## 3 Results and Discussion
### Analysis of Plasmid Presence and Antibiotic Resistance Genes
#### 3.6.1. Trepene-Related Gene Clusters
In the upper subregion, XIJ14784.1 and XIJ14785.1 show similarity to a heme-degrading domain-containing protein and a Gfo/Idh/MocA family oxidoreductase, respectively. The spacing between protein-coding regions is indicated by “+” or “\(-\)” signs. The antiSMASH analysis of the complete genome sequence of _Lentzea_ sp. JNUCC 0626 revealed that BGC region 6 shares 100% genetic similarity with the isorenierateene BGC from _S. griseus_ subsp. _griseus_ NBRC 13350 (GenBank: AP009493). Isorenierate, a carotenoid pigment, is synthesized by a gene cluster containing key biosynthetic genes, such as phytoene synthase, phytoene desaturase, lycopene cyclase, and a methyltransferase. In _S. griseus_, the isorenierateene BGC consists of seven genes: _crtY_ (lycopene cyclase), _crtT_ (methyltransferase), _crtU_ (\(\beta\)-carotene desaturase/methylase), _crtV_ (methylesterase), _crtB_ (phytoene synthase), _crtI_ (phytoene dehydrogenase), and _crtE_ (geranylgeranyl pyrophosphate synthase). In contrast, the isorenieratee BGC from _Streptomyces argillaceous_ ATCC 12956 (GenBank: LT989886) includes an additional gene encoding a sigma-70 family RNA polymerase sigma factor (_crtQ_), bringing the total to eight genes. In _Lentzea_ sp. JNUCC 0626, BGC region 6 also contains the seven essential genes (_crtY_, _crtT_, _crtU_, _crtV_, _crtB_, _crtI_, and _crtE_), as shown in Figure 4 and Table S9. However, unlike _S. griseus_ and _S. argillaceous_, which have lycopene cyclase genes with 413 and 396 amino acids, respectively, JNUCC 0626 has two smaller lycopene cyclase genes, _crtY1_ (117 aa) and _crtY2_ (105 aa). Furthermore, instead of the sigma factor _crtQ_ found in _S. argillaceous_, BGC region 6 of _Lentzea_ sp. JNUCC 0626 contains two regulatory genes: a MerR family transcriptional regulator (XIJ15578, 287 aa) and a WhiB family transcriptional regulator (XIJ15579, 95 aa). Of particular note is the presence of two proteins, XJ15576 and XJ15577, within the middle region of the _L. jejuni_s isorenieratee BGC. Structural homologs for these proteins were not identified through AlphaFold or Swiss-Prot. However, TrEMBL predicted that these proteins are similar to flavin-containing amine oxidoreductase and deoxyribodipyrimidine photolyase, both derived from _Lentzea_ species. Additionally, SWISS-MODEL and HHPred analyses indicated that protein XJ15576 resembles protoporphyrinogen oxidase from _Bacillus subtilis_ (PDB: 3i6d), _Myxococcus xanthus_ (PDB: 2 IVE), and _Exiguobacterium_ sp. 255-15 (PDB: 3 LOV), while protein XJ15577 shares structural similarity with cryptochrome B from _Rlodobacter sphaeroides_ (PDB: 3 ZXS), as well as bacterial photolyases from _Agrobacteriumium tunefaciens_ (PDB: 4 DJA) and _Vibrio cholerae_ (PDB: 8A1H). Cryptochrome B and photolyases are evolutionarily related photoreceptors. While they share structural similarities, cryptochrome B primarily functions in light signaling, such as regulating circadian rhythms, whereas photolyases play a role in DNA repair by fixing UV-induced damage. Although the relationship between cryptochrome B and terpene synthesis remains unclear, it is plausible that cryptochrome B could influence terpene biosynthesis, given that terpene biosynthesis is often responsive to environmental factors such as light. Cryptochrome B might regulate the expression or activity of enzymes involved in terpene synthesis, potentially linking circadian regulation and metabolic pathways to terpene biosynthesis. Figure 4: Isorenieratee gene cluster within BGC region 6 of the _Lentzea_ sp. JNUCC 0626 genome. XJ15576, XJ15577, and XJ15583, located near the isorenieratee gene cluster, show similarity to an NAD(P)/FAD-dependent oxidoreductase, a cryptochrome/photolyase family protein, and an alpha/beta hydrolase, respectively. BGC Region 23 Derived from _Lentzea_ sp. JNUCC 0626  
As shown in Figure S3 and Table S10, BGC region 23 contains two terpene biosynthesis-related genes: Type I geranylgeranyl diphosphate synthase (XIJ18858, 353 aa) and a phytoene/squalene synthase family protein (XIJ18860, 296 aa).