Single-molecule FRET reveals the energy landscape of the full-length SAM-I riboswitch

S-adenosyl-L-methionine (SAM) ligand binding induces major structural changes in SAM-I riboswitches, through which gene expression is regulated via transcription termination. Little is known about the conformations and motions governing the function of the full-length Bacillus subtilis yitJ SAM-I riboswitch. Therefore, we have explored its conformational energy landscape as a function of Mg^2+ and SAM ligand concentrations using single-molecule Förster resonance energy transfer (smFRET) microscopy and hidden Markov modeling analysis. We resolved four conformational states both in the presence and the absence of SAM and determined their Mg^2+-dependent fractional populations and conformational dynamics, including state lifetimes, interconversion rate coefficients and equilibration timescales. Riboswitches with terminator and antiterminator folds coexist, and SAM binding only gradually shifts the populations toward terminator states. We observed a pronounced acceleration of conformational transitions upon SAM binding, which may be crucial for off-switching during the brief decision window before expression of the downstream gene

Data from: Genetic variation and structure in the neotropical tree, Manilkara zapota (L) P. Royen (Sapotaceae) used by the ancient Maya

Manilkara zapota is a tropical tree species that was used by the ancient Maya in construction of their temples and as a source for fruit. Although this has been supported by ethnographic and paleoethnobotanical data, we used genetic approaches to estimate variation and structure in modern populations of this neotropical tree species to discern if genetic patterns were consistent with earlier influences of ancient Maya management or if they could be explained by the natural history of the species. Nine microsatellite markers, consisting of seven novel markers and two markers identified in a related species, were used to characterize the genetic diversity and population genetic structure in three populations of M. zapota collected from reforested, historically urbanized ancient Maya ceremonial centers in Guatemala and Belize, from home gardens in Guatemala, and from a number of cultivars. Levels of genetic variation were slightly higher in forest populations (H O = 0.447) than in gardens (0.430) and cultivated varieties of M. zapota (0.351). We observed low but significant population substructuring (θ = 0.01) between sites 90 km apart, and minimal evidence of inbreeding. Substantial levels of genetic diversity with minimal genetic structure in M. zapota are consistent with movement of the ancient Maya as they possibly carried fruits and seedlings during immigration, but they may more likely reflect natural processes such as seed and pollen being dispersed widely throughout the tropical forest