Genomic-driven discovery of an amidinohydrolase involved in the biosynthesis of mediomycin A
Clethramycin (1) and mediomycin A (2) belong to the linear polyene polyketide (LPP) family of antibiotics that exhibit potent antifungal activity. Structural similarities exist between 1 and 2, except that 2 contains an amino moiety substituted for the guanidino moiety. Herein, the draft genome sequence of Streptomyces mediocidicus ATCC23936, a strain which produces both 1 and 2, was obtained through de novo sequencing. Bioinformatic analysis of the genome revealed a clethramycin (cle) gene cluster that contained 25 open reading frames (orfs). However, amidinohydrolase for 2 formation was not found in the cle gene cluster. Further genomic analysis revealed an amidinohydrolase MedX, which can hydrolyse the guanidino form (1) into the amino form (2) via heterologous co-expression of the cle cluster in Streptomyces lividans or by in vitro catalysis. These results also suggest the feasibility of engineering novel LPPs for drug discovery by manipulating the biosynthetic machinery of S. mediocidicus.
KeywordsBiosynthesis Clethramycin Mediomycin A Amidinohydrolase Linear polyene polyketides (LPPs)
We thank Dr. Mei Ge, Shanghai Laiyi Center for Biopharmaceuticals R & D, for providing S. mediocidicus ATCC23936.
This work was supported by grants from Tianjin science and technology plan projects (no. 16YFZCSY01000).
Compliance with ethical standards
Conflict of interest
The authors declare that they have no conflict of interest.
This article does not contain any studies with human participants or animals performed by any of the authors.
- Banskota AH, Mcalpine JD, Ibrahim A, Aouidate M, Piraee M, Alarco AM, Farnet CM, Zazopoulos E (2006) Genomic analyses lead to novel secondary metabolites. Part 3. ECO-0501, a novel antibacterial of a new class. J Antibiot 59(9):533–542. https://doi.org/10.1038/ja.2006.74 CrossRefPubMedGoogle Scholar
- Elkins JM, Clifton IJ, Hernández H, Doan LX, Robinson CV, Schofield CJ, Hewitson KS (2002) Oligomeric structure of proclavaminic acid amidino hydrolase: evolution of a hydrolytic enzyme in clavulanic acid biosynthesis. Biochem J 366(2):423–434. https://doi.org/10.1042/bj20020125 CrossRefPubMedPubMedCentralGoogle Scholar
- Furumai T, Yamakawa T, Yoshida R, Igarashi Y (2003) Clethramycin, a new inhibitor of pollen tube growth with antifungal activity from Streptomyces hygroscopicus TP-A0623. I. Screening, taxonomy, fermentation, isolation and biological properties. J Antibiot 56(8):700–704. https://doi.org/10.7164/antibiotics.56.700 CrossRefPubMedGoogle Scholar
- Gust B, Challis GL, Fowler K, Kieser T, Chater KF (2003) PCR-targeted Streptomyces gene replacement identifies a protein domain needed for biosynthesis of the sesquiterpene soil odor geosmin. Proc Natl Acad Sci U S A 100(4):1541–1546. https://doi.org/10.1073/pnas.0337542100 CrossRefPubMedPubMedCentralGoogle Scholar
- Hornung A, Bertazzo M, Dziarnowski A, Schneider K, Welzel K, Wohlert SE, Holzenkämpfer M, Nicholson GJ, Bechthold A, Süssmuth RD (2007) A genomic screening approach to the structure-guided identification of drug candidates from natural sources. Chembiochem 8(7):757–766. https://doi.org/10.1002/cbic.200600375 CrossRefPubMedGoogle Scholar
- Igarashi Y, Iwashita T, Fujita T, Naoki H, Yamakawa T, Yoshida R, Furuma T (2003) Clethramycin, a new inhibitor of pollen tube growth with antifungal activity from Streptomyces hygroscopicus TP-A0623. II. Physico-chemical properties and structure determination. J Antibiot 56(8):705–708. https://doi.org/10.7164/antibiotics.56.705 CrossRefPubMedGoogle Scholar
- Lee SJ, Kim DJ, Kim HS, Lee BI, Yoon HJ, Yoon JY, Kim KH, Jang JY, Im HN, An DR (2011) Crystal structures of Pseudomonas aeruginosa guanidinobutyrase and guanidinopropionase, members of the ureohydrolase superfamily. J Struct Biol 175(3):329–338. https://doi.org/10.1016/j.jsb.2011.05.002 CrossRefPubMedGoogle Scholar
- Mcalpine JB, Bachmann BO, Piraee M, Tremblay S, Alarco AM, Zazopoulos E, Farnet CM (2005) Microbial genomics as a guide to drug discovery and structural elucidation: ECO-02301, a novel antifungal agent, as an example. J Nat Prod 68(4):493–496. https://doi.org/10.1021/np0401664 CrossRefPubMedGoogle Scholar
- Nei M, Kumar S (2000) Molecular evolution and phylogenetics. Oxford University Press, USAGoogle Scholar
- Sbaraini N, Andreis FC, Thompson CE, Guedes RLM, Junges Â, Campos T, Staats CC, Vainstein MH, Vasconcelos ATRD, Schrank A (2017) Genome-wide analysis of secondary metabolite gene clusters in ophiostoma ulmi and ophiostoma novo-ulmi reveals a fujikurin-like gene cluster with a putative role in infection. Front Microbiol 8:1063. https://doi.org/10.3389/fmicb.2017.01063 CrossRefPubMedPubMedCentralGoogle Scholar
- Zhang L, Hashimoto T, Qin B, Hashimoto J, Kozone I, Kawahara T, Okada M, Awakawa T, Ito T, Asakawa Y, Ueki M, Takahashi S, Osada H, Wakimoto T, Ikeda H, Shin-Ya K, Abe I (2017) Characterization of giant modular PKSs provides insight into genetic mechanism for structural diversification of aminopolyol polyketides. Angew Chem Int Ed Engl 56(7):1740–1745. https://doi.org/10.1002/anie.201611371 CrossRefPubMedGoogle Scholar