Metal Ion-Mediated Nucleobase Recognition by the ZTP Riboswitch

Trausch, J.J.; Marcano-Velázquez, Joan G.; Matyjasik, M.M.; Batey, Robert T.

doi:10.1016/j.chembiol.2015.06.007

Cited by 47 publications

(62 citation statements)

References 62 publications

(95 reference statements)

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“…For example, representatives of the GEMM (Weinberg et al 2007) and pfl ) orphans have since been proven to respond, respectively, to c-di-GMP (Sudarsan et al 2008;Kulshina et al 2009;Smith et al 2009) and ZTP (Jones and Ferré-D'Amaré 2015;Kim et al 2015;Ren et al 2015;Trausch et al 2015). A general theme is that the natural ligands for these long-standing riboswitch candidates remained mysterious because either the ligands, the biological processes regulated by the ligands, or both, were obscure or even entirely unknown.…”

Section: Orphan and Other Riboswitch Candidatesmentioning

confidence: 99%

Riboswitch diversity and distribution

McCown

Corbino

Stav

et al. 2017

RNA

400

516

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Riboswitches are commonly used by bacteria to detect a variety of metabolites and ions to regulate gene expression. To date, nearly 40 different classes of riboswitches have been discovered, experimentally validated, and modeled at atomic resolution in complex with their cognate ligands. The research findings produced since the first riboswitch validation reports in 2002 reveal that these noncoding RNA domains exploit many different structural features to create binding pockets that are extremely selective for their target ligands. Some riboswitch classes are very common and are present in bacteria from nearly all lineages, whereas others are exceedingly rare and appear in only a few species whose DNA has been sequenced. Presented herein are the consensus sequences, structural models, and phylogenetic distributions for all validated riboswitch classes. Based on our findings, we predict that there are potentially many thousands of distinct bacterial riboswitch classes remaining to be discovered, but that the rarity of individual undiscovered classes will make it increasingly difficult to find additional examples of this RNA-based sensory and gene control mechanism.

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Section: Orphan and Other Riboswitch Candidatesmentioning

confidence: 99%

Riboswitch diversity and distribution

McCown

Corbino

Stav

et al. 2017

RNA

400

516

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“…A ZTP (5-amino 4-imidazole carboxamide riboside 5 ′ -triphosphate) riboswitch can up-regulate de novo purine synthesis in response to increased intracellular levels of ZTP or ZMP (Trausch et al 2015). The sequence of the ZTP riboswitch structure is of 60 nt:…”

Section: Puzzle 13: Ztp Riboswitchmentioning

confidence: 99%

RNA-Puzzles Round III: 3D RNA structure prediction of five riboswitches and one ribozyme

Miao

Adamiak

Antczak

et al. 2017

RNA

180

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RNA-Puzzles is a collective experiment in blind 3D RNA structure prediction. We report here a third round of RNA-Puzzles. Five puzzles, 4, 8, 12, 13, 14, all structures of riboswitch aptamers and puzzle 7, a ribozyme structure, are included in this round of the experiment. The riboswitch structures include biological binding sites for small molecules (S-adenosyl methionine, cyclic diadenosine monophosphate, 5-amino 4-imidazole carboxamide riboside 5 ′ -triphosphate, glutamine) and proteins (YbxF), and one set describes large conformational changes between ligand-free and ligand-bound states. The Varkud satellite ribozyme is the most recently solved structure of a known large ribozyme. All puzzles have established biological functions and require structural understanding to appreciate their molecular mechanisms. Through the use of fast-track experimental data, including multidimensional chemical mapping, and accurate prediction of RNA secondary structure, a large portion of the contacts in 3D have been predicted correctly leading to similar topologies for the top ranking predictions. Template-based and homologyderived predictions could predict structures to particularly high accuracies. However, achieving biological insights from de novo prediction of RNA 3D structures still depends on the size and complexity of the RNA. Blind computational predictions of RNA structures already appear to provide useful structural information in many cases. Similar to the previous RNA-Puzzles Round II experiment, the prediction of non-Watson-Crick interactions and the observed high atomic clash scores reveal a notable need for an algorithm of improvement. All prediction models and assessment results are available at http://ahsoka.ustrasbg.fr/rnapuzzles/.

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“…In the September 2015 issue of Nature Structural & Molecular Biology, Jones and Ferré-D' Amaré 5 describe the structure of the ZTP riboswitch from Fusobacterium ulcerans bound to a ZMP ligand, solved by X-ray crystallography to a resolution of 2.8 Å. Two other structures of this complex from different bacterial species have also been presented, by the Batey laboratory (1.8 Å) 6 and the Patel laboratory (2.9 Å) 7 . These three structures and associated analysis together provide exciting new insight into the strategies available to riboswitches to bind their ligands.…”

Section: Terminator Ztpmentioning

confidence: 95%

“…In conclusion, structural studies such as these [5][6][7] continue to teach important lessons about the diverse ways in which RNA can recognize small-molecule ligands, raising new riboswitch is formed before ligand binding, but this structure is likely to be unstable and more conformationally dynamic, and the ligandbinding pocket may be flexible. If so, then these structures suggest that ligand-coupled magnesium positioning may be part of the mechanism by which ligand recognition 'locks down' a loosely formed binding-site structure to stabilize a specific riboswitch conformation.…”

Section: Terminator Ztpmentioning

confidence: 99%