In bacteria, many genes involved in the biosynthesis of cofactors such as thiamine pyrophosphate (TPP) are regulated by riboswitches, regions in the 5 end of mRNAs to which the cofactor binds, thereby affecting translation and/or transcription. TPP riboswitches have now been identified in fungi, in which they alter mRNA splicing. Here, we show that addition of thiamine to cultures of the model green alga Chlamydomonas reinhardtii alters splicing of transcripts for the THI4 and THIC genes, encoding the first enzymes of the thiazole and pyrimidine branches of thiamine biosynthesis, respectively, concomitant with an increase in intracellular thiamine and TPP levels. Comparison with Volvox carteri, a related alga, revealed highly conserved regions within introns of these genes. Inspection of the sequences identified TPP riboswitch motifs, and RNA transcribed from the regions binds TPP in vitro. The THI4 riboswitch, but not the promoter region, was found to be necessary and sufficient for thiamine to repress expression of a luciferase-encoding reporter construct in vivo. The pyr1 mutant of C. reinhardtii, which is resistant to the thiamine analogue pyrithiamine, has a mutation in the THI4 riboswitch that prevents the THI4 gene from being repressed by TPP. By the use of these riboswitches, thiamine biosynthesis in C. reinhardtii can be effectively regulated at physiological concentrations of the vitamin.regulation of metabolism ͉ Chlamydomonas reinhardtii ͉ luciferase reporter gene ͉ alternative splicing of mRNA T hiamine (vitamin B 1 ) is synthesized via a branched pathway ( Fig. 1) from the condensation of a thiazole and a pyrimidine moiety to make thiamine monophosphate (TMP). This is then phosphorylated to make thiamine pyrophosphate (TPP), the active cofactor, either directly in prokaryotes, or by dephosphorylation followed by pyrophosphorylation in eukaryotes. Like many cofactors, the level of TPP within the cell is low, the majority of it being associated with its cognate enzymes, which are part of the central respiratory pathways. The biosynthetic pathway is carefully regulated to ensure that TPP production meets cellular demand, usually by regulation of gene expression for one or more of the enzymes, and in bacteria and fungi exogenous thiamine severely represses gene expression (1, 2).In bacteria, an important TPP regulatory mechanism is mediated via riboswitches in one or more of the thiamine biosynthesis genes. Riboswitches are short sequences in mRNAs that bind metabolites directly, without the need for intermediary proteins. Binding of the ligand alters the secondary structure of the RNA, thereby regulating expression of the gene, typically by premature transcription termination and/or initiation of translation (3, 4). Until recently, most of the work on riboswitches was carried out in prokaryotic systems. Now, TPP riboswitches have been found in the 5Ј UTR of genes for thiamine biosynthetic enzymes in the fungi Aspergillus oryzae and Neurospora crassa, where they appear to operate by causing alternative...