Analysis of sRNAs and Their mRNA Targets in Sinorhizobium meliloti: Focus on Half-Life Determination

Regulation of gene expression at the level of RNA and/or by regulatory RNA is an integral part of the regulatory circuits in all living cells. In bacteria, transcription and translation can be coupled, enabling regulation by transcriptional attenuation, a mechanism based on mutually exclusive structures in nascent mRNA. Transcriptional attenuation gives rise to small RNAs that are well suited to act in trans by either base pairing or ligand binding. Examples of 5'-UTR-derived sRNAs in the alpha-proteobacterium Sinorhizobium meliloti are the sRNA rnTrpL of the tryptophan attenuator and SAM-II riboswitch sRNAs. Analyses addressing RNA-based gene regulation often include measurements of steady-state levels and of half-lives of specific sRNAs and mRNAs. Using such measurements, recently we have shown that the tryptophan attenuator responds to translation inhibition by tetracycline and that SAM-II riboswitches stabilize RNA. Here we discuss our experience in using alternative RNA purification methods for analysis of sRNA and mRNA of S. meliloti. Additionally, we show that other translational inhibitors (besides tetracycline) also cause attenuation giving rise to the rnTrpL sRNA. Furthermore, we discuss the importance of considering RNA stability changes under different conditions and describe in detail a robust and fast method for mRNA half-life determination. The latter includes rifampicin treatment, RNA isolation using commercially available columns, and mRNA analysis by reverse transcription followed by quantitative PCR (RT-qPCR). The latter can be performed as a one-step procedure or in a strand-specific manner using the same commercial kit and a spike-in transcript as a reference.