Category Ranking
98%
Total Visits
921
Avg Visit Duration
2 minutes
Citations
20
Article Abstract
The SAM-I riboswitch is a cis-acting element of genetic control found in bacterial mRNAs that specifically binds S-adenosylmethionine (SAM). We previously determined the 2.9-A X-ray crystal structure of the effector-binding domain of this RNA element, revealing details of RNA-ligand recognition. To improve this structure, variations were made to the RNA sequence to alter lattice contacts, resulting in a 0.5-A improvement in crystallographic resolution and allowing for a more accurate refinement of the crystallographic model. The basis for SAM specificity was addressed by a structural analysis of the RNA complexed to S-adenosylhomocysteine (SAH) and sinefungin and by measuring the affinity of SAM and SAH for a series of mutants using isothermal titration calorimetry. These data illustrate the importance of two universally conserved base pairs in the RNA that form electrostatic interactions with the positively charged sulfonium group of SAM, thereby providing a basis for discrimination between SAM and SAH.
Download full-text PDF |
Source |
|---|---|
| http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2822714 | PMC |
| http://dx.doi.org/10.1016/j.jmb.2009.12.007 | DOI Listing |
Publication Analysis
Top Keywords
Similar Publications
Template switching enables chemical probing of native RNA structures.
RNA
December 2024
Department of Biological Chemistry, Center for RNA Biomedicine, Rogel Cancer Center, University of Michigan Medical School, Ann Arbor, Michigan 48109, USA
RNAs are often studied in nonnative sequence contexts to facilitate structural studies. However, seemingly innocuous changes to an RNA sequence may perturb the native structure and generate inaccurate or ambiguous structural models. To facilitate the investigation of native RNA secondary structure by selective 2' hydroxyl acylation analyzed by primer extension (SHAPE), we engineered an approach that couples minimal enzymatic steps to RNA chemical probing and mutational profiling (MaP) reverse transcription (RT) methods-a process we call template switching and mutational profiling (Switch-MaP).
View Article and Find Full Text PDFFunctional Validation of SAM Riboswitch Element A from .
Biochemistry
October 2024
Department of Chemistry, University of Michigan, Ann Arbor, Michigan 48109, United States.
SreA is one of seven candidate -adenosyl methionine (SAM) class I riboswitches identified in , a saprophyte and opportunistic foodborne pathogen. SreA precedes genes encoding a methionine ATP-binding cassette (ABC) transporter, which imports methionine and is presumed to regulate transcription of its downstream genes in a SAM-dependent manner. The proposed role of SreA in controlling the transcription of genes encoding an ABC transporter complex may have important implications for how the bacteria senses and responds to the availability of the metabolite SAM in the diverse environments in which persists.
View Article and Find Full Text PDFGenerative Modeling of RNA Sequence Families with Restricted Boltzmann Machines.
Methods Mol Biol
September 2024
Laboratory of Physics of the Ecole Normale Supérieure, CNRS UMR 8023 & PSL Research, Paris, France.
In this chapter, we discuss the potential application of Restricted Boltzmann machines (RBM) to model sequence families of structured RNA molecules. RBMs are a simple two-layer machine learning model able to capture intricate sequence dependencies induced by secondary and tertiary structure, as well as mechanisms of structural flexibility, resulting in a model that can be successfully used for the design of allosteric RNA such as riboswitches. They have recently been experimentally validated as generative models for the SAM-I riboswitch aptamer domain sequence family.
View Article and Find Full Text PDFA sensitive and scalable fluorescence anisotropy single stranded RNA targeting approach for monitoring riboswitch conformational states.
Nucleic Acids Res
April 2024
Department of Chemistry, Faculty of Science, McGill University, Montreal, QC H3A 0B8, Canada.
The capacity of riboswitches to undergo conformational changes in response to binding their native ligands is closely tied to their functional roles and is an attractive target for antimicrobial drug design. Here, we established a probe-based fluorescence anisotropy assay to monitor riboswitch conformational switching with high sensitivity and throughput. Using the Bacillus subtillis yitJ S-Box (SAM-I), Fusobacterium nucleatum impX RFN element of (FMN) and class-I cyclic-di-GMP from Vibrio cholerae riboswitches as model systems, we developed short fluorescent DNA probes that specifically recognize either ligand-free or -bound riboswitch conformational states.
View Article and Find Full Text PDFA spermidine riboswitch class in bacteria exploits a close variant of an aptamer for the enzyme cofactor S-adenosylmethionine.
Cell Rep
December 2023
Department of Molecular, Cellular and Developmental Biology, Yale University, New Haven, CT 06520-8103, USA; Howard Hughes Medical Institute, Yale University, New Haven, CT 06520-8103, USA; Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT 06520-8103, USA. Electroni
Natural polyamines such as spermidine and spermine cations have characteristics that make them highly likely to be sensed by riboswitches, such as their general affinity to polyanionic RNA and their broad contributions to cell physiology. Despite previous claims that polyamine riboswitches exist, evidence of their biological functions has remained unconvincing. Here, we report that rare variants of bacterial S-adenosylmethionine-I (SAM-I) riboswitches reject SAM and have adapted to selectively sense spermidine.
View Article and Find Full Text PDF