- and sex-matched controls were randomly selected from the background population. Electrocardiograms were manually analyzed using the Minnesota Coding System, looking for evidence of previous myocardial infarction (MI), atrial fibrillation (AF) or atrial flutter (AFl), and left ventricular hypertrophy (LVH). RESULTS: In Hai, there were 93 cases and 241 controls with codable electrocardiograms, and in Dar-es-Salaam, there were 39 cases and 72 controls with codable electrocardiograms. Comparing cases and controls, there was a higher prevalence of MI and AF or AFl (but not LVH) in cases compared with controls. CONCLUSIONS: This is the first published study of ECG assessment of CAD and other stroke risk factors in an incident population of stroke cases in sub-Saharan Africa. It suggests that concomitant CAD in black African stroke cases is more common than previously suggested.

Broadly conserved FlgV controls flagellar assembly and Borrelia burgdorferi dissemination in mice.

Flagella propel pathogens through their environments yet are expensive to synthesize and are immunogenic. Thus, complex hierarchical regulatory networks control flagellar gene expression. Spirochetes are highly motile bacteria, but peculiarly in the Lyme spirochete Borrelia burgdorferi, the archetypal flagellar regulator σ28 is absent. We rediscovered gene bb0268 in B. burgdorferi as flgV, a broadly-conserved gene in the flagellar superoperon alongside σ28 in many Spirochaetes, Firmicutes and other phyla, with distant homologs in Epsilonproteobacteria. We found that B. burgdorferi FlgV is localized within flagellar motors. B. burgdorferi lacking flgV construct fewer and shorter flagellar filaments and are defective in cell division and motility. During the enzootic cycle, B. burgdorferi lacking flgV survive and replicate in Ixodes ticks but are attenuated for dissemination and infection in mice. Our work defines infection timepoints when spirochete motility is most crucial and implicates FlgV as a broadly distributed structural flagellar component that modulates flagellar assembly.

Epigonal conditioned media from bonnethead shark, Sphyrna tiburo, induces apoptosis in a T-cell leukemia cell line, Jurkat E6-1.

Representatives of Subclass Elasmobranchii are cartilaginous fish whose members include sharks, skates, and rays. Because of their unique phylogenetic position of being the most primitive group of vertebrates to possess all the components necessary for an adaptive immune system, the immune regulatory compounds they possess may represent the earliest evolutionary forms of novel compounds with the potential for innovative therapeutic applications. Conditioned medium, generated from short term culture of cells from the epigonal organ of bonnethead sharks (Sphyrna tiburo), has been shown to have potent reproducible cytotoxic activity against a variety of human tumor cell lines in vitro. Existing data suggest that epigonal conditioned medium (ECM) exerts this cytotoxic activity through induction of apoptosis in target cells. This manuscript describes apoptosis induction in a representative tumor cell line, Jurkat E6-1, in response to treatment with ECM at concentrations of 1 and 2 mg/mL. Data indicate that ECM exposure initiates the mitochondrial pathway of apoptosis through activation of caspase enzymes. Future purification of ECM components may result in the isolation of an immune-regulatory compound with potential therapeutic benefit for treatment of human cancer.

Extensive diversity in RNA termination and regulation revealed by transcriptome mapping for the Lyme pathogen B. burgdorferi.

Transcription termination is an essential and dynamic process that can tune gene expression in response to diverse molecular signals. Yet, the genomic positions, molecular mechanisms, and regulatory consequences of termination have only been studied thoroughly in model bacteria. We employed complementary RNA-seq approaches to map RNA ends for the transcriptome of the spirochete Borrelia burgdorferi - the etiological agent of Lyme disease. By systematically mapping B. burgdorferi RNA ends at single nucleotide resolution, we delineated complex gene arrangements and operons and mapped untranslated regions (UTRs) and small RNAs (sRNAs). We experimentally tested modes of B. burgdorferi transcription termination and compared our findings to observations in E. coli , P. aeruginosa , and B. subtilis . We discovered 63% of B. burgdorferi RNA 3' ends map upstream or internal to open reading frames (ORFs), suggesting novel mechanisms of regulation. Northern analysis confirmed the presence of stable 5' derived RNAs from mRNAs encoding gene products involved in the unique infectious cycle of B. burgdorferi . We suggest these RNAs resulted from premature termination and regulatory events, including forms of cis- acting regulation. For example, we documented that the polyamine spermidine globally influences the generation of truncated mRNAs. In one case, we showed that high spermidine concentrations increased levels of RNA fragments derived from an mRNA encoding a spermidine import system, with a concomitant decrease in levels of the full- length mRNA. Collectively, our findings revealed new insight into transcription termination and uncovered an abundance of potential RNA regulators.

Extensive diversity in RNA termination and regulation revealed by transcriptome mapping for the Lyme pathogen Borrelia burgdorferi.

Transcription termination is an essential and dynamic process that can tune gene expression in response to diverse molecular signals. Yet, the genomic positions, molecular mechanisms, and regulatory consequences of termination have only been studied thoroughly in model bacteria. Here, we use several RNA-seq approaches to map RNA ends for the transcriptome of the spirochete Borrelia burgdorferi - the etiological agent of Lyme disease. We identify complex gene arrangements and operons, untranslated regions and small RNAs. We predict intrinsic terminators and experimentally test examples of Rho-dependent transcription termination. Remarkably, 63% of RNA 3' ends map upstream of or internal to open reading frames (ORFs), including genes involved in the unique infectious cycle of B. burgdorferi. We suggest these RNAs result from premature termination, processing and regulatory events such as cis-acting regulation. Furthermore, the polyamine spermidine globally influences the generation of truncated mRNAs. Collectively, our findings provide insights into transcription termination and uncover an abundance of potential RNA regulators in B. burgdorferi.

Structures and phase transitions of CePd3+xGa8-x: new variants of the BaHg11 structure type.

New distorted variants of the cubic BaHg11 structure type have been synthesized in Ga flux. Multiple phases of CePd3+xGa8-x, which include an orthorhombic Pmmn structure (x = 3.21(2)), a rhombohedral R3m structure (x = 3.13(4)), and a cubic Fm3m superstructure (x = 2.69(6)), form preferentially depending on reaction cooling rate and isolation temperature. Differential thermal analysis and in situ temperature-dependent powder X-ray diffraction patterns show a reversible phase transition at approximately 640 °C between the low temperature orthorhombic and rhombohedral structures and the high temperature cubic superstructure. Single crystal X-ray diffraction experiments indicate that the general structure of BaHg11, including the intersecting planes of a kagomé-type arrangement of Ce atoms, is only slightly distorted in the low temperature phases. A combination of Kondo, crystal electric field, and magnetic frustration effects may be present, resulting in low temperature anomalies in magnetic susceptibility, electrical resistivity, and heat capacity measurements. In addition to CePd3+xGa8-x, the rare earth analogues REPd3+xGa8-x, RE = La, Nd, Sm, Tm, and Yb, were successfully synthesized and also crystallize in one of the lower symmetry space groups.

The Value of Vaccines: A Tale of Two Parts.

Vaccines are essential to ensuring a nation's health, wellbeing and prosperity. After the coronavirus pandemic commenced, the Australian Government introduced social restrictions to constrain virus transmission, seeing significant economic impacts. Reflecting the extraordinary circumstances, subsequent vaccination rollout forwent usual health technology assessment (HTA) processes, facilitating restrictions removal and leading to societal and economic recovery. However, in 'usual' circumstances, HTA may not consider such broader effects of vaccines, making it challenging for them to achieve timely funding. We used detailed modelling to compare economic impacts under continued lockdowns against population-wide vaccination rollout between January 2020 and June 2023 and examined global HTA vaccine evaluation methodologies and efforts to develop broader valuation approaches. Australian gross domestic product reduces by approximately AUD 395 billion with lockdowns. With vaccination rollout, this effect is approximately AUD 214bn, a positive incremental impact of AUD 181bn. Vaccination contributes to large estimated positive effects for tourism (AUD 28bn) and education (AUD 26bn) exports, employment (142,000 jobs) and government finances (AUD 259bn). Conversely, global HTA methods generally only consider direct patient health outcomes and healthcare system-related costs, with broader effects usually not impacting funding decisions. Our results suggest that recent efforts to propose broader HTA valuation frameworks warrant further policy consideration.

Early immersion in a dedicated one-month Anesthesiology Professional Practice rotation for Post-Graduate Year-1 interns is associated with an increase in scholarly activity during residency.

STUDY OBJECTIVE: Despite the Accreditation Council for Graduate Medical Education scholarly activity requirement, incorporating education on scholarly fundamentals into residency is challenging. We designed and implemented an academic non-clinical rotation for Post Graduate Year-1 (PGY-1) interns and its association with subsequent resident scholarly productivity was determined. We hypothesized that early immersion in such a rotation would be associated with increased scholarly activity during residency. DESIGN: Retrospective educational comparative study, of two cohorts of anesthesiology residents in the graduating classes of 2015-2020. SETTING: Large anesthesiology residency program at a U.S. academic medical center. INTERVENTION: A one-month academic rotation titled Anesthesia Professional Practice for PGY-1 interns has been implemented since 2014. The rotation curriculum broadly covers important topics for scholarly projects and provides introductions to academic faculty and institutional resources. MEASUREMENTS: The scholarly products (abstracts, publications, book chapters, research protocols, and grant applications) were quantified using Scholarly Activity Points, a previously described metric that accounts for significance and the resident's contribution. Total Scholarly Activity Points for each resident and number of publications prior to residency were determined for both cohorts. Segmented regression was employed with Scholarly Activity Points as the outcome; participation in the early immersion rotation and prior publications were used as input variables. MAIN RESULTS: Resident participation in the early immersion rotation was significantly associated with higher Scholarly Activity Points. The confounding variable of pre-residency publication count was not significantly correlated to this increase. CONCLUSIONS: Immersion in a one-month academic program during PGY-1 internship may contribute to increased scholarly productivity during residency.

The impacts of COVID-19 containment on the Australian economy and its agricultural and mining industries.

We simulate the economic impacts of the COVID-19 pandemic on the Australian economy using VURM, a detailed computable general equilibrium model for Australia. We identify five sources of economic perturbations: changes to productivity due to changing work practices, changes in household demand imposed by voluntary and mandated social distancing behaviour, changes in international trade due to a weakened world economy and severe curtailment of international travel, reduced population growth due to lower net migration and large debt-financed fiscal stimulus. Variants of these shocks and associated recovery paths are simulated in VURM, with three scenarios describing potential recovery arcs. The macroeconomic and industry impacts are reported for each scenario. Ultimately, our focus is on the impact on output and employment in the agriculture and mining sectors, and on their likely recovery prospects. At the peak of economic impacts, output in these sectors declines by about 6 per cent relative to a no-COVID baseline. Compared to the economy-wide average, the decline in agriculture and mining output is small. This can be explained by relatively minor impacts on work practices, relatively low negative impacts on demand for intensive agriculture (helped by fiscal supports for households) and relatively low disruption to export demand.

Regulatory roles of Escherichia coli 5' UTR and ORF-internal RNAs detected by 3' end mapping.

Many bacterial genes are regulated by RNA elements in their 5´ untranslated regions (UTRs). However, the full complement of these elements is not known even in the model bacterium Escherichia coli. Using complementary RNA-sequencing approaches, we detected large numbers of 3´ ends in 5´ UTRs and open reading frames (ORFs), suggesting extensive regulation by premature transcription termination. We documented regulation for multiple transcripts, including spermidine induction involving Rho and translation of an upstream ORF for an mRNA encoding a spermidine efflux pump. In addition to discovering novel sites of regulation, we detected short, stable RNA fragments derived from 5´ UTRs and sequences internal to ORFs. Characterization of three of these transcripts, including an RNA internal to an essential cell division gene, revealed that they have independent functions as sRNA sponges. Thus, these data uncover an abundance of cis- and trans-acting RNA regulators in bacterial 5´ UTRs and internal to ORFs.

In most organisms, specific segments of a cell's genetic information are copied to form single-stranded molecules of various sizes and purposes. Each of these RNA molecules, as they are known, is constructed as a chain that starts at the 5´ end and terminates at the 3´ end. Certain RNAs carry the information present in a gene, which provides the instructions that a cell needs to build proteins. Some, however, are 'non-coding' and instead act to fine-tune the activity of other RNAs. These regulatory RNAs can be separate from the RNAs they control, or they can be embedded in the very sequences they regulate; new evidence also shows that certain regulatory RNAs can act in both ways. Many regulatory RNAs are yet to be catalogued, even in simple, well-studied species such as the bacterium Escherichia coli. Here, Adams et al. aimed to better characterize the regulatory RNAs present in E. coli by mapping out the 3´ ends of every RNA molecule in the bacterium. This revealed many new regulatory RNAs and offered insights into where these sequences are located. For instance, the results show that several of these RNAs were embedded within RNA produced from larger genes. Some were nested in coding RNAs, and were parts of a longer RNA sequence that is adjacent to the protein coding segment. Others, however, were present within the instructions that code for a protein. The work by Adams et al. reveals that regulatory RNAs can be located in unexpected places, and provides a method for identifying them. This can be applied to other types of bacteria, in particular in species with few known RNA regulators.

Prevalence of small base-pairing RNAs derived from diverse genomic loci.

Small RNAs (sRNAs) that act by base-pairing have been shown to play important roles in fine-tuning the levels and translation of their target transcripts across a variety of model and pathogenic organisms. Work from many different groups in a wide range of bacterial species has provided evidence for the importance and complexity of sRNA regulatory networks, which allow bacteria to quickly respond to changes in their environment. However, despite the expansive literature, much remains to be learned about all aspects of sRNA-mediated regulation, particularly in bacteria beyond the well-characterized Escherichia coli and Salmonella enterica species. Here we discuss what is known, and what remains to be learned, about the identification of regulatory base-pairing RNAs produced from diverse genomic loci including how their expression is regulated. This article is part of a Special Issue entitled: RNA and gene control in bacteria edited by Dr. M. Guillier and F. Repoila.