New RNA motifs suggest an expanded scope for riboswitches in bacterial genetic control

Abstract

The expression of certain genes involved in fundamental metabolism is regulated by metabolite-binding ''riboswitch'' elements embedded within their corresponding mRNAs. We have identified at least six additional elements within the Bacillus subtilis genome that exhibit characteristics of riboswitch function (glmS, gcvT, ydaO͞yuaA, ykkC͞yxkD, ykoK, and yybP͞ykoY). These motifs exhibit extensive sequence and secondary-structure conservation among many bacterial species and occur upstream of related genes. The element located upstream of the glmS gene in Grampositive organisms functions as a metabolite-dependent ribozyme that responds to glucosamine-6-phosphate. Other motifs form complex folded structures when transcribed as RNA molecules and carry intrinsic terminator structures. These findings indicate that riboswitches serve as a major genetic regulatory mechanism for the control of metabolic genes in many microbial species. R iboswitches are highly structured domains within mRNAs that precisely sense metabolites and control gene expression (1). These RNA elements are capable of binding to a variety of target compounds and subsequently modulating transcription and translation with performance characteristics that are similar to those of protein genetic factors. Typically, each riboswitch is composed of a conserved metabolite-binding domain (aptamer) located upstream of a variable sequence region (expression platform) that dictates the level of gene expression. Allosteric changes brought about by metabolite binding to the aptamer are harnessed by the expression platform to modulate the expression of the adjacent gene or operon. Riboswitches are versatile genetic control elements. In some instances, both transcription and translation control are used by the same aptamer class in the same prokaryotic organism (e.g., see ref.2). Evidence also shows that riboswitches can use mRNA-processing events to modulate gene expression (3, 4).The various metabolites that are detected by known riboswitches are of fundamental importance to living systems (5). On this basis, we have speculated that modern riboswitches might be the remaining representatives of an ancient metabolitemonitoring system that was present in the RNA World (5-9). The wide distribution of some riboswitch classes among microbes (e.g., see refs. 5 and 9-14) and the presence of metabolitebinding RNA domains in eukaryotes (4) support this hypothesis. Each of the seven classes of riboswitches reported (1, 5) was examined for metabolite-binding function because published genetic evidence showed that these elements were important for genetic control. Because the regulation of many metabolism genes has not been characterized in detail, it is possible that numerous other metabolite-binding RNA motifs exist in nature.The riboswitches known to be present in prokaryotes are typically located in noncoding or intergenic regions (IGRs). Therefore, the examination of unusually long IGRs for indications of conserved sequence and secondary-structure elements should yield new...

Confirmation of a second natural preQ1 aptamer class in Streptococcaceae bacteria

“…The aptamer of each riboswitch class usually is well conserved due to constraints imposed by the ligand binding site. This conservation of aptamer sequences and structures makes bioinformatics analyses of genomic sequences an effective tool for identifying new riboswitch candidates (e.g., Rodionov et al 2002Rodionov et al , 2003Barrick et al 2004;AbreuGoodger and Merino 2005;Corbino et al 2005;Weinberg et al 2007). In contrast, expression platforms may vary considerably and utilize diverse genetic regulatory mechanisms such as transcription termination and translation inhibition (Mandal and Breaker 2004b).…”

“…We have used bioinformatics searches to discover numerous riboswitches and riboswitch candidates (e.g., Barrick et al 2004;Corbino et al 2005). Most recently, we reported the discovery of 22 RNA motifs using the CMfinder pipeline ) that was applied to search several hundred bacterial genomes ).…”

Structural features of metabolite-sensing riboswitches

“…As an example of a potential non-metabolite ligand, levels of intracellular metal ions have been proposed to regulate the expression of the Salmonella enterica mgtA gene via an RNA element located within its 5′ UTR [63]. Additionally, a broadly distributed orphan riboswitch class appears to regulate the expression of an MgtE-family magnesium transporter (ykoK) in Bacillus subtilis as well as many genes responsible for metal uptake in other organisms [64,65], allowing one to wonder whether multiple classes of RNAs could function as metal ion sensors. The utilization of better bioinformatic search algorithms and genetic screens could uncover additional examples of structural noncoding RNAs, including new riboswitches.…”

Evolutionary patterns of non-coding RNAs

“…The search for additional elements is ongoing, e.g. [20,242]. The program Riboswitch finder [25] utilizes consensus motifs of known elements to detect new prokaryotes riboswitches.…”