Abstract:

In this paper, we investigate the nonlinear dynamic behavior of TPP (thiamine pyrophosphate) riboswitches in E. coli (Escherichia coli). TPP riboswitches are highly conserved RNA regulatory elements, embedded within the 5' untranslated region of three TPP biosynthesis operons. The three operons thiCEFSGH, thiMD, and thiBPQ are involved in the biosynthesis, salvage, and transport of TPP, respectively. TPP riboswitches modulate their expressions in response to changing TPP concentration, without involving protein cofactors. Interestingly, the expression of thiMD is regulated at the translational level, while that of thiCEFSGH at both levels of transcription and translation. We develop a mathematical model of the TPP riboswitch’s regulatory system possessed by thiCEFSGH and thiMD, so as to simulate the time-course experiments of TPP biosynthesis in E. coli. The simulation results are validated against three sets of reported experimental data in order to gain insight into the nature of steady states and the stability of TPP riboswitches, and to explain the biological significance of regulating at level of transcription or translation, or even both. Our findings suggest that in the TPP biosynthesis pathway of E. coli, the biological effect of down-regulating thiCEFSGH operon at the translational level by TPP riboswitch is less prominent than that at the transcriptional level. 

Keywords: riboswitches; RNA; gene regulation; nonlinear, deterministic;

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