# Effect of PAS-LuxR Family Regulators on the Secondary Metabolism of _Streptomyces_
## 3 Regulation of Related Product Biosynthesis by PAS-LuxR Family Regulators
### Regulation of Polyene Macrolide Biosynthesis by PAS-LuxR Family Regulators  
#### 3.1.1 Vertical Regulatory System Formed with SARP-LAL and PAS-LuxR Family Regulators  
The PAS-LuxR family of regulators was first reported in the pimaricin pathway; a tetraene macrolide produced by _S. natalensis_ ATCC 27448 is also produced by _S. dattanoogensis_, _S. lydicus_, and _S. gilvosporeus_[19]. The pimaricin pathway in _S. natalensis_ involves two positive regulators, namely, the PAS-LuxR family regulator PimM and the SARP-LAL family regulator PimR. PimM affects the biosynthesis of pimaricin by regulating the transcription of PKS genes (_pimS0_, _pimS1_, _pimS2_, _pimS3_, and _pimS4_), oxidoreductase genes (_pimD_, _pimF_, and _pimG_), glycosylation genes (_pimC_, _pimI_), and _pimK_), transporter genes (_pimA_ and _pimB_), and the thioester hydrolase gene (_pimI_). However, _pimE_, _pimH_, _pimM_, and _pimR_ are not regulated by PimM. PimR affects pimaricin biosynthesis indirectly by regulating _pimM_ through binding to the site of TGGCAAAGAAGCGCGCAGGTGTCGCAAG with the heptameric repeats in the promoter of _pimM_. In combination with the regulatory role of PimM, a vertical regulatory  
Figure 5: Simulated secondary structures of C-terminal HTH motif of PAS-LuxR family regulators by SWISS-MODEL on [[https://swissmodel.expasy.org/](https://swissmodel.expasy.org/)]([https://swissmodel.expasy.org/](https://swissmodel.expasy.org/)), accessed on 25 July 2022.  
system is formed between the two regulators [20]. The pimaricin biosynthetic gene cluster in _S. chattauogensis_ has 17 open reading frames, including two regulatory genes, namely, _scnRI_ and _scnRII_, which correspond to _pimR_ and _pimM_ with sequence identities of 85% and 96%, respectively [21; 22; 23]. ScnRII also belongs to the PAS-LuxR family. The analysis of ScnRII (192 aa) revealed that it has 99% sequence identity with the positive regulator Aurj3M of _S. aureusvicus_ and 96% amino acid similarity with PimM. Genes _scnA_, _scnE_, _scnD_, and _scnRII_ are partially regulated by ScnRI, while _scnS1_ and _scnT_ are not regulated by ScnRI. ScnRII affects pimaricin biosynthesis by regulating eight genes, namely, _scnA_, _scnE_, _scnD_, _scnI_, _scnI_, _scnK_, _scnS1_, and _scnS2_, which bind to the promoters of the above genes and recruit RNA polymerase to initiate their transcription, forming a vertical regulatory system [24]. Considering the difference in the target genes regulated by PimM and ScnRII, the amino acid sequences of these two regulators were analyzed independently. The results reveal that 186 aa out of 192 aa are identical. The six amino acid residues that did not match appeared in the PAS structural domain, and the genes within the two gene clusters were not identical, which may account for their different regulatory mechanisms. The SInM in pimaricin producer _S. hydicus_ A02 is a member of the PAS-LuxR family [25]. The identities of _slnM_ with _scnRII_ and _pimM_ genes are both 96%. However, the identity of SInM with ScnRII was higher than that with PimM or SgnRII, as indicated by the closer relationship between SInM and ScnRII in Figure 6.  
The biosynthetic gene clusters of pimaricin have not been reported in _S. gilvosporeus_[26]. Filipin is a 28-membered cyclopentenyl macrolide produced by _S. avemitillis_, _S. filipinensis_, and _S. milaraensis_[27; 28; 29], of which the most detailed biosynthetic process has been reported in _S. avemitilis_. Similar to pimaricin, the filipin pathway has two different regulators, namely, the SARP-LAL family regulator PteR and the PAS-LuxR family regulator PteF. PteR is homologous to PimM. The transcription of all PKS genes (_pteA1_, _pteA2_, _pteA3_, _pteA4_, and _pteA5_) are significantly reduced in the _pteF_-disrupted strain (_ApteF_), in which the expression of _pteA3_, _pteA4_, and _pteA5_ significantly differed, suggesting that _pteF_ has a direct or indirect regulatory effect on these genes [30].