Sensing Small Molecules by Nascent RNA

Abstract

Thiamin and riboflavin are precursors of essential coenzymes-thiamin pyrophosphate (TPP) and flavin mononucleotide (FMN)/flavin adenine dinucleotide (FAD), respectively. In Bacillus spp, genes responsible for thiamin and riboflavin biosynthesis are organized in tightly controllable operons. Here, we demonstrate that the feedback regulation of riboflavin and thiamin genes relies on a novel transcription attenuation mechanism. A unique feature of this mechanism is the formation of specific complexes between a conserved leader region of the cognate RNA and FMN or TPP. In each case, the complex allows the termination hairpin to form and interrupt transcription prematurely. Thus, sensing small molecules by nascent RNA controls transcription elongation of riboflavin and thiamin operons and possibly other bacterial operons as well.

The L box regulon: Lysine sensing by leader RNAs of bacterial lysine biosynthesis genes

“…Binding of uncharged tRNA and small molecules such as thiamine pyrophosphate, flavin mononucleotide, SAM, and guanine has been shown to control premature transcription termination (12,(15)(16)(17)(18)(19)(20); it has been suggested that riboflavin and thiamine biosynthesis genes in Gram-negative bacteria are instead regulated at the level of translation initiation (17)(18)(19). In this study, we find that the B. subtilis lysC gene is regulated by direct interaction of lysine, the final product of the lysine biosynthesis pathway, with the lysC leader RNA.…”

“…The S box regulatory system also involves transcription termination, but in this case the regulated genes respond in concert to a single effector, Sadenosylmethionine (SAM), which binds to the leader RNA and promotes a structural rearrangement that stabilizes the terminator helix (14)(15)(16). Similarly, thiamine pyrophosphate, flavin mononucleotide, and guanine regulate thiamine, riboflavin, and purine biosynthesis genes, respectively, via direct interaction with the leader RNA (17)(18)(19)(20). There are also many systems in which modulation of the leader RNA structure is determined by binding of a regulatory protein that responds to the availability of the effector molecule.…”

The riboswitch-mediated control of sulfur metabolism in bacteria

“…1). Recently, three regulons responsible for vitamin biosynthesis have been shown to use flavinmononucleotide, thiamin pyrophosphate (TPP), and adenosyl-cobalamin to directly bind their cognate leader RNAs, changing their structures and functions (2)(3)(4)(5). Such leader RNA aptamers were called riboswitches to reflect their unique ability to switch between two conformations in response to binding of a small molecule without the help of proteins (3,5,6).…”

“…Recently, three regulons responsible for vitamin biosynthesis have been shown to use flavinmononucleotide, thiamin pyrophosphate (TPP), and adenosyl-cobalamin to directly bind their cognate leader RNAs, changing their structures and functions (2)(3)(4)(5). Such leader RNA aptamers were called riboswitches to reflect their unique ability to switch between two conformations in response to binding of a small molecule without the help of proteins (3,5,6). The evolutionarily conserved sequences encoding vitamin-sensing riboswitches have been found in the genomes of many Gram-positive and Gram-negative bacteria (7)(8)(9)(10), and also in some archaea (10), fungi, and plant species (A.S.M.…”

“…The striking similarity in overall organization of the S-box leader to the recently characterized thiamin (thi-box) and riboflavin (rfn-box) riboswitches (4,5) and the apparent absence of a protein candidate for its regulation prompted us to test whether the S-box leader RNA also functions as a riboswitch. Using a minimal reconstituted transcription system lacking any additional factors, we demonstrate that SAM, but not other metabolites, directly binds S-box RNA to stabilize its antiantitermination structure, thus causing termination of the leader transcript.…”