On 2016 Aug 04, Martine Crasnier-Mednansky commented:

Expression of crp in Escherichia coli was found 'not to be' post-transcriptionally regulated by sRNAs including SdsR (Lee HJ, 2016). In sharp contrast, this paper reports SdsR 'strongly' affects the expression of crp in Salmonella typhimurium. What causes such discrepancy?

In all fairness, Lee HJ, 2016 noted "a few sRNAs [which included SdrS] were close to the two-fold cutoff for repression of crp" and also noted "our translational fusions will only detect regulation in the 5’ UTR and the first 20 codons of the targets". Therefore, it was prudently suggested that expression of crp was not affected by sRNAs.

Here, the authors observed a two-fold repression of crp by SdsR using whole genome microarray (table 1), and an almost 2-fold repression using a gfp reporter fusion (figure 1B). Thus it appears there is no data discrepancy between the present work and Lee HJ, 2016.

The contention by the authors SdsR strongly affects the expression of crp is in relation to data obtained with sRNA CyaR (as reported in figure 6). Figure 6A indicates that, in early stationary phase, there is no synthesis of SdsR. SdsR appears at +3h when the cells are supposedly well advanced in the stationary phase. This suggests regulation by SdsR occurs late in the stationary phase, as mentioned by the authors. Figure 6A also indicates constitutive SdsR is overly expressed, and most importantly the correlation between SdsR and crp mRNA is not straightforward, as observed by comparing lane 4 and 10 (or 11) in figure 6A.

CyaR expression is positively regulated by CRP-cAMP (De Lay N, 2009), therefore a carbon source triggering a relatively high cAMP level as compared to glucose (maltose in this paper), caused an increase in the CyaR level both in the presence and absence of SdsR (figure 6B, lane 1 to 8). With SdsR overly expressed, the CyaR level significantly decreased for cells grown on maltose (figure 6B, lane 11 and 12). The authors concluded lack of CyaR is related to the repression of crp by SdsR yet the level of CRP was not monitored.

It is reasonable to conclude regulation of crp expression by sRNAs does not appear physiologically relevant during growth or entry into stationary phase. However, this regulation may be significant upon accumulation of SdsR in nutrient-limited cells. If this is the case, CRP-dependent synthesis of post-exponential starvation proteins, which are not essential for survival (Schultz JE, 1988), will gradually be shut off. This attempted proposal is grounded in data from Lévi-Meyrueis C, 2014 indicating lack of SdsR results in impaired competitive fitness however only after 2 to 3 days in stationary phase.

On 2016 Aug 04, Martine Crasnier-Mednansky commented:

Expression of crp in Escherichia coli was found 'not to be' post-transcriptionally regulated by sRNAs including SdsR (Lee HJ, 2016). In sharp contrast, this paper reports SdsR 'strongly' affects the expression of crp in Salmonella typhimurium. What causes such discrepancy?

In all fairness, Lee HJ, 2016 noted "a few sRNAs [which included SdrS] were close to the two-fold cutoff for repression of crp" and also noted "our translational fusions will only detect regulation in the 5’ UTR and the first 20 codons of the targets". Therefore, it was prudently suggested that expression of crp was not affected by sRNAs.

Here, the authors observed a two-fold repression of crp by SdsR using whole genome microarray (table 1), and an almost 2-fold repression using a gfp reporter fusion (figure 1B). Thus it appears there is no data discrepancy between the present work and Lee HJ, 2016.

The contention by the authors SdsR strongly affects the expression of crp is in relation to data obtained with sRNA CyaR (as reported in figure 6). Figure 6A indicates that, in early stationary phase, there is no synthesis of SdsR. SdsR appears at +3h when the cells are supposedly well advanced in the stationary phase. This suggests regulation by SdsR occurs late in the stationary phase, as mentioned by the authors. Figure 6A also indicates constitutive SdsR is overly expressed, and most importantly the correlation between SdsR and crp mRNA is not straightforward, as observed by comparing lane 4 and 10 (or 11) in figure 6A.

CyaR expression is positively regulated by CRP-cAMP (De Lay N, 2009), therefore a carbon source triggering a relatively high cAMP level as compared to glucose (maltose in this paper), caused an increase in the CyaR level both in the presence and absence of SdsR (figure 6B, lane 1 to 8). With SdsR overly expressed, the CyaR level significantly decreased for cells grown on maltose (figure 6B, lane 11 and 12). The authors concluded lack of CyaR is related to the repression of crp by SdsR yet the level of CRP was not monitored.

It is reasonable to conclude regulation of crp expression by sRNAs does not appear physiologically relevant during growth or entry into stationary phase. However, this regulation may be significant upon accumulation of SdsR in nutrient-limited cells. If this is the case, CRP-dependent synthesis of post-exponential starvation proteins, which are not essential for survival (Schultz JE, 1988), will gradually be shut off. This attempted proposal is grounded in data from Lévi-Meyrueis C, 2014 indicating lack of SdsR results in impaired competitive fitness however only after 2 to 3 days in stationary phase.