Comparative Analyses of Cytochrome P450s and Those Associated with Secondary Metabolism in Bacillus Species
Abstract
:1. Introduction
2. Results and Discussion
2.1. Bacillus Species Have the Lowest Number of P450s
2.2. Bacillus Species Have the Lowest Number of P450 Families and Subfamilies’
2.3. Bacillus Species Have the Lowest Number of Secondary Metabolite BGCs
2.4. Large Number of P450s Found to Be Part of Secondary Metabolites BGCs in Bacillus Species
2.5. Bacillus P450s Indeed Involved in the Synthesis of Secondary Metabolites
3. Materials and Methods
3.1. Species and Database
3.2. Genome Data Mining and Annotation of P450s
3.3. Phylogenetic Analysis of P450s
3.4. P450 Diversity Percentage Analysis
3.5. Generation of P450 Profile Heat-Maps
3.6. Secondary Metabolite BGCs Analysis
3.7. Comparative Analysis of P450s
4. Conclusions
Supplementary Materials
Author Contributions
Funding
Acknowledgments
Conflicts of Interest
References
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Species Name | Cluster Number | Type of BGCs | P450 Name |
---|---|---|---|
Bacillus subtilis subsp. subtilis 168 | 4 | Nrps-Transatpks-Otherks | CYP134A1 |
10 | Other | CYP134A1 | |
Bacillus subtilis subsp. subtilis RO-NN-1 | 3 | Nrps-Transatpks-Otherks | CYP107K1 |
Bacillus subtilis subsp. subtilis BSP1 | 8 | Transatpks-Otherks-Nrps | CYP107K1 |
Bacillus subtilis subsp. subtilis 6051-HGW | 4 | Nrps-Transatpks-Otherks | CYP107K1 |
10 | Other | CYP107K1 | |
Bacillus subtilis subsp. subtilis BAB-1 | 4 | Nrps-Transatpks-Otherks | CYP107K1 |
Bacillus subtilis subsp. subtilis AG1839 | 4 | Nrps-Transatpks-Otherks | CYP107K1 |
10 | Other | CYP107K1 | |
Bacillus subtilis subsp. subtilis JH642 | 4 | Nrps-Transatpks-Otherks | CYP107K1 |
10 | Other | CYP134A1 | |
Bacillus subtilis subsp. subtilis OH 131.1 | 1 | Lantipeptide | CYP152A1 |
4 | Nrps-Transatpks-Otherks | CYP107K1 | |
9 | Other | CYP134A1 | |
Bacillus subtilis subsp. spizizenii W23 | 1 | Phosphonate | CYP152A1 |
4 | Nrps-Transatpks-Otherks | CYP107K1 | |
10 | Other | CYP134A1 | |
Bacillus subtilis subsp. spizizenii TU-B-10 | 3 | Nrps-Transatpks-Otherks | CYP107K1 |
9 | Other | CYP134A1 | |
Bacillus subtilis BSn5 | 4 | Other | CYP102A48 |
8 | Lantipeptide | CYP152A1 | |
11 | Nrps-Transatpks-Otherks | CYP107K1 | |
Bacillus subtilis QB928 | 4 | Nrps-Transatpks-Otherks | CYP107K1 |
10 | Other | CYP134A1 | |
Bacillus subtilis XF-1 | 4 | Nrps-Transatpks-Otherks | CYP107K1 |
Bacillus subtilis PY79 | 4 | Nrps-Transatpks-Otherks | CYP107K1 |
9 | Other | CYP134A1 | |
Bacillus licheniformis ATCC 14580 | 7 | Other | CYP134A5 |
Bacillus licheniformis DSM 13 = ATCC 14580 | 7 | Other | CYP134A5 |
Bacillus paralicheniformis | 10 | Other | CYP134A5 |
Bacillus velezensis FZB42 | 5 | Transatpks-Nrps | CYP107K3 |
6 | Transatpks-Nrps | CYP107H4 | |
9 | Transatpks | CYP113L1 | |
Bacillus velezensis CAU B946 | 5 | Transatpks-Nrps | CYP107K3 |
6 | Transatpks-Nrps | CYP107H4 | |
9 | Transatpks | CYP113L1 | |
Bacillus velezensis YAU B9601-Y2 | 5 | Transatpks | CYP107K3 |
6 | Transatpks-Nrps | CYP107K3 | |
7 | Transatpks-Nrps | CYP107H4 | |
10 | Transatpks | CYP113L1 | |
Bacillus velezensis AS43.3 | 6 | Transatpks | CYP107K3 |
7 | Transatpks-Nrps | CYP113L1 | |
10 | Transatpks | CYP113L1 | |
Bacillus velezensis UCMB5036 | 5 | Transatpks-Nrps | CYP107K3 |
6 | Transatpks-Nrps | CYP107H4 | |
9 | Bacteriocin-Nrps | CYP113L1 | |
Bacillus velezensis UCMB5033 | 6 | Transatpks-Nrps | CYP107K3 |
7 | Transatpks-Nrps | CYP107H4 | |
10 | Transatpks | CYP113L1 | |
Bacillus velezensis UCMB5113 | 7 | Transatpks-Nrps | CYP107K3 |
8 | Transatpks-Nrps | CYP107H4 | |
11 | Transatpks | CYP113L1 | |
Bacillus velezensis NAU-B3 | 3 | Transatpks | CYP113L1 |
6 | Transatpks-Nrps | CYP107H4 | |
7 | Transatpks-Nrps | CYP107K3 | |
Bacillus velezensis TrigoCor1448 | 5 | Transatpks-Nrps | CYP107K3 |
6 | Transatpks-Nrps | CYP107H4 | |
Bacillus velezensis SQR9 | 6 | Transatpks-Nrps | CYP107K3 |
7 | Transatpks-Nrps | CYP107H4 | |
10 | Transatpks | CYP113L1 | |
Bacillus velezensis | 6 | Transatpks-Nrps | CYP107K3 |
7 | Transatpks-Nrps | CYP107H4 | |
10 | Transatpks | CYP113L1 | |
Bacillus amyloliquefaciens DSM 7 | 5 | Transatpks-Nrps | CYP107K3 |
6 | Transatpks-Nrps | CYP107H2 | |
Bacillus amyloliquefaciens TA208 | 7 | Transatpks-Nrps | CYP107H2 |
8 | Transatpks-Nrps | CYP107K3 | |
Bacillus amyloliquefaciens LL3 | 5 | Transatpks-Nrps | CYP107K3 |
6 | Transatpks-Nrps | CYP107H2 | |
Bacillus amyloliquefaciens XH7 | 7 | Transatpks-Nrps | CYP107H2 |
8 | Transatpks-Nrps | CYP107K3 | |
Bacillus amyloliquefaciens Y2 | 6 | Transatpks-Nrps | CYP107K3 |
7 | Transatpks-Nrps | CYP107H4 | |
10 | Transatpks | CYP113L1 | |
Bacillus amyloliquefaciens IT-45 | 3 | Transatpks | CYP113L1 |
6 | Transatpks-Nrps | CYP107H4 | |
7 | Transatpks-Nrps | CYP107K3 | |
Bacillus amyloliquefaciens CC178 | 6 | Transatpks-Nrps | CYP107H4 |
9 | Transatpks | CYP113L1 | |
Bacillus amyloliquefaciens LFB112 | 7 | Transatpks-Nrps | CYP107K3 |
8 | Transatpks-Nrps | CYP107H4 | |
11 | Transatpks | CYP113L1 | |
Bacillus atrophaeus 1942 | 3 | Nrps-Transatpks-Otherks | CYP107K2 |
10 | Nrps | CYP152A9 | |
Bacillus atrophaeus NRS 1221A | 3 | Nrps-Transatpks-Otherks | CYP107K2 |
10 | Nrps | CYP152A9 | |
Bacillus vallismortis | 6 | Transatpks-Nrps | CYP107K3 |
7 | Transatpks-Nrps | CYP107H4 | |
10 | Transatpks | CYP113L1 | |
Bacillus pumilus SH-B9 | 8 | Nrps | CYP109B6 |
Bacillus sp. JS | 4 | Nrps-Transatpks-Otherks | CYP107K1 |
Bacillus sp. Pc3 | 1 | Bacteriocin-Transatpks-Nrps | CYP107H4 |
2 | Transatpks-Nrps | CYP107K3 | |
10 | Transatpks | CYP113L1 | |
Bacillus sp. BH072 | 8 | Transatpks-Nrps | CYP107K3 |
9 | Transatpks-Nrps | CYP107H4 | |
12 | Transatpks | CYP107H4 | |
Bacillus sp. YP1 | 4 | Nrps-Transatpks-Otherks | CYP107K1 |
Bacillus sp. BS34A | 4 | Nrps-Transatpks-Otherks | CYP107K1 |
10 | Other | CYP134A1 | |
Bacillus sp. LM 4-2 | 3 | Nrps-Transatpks-Otherks | CYP107K1 |
7 | Other | CYP102A48 | |
9 | Other | CYP134A1 | |
Bacillus gibsonii | 1 | Nrps-Transatpks-Otherks | CYP107K1 |
6 | Other | CYP134A1 | |
9 | Lantipeptide | CYP152A1 | |
Bacillus xiamenensis | 2 | Nrps | CYP1179A4 |
Bacillus altitudinis | 2 | Nrps | CYP1179A4 |
8 | Nrps | CYP109B5 | |
Bacillus sp. SDLI1 | 3 | Transatpks-Nrps | CYP107H4 |
4 | Transatpks-Nrps | CYP107K3 | |
11 | Transatpks | CYP113L1 |
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Mthethwa, B.C.; Chen, W.; Ngwenya, M.L.; Kappo, A.P.; Syed, P.R.; Karpoormath, R.; Yu, J.-H.; Nelson, D.R.; Syed, K. Comparative Analyses of Cytochrome P450s and Those Associated with Secondary Metabolism in Bacillus Species. Int. J. Mol. Sci. 2018, 19, 3623. https://doi.org/10.3390/ijms19113623
Mthethwa BC, Chen W, Ngwenya ML, Kappo AP, Syed PR, Karpoormath R, Yu J-H, Nelson DR, Syed K. Comparative Analyses of Cytochrome P450s and Those Associated with Secondary Metabolism in Bacillus Species. International Journal of Molecular Sciences. 2018; 19(11):3623. https://doi.org/10.3390/ijms19113623
Chicago/Turabian StyleMthethwa, Bongumusa Comfort, Wanping Chen, Mathula Lancelot Ngwenya, Abidemi Paul Kappo, Puleng Rosinah Syed, Rajshekhar Karpoormath, Jae-Hyuk Yu, David R. Nelson, and Khajamohiddin Syed. 2018. "Comparative Analyses of Cytochrome P450s and Those Associated with Secondary Metabolism in Bacillus Species" International Journal of Molecular Sciences 19, no. 11: 3623. https://doi.org/10.3390/ijms19113623
APA StyleMthethwa, B. C., Chen, W., Ngwenya, M. L., Kappo, A. P., Syed, P. R., Karpoormath, R., Yu, J.-H., Nelson, D. R., & Syed, K. (2018). Comparative Analyses of Cytochrome P450s and Those Associated with Secondary Metabolism in Bacillus Species. International Journal of Molecular Sciences, 19(11), 3623. https://doi.org/10.3390/ijms19113623