## 3 Discussion  
In this study, the abundance of 332 proteins, including proteins of the transcriptional apparatus and one or two components transcriptional regulators, was quantified in _SL_ and _SC_ grown in conditions of either phosphate limitation or proficiency. The abundance of the vast majority of these proteins greatly differed between the two strains and responded differently to Pi availability, whereas only a minority had a similar abundance and responded in a similar way to Pi availability in both strains. An important outcome of this paper is that the regulatory proteins GlnRI/SCO4159/SLI_4154 (cluster G) [70; 86; 173] and MtrA/SCO3013/SLI_3005 (cluster H) [180; 181], involved in the positive and negative control of nitrogen metabolism, respectively, were poorly abundant in _SC_ compared to _SL_ and this was correlated with the very low abundance of proteins involved in nitrogen up-take and assimilation in _SC_ compared to _SL_, as reported in [PERSON] et al. [9]. Consequently, _SC_ most likely suffers from severe nitrogen stress. GlnRI activates the expression of genes involved in N uptake and assimilation [86] and is, as expected, more abundant in Pi proficiency than in Pi limitation in _SL_, since in this condition the negative effect that PhoP exerts on GlnRI expression is relieved [199]. However, this up-regulation does not occur in _SC_. Consistently, proteins whose expression is under the positive control of GlnR such as the ammonium transporter AmtB/SCO5583, the glutamine synthases GSI/SCO2198/GlnA and GSII/SCO2210, as well as the regulator SCO2958/NnaR and its regulatory targets essential for nitrate and nitrite assimilation [70; 86; 173] were far more abundant in Pi proficiency than in Pi limitation in _SL_ but not in _SC_ (Figure 8 of [9]). In contrast, the regulator MtrA, which represses the expression of GlnRI and that of the genes under its positive control [181], is clearly more abundant in Pi limitation than in Pi proficiency in _SL_ but not in _SC_. This study thus revealed that GlnRI that positively controls the expression of genes involved in N up-take and assimilation is more abundant in Pi proficiency than in Pi limitation, whereas MtrA, which negatively controls the expression of these genes, is more abundant in Pi limitation than in Pi proficiency, in _SL_. The interplay between these two regulators thus adjusts N up-take and assimilation to Pi availability. However, in _SC_, such regulation is altered, and these two regulators remain poorly abundant in both Pi conditions. This is obviously correlated with the poor expression of genes encoding proteins involved in nitrogen up-take and assimilation. Interestingly, these two regulators are known to be phosphorylated and this phosphorylation stimulates the repressing function of MtrA [200] but impairs the activating function of GlnRI [201]. In _SC_, the phosphorylation of MtrA could thus contribute to the weak expression of GlnRI and the activating function of the latter would be impaired by its phosphorylation, resulting in poor expression of its target genes (Figure 7 of [9]). We hypothesize that the extensive phosphorylation of these regulators might be promoted in _SC_ by the high ATP content of this strain [10], which is thought to be linked to the highly active oxidative metabolism of this strain [9; 12], as well as to the high abundance of the complex I of the respiratory chain in _SC_, in both Pi conditions (Figure 5 of [9]). The reduced abundance, in _SC_ compared to _SL_, of the glutamine synthases GlnA/SCO2198 and GSII/SCO2210, to a lesser extent (Figures 6 and S3A of [9]), and of other enzymes involved directly or indirectly (via serine biosynthesis) in the biosynthesis of alanine and glycine (Figure S3A of [9]) is likely to limit the availability of these three amino acids as well as that of the N containing compound, N acetyl glucosamine (GlcNAc), which are constitutive of the peptidoglycan cell wall [202].