# Genome-Wide Analysis Reveals the Secondary Metabolome in _Streptomyces kanasensis_ ZX01
## 3 Results and Discussion
### Regulators for Secondary Metabolism in S. kanasensis ZX01 Genome  
Secondary metabolism has a complex regulatory network in _Streptomyces_. Pathway-specific regulatory genes, where each controls one antibiotic biosynthetic pathway, are at the bottom of the regulatory network, such as _actII-or4_, _redD_, _cdaR_ and _mmyR_[20]. Global regulators perform the highest-level regulation and affect the morphological and physiological differentiation. There are at least 466 putative regulators in _S. kanasensis_ ZX01 genome, belonging to LuxR, MerR, MarR, AraC, GntR, ArsR family, et al. Some of them, as positive or negative regulators, probably have effects on the secondary metabolism. For examples, _nsdA_ negatively regulates the sporulation and antibiotic production in _Streptomyces_. The _nsdA_ disruption caused the overproduction of spores and three antibiotics (actinorhodin, calcium-independent antibiotic, epoxycyclopentanone methylenomycin) in _S. coelicolor_[21]. The _Streptomyces bingchenensis_\(\Delta\)_nsdA_ mutant produced more pigments and spores; meanwhile, milbemycin A4 and nanchangmycin were over-produced in the \(\Delta\)_nsdA_ mutant [22]. \begin{table}
\begin{tabular}{c c c c c c c} \hline \hline \multirow{2}{*}{**Cluster**} & \multirow{2}{*}{**Type**} & \multirow{2}{*}{**GenBank ID**} & \multicolumn{2}{c}{**Location**} & \multicolumn{2}{c}{**Most Similar Known**} & \multirow{2}{*}{**Similarity (\%) \(\star\)**} \\ \cline{3-4} \cline{6-7}  & & & **From** & & **To** & & **Biosynthetic Gene Cluster** \\ \hline
11 & Phosphonate & LNSV01000030 & 1 & 34405 & Azinomycin B & 6 \\
12 & Bacteriocn & LNSV01000030 & 45699 & 57147 & Enduracidin & 6 \\
13 & Ecotine & LNSV01000074 & 2911 & 13309 & Ecotine & 100 \\
14 & Lassopeptide & LNSV0100003 & 18630 & 41325 & Collismycin A & 7 \\
15 & Thiophene & LNSV01000094 & 1 & 22641 & Granaticin & 8 \\
16 & T1 pks & LNSV01000017 & 13669 & 61120 & Monensin & 5 \\
17 & T1 pks-Otherks & LNSV01000001 & 32321 & 84798 & - & - \\
18 & Tipks-Butyrolactone-NRPs & LNSV01000041 & 1 & 58607 & Micromonolactam & 100 \\
19 & T3 pks & LNSV01000059 & 19531 & 42521 & Merchorlin & 4 \\
20 & Otheris-Phenazine & LNSV01000010 & 440 & 49063 & Esmeraldin & 64 \\
21 & NRPs & LNSV01000098 & 1 & 22529 & - & - \\ \hline \hline \end{tabular}  
* Secondary metabolite types detected by antisMASH 4.0: T1 pks, Type I polyketide synthase (PKS) cluster; T3 pks, Type III PKS cluster; Ohreks, cluster containing some PKS modules that does not fit into any other type. NRPs, Nonribosomal peptide synthetase cluster; The “similarity” means the percentage of the homologous genes in the query cluster that are present in the hit cluster. According to the definition by the antiSMASH, the homologous genes were selected by BLAST e-value \(<\) 10\({}^{-5}\), 30% minimal sequence identity, shortest BLAST alignment covers over \(>\)25% of the sequence.  
\end{table} 
Table 1: _Cont._In the genome of _S. kanasensis_ ZX01 _nsdA_ is also present, and affects secondary metabolism and antibiotics. Glycoprotein GP-1 is a secondary metabolite with antiviral activity, producing by _S. kanasensis_ ZX01. The \(\Delta\)_nsdA_ mutant of _S. kanasensis_ ZX01 produced more spores and aerial hyphae than the wild strain on plate medium or liquid medium, and the production of GP-1 dramatically increased as well (Figure 3). Therefore, the global regulator, _nsdA_, affects colonial morphology and secondary metabolism of antibiotic or non-antibiotic. Figure 1: **Proposed PKS/NRPs module and domain organization in five clusters. ** PKS: polyketide biosynthesis, NRPs: nonribosomal peptide synthetase, KS: ketosynthes, AT: acyltransferase, DH: dehydatase, ER: enoyl reductase, KR: ketoreductase, ACP: acyl carrier protein, cMT: C-methyl transferase, PCP: peptidyl carrier protein, C: condensation, A: adenylation, PDN: PKS docking N-term, PDC: PKS docking C-term, NCN: NRPS-COM N-term, TE: thioesterase. Figure 2: Expression difference of PKS and NRPs genes in _S.