## 2 Results
### Transcriptional Regulators and Sensory Histidine Kinases
#### 2.2.3 Cluster C: Regulators More Abundant in _SC_ than in _SL_ in Both Pi Conditions  
Cluster C includes 53 regulators (Figure 4):  
Two regulatory systems able to sense nitric oxide (NO), the TCS OdsK/SCO0203-OdsR/SCO0204 [94] also called DevS/R [95], and NsrR/SCO7427 which positively controls the expression of NO-detoxifying flavohemoglobins hmpA1/SCO7428 and hpmA2/SCO7094 [96; 97]. The RR OdsR regulates the expression of genes of the dormancy/survival regulon [94]. Proteins of the OdsR regulon fall into two groups, highly and poorly expressed in _SC_, and conversely in _SL_ (Figure S11C of [9]). Intracellular NO is thought to inhibit the auto-phosphorylation of the SHK DevS/OdsK which becomes unable to phosphorylate the RR DevR/OdsR [95]. Un-phosphorylated OdsR is unable to interact with the promoter region of _actII-ORF4_ to activate its expression [95]. NO thus has an indirect negative effect on ACT biosynthesis. Since _SC_ produces ACT abundantly, it might be legitimate to propose that little NO is generated in _SC_, and this would be consistent with the previously mentioned reduced N availability in this strain. Cluster C also includes 2 two regulators involved in the response to OsS or OxS:  
The SHK OhkA/SCO1596 and its cognate RR OrrA/SCO3008 (Cluster D2). This TCS is involved in osmoadaptation [98] and has a negative impact on RED and ACT biosynthesis [99; 100]. The regulator WbIA that is a target of the OrrA was identified as a down-regulator of the expression of genes involved in the resistance to OxS [101]. Since OxS was proposed to be an important trigger of ACT biosynthesis [8; 12], this can explain the negative impact that WbIA exerts on ACT biosynthesis [102]. The protein kinase RsfA/SCO4677 that phosphorylates and thus inactivates the function of the anti-sigma factor antagonist BldG/SCO3549 [25] that is involved in the regulation of the activity of the OsS responsive SigH factor [26]. * The regulator Rex SCO3320 [103] that responds to NAD+/NADH poise and represses the transcription of numerous genes, including its own and that of genes encoding subunits of the complex I/NADH dehydrogenase of the respiratory chain, (_unoABCDE-FGHIJKLMN/sco4562-75_) and of the ATP synthase (_atplBEFHAGDC/sco5366-74_). The repressing effect of Rex is alleviated when the intracellular NADH concentration is high [103], as is likely to be the case in \(SC\) that is characterized by an oxidative metabolism [10]. Interestingly, the sub-units of the complex I of the respiratory chain were far more abundant in \(SC\) than in \(SL\), in both Pi conditions (Figure 5 of [9]). * SCO6992/AbsR1, a member of the Abrc3 regulon [76,78] that has a positive impact on RED and ACT biosynthesis [104]. * The RR CutR/SC05862 of the TCS CutS/CutR, thought to be involved in the regulation of copper homeostasis [105], has a negative impact on RED and ACT biosynthesis [106]. * SCO6008/Rosk7B7 that negatively regulates the expression of the xylose transporter operon _xylFGH_, has a rather a positive impact on ACT biosynthesis but a negative one on RED and CDA biosynthesis [107,108]. Figure 4: Cluster C, heatmap representation of transcriptional regulators and sensory histidine kinases more abundant in \(SC\) than in \(SL\) in both Pi conditions. 2.2.4 Cluster D: Regulatory Proteins More Abundant in Pi Proficiency than in Pi Limitation in \(Sc\)  
Cluster D could be divided into three sub-clusters: D1 and D2 and D3 (Figure 5). Most of these regulators have a positive or a negative impact on antibiotic production. The 18 regulators of sub-cluster D1 were more abundant in Pi proficiency than in Pi limitation at both time points in \(SC\) but some of them were also abundant in Pi limitation at 48 h in \(SC\). This sub-cluster includes:  
* The regulator DasR/SCO5231 which is known to repress the expression of genes involved in the up-take and catabolism of N-acetyl glucosamine [109].