The regulation mechanism of yitJ and metF riboswitches

Journal Article · Tue Jul 28 04:00:00 EDT 2015 · Journal of Chemical Physics

DOI:https://doi.org/10.1063/1.4927390· OSTI ID:22493475

Gong, Sha; Wang, Yujie; Zhang, Wenbing ^[1]

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1. Department of Physics, Wuhan University, Wuhan, Hubei 430072 (China)

Riboswitches which function at the transcriptional level are sensitive to cotranscriptional folding. Based on the recently proposed theory of cotranscriptional folding, we developed a transition node approximation method to effectively decrease the conformation space of long RNA chains. Our results indicate that this approximation is reliable for calculating the cotranscriptional folding kinetics of long mRNA chains. We theoretically studied the cotranscriptional folding behavior of the yitJ and metF riboswitches in the absence/presence of S-adenosylmethionine. Although the two S-box riboswitches have similar OFF-state structures and share common features of riboswitches operated at the transcriptional level, their regulation mechanisms are different. The yitJ riboswitch is regulated by a combination of thermodynamic and kinetic mechanisms, while the metF riboswitch is solely kinetically controlled. For the yitJ riboswitch, transcriptional pausing at the U-stretch directly following the terminator decreases the amount of ligand required to trigger the switch. The different regulation mechanisms and binding affinities of the two riboswitches result from the different lengths of the anti-terminator helix, which in yitJ is short and only disrupts helix P1 of the riboswitch aptamer, but in metF is long and breaks both the helices P1 and P4.

• OSTI ID: 22493475
• Journal Information: Journal of Chemical Physics, Journal Name: Journal of Chemical Physics Journal Issue: 4 Vol. 143; ISSN JCPSA6; ISSN 0021-9606
• Country of Publication: United States
• Language: English

Related Subjects

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CHEMISTRY
60 APPLIED LIFE SCIENCES
AFFINITY
FUNCTIONS
KINETICS
LENGTH
LIGANDS
MESSENGER-RNA
REGULATIONS
SPACE
TRANSCRIPTION