\"The SAM-I riboswitch is a cis-acting element of genetic control found in bacte

Question

"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."

Question?

c. Predict the effect of a mutation of one of the two universally conserved base pairs in the RNA.

d. Describe what happens to the riboswitch (in cis) in the presence of SAM and in the absence of SAM.

Explanation / Answer

c. Predict the effect of a mutation of one of the two universally conserved base pairs in the RNA?

Based on the article by, (Huck, 2004): “Conserved tertiary base pairing ensures proper RNA folding and efficient assembly of the signal recognition particle Alu domain” it can be concluded that the effect of a mutation of one of the two universally conserved base pairs in the RNA will lead to conformational changes of the RNA leading to changes in structure which in turn will lead to changes in signal transduction associated with it.

d. Describe what happens to the riboswitch (in cis) in the presence of SAM and in the absence of SAM.

Since, Riboswitches are cis-acting mRNA regulatory elements that modulate gene expression through their ability to bind small molecule metabolites with high specificity (Montange and Batey, 2008). There is structural heterogeneity in a free state riboswitch aptamer domain and magnesium and SAM binding reshapes the folding landscape, (Stoddard, 2010)

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