A variant riboswitch aptamer class for S-adenosylmethionine common in marine bacteria

Abstract

Riboswitches that sense S-adenosylmethionine (SAM) are widely distributed throughout a variety of bacterial lineages. Four classes of SAM-binding riboswitches have been reported to date, constituting the most diverse collection of riboswitch classes that sense the same compound. Three of these classes, termed SAM-I, SAM-II, and SAM-III represent unique structures that form distinct binding pockets for the ligand. SAM-IV riboswitches carry different conserved sequence and structural features compared to other SAM riboswitches, but nucleotides and substructures corresponding to the ligand binding pocket are identical to SAM-I aptamers. In this article, we describe a fifth class of SAM binding aptamer, which we have termed SAM-V. SAM-V was discovered by analyzing GC-rich intergenic regions preceding metabolic genes in the marine a-proteobacterium ''Candidatus Pelagibacter ubique.'' Although the motif is nearly unrepresented in cultured bacteria whose genomes have been completely sequenced, SAM-V is prevalent in marine metagenomic sequences. The consensus sequence and structure of SAM-V show some similarities to that of the SAM-II riboswitch, and it is likely that the two aptamers form similar ligand binding pockets. In addition, we identified numerous examples of a tandem SAM-II/SAM-V aptamer architecture. In this arrangement, the SAM-II aptamer is always positioned 59 of the SAM-V aptamer and the SAM-II aptamer is followed by a predicted intrinsic transcription terminator stem. The SAM-V aptamer, however, appears to use a ribosome binding site occlusion mechanism for genetic regulation. This tandem riboswitch arrangement exhibits an architecture that can potentially control both the transcriptional and translational stages of gene expression.

Tuning a riboswitch response through structural extension of a pseudoknot

“…Although the relatively small size of the preQ 1 -II, SAM-II, and SAH riboswitches (∼50 nt) may significantly reduce the complexity of the folding landscape, the present investigations demonstrating the impact of the P4 stem-loop element insertion on the kinetic and structural features of the preQ 1 -II riboswitch argue that substantial challenges remain toward gaining a complete understanding of even the most compact aptamer folds. Larger (100-to 200-nt) riboswitches such as SAM-I and B 12 riboswitches, and the glmS riboswitch-ribozyme also contain pseudoknots as integral structural components (Table S4). In the case of the SAM-I riboswitch, a helical extension (P4) is located immediately 3′ to the pseudoknot and its deletion reduces ligand binding affinity (43).…”

“…In the simplest form, the SD sequence overlaps with the metabolite-sensitive aptamer domain at its downstream end. Representative examples include the S-adenosylmethionine class II (SAM-II) (10) and the S-adenosylhomocysteine (SAH) riboswitches (11,12), as well as prequeuosine class I (preQ 1 -I) and II (preQ 1 -II) riboswitches (13,14). The secondary structures of these four short RNA families contain a pseudoknot fold that is central to their gene regulation capacity.…”

Downward causation by information control in micro-organisms

“…on May 11, 2018 http://rsfs.royalsocietypublishing.org/ Downloaded from different bacteria species [44,61] (figure 3e). These examples are far from being isolated cases and would require a thorough investigation.…”

An expanded collection and refined consensus model of glmS ribozymes

“…We utilized a bioinformatics search strategy that has previously yielded different types of riboswitch or ribozyme structural variants (Barrick et al 2005;Kim et al 2007;Weinberg et al 2008;Weinberg and Breaker 2011;Perreault et al 2011). We also used a different search strategy that has previously uncovered several new noncoding RNAs (ncRNAs) as well as a new class of S-adenosylmethionine-binding riboswitches Poiata et al 2009). Our searches revealed additional consensus glmS ribozymes that were previously unknown, glmS ribozymes with novel genetic associations, and new types of structural variants.…”