Top-down synthetic biology approach for titer improvement of clinically important antibiotic daptomycin in Streptomyces roseosporus

Ji, Chang-Hun; Kim, Hiyoung; Je, Hyun-Woo; Kwon, Haeun; Lee, Dong‐Ho; Kang, Hahk‐Soo

doi:10.1016/j.ymben.2021.10.013

Cited by 18 publications

(13 citation statements)

References 57 publications

Supporting

Mentioning

Contrasting

Order By: Relevance

“…Improving key gene expressions levels in BGCs usually contributes to higher productions of target secondary metabolites. For example, the transcriptome analysis revealed that the insufficient transcription of dpt genes was probably the major factor contributing to the low daptomycin production in the native producer S. roseosporus NRRL 11379, and improving gene expression by promoter engineering resulted in significant improvement in lipopeptide production ( Ji et al, 2022 ). We speculated that the consistency of gene expression in the late fermentation stage was the key factor for the enhanced erythromycin production in the high-producing strain S0, while the insufficient transcription of ery genes would lead to low yield in the wild-type host.…”

Section: Resultsmentioning

confidence: 99%

Droplet-Microfluidic-Based Promoter Engineering and Expression Fine-Tuning for Improved Erythromycin Production in Saccharopolyspora erythraea NRRL 23338

Yun

Zhang

et al. 2022

Front. Bioeng. Biotechnol.

View full text Add to dashboard Cite

Erythromycin is a clinically important drug produced by the rare actinomycete Saccharopolyspora erythraea. In the wide-type erythromycin producer S. erythraea NRRL 23338, there is a lack of systematical method for promoter engineering as well as a well-characterized promoter panel for comprehensive metabolic engineering. Here we demonstrated a systematical promoter acquiring process including promoter characterization, engineering and high-throughput screening by the droplet-microfluidic based platform in S. erythraea NRRL 23338, and rapidly obtained a panel of promoters with 21.5-fold strength variation for expression fine-tuning in the native host. By comparative qRT-PCR of S. erythraea NRRL 23338 and a high-producing strain S0, potential limiting enzymes were identified and overexpressed individually using two screened synthetic promoters. As a result, erythromycin production in the native host was improved by as high as 137.24 folds by combinational gene overexpression. This work enriches the accessible regulatory elements in the important erythromycin-producing strain S. erythraea NRRL 23338, and also provides a rapid and systematic research paradigm of promoter engineering and expression fine-tuning in the similar filamentous actinomycete hosts.

show abstract

Section: Resultsmentioning

confidence: 99%

Droplet-Microfluidic-Based Promoter Engineering and Expression Fine-Tuning for Improved Erythromycin Production in Saccharopolyspora erythraea NRRL 23338

Yun

Zhang

et al. 2022

Front. Bioeng. Biotechnol.

View full text Add to dashboard Cite

show abstract

“…According to the model, we improved daptomycin production to 36.3 mg/l with an increase of 111% by knocking out kynurenine-related genes, such as orf3344 and orf3242 ( Figure 2B ). However, co-overexpression of other related genes, such as dptJ , orf3245 , and orf3243 , made daptomycin production decrease by 26% ( Figure 2B ) and this may be due to the excessive accumulation of some intermediates, which affect the further synthesis of L-Kyn ( Ji et al, 2021 ) or are toxic to the cell itself, thereby affecting the accumulation of daptomycin. The underlying mechanisms may be complicated.…”

Section: Discussionmentioning

confidence: 99%

“…In addition to the red pigment, the production process of daptomycin is also accompanied by other byproducts, such as homologs of daptomycin. Although deleting branched-chain α-keto acid dehydrogenase (BKD) enzyme complex could remove homologs of daptomycin containing branched-chain fatty acids (BCFAs), it introduced new homologs of daptomycin with straight-chain fatty acids ( Ji et al, 2021 ). Therefore, in future studies, other methods should be considered to completely solve the problem of daptomycin homologs, such as the directed evolution of DptE, an acyl AMP ligase, on improving its substrate selectivity.…”

Section: Discussionmentioning

confidence: 99%

“…Finally, we further increased daptomycin to 105 mg/l with an increase of 40% by introducing an extra copy of daptomycin BGC, which implied that multicopy of BGC can efficiently enhance the biosynthesis of daptomycin ( Figure 3A ). According to previous studies, the overall transcriptional level of dpt BGC is too low to meet the efficient production of daptomycin in S. roseosporus ( Ji et al, 2021 ). Recently, Lu’s team developed an integrase-mediated multicopy system used for the integration of 3–5 copies BGCs into Streptomyces genomes.…”

Section: Discussionmentioning

confidence: 99%

See 1 more Smart Citation

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

Lyu

Fang

et al. 2022

Front. Microbiol.

View full text Add to dashboard Cite

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 Streptomyces roseosporus 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 arpA and phaR), byproduct engineering (i.e., removing pigment), multicopy biosynthetic gene cluster (BGC), and fermentation process engineering (i.e., enhancing O2 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.

show abstract

“…Unfortunately, similar to other antibiotic natural producers, “wild-type” S. roseosporus has low daptomycin titers ( Ye et al, 2014 ). Recently, Ji et al, using a “top-down” synthetic biology approach, achieved an increase in total lipopeptide production up to ∼2,300%, where up to 40% was daptomycin ( Ji et al, 2022 ).…”

Section: Genetic Engineering To Modify Antibioticsmentioning

confidence: 99%

Synthetic Biology Tools for Engineering Microbial Cells to Fight Superbugs

León-Buitimea

Balderas-Cisneros

Garza-Cárdenas

et al. 2022

Front. Bioeng. Biotechnol.

View full text Add to dashboard Cite

With the increase in clinical cases of bacterial infections with multiple antibiotic resistance, the world has entered a health crisis. Overuse, inappropriate prescribing, and lack of innovation of antibiotics have contributed to the surge of microorganisms that can overcome traditional antimicrobial treatments. In 2017, the World Health Organization published a list of pathogenic bacteria, including Enterococcus faecium, Staphylococcus aureus, Klebsiella pneumoniae, Acinetobacter baumannii, Pseudomonas aeruginosa, and Escherichia coli (ESKAPE). These bacteria can adapt to multiple antibiotics and transfer their resistance to other organisms; therefore, studies to find new therapeutic strategies are needed. One of these strategies is synthetic biology geared toward developing new antimicrobial therapies. Synthetic biology is founded on a solid and well-established theoretical framework that provides tools for conceptualizing, designing, and constructing synthetic biological systems. Recent developments in synthetic biology provide tools for engineering synthetic control systems in microbial cells. Applying protein engineering, DNA synthesis, and in silico design allows building metabolic pathways and biological circuits to control cellular behavior. Thus, synthetic biology advances have permitted the construction of communication systems between microorganisms where exogenous molecules can control specific population behaviors, induce intracellular signaling, and establish co-dependent networks of microorganisms.

show abstract

Top-down synthetic biology approach for titer improvement of clinically important antibiotic daptomycin in Streptomyces roseosporus

Cited by 18 publications

References 57 publications

Droplet-Microfluidic-Based Promoter Engineering and Expression Fine-Tuning for Improved Erythromycin Production in Saccharopolyspora erythraea NRRL 23338

Droplet-Microfluidic-Based Promoter Engineering and Expression Fine-Tuning for Improved Erythromycin Production in Saccharopolyspora erythraea NRRL 23338

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

Synthetic Biology Tools for Engineering Microbial Cells to Fight Superbugs

Contact Info

Product

Resources

About