A comprehensive genomic and growth proteomic analysis of antitumor lipopeptide bacillomycin Lb biosynthesis in Bacillus amyloliquefaciens X030
Lipopeptides (such as iturin, fengycin, and surfactin) from Bacillus possess antibacterial, antifungal, and antiviral activities and have important application in agriculture and pharmaceuticals. Although unremitting efforts have been devoted to improve lipopeptide production by designing gene regulatory circuits or optimizing fermentation process, little attention has been paid to utilizing multi-omics for systematically mining core genes and proteins during the bacterial growth cycle. Here, lipopeptide bacillomycin Lb from new Bacillus amyloliquefaciens X030 was isolated and first found to have anticancer activity in various cancer cells (such as SMMC-7721 and MDA-MB-231). A comprehensive genomic and growth proteomic analysis of X030 revealed bacillomycin Lb biosynthetic gene cluster, key enzymes and potential regulatory proteins (PerR, PhoP, CcpA, and CsfB), and novel links between primary metabolism and bacillomycin Lb production in X030. The antitumor activity of the fermentation supernatant supplemented with amino acids (such as glutamic acid) and sucrose was significantly increased, verifying the role of key metabolic switches in the metabolic regulatory network. Quantitative real-time PCR analysis confirmed that 7 differential expressed genes exhibited a positive correlation between changes at transcriptional and translational levels. The study not only will stimulate the deeper and wider antitumor study of lipopeptides but also provide a comprehensive database, which promotes an in-depth analysis of pathways and networks for complex events in lipopeptide biosynthesis and regulation and gives great help in improving the yield of bacillomycin Lb (media optimization, genetic modification, or pathway engineering).
KeywordsGenomics Growth proteomics Bacillomycin Lb Lipopeptide Anticancer
This work was financially supported by the National key Research and Development program of China (2017YFD0201201), the National Natural Science Foundation of China (31370116), and the Cooperative Innovation Center of Engineering and New Products for Developmental Biology of Hunan Province (20134486).
Compliance with ethical standards
This study did not involve any research involving human participants or animals.
Conflict of interest
The authors declare that they have no conflict of interest.
- Bartolini M, Cogliati S, Vileta D, Bauman C, Ramirez W, Grau R (2019) The stress-responsive alternative sigma factor SigB plays a positive role in the antifungal proficiency of Bacillus subtilis. Appl Environ Microbiol 85. https://doi.org/10.1128/AEM.00178-19
- Belbahri L, Chenari Bouket A, Rekik I, Alenezi FN, Vallat A, Luptakova L, Petrovova E, Oszako T, Cherrad S, Vacher S, Rateb ME (2017) Comparative genomics of Bacillus amyloliquefaciens strains reveals a core genome with traits for habitat adaptation and a secondary metabolites rich accessory genome. Front Microbiol 8:1438. https://doi.org/10.3389/fmicb.2017.01438 PubMedGoogle Scholar
- D'Souza C, Nakano MM, Zuber P (1994) Identification of comS, a gene of the srfA operon that regulates the establishment of genetic competence in Bacillus subtilis. Proc Natl Acad Sci U S A 91(20):9397–9401. https://doi.org/10.1073/pnas.91.20.9397
- Hu Y, Nan F, Maina SW, Guo J, Wu S, Xin Z (2018) Clone of plipastatin biosynthesis gene cluster by transformation-associated recombination technique and high efficient expression in model organism Bacillus subtilis. J Biotechnol 288:1–8. https://doi.org/10.1016/j.jbiotec.2018.10.006 PubMedGoogle Scholar
- Lim SM, Yoon M-Y, Choi GJ, Choi YH, Jang KS, Shin TS, Park HW, Yu NH, Kim YH, Kim J-C (2017) Diffusible and volatile antifungal compounds produced by an antagonistic Bacillus velezensis G341 against various phytopathogenic fungi. Plant Pathol J 33(5):488–498. https://doi.org/10.5423/ppj.oa.04.2017.0073 PubMedGoogle Scholar
- Luo Y, Ding X, Xia L, Huang F, Li W, Huang S, Tang Y, Sun Y (2011) Comparative proteomic analysis of Saccharopolyspora spinosa SP06081 and PR2 strains reveals the differentially expressed proteins correlated with the increase of spinosad yield. Proteome Sci 9:40. https://doi.org/10.1186/1477-5956-9-40 PubMedGoogle Scholar
- Salzberg LI, Botella E, Hokamp K, Antelmann H, Maass S, Becher D, Noone D, Devine KM (2015) Genome-wide analysis of phosphorylated PhoP binding to chromosomal DNA reveals several novel features of the PhoPR-mediated phosphate limitation response in Bacillus subtilis. J Bacteriol 197(8):1492–1506. https://doi.org/10.1128/JB.02570-14 PubMedGoogle Scholar
- Smith DDN, Williams AN, Verrett JN, Bergbusch NT, Manning V, Trippe K, Stavrinides J (2019) Resistance to two vinylglycine antibiotic analogs is conferred by inactivation of two separate amino acid transporters in Erwinia amylovora. J Bacteriol 201(9). https://doi.org/10.1128/JB.00658-18
- Soussi S, Essid R, Hardouin J, Gharbi D, Elkahoui S, Tabbene O, Cosette P, Jouenne T, Limam F (2018) Utilization of grape seed flour for antimicrobial lipopeptide production by Bacillus amyloliquefaciens C5 strain. Appl Biochem Biotechnol 187(4):1460–1474. https://doi.org/10.1007/s12010-018-2885-1 PubMedGoogle Scholar
- Yang Q, Ding X, Liu X, Liu S, Sun Y, Yu Z, Hu S, Rang J, He H, He L, Xia L (2014) Differential proteomic profiling reveals regulatory proteins and novel links between primary metabolism and spinosad production in Saccharopolyspora spinosa. Microb Cell Factories 13(1):27. https://doi.org/10.1186/1475-2859-13-27 Google Scholar
- Zhou M, Liu F, Yang X, Jin J, Dong X, Zeng K-W, Liu D, Zhang Y, Ma M, Yang D (2018b) Bacillibactin and bacillomycin analogues with cytotoxicities against human cancer cell lines from marine Bacillus sp PKU-MA00093 and PKU-MA00092. Mar Drugs 16(1):22. https://doi.org/10.3390/md16010022 Google Scholar