Talk:SAM riboswitch (S-box leader)

moved out of unassessed on the genetics project

1/19/17 DennisPietras (talk) 19:06, 19 January 2017 (UTC)

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Text deletion 30 May 2009

Deleted this text:

"However, ribosomal protein binding can specifically binds the SAM kink-turn and stabilize the kink and facilitates the folding."

Is there a reference supporting this statement, and which ribosomal protein? I hadn't heard of this. Zashaw (talk) 22:14, 30 May 2009 (UTC)

Delete this recently added text:

"When the SAM riboswitch is bound by SAM a pseudoknot is stabilised resulting in rho-independent transcription termination. "

The cited paper describes the pseudoknot, but I couldn't find where it suggests that stabilization of the pseudoknot results in transcription termination, or that the pseudoknot is particularly important for regulation. In fact, when the paper says

"In-line probing of several different SAM-I riboswitches revealed that key nucleotides in L2, J3/4 and J4/1 involved in the formation of this region of tertiary structure are protected from cleavage in the absence and presence of SAM6, 18 indicating that these structures are not ligand dependent."

I think it's saying that the pseudoknot (formed with L2 and J3/4) is not stabilized by SAM, the ligand, although I haven't read this paper for some years. Another issue is that only some SAM riboswitches are believed to be regulated via the formation of rho-independent transcription terminators, while many others are, for example, believed to be regulated by sequestering the Shine-Dalgarno site. The reference is a good one, as it gives the atomic-resolution structure of the RNA, but that reference is already cited later in the article. Zashaw (talk) 00:46, 31 March 2012 (UTC)

References