Riboswitch-dependent gene regulation and its evolution in the plant kingdom

Abstract

Riboswitches are natural RNA sensors that affect gene control via their capacity to bind small molecules. Their prevalence in higher eukaryotes is unclear. We discovered a post-transcriptional mechanism in plants that uses a riboswitch to control a metabolic feedback loop through differential processing of the precursor RNA 3 terminus. When cellular thiamin pyrophosphate (TPP) levels rise, metabolite sensing by the riboswitch located in TPP biosynthesis genes directs formation of an unstable splicing product, and consequently TPP levels drop. When transformed in plants, engineered TPP riboswitches can act autonomously to modulate gene expression. In an evolutionary perspective, a TPP riboswitch is also present in ancient plant taxa, suggesting that this mechanism is active since vascular plants emerged 400 million years ago.Supplemental material is available at http://www.genesdev.org.Received June 5, 2007; revised version accepted September 24, 2007. Riboswitches are regions in mRNA that act as metabolite sensors. These selectively bind small molecule targets such as vitamins, amino acids, and nucleotides through a conserved sensor domain. Upon substrate binding, the conformation of a variable "expression platform" coupled to the sensor domain is changed, and this can affect different modes of gene control including transcription termination, translation initiation, or mRNA processing (Mandal and Breaker 2004;Nudler and Mironov 2004;Coppins et al. 2007). Notably, riboswitches exert their functions without the need for protein cofactors Winkler et al. 2002). In most cases, they act in feedback regulation mechanisms; once the level of an end product in a metabolic pathway rises, riboswitch binding occurs, triggering a repression of gene expression in the same pathway. The substrate specificity of riboswitches is extremely high, allowing them to perform their activity amid the presence of numerous related compounds (Sudarsan et al. 2005). In prokaryotes, genetic control mediated by riboswitches is a prevalent phenomenon, and the dozen riboswitches identified to date regulate >3% of all bacterial genes (Nudler 2006).Thiamin pyrophosphate (TPP) is a coenzyme derived from vitamin B1 (thiamin) that is synthesized by bacteria, fungi, and plants, and serves as a dietary requirement for humans and other animals. It is an obligatory cofactor that plays an important role in amino acid and carbohydrate metabolism; thus, fine control of its levels is essential for the viability of all living cells. TPP-binding riboswitches, first identified in Bacillus subtilis and Escherichia coli Winkler et al. 2002), exist in the genomes of species belonging to most bacterial phyla (Rodionov et al. 2002). Binding of TPP by the riboswitch down-regulates expression of thiamin biosynthesis genes by inducing either the formation of a transcription terminator hairpin or the formation of a Shine-Dalgarno sequester hairpin Rodionov et al. 2002;Winkler et al. 2002). Much less is known about riboswitch-mediated gene control in eukaryotic organ...

Complexity of the Alternative Splicing Landscape in Plants

“…This work opens new avenues for the conditional expression of multiple genes at the splicing level by incorporating the same suicide exon into the transgenes. In another case, addition of the TPP riboswitch in THIC to a reporter construct resulted in metabolite-dependent regulation of reporter gene expression, with decreased expression under high TPP levels (Bocobza et al, 2007), suggesting a potential use of riboswitches for conditional expression of transgenes. Expression of a bacterial RNA chaperone that modulates RNA structure has also been shown to confer abiotic stress tolerance in maize under field conditions and increase yield (Castiglioni et al, 2008).…”

“…The location of a TPP binding aptamer within the pre-mRNA can be in the 59UTR, 39UTR, or coding region (Wachter, 2010). In Arabidopsis and other plants, conserved TPP riboswitches in the 39UTR of the THIAMINE C SYNTHASE (THIC) gene regulate thiamine metabolism (Bocobza et al, 2007;Wachter et al, 2007). The binding of TPP to an aptamer changes the splicing pattern of pre-mRNA by masking a splice site resulting in a splice variant with a retained intron, which is less stable.…”

Thermodynamic analysis of ligand binding and ligand binding-induced tertiary structure formation by the thiamine pyrophosphate riboswitch

“…At present, it is the riboswitch with the broadest known phylogenetic distribution (Kubodera et al 2003;Sudarsan et al 2003;Bocobza et al 2007;Cheah et al 2007) and has been shown to be a target of an antibacterial compound (Sudarsan et al 2005). Crystal structures have been reported of the aptamer domains of the TPP-responsive riboswitches thiM from Escherichia coli (Edwards and Ferré-D'Amaré 2006;Serganov et al 2006) and thiC from Arabidopsis thaliana (Thore et al 2006), both in complex with TPP.…”

Genome-Wide Characterization of the HD-ZIP IV Transcription Factor Family in Maize: Preferential Expression in the Epidermis

“…In the case of exon 8, the new intron is positioned just downstream of the coding region in the 3# UTR. The splicing of this intron may play a role in transcript stability, as suggested by the precedent of the Arabidopsis THIAMINE C SYNTHASE A gene (Bocobza et al, 2007).…”