The cspA mRNA is a thermosensor that modulates translation of the cold-shock protein CspA

RNA helicases and remodeling proteins

It is becoming increasingly clear that RNA molecules play a major role in all aspects of metabolism. The conformational state and stability of RNA are controlled by RNA remodeling proteins, which are ubiquitous motor proteins in the cell. Here, we review advances in our understanding of the structure and function of three major structural families of RNA remodeling proteins, the hexameric ring proteins, the processive monomeric RNA translocase/helicases, and the functionally diverse DEAD-box remodeling proteins. New studies have revealed molecular mechanisms for coupling between ATP hydrolysis and unwinding, the physical basis for regulatory control by cofactors, and novel functions for RNA remodeling proteins.

Understanding the transcriptome through RNA structure

RNA structure is crucial for gene regulation and function. In the past, transcriptomes have largely been parsed by primary sequences and expression levels, but it is now becoming feasible to annotate and compare transcriptomes based on RNA structure. In addition to computational prediction methods, the recent advent of experimental techniques to probe RNA structure by high-throughput sequencing has enabled genome-wide measurements of RNA structure and has provided the first picture of the structural organization of a eukaryotic transcriptome - the 'RNA structurome'. With additional advances in method refinement and interpretation, structural views of the transcriptome should help to identify and validate regulatory RNA motifs that are involved in diverse cellular processes and thereby increase understanding of RNA function.

New insights into riboswitch regulation mechanisms

Riboswitches are genetic elements located in non-coding regions of some messenger RNAs (mRNAs) that are present in all three domains of life. The binding of ligands to riboswitches induces conformational changes in the mRNA molecule, resulting in modulation of gene transcription, or RNA splicing, translation or stability. This mechanism of regulation is particularly widespread in bacteria and allows a direct response to various metabolic changes. A large number of riboswitches have been discovered in the last few years, suggesting the existence of a huge diversity of regulatory ligands and genetic mechanisms of regulation. This review focuses on recent discoveries in riboswitch regulatory mechanisms as well as current outstanding challenges.

Genome-wide identification of transcription start sites yields a novel thermosensing RNA and new cyclic AMP receptor protein-regulated genes in Escherichia coli

Intergenic regions often contain regulatory elements that control the expression of flanking genes. Using a deep-sequencing approach, we identified numerous new transcription start sites in Escherichia coli, yielding a new thermosensing regulatory RNA and seven genes previously unknown to be under the control of the global regulator CRP.

Rfam: Wikipedia, clans and the "decimal" release

The Rfam database aims to catalogue non-coding RNAs through the use of sequence alignments and statistical profile models known as covariance models. In this contribution, we discuss the pros and cons of using the online encyclopedia, Wikipedia, as a source of community-derived annotation. We discuss the addition of groupings of related RNA families into clans and new developments to the website. Rfam is available on the Web at http://rfam.sanger.ac.uk.

RNA folding in living cells

RNA folding is the most essential process underlying RNA function. While significant progress has been made in understanding the forces driving RNA folding in vitro, exploring the rules governing intracellular RNA structure formation is still in its infancy. The cellular environment hosts a great diversity of factors that potentially influence RNA folding in vivo. For example, the nature of transcription and translation is known to shape the folding landscape of RNA molecules. Trans-acting factors such as proteins, RNAs and metabolites, among others, are also able to modulate the structure and thus the fate of an RNA. Here we summarize the ongoing efforts to uncover how RNA folds in living cells.

RNA remodeling and gene regulation by cold shock proteins

One of the many important consequences that temperature down-shift has on cells is stabilization of secondary structures of RNAs. This stabilization has wide-spread effects, such as inhibition of expression of several genes due to termination of their transcription and inefficient RNA degradation that adversely affect cell growth at low temperature. Several cold shock proteins are produced to counteract these effects and thus allow cold acclimatization of the cell. The main RNA modulating cold shock proteins of E. coli can be broadly divided into two categories, (1) the CspA family proteins, which mainly affect the transcription and possibly translation at low temperature through their RNA chaperoning function and (2) RNA helicases and exoribonucleases that stimulate RNA degradation at low temperature through their RNA unwinding activity.

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.

Riboswitches as hormone receptors: hypothetical cytokinin-binding riboswitches in Arabidopsis thaliana

Background

Riboswitches are mRNA elements that change conformation when bound to small molecules. They are known to be key regulators of biosynthetic pathways in both prokaryotes and eukaryotes.

Presentation of the Hypothesis

The hypothesis presented here is that riboswitches function as receptors in hormone perception. We propose that riboswitches initiate or integrate signaling cascades upon binding to classic signaling molecules. The molecular interactions for ligand binding and gene expression control would be the same as for biosynthetic pathways, but the context and the cadre of ligands to consider is dramatically different. The hypothesis arose from the observation that a compound used to identify adenine binding RNA sequences is chemically similar to the classic plant hormone, or growth regulator, cytokinin. A general tenet of the hypothesis is that riboswitch-binding metabolites can be used to make predictions about chemically related signaling molecules. In fact, all cell permeable signaling compounds can be considered as potential riboswitch ligands. The hypothesis is plausible, as demonstrated by a cursory review of the transcriptome and genome of the model plant Arabidopsis thaliana for transcripts that i) contain an adenine aptamer motif, and ii) are also predicted to be cytokinin-regulated. Here, one gene, CRK10 (for Cysteine-rich Receptor-like Kinase 10, At4g23180), contains an adenine aptamer-related sequence and is down-regulated by cytokinin approximately three-fold in public gene expression data. To illustrate the hypothesis, implications of cytokinin-binding to the CRK10 mRNA are discussed.

Testing the hypothesis

At the broadest level, screening various cell permeable signaling molecules against random RNA libraries and comparing hits to sequence and gene expression data bases could determine how broadly the hypothesis applies. Specific cases, such as CRK10 presented here, will require experimental validation of direct ligand binding, altered RNA conformation, and effect on gene expression. Each case will be different depending on the signaling pathway and the physiology involved.

Implications of the hypothesis

This would be a very direct signal perception mechanism for regulating gene expression; rivaling animal steroid hormone receptors, which are frequently ligand dependent transcription initiation factors. Riboswitch-regulated responses could occur by modulating target RNA stability, translatability, and alternative splicing - all known expression platforms used in riboswitches. The specific illustration presented, CRK10, implies a new mechanism for the perception of cytokinin, a classic plant hormone. Experimental support for the hypothesis would add breadth to the growing list of important functions attributed to riboswitches.

Reviewers

This article was reviewed by Anthony Poole, Rob Knight, Mikhail Gelfand.

Ice as a protocellular medium for RNA replication

A crucial transition in the origin of life was the emergence of an informational polymer capable of self-replication and its compartmentalization within protocellular structures. We show that the physicochemical properties of ice, a simple medium widespread on a temperate early Earth, could have mediated this transition prior to the advent of membraneous protocells. Ice not only promotes the activity of an RNA polymerase ribozyme but also protects it from hydrolytic degradation, enabling the synthesis of exceptionally long replication products. Ice furthermore relieves the dependence of RNA replication on prebiotically implausible substrate concentrations, while providing quasicellular compartmentalization within the intricate microstructure of the eutectic phase. Eutectic ice phases had previously been shown to promote the de novo synthesis of nucleotide precursors, as well as the condensation of activated nucleotides into random RNA oligomers. Our results support a wider role for ice as a predisposed environment, promoting all the steps from prebiotic synthesis to the emergence of RNA self-replication and precellular Darwinian evolution.

Very rapid induction of a cold shock protein by temperature downshift in Thermus thermophilus

A rapid temperature downshift induces the expression of many proteins termed 'cold-induced' proteins. Although some of these proteins are known to participate in metabolism, transcription, translation and protein folding, processes that are affected by cold stress, it has not yet been identified which proteins sense the temperature downshift. Here we analyzed the mRNA expression profiles of genes induced immediately following a temperature downshift in Thermus thermophilus HB8. The cold shock protein gene ttcsp2 displayed the most rapid and drastic increase in mRNA. ttcsp2 mRNA was induced at 30s after temperature downshift, although ttCSP2 protein was first detected at 10 min. A temperature-dependent secondary structure was predicted to form in the 5'-untranslated region, including the Shine-Dalgarno sequence, of ttcsp2 mRNA. Stabilization of this secondary structure at 45 degrees C was assumed to prevent degradation of ttcsp2 mRNA and to slow translation. Thus, ttCSP2 is considered to act as a 'thermosensor' during temperature downshift through changes in its secondary structure.

Interactions of the RNA-binding protein Hfq with cspA mRNA, encoding the major cold shock protein

CspA, a small protein that is highly induced by cold shock, is encoded by a monocistronic mRNA of 428 nucleotides (nt) whose half-life and abundance are greatly increased following cold shock. We show here that in vitro cspA mRNA can bind multiple copies of Hfq, a hexameric Sm-like protein which promotes a variety of RNA-RNA interactions. Binding of the first Hfq hexamer occurs with an apparent K(d) (dissociation constant) of <40 nM; up to seven additional hexamers can bind sequentially at higher concentrations. Known ligands of Hfq, including the small regulatory RNA, RyhB, compete with cspA mRNA. Several experiments suggest that the first binding site to be occupied by Hfq is located at or near the 3' end of cspA mRNA. The consequences of limited Hfq binding in vitro include nearly total inhibition of RNase E cleavage at a site approximately 35 nt from the 3' end of the mRNA, stimulation of polyadenylation by poly(A) polymerase 1, and subsequent exonucleolytic degradation by polynucleotide phosphorylase. We propose that Hfq may play a facilitating role in the metabolism of cspA mRNA.

RNA-mediated regulation in bacteria: from natural to artificial systems

Bacteria use various means of RNA-mediated gene regulation. Regulatory RNAs include mRNA leaders that affect expression in cis or in trans, non-coding RNAs that trap regulatory proteins or interact with one or multiple target mRNAs, and RNAs that protect the bacteria against foreign and invasive DNA. The aim of this review is to outline the basic principles of bacterial RNA-mediated regulation, with a special focus on both cis-acting regulatory regions of mRNAs and antisense RNAs (asRNAs), and to give a brief overview of selected examples of RNA-based technology that have paved the way for biotechnological applications.

RNA switches out in the cold

In this issue of Molecular Cell, Giuliodori et al. (2010) describe a cold-induced genetic switch made of RNA. Could thermo-sensing RNAs be among the most common types of RNA genetic switches?