An internal loop region is responsible for inherent target specificity of bacterial cold-shock proteins.

Cold-shock proteins (Csps), of around 70 amino acids, share a protein fold for the cold-shock domain (CSD) that contains RNA-binding motifs, RNP1 and RNP2, and constitute one family of bacterial RNA-binding proteins. Despite similar amino acid composition, Csps have been shown to individually possess inherent specific functions. Here, we identify the molecular differences in Csps that allow selective recognition of RNA targets.

Coming in out of the cold: Rho-dependent termination contributes to adaptation to cold shock.

During cold shock, bacteria shut down translation of all but a set of cold-shock proteins critical for recovery; in this issue of Molecular Cell, Delaleau et al. show that Rho-dependent transcription termination plays an important role in cold adaptation, via temperature-regulated termination of the cold-shock protein mRNAs.

Complete genome sequence of CS-K2, isolated from freshwater lake sediments in Bavaria, Germany.

CS-K2 is a Gram-negative bacterium first isolated from the sediment of the littoral zone of a freshwater lake in Germany. We here present the complete annotated genome sequence of this thiosulfate-oxidizing bacterium, spanning 3.54 Mb and encoding 3,192 protein-coding sequences.

Identification of Attenuators of Transcriptional Termination: Implications for RNA Regulation in Escherichia coli.

The regulatory function of many bacterial small RNAs (sRNAs) requires the binding of the RNA chaperone Hfq to the 3' portion of the sRNA intrinsic terminator, and therefore sRNA signaling might be regulated by modulating its terminator. Here, using a multicopy screen developed with the terminator of sRNA SgrS, we identified an sRNA gene () and three protein-coding genes (, , and ) that attenuate SgrS termination in Escherichia coli. Analyses of CyaR and YgjH, a putative tRNA binding protein, suggested that the CyaR activity was indirect and the effect of YgjH was moderate.

Regulation of Transcription Termination of Small RNAs and by Small RNAs: Molecular Mechanisms and Biological Functions.

Accurate and efficient transcription termination is an important step for cells to generate functional RNA transcripts. In bacteria, two mechanisms are responsible for terminating transcription: intrinsic (Rho-independent) termination and Rho-dependent termination. Growing examples suggest that neither type of transcription termination is static, but instead are highly dynamic and regulated.

Mechanism and physiological significance of autoregulation of the gene.

The RNA chaperone Hfq plays a critical role in sRNA-mediated gene regulation in enteric bacteria. The major role of Hfq is to stimulate base-pairing between sRNAs and target mRNAs by binding both RNAs through three RNA-binding surfaces. To understand the post-transcriptional network exerted by Hfq and its associated sRNAs, it is important to know how the cellular concentration of Hfq is regulated.

The effect of visual cues on performance in the ultimatum game in individuals with autism spectrum disorder.

The Ultimatum Game (UG) allows for the assessment of altruistic behavior as well as the perception of fairness. We examined the effects of visual social cues (gaze of others), factors associated with autism, and trust on UG performance in typical adults (TAs) and individuals with autism spectrum disorder (ASD). We hypothesized that individuals with ASD would be less affected by visual social cues than TAs.

Role of the terminator hairpin in the biogenesis of functional Hfq-binding sRNAs.

Rho-independent transcription terminators of the genes encoding bacterial Hfq-binding sRNAs possess a set of seven or more T residues at the 3' end, as noted in previous studies. Here, we have studied the role of the terminator hairpin in the biogenesis of sRNAs focusing on SgrS and RyhB in We constructed variant sRNA genes in which the GC-rich inverted repeat sequences are extended to stabilize the terminator hairpins. We demonstrate that the extension of the hairpin stem leads to generation of heterogeneous transcripts in which the poly(U) tail is shortened.

Inhibition of Phagocytic Killing of Escherichia coli in Drosophila Hemocytes by RNA Chaperone Hfq.

An RNA chaperone of Escherichia coli, called host factor required for phage Qβ RNA replication (Hfq), forms a complex with small noncoding RNAs to facilitate their binding to target mRNA for the alteration of translation efficiency and stability. Although the role of Hfq in the virulence and drug resistance of bacteria has been suggested, how this RNA chaperone controls the infectious state remains unknown. In the present study, we addressed this issue using Drosophila melanogaster as a host for bacterial infection.

Insights into transcription termination of Hfq-binding sRNAs of Escherichia coli and characterization of readthrough products.

The genes encoding Hfq-dependent sRNAs possess a typical Rho-independent transcription terminator. Here, we have studied the molecular events occurring at Rho-independent terminators of sRNA genes, focusing on two well-characterized Hfq-binding sRNAs, SgrS and RyhB. We constructed several hybrid genes in which the DNA sequence corresponding to a strong Rho-independent terminator was placed just downstream from the Rho-independent terminators of sRNA genes.

Photo-induced regulation of the chromatic adaptive gene expression by Anabaena sensory rhodopsin.

Rhodopsin molecules are photochemically reactive membrane-embedded proteins, with seven transmembrane α-helices, which bind the chromophore retinal (vitamin A aldehyde). They are roughly divided into two groups according to their basic functions: (i) ion transporters such as proton pumps, chloride pumps, and cation channels; and (ii) photo-sensors such as sensory rhodopsin from microbes and visual pigments from animals. Anabaena sensory rhodopsin (ASR), found in 2003 in the cyanobacterium Anabaena PCC7120, is categorized as a microbial sensory rhodopsin.

Detection of sRNA-mRNA interactions by electrophoretic mobility shift assay.

Electrophoretic mobility shift assay is a simple, rapid, and sensitive technique to analyze the RNA-RNA interaction. A (32)P-labeled RNA is incubated with another unlabeled RNA and subjected to electrophoresis on a native polyacrylamide gel. If two RNA molecules base pair stably, the movement of the probe RNA through the gel is retarded resulting in a characteristic band corresponding to the RNA duplex.

The functional Hfq-binding module of bacterial sRNAs consists of a double or single hairpin preceded by a U-rich sequence and followed by a 3' poly(U) tail.

Hfq-dependent sRNAs contain, at least, an mRNA base-pairing region, an Hfq-binding site, and a Rho-independent terminator. Recently, we found that the terminator poly(U) of Escherichia coli sRNAs is essential for Hfq binding and therefore for riboregulation. In this study, we tried to identify additional components within Hfq-binding sRNAs required for efficient Hfq binding by using SgrS as a model.

PolyU tail of rho-independent terminator of bacterial small RNAs is essential for Hfq action.

Major bacterial small RNAs (sRNAs) regulate the translation and stability of target mRNAs through base pairing with the help of the RNA chaperone Hfq. The Hfq-dependent sRNAs consist of three basic elements, mRNA base-pairing region, Hfq-binding site, and rho-independent terminator. Although the base-pairing region and the terminator are well documented in many sRNAs, the Hfq-binding site is less well-defined except that Hfq binds RNA with a preference for AU-rich sequences.

RNase E action at a distance: degradation of target mRNAs mediated by an Hfq-binding small RNA in bacteria.

A major class of bacterial small RNAs (sRNAs), along with RNA-binding protein Hfq and endoribonuclease RNase E, acts on target mRNAs through base-pairing, leading to translational repression and rapid degradation of the mRNAs. In this issue of Genes & Development, Prévost and colleagues (pp. 385-396) demonstrate by using the well-characterized sRNA RyhB that RNase E cleavage at sites distal from the pairing region triggers degradation of target mRNAs.

Hfq binding at RhlB-recognition region of RNase E is crucial for the rapid degradation of target mRNAs mediated by sRNAs in Escherichia coli.

An RNA chaperon Hfq along with Hfq-binding sRNAs stably binds to RNase E in Escherichia coli. The role of the Hfq-RNase E interaction is to recruit RNase E to target mRNAs of sRNAs resulting in the rapid degradation of the mRNA-sRNA hybrid. The C-terminal scaffold region of RNase E is responsible for the interaction with Hfq.

A minimal base-pairing region of a bacterial small RNA SgrS required for translational repression of ptsG mRNA.

Escherichia coli SgrS is an Hfq-binding small RNA that is induced under glucose-phosphate stress to cause translational repression and RNase E-dependent rapid degradation of ptsG mRNA encoding the major glucose transporter. A 31-nt-long stretch in the 3' region of SgrS is partially complementary to the translation initiation region of ptsG mRNA. We showed previously that SgrS alone causes translational repression when pre-annealed with ptsG mRNA by a high-temperature treatment in vitro.

The Plasmodium HU homolog, which binds the plastid DNA sequence-independent manner, is essential for the parasite's survival.

The nuclear genome of the human malaria parasite Plasmodium falciparum encodes a homolog of the bacterial HU protein (PfHU). In this study, we characterised PfHU's physiological function. PfHU, which is targeted exclusively to the parasite's plastid, bound its natural target--the plastid DNA--sequence-independently and complemented lack of HU in Escherichia coli.

Analyses of mRNA destabilization and translational inhibition mediated by Hfq-binding small RNAs.

A major class of bacterial small RNAs binds to an RNA chaperone Hfq and acts via imperfect base pairing to regulate the translation and stability of target mRNAs under specific physiological conditions. SgrS, an example for this class of small RNAs, is induced in response to the accumulation of glucose phosphates and downregulates the ptsG mRNA, which encodes the glucose transporter IICB(Glc) in Escherichia coli. SgrS forms a specific ribonucleoprotein complex with RNase E through Hfq.

RNA, but not protein partners, is directly responsible for translational silencing by a bacterial Hfq-binding small RNA.

SgrS is an Hfq-binding small RNA that is induced under glucose phosphate stress in Escherichia coli. It forms a specific ribo nucleo protein complex with Hfq and RNase E resulting in translational repression and rapid degradation of ptsG mRNA, encoding the glucose transporter. Here, we report translational silencing of ptsG mRNA in a defined in vitro system.

Cleavage of mRNAs and role of tmRNA system under amino acid starvation in Escherichia coli.

We have shown previously that ribosome stalling during translation caused by various reasons leads to mRNA cleavage, resulting in non-stop mRNAs that are eliminated in a tmRNA-dependent manner. Amino acid starvation is a physiological condition in which ribosome stalling is expected to occur more frequently. Here we demonstrate that mRNA cleavage is induced by amino acid starvation, resulting in accumulation of truncated mRNAs in cells lacking tmRNA.