## 2 Results
### Transcriptional Regulators and Sensory Histidine Kinases
* The SOS regulatory protein LexA/SCO5803 that positively controls the expression of the recombination protein RecA/SCO5769 [68]. Consistently, LexA and RecA were more abundant in Pi proficiency than in Pi limitation in _SL_ but RecA was similarly and highly abundant in both Pi conditions in _SC_ (Figure S8 of [9]) indicating a situation of stress. * The gene encoding the regulator SCO1614 that is located in divergence of an ethanolamine utilization pathway [69]. Sub-cluster A3 includes 3 proteins involved into the regulation of nitrogen metabolism: the regulator SCO2958/nnaR, the adenylyltransferase GlnID/SCO5585, and the nitrogen sensor protein GlnK/SCO5584. NnaR is a regulatory target of the nitrogen regulator GlnR/SCO4159 and acts as a co-activator of the latter [70]. NnaR directly positively controls the expression of the genes narK (nitrate extrusion protein, SCO2959), nirB (nitrite  
Figure 2: Cluster A, heatmap representation of transcriptional regulators and sensory histidine kinases more abundant in Pi proficiency than in Pi limitation in both strains. Cluster A that can be divided into 3 sub-clusters A1, A2 and A3. Sub-cluster A1 includes 22 regulators rather more abundant in Pi proficiency than in Pi limitation in both strains. The sub-clusters A2 and A3 both include 16 regulators that were similarly abundant in _SL_ and _SC_ in Pi proficiency at both time points but also abundant in _SL_ in Pi limitation at 60 h.  
reductase, SCO2486-87), nirA (nitrite/sulphite reductase SCO6102), and nasA (nitrate reductase SCO2473) that are essential for nitrate and nitrite assimilation [70]. NnaR was more abundant in Pi proficiency than in Pi limitation in both species, but NnaR was far less abundant in _SC_ than in _SL_ in both Pi conditions. Consistently all the NnaR target proteins were far more abundant in Pi proficiency than in Pi limitation in _SL_ but not in _SC_ (Figure 7 of [9]). GlnD adenylates GlnK/SC05584 [71] which has a positive impact on antibiotic production and morphological differentiation [72]. The low abundance of all these proteins in Pi proficiency in _SC_ likely limits its ability to assimilate nitrate/nitrite and should result in severe nitrogen limitation in _SC_. This cluster also includes the orphan RR SCO2281/Aor1 that has a positive impact on antibiotic biosynthesis and morphological differentiation [73]. In an aor1 mutant of _SC_, genes of the SigB regulon were up-regulated, suggesting a link with OsS [53; 74]. 2.2 Cluster B: Regulatory Proteins More Abundant in Pi Limitation than in Pi Proficiency in Both Strains  
Cluster B could be divided into three sub-clusters: B1, B2, and B3 (Figure 3). Sub-cluster B1 includes 6 proteins more abundant in _SC_ than in _SL_ in both Pi conditions but also abundant in _SL_ in Pi limitation at 48 h. Sub-cluster B1 includes:  
* The SHK CseC/SCO3359 of the TCS _cseC/cseB_ belongs to an operon constituted also by _cseA_ (lipoprotein) and _sigE_. This TCS activates the transcription of _sigE/sco3356_, in response to the alteration of the cell envelope [47; 75]. Consistently, SigE was far more abundant in _SC_ than in _SL_ in both Pi conditions (Figure 1). This indicated that damages to the cell wall occur independently of Pi availability in _SC_. * AbrC1/SCO4598 is part of an atypical TCS constituted of 2 SHK (AbrC1/SCO4598 and AbrC2/SCO4597) and of the RR AbrC3/SCO4596 [76]. The genes encoding this TCS are located in divergence of genes encoding sub-units of NADH dehydrogenase (SCO4599-SCO4608) which were far more abundant in _SC_ than in _SL_ in both Pi conditions (Figure 5 of [9]). This TCS has a positive impact on antibiotic production and morphological differentiation in _SC_[76; 77; 78]. * The regulator BldB/SCO5723 that has a positive impact on antibiotic production and morphological differentiation [79]. Sub-cluster B2 includes 22 proteins clearly more abundant in Pi limitation than in Pi proficiency in both strains.