1
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Klauer RR, Hansen DA, Wu D, Monteiro LMO, Solomon KV, Blenner MA. Biological Upcycling of Plastics Waste. Annu Rev Chem Biomol Eng 2024; 15:315-342. [PMID: 38621232 DOI: 10.1146/annurev-chembioeng-100522-115850] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/17/2024]
Abstract
Plastic wastes accumulate in the environment, impacting wildlife and human health and representing a significant pool of inexpensive waste carbon that could form feedstock for the sustainable production of commodity chemicals, monomers, and specialty chemicals. Current mechanical recycling technologies are not economically attractive due to the lower-quality plastics that are produced in each iteration. Thus, the development of a plastics economy requires a solution that can deconstruct plastics and generate value from the deconstruction products. Biological systems can provide such value by allowing for the processing of mixed plastics waste streams via enzymatic specificity and using engineered metabolic pathways to produce upcycling targets. We focus on the use of biological systems for waste plastics deconstruction and upcycling. We highlight documented and predicted mechanisms through which plastics are biologically deconstructed and assimilated and provide examples of upcycled products from biological systems. Additionally, we detail current challenges in the field, including the discovery and development of microorganisms and enzymes for deconstructing non-polyethylene terephthalate plastics, the selection of appropriate target molecules to incentivize development of a plastic bioeconomy, and the selection of microbial chassis for the valorization of deconstruction products.
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Affiliation(s)
- Ross R Klauer
- Department of Chemical and Biomolecular Engineering, University of Delaware, Newark, Delaware, USA; ,
| | - D Alex Hansen
- Department of Chemical and Biomolecular Engineering, University of Delaware, Newark, Delaware, USA; ,
| | - Derek Wu
- Department of Chemical and Biomolecular Engineering, University of Delaware, Newark, Delaware, USA; ,
| | | | - Kevin V Solomon
- Department of Chemical and Biomolecular Engineering, University of Delaware, Newark, Delaware, USA; ,
| | - Mark A Blenner
- Department of Chemical and Biomolecular Engineering, University of Delaware, Newark, Delaware, USA; ,
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2
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Liu C, Gao C, Song L, Li X, Chen X, Wu J, Song W, Wei W, Liu L. Fine-Tuning Pyridoxal 5'-Phosphate Synthesis in Escherichia coli for Cadaverine Production in Minimal Culture Media. ACS Synth Biol 2024; 13:1820-1830. [PMID: 38767944 DOI: 10.1021/acssynbio.4c00102] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/22/2024]
Abstract
Cadaverine is a critical C5 monomer for the production of polyamides. Pyridoxal 5'-phosphate (PLP), as a crucial cofactor for the key enzyme lysine decarboxylase in the cadaverine biosynthesis pathway, has seen a persistent shortage, leading to limitations in cadaverine production. To address this issue, a dual-pathway strategy was implemented, synergistically enhancing both endogenous and heterologous PLP synthesis modules and resulting in improved PLP synthesis. Subsequently, a growth-stage-dependent molecular switch was introduced to balance the precursor competition between PLP synthesis and cell growth. Additionally, a PLP sensor-based negative feedback circuit was constructed by integrating a newly identified PLP-responsive promoter PygjH and an arabinose-regulated system, dynamically regulating the expression of the PLP synthetic genes and preventing excessive intracellular PLP accumulation. The optimal strain, L18, cultivated in the minimal medium AM1, demonstrated cadaverine production with a titer, yield, and productivity of 64.03 g/L, 0.23 g/g glucose, and 1.33 g/L/h, respectively. This represents the highest titer reported to date in engineered Escherichia coli by fed-batch fermentation in a minimal medium.
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Affiliation(s)
- Cunping Liu
- School of Biotechnology and Key Laboratory of Industrial Biotechnology of Ministry of Education, Jiangnan University, Wuxi 214122, China
| | - Cong Gao
- School of Biotechnology and Key Laboratory of Industrial Biotechnology of Ministry of Education, Jiangnan University, Wuxi 214122, China
| | - Longfei Song
- School of Biotechnology and Key Laboratory of Industrial Biotechnology of Ministry of Education, Jiangnan University, Wuxi 214122, China
| | - Xiaomin Li
- School of Biotechnology and Key Laboratory of Industrial Biotechnology of Ministry of Education, Jiangnan University, Wuxi 214122, China
| | - Xiulai Chen
- School of Biotechnology and Key Laboratory of Industrial Biotechnology of Ministry of Education, Jiangnan University, Wuxi 214122, China
| | - Jing Wu
- School of Life Sciences and Health Engineering, Jiangnan University, Wuxi 214122, China
| | - Wei Song
- School of Life Sciences and Health Engineering, Jiangnan University, Wuxi 214122, China
| | - Wanqing Wei
- School of Biotechnology and Key Laboratory of Industrial Biotechnology of Ministry of Education, Jiangnan University, Wuxi 214122, China
| | - Liming Liu
- School of Biotechnology and Key Laboratory of Industrial Biotechnology of Ministry of Education, Jiangnan University, Wuxi 214122, China
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3
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Liu J, Ou Y, Xu JZ, Rao ZM, Zhang WG. L-lysine production by systems metabolic engineering of an NADPH auto-regulated Corynebacterium glutamicum. BIORESOURCE TECHNOLOGY 2023; 387:129701. [PMID: 37604260 DOI: 10.1016/j.biortech.2023.129701] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/02/2023] [Revised: 08/17/2023] [Accepted: 08/18/2023] [Indexed: 08/23/2023]
Abstract
Here, the systems metabolic engineering of L-lysine-overproducing Corynebacterium glutamicum is described to create a highly efficient microorganism producer. The key chromosomal mutations associated with L-lysine synthesis were identified based on whole-genome sequencing. The carbon flux was subsequently redirected into the L-lysine synthesis pathway and increased the availability of energy and product transport systems required for L-lysine synthesis. In addition, a promoter library sensitive to intracellular L-lysine concentration was constructed and applied to regulate the NADPH pool dynamically. In the fed-batch fermentation experiment, the L-lysine titer of the final engineered strain was 223.4 ± 6.5 g/L. This study is the first to improve L-lysine production by enhancing ATP supply and NADPH self-regulation to improve the intracellular environment.
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Affiliation(s)
- Jie Liu
- The Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, 1800(#) Lihu Road, WuXi 214122, People's Republic of China
| | - Ying Ou
- The Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, 1800(#) Lihu Road, WuXi 214122, People's Republic of China
| | - Jian-Zhong Xu
- The Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, 1800(#) Lihu Road, WuXi 214122, People's Republic of China
| | - Zhi-Ming Rao
- The Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, 1800(#) Lihu Road, WuXi 214122, People's Republic of China; National Engineering Laboratory for Cereal Fermentation Technology, School of Biotechnology, Jiangnan University, 1800(#) Lihu Road, WuXi 214122, People's Republic of China
| | - Wei-Guo Zhang
- The Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, 1800(#) Lihu Road, WuXi 214122, People's Republic of China.
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4
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Liu M, He K, Bi H, Wang M, Chen B, Tan T, Zhang Y. Metabolic Engineering for Effective Synthesis of 2-Hydroxyadipate. ACS Synth Biol 2023; 12:2475-2486. [PMID: 37527188 DOI: 10.1021/acssynbio.3c00362] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/03/2023]
Abstract
Adipic acid is an important monomer in the synthesis of nylon-6,6. In recent years, the biosynthesis of adipic acid has received more and more attention. The pathway with l-lysine as a precursor has potential for adipic acid synthesis, and 2-hydroxyadipate is a key intermediate metabolite in this pathway. In this Letter, the biosynthesis pathway of 2-hydroxyadipate was constructed in Escherichia coli. Through enhancement of precursor synthesis and cofactors regulation, 7.11 g/L of 2-hydroxyadipate was produced in the 5 L bioreactor, which verified the scale-up potential of 2-hydroxyadipate production. Furthermore, 11.1 g/L of 2-hydroxyadipate was produced in the 5 L bioreactor on the basis of potential optimization strategies via transcriptome analysis. This is the first time for the biosynthesis of 2-hydroxyadipate. The results lay a solid foundation for the biosynthesis of adipic acid and the production of bionylon.
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Affiliation(s)
- Meng Liu
- National Energy R&D Center for Biorefinery, Beijing Key Laboratory of Bioprocess, Beijing University of Chemical Technology, Beijing, 15th Beisanhuan East Road, Beijing, 100029, PR China
| | - Keqin He
- National Energy R&D Center for Biorefinery, Beijing Key Laboratory of Bioprocess, Beijing University of Chemical Technology, Beijing, 15th Beisanhuan East Road, Beijing, 100029, PR China
| | - Haoran Bi
- National Energy R&D Center for Biorefinery, Beijing Key Laboratory of Bioprocess, Beijing University of Chemical Technology, Beijing, 15th Beisanhuan East Road, Beijing, 100029, PR China
| | - Meng Wang
- National Energy R&D Center for Biorefinery, Beijing Key Laboratory of Bioprocess, Beijing University of Chemical Technology, Beijing, 15th Beisanhuan East Road, Beijing, 100029, PR China
| | - Biqiang Chen
- National Energy R&D Center for Biorefinery, Beijing Key Laboratory of Bioprocess, Beijing University of Chemical Technology, Beijing, 15th Beisanhuan East Road, Beijing, 100029, PR China
| | - Tianwei Tan
- National Energy R&D Center for Biorefinery, Beijing Key Laboratory of Bioprocess, Beijing University of Chemical Technology, Beijing, 15th Beisanhuan East Road, Beijing, 100029, PR China
| | - Yang Zhang
- National Energy R&D Center for Biorefinery, Beijing Key Laboratory of Bioprocess, Beijing University of Chemical Technology, Beijing, 15th Beisanhuan East Road, Beijing, 100029, PR China
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Yang C, Peng Z, Yang L, Du B, Guo C, Sui S, Wang J, Li J, Wang J, Li N. Design and application of artificial rare L-lysine codons in Corynebacterium glutamicum. Front Bioeng Biotechnol 2023; 11:1194511. [PMID: 37324439 PMCID: PMC10268032 DOI: 10.3389/fbioe.2023.1194511] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2023] [Accepted: 05/16/2023] [Indexed: 06/17/2023] Open
Abstract
Background: L-lysine is widely used in the feed, food, and pharmaceutical industries, and screening for high L-lysine-producing strains has become a key goal for the industry. Methods: We constructed the rare L-lysine codon AAA by corresponding tRNA promoter replacement in C. glutamicum. Additionally, a screening marker related to the intracellular L-lysine content was constructed by converting all L-lysine codons of enhanced green fluorescent protein (EGFP) into the artificial rare codon AAA. The artificial EGFP was then ligated into pEC-XK99E and transformed into competent Corynebacterium glutamicum 23604 cells with the rare L-lysine codon. After atmospheric and room-temperature plasma mutation and induction culture, 55 mutants (0.01% of total cells) with stronger fluorescence were sorted using flow cytometry, and further screened by fermentation in a 96-deep-well plate and 500 mL shaker. Results: The fermentation results showed that the L-lysine production was increased by up to 9.7% in the mutant strains with higher fluorescence intensities, and that the highest screening positive rate was 69%, compared with that in the wild-type strain. Conclusion: The application of artificially constructed rare codons in this study represents an efficient, accurate, and simple method for screening other amino acid-producing microorganisms.
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Affiliation(s)
- Cuiping Yang
- Department of Biological Engineering, Qilu University of Technology, Jinan, China
| | - Zehao Peng
- Department of Biological Engineering, Qilu University of Technology, Jinan, China
| | - Lu Yang
- Department of Biological Engineering, Qilu University of Technology, Jinan, China
| | - Bowen Du
- Department of Biological Engineering, Qilu University of Technology, Jinan, China
| | | | - Songsen Sui
- Zhucheng Dongxiao Biotechnology Co., Ltd., Zhucheng, China
| | - Jianbin Wang
- Zhucheng Dongxiao Biotechnology Co., Ltd., Zhucheng, China
| | - Junlin Li
- Zhucheng Dongxiao Biotechnology Co., Ltd., Zhucheng, China
| | - Junqing Wang
- Department of Biological Engineering, Qilu University of Technology, Jinan, China
- State Key Laboratory of Biobased Material and Green Papermaking (LBMP), Qilu University of Technology, Jinan, China
| | - Nan Li
- College of Biotechnology, Tianjin University of Science and Technology, Tianjin, China
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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] [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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7
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Hayes G, Laurel M, MacKinnon D, Zhao T, Houck HA, Becer CR. Polymers without Petrochemicals: Sustainable Routes to Conventional Monomers. Chem Rev 2023; 123:2609-2734. [PMID: 36227737 PMCID: PMC9999446 DOI: 10.1021/acs.chemrev.2c00354] [Citation(s) in RCA: 27] [Impact Index Per Article: 27.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Access to a wide range of plastic materials has been rationalized by the increased demand from growing populations and the development of high-throughput production systems. Plastic materials at low costs with reliable properties have been utilized in many everyday products. Multibillion-dollar companies are established around these plastic materials, and each polymer takes years to optimize, secure intellectual property, comply with the regulatory bodies such as the Registration, Evaluation, Authorisation and Restriction of Chemicals and the Environmental Protection Agency and develop consumer confidence. Therefore, developing a fully sustainable new plastic material with even a slightly different chemical structure is a costly and long process. Hence, the production of the common plastic materials with exactly the same chemical structures that does not require any new registration processes better reflects the reality of how to address the critical future of sustainable plastics. In this review, we have highlighted the very recent examples on the synthesis of common monomers using chemicals from sustainable feedstocks that can be used as a like-for-like substitute to prepare conventional petrochemical-free thermoplastics.
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Affiliation(s)
- Graham Hayes
- Department of Chemistry, University of Warwick, CV4 7ALCoventry, United Kingdom
| | - Matthew Laurel
- Department of Chemistry, University of Warwick, CV4 7ALCoventry, United Kingdom
| | - Dan MacKinnon
- Department of Chemistry, University of Warwick, CV4 7ALCoventry, United Kingdom
| | - Tieshuai Zhao
- Department of Chemistry, University of Warwick, CV4 7ALCoventry, United Kingdom
| | - Hannes A Houck
- Department of Chemistry, University of Warwick, CV4 7ALCoventry, United Kingdom.,Institute of Advanced Study, University of Warwick, CV4 7ALCoventry, United Kingdom
| | - C Remzi Becer
- Department of Chemistry, University of Warwick, CV4 7ALCoventry, United Kingdom
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8
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Catalytic Production of Functional Monomers from Lysine and Their Application in High-Valued Polymers. Catalysts 2022. [DOI: 10.3390/catal13010056] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022] Open
Abstract
Lysine is a key raw material in the chemical industry owing to its sustainability, mature fermentation process and unique chemical structure, besides being an important nutritional supplement. Multiple commodities can be produced from lysine, which thus inspired various catalytic strategies for the production of these lysine-based chemicals and their downstream applications in functional polymer production. In this review, we present a fundamental and comprehensive study on the catalytic production process of several important lysine-based chemicals and their application in highly valued polymers. Specifically, we first focus on the synthesis process and some of the current industrial production methods of lysine-based chemicals, including ε-caprolactam, α-amino-ε-caprolactam and its derivatives, cadaverine, lysinol and pipecolic acid. Second, the applications and prospects of these lysine-based monomers in functional polymers are discussed such as derived poly (lysine), nylon-56, nylon-6 and its derivatives, which are all of growing interest in pharmaceuticals, human health, textile processes, fire control and electronic manufacturing. We finally conclude with the prospects of the development of both the design and synthesis of new lysine derivatives and the expansion of the as-synthesized lysine-based monomers in potential fields.
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9
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Liu J, Xu JZ, Rao ZM, Zhang WG. An enzymatic colorimetric whole-cell biosensor for high-throughput identification of lysine overproducers. Biosens Bioelectron 2022; 216:114681. [PMID: 36087402 DOI: 10.1016/j.bios.2022.114681] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2022] [Revised: 08/17/2022] [Accepted: 08/30/2022] [Indexed: 11/02/2022]
Abstract
L-lysine is a crucial nutrient for both humans and animals, and its main commercial use is as a supplement in animal feed to promote chicken and other animal growth. Fluorescence biosensors based on the transcriptional regulator have been developed for high-throughput screening of L-lysine producers. However, due to its inability to specifically detect lysine, this fluorescent biosensor cannot be employed to screen high-yielding strains. Here, we present a novel technique for observing L-lysine concentrations within individual Corynebacterium glutamicum cells. The transcriptional regulator LysG and its binding site, as well as the phytoene desaturase that catalyzes the synthesis of the red pigment, make up the functional core of the biosensor. The lysine-sensitive mutant LysG(E123Y, E125A), which improved the sensitivity of biosensors, was generated by site-directed saturation mutagenesis. In addition, we increased the lysine-induced chromogenic biosensor response to 320 mM by optimizing the L-lysine export mechanism and the pathway for the synthesis of lycopene precursors. The direct identification of producers with elevated L-lysine accumulation is thus made straightforward by colorimetric screening. Lys-8, a lysine producer with a maximum lysine titer of 316.2 mM, was sorted out based on the biosensor. The enzymatic colorimetric biosensor constructed here is a simple tool with great potential for the development of high-level lysine-producing C. glutamicum.
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Affiliation(s)
- Jie Liu
- The Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, 1800(#)Lihu Road, WuXi, 214122, PR China
| | - Jian-Zhong Xu
- The Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, 1800(#)Lihu Road, WuXi, 214122, PR China
| | - Zhi-Ming Rao
- The Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, 1800(#)Lihu Road, WuXi, 214122, PR China; National Engineering Laboratory for Cereal Fermentation Technology, School of Biotechnology, Jiangnan University, 1800(#)Lihu Road, WuXi, 214122, PR China
| | - Wei-Guo Zhang
- The Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, 1800(#)Lihu Road, WuXi, 214122, PR China.
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10
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Teseo S, Otani S, Brinch C, Leroy S, Ruiz P, Desvaux M, Forano E, Aarestrup FM, Sapountzis P. A global phylogenomic and metabolic reconstruction of the large intestine bacterial community of domesticated cattle. MICROBIOME 2022; 10:155. [PMID: 36155629 PMCID: PMC9511753 DOI: 10.1186/s40168-022-01357-1] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/21/2022] [Accepted: 08/24/2022] [Indexed: 05/30/2023]
Abstract
BACKGROUND The large intestine is a colonization site of beneficial microbes complementing the nutrition of cattle but also of zoonotic and animal pathogens. Here, we present the first global gene catalog of cattle fecal microbiomes, a proxy of the large intestine microbiomes, from 436 metagenomes from six countries. RESULTS Phylogenomics suggested that the reconstructed genomes and their close relatives form distinct branches and produced clustering patterns that were reminiscent of the metagenomics sample origin. Bacterial taxa had distinct metabolic profiles, and complete metabolic pathways were mainly linked to carbohydrates and amino acids metabolism. Dietary changes affected the community composition, diversity, and potential virulence. However, predicted enzymes, which were part of complete metabolic pathways, remained present, albeit encoded by different microbes. CONCLUSIONS Our findings provide a global insight into the phylogenetic relationships and the metabolic potential of a rich yet understudied bacterial community and suggest that it provides valuable services to the host. However, we tentatively infer that members of that community are not irreplaceable, because similar to previous findings, symbionts of complex bacterial communities of mammals are expendable if there are substitutes that can perform the same task. Video Abstract.
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Affiliation(s)
- S Teseo
- School of Biological Sciences, Nanyang Technological University, Singapore, Singapore
| | - S Otani
- National Food Institute, Technical University of Denmark, Kongens Lyngby, Denmark
| | - C Brinch
- National Food Institute, Technical University of Denmark, Kongens Lyngby, Denmark
| | - S Leroy
- Université Clermont Auvergne, INRAE, UMR 0454 MEDIS, Clermont-Ferrand, France
| | - P Ruiz
- Université Clermont Auvergne, INRAE, UMR 0454 MEDIS, Clermont-Ferrand, France
| | - M Desvaux
- Université Clermont Auvergne, INRAE, UMR 0454 MEDIS, Clermont-Ferrand, France
| | - E Forano
- Université Clermont Auvergne, INRAE, UMR 0454 MEDIS, Clermont-Ferrand, France
| | - F M Aarestrup
- National Food Institute, Technical University of Denmark, Kongens Lyngby, Denmark
| | - P Sapountzis
- Université Clermont Auvergne, INRAE, UMR 0454 MEDIS, Clermont-Ferrand, France.
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11
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Wang J, Yang J, Shi G, Li W, Ju Y, Wei L, Liu J, Xu N. Transcriptome profiles of high-lysine adaptation reveal insights into osmotic stress response in Corynebacterium glutamicum. Front Bioeng Biotechnol 2022; 10:933325. [PMID: 36017356 PMCID: PMC9395588 DOI: 10.3389/fbioe.2022.933325] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2022] [Accepted: 07/06/2022] [Indexed: 12/05/2022] Open
Abstract
Corynebacterium glutamicum has been widely and effectively used for fermentative production of l-lysine on an industrial scale. However, high-level accumulation of end products inevitably leads to osmotic stress and hinders further increase of l-lysine production. At present, the underlying mechanism by which C. glutamicum cells adapt to high-lysine-induced osmotic stress is still unclear. In this study, we conducted a comparative transcriptomic analysis by RNA-seq to determine gene expression profiles under different high-lysine stress conditions. The results indicated that the increased expression of some metabolic pathways such as sulfur metabolism and specific amino acid biosynthesis might offer favorable benefits for high-lysine adaptation. Functional assays of 18 representative differentially expressed genes showed that the enhanced expression of multiple candidate genes, especially grpE chaperon, conferred high-lysine stress tolerance in C. glutamicum. Moreover, DNA repair component MutT and energy-transducing NADH dehydrogenase Ndh were also found to be important for protecting cells against high-lysine-induced osmotic stress. Taken together, these aforementioned findings provide broader views of transcriptome profiles and promising candidate targets of C. glutamicum for the adaptation of high-lysine stress during fermentation.
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Affiliation(s)
- Jian Wang
- College of Biological and Agricultural Engineering, Jilin University, Changchun, China
| | - Jian Yang
- College of Biological and Agricultural Engineering, Jilin University, Changchun, China
| | - Guoxin Shi
- College of Biological and Agricultural Engineering, Jilin University, Changchun, China
| | - Weidong Li
- College of Biological and Agricultural Engineering, Jilin University, Changchun, China
| | - Yun Ju
- School of Food Engineering and Biotechnology, Tianjin University of Science and Technology, Tianjin, China
| | - Liang Wei
- Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, China
| | - Jun Liu
- Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, China
- Key Laboratory of Systems Microbial Biotechnology, Chinese Academy of Sciences, Tianjin, China
| | - Ning Xu
- Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, China
- Key Laboratory of Systems Microbial Biotechnology, Chinese Academy of Sciences, Tianjin, China
- *Correspondence: Ning Xu,
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12
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Jie-Liu, Xu JZ, Rao ZM, Zhang WG. Industrial production of L-lysine in Corynebacterium glutamicum: progress and prospects. Microbiol Res 2022; 262:127101. [DOI: 10.1016/j.micres.2022.127101] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2022] [Revised: 06/11/2022] [Accepted: 06/22/2022] [Indexed: 11/24/2022]
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13
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Metabolic engineering of Corynebacterium glutamicum for de novo production of 3-hydroxycadaverine. CURRENT RESEARCH IN BIOTECHNOLOGY 2022. [DOI: 10.1016/j.crbiot.2021.12.004] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022] Open
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14
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Tsuge Y, Yamaguchi A. Physiological characteristics of Corynebacterium glutamicum as a cell factory under anaerobic conditions. Appl Microbiol Biotechnol 2021; 105:6173-6181. [PMID: 34402937 DOI: 10.1007/s00253-021-11474-w] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2021] [Revised: 07/14/2021] [Accepted: 07/15/2021] [Indexed: 12/25/2022]
Abstract
Corynebacterium glutamicum, a gram-positive and facultative anaerobic bacterium, is widely used for the industrial production of amino acids, such as L-glutamate and L-lysine. C. glutamicum grows and produces amino acids under aerobic conditions. When restricted under anaerobic conditions, it produces organic acids, such as L-lactate and succinate, through metabolic shift. With the increasing threat of global warming, these organic acids have drawn considerable attention as bio-based plastic monomers. In addition to the organic acids, the anaerobic bioprocess is also used to produce other value-added compounds, including isobutanol, ethanol, 3-methyl-1-butanol, 2,3-butanediol, L-alanine, and L-valine. Therefore, C. glutamicum is now a versatile cell factory for producing a wide variety of useful chemicals under both aerobic and anaerobic conditions. The growth and metabolism of the bacterium depend on the oxygen levels, which modulate the rearrangement of the carbon flux by reprogramming gene expression patterns and intracellular redox states. Anaerobic cell growth and L-lysine production as well as aerobic succinate production have been demonstrated by engineering the metabolic pathways or supplying a terminal electron acceptor instead of oxygen. In this review, we discuss the physiological and metabolic changes in C. glutamicum associated with its application as a cell factory under different oxygen states. Physiological switching in bacteria is initiated with the sensing of oxygen availability. While such a sensor has not been identified in C. glutamicum yet, the molecular mechanism for oxygen sensing in related bacteria is also discussed. KEY POINTS: • C. glutamicum produces a wide variety of useful compounds under anaerobic conditions. • C. glutamicum is a versatile cell factory under both aerobic and anaerobic conditions. • Metabolic fate can be overcome by engineering metabolic pathways.
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Affiliation(s)
- Yota Tsuge
- Institute for Frontier Science Initiative, Kanazawa University, Kakuma-machi, Kanazawa, Ishikawa, 920-1192, Japan.
- Graduate School of Natural Science and Technology, Kanazawa University, Kakuma-machi, Kanazawa, Ishikawa, 920-1192, Japan.
| | - Akira Yamaguchi
- Graduate School of Natural Science and Technology, Kanazawa University, Kakuma-machi, Kanazawa, Ishikawa, 920-1192, Japan
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15
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Hoffmann SL, Kohlstedt M, Jungmann L, Hutter M, Poblete-Castro I, Becker J, Wittmann C. Cascaded valorization of brown seaweed to produce l-lysine and value-added products using Corynebacterium glutamicum streamlined by systems metabolic engineering. Metab Eng 2021; 67:293-307. [PMID: 34314893 DOI: 10.1016/j.ymben.2021.07.010] [Citation(s) in RCA: 25] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2020] [Revised: 06/23/2021] [Accepted: 07/22/2021] [Indexed: 12/15/2022]
Abstract
Seaweeds emerge as promising third-generation renewable for sustainable bioproduction. In the present work, we valorized brown seaweed to produce l-lysine, the world's leading feed amino acid, using Corynebacterium glutamicum, which was streamlined by systems metabolic engineering. The mutant C. glutamicum SEA-1 served as a starting point for development because it produced small amounts of l-lysine from mannitol, a major seaweed sugar, because of the deletion of its arabitol repressor AtlR and its engineered l-lysine pathway. Starting from SEA-1, we systematically optimized the microbe to redirect excess NADH, formed on the sugar alcohol, towards NADPH, required for l-lysine synthesis. The mannitol dehydrogenase variant MtlD D75A, inspired by 3D protein homology modelling, partly generated NADPH during the oxidation of mannitol to fructose, leading to a 70% increased l-lysine yield in strain SEA-2C. Several rounds of strain engineering further increased NADPH supply and l-lysine production. The best strain, SEA-7, overexpressed the membrane-bound transhydrogenase pntAB together with codon-optimized gapN, encoding NADPH-dependent glyceraldehyde 3-phosphate dehydrogenase, and mak, encoding fructokinase. In a fed-batch process, SEA-7 produced 76 g L-1l-lysine from mannitol at a yield of 0.26 mol mol-1 and a maximum productivity of 2.1 g L-1 h-1. Finally, SEA-7 was integrated into seaweed valorization cascades. Aqua-cultured Laminaria digitata, a major seaweed for commercial alginate, was extracted and hydrolyzed enzymatically, followed by recovery and clean-up of pure alginate gum. The residual sugar-based mixture was converted to l-lysine at a yield of 0.27 C-mol C-mol-1 using SEA-7. Second, stems of the wild-harvested seaweed Durvillaea antarctica, obtained as waste during commercial processing of the blades for human consumption, were extracted using acid treatment. Fermentation of the hydrolysate using SEA-7 provided l-lysine at a yield of 0.40 C-mol C-mol-1. Our findings enable improvement of the efficiency of seaweed biorefineries using tailor-made C. glutamicum strains.
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Affiliation(s)
- Sarah Lisa Hoffmann
- Institute of Systems Biotechnology, Saarland University, Saarbrücken, Germany
| | - Michael Kohlstedt
- Institute of Systems Biotechnology, Saarland University, Saarbrücken, Germany
| | - Lukas Jungmann
- Institute of Systems Biotechnology, Saarland University, Saarbrücken, Germany
| | - Michael Hutter
- Centre for Bioinformatics, Saarland University, Saarbrücken, Germany
| | | | - Judith Becker
- Institute of Systems Biotechnology, Saarland University, Saarbrücken, Germany
| | - Christoph Wittmann
- Institute of Systems Biotechnology, Saarland University, Saarbrücken, Germany.
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16
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Huang Y, Ji X, Ma Z, Łężyk M, Xue Y, Zhao H. Green chemical and biological synthesis of cadaverine: recent development and challenges. RSC Adv 2021; 11:23922-23942. [PMID: 35479032 PMCID: PMC9036910 DOI: 10.1039/d1ra02764f] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2021] [Accepted: 06/29/2021] [Indexed: 11/21/2022] Open
Abstract
Cadaverine has great potential to be used as an important monomer for the development of a series of high value-added products with market prospects. The most promising strategies for cadaverine synthesis involve using green chemical and bioconversion technologies. Herein, the review focuses on the progress and strategies towards the green chemical synthesis and biosynthesis of cadaverine. Specifically, we address the specific biosynthetic pathways of cadaverine from different substrates as well as extensively discussing the origination, structure and catalytic mechanism of the key lysine decarboxylases. The advanced strategies for process intensification, the separation and purification of cadaverine have been summarized. Furthermore, the challenging issues of the environmental, economic, and applicable impact for cadaverine production are also highlighted. This review concludes with the promising outlooks of state-of-the-art applications of cadaverine along with some insights toward their challenges and potential improvements.
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Affiliation(s)
- Yuhong Huang
- Beijing Key Laboratory of Ionic Liquids Clean Process, CAS Key Laboratory of Green Process and Engineering, State Key Laboratory of Multiphase Complex Systems, Institute of Process Engineering, Chinese Academy of Sciences Beijing 100190 China
- Innovation Academy for Green Manufacture, Chinese Academy of Sciences Beijing 100190 China
- Zhengzhou Institute of Emerging Industrial Technology Zhengzhou City Henan 450000 China
- Zhongke Langfang Institute of Process Engineering Langfang 065001 China
| | - Xiuling Ji
- Beijing Key Laboratory of Ionic Liquids Clean Process, CAS Key Laboratory of Green Process and Engineering, State Key Laboratory of Multiphase Complex Systems, Institute of Process Engineering, Chinese Academy of Sciences Beijing 100190 China
| | - Zhanling Ma
- Zhengzhou Institute of Emerging Industrial Technology Zhengzhou City Henan 450000 China
| | - Mateusz Łężyk
- Water Supply and Bioeconomy Division, Faculty of Environmental Engineering and Energy, Poznan University of Technology Berdychowo 4 60-965 Poznan Poland
| | - Yaju Xue
- Beijing Key Laboratory of Ionic Liquids Clean Process, CAS Key Laboratory of Green Process and Engineering, State Key Laboratory of Multiphase Complex Systems, Institute of Process Engineering, Chinese Academy of Sciences Beijing 100190 China
| | - Hai Zhao
- Innovation Academy for Green Manufacture, Chinese Academy of Sciences Beijing 100190 China
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Tokuyama K, Shimodaira Y, Kodama Y, Matsui R, Kusunose Y, Fukushima S, Nakai H, Tsuji Y, Toya Y, Matsuda F, Shimizu H. Soft-sensor development for monitoring the lysine fermentation process. J Biosci Bioeng 2021; 132:183-189. [PMID: 33958301 DOI: 10.1016/j.jbiosc.2021.04.002] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2021] [Revised: 04/06/2021] [Accepted: 04/11/2021] [Indexed: 10/21/2022]
Abstract
Monitoring cell growth and target production in working fermentors is important for stabilizing high level production. In this study, we developed a novel soft sensor for estimating the concentration of a target product (lysine), substrate (sucrose), and bacterial cell in commercially working fermentors using machine learning combined with available on-line process data. The lysine concentration was accurately estimated in both linear and nonlinear models; however, the nonlinear models were also suitable for estimating the concentrations of sucrose and bacterial cells. Data enhancement by time interpolation improved the model prediction accuracy and eliminated unnecessary fluctuations. Furthermore, the soft sensor developed based on the dataset of the same process parameters in multiple fermentor tanks successfully estimated the fermentation behavior of each tank. Machine learning-based soft sensors may represent a novel monitoring system for digital transformation in the field of biotechnological processes.
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Affiliation(s)
- Kento Tokuyama
- DX Promotion Department, Ajinomoto Co., Inc., 1-15-1 Kyobashi, Chuo-ku, Tokyo 104-8315, Japan
| | - Yoshiki Shimodaira
- DX Promotion Department, Ajinomoto Co., Inc., 1-15-1 Kyobashi, Chuo-ku, Tokyo 104-8315, Japan
| | - Yohei Kodama
- Institute for Innovation, Ajinomoto Co., Inc., 1-1 Suzuki-cho, Kawasaki-ku, Kawasaki, Kanagawa 210-8681, Japan
| | - Ryuzo Matsui
- Institute for Innovation, Ajinomoto Co., Inc., 1-1 Suzuki-cho, Kawasaki-ku, Kawasaki, Kanagawa 210-8681, Japan
| | - Yasuhiro Kusunose
- Institute for Innovation, Ajinomoto Co., Inc., 1-1 Suzuki-cho, Kawasaki-ku, Kawasaki, Kanagawa 210-8681, Japan
| | - Shunsuke Fukushima
- Ajinomoto Animal Nutrition Europe S.A.S., 60, rue de Vaux, CS18018, 80084 Amiens Cedex 2, France
| | - Hiroaki Nakai
- Ajinomoto Animal Nutrition Europe S.A.S., 60, rue de Vaux, CS18018, 80084 Amiens Cedex 2, France
| | - Yuichiro Tsuji
- Ajinomoto Animal Nutrition Europe S.A.S., 60, rue de Vaux, CS18018, 80084 Amiens Cedex 2, France
| | - Yoshihiro Toya
- Department of Bioinformatic Engineering, Graduate School of Information Science and Technology, Osaka University, 1-5 Yamadaoka, Suita, Osaka 565-0871, Japan
| | - Fumio Matsuda
- Department of Bioinformatic Engineering, Graduate School of Information Science and Technology, Osaka University, 1-5 Yamadaoka, Suita, Osaka 565-0871, Japan
| | - Hiroshi Shimizu
- Department of Bioinformatic Engineering, Graduate School of Information Science and Technology, Osaka University, 1-5 Yamadaoka, Suita, Osaka 565-0871, Japan.
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18
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Wang J, Gao C, Chen X, Liu L. Expanding the lysine industry: biotechnological production of l-lysine and its derivatives. ADVANCES IN APPLIED MICROBIOLOGY 2021; 115:1-33. [PMID: 34140131 DOI: 10.1016/bs.aambs.2021.02.001] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Abstract
l-lysine is an essential amino acid that contains various functional groups including α-amino, ω-amino, and α-carboxyl groups, exhibiting high reaction potential. The derivatization of these functional groups produces a series of value-added chemicals, such as cadaverine, glutarate, and d-lysine, that are widely applied in the chemical synthesis, cosmetics, food, and pharmaceutical industries. Here, we review recent advances in the biotechnological production of l-lysine and its derivatives and expatiate key technological strategies. Furthermore, we also discuss the existing challenges and potential strategies for more efficient production of these chemicals.
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Affiliation(s)
- Jiaping Wang
- State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi, China; Key Laboratory of Industrial Biotechnology, Ministry of Education, Jiangnan University, Wuxi, China; International Joint Laboratory on Food Safety, Jiangnan University, Wuxi, China
| | - Cong Gao
- State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi, China; Key Laboratory of Industrial Biotechnology, Ministry of Education, Jiangnan University, Wuxi, China; International Joint Laboratory on Food Safety, Jiangnan University, Wuxi, China
| | - Xiulai Chen
- State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi, China; Key Laboratory of Industrial Biotechnology, Ministry of Education, Jiangnan University, Wuxi, China; International Joint Laboratory on Food Safety, Jiangnan University, Wuxi, China
| | - Liming Liu
- State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi, China; Key Laboratory of Industrial Biotechnology, Ministry of Education, Jiangnan University, Wuxi, China; International Joint Laboratory on Food Safety, Jiangnan University, Wuxi, China.
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19
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Glutaric acid production by systems metabolic engineering of an l-lysine-overproducing Corynebacterium glutamicum. Proc Natl Acad Sci U S A 2020; 117:30328-30334. [PMID: 33199604 DOI: 10.1073/pnas.2017483117] [Citation(s) in RCA: 44] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
Abstract
There is increasing industrial demand for five-carbon platform chemicals, particularly glutaric acid, a widely used building block chemical for the synthesis of polyesters and polyamides. Here we report the development of an efficient glutaric acid microbial producer by systems metabolic engineering of an l-lysine-overproducing Corynebacterium glutamicum BE strain. Based on our previous study, an optimal synthetic metabolic pathway comprising Pseudomonas putida l-lysine monooxygenase (davB) and 5-aminovaleramide amidohydrolase (davA) genes and C. glutamicum 4-aminobutyrate aminotransferase (gabT) and succinate-semialdehyde dehydrogenase (gabD) genes, was introduced into the C. glutamicum BE strain. Through system-wide analyses including genome-scale metabolic simulation, comparative transcriptome analysis, and flux response analysis, 11 target genes to be manipulated were identified and expressed at desired levels to increase the supply of direct precursor l-lysine and reduce precursor loss. A glutaric acid exporter encoded by ynfM was discovered and overexpressed to further enhance glutaric acid production. Fermentation conditions, including oxygen transfer rate, batch-phase glucose level, and nutrient feeding strategy, were optimized for the efficient production of glutaric acid. Fed-batch culture of the final engineered strain produced 105.3 g/L of glutaric acid in 69 h without any byproduct. The strategies of metabolic engineering and fermentation optimization described here will be useful for developing engineered microorganisms for the high-level bio-based production of other chemicals of interest to industry.
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20
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Sato N, Kishida M, Nakano M, Hirata Y, Tanaka T. Metabolic Engineering of Shikimic Acid-Producing Corynebacterium glutamicum From Glucose and Cellobiose Retaining Its Phosphotransferase System Function and Pyruvate Kinase Activities. Front Bioeng Biotechnol 2020; 8:569406. [PMID: 33015020 PMCID: PMC7511668 DOI: 10.3389/fbioe.2020.569406] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2020] [Accepted: 08/19/2020] [Indexed: 01/23/2023] Open
Abstract
The production of aromatic compounds by microbial production is a promising and sustainable approach for producing biomolecules for various applications. We describe the metabolic engineering of Corynebacterium glutamicum to increase its production of shikimic acid. Shikimic acid and its precursor-consuming pathways were blocked by the deletion of the shikimate kinase, 3-dehydroshikimate dehydratase, shikimate dehydratase, and dihydroxyacetone phosphate phosphatase genes. Plasmid-based expression of shikimate pathway genes revealed that 3-deoxy-D-arabino-heptulosonate 7-phosphate (DAHP) synthase, encoded by aroG, and DHQ synthase, encoded by aroB, are key enzymes for shikimic acid production in C. glutamicum. We constructed a C. glutamicum strain with aroG, aroB and aroE3 integrated. This strain produced 13.1 g/L of shikimic acid from 50 g/L of glucose, a yield of 0.26 g-shikimic acid/g-glucose, and retained both its phosphotransferase system and its pyruvate kinase activity. We also endowed β-glucosidase secreting ability to this strain. When cellobiose was used as a carbon source, the strain produced shikimic acid at 13.8 g/L with the yield of 0.25 g-shikimic acid/g-glucose (1 g of cellobiose corresponds to 1.1 g of glucose). These results demonstrate the feasibility of producing shikimic acid and its derivatives using an engineered C. glutamicum strain from cellobiose as well as glucose.
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Affiliation(s)
- Naoki Sato
- Department of Chemical Science and Engineering, Graduate School of Engineering, Kobe University, Kobe, Japan
| | - Mayumi Kishida
- Department of Chemical Science and Engineering, Graduate School of Engineering, Kobe University, Kobe, Japan
| | - Mariko Nakano
- Department of Chemical Science and Engineering, Graduate School of Engineering, Kobe University, Kobe, Japan
| | - Yuuki Hirata
- Department of Chemical Science and Engineering, Graduate School of Engineering, Kobe University, Kobe, Japan
| | - Tsutomu Tanaka
- Department of Chemical Science and Engineering, Graduate School of Engineering, Kobe University, Kobe, Japan
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21
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Saez-Jimenez V, Maršić ŽS, Lambrughi M, Shin JH, van Havere R, Papaleo E, Olsson L, Mapelli V. Structure-function investigation of 3-methylaspartate ammonia lyase reveals substrate molecular determinants for the deamination reaction. PLoS One 2020; 15:e0233467. [PMID: 32437404 PMCID: PMC7241714 DOI: 10.1371/journal.pone.0233467] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2020] [Accepted: 05/05/2020] [Indexed: 12/03/2022] Open
Abstract
The enzymatic reactions leading to the deamination of β-lysine, lysine, or 2-aminoadipic acid are of great interest for the metabolic conversion of lysine to adipic acid. Enzymes able to carry out these reactions are not known, however ammonia lyases (EC 4.3.1.-) perform deamination on a wide range of substrates. We have studied 3-methylaspartate ammonia lyase (MAL, EC 4.3.1.2) as a potential candidate for protein engineering to enable deamination towards β-lysine, that we have shown to be a competitive inhibitor of MAL. We have characterized MAL activity, binding and inhibition properties on six different compounds that would allow to define the molecular determinants necessary for MAL to deaminate our substrate of interest. Docking calculations showed that β-lysine as well as the other compounds investigated could fit spatially into MAL catalytic pocket, although they probably are weak or very transient binders and we identified molecular determinants involved in the binding of the substrate. The hydrophobic interactions formed by the methyl group of 3-methylaspartic acid, together with the presence of the amino group on carbon 2, play an essential role in the appropriate binding of the substrate. The results showed that β-lysine is able to fit and bind in MAL catalytic pocket and can be potentially converted from inhibitor to substrate of MAL upon enzyme engineering. The characterization of the binding and inhibition properties of the substrates tested here provide the foundation for future and more extensive studies on engineering MAL that could lead to a MAL variant able to catalyse this challenging deamination reaction.
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Affiliation(s)
- Veronica Saez-Jimenez
- Division of Industrial Biotechnology, Department of Biology and Biological Engineering, Chalmers University of Technology, Gothenburg, Sweden
| | - Željka Sanader Maršić
- Computational Biology Laboratory, Danish Cancer Society Research Center, Copenhagen, Denmark
| | - Matteo Lambrughi
- Computational Biology Laboratory, Danish Cancer Society Research Center, Copenhagen, Denmark
| | - Jae Ho Shin
- Division of Industrial Biotechnology, Department of Biology and Biological Engineering, Chalmers University of Technology, Gothenburg, Sweden
| | - Robin van Havere
- Division of Industrial Biotechnology, Department of Biology and Biological Engineering, Chalmers University of Technology, Gothenburg, Sweden
| | - Elena Papaleo
- Computational Biology Laboratory, Danish Cancer Society Research Center, Copenhagen, Denmark
| | - Lisbeth Olsson
- Division of Industrial Biotechnology, Department of Biology and Biological Engineering, Chalmers University of Technology, Gothenburg, Sweden
| | - Valeria Mapelli
- Division of Industrial Biotechnology, Department of Biology and Biological Engineering, Chalmers University of Technology, Gothenburg, Sweden
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22
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Rui J, You S, Zheng Y, Wang C, Gao Y, Zhang W, Qi W, Su R, He Z. High-efficiency and low-cost production of cadaverine from a permeabilized-cell bioconversion by a Lysine-induced engineered Escherichia coli. BIORESOURCE TECHNOLOGY 2020; 302:122844. [PMID: 32006927 DOI: 10.1016/j.biortech.2020.122844] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/29/2019] [Revised: 01/15/2020] [Accepted: 01/16/2020] [Indexed: 06/10/2023]
Abstract
Cadaverine is the monomer of bio-based nylons polyamide 5.4, 5.6 and 5.10. In this study, a litre-scale integrated strategy was developed for high-efficiency and low-cost production of cadaverine using an engineered Escherichia coli. Firstly, the engineered strain BL21-Pcad-CadA induced by cheap l-lysine-HCl instead of IPTG was constructed. Then the permeabilized cells were served as the biocatalyst for the production of cadaverine, because the enhanced permeability facilitated the mass transfer of the substrate and the release of products. After the replacement of industrial materials and the solution of the scale-up permeabilization process, cadaverine concentration reached 205 g/L with the yield of 92.1% after 20 h in a 2 L bioconversion system, achieving the level of industrial production. Furthermore, the costs of industrial materials for 2 L integrated strategy ($2.78) was only 1/11 of the lab reagents ($30.88). Therefore, the proposed strategy is a promising candidate for the industrial process of cadaverine.
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Affiliation(s)
- Jinqiu Rui
- Chemical Engineering Research Center, School of Chemical Engineering and Technology, Tianjin University, Tianjin 300072, PR China
| | - Shengping You
- Chemical Engineering Research Center, School of Chemical Engineering and Technology, Tianjin University, Tianjin 300072, PR China; Tianjin Key Laboratory of Membrane Science and Desalination Technology, Tianjin University, Tianjin 300072, PR China
| | - Yunxin Zheng
- Chemical Engineering Research Center, School of Chemical Engineering and Technology, Tianjin University, Tianjin 300072, PR China
| | - Chengyu Wang
- Chemical Engineering Research Center, School of Chemical Engineering and Technology, Tianjin University, Tianjin 300072, PR China
| | - Yingtong Gao
- Chemical Engineering Research Center, School of Chemical Engineering and Technology, Tianjin University, Tianjin 300072, PR China
| | - Wei Zhang
- Ever-Sky Bioscience (Tianjin) Co., Ltd., PR China
| | - Wei Qi
- Chemical Engineering Research Center, School of Chemical Engineering and Technology, Tianjin University, Tianjin 300072, PR China; State Key Laboratory of Chemical Engineering, Tianjin University, Tianjin 300072, PR China; Collaborative Innovation Center of Chemical Science and Engineering (Tianjin), Tianjin 300072, PR China; Tianjin Key Laboratory of Membrane Science and Desalination Technology, Tianjin University, Tianjin 300072, PR China.
| | - Rongxin Su
- Chemical Engineering Research Center, School of Chemical Engineering and Technology, Tianjin University, Tianjin 300072, PR China; State Key Laboratory of Chemical Engineering, Tianjin University, Tianjin 300072, PR China; Collaborative Innovation Center of Chemical Science and Engineering (Tianjin), Tianjin 300072, PR China; Tianjin Key Laboratory of Membrane Science and Desalination Technology, Tianjin University, Tianjin 300072, PR China
| | - Zhimin He
- Chemical Engineering Research Center, School of Chemical Engineering and Technology, Tianjin University, Tianjin 300072, PR China; State Key Laboratory of Chemical Engineering, Tianjin University, Tianjin 300072, PR China
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23
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Production of nonnatural straight-chain amino acid 6-aminocaproate via an artificial iterative carbon-chain-extension cycle. Metab Eng 2019; 55:23-32. [DOI: 10.1016/j.ymben.2019.06.009] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2019] [Revised: 06/13/2019] [Accepted: 06/15/2019] [Indexed: 12/23/2022]
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24
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Hommes A, Heeres HJ, Yue J. Catalytic Transformation of Biomass Derivatives to Value‐Added Chemicals and Fuels in Continuous Flow Microreactors. ChemCatChem 2019. [DOI: 10.1002/cctc.201900807] [Citation(s) in RCA: 50] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Affiliation(s)
- Arne Hommes
- Department of Chemical Engineering Engineering and Technology Institute GroningenUniversity of Groningen Nijenborgh 4 Groningen 9747 AG The Netherlands
| | - Hero Jan Heeres
- Department of Chemical Engineering Engineering and Technology Institute GroningenUniversity of Groningen Nijenborgh 4 Groningen 9747 AG The Netherlands
| | - Jun Yue
- Department of Chemical Engineering Engineering and Technology Institute GroningenUniversity of Groningen Nijenborgh 4 Groningen 9747 AG The Netherlands
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An economically and environmentally acceptable synthesis of chiral drug intermediate l-pipecolic acid from biomass-derived lysine via artificially engineered microbes. ACTA ACUST UNITED AC 2018; 45:405-415. [DOI: 10.1007/s10295-018-2044-2] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2018] [Accepted: 04/29/2018] [Indexed: 12/29/2022]
Abstract
Abstract
Deficiency in petroleum resources and increasing environmental concerns have pushed a bio-based economy to be built, employing a highly reproducible, metal contaminant free, sustainable and green biomanufacturing method. Here, a chiral drug intermediate l-pipecolic acid has been synthesized from biomass-derived lysine. This artificial bioconversion system involves the coexpression of four functional genes, which encode l-lysine α-oxidase from Scomber japonicus, glucose dehydrogenase from Bacillus subtilis, Δ1-piperideine-2-carboxylase reductase from Pseudomonas putida, and lysine permease from Escherichia coli. Besides, a lysine degradation enzyme has been knocked out to strengthen the process in this microbe. The overexpression of LysP improved the l-pipecolic acid titer about 1.6-folds compared to the control. This engineered microbial factory showed the highest l-pipecolic acid production of 46.7 g/L reported to date and a higher productivity of 2.41 g/L h and a yield of 0.89 g/g. This biotechnological l-pipecolic acid production is a simple, economic, and green technology to replace the presently used chemical synthesis.
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