Switching the light on plant riboswitches

Department of Plant Sciences, Weizmann Institute of Science, PO Box 26, Rehovot 76100, Israel.
Trends in Plant Science (Impact Factor: 12.93). 10/2008; 13(10):526-33. DOI: 10.1016/j.tplants.2008.07.004
Source: PubMed


Riboswitches are natural RNA sensors that affect post-transcriptional processes via their capacity to bind small molecules. To date, these mRNA structures have been shown to regulate the biosynthesis of essential metabolites, including vitamins and amino acids. Although bacterial riboswitches are widespread and characterized, only a single eukaryotic, thiamin-pyrophosphate-binding riboswitch has recently been discovered to direct gene expression by regulating mRNA splicing in fungi, green algae and land plants. It is unclear how widespread riboswitches are and what additional roles they have in eukaryotes. When engineered in plants, riboswitches can function autonomously to modulate gene expression. These discoveries not only trigger novel findings regarding RNA switches in plants, but also spur the exploitation of riboswitches for monitoring metabolite concentrations in planta.

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Available from: Samuel Bocobza, Jun 16, 2014
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    • "Only the riboswitch class responding to TPP has been found in eukaryotes, although bacteria have numerous classes (Wachter, 2010; Breaker, 2011). In plants, control of functionally related genes without the involvement of additional proteins is thought to reduce response rates and energy costs associated with thiamine biosynthesis (Bocobza and Aharoni, 2008). This efficient form of regulation would seem particularly advantageous for eukaryotic phytoplankton in marine systems where B 1 and nutrients are often at low concentrations (Sanudo-Wilhelmy et al., 2012; Carini et al., 2014). "
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    ABSTRACT: Vitamin B1 (thiamine pyrophosphate, TPP) is essential to all life but scarce in ocean surface waters. In many bacteria and a few eukaryotic groups thiamine biosynthesis genes are controlled by metabolite-sensing mRNA-based gene regulators known as riboswitches. Using available genome sequences and transcriptomes generated from ecologically important marine phytoplankton, we identified 31 new eukaryotic riboswitches. These were found in alveolate, cryptophyte, haptophyte and rhizarian phytoplankton as well as taxa from two lineages previously known to have riboswitches (green algae and stramenopiles). The predicted secondary structures bear hallmarks of TPP-sensing riboswitches. Surprisingly, most of the identified riboswitches are affiliated with genes of unknown function, rather than characterized thiamine biosynthesis genes. Using qPCR and growth experiments involving two prasinophyte algae, we show that expression of these genes increases significantly under vitamin B1-deplete conditions relative to controls. Pathway analyses show that several algae harboring the uncharacterized genes lack one or more enzymes in the known TPP biosynthesis pathway. We demonstrate that one such alga, the major primary producer Emiliania huxleyi, grows on 4-amino-5-hydroxymethyl-2-methylpyrimidine (a thiamine precursor moiety) alone, although long thought dependent on exogenous sources of thiamine. Thus, overall, we have identified riboswitches in major eukaryotic lineages not known to undergo this form of gene regulation. In these phytoplankton groups, riboswitches are often affiliated with widespread thiamine-responsive genes with as yet uncertain roles in TPP pathways. Further, taxa with 'incomplete' TPP biosynthesis pathways do not necessarily require exogenous vitamin B1, making vitamin control of phytoplankton blooms more complex than the current paradigm suggests.The ISME Journal advance online publication, 29 August 2014; doi:10.1038/ismej.2014.146.
    Full-text · Article · Nov 2014 · The ISME Journal
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    • "The THI-box is a particularly intriguing example of a riboswitch, as it is found in a wide range of bacteria, archaea, and eukaryotes, and functions in a variety of contexts. The TPP riboswitch is the only known eukaryotic riboswitch identified to date (Bocobza and Aharoni, 2008). "
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    ABSTRACT: Motivation: Riboswitches are short sequences of messenger RNA that can change their structural conformation to regulate the expression of adjacent genes. Computational prediction of putative riboswitches can provide direction to molecular biologists studying riboswitch-mediated gene expression. Results: The Denison Riboswitch Detector (DRD) is a new computational tool with a Web interface that can quickly identify putative riboswitches in DNA sequences on the scale of bacterial genomes. Riboswitch descriptions are easily modifiable and new ones are easily created. The underlying algorithm converts the problem to a 'heaviest path' problem on a multipartite graph, which is then solved using efficient dynamic programming. We show that DRD can achieve ∼ 88-99% sensitivity and >99.99% specificity on 13 riboswitch families. Availability and implementation: DRD is available at
    Full-text · Article · Jul 2014 · Bioinformatics
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    • "Riboswitches that regulate pre - mRNA splicing have recently been identified in land plants , algae , and fungi where a small molecule regulates splicing by modulating RNA structure . In these organisms , AS of pre - mRNAs encoding proteins involved in thiamine metabolism is modulated by a metabolite ( thiamin - pyrophosphate [ TPP ] ) binding riboswitch ( Bocobza and Aharoni , 2008 ; Wachter , 2010 ) . Three TPP switches were identified in the fungus Neurospora crassa ( Cheah et al . "
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    ABSTRACT: Alternative splicing (AS) of precursor mRNAs (pre-mRNAs) from multiexon genes allows organisms to increase their coding potential and regulate gene expression through multiple mechanisms. Recent transcriptome-wide analysis of AS using RNA sequencing has revealed that AS is highly pervasive in plants. Pre-mRNAs from over 60% of intron-containing genes undergo AS to produce a vast repertoire of mRNA isoforms. The functions of most splice variants are unknown. However, emerging evidence indicates that splice variants increase the functional diversity of proteins. Furthermore, AS is coupled to transcript stability and translation through nonsense-mediated decay and microRNA-mediated gene regulation. Widespread changes in AS in response to developmental cues and stresses suggest a role for regulated splicing in plant development and stress responses. Here, we review recent progress in uncovering the extent and complexity of the AS landscape in plants, its regulation, and the roles of AS in gene regulation. The prevalence of AS in plants has raised many new questions that require additional studies. New tools based on recent technological advances are allowing genome-wide analysis of RNA elements in transcripts and of chromatin modifications that regulate AS. Application of these tools in plants will provide significant new insights into AS regulation and crosstalk between AS and other layers of gene regulation.
    Full-text · Article · Oct 2013 · The Plant Cell
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