Enhanced Natamycin production in Streptomyces gilvosporeus through phosphate tolerance screening and transcriptome-based analysis of high-yielding mechanisms.

Publisher: BioMed Central Country of Publication: England NLM ID: 101139812 Publication Model: Electronic Cited Medium: Internet ISSN: 1475-2859 (Electronic) Linking ISSN: 14752859 NLM ISO Abbreviation: Microb Cell Fact Subsets: MEDLINE

Original Publication: London : BioMed Central, [2002-

Streptomyces*/metabolism ; Streptomyces*/genetics ; Natamycin*/biosynthesis ; Phosphates*/metabolism; Gene Expression Profiling ; Transcriptome ; Multigene Family

Competing Interests: Declarations. Ethics approval and consent to participate: All authors read and approved the final manuscript and related ethics. Consent for publication: All authors consent to this manuscript for publication after revising this final form. Competing interests: The authors declare no competing interests.
Background: Natamycin is a natural antibiotic with broad-spectrum antifungal activity, widely used in food preservation, medicine, and biological control. However, the relatively low biosynthetic capacity of producing strains limits further industrialization and broader applications of natamycin. Due to the complexity of cellular metabolism, evolutionary engineering is required for developing strains with enhanced natamycin biosynthetic capacity.
Results: Here, protoplast fusion combined with phosphate tolerance screening was employed for the first time to enhance natamycin production of Streptomyces gilvosporeus. A high-yielding strain, GR-2, was obtained, with natamycin production twice that of the original strain. Transcriptomic analysis revealed that the natamycin biosynthetic gene cluster and several primary metabolic pathways were significantly upregulated in GR-2, likely contributing to its high production performance. Further experiments, including amino acid addition and reverse engineering, confirmed that branched-chain amino acid, nitrogen, and phosphate metabolism play crucial roles in promoting natamycin production. Silencing of the phosphate metabolism transcriptional regulators PhoP and PhoR led to a decreased expression of natamycin biosynthetic genes and significantly reduced natamycin production, highlighting the key role of these regulators in S. gilvosporeus. Based on omics data, co-expression of phoP and phoR in GR-2 resulted in the engineered strain GR2-P3, which exhibited a 25% increase in natamycin production in shake flasks. In a 5 L fermenter, GR2-P3 achieved a natamycin production of 12.2 ± 0.6 g·L⁻¹, the highest yield reported for S. gilvosporeus to date.
Conclusions: Our findings suggest that the high production performance of GR-2 is primarily due to the upregulation of the natamycin biosynthetic gene cluster and genes related to precursor supply. Increasing the intracellular supply of valine and glutamate significantly enhanced natamycin production. Additionally, the natamycin biosynthetic gene cluster is likely positively regulated by PhoP and PhoR. Our work presents a novel strategy for strain screening and evolution to improve natamycin production and identifies novel molecular targets for metabolic engineering.
(© 2025. The Author(s).)

Metab Eng. 2007 Mar;9(2):217-27. (PMID: 17142079)
Int J Nanomedicine. 2019 Apr 08;14:2515-2531. (PMID: 31040672)
J Microbiol Biotechnol. 2016 Feb;26(2):241-7. (PMID: 26502732)
mBio. 2024 Sep 11;15(9):e0164224. (PMID: 39152718)
Biotechnol Biofuels Bioprod. 2022 May 14;15(1):50. (PMID: 35568955)
J Glob Antimicrob Resist. 2013 Jun;1(2):109-113. (PMID: 27873577)
Prep Biochem Biotechnol. 2017 Oct 21;47(9):939-944. (PMID: 28816611)
Microbiol Res. 2022 Sep;262:127077. (PMID: 35688098)
Adv Exp Med Biol. 2022;1362:135-150. (PMID: 35288878)
Proc Natl Acad Sci U S A. 2003 May 13;100(10):6133-8. (PMID: 12730372)
ACS Synth Biol. 2020 Apr 17;9(4):814-826. (PMID: 32202411)
J Biol Chem. 1999 Apr 9;274(15):10133-9. (PMID: 10187796)
Microb Cell Fact. 2024 Mar 27;23(1):94. (PMID: 38539197)
ACS Synth Biol. 2020 Dec 18;9(12):3236-3244. (PMID: 33186034)
J Ind Microbiol Biotechnol. 2019 May;46(5):725-737. (PMID: 30712141)
Methods Enzymol. 2009;459:215-42. (PMID: 19362642)
Mol Genet Genomics. 2012 Jul;287(7):565-73. (PMID: 22643908)
BMC Biotechnol. 2019 Jul 16;19(1):46. (PMID: 31311527)
Int J Mol Sci. 2020 Feb 14;21(4):. (PMID: 32075107)
Pest Manag Sci. 2024 Apr;80(4):1981-1990. (PMID: 38087429)
Int J Mol Sci. 2022 Sep 05;23(17):. (PMID: 36077572)
Appl Microbiol Biotechnol. 2020 May;104(10):4471-4482. (PMID: 32221688)
Food Chem. 2016 Mar 1;194:928-37. (PMID: 26471636)
Microbiol Res. 2015 Apr;173:25-33. (PMID: 25801968)
Microbiol Spectr. 2023 Sep 11;:e0087923. (PMID: 37695060)
Sheng Wu Gong Cheng Xue Bao. 2015 May;31(5):744-51. (PMID: 26571695)
Biomolecules. 2021 May 12;11(5):. (PMID: 34065948)
J Environ Manage. 2022 Nov 1;321:115856. (PMID: 35985261)
BMC Genomics. 2018 Jun 14;19(1):457. (PMID: 29898657)
Front Endocrinol (Lausanne). 2021 Oct 29;12:757088. (PMID: 34777253)
Int J Mol Sci. 2022 Jun 09;23(12):. (PMID: 35742917)
J Appl Genet. 2021 Feb;62(1):165-182. (PMID: 33415709)
Int J Biol Sci. 2022 Mar 6;18(6):2304-2316. (PMID: 35414794)
Mol Microbiol. 2009 Apr;72(1):53-68. (PMID: 19220751)
Microb Cell Fact. 2022 May 14;21(1):83. (PMID: 35568948)
Microb Cell Fact. 2021 Mar 9;20(1):66. (PMID: 33750383)
Int J Mol Sci. 2022 Jan 05;23(1):. (PMID: 35008994)
Front Microbiol. 2022 Mar 22;12:813993. (PMID: 35392450)
Appl Microbiol Biotechnol. 2021 May;105(10):4017-4031. (PMID: 33950280)
Bioresour Technol. 2019 Feb;273:377-385. (PMID: 30453252)
Microbiol Res. 2017 Dec;205:80-87. (PMID: 28942849)
J Antibiot (Tokyo). 2017 Nov 01;:. (PMID: 29089595)
Food Sci Biotechnol. 2022 Oct 31;32(3):341-352. (PMID: 36778090)
Microb Cell Fact. 2019 Nov 27;18(1):206. (PMID: 31775761)
Commun Biol. 2022 May 9;5(1):432. (PMID: 35534536)
Microbiology (Reading). 2011 May;157(Pt 5):1300-1311. (PMID: 21330439)
Int Microbiol. 2020 Aug;23(3):441-451. (PMID: 31927642)
ACS Synth Biol. 2019 Apr 19;8(4):866-875. (PMID: 30865822)

JUSRP123040 The Fundamental Research Funds for the Central Universities; KLIB-KF202206 Program of the Key Laboratory of Industrial Biotechnology, Ministry of Education, China; 2020YFA0907700 National Key R&D Program of China; BE2022703 Key R&D Program of Jiangsu Province; CX(24)3086l Jiangsu Agricultural Science And Technology Innovation Fund

Keywords: Streptomyces gilvosporeus; Comparative transcriptomics; Natamycin; Phosphate-tolerance screening; Transcriptional regulation

8O0C852CPO (Natamycin)
0 (Phosphates)

Date Created: 20250402 Date Completed: 20250403 Latest Revision: 20250405

20250407

PMC11963449

10.1186/s12934-025-02696-y

40176084