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Figure 1 | BMC Genomics

Figure 1

From: Prediction of Sinorhizobium meliloti sRNA genes and experimental detection in strain 2011

Figure 1

Northern blot analysis of putative sRNAs encoded in the chromosome of S. meliloti strain 2011. Total RNA was isolated from S. meliloti 2011 cells grown at 28°C with agitation (120 rpm) in RDM minimal medium and harvested at OD600 = 0.5 (Exp) or at OD600 = 3.9 (Stat). Total RNA was also isolated from cells subjected to high salt stress (NaCl; 0.3 M NaCl in RDM, OD600 = 0.55), membrane stress (EtOH; RDM with 2% v/v ethanol, OD600 = 1.6; or SDS; RDM with 0.1% w/v SDS; OD600 = 1.0), phosphate starvation (-P; RDM with 0.1 mM phosphate and 10 mM MOPS pH 7.0, OD600 = 1.0), oxidative stress (H2O2; RDM with 0.1 mM H2O2, OD600 = 1.1), heat stress (37°; RDM grown at 37°C, OD600 = 0.95) and acid stress (pH 5.5; treatment of exponential phase cells at OD600 = 0.5 during 90 min at pH 5.5 before harvest). Northern hybridizations were done with PCR-generated digoxigenin-labeled dsDNA probes directed against the entire IgR or an internal fragment (see Figure 2 and Additional file 2 for further details). RNA molecular weight markers (with their sizes indicated in nt with small arrows at the left of each panel) were run with each set of RNA samples for estimation of transcript size. As exposure times were optimized for visualization here, the signal intensity does not indicate relative abundance of detected transcripts between different IgRs. Hybridization signals were quantified with ImageJ software, normalized to the amount of 5S RNA, 4.5S RNA and tRNA bands detected in silver stained gels present in each sample (bottom panel) and plotted in a bar graph shown below each Northern blot. The band intensity units are relative to the normalized amount present in Exp cells, which were set as 1.0.

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