Abstract
Riboswitches are non-coding RNA molecules that regulate gene expression by binding to specific ligands. They are primarily found in bacteria. However, one riboswitch type, the thiamin pyrophosphate (TPP) riboswitch, has also been described in some plants, marine protists and fungi. We find that riboswitches are widespread in the budding yeasts (Saccharomycotina), and they are most common in homologs of DUR31, originally described as a spermidine transporter. We show that DUR31 (an ortholog of N. crassa gene NCU01977) encodes a thiamin transporter in Candida species. Using an RFP/riboswitch expression system, we show that the functional elements of the riboswitch are contained within the native intron of DUR31 from Candida parapsilosis, and that the riboswitch regulates splicing in a thiamin-dependent manner when RFP is constitutively expressed. The DUR31 gene has been lost from Saccharomyces, and may have been displaced by an alternative thiamin transporter. TPP riboswitches are also present in other putative transporters in yeasts and filamentous fungi. However, they are rare in thiamin biosynthesis genes THI4 and THI5 in the Saccharomycotina, and have been lost from all genes in the sequenced species in the family Saccharomycetaceae, including S. cerevisiae.
Highlights
Riboswitches are RNA regulatory elements that are located within messenger RNA, and control gene expression [1]
Expression of thiamin biosynthesis genes and of thiamin transporters is strictly regulated in response to the presence of thiamin
Expression of thiamin biosynthesis genes is regulated by thiamin pyrophosphate (TPP) riboswitches, RNA regulatory elements that are located within messenger RNA
Summary
Riboswitches are RNA regulatory elements that are located within messenger RNA, and control gene expression [1]. Binding of the ligand or changing the temperature or pH disrupts the secondary structure of the riboswitch. Bacterial riboswitches are usually located in 5’ UTR regions, and control initiation of translation or premature termination of transcription. In eukaryotes only one type of riboswitch has been identified, which binds thiamin pyrophosphate (TPP, a derivative of thiamin). TPP riboswitches regulate expression of thiamin synthesis genes in algae and marine phytoplankton [7], plants [8, 9] and filamentous fungi [10, 11], and probably in oomycetes [12]. Eukaryotic riboswitches are often located within introns, and they function by regulating splicing
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