Improving the Yield and Quality of Daptomycin in by Multilevel Metabolic Engineering

Overview

Journal Front Microbiol

Specialty Microbiology

Date 2022 May 5

PMID 35509317

Authors

Zhong-Yuan Lyu

Qing-Ting Bu

Jiao-Le Fang

Chen-Yang Zhu

Wei-Feng Xu

Lie Ma

Wen-Li Gao

Xin-Ai Chen

Yong-Quan Li

Affiliations

Soon will be listed here.

Abstract

Daptomycin is a cyclic lipopeptide antibiotic with a significant antibacterial action against antibiotic-resistant Gram-positive bacteria. Despite numerous attempts to enhance daptomycin yield throughout the years, the production remains unsatisfactory. This study reports the application of multilevel metabolic engineering strategies in to reconstruct high-quality daptomycin overproducing strain L2797-VHb, including precursor engineering (i.e., refactoring kynurenine pathway), regulatory pathway reconstruction (i.e., knocking out negative regulatory genes and ), byproduct engineering (i.e., removing pigment), multicopy biosynthetic gene cluster (BGC), and fermentation process engineering (i.e., enhancing O supply). The daptomycin titer of L2797-VHb arrived at 113 mg/l with 565% higher comparing the starting strain L2790 (17 mg/l) in shake flasks and was further increased to 786 mg/l in 15 L fermenter. This multilevel metabolic engineering method not only effectively increases daptomycin production, but can also be applied to enhance antibiotic production in other industrial strains.

Citing Articles

Overproduction of endusamycin in subsp. .

Chang Y, Liu Z, Deng Z, Liu T Synth Syst Biotechnol. 2025; 10(2):523-531.

PMID: 40061181 PMC: 11889735. DOI: 10.1016/j.synbio.2025.02.004.

The Transcriptional Regulator DhyR Positively Modulates Daptomycin Biosynthesis in Streptomyces roseosporus.

He F, Liu X, Wang H, Li X, Wu Y, Zhang D Microb Biotechnol. 2025; 18(3):e70110.

PMID: 40025688 PMC: 11872808. DOI: 10.1111/1751-7915.70110.

Metabolic engineering of for high-level production of pneumocandin B.

Zhang X, Cheng S, Yang J, Lu L, Deng Z, Bian G Synth Syst Biotechnol. 2025; 10(2):381-390.

PMID: 39830076 PMC: 11742615. DOI: 10.1016/j.synbio.2024.12.008.

Metabolic engineering of Streptomyces roseosporus for increased production of clinically important antibiotic daptomycin.

Li X, Sang Z, Zhao X, Wen Y Microb Biotechnol. 2024; 17(11):e70038.

PMID: 39487765 PMC: 11530997. DOI: 10.1111/1751-7915.70038.

Stepwise increase of fidaxomicin in an engineered heterologous host through multi-level metabolic engineering.

Xie H, Su Y, Bu Q, Li Y, Zhao Q, Du Y Synth Syst Biotechnol. 2024; 9(4):766-774.

PMID: 39021363 PMC: 11253128. DOI: 10.1016/j.synbio.2024.06.004.

References

Wentzel A, Bruheim P, Overby A, Jakobsen O, Sletta H, Omara W . Optimized submerged batch fermentation strategy for systems scale studies of metabolic switching in Streptomyces coelicolor A3(2). BMC Syst Biol. 2012; 6:59. PMC: 3431225. DOI: 10.1186/1752-0509-6-59. View

Mironczuk A, Kosiorowska K, Biegalska A, Rakicka-Pustulka M, Szczepanczyk M, Dobrowolski A . Heterologous overexpression of bacterial hemoglobin VHb improves erythritol biosynthesis by yeast Yarrowia lipolytica. Microb Cell Fact. 2019; 18(1):176. PMC: 6794898. DOI: 10.1186/s12934-019-1231-9. View

Murakami T, Burian J, Yanai K, Bibb M, Thompson C . A system for the targeted amplification of bacterial gene clusters multiplies antibiotic yield in Streptomyces coelicolor. Proc Natl Acad Sci U S A. 2011; 108(38):16020-5. PMC: 3179087. DOI: 10.1073/pnas.1108124108. View

Staunton J, Weissman K . Polyketide biosynthesis: a millennium review. Nat Prod Rep. 2001; 18(4):380-416. DOI: 10.1039/a909079g. View

Miao V, Coeffet-LeGal M, Brian P, Brost R, Penn J, Whiting A . Daptomycin biosynthesis in Streptomyces roseosporus: cloning and analysis of the gene cluster and revision of peptide stereochemistry. Microbiology (Reading). 2005; 151(Pt 5):1507-1523. DOI: 10.1099/mic.0.27757-0. View

Chari R, Yeo N, Chavez A, Church G . sgRNA Scorer 2.0: A Species-Independent Model To Predict CRISPR/Cas9 Activity. ACS Synth Biol. 2017; 6(5):902-904. PMC: 5793212. DOI: 10.1021/acssynbio.6b00343. View

Bednarz B, Millan-Oropeza A, Kotowska M, Swiat M, Quispe Haro J, Henry C . Coelimycin Synthesis Activatory Proteins Are Key Regulators of Specialized Metabolism and Precursor Flux in A3(2). Front Microbiol. 2021; 12:616050. PMC: 8062868. DOI: 10.3389/fmicb.2021.616050. View

Aziz R, Bartels D, Best A, DeJongh M, Disz T, Edwards R . The RAST Server: rapid annotations using subsystems technology. BMC Genomics. 2008; 9:75. PMC: 2265698. DOI: 10.1186/1471-2164-9-75. View

Luo S, Chen X, Mao X, Li Y . Regulatory and biosynthetic effects of the bkd gene clusters on the production of daptomycin and its analogs A21978C. J Ind Microbiol Biotechnol. 2018; 45(4):271-279. DOI: 10.1007/s10295-018-2011-y. View

10.

Wang F, Ren N, Luo S, Chen X, Mao X, Li Y . DptR2, a DeoR-type auto-regulator, is required for daptomycin production in Streptomyces roseosporus. Gene. 2014; 544(2):208-15. DOI: 10.1016/j.gene.2014.04.044. View

11.

Choi S, Nah H, Choi S, Kim E . Heterologous Expression of Daptomycin Biosynthetic Gene Cluster Via Artificial Chromosome Vector System. J Microbiol Biotechnol. 2019; 29(12):1931-1937. DOI: 10.4014/jmb.1909.09022. View

12.

Wittmann M, Linne U, Pohlmann V, Marahiel M . Role of DptE and DptF in the lipidation reaction of daptomycin. FEBS J. 2008; 275(21):5343-54. DOI: 10.1111/j.1742-4658.2008.06664.x. View

13.

Li L, Wei K, Liu X, Wu Y, Zheng G, Chen S . aMSGE: advanced multiplex site-specific genome engineering with orthogonal modular recombinases in actinomycetes. Metab Eng. 2018; 52:153-167. DOI: 10.1016/j.ymben.2018.12.001. View

14.

Lin C, Zhang Y, Wu J, Xie R, Qiao J, Zhao G . Regulatory Patterns of Crp on Monensin Biosynthesis in . Microorganisms. 2020; 8(2). PMC: 7074812. DOI: 10.3390/microorganisms8020271. View

15.

Luo S, Chen X, Mao X, Li Y . Transposon-based identification of a negative regulator for the antibiotic hyper-production in Streptomyces. Appl Microbiol Biotechnol. 2018; 102(15):6581-6592. DOI: 10.1007/s00253-018-9103-5. View

16.

Zhou T, Kim B, Zhong J . Enhanced production of validamycin A in Streptomyces hygroscopicus 5008 by engineering validamycin biosynthetic gene cluster. Appl Microbiol Biotechnol. 2014; 98(18):7911-22. DOI: 10.1007/s00253-014-5943-9. View

17.

Liao G, Wang L, Liu Q, Guan F, Huang Y, Hu C . Manipulation of kynurenine pathway for enhanced daptomycin production in Streptomyces roseosporus. Biotechnol Prog. 2013; 29(4):847-52. DOI: 10.1002/btpr.1740. View

18.

Li H, Gao W, Cui Y, Pan Y, Liu G . Remarkable enhancement of bleomycin production through precise amplification of its biosynthetic gene cluster in Streptomyces verticillus. Sci China Life Sci. 2021; 65(6):1248-1256. DOI: 10.1007/s11427-021-1998-8. View

19.

Li H, Zhang D, Yue T, Jiang L, Yu X, Zhao P . Improved polysaccharide production in a submerged culture of Ganoderma lucidum by the heterologous expression of Vitreoscilla hemoglobin gene. J Biotechnol. 2015; 217:132-7. DOI: 10.1016/j.jbiotec.2015.11.011. View

20.

Barbuto Ferraiuolo S, Cammarota M, Schiraldi C, Restaino O . Streptomycetes as platform for biotechnological production processes of drugs. Appl Microbiol Biotechnol. 2021; 105(2):551-568. PMC: 7780072. DOI: 10.1007/s00253-020-11064-2. View