Abstract
The bacterium Saccharothrix syringae NRRL B-16468 is the producer of nocamycin I and nocamycin II which feature tetramic acid and bicyclic ketal groups. In this study, we presented the complete genome of S. syringae NRRL B-16468 obtained from ARS Culture Collection. It contains a circular chromosome of 10,929,570 bp with an average GC content of 73.49%, 9316 genes, 12 rRNAs and 54 tRNAs. Bioinformatics analyses of the genome has demonstrated that it harbors 55 putative biosynthetic gene clusters (BGCs) involved in synthesizing diverse secondary metabolites. The backbones of the natural products synthesized by these BGCs encoding for type I polyketide synthase (PKS), non-ribosomal peptide synthetase (NRPS) and hybrid type I PKS-NRPS were analyzed, furthermore, the natural products synthesized by these BGCs with > 40% similarity to known BGCs were described in detail. The complete genome of S. syringae reveals its capacity in producing diverse bioactive natural products, and it will also shed lights on mining novel secondary metabolites from S. syringae through rational strategies.
Similar content being viewed by others
References
Monciardini P, Iorio M, Maffioli S, Sosio M, Donadio S (2014) Discovering new bioactive molecules from microbial sources. Microb Biotechnol 7(3):209–220
Okada BK, Seyedsayamdost MR (2017) Antibiotic dialogues: induction of silent biosynthetic gene clusters by exogenous small molecules. FEMS Microbiol Rev 41(1):19–33
Strobel T, Al-Dilaimi A, Blom J, Gessner A, Kalinowski J, Luzhetska M, Pühler A, Szczepanowski R, Bechthold A, Rückert C (2012) Complete genome sequence of Saccharothrix espanaensis DSM 44229(T) and comparison to the other completely sequenced Pseudonocardiaceae. BMC Genom 13:465
Liu C, Fan D, Li Y, Chen Y, Huang L, Yan X (2018) Transcriptome analysis of Valsa mali reveals its response mechanism to the biocontrol actinomycete Saccharothrix yanglingensis Hhs.015. BMC Microbiol 18(1):90
Lu S, Nishimura S, Takenaka K, Ito M, Kato T, Kakeya H (2018) Discovery of presaccharothriolide X, a retro-Michael reaction product of saccharothriolide B, from the rare actinomycete Saccharothrix sp. A1506. Org Lett 20(15):4406–4410
Gauze GF, Sveshnikova MA, Ukholina RS, Komarova GN, Bazhanov VS (1977) Formation of a new antibiotic, nocamycin, by a culture of Nocardiopsis syringae sp. Nov. Antibiotiki 22(6):483–486
Mo X, Shi C, Gui C, Zhang Y, Ju J, Wang Q (2017) Identification of nocamycin biosynthetic gene cluster from Saccharothrix syringae NRRL B-16468 and generation of new nocamycin derivatives by manipulating gene cluster. Microb Cell Fact 16(1):100
Mo X, Gui C, Wang Q (2017) Elucidation of a carboxylate O-methyltransferase NcmP in nocamycin biosynthetic pathway. Bioorg Med Chem Lett 27(18):4431–4435
Li R, Li Y, Kristiansen K, Wang J (2008) SOAP: short oligonucleotide alignment program. Bioinformatics 24(5):713–714
Koren S, Walenz BP, Berlin K, Miller JR, Bergman NH, Phillippy AM (2017) Canu: scalable and accurate long-read assembly via adaptive k-mer weighting and repeat separation. Genome Res 27(5):722–736
Huerta-Cepas J, Szklarczyk D, Forslund K, Cook H, Heller D, Walter MC, Rattei T, Mende DR, Sunagawa S, Kuhn M, Jensen LJ, von Mering C, Bork P (2016) eggNOG 4.5: a hierarchical orthology framework with improved functional annotations for eukaryotic, prokaryotic and viral sequences. Nucleic Acids Res 44(D1):D286-293
Blin K, Shaw S, Steinke K, Villebro R, Ziemert N, Lee SY, Medema MH, Weber T (2019) antiSMASH 5.0: updates to the secondary metabolite genome mining pipeline. Nucleic Acids Res 47(W1):W81–W87
León B, Navarro G, Dickey BJ, Stepan G, Tsai A, Jones GS, Morales ME, Barnes T, Ahmadyar S, Tsiang M, Geleziunas R, Cihlar T, Pagratis N, Tian Y, Yu H, Linington RG (2015) Abyssomicin 2 reactivates latent HIV-1 by a PKC- and HDAC-independent mechanism. Org Lett 17(2):262–265
Wang Q, Song F, Xiao X, Huang P, Li L, Monte A, Abdel-Mageed WM, Wang J, Guo H, He W, Xie F, Dai H, Liu M, Chen C, Xu H, Liu M, Piggott AM, Liu X, Capon RJ, Zhang L (2013) Abyssomicins from the South China Sea deep-sea sediment Verrucosispora sp.: natural thioether Michael addition adducts as antitubercular prodrugs. Angew Chem Int Ed 52(4):1231–1234
Huang P, Xie F, Ren B, Wang Q, Wang J, Wang Q, Abdel-Mageed WM, Liu M, Han J, Oyeleye A, Shen J, Song F, Dai H, Liu X, Zhang L (2016) Anti-MRSA and anti-TB metabolites from marine-derived Verrucosispora sp. MS100047. Appl Microbiol Biotechnol 100(17):7437–7447
Gottardi EM, Krawczyk JM, von Suchodoletz H, Schadt S, Mühlenweg A, Uguru GC, Pelzer S, Fiedler HP, Bibb MJ, Stach JE, Süssmuth RD (2011) Abyssomicin biosynthesis: formation of an unusual polyketide, antibiotic-feeding studies and genetic analysis. ChemBioChem 12(9):1401–1410
Blodgett JA, Oh DC, Cao S, Currie CR, Kolter R, Clardy J (2010) Common biosynthetic origins for polycyclic tetramate macrolactams from phylogenetically diverse bacteria. Proc Natl Acad Sci USA 107(26):11692–11697
Zhang G, Zhang W, Saha S, Zhang C (2016) Recent advances in discovery, biosynthesis and genome mining of medicinally relevant polycyclic tetramate macrolactams. Curr Top Med Chem 16(15):1727–1739
Schmoock G, Pfennig F, Jewiarz J, Schlumbohm W, Laubinger W, Schauwecker F, Keller U (2005) Functional cross-talk between fatty acid synthesis and nonribosomal peptide synthesis in quinoxaline antibiotic-producing Streptomycetes. J Biol Chem 280(6):4339–4349
Watanabe K, Hotta K, Nakaya M, Praseuth AP, Wang CC, Inada D, Takahashi K, Fukushi E, Oguri H, Oikawa H (2009) Escherichia coli allows efficient modular incorporation of newly isolated quinomycin biosynthetic biosynthetic enzyme into echinomycin biosynthetic pathway for rational design and synthesisof potent antibiotic unnatural natural product. J Am Chem Soc 131(26):9347–9353
Pu JY, Peng C, Tang MC, Zhang Y, Guo JP, Song LQ, Hua Q, Tang GL (2013) Naphthyridinomycin biosynthesis revealing the use of leader peptide to guide nonribosomal peptide assembly. Org Lett 15(14):3674–3677
Giessen TW, Franke KB, Knappe TA, Kraas FI, Bosello M, Xie X, Linne U, Marahiel MA (2012) Isolation, structure elucidation, and biosynthesis of an unusual hydroxamic acid ester-containing siderophore from Actinosynnema mirum. J Nat Prod 75(5):905–914
Udwary DW, Zeigler L, Asolkar RN, Singan V, Lapidus A, Fenical W, Jensen PR, Moore BS (2007) Genome sequencing reveals complex secondary metabolome in the marine actinomycete Salinispora tropica. Proc Natl Acad Sci USA 104(25):10376–10381
Acknowledgements
This work was supported by Grants from the National Natural Science Foundation of China (No. 31300063), Research Foundation for Advanced Talents of Qingdao Agricultural University (No. 631301), and Open Research Project from Guangdong Key Laboratory of Marine Materia Medica (No. LMM2019-1).
Author information
Authors and Affiliations
Contributions
XM conceived and performed the experiments. XM and SY analyzed the data and wrote the manuscript. All authors read the approved the manuscript.
Corresponding author
Ethics declarations
Conflict of interest
All the authors declare no conflict of interests with respect to this paper.
Research Involving Human and Animal Participants
This research does not contain any studies with human participants or animals performed by any of the authors.
Additional information
Publisher's Note
Springer Nature remains neutral with regard to jurisdictional claims in published maps and institutional affiliations.
Electronic supplementary material
Below is the link to the electronic supplementary material.
Rights and permissions
About this article
Cite this article
Mo, X., Yang, S. Complete Genome of Nocamycin-Producing Strain Saccharothrix syringae NRRL B-16468 Reveals the Biosynthetic Potential for Secondary Metabolites. Curr Microbiol 78, 107–113 (2021). https://doi.org/10.1007/s00284-020-02272-0
Received:
Accepted:
Published:
Issue Date:
DOI: https://doi.org/10.1007/s00284-020-02272-0