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Stegmüller J, Rodríguez Estévez M, Shu W, Gläser L, Myronovskyi M, Rückert-Reed C, Kalinowski J, Luzhetskyy A, Wittmann C. Systems metabolic engineering of the primary and secondary metabolism of Streptomyces albidoflavus enhances production of the reverse antibiotic nybomycin against multi-resistant Staphylococcus aureus. Metab Eng 2024; 81:123-143. [PMID: 38072358 DOI: 10.1016/j.ymben.2023.12.004] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2023] [Revised: 11/17/2023] [Accepted: 12/01/2023] [Indexed: 01/23/2024]
Abstract
Nybomycin is an antibiotic compound with proven activity against multi-resistant Staphylococcus aureus, making it an interesting candidate for combating these globally threatening pathogens. For exploring its potential, sufficient amounts of nybomycin and its derivatives must be synthetized to fully study its effectiveness, safety profile, and clinical applications. As native isolates only accumulate low amounts of the compound, superior producers are needed. The heterologous cell factory S. albidoflavus 4N24, previously derived from the cluster-free chassis S. albidoflavus Del14, produced 860 μg L-1 of nybomycin, mainly in the stationary phase. A first round of strain development modulated expression of genes involved in supply of nybomycin precursors under control of the common Perm* promoter in 4N24, but without any effect. Subsequent studies with mCherry reporter strains revealed that Perm* failed to drive expression during the product synthesis phase but that use of two synthetic promoters (PkasOP* and P41) enabled strong constitutive expression during the entire process. Using PkasOP*, several rounds of metabolic engineering successively streamlined expression of genes involved in the pentose phosphate pathway, the shikimic acid pathway, supply of CoA esters, and nybomycin biosynthesis and export, which more than doubled the nybomycin titer to 1.7 mg L-1 in the sixth-generation strain NYB-6B. In addition, we identified the minimal set of nyb genes needed to synthetize the molecule using single-gene-deletion strains. Subsequently, deletion of the regulator nybW enabled nybomycin production to begin during the growth phase, further boosting the titer and productivity. Based on RNA sequencing along the created strain genealogy, we discovered that the nyb gene cluster was unfavorably downregulated in all advanced producers. This inspired removal of a part and the entire set of the four regulatory genes at the 3'-end nyb of the cluster. The corresponding mutants NYB-8 and NYB-9 exhibited marked further improvement in production, and the deregulated cluster was combined with all beneficial targets from primary metabolism. The best strain, S. albidoflavus NYB-11, accumulated up to 12 mg L-1 nybomycin, fifteenfold more than the basic strain. The absence of native gene clusters in the host and use of a lean minimal medium contributed to a selective production process, providing an important next step toward further development of nybomycin.
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Affiliation(s)
- Julian Stegmüller
- Institute of Systems Biotechnology, Saarland University, Saarbrücken, Germany
| | | | - Wei Shu
- Institute of Systems Biotechnology, Saarland University, Saarbrücken, Germany
| | - Lars Gläser
- Institute of Systems Biotechnology, Saarland University, Saarbrücken, Germany
| | - Maksym Myronovskyi
- Department of Pharmaceutical Biotechnology, Saarland University, Saarbrücken, Germany
| | | | - Jörn Kalinowski
- Center for Biotechnology, Bielefeld University, Bielefeld, Germany
| | - Andriy Luzhetskyy
- Department of Pharmaceutical Biotechnology, Saarland University, Saarbrücken, Germany
| | - Christoph Wittmann
- Institute of Systems Biotechnology, Saarland University, Saarbrücken, Germany.
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Yang F, Wang H, Zhao C, Zhang L, Liu X, Park H, Yuan Y, Ye JW, Wu Q, Chen GQ. Metabolic engineering of Halomonas bluephagenesis for production of five carbon molecular chemicals derived from L-lysine. Metab Eng 2024; 81:227-237. [PMID: 38072357 DOI: 10.1016/j.ymben.2023.12.001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2023] [Revised: 10/28/2023] [Accepted: 12/01/2023] [Indexed: 12/31/2023]
Abstract
5-Aminovaleric acid (5-AVA), 5-hydroxyvalerate (5HV), copolymer P(3HB-co-5HV) of 3-hydroxybutyrate (3HB) and 5HV were produced from L-lysine as a substrate by recombinant Halomonas bluephagenesis constructed based on codon optimization, deletions of competitive pathway and L-lysine export protein, and three copies of davBA genes encoding L-lysine monooxygenase (DavB) and 5-aminovaleramide amidohydrolase (DavA) inserted into its genome to form H. bluephagenesis YF117ΔgabT1+2, which produced 16.4 g L-1 and 67.4 g L-1 5-AVA in flask cultures and in 7 L bioreactor, respectively. It was able to de novo synthesize 5-AVA from glucose by L-lysine-overproducing H. bluephagenesis TD226. Corn steep liquor was used instead of yeast extract for cost reduction during the 5-AVA production. Using promoter engineering based on Pporin mutant library for downstream genes, H. bluephagenesis YF117 harboring pSEVA341-Pporin42-yqhDEC produced 6 g L-1 5HV in shake flask growth, while H. bluephagenesis YF117 harboring pSEVA341-Pporin42-yqhDEC-Pporin278-phaCRE-abfT synthesized 42 wt% P(3HB-co-4.8 mol% 5HV) under the same condition. Thus, H. bluephagenesis was successfully engineered to produce 5-AVA and 5HV in supernatant and intracellular P(3HB-co-5HV) utilizing L-lysine as the substrate.
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Affiliation(s)
- Fang Yang
- School of Life Sciences, Tsinghua University, Beijing, 100084, China
| | - Huan Wang
- School of Life Sciences, Tsinghua University, Beijing, 100084, China
| | - Cuihuan Zhao
- School of Life Sciences, Tsinghua University, Beijing, 100084, China
| | - Lizhan Zhang
- School of Life Sciences, Tsinghua University, Beijing, 100084, China
| | - Xu Liu
- PhaBuilder Biotech Co. Ltd., Shunyi District, Zhaoquan Ying, Beijing, 101309, China
| | - Helen Park
- School of Life Sciences, Tsinghua University, Beijing, 100084, China
| | - Yiping Yuan
- School of Life Sciences, Tsinghua University, Beijing, 100084, China
| | - Jian-Wen Ye
- School of Life Sciences, Tsinghua University, Beijing, 100084, China
| | - Qiong Wu
- School of Life Sciences, Tsinghua University, Beijing, 100084, China
| | - Guo-Qiang Chen
- School of Life Sciences, Tsinghua University, Beijing, 100084, China; Center for Synthetic and Systems Biology, Tsinghua University, Beijing, 100084, China; Tsinghua-Peking Center for Life Sciences, Beijing, China; MOE Key Lab of Industrial Biocatalysis, Dept Chemical Engineering, Tsinghua University, Beijing, 100084, China.
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Jovanovic Gasovic S, Dietrich D, Gläser L, Cao P, Kohlstedt M, Wittmann C. Multi-omics view of recombinant Yarrowia lipolytica: Enhanced ketogenic amino acid catabolism increases polyketide-synthase-driven docosahexaenoic production to high selectivity at the gram scale. Metab Eng 2023; 80:45-65. [PMID: 37683719 DOI: 10.1016/j.ymben.2023.09.003] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2023] [Revised: 09/04/2023] [Accepted: 09/04/2023] [Indexed: 09/10/2023]
Abstract
DHA is a marine PUFA of commercial value, given its multiple health benefits. The worldwide emerging shortage in DHA supply has increased interest in microbial cell factories that can provide the compound de novo. In this regard, the present work aimed to improve DHA production in the oleaginous yeast strain Y. lipolytica Af4, which synthetized the PUFA via a heterologous myxobacterial polyketide synthase (PKS)-like gene cluster. As starting point, we used transcriptomics, metabolomics, and 13C-based metabolic pathway profiling to study the cellular dynamics of Y. lipolytica Af4. The shift from the growth to the stationary DHA-production phase was associated with fundamental changes in carbon core metabolism, including a strong upregulation of the PUFA gene cluster, as well as an increase in citrate and fatty acid degradation. At the same time, the intracellular levels of the two DHA precursors acetyl-CoA and malonyl-CoA dropped by up to 98% into the picomolar range. Interestingly, the degradation pathways for the ketogenic amino acids l-lysine, l-leucine, and l-isoleucine were transcriptionally activated, presumably to provide extra acetyl-CoA. Supplementation with small amounts of these amino acids at the beginning of the DHA production phase beneficially increased the intracellular CoA-ester pools and boosted the DHA titer by almost 40%. Isotopic 13C-tracer studies revealed that the supplements were efficiently directed toward intracellular CoA-esters and DHA. Hereby, l-lysine was found to be most efficient, as it enabled long-term activation, due to storage within the vacuole and continuous breakdown. The novel strategy enabled DHA production in Y. lipolytica at the gram scale for the first time. DHA was produced at a high selectivity (27% of total fatty acids) and free of the structurally similar PUFA DPA, which facilitates purification for high-value medical applications that require API-grade DHA. The assembled multi-omics picture of the central metabolism of Y. lipolytica provides valuable insights into this important yeast. Beyond our work, the enhanced catabolism of ketogenic amino acids seems promising for the overproduction of other compounds in Y. lipolytica, whose synthesis is limited by the availability of CoA ester precursors.
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Affiliation(s)
| | - Demian Dietrich
- Institute of Systems Biotechnology, Saarland University, Germany
| | - Lars Gläser
- Institute of Systems Biotechnology, Saarland University, Germany
| | - Peng Cao
- Institute of Systems Biotechnology, Saarland University, Germany
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Beganovic S, Rückert-Reed C, Sucipto H, Shu W, Gläser L, Patschkowski T, Struck B, Kalinowski J, Luzhetskyy A, Wittmann C. Systems biology of industrial oxytetracycline production in Streptomyces rimosus: the secrets of a mutagenized hyperproducer. Microb Cell Fact 2023; 22:222. [PMID: 37898787 PMCID: PMC10612213 DOI: 10.1186/s12934-023-02215-x] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2023] [Accepted: 09/26/2023] [Indexed: 10/30/2023] Open
Abstract
BACKGROUND Oxytetracycline which is derived from Streptomyces rimosus, inhibits a wide range of bacteria and is industrially important. The underlying biosynthetic processes are complex and hinder rational engineering, so industrial manufacturing currently relies on classical mutants for production. While the biochemistry underlying oxytetracycline synthesis is known to involve polyketide synthase, hyperproducing strains of S. rimosus have not been extensively studied, limiting our knowledge on fundamental mechanisms that drive production. RESULTS In this study, a multiomics analysis of S. rimosus is performed and wild-type and hyperproducing strains are compared. Insights into the metabolic and regulatory networks driving oxytetracycline formation were obtained. The overproducer exhibited increased acetyl-CoA and malonyl CoA supply, upregulated oxytetracycline biosynthesis, reduced competing byproduct formation, and streamlined morphology. These features were used to synthesize bhimamycin, an antibiotic, and a novel microbial chassis strain was created. A cluster deletion derivative showed enhanced bhimamycin production. CONCLUSIONS This study suggests that the precursor supply should be globally increased to further increase the expression of the oxytetracycline cluster while maintaining the natural cluster sequence. The mutagenized hyperproducer S. rimosus HP126 exhibited numerous mutations, including large genomic rearrangements, due to natural genetic instability, and single nucleotide changes. More complex mutations were found than those typically observed in mutagenized bacteria, impacting gene expression, and complicating rational engineering. Overall, the approach revealed key traits influencing oxytetracycline production in S. rimosus, suggesting that similar studies for other antibiotics could uncover general mechanisms to improve production.
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Affiliation(s)
- Selma Beganovic
- Institute of Systems Biotechnology, Saarland University, Campus A1 5, 66123, Saarbrücken, Germany
| | | | - Hilda Sucipto
- Department of Pharmacy, Saarland University, Saarbrücken, Germany
| | - Wei Shu
- Institute of Systems Biotechnology, Saarland University, Campus A1 5, 66123, Saarbrücken, Germany
| | - Lars Gläser
- Institute of Systems Biotechnology, Saarland University, Campus A1 5, 66123, Saarbrücken, Germany
| | | | - Ben Struck
- Centre for Biotechnology, Bielefeld University, Bielefeld, Germany
| | - Jörn Kalinowski
- Centre for Biotechnology, Bielefeld University, Bielefeld, Germany
| | | | - Christoph Wittmann
- Institute of Systems Biotechnology, Saarland University, Campus A1 5, 66123, Saarbrücken, Germany. *
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Dietrich D, Jovanovic-Gasovic S, Cao P, Kohlstedt M, Wittmann C. Refactoring the architecture of a polyketide gene cluster enhances docosahexaenoic acid production in Yarrowia lipolytica through improved expression and genetic stability. Microb Cell Fact 2023; 22:199. [PMID: 37773137 PMCID: PMC10540379 DOI: 10.1186/s12934-023-02209-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2023] [Accepted: 09/20/2023] [Indexed: 10/01/2023] Open
Abstract
BACKGROUND Long-chain polyunsaturated fatty acids (LC-PUFAs), such as docosahexaenoic acid (DHA), are essential for human health and have been widely used in the food and pharmaceutical industries. However, the limited availability of natural sources, such as oily fish, has led to the pursuit of microbial production as a promising alternative. Yarrowia lipolytica can produce various PUFAs via genetic modification. A recent study upgraded Y. lipolytica for DHA production by expressing a four-gene cluster encoding a myxobacterial PKS-like PUFA synthase, reducing the demand for redox power. However, the genetic architecture of gene expression in Y. lipolytica is complex and involves various control elements, offering space for additional improvement of DHA production. This study was designed to optimize the expression of the PUFA cluster using a modular cloning approach. RESULTS Expression of the monocistronic cluster with each gene under the control of the constitutive TEF promoter led to low-level DHA production. By using the minLEU2 promoter instead and incorporating additional upstream activating UAS1B4 sequences, 5' promoter introns, and intergenic spacers, DHA production was increased by 16-fold. The producers remained stable over 185 h of cultivation. Beneficially, the different genetic control elements acted synergistically: UAS1B elements generally increased expression, while the intron caused gene-specific effects. Mutants with UAS1B16 sequences within 2-8 kb distance, however, were found to be genetically unstable, which limited production performance over time, suggesting the avoidance of long repetitive sequence blocks in synthetic multigene clusters and careful monitoring of genetic stability in producing strains. CONCLUSIONS Overall, the results demonstrate the effectiveness of synthetic heterologous gene clusters to drive DHA production in Y. lipolytica. The combinatorial exploration of different genetic control elements allowed the optimization of DHA production. These findings have important implications for developing Y. lipolytica strains for the industrial-scale production of valuable polyunsaturated fatty acids.
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Affiliation(s)
- Demian Dietrich
- Institute of Systems Biotechnology, Saarland University, Saarbrücken, Germany
| | | | - Peng Cao
- Institute of Systems Biotechnology, Saarland University, Saarbrücken, Germany
| | - Michael Kohlstedt
- Institute of Systems Biotechnology, Saarland University, Saarbrücken, Germany
| | - Christoph Wittmann
- Institute of Systems Biotechnology, Saarland University, Saarbrücken, Germany.
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Zhao X, Wu Y, Feng T, Shen J, Lu H, Zhang Y, Chou HH, Luo X, Keasling JD. Dynamic upregulation of the rate-limiting enzyme for valerolactam biosynthesis in Corynebacterium glutamicum. Metab Eng 2023; 77:89-99. [PMID: 36933819 DOI: 10.1016/j.ymben.2023.02.005] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2022] [Revised: 01/26/2023] [Accepted: 02/13/2023] [Indexed: 03/18/2023]
Abstract
Valerolactam is a monomer used to manufacture high-value nylon-5 and nylon-6,5. However, the biological production of valerolactam has been limited by the inadequate efficiency of enzymes to cyclize 5-aminovaleric acid to produce valerolactam. In this study, we engineered Corynebacterium glutamicum with a valerolactam biosynthetic pathway consisting of DavAB from Pseudomonas putida to convert L-lysine to 5-aminovaleric acid and β-alanine CoA transferase (Act) from Clostridium propionicum to produce valerolactam from 5-aminovaleric acid. Most of the L-lysine was converted into 5-aminovaleric acid, but promoter optimization and increasing the copy number of Act were insufficient to significantly improve the titer of valerolactam. To eliminate the bottleneck at Act, we designed a dynamic upregulation system (a positive feedback loop based on the valerolactam biosensor ChnR/Pb). We used laboratory evolution to engineer ChnR/Pb to have higher sensitivity and a higher dynamic output range, and the engineered ChnR-B1/Pb-E1 system was used to overexpress the rate-limiting enzymes (Act/ORF26/CaiC) that cyclize 5-aminovaleric acid into valerolactam. In glucose fed-batch culture, we obtained 12.33 g/L valerolactam from the dynamic upregulation of Act, 11.88 g/L using ORF26, and 12.15 g/L using CaiC. Our engineered biosensor (ChnR-B1/Pb-E1 system) was also sensitive to 0.01-100 mM caprolactam, which suggests that this dynamic upregulation system can be used to enhance caprolactam biosynthesis in the future.
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Affiliation(s)
- Xixi Zhao
- Center for Synthetic Biochemistry, Shenzhen Institute of Synthetic Biology, Shenzhen Institutes of Advanced Technology, Chinese Academy of Sciences, Shenzhen, 518055, China; CAS Key Laboratory of Quantitative Engineering Biology, Shenzhen Institute of Synthetic Biology, Shenzhen Institutes of Advanced Technology, Chinese Academy of Sciences, Shenzhen, 518055, China
| | - Yanling Wu
- Center for Synthetic Biochemistry, Shenzhen Institute of Synthetic Biology, Shenzhen Institutes of Advanced Technology, Chinese Academy of Sciences, Shenzhen, 518055, China; CAS Key Laboratory of Quantitative Engineering Biology, Shenzhen Institute of Synthetic Biology, Shenzhen Institutes of Advanced Technology, Chinese Academy of Sciences, Shenzhen, 518055, China; University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Tingye Feng
- Center for Synthetic Biochemistry, Shenzhen Institute of Synthetic Biology, Shenzhen Institutes of Advanced Technology, Chinese Academy of Sciences, Shenzhen, 518055, China; CAS Key Laboratory of Quantitative Engineering Biology, Shenzhen Institute of Synthetic Biology, Shenzhen Institutes of Advanced Technology, Chinese Academy of Sciences, Shenzhen, 518055, China
| | - Junfeng Shen
- Center for Synthetic Biochemistry, Shenzhen Institute of Synthetic Biology, Shenzhen Institutes of Advanced Technology, Chinese Academy of Sciences, Shenzhen, 518055, China; CAS Key Laboratory of Quantitative Engineering Biology, Shenzhen Institute of Synthetic Biology, Shenzhen Institutes of Advanced Technology, Chinese Academy of Sciences, Shenzhen, 518055, China
| | - Huan Lu
- Center for Synthetic Biochemistry, Shenzhen Institute of Synthetic Biology, Shenzhen Institutes of Advanced Technology, Chinese Academy of Sciences, Shenzhen, 518055, China; CAS Key Laboratory of Quantitative Engineering Biology, Shenzhen Institute of Synthetic Biology, Shenzhen Institutes of Advanced Technology, Chinese Academy of Sciences, Shenzhen, 518055, China
| | - Yunfeng Zhang
- Center for Synthetic Biochemistry, Shenzhen Institute of Synthetic Biology, Shenzhen Institutes of Advanced Technology, Chinese Academy of Sciences, Shenzhen, 518055, China; CAS Key Laboratory of Quantitative Engineering Biology, Shenzhen Institute of Synthetic Biology, Shenzhen Institutes of Advanced Technology, Chinese Academy of Sciences, Shenzhen, 518055, China
| | - Howard H Chou
- Center for Synthetic Biochemistry, Shenzhen Institute of Synthetic Biology, Shenzhen Institutes of Advanced Technology, Chinese Academy of Sciences, Shenzhen, 518055, China; CAS Key Laboratory of Quantitative Engineering Biology, Shenzhen Institute of Synthetic Biology, Shenzhen Institutes of Advanced Technology, Chinese Academy of Sciences, Shenzhen, 518055, China; University of Chinese Academy of Sciences, Beijing, 100049, China; Shenzhen Key Laboratory for the Intelligent Microbial Manufacturing of Medicines, Shenzhen Institutes of Advanced Technology, Chinese Academy of Sciences, Shenzhen, 518055, China
| | - Xiaozhou Luo
- Center for Synthetic Biochemistry, Shenzhen Institute of Synthetic Biology, Shenzhen Institutes of Advanced Technology, Chinese Academy of Sciences, Shenzhen, 518055, China; CAS Key Laboratory of Quantitative Engineering Biology, Shenzhen Institute of Synthetic Biology, Shenzhen Institutes of Advanced Technology, Chinese Academy of Sciences, Shenzhen, 518055, China; University of Chinese Academy of Sciences, Beijing, 100049, China; Shenzhen Key Laboratory for the Intelligent Microbial Manufacturing of Medicines, Shenzhen Institutes of Advanced Technology, Chinese Academy of Sciences, Shenzhen, 518055, China.
| | - Jay D Keasling
- Center for Synthetic Biochemistry, Shenzhen Institute of Synthetic Biology, Shenzhen Institutes of Advanced Technology, Chinese Academy of Sciences, Shenzhen, 518055, China; Joint BioEnergy Institute, Lawrence Berkeley National Laboratory, Emeryville, CA, 94608, USA; Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA; QB3 Institute, University of California, Berkeley, CA, 94720, USA; Department of Chemical and Biomolecular Engineering and Department of Bioengineering, University of California, Berkeley, CA, 94720, USA; The Novo Nordisk Foundation Center for Biosustainability, Technical University Denmark, Kemitorvet, Building 220, Kongens Lyngby, 2800, Denmark
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Pauli S, Kohlstedt M, Lamber J, Weiland F, Becker J, Wittmann C. Systems metabolic engineering upgrades Corynebacterium glutamicum for selective high-level production of the chiral drug precursor and cell-protective extremolyte L-pipecolic acid. Metab Eng 2023; 77:100-117. [PMID: 36931556 DOI: 10.1016/j.ymben.2023.03.006] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2022] [Revised: 03/02/2023] [Accepted: 03/14/2023] [Indexed: 03/17/2023]
Abstract
The nonproteinogenic cyclic metabolite l-pipecolic acid is a chiral precursor for the synthesis of various commercial drugs and functions as a cell-protective extremolyte and mediator of defense in plants, enabling high-value applications in the pharmaceutical, medical, cosmetic, and agrochemical markets. To date, the production of the compound is unfavorably fossil-based. Here, we upgraded the strain Corynebacterium glutamicum for l-pipecolic acid production using systems metabolic engineering. Heterologous expression of the l-lysine 6-dehydrogenase pathway, apparently the best route to be used in the microbe, yielded a family of strains that enabled successful de novo synthesis from glucose but approached a limit of performance at a yield of 0.18 mol mol-1. Detailed analysis of the producers at the transcriptome, proteome, and metabolome levels revealed that the requirements of the introduced route were largely incompatible with the cellular environment, which could not be overcome after several further rounds of metabolic engineering. Based on the gained knowledge, we based the strain design on l-l-lysine 6-aminotransferase instead, which enabled a substantially higher in vivo flux toward l-pipecolic acid. The tailormade producer C. glutamicum PIA-7 formed l-pipecolic acid up to a yield of 562 mmol mol-1, representing 75% of the theoretical maximum. Ultimately, the advanced mutant PIA-10B achieved a titer of 93 g L-1 in a fed-batch process on glucose, outperforming all previous efforts to synthesize this valuable molecule de novo and even approaching the level of biotransformation from l-lysine. Notably, the use of C. glutamicum allows the safe production of GRAS-designated l-pipecolic acid, providing extra benefit toward addressing the high-value pharmaceutical, medical, and cosmetic markets. In summary, our development sets a milestone toward the commercialization of biobased l-pipecolic acid.
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Affiliation(s)
- Sarah Pauli
- Institute for Systems Biotechnology, Saarland University, Saarbrücken, Germany
| | - Michael Kohlstedt
- Institute for Systems Biotechnology, Saarland University, Saarbrücken, Germany
| | - Jessica Lamber
- Institute for Systems Biotechnology, Saarland University, Saarbrücken, Germany
| | - Fabia Weiland
- Institute for Systems Biotechnology, Saarland University, Saarbrücken, Germany
| | - Judith Becker
- Institute for Systems Biotechnology, Saarland University, Saarbrücken, Germany
| | - Christoph Wittmann
- Institute for Systems Biotechnology, Saarland University, Saarbrücken, Germany.
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8
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Christmann J, Cao P, Becker J, Desiderato CK, Goldbeck O, Riedel CU, Kohlstedt M, Wittmann C. High-efficiency production of the antimicrobial peptide pediocin PA-1 in metabolically engineered Corynebacterium glutamicum using a microaerobic process at acidic pH and elevated levels of bivalent calcium ions. Microb Cell Fact 2023; 22:41. [PMID: 36849884 PMCID: PMC9969654 DOI: 10.1186/s12934-023-02044-y] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2022] [Accepted: 02/16/2023] [Indexed: 03/01/2023] Open
Abstract
BACKGROUND Pediocin PA-1 is a bacteriocin of recognized value with applications in food bio-preservation and the medical sector for the prevention of infection. To date, industrial manufacturing of pediocin PA-1 is limited by high cost and low-performance. The recent establishment of the biotechnological workhorse Corynebacterium glutamicum as recombinant host for pediocin PA-1 synthesis displays a promising starting point towards more efficient production. RESULTS Here, we optimized the fermentative production process. Following successful simplification of the production medium, we carefully investigated the impact of dissolved oxygen, pH value, and the presence of bivalent calcium ions on pediocin production. It turned out that the formation of the peptide was strongly supported by an acidic pH of 5.7 and microaerobic conditions at a dissolved oxygen level of 2.5%. Furthermore, elevated levels of CaCl2 boosted production. The IPTG-inducible producer C. glutamicum CR099 pXMJ19 Ptac pedACDCg provided 66 mg L-1 of pediocin PA-1 in a two-phase batch process using the optimized set-up. In addition, the novel constitutive strain Ptuf pedACDCg allowed successful production without the need for IPTG. CONCLUSIONS The achieved pediocin titer surpasses previous efforts in various microbes up to almost seven-fold, providing a valuable step to further explore and develop this important bacteriocin. In addition to its high biosynthetic performance C. glutamicum proved to be highly robust under the demanding producing conditions, suggesting its further use as host for bacteriocin production.
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Affiliation(s)
- Jens Christmann
- grid.11749.3a0000 0001 2167 7588Institute for Systems Biotechnology, Saarland University, Saarbrücken, Germany
| | - Peng Cao
- grid.11749.3a0000 0001 2167 7588Institute for Systems Biotechnology, Saarland University, Saarbrücken, Germany
| | - Judith Becker
- grid.11749.3a0000 0001 2167 7588Institute for Systems Biotechnology, Saarland University, Saarbrücken, Germany
| | - Christian K. Desiderato
- grid.6582.90000 0004 1936 9748Institute of Microbiology and Biotechnology, University of Ulm, Ulm, Germany
| | - Oliver Goldbeck
- grid.6582.90000 0004 1936 9748Institute of Microbiology and Biotechnology, University of Ulm, Ulm, Germany
| | - Christian U. Riedel
- grid.6582.90000 0004 1936 9748Institute of Microbiology and Biotechnology, University of Ulm, Ulm, Germany
| | - Michael Kohlstedt
- grid.11749.3a0000 0001 2167 7588Institute for Systems Biotechnology, Saarland University, Saarbrücken, Germany
| | - Christoph Wittmann
- Institute for Systems Biotechnology, Saarland University, Saarbrücken, Germany.
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Pu W, Chen J, Zhou Y, Qiu H, Shi T, Zhou W, Guo X, Cai N, Tan Z, Liu J, Feng J, Wang Y, Zheng P, Sun J. Systems metabolic engineering of Escherichia coli for hyper-production of 5‑aminolevulinic acid. Biotechnol Biofuels Bioprod 2023; 16:31. [PMID: 36829220 PMCID: PMC9951541 DOI: 10.1186/s13068-023-02280-9] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/13/2022] [Accepted: 02/09/2023] [Indexed: 02/26/2023]
Abstract
BACKGROUND 5-Aminolevulinic acid (5-ALA) is a promising biostimulant, feed nutrient, and photodynamic drug with wide applications in modern agriculture and therapy. Although microbial production of 5-ALA has been improved realized by using metabolic engineering strategies during the past few years, there is still a gap between the present production level and the requirement of industrialization. RESULTS In this study, pathway, protein, and cellular engineering strategies were systematically employed to construct an industrially competitive 5-ALA producing Escherichia coli. Pathways involved in precursor supply and product degradation were regulated by gene overexpression and synthetic sRNA-based repression to channel metabolic flux to 5-ALA biosynthesis. 5-ALA synthase was rationally engineered to release the inhibition of heme and improve the catalytic activity. 5-ALA transport and antioxidant defense systems were targeted to enhance cellular tolerance to intra- and extra-cellular 5-ALA. The final engineered strain produced 30.7 g/L of 5-ALA in bioreactors with a productivity of 1.02 g/L/h and a yield of 0.532 mol/mol glucose, represent a new record of 5-ALA bioproduction. CONCLUSIONS An industrially competitive 5-ALA producing E. coli strain was constructed with the metabolic engineering strategies at multiple layers (protein, pathway, and cellular engineering), and the strategies here can be useful for developing industrial-strength strains for biomanufacturing.
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Affiliation(s)
- Wei Pu
- grid.458513.e0000 0004 1763 3963Key Laboratory of Systems Microbial Biotechnology, Chinese Academy of Sciences, Tianjin Institute of Industrial Biotechnology, Tianjin, 300308 China ,National Technology Innovation Center of Synthetic Biology, Tianjin, 300308 China
| | - Jiuzhou Chen
- grid.458513.e0000 0004 1763 3963Key Laboratory of Systems Microbial Biotechnology, Chinese Academy of Sciences, Tianjin Institute of Industrial Biotechnology, Tianjin, 300308 China ,National Technology Innovation Center of Synthetic Biology, Tianjin, 300308 China
| | - Yingyu Zhou
- grid.458513.e0000 0004 1763 3963Key Laboratory of Systems Microbial Biotechnology, Chinese Academy of Sciences, Tianjin Institute of Industrial Biotechnology, Tianjin, 300308 China ,grid.413109.e0000 0000 9735 6249College of Biotechnology, Tianjin University of Science and Technology, Tianjin, 300457 China
| | - Huamin Qiu
- grid.458513.e0000 0004 1763 3963Key Laboratory of Systems Microbial Biotechnology, Chinese Academy of Sciences, Tianjin Institute of Industrial Biotechnology, Tianjin, 300308 China ,grid.410726.60000 0004 1797 8419University of Chinese Academy of Sciences, Beijing, 100049 China
| | - Tuo Shi
- grid.458513.e0000 0004 1763 3963Key Laboratory of Systems Microbial Biotechnology, Chinese Academy of Sciences, Tianjin Institute of Industrial Biotechnology, Tianjin, 300308 China ,National Technology Innovation Center of Synthetic Biology, Tianjin, 300308 China
| | - Wenjuan Zhou
- grid.458513.e0000 0004 1763 3963Key Laboratory of Systems Microbial Biotechnology, Chinese Academy of Sciences, Tianjin Institute of Industrial Biotechnology, Tianjin, 300308 China ,National Technology Innovation Center of Synthetic Biology, Tianjin, 300308 China
| | - Xuan Guo
- grid.458513.e0000 0004 1763 3963Key Laboratory of Systems Microbial Biotechnology, Chinese Academy of Sciences, Tianjin Institute of Industrial Biotechnology, Tianjin, 300308 China ,National Technology Innovation Center of Synthetic Biology, Tianjin, 300308 China
| | - Ningyun Cai
- grid.458513.e0000 0004 1763 3963Key Laboratory of Systems Microbial Biotechnology, Chinese Academy of Sciences, Tianjin Institute of Industrial Biotechnology, Tianjin, 300308 China ,grid.413109.e0000 0000 9735 6249College of Biotechnology, Tianjin University of Science and Technology, Tianjin, 300457 China
| | - Zijian Tan
- grid.458513.e0000 0004 1763 3963Key Laboratory of Systems Microbial Biotechnology, Chinese Academy of Sciences, Tianjin Institute of Industrial Biotechnology, Tianjin, 300308 China ,National Technology Innovation Center of Synthetic Biology, Tianjin, 300308 China
| | - Jiao Liu
- grid.458513.e0000 0004 1763 3963Key Laboratory of Systems Microbial Biotechnology, Chinese Academy of Sciences, Tianjin Institute of Industrial Biotechnology, Tianjin, 300308 China ,National Technology Innovation Center of Synthetic Biology, Tianjin, 300308 China
| | - Jinhui Feng
- grid.458513.e0000 0004 1763 3963Key Laboratory of Systems Microbial Biotechnology, Chinese Academy of Sciences, Tianjin Institute of Industrial Biotechnology, Tianjin, 300308 China ,National Technology Innovation Center of Synthetic Biology, Tianjin, 300308 China
| | - Yu Wang
- Key Laboratory of Systems Microbial Biotechnology, Chinese Academy of Sciences, Tianjin Institute of Industrial Biotechnology, Tianjin, 300308, China. .,National Technology Innovation Center of Synthetic Biology, Tianjin, 300308, China. .,University of Chinese Academy of Sciences, Beijing, 100049, China.
| | - Ping Zheng
- Key Laboratory of Systems Microbial Biotechnology, Chinese Academy of Sciences, Tianjin Institute of Industrial Biotechnology, Tianjin, 300308, China. .,National Technology Innovation Center of Synthetic Biology, Tianjin, 300308, China. .,University of Chinese Academy of Sciences, Beijing, 100049, China.
| | - Jibin Sun
- grid.458513.e0000 0004 1763 3963Key Laboratory of Systems Microbial Biotechnology, Chinese Academy of Sciences, Tianjin Institute of Industrial Biotechnology, Tianjin, 300308 China ,National Technology Innovation Center of Synthetic Biology, Tianjin, 300308 China ,grid.410726.60000 0004 1797 8419University of Chinese Academy of Sciences, Beijing, 100049 China
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10
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Zha J, Zhao Z, Xiao Z, Eng T, Mukhopadhyay A, Koffas MA, Tang YJ. Biosystem design of Corynebacterium glutamicum for bioproduction. Curr Opin Biotechnol 2023; 79:102870. [PMID: 36549106 DOI: 10.1016/j.copbio.2022.102870] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2022] [Revised: 11/13/2022] [Accepted: 11/24/2022] [Indexed: 12/24/2022]
Abstract
Corynebacterium glutamicum, a natural glutamate-producing bacterium adopted for industrial production of amino acids, has been extensively explored recently for high-level biosynthesis of amino acid derivatives, bulk chemicals such as organic acids and short-chain alcohols, aromatics, and natural products, including polyphenols and terpenoids. Here, we review the recent advances with a focus on biosystem design principles, metabolic characterization and modeling, omics analysis, utilization of nonmodel feedstock, emerging CRISPR (Clustered Regularly Interspaced Short Palindromic Repeats) tools for Corynebacterium strain engineering, biosensors, and novel strains of C. glutamicum. Future research directions for developing C. glutamicum cell factories are also discussed.
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Affiliation(s)
- Jian Zha
- School of Food and Biological Engineering, Shaanxi University of Science and Technology, Xi'an, Shaanxi 710021, China
| | - Zhen Zhao
- School of Food and Biological Engineering, Shaanxi University of Science and Technology, Xi'an, Shaanxi 710021, China
| | - Zhengyang Xiao
- Department of Energy, Environmental and Chemical Engineering, Washington University in Saint Louis, MO 63130, USA
| | - Thomas Eng
- Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Aindrila Mukhopadhyay
- Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Mattheos Ag Koffas
- Department of Chemical and Biological Engineering, Rensselaer Polytechnic Institute, Troy, NY 12180, USA; Center for Biotechnology and Interdisciplinary Studies, Rensselaer Polytechnic Institute, Troy, NY 12180, USA
| | - Yinjie J Tang
- Department of Energy, Environmental and Chemical Engineering, Washington University in Saint Louis, MO 63130, USA.
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11
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Son J, Sohn YJ, Baritugo KA, Jo SY, Song HM, Park SJ. Recent advances in microbial production of diamines, aminocarboxylic acids, and diacids as potential platform chemicals and bio-based polyamides monomers. Biotechnol Adv 2023; 62:108070. [PMID: 36462631 DOI: 10.1016/j.biotechadv.2022.108070] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2022] [Revised: 11/16/2022] [Accepted: 11/24/2022] [Indexed: 12/03/2022]
Abstract
Recently, bio-based manufacturing processes of value-added platform chemicals and polymers in biorefineries using renewable resources have extensively been developed for sustainable and carbon dioxide (CO2) neutral-based industry. Among them, bio-based diamines, aminocarboxylic acids, and diacids have been used as monomers for the synthesis of polyamides having different carbon numbers and ubiquitous and versatile industrial polymers and also as precursors for further chemical and biological processes to afford valuable chemicals. Until now, these platform bio-chemicals have successfully been produced by biorefinery processes employing enzymes and/or microbial host strains as main catalysts. In this review, we discuss recent advances in bio-based production of diamines, aminocarboxylic acids, and diacids, which has been developed and improved by systems metabolic engineering strategies of microbial consortia and optimization of microbial conversion processes including whole cell bioconversion and direct fermentative production.
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Affiliation(s)
- Jina Son
- Department of Chemical Engineering and Materials Science, Graduate Program in System Health Science and Engineering, Ewha Womans University, 52 Ewhayeodae-gil, Seodaemun-gu, Seoul 03760, Republic of Korea
| | - Yu Jung Sohn
- Department of Chemical Engineering and Materials Science, Graduate Program in System Health Science and Engineering, Ewha Womans University, 52 Ewhayeodae-gil, Seodaemun-gu, Seoul 03760, Republic of Korea
| | - Kei-Anne Baritugo
- Department of Chemical Engineering and Materials Science, Graduate Program in System Health Science and Engineering, Ewha Womans University, 52 Ewhayeodae-gil, Seodaemun-gu, Seoul 03760, Republic of Korea
| | - Seo Young Jo
- Department of Chemical Engineering and Materials Science, Graduate Program in System Health Science and Engineering, Ewha Womans University, 52 Ewhayeodae-gil, Seodaemun-gu, Seoul 03760, Republic of Korea
| | - Hye Min Song
- Department of Chemical Engineering and Materials Science, Graduate Program in System Health Science and Engineering, Ewha Womans University, 52 Ewhayeodae-gil, Seodaemun-gu, Seoul 03760, Republic of Korea
| | - Si Jae Park
- Department of Chemical Engineering and Materials Science, Graduate Program in System Health Science and Engineering, Ewha Womans University, 52 Ewhayeodae-gil, Seodaemun-gu, Seoul 03760, Republic of Korea.
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12
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Weiland F, Barton N, Kohlstedt M, Becker J, Wittmann C. Systems metabolic engineering upgrades Corynebacterium glutamicum to high-efficiency cis, cis-muconic acid production from lignin-based aromatics. Metab Eng 2023; 75:153-69. [PMID: 36563956 DOI: 10.1016/j.ymben.2022.12.005] [Citation(s) in RCA: 11] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2022] [Revised: 12/14/2022] [Accepted: 12/17/2022] [Indexed: 12/24/2022]
Abstract
Lignin displays a highly challenging renewable. To date, massive amounts of lignin, generated in lignocellulosic processing facilities, are for the most part merely burned due to lacking value-added alternatives. Aromatic lignin monomers of recognized relevance are in particular vanillin, and to a lesser extent vanillate, because they are accessible at high yield from softwood-lignin using industrially operated alkaline oxidative depolymerization. Here, we metabolically engineered C. glutamicum towards cis, cis-muconate (MA) production from these key aromatics. Starting from the previously created catechol-based producer C. glutamicum MA-2, systems metabolic engineering first discovered an unspecific aromatic aldehyde reductase that formed aromatic alcohols from vanillin, protocatechualdehyde, and p- hydroxybenzaldehyde, and was responsible for the conversion up to 57% of vanillin into vanillyl alcohol. The alcohol was not re-consumed by the microbe later, posing a strong drawback on the producer. The identification and subsequent elimination of the encoding fudC gene completely abolished vanillyl alcohol formation. Second, the initially weak flux through the native vanillin and vanillate metabolism was enhanced up to 2.9-fold by implementing synthetic pathway modules. Third, the most efficient protocatechuate decarboxylase AroY for conversion of the midstream pathway intermediate protocatechuate into catechol was identified out of several variants in native and codon optimized form and expressed together with the respective helper proteins. Fourth, the streamlined modules were all genomically combined which yielded the final strain MA-9. MA-9 produced bio-based MA from vanillin, vanillate, and seven structurally related aromatics at maximum selectivity. In addition, MA production from softwood-based vanillin, obtained through alkaline depolymerization, was demonstrated.
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Jungmann L, Hoffmann SL, Lang C, De Agazio R, Becker J, Kohlstedt M, Wittmann C. High-efficiency production of 5-hydroxyectoine using metabolically engineered Corynebacterium glutamicum. Microb Cell Fact 2022; 21:274. [PMID: 36578077 PMCID: PMC9798599 DOI: 10.1186/s12934-022-02003-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2022] [Accepted: 12/17/2022] [Indexed: 12/29/2022] Open
Abstract
BACKGROUND Extremolytes enable microbes to withstand even the most extreme conditions in nature. Due to their unique protective properties, the small organic molecules, more and more, become high-value active ingredients for the cosmetics and the pharmaceutical industries. While ectoine, the industrial extremolyte flagship, has been successfully commercialized before, an economically viable route to its highly interesting derivative 5-hydroxyectoine (hydroxyectoine) is not existing. RESULTS Here, we demonstrate high-level hydroxyectoine production, using metabolically engineered strains of C. glutamicum that express a codon-optimized, heterologous ectD gene, encoding for ectoine hydroxylase, to convert supplemented ectoine in the presence of sucrose as growth substrate into the desired derivative. Fourteen out of sixteen codon-optimized ectD variants from phylogenetically diverse bacterial and archaeal donors enabled hydroxyectoine production, showing the strategy to work almost regardless of the origin of the gene. The genes from Pseudomonas stutzeri (PST) and Mycobacterium smegmatis (MSM) worked best and enabled hydroxyectoine production up to 97% yield. Metabolic analyses revealed high enrichment of the ectoines inside the cells, which, inter alia, reduced the synthesis of other compatible solutes, including proline and trehalose. After further optimization, C. glutamicum Ptuf ectDPST achieved a titre of 74 g L-1 hydroxyectoine at 70% selectivity within 12 h, using a simple batch process. In a two-step procedure, hydroxyectoine production from ectoine, previously synthesized fermentatively with C. glutamicum ectABCopt, was successfully achieved without intermediate purification. CONCLUSIONS C. glutamicum is a well-known and industrially proven host, allowing the synthesis of commercial products with granted GRAS status, a great benefit for a safe production of hydroxyectoine as active ingredient for cosmetic and pharmaceutical applications. Because ectoine is already available at commercial scale, its use as precursor appears straightforward. In the future, two-step processes might provide hydroxyectoine de novo from sugar.
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Affiliation(s)
- Lukas Jungmann
- grid.11749.3a0000 0001 2167 7588Institute of Systems Biotechnology, Saarland University, Campus A1.5, Saarbrücken, Germany
| | - Sarah Lisa Hoffmann
- grid.11749.3a0000 0001 2167 7588Institute of Systems Biotechnology, Saarland University, Campus A1.5, Saarbrücken, Germany
| | - Caroline Lang
- grid.11749.3a0000 0001 2167 7588Institute of Systems Biotechnology, Saarland University, Campus A1.5, Saarbrücken, Germany
| | - Raphaela De Agazio
- grid.11749.3a0000 0001 2167 7588Institute of Systems Biotechnology, Saarland University, Campus A1.5, Saarbrücken, Germany
| | - Judith Becker
- grid.11749.3a0000 0001 2167 7588Institute of Systems Biotechnology, Saarland University, Campus A1.5, Saarbrücken, Germany
| | - Michael Kohlstedt
- grid.11749.3a0000 0001 2167 7588Institute of Systems Biotechnology, Saarland University, Campus A1.5, Saarbrücken, Germany
| | - Christoph Wittmann
- grid.11749.3a0000 0001 2167 7588Institute of Systems Biotechnology, Saarland University, Campus A1.5, Saarbrücken, Germany
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