ArticleGenome biology2005
Evidence for a second class of S-adenosylmethionine riboswitches and other regulatory RNA motifs in alpha-proteobacteria.
Article in Genome biology, 2005. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 127 papers.
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Who cites it
127 citing papers in PubMed, 236 citations in OpenAlex.
- A cooperative effect of ligands, MgThe Journal of biological chemistry · 2026Article
- Structure and catalytic activity of the SAM-utilizing ribozyme SAMURI.Nature chemical biology · 2026Article
- Predicted bacterial uRBSs reveal translational coupling and ribosome-mediated RBS occlusion as gene-controlling mechanisms.microLife · 2026Article
- Evidence that ribosomal protein bS21 is a component of the OLE ribonucleoprotein complex.RNA biology · 2025Article
- Implications for OLE RNA as a natural integral membrane RNA.RNA (New York, N.Y.) · 2025Review
- Modeling riboswitches: The impact of concentration of MgBiophysical journal · 2025Article
- Linker-Mediated Inactivation of the SAM-II Domain in the Tandem SAM-II/SAM-V Riboswitch.International journal of molecular sciences · 2024Article
- The Role of General Acid Catalysis in the Mechanism of an Alkyl Transferase Ribozyme.ACS catalysis · 2024Article
- The current riboswitch landscape inMicrobiology (Reading, England) · 2024Review
- Article
- A spermidine riboswitch class in bacteria exploits a close variant of an aptamer for the enzyme cofactor S-adenosylmethionine.Cell reports · 2023Article
- Linking folding dynamics and function of SAM/SAH riboswitches at the single molecule level.Nucleic acids research · 2023Article
- Magnesium ions mediate ligand binding and conformational transition of the SAM/SAH riboswitch.Communications biology · 2023Article
- Magnesium ions mediate ligand binding and conformational transition of the SAM/SAH riboswitch.bioRxiv : the preprint server for biology · 2023Article
- Discovering riboswitches: the past and the future.Trends in biochemical sciences · 2023Review
- Variants of the guanine riboswitch class exhibit altered ligand specificities for xanthine, guanine, or 2'-deoxyguanosine.Proceedings of the National Academy of Sciences of the United States of America · 2022Article
- Architectures and complex functions of tandem riboswitches.RNA biology · 2022Article
- Incoherent dual regulation by a SAM-II riboswitch controlling translation at a distance.RNA biology · 2022Article
- Comprehensive discovery of novel structured noncoding RNAs in 26 bacterial genomes.RNA biology · 2021Article
- Riboswitch Mechanisms: New Tricks for an Old Dog.Biochemistry. Biokhimiia · 2021Review
67 more citing papers are in PubMed but not listed here.
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Authors and funding
9 authors at 2 institutions in 1 country.
Funding
Abstract
backgroundRiboswitches are RNA elements in the 5' untranslated leaders of bacterial mRNAs that directly sense the levels of specific metabolites with a structurally conserved aptamer domain to regulate expression of downstream genes. Riboswitches are most common in the genomes of low GC Gram-positive bacteria (for example, Bacillus subtilis contains examples of all known riboswitches), and some riboswitch classes seem to be restricted to this group.
resultsWe used comparative sequence analysis and structural probing to identify five RNA elements (serC, speF, suhB, ybhL, and metA) that reside in the intergenic regions of Agrobacterium tumefaciens and many other alpha-proteobacteria. One of these, the metA motif, is found upstream of methionine biosynthesis genes and binds S-adenosylmethionine (SAM). This natural aptamer most likely functions as a SAM riboswitch (SAM-II) with a consensus sequence and structure that is distinct from the class of SAM riboswitches (SAM-I) predominantly found in Gram-positive bacteria. The minimal functional SAM-II aptamer consists of fewer than 70 nucleotides, which form a single stem and a pseudoknot. Despite its simple architecture and lower affinity for SAM, the SAM-II aptamer strongly discriminates against related compounds.
conclusionSAM-II is the only metabolite-binding riboswitch class identified so far that is not found in Gram-positive bacteria, and its existence demonstrates that biological systems can use multiple RNA structures to sense a single chemical compound. The two SAM riboswitches might be 'RNA World' relics that were selectively retained in certain bacterial lineages or new motifs that have emerged since the divergence of the major bacterial groups.
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Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.