Maestro of regulation: Riboswitches orchestrate gene expression at the levels of translation, transcription and mRNA decay

Abstract

Riboswitches are RNA regulators that control gene expression by modulating their structure in response to metabolite binding. The study of mechanisms by which riboswitches modulate gene expression is crucial to understand how riboswitches are involved in maintaining cellular homeostasis. Previous reports indicate that riboswitches can control gene expression at the level of translation, transcription or mRNA decay. However, there are very few described examples where riboswitches regulate multiple steps in gene expression. Recent studies of a translation-regulating, TPP-dependent riboswitch have revealed that ligand binding is also involved in the control of mRNA levels. In this model, TPP binding to the riboswitch leads to the inhibition of translation, which in turn allows for Rho-dependent transcription termination. Thus, mRNA levels are indirectly controlled through ribosome occupancy. This is in contrast to other riboswitches that directly control mRNA levels by modulating the access of regulatory sequences involved in either Rho-dependent transcription termination or RNase E cleavage activity. Together, these findings indicate that riboswitches modulate both translation initiation and mRNA levels using multiple strategies that direct the outcome of gene expression.

Keywords: Genetic regulation; Rho transcription termination; Riboswitch; translation.

Figure 1.

The expression of thiM is modulated through Rho-dependent transcription termination. RNase H cleavage assays show that a region (black) is protected in the presence of Rho, consistent with the presence of a rut. Rho-dependent transcription termination sites identified in vitro are shown in gray and codons (cd) 9, 20, 34 and 40 are underlined.

Figure 2.

Indirect and direct control mechanisms used to regulate mRNA levels. A) The indirect control mechanism primarily relies on the modulation of translation initiation. Upon translation inhibition, a rut becomes accessible to Rho binding, leading to transcription termination. B) The direct control mechanism is performed by directly modulating the access of rut, which is dictated by ligand-dependent riboswitch conformational changes. Both indirect and direct control mechanisms rely on the inhibition of ribosome binding to the RBS in the ligand-bound state.