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Mitsui R, Kondo A, Shirai T. Production of (R)-citramalate by engineered Saccharomyces cerevisiae. Metab Eng Commun 2024; 19:e00247. [PMID: 39246525 PMCID: PMC11379666 DOI: 10.1016/j.mec.2024.e00247] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2024] [Revised: 07/01/2024] [Accepted: 08/06/2024] [Indexed: 09/10/2024] Open
Abstract
The budding yeast, Saccharomyces cerevisiae, has a high tolerance to organic acids and alcohols, and thus grows well under toxic concentrations of various compounds in the culture medium, potentially allowing for highly efficient compound production. (R)-citramalate is a raw material for methyl methacrylate and can be used as a metabolic intermediate in the biosynthesis of higher alcohols. (R)-citramalate is synthesized from pyruvate and acetyl-CoA. Unlike Escherichia coli, S. cerevisiae has organelles, and its intracellular metabolites are compartmentalized, preventing full use of intracellular acetyl-CoA. Therefore, in this study, to increase the amount of cytosolic acetyl-CoA for highly efficient production of (R)-citramalate, we inhibited the transport of cytosolic acetyl-CoA and pyruvate to the mitochondria. We also constructed a heterologous pathway to supply cytosolic acetyl-CoA. Additionally, we attempted to export (R)-citramalate from cells by expressing a heterologous dicarboxylate transporter gene. We evaluated the effects of these approaches on (R)-citramalate production and constructed a final strain by combining these positive approaches. The resulting strain produced 16.5 mM (R)-citramalate in batch culture flasks. This is the first report of (R)-citramalate production by recombinant S. cerevisiae, and the (R)-citramalate production by recombinant yeast achieved in this study was the highest reported to date.
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Affiliation(s)
- Ryosuke Mitsui
- Center for Sustainable Resource Science, RIKEN, 1-7-22, Suehiro-cho, Tsurumi-ku, Yokohama, Kanagawa, 230-0045, Japan
| | - Akihiko Kondo
- Center for Sustainable Resource Science, RIKEN, 1-7-22, Suehiro-cho, Tsurumi-ku, Yokohama, Kanagawa, 230-0045, Japan
- Graduate School of Science, Technology and Innovation, Kobe University, 1-1 Rokkodai, Nada, Kobe, 657-8501, Japan
| | - Tomokazu Shirai
- Center for Sustainable Resource Science, RIKEN, 1-7-22, Suehiro-cho, Tsurumi-ku, Yokohama, Kanagawa, 230-0045, Japan
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Wang T, Ye P, Xu X, Lu M, Zhang X, Li N. Metabolic engineering combined with site-directed saturated mutations of α-keto acid decarboxylase for efficient production of 6-aminocaproic acid and 1,6-hexamethylenediamine. Biotechnol Bioeng 2024; 121:3329-3337. [PMID: 38956978 DOI: 10.1002/bit.28795] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2024] [Revised: 06/21/2024] [Accepted: 06/24/2024] [Indexed: 07/04/2024]
Abstract
6-Aminocaproic acid (6ACA) and 1,6-hexamethylenediamine (HMDA) are key precursors for nylon synthesis, and both are produced using petroleum-based chemical processes. However, the utilization of bio-based raw materials for biological production of monomers is crucial for nylon industry. In this study, we demonstrated that metabolic engineering of Escherichia coli and selected mutations of α-keto acid decarboxylase successfully synthesized 6ACA and HMDA. An artificial iterative cycle from l-lysine to chain-extended α-ketoacids was introduced into Escherichia coli BL21 (DE3). Then, the extended α-ketoacids were decarboxylated and oxidized for 6ACA production. Overexpression of catalase (KatE) combined with the site-directed mutations of α-isopropylmalate synthase (LeuA) contributed synergistic enhancement effect on synthesis of 6ACA, resulting in a 1.3-fold increase in 6ACA titer. Selected mutations in α-keto acid decarboxylase (KivD) improved its specificity and 170.00 ± 5.57 mg/L of 6ACA with a yield of 0.13 mol/mol (6ACA/l-lysine hydrochloride) was achieved by shake flask cultivation of the engineered strain with the KivD# (F381Y/V461I). Meanwhile, the engineered E. coli could accumulate 84.67 ± 4.04 mg/L of HMDA with a yield of 0.08 mol/mol (HMDA/l-lysine hydrochloride) by replacing aldehyde dehydrogenase with bi-aminotransferases. This achievement marks a significant advancement in the biological synthesis of 6-carbon compounds, since the biosynthetic pathways of HMDA are rarely identified.
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Affiliation(s)
- Tiantian Wang
- Innovation Center for Textile Science and Technology, College of Biological Science and Medical Engineering, Donghua University, Shanghai, People's Republic of China
| | - Pan Ye
- Innovation Center for Textile Science and Technology, College of Biological Science and Medical Engineering, Donghua University, Shanghai, People's Republic of China
| | - Xue Xu
- Innovation Center for Textile Science and Technology, College of Biological Science and Medical Engineering, Donghua University, Shanghai, People's Republic of China
| | - Mengqing Lu
- Innovation Center for Textile Science and Technology, College of Biological Science and Medical Engineering, Donghua University, Shanghai, People's Republic of China
| | - Xinyu Zhang
- Innovation Center for Textile Science and Technology, College of Biological Science and Medical Engineering, Donghua University, Shanghai, People's Republic of China
| | - Naiqiang Li
- Innovation Center for Textile Science and Technology, College of Biological Science and Medical Engineering, Donghua University, Shanghai, People's Republic of China
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3
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Kang Y, Xiao K, Wang D, Peng Z, Luo R, Liu X, Hu L, Hu G. Metabolic Engineering of Saccharomyces cerevisiae for High-Level Production of l-Pipecolic Acid from Glucose. ACS Synth Biol 2024. [PMID: 39267441 DOI: 10.1021/acssynbio.4c00464] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 09/17/2024]
Abstract
l-Pipecolic acid (L-PA), an essential chiral cyclic nonprotein amino acid, is gaining prominence in the food and pharmaceutical sectors due to its wide-ranging biological and pharmacological properties. Historically, L-PA has been synthesized chemically for commercial purposes. This study introduces a novel and efficient microbial production method for L-PA using engineered strain Saccharomyces cerevisiae BY4743. Initially, an optimized biosynthetic pathway was constructed within S. cerevisiae, converting glucose to L-PA with a yield of 0.60 g/L in a 250 mL shake flask in vivo. Subsequently, a multifaceted engineering strategy was implemented to enhance L-PA production: substrate-enzyme affinity modification, global transcription machinery engineering modification, and Kozak sequence optimization for enhanced L-PA production. Approaches above led to an impressive 8.6-fold increase in L-PA yield, reaching 5.47 g/L in shake flask cultures. Further scaling up in a 5 L fed-batch fermenter achieved a remarkable L-PA concentration of 74.54 g/L. This research offers innovative insights into the industrial-scale production of L-PA.
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Affiliation(s)
- Yaqi Kang
- Department of Chemical Engineering, School of Chemistry and Chemical Engineering, Chongqing University, Chongqing 401331, PR China
| | - Kaixing Xiao
- Department of Chemical Engineering, School of Chemistry and Chemical Engineering, Chongqing University, Chongqing 401331, PR China
| | - Dan Wang
- Department of Chemical Engineering, School of Chemistry and Chemical Engineering, Chongqing University, Chongqing 401331, PR China
| | - Zhiyao Peng
- Department of Chemical Engineering, School of Chemistry and Chemical Engineering, Chongqing University, Chongqing 401331, PR China
| | - Ruoshi Luo
- Department of Chemical Engineering, School of Chemistry and Chemical Engineering, Chongqing University, Chongqing 401331, PR China
| | - Xuemei Liu
- Department of Chemical Engineering, School of Chemistry and Chemical Engineering, Chongqing University, Chongqing 401331, PR China
| | - Lin Hu
- Department of Chemical Engineering, School of Chemistry and Chemical Engineering, Chongqing University, Chongqing 401331, PR China
| | - Ge Hu
- Department of Chemical Engineering, School of Chemistry and Chemical Engineering, Chongqing University, Chongqing 401331, PR China
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Stewart LE, Owens SL, Ahmed SR, Lang Harman RM, Mori S. Characterization of HphA: The First Enzyme in the Homologation Pathway of l-Phenylalanine and l-Tyrosine. Chembiochem 2024; 25:e202400369. [PMID: 38896437 PMCID: PMC11382533 DOI: 10.1002/cbic.202400369] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2024] [Revised: 05/31/2024] [Accepted: 06/18/2024] [Indexed: 06/21/2024]
Abstract
Homologation of amino acids is the insertion or deletion of a methylene group to their side chain, which is a relatively uncommon chemical transformation observed in peptide natural product (NP) structure. Homologated amino acids can potentially make the NP more stable in a biological system, but its biosynthesis is yet to be understood. This study biochemically characterized the first of three unexplored enzymes in the homologation pathway of l-phenylalanine and l-tyrosine. Previously proposed reactions catalyzed by HphA were confirmed by reversed-phase high-performance liquid chromatography and tandem mass spectrometry analysis. The substrate profile and kinetic parameters showed high selectivity for the natural substrates and their close analogs. The comparability of HphA to homologous enzymes in primary metabolic pathways, 2-isopropylmate synthase and homocitrate synthase which are involved in l-leucine and l-lysine biosynthesis, respectively, was validated by bioinformatical and site-directed mutagenesis studies. The knowledge obtained from this study has deepened the understanding of the homologation of amino acids, which can lead to future combinatorial biosynthesis and metabolic engineering studies.
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Affiliation(s)
- Laura E Stewart
- Department of Chemistry and Biochemistry, Augusta University, 1120 15th Street, Augusta, GA 30912, USA
| | - Skyler L Owens
- Department of Chemistry and Biochemistry, Augusta University, 1120 15th Street, Augusta, GA 30912, USA
| | - Shopno R Ahmed
- Department of Chemistry and Biochemistry, Augusta University, 1120 15th Street, Augusta, GA 30912, USA
| | - Rebecca M Lang Harman
- Department of Chemistry and Biochemistry, Augusta University, 1120 15th Street, Augusta, GA 30912, USA
| | - Shogo Mori
- Department of Chemistry and Biochemistry, Augusta University, 1120 15th Street, Augusta, GA 30912, USA
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Chen Z, Yu S, Liu J, Guo L, Wu T, Duan P, Yan D, Huang C, Huo Y. Concentration Recognition-Based Auto-Dynamic Regulation System (CRUISE) Enabling Efficient Production of Higher Alcohols. ADVANCED SCIENCE (WEINHEIM, BADEN-WURTTEMBERG, GERMANY) 2024; 11:e2310215. [PMID: 38626358 PMCID: PMC11187965 DOI: 10.1002/advs.202310215] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/26/2023] [Revised: 03/12/2024] [Indexed: 04/18/2024]
Abstract
Microbial factories lacking the ability of dynamically regulating the pathway enzymes overexpression, according to in situ metabolite concentrations, are suboptimal, especially when the metabolic intermediates are competed by growth and chemical production. The production of higher alcohols (HAs), which hijacks the amino acids (AAs) from protein biosynthesis, minimizes the intracellular concentration of AAs and thus inhibits the host growth. To balance the resource allocation and maintain stable AA flux, this work utilizes AA-responsive transcriptional attenuator ivbL and HA-responsive transcriptional activator BmoR to establish a concentration recognition-based auto-dynamic regulation system (CRUISE). This system ultimately maintains the intracellular homeostasis of AA and maximizes the production of HA. It is demonstrated that ivbL-driven enzymes overexpression can dynamically regulate the AA-to-HA conversion while BmoR-driven enzymes overexpression can accelerate the AA biosynthesis during the HA production in a feedback activation mode. The AA flux in biosynthesis and conversion pathways is balanced via the intracellular AA concentration, which is vice versa stabilized by the competition between AA biosynthesis and conversion. The CRUISE, further aided by scaffold-based self-assembly, enables 40.4 g L-1 of isobutanol production in a bioreactor. Taken together, CRUISE realizes robust HA production and sheds new light on the dynamic flux control during the process of chemical production.
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Affiliation(s)
- Zhenya Chen
- Key Laboratory of Molecular Medicine and BiotherapyAerospace Center HospitalSchool of Life ScienceBeijing Institute of TechnologyHaidian DistrictNo. 5 South Zhongguancun StreetBeijing100081China
- Tangshan Research InstituteBeijing Institute of Technology, No. 57, South Jianshe Road, Lubei DistrictTangshanHebei063000China
| | - Shengzhu Yu
- Key Laboratory of Molecular Medicine and BiotherapyAerospace Center HospitalSchool of Life ScienceBeijing Institute of TechnologyHaidian DistrictNo. 5 South Zhongguancun StreetBeijing100081China
| | - Jing Liu
- Key Laboratory of Molecular Medicine and BiotherapyAerospace Center HospitalSchool of Life ScienceBeijing Institute of TechnologyHaidian DistrictNo. 5 South Zhongguancun StreetBeijing100081China
| | - Liwei Guo
- Key Laboratory of Molecular Medicine and BiotherapyAerospace Center HospitalSchool of Life ScienceBeijing Institute of TechnologyHaidian DistrictNo. 5 South Zhongguancun StreetBeijing100081China
| | - Tong Wu
- Key Laboratory of Molecular Medicine and BiotherapyAerospace Center HospitalSchool of Life ScienceBeijing Institute of TechnologyHaidian DistrictNo. 5 South Zhongguancun StreetBeijing100081China
| | - Peifeng Duan
- Key Laboratory of Molecular Medicine and BiotherapyAerospace Center HospitalSchool of Life ScienceBeijing Institute of TechnologyHaidian DistrictNo. 5 South Zhongguancun StreetBeijing100081China
| | - Dongli Yan
- Key Laboratory of Molecular Medicine and BiotherapyAerospace Center HospitalSchool of Life ScienceBeijing Institute of TechnologyHaidian DistrictNo. 5 South Zhongguancun StreetBeijing100081China
| | - Chaoyong Huang
- Key Laboratory of Molecular Medicine and BiotherapyAerospace Center HospitalSchool of Life ScienceBeijing Institute of TechnologyHaidian DistrictNo. 5 South Zhongguancun StreetBeijing100081China
| | - Yi‐Xin Huo
- Key Laboratory of Molecular Medicine and BiotherapyAerospace Center HospitalSchool of Life ScienceBeijing Institute of TechnologyHaidian DistrictNo. 5 South Zhongguancun StreetBeijing100081China
- Tangshan Research InstituteBeijing Institute of Technology, No. 57, South Jianshe Road, Lubei DistrictTangshanHebei063000China
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Nie M, Wang J, Chen Z, Cao C, Zhang K. Systematic engineering enables efficient biosynthesis of L-phenylalanine in E. coli from inexpensive aromatic precursors. Microb Cell Fact 2024; 23:12. [PMID: 38183119 PMCID: PMC10768146 DOI: 10.1186/s12934-023-02282-0] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2023] [Accepted: 12/19/2023] [Indexed: 01/07/2024] Open
Abstract
BACKGROUND L-phenylalanine is an essential amino acid with various promising applications. The microbial pathway for L-phenylalanine synthesis from glucose in wild strains involves lengthy steps and stringent feedback regulation that limits the production yield. It is attractive to find other candidates, which could be used to establish a succinct and cost-effective pathway for L-phenylalanine production. Here, we developed an artificial bioconversion process to synthesize L-phenylalanine from inexpensive aromatic precursors (benzaldehyde or benzyl alcohol). In particular, this work opens the possibility of L-phenylalanine production from benzyl alcohol in a cofactor self-sufficient system without any addition of reductant. RESULTS The engineered L-phenylalanine biosynthesis pathway comprises two modules: in the first module, aromatic precursors and glycine were converted into phenylpyruvate, the key precursor for L-phenylalanine. The highly active enzyme combination was natural threonine aldolase LtaEP.p and threonine dehydratase A8HB.t, which could produce phenylpyruvate in a titer of 4.3 g/L. Overexpression of gene ridA could further increase phenylpyruvate production by 16.3%, reaching up to 5 g/L. The second module catalyzed phenylpyruvate to L-phenylalanine, and the conversion rate of phenylpyruvate was up to 93% by co-expressing PheDH and FDHV120S. Then, the engineered E. coli containing these two modules could produce L-phenylalanine from benzaldehyde with a conversion rate of 69%. Finally, we expanded the aromatic precursors to produce L-phenylalanine from benzyl alcohol, and firstly constructed the cofactor self-sufficient biosynthetic pathway to synthesize L-phenylalanine without any additional reductant such as formate. CONCLUSION Systematical bioconversion processes have been designed and constructed, which could provide a potential bio-based strategy for the production of high-value L-phenylalanine from low-cost starting materials aromatic precursors.
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Affiliation(s)
- Mengzhen Nie
- Zhejiang University, Hangzhou, 310027, Zhejiang, China
- Center of Synthetic Biology and Integrated Bioengineering, School of Engineering, Westlake University, Hangzhou, 310030, Zhejiang, China
| | - Jingyu Wang
- Center of Synthetic Biology and Integrated Bioengineering, School of Engineering, Westlake University, Hangzhou, 310030, Zhejiang, China
| | - Zeyao Chen
- Zhejiang University, Hangzhou, 310027, Zhejiang, China
- Center of Synthetic Biology and Integrated Bioengineering, School of Engineering, Westlake University, Hangzhou, 310030, Zhejiang, China
| | - Chenkai Cao
- Zhejiang University, Hangzhou, 310027, Zhejiang, China
- Center of Synthetic Biology and Integrated Bioengineering, School of Engineering, Westlake University, Hangzhou, 310030, Zhejiang, China
| | - Kechun Zhang
- Center of Synthetic Biology and Integrated Bioengineering, School of Engineering, Westlake University, Hangzhou, 310030, Zhejiang, China.
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Liu H, Yu H, Gao R, Ge F, Zhao R, Lu X, Wang T, Liu H, Yang C, Xia Y, Xun L. A Zero-Valent Sulfur Transporter Helps Podophyllotoxin Uptake into Bacterial Cells in the Presence of CTAB. Antioxidants (Basel) 2023; 13:27. [PMID: 38247452 PMCID: PMC10812762 DOI: 10.3390/antiox13010027] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2023] [Revised: 12/16/2023] [Accepted: 12/18/2023] [Indexed: 01/23/2024] Open
Abstract
Podophyllotoxin (PTOX) is naturally produced by the plant Podophyllum species. Some of its derivatives are anticancer drugs, which are produced mainly by using chemical semi-synthesis methods. Recombinant bacteria have great potential in large-scale production of the derivatives of PTOX. In addition to introducing the correct enzymes, the transportation of PTOX into the cells is an important factor, which limits its modification in the bacteria. Here, we improved the cellular uptake of PTOX into Escherichia coli with the help of the zero-valent sulfur transporter YedE1E2 in the presence of cetyltrimethylammonium bromide (CTAB). CTAB promoted the uptake of PTOX, but induced the production of reactive oxygen species. A protein complex (YedE1E2) of YedE1 and YedE2 enabled E. coli cells to resist CTAB by reducing reactive oxygen species, and YedE1E2 was a hypothetical transporter. Further investigation showed that YedE1E2 facilitated the uptake of extracellular zero-valent sulfur across the cytoplasmic membrane and the formation of glutathione persulfide (GSSH) inside the cells. The increased GSSH minimized oxidative stress. Our results indicate that YedE1E2 is a zero-valent sulfur transporter and it also facilitates CTAB-assisted uptake of PTOX by recombinant bacteria.
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Affiliation(s)
- Honglei Liu
- State Key Laboratory of Microbial Technology, Shandong University, 72 Binhai Road, Qingdao 266237, China; (H.L.); (H.Y.); (R.G.); (F.G.); (R.Z.); (X.L.); (T.W.); (H.L.); (C.Y.)
| | - Huiyuan Yu
- State Key Laboratory of Microbial Technology, Shandong University, 72 Binhai Road, Qingdao 266237, China; (H.L.); (H.Y.); (R.G.); (F.G.); (R.Z.); (X.L.); (T.W.); (H.L.); (C.Y.)
| | - Rui Gao
- State Key Laboratory of Microbial Technology, Shandong University, 72 Binhai Road, Qingdao 266237, China; (H.L.); (H.Y.); (R.G.); (F.G.); (R.Z.); (X.L.); (T.W.); (H.L.); (C.Y.)
- Shandong Provincial Key Laboratory of Test Technology on Food Quality and Safety, Institute of Quality Standard and Testing Technology for Agro-Products, Shandong Academy of Agricultural Sciences, Jinan 250100, China
| | - Fulin Ge
- State Key Laboratory of Microbial Technology, Shandong University, 72 Binhai Road, Qingdao 266237, China; (H.L.); (H.Y.); (R.G.); (F.G.); (R.Z.); (X.L.); (T.W.); (H.L.); (C.Y.)
| | - Rui Zhao
- State Key Laboratory of Microbial Technology, Shandong University, 72 Binhai Road, Qingdao 266237, China; (H.L.); (H.Y.); (R.G.); (F.G.); (R.Z.); (X.L.); (T.W.); (H.L.); (C.Y.)
| | - Xia Lu
- State Key Laboratory of Microbial Technology, Shandong University, 72 Binhai Road, Qingdao 266237, China; (H.L.); (H.Y.); (R.G.); (F.G.); (R.Z.); (X.L.); (T.W.); (H.L.); (C.Y.)
| | - Tianqi Wang
- State Key Laboratory of Microbial Technology, Shandong University, 72 Binhai Road, Qingdao 266237, China; (H.L.); (H.Y.); (R.G.); (F.G.); (R.Z.); (X.L.); (T.W.); (H.L.); (C.Y.)
| | - Huaiwei Liu
- State Key Laboratory of Microbial Technology, Shandong University, 72 Binhai Road, Qingdao 266237, China; (H.L.); (H.Y.); (R.G.); (F.G.); (R.Z.); (X.L.); (T.W.); (H.L.); (C.Y.)
| | - Chunyu Yang
- State Key Laboratory of Microbial Technology, Shandong University, 72 Binhai Road, Qingdao 266237, China; (H.L.); (H.Y.); (R.G.); (F.G.); (R.Z.); (X.L.); (T.W.); (H.L.); (C.Y.)
| | - Yongzhen Xia
- State Key Laboratory of Microbial Technology, Shandong University, 72 Binhai Road, Qingdao 266237, China; (H.L.); (H.Y.); (R.G.); (F.G.); (R.Z.); (X.L.); (T.W.); (H.L.); (C.Y.)
| | - Luying Xun
- State Key Laboratory of Microbial Technology, Shandong University, 72 Binhai Road, Qingdao 266237, China; (H.L.); (H.Y.); (R.G.); (F.G.); (R.Z.); (X.L.); (T.W.); (H.L.); (C.Y.)
- School of Molecular Biosciences, Washington State University, Pullman, WA 99164-7520, USA
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Bi Y, Wang J, Li J, Chou HH, Ren T, Li J, Zhang K. Engineering acetylation platform for the total biosynthesis of D-amino acids. Metab Eng 2023; 80:25-32. [PMID: 37689258 DOI: 10.1016/j.ymben.2023.09.001] [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] [Received: 07/18/2023] [Revised: 08/29/2023] [Accepted: 09/03/2023] [Indexed: 09/11/2023]
Abstract
Optically pure D-amino acids are key chemicals with various applications. Although the production of specific D-amino acids has been achieved by chemical synthesis or with in vitro enzyme catalysts, it is challenging to convert a simple carbon source into D-amino acids with high efficiency. Here, we design an artificial metabolic pathway by engineering bacteria to heterologously express racemase and N-acetyltransferase to produce N-acetyl-D-amino acids from L-amino acids. This new platform allows the cytotoxicity of D-amino acids to be avoided. The universal potential of this acetylation protection strategy for effectively synthesizing optically pure D-amino acids is demonstrated by testing sixteen amino acid targets. Furthermore, we combine pathway optimization and metabolic engineering in Escherichia coli and achieve practically useful efficiency with four specific examples, including N-acetyl-D-valine, N-acetyl-D-serine, N-acetyl-D-phenylalanine and N-acetyl-D-phenylglycine, with titers reaching 5.65 g/L, 5.25 g/L, 8.025 g/L and 130 mg/L, respectively. This work opens up opportunities for synthesizing D-amino acids directly from simple carbon sources, avoiding costly and unsustainable conventional approaches.
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Affiliation(s)
- Yanqi Bi
- Fudan University, 220 Handan Road, Shanghai, 201100, China; School of Engineering, Westlake University, Hangzhou, Zhejiang Province, China; Institute of Advanced Technology, Westlake Institute for Advanced Study, 18 Shilongshan Road, Hangzhou, 310024, Zhejiang Province, China
| | - Jingyu Wang
- School of Engineering, Westlake University, Hangzhou, Zhejiang Province, China; Institute of Advanced Technology, Westlake Institute for Advanced Study, 18 Shilongshan Road, Hangzhou, 310024, Zhejiang Province, China
| | - Jialong Li
- School of Engineering, Westlake University, Hangzhou, Zhejiang Province, China; Institute of Advanced Technology, Westlake Institute for Advanced Study, 18 Shilongshan Road, Hangzhou, 310024, Zhejiang Province, China
| | - Hsiang-Hui Chou
- School of Engineering, Westlake University, Hangzhou, Zhejiang Province, China; Institute of Advanced Technology, Westlake Institute for Advanced Study, 18 Shilongshan Road, Hangzhou, 310024, Zhejiang Province, China
| | - Tianhua Ren
- School of Engineering, Westlake University, Hangzhou, Zhejiang Province, China; Institute of Advanced Technology, Westlake Institute for Advanced Study, 18 Shilongshan Road, Hangzhou, 310024, Zhejiang Province, China
| | - Jinlin Li
- School of Engineering, Westlake University, Hangzhou, Zhejiang Province, China; Institute of Advanced Technology, Westlake Institute for Advanced Study, 18 Shilongshan Road, Hangzhou, 310024, Zhejiang Province, China
| | - Kechun Zhang
- School of Engineering, Westlake University, Hangzhou, Zhejiang Province, China; Institute of Advanced Technology, Westlake Institute for Advanced Study, 18 Shilongshan Road, Hangzhou, 310024, Zhejiang Province, China.
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9
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Sen O, Hinks J, Lin Q, Lin Q, Kjelleberg S, Rice SA, Seviour T. Escherichia coli displays a conserved membrane proteomic response to a range of alcohols. BIOTECHNOLOGY FOR BIOFUELS AND BIOPRODUCTS 2023; 16:147. [PMID: 37789404 PMCID: PMC10546733 DOI: 10.1186/s13068-023-02401-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/20/2023] [Accepted: 09/18/2023] [Indexed: 10/05/2023]
Abstract
BACKGROUND Alcohol is a good and environment-friendly fuel that can be microbially produced, capable of eliminating many of the limitations of the present-day fossil fuels. However, the inherent toxic nature of alcohols to the microbial cells leads to end-product inhibition that limits large-scale alcohol production by fermentation. Fundamental knowledge about the stress responses of microorganisms to alcohols would greatly facilitate to improve the microbial alcohol tolerance. The current study elucidates and compares the changes in the membrane proteome of Escherichia coli in response to a range of alcohols. RESULTS Although alcohol toxicity increased exponentially with alcohol chain length (2-6 carbon), similar stress responses were observed in the inner and outer membrane proteome of E. coli in the presence of 2-, 4- and 6-carbon alcohols at the MIC50. This pertains to: (1) increased levels of inner membrane transporters for uptake of energy-producing metabolites, (2) reduced levels of non-essential proteins, associated with anaerobic, carbon starvation and osmotic stress, for energy conservation, (3) increased levels of murein degrading enzymes (MltA, EmtA, MliC and DigH) promoting cell elongation and 4) reduced levels of most outer membrane β-barrel proteins (LptD, FadL, LamB, TolC and BamA). Major outer membrane β-barrel protein OmpC, which is known to contribute to ethanol tolerance and membrane integrity, was notably reduced by alcohol stress. While LPS is important for OmpC trimerisation, LPS release by EDTA did not lower OmpC levels. This suggests that LPS release, which is reported under alcohol stress, does not contribute to the reduced levels of OmpC in the presence of alcohol. CONCLUSIONS Since alcohol primarily targets the integrity of the membrane, maintenance of outer membrane OmpC levels in the presence of alcohol might help in the survival of E. coli to higher alcohol concentrations. The study provides important information about the membrane protein responses of E. coli to a range of alcohols, which can be used to develop targeted strategies for increased microbial alcohol tolerance and hence bioalcohol production.
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Affiliation(s)
- Oishi Sen
- Singapore Centre for Environmental Life Sciences Engineering, Nanyang Technological University, Singapore, Singapore
- School of Biological Sciences, Nanyang Technological University, Singapore, Singapore
| | - Jamie Hinks
- Singapore Centre for Environmental Life Sciences Engineering, Nanyang Technological University, Singapore, Singapore
| | - Qifeng Lin
- Department of Biological Sciences, Faculty of Science, National University of Singapore, Singapore, Singapore
| | - Qingsong Lin
- Department of Biological Sciences, Faculty of Science, National University of Singapore, Singapore, Singapore
| | - Staffan Kjelleberg
- Singapore Centre for Environmental Life Sciences Engineering, Nanyang Technological University, Singapore, Singapore
- School of Biological Sciences, Nanyang Technological University, Singapore, Singapore
- School of Biological, Earth and Environmental Sciences, University of New South Wales, Sydney, 2052, Australia
| | - Scott A Rice
- Singapore Centre for Environmental Life Sciences Engineering, Nanyang Technological University, Singapore, Singapore
- The Australian Institute for Microbiology and Immunology, University of Technology Sydney, Sydney, 2007, Australia
- CSIRO, Agriculture and Food, Westmead and Microbiomes for One Systems Health, Sydney, Australia
| | - Thomas Seviour
- Singapore Centre for Environmental Life Sciences Engineering, Nanyang Technological University, Singapore, Singapore.
- WATEC Aarhus University Centre for Water Technology, Universitetsbyen 36, Bldg 1783, 8000, Aarhus, Denmark.
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10
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Nie M, Wang J, Zhang K. A novel strategy for L-arginine production in engineered Escherichia coli. Microb Cell Fact 2023; 22:138. [PMID: 37495979 PMCID: PMC10373293 DOI: 10.1186/s12934-023-02145-8] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2023] [Accepted: 07/10/2023] [Indexed: 07/28/2023] Open
Abstract
BACKGROUND L-arginine is an important amino acid with applications in diverse industrial and pharmaceutical fields. N-acetylglutamate, synthesized from L-glutamate and acetyl-CoA, is a precursor of the L-arginine biosynthetic branch in microorganisms. The enzyme that produces N-acetylglutamate, N-acetylglutamate synthase, is allosterically inhibited by L-arginine. L-glutamate, as a central metabolite, provides carbon backbone for diverse biological compounds besides L-arginine. When glucose is the sole carbon source, the theoretical maximum carbon yield towards L-arginine is 96.7%, but the experimental highest yield was 51%. The gap of L-arginine yield indicates the regulation complexity of carbon flux and energy during the L-arginine biosynthesis. Besides endogenous biosynthesis, N-acetylglutamate, the key precursor of L-arginine, can be obtained by chemical acylation of L-glutamate with a high yield of 98%. To achieve high-yield production of L-arginine, we demonstrated a novel approach by directly feeding precursor N-acetylglutamate to engineered Escherichia coli. RESULTS We reported a new approach for the high yield of L-arginine production in E. coli. Gene argA encoding N-acetylglutamate synthase was deleted to disable endogenous biosynthesis of N-acetylglutamate. The feasibility of external N-acetylglutamate towards L-arginine was verified via growth assay in argA- strain. To improve L-arginine production, astA encoding arginine N-succinyltransferase, speF encoding ornithine decarboxylase, speB encoding agmatinase, and argR encoding an arginine responsive repressor protein were disrupted. Based on overexpression of argDGI, argCBH operons, encoding enzymes of the L-arginine biosynthetic pathway, ~ 4 g/L L-arginine was produced in shake flask fermentation, resulting in a yield of 0.99 mol L-arginine/mol N-acetylglutamate. This strain was further engineered for the co-production of L-arginine and pyruvate by removing genes adhE, ldhA, poxB, pflB, and aceE, encoding enzymes involved in the conversion and degradation of pyruvate. The resulting strain was shown to produce 4 g/L L-arginine and 11.3 g/L pyruvate in shake flask fermentation. CONCLUSIONS Here, we developed a novel approach to avoid the strict regulation of L-arginine on ArgA and overcome the metabolism complexity in the L-arginine biosynthesis pathway. We achieve a high yield of L-arginine production from N-acetylglutamate in E. coli. Co-production pyruvate and L-arginine was used as an example to increase the utilization of input carbon sources.
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Affiliation(s)
- Mengzhen Nie
- Zhejiang University, Hangzhou, 310027 Zhejiang China
- Center of Synthetic Biology and Integrated Bioengineering, School of Engineering, Westlake University, Hangzhou, 310030 Zhejiang China
| | - Jingyu Wang
- Center of Synthetic Biology and Integrated Bioengineering, School of Engineering, Westlake University, Hangzhou, 310030 Zhejiang China
| | - Kechun Zhang
- Center of Synthetic Biology and Integrated Bioengineering, School of Engineering, Westlake University, Hangzhou, 310030 Zhejiang China
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11
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Su H, Lin J. Biosynthesis pathways of expanding carbon chains for producing advanced biofuels. BIOTECHNOLOGY FOR BIOFUELS AND BIOPRODUCTS 2023; 16:109. [PMID: 37400889 DOI: 10.1186/s13068-023-02340-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Subscribe] [Scholar Register] [Received: 12/01/2022] [Accepted: 05/11/2023] [Indexed: 07/05/2023]
Abstract
Because the thermodynamic property is closer to gasoline, advanced biofuels (C ≥ 6) are appealing for replacing non-renewable fossil fuels using biosynthesis method that has presented a promising approach. Synthesizing advanced biofuels (C ≥ 6), in general, requires the expansion of carbon chains from three carbon atoms to more than six carbon atoms. Despite some specific biosynthesis pathways that have been developed in recent years, adequate summary is still lacking on how to obtain an effective metabolic pathway. Review of biosynthesis pathways for expanding carbon chains will be conducive to selecting, optimizing and discovering novel synthetic route to obtain new advanced biofuels. Herein, we first highlighted challenges on expanding carbon chains, followed by presentation of two biosynthesis strategies and review of three different types of biosynthesis pathways of carbon chain expansion for synthesizing advanced biofuels. Finally, we provided an outlook for the introduction of gene-editing technology in the development of new biosynthesis pathways of carbon chain expansion.
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Affiliation(s)
- Haifeng Su
- Key Laboratory of Degraded and Unused Land Consolidation Engineering, The Ministry of Natural and Resources, Xian, 710075, Shanxi, China
| | - JiaFu Lin
- Antibiotics Research and Re-Evaluation Key Laboratory of Sichuan Province, Sichuan Industrial Institute of Antibiotics, School of Pharmacy, Chengdu University, Chengdu, 610106, China.
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12
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Huang T, Ma Y. Advances in biosynthesis of higher alcohols in Escherichia coli. World J Microbiol Biotechnol 2023; 39:125. [PMID: 36941474 DOI: 10.1007/s11274-023-03580-w] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2023] [Accepted: 03/13/2023] [Indexed: 03/23/2023]
Abstract
In recent years, the development of green energy to replace fossil fuels has been the focus of research. Higher alcohols are important biofuels and chemicals. The production of higher alcohols in microbes has gained attention due to its environmentally friendly character. Higher alcohols have been synthesized in model microorganism Escherichia coli, and the production has reached the gram level through enhancement of metabolic flow, the balance of reducing power and the optimization of fermentation processes. Sustainable bio-higher alcohols production is expected to replace fossil fuels as a green and renewable energy source. Therefore, this review summarizes the latest developments in producing higher alcohols (C3-C6) by E. coli, elucidate the main bottlenecks limiting the biosynthesis of higher alcohols, and proposes potential engineering strategies of improving the production of biological higher alcohols. This review would provide a theoretical basis for further research on higher alcohols production by E. coli.
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Affiliation(s)
- Tong Huang
- Department of Biochemical Engineering, School of Chemical Engineering and Technology, Tianjin University, Tianjin, 300072, People's Republic of China
| | - Yuanyuan Ma
- Department of Biochemical Engineering, School of Chemical Engineering and Technology, Tianjin University, Tianjin, 300072, People's Republic of China.
- School of Marin Science and Technology, Tianjin University, Tianjin, 300072, China.
- R&D Center for Petrochemical Technology, Tianjin University, Tianjin, 300072, China.
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13
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Orrego AH, Rubanu MG, López IL, Andrés-Sanz D, García-Marquina G, Pieslinger GE, Salassa L, López-Gallego F. ATP-Independent and Cell-Free Biosynthesis of β-Hydroxy Acids Using Vinyl Esters as Smart Substrates. Angew Chem Int Ed Engl 2023; 62:e202218312. [PMID: 36718873 DOI: 10.1002/anie.202218312] [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: 12/12/2022] [Revised: 01/30/2023] [Accepted: 01/31/2023] [Indexed: 02/01/2023]
Abstract
In vitro biosynthetic pathways that condense and reduce molecules through coenzyme A (CoASH) activation demand energy and redox power in the form of ATP and NAD(P)H, respectively. These coenzymes must be orthogonally recycled by ancillary reactions that consume chemicals, electricity, or light, impacting the atom economy and/or the energy consumption of the biosystem. In this work, we have exploited vinyl esters as dual acyl and electron donor substrates to synthesize β-hydroxy acids through a non-decarboxylating Claisen condensation, reduction and hydrolysis stepwise cascade, including a NADH recycling step, catalyzed by a total of 4 enzymes. Herein, the chemical energy to activate the acyl group with CoASH and the redox power for the reduction are embedded into the vinyl esters. Upon optimization, this self-sustaining cascade reached a titer of (S)-3-hydroxy butyrate of 24 mM without requiring ATP and simultaneously recycling CoASH and NADH. This work illustrates the potential of in vitro biocatalysis to transform simple molecules into multi-functional ones.
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Affiliation(s)
- Alejandro H Orrego
- Heterogeneous Biocatalysis laboratory. Center for Cooperative Research in Biomaterials (CIC biomaGUNE)-Basque Research and Technology Alliance (BRTA), Paseo de Miramón,182., 20014, Donostia-San Sebastián, Spain
| | - Maria Grazia Rubanu
- Heterogeneous Biocatalysis laboratory. Center for Cooperative Research in Biomaterials (CIC biomaGUNE)-Basque Research and Technology Alliance (BRTA), Paseo de Miramón,182., 20014, Donostia-San Sebastián, Spain
| | - Idania L López
- Heterogeneous Biocatalysis laboratory. Center for Cooperative Research in Biomaterials (CIC biomaGUNE)-Basque Research and Technology Alliance (BRTA), Paseo de Miramón,182., 20014, Donostia-San Sebastián, Spain
| | - Daniel Andrés-Sanz
- Heterogeneous Biocatalysis laboratory. Center for Cooperative Research in Biomaterials (CIC biomaGUNE)-Basque Research and Technology Alliance (BRTA), Paseo de Miramón,182., 20014, Donostia-San Sebastián, Spain
| | - Guillermo García-Marquina
- Heterogeneous Biocatalysis laboratory. Center for Cooperative Research in Biomaterials (CIC biomaGUNE)-Basque Research and Technology Alliance (BRTA), Paseo de Miramón,182., 20014, Donostia-San Sebastián, Spain
| | - German E Pieslinger
- CONICET-Universidad de Buenos Aires. Instituto de Química y Fisicoquímica Biológicas (IQUIFIB), Buenos Aires, Argentina.,Donostia International Physics Center, Paseo Manuel de Lardizabal 4, 20018, Donostia, Spain
| | - Luca Salassa
- Donostia International Physics Center, Paseo Manuel de Lardizabal 4, 20018, Donostia, Spain.,Polimero eta Material Aurreratuak: Fisika, Kimika eta Teknologia, Kimika Fakultatea, Euskal Herriko Unibertsitatea UPV/EHU, Paseo Manuel de Lardizabal 3, 20018, Donostia, Spain.,Ikerbasque, Basque Foundation for Science, Plaza Euskadi, 5., 48009, . Bilbao, Spain
| | - Fernando López-Gallego
- Heterogeneous Biocatalysis laboratory. Center for Cooperative Research in Biomaterials (CIC biomaGUNE)-Basque Research and Technology Alliance (BRTA), Paseo de Miramón,182., 20014, Donostia-San Sebastián, Spain.,Ikerbasque, Basque Foundation for Science, Plaza Euskadi, 5., 48009, . Bilbao, Spain
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14
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Shu L, Gu J, Wang Q, Sun S, Cui Y, Fell J, Mak WS, Siegel JB, Shi J, Lye GJ, Baganz F, Hao J. The pyruvate decarboxylase activity of IpdC is a limitation for isobutanol production by Klebsiella pneumoniae. BIOTECHNOLOGY FOR BIOFUELS AND BIOPRODUCTS 2022; 15:41. [PMID: 35501883 PMCID: PMC9063327 DOI: 10.1186/s13068-022-02144-8] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/09/2021] [Accepted: 04/17/2022] [Indexed: 11/15/2022]
Abstract
Background Klebsiella pneumoniae contains an endogenous isobutanol synthesis pathway. The ipdC gene annotated as an indole-3-pyruvate decarboxylase (Kp-IpdC), was identified to catalyze the formation of isobutyraldehyde from 2-ketoisovalerate. Results Compared with 2-ketoisovalerate decarboxylase from Lactococcus lactis (KivD), a decarboxylase commonly used in artificial isobutanol synthesis pathways, Kp-IpdC has an 2.8-fold lower Km for 2-ketoisovalerate, leading to higher isobutanol production without induction. However, expression of ipdC by IPTG induction resulted in a low isobutanol titer. In vitro enzymatic reactions showed that Kp-IpdC exhibits promiscuous pyruvate decarboxylase activity, which adversely consume the available pyruvate precursor for isobutanol synthesis. To address this, we have engineered Kp-IpdC to reduce pyruvate decarboxylase activity. From computational modeling, we identified 10 amino acid residues surrounding the active site for mutagenesis. Ten designs consisting of eight single-point mutants and two double-point mutants were selected for exploration. Mutants L546W and T290L that showed only 5.1% and 22.1% of catalytic efficiency on pyruvate compared to Kp-IpdC, were then expressed in K. pneumoniae for in vivo testing. Isobutanol production by K. pneumoniae T290L was 25% higher than that of the control strain, and a final titer of 5.5 g/L isobutanol was obtained with a substrate conversion ratio of 0.16 mol/mol glucose. Conclusions This research provides a new way to improve the efficiency of the biological route of isobutanol production. Supplementary Information The online version contains supplementary material available at 10.1186/s13068-022-02144-8. Kp-IpdC is more efficient than KivD for 2-ketoisovalerate decarboxylation. Pyruvate decarboxylase activity is a limitation of Kp-IpdC. T290L variant exhibits a decreased pyruvate decarboxylase activity. Isobutanol production by K. pneumoniae T290L was improved.
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15
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Gulevich AY, Skorokhodova AY, Debabov VG. Evaluation of the Efficiency of Functional Reversal of Fatty Acid Β-Oxidation in Escherichia coli upon the Action of Various Native Acyl-CoA Dehydrogenases. APPL BIOCHEM MICRO+ 2022. [DOI: 10.1134/s0003683822040196] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
Abstract
Abstract
Using Escherichia coli strain MG1655 lacIQ, ∆ackA-pta, ∆poxB, ∆ldhA, ∆adhE, ∆fadE, PL‑SDφ10-atoB, Ptrc-ideal-4-SDφ10-fadB, PL-SDφ10-tesB, ∆yciA as a core strain, the efficiency of the reversal of fatty acid β-oxidation upon the action of native cellular enzymes capable of serving as acyl-CoA dehydrogenases was examined. Increased expression of fadE, fabI, and ydiO/ydiQRST genes encoding the corresponding enzymes was ensured in derivatives of the core strain by substituting their native regulatory regions with artificial regulatory element Ptrc-ideal-4-SDφ10. A three-turn reversal of the cycle in the engineered recombinants was demonstrated that was accompanied by considerable secretion of butyric, caproic, and caprylic acids. The highest level of six- and eight-carbon carboxylates production was achieved upon the overexpression of the fabI gene, while the lowest levels of secretion of the corresponding compounds were demonstrated by the strain with the enhanced expression of the ydiO and ydiQRST genes. The recombinant with the individually enhanced expression of ydiO did not produce detectable amounts of the derivatives of the complete and successful β-oxidation reversal.
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16
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Seo H, Giannone RJ, Yang YH, Trinh CT. Proteome reallocation enables the selective de novo biosynthesis of non-linear, branched-chain acetate esters. Metab Eng 2022; 73:38-49. [PMID: 35561848 DOI: 10.1016/j.ymben.2022.05.003] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2022] [Revised: 04/21/2022] [Accepted: 05/06/2022] [Indexed: 10/25/2022]
Abstract
The one-carbon recursive ketoacid elongation pathway is responsible for making various branched-chain amino acids, aldehydes, alcohols, and acetate esters in living cells. Controlling selective microbial biosynthesis of these target molecules at high efficiency is challenging due to enzyme promiscuity, regulation, and metabolic burden. In this study, we present a systematic modular design approach to control proteome reallocation for selective microbial biosynthesis of branched-chain acetate esters. Through pathway modularization, we partitioned the branched-chain ester pathways into four submodules including keto-isovalerate submodule for converting pyruvate to keto-isovalerate, ketoacid elongation submodule for producing longer carbon-chain keto-acids, ketoacid decarboxylase submodule for converting ketoacids to alcohols, and alcohol acyltransferase submodule for producing branched-chain acetate esters by condensing alcohols and acetyl-CoA. By systematic manipulation of pathway gene replication and transcription, enzyme specificity of the first committed steps of these submodules, and downstream competing pathways, we demonstrated selective microbial production of isoamyl acetate over isobutyl acetate. We found that the optimized isoamyl acetate pathway globally redistributed the amino acid fractions in the proteomes and required up to 23-31% proteome reallocation at the expense of other cellular resources, such as those required to generate precursor metabolites and energy for growth and amino acid biosynthesis. From glucose fed-batch fermentation, the engineered strains produced isoamyl acetate up to a titer of 8.8 g/L (>0.25 g/L toxicity limit), a yield of 0.22 g/g (61% of maximal theoretical value), and 86% selectivity, achieving the highest titers, yields and selectivity of isoamyl acetate reported to date.
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Affiliation(s)
- Hyeongmin Seo
- Department of Chemical and Biomolecular Engineering, The University of Tennessee, Knoxville, TN, USA; Center of Bioenergy Innovation, Oak Ridge National Laboratory, Oak Ridge, TN, USA
| | - Richard J Giannone
- Center of Bioenergy Innovation, Oak Ridge National Laboratory, Oak Ridge, TN, USA; Chemical Sciences Division, Oak Ridge National Laboratory, Oak Ridge, TN, 37830, USA
| | - Yung-Hun Yang
- Department of Biological Engineering, Konkuk University, Seoul, South Korea
| | - Cong T Trinh
- Department of Chemical and Biomolecular Engineering, The University of Tennessee, Knoxville, TN, USA; Center of Bioenergy Innovation, Oak Ridge National Laboratory, Oak Ridge, TN, USA.
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17
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Salmerón I, Guzmán CLA, Sánchez VHR, Reyes IP, Mata JS, Cisneros de la Cueva S. Hydrogen and alcohols production by Serratia sp. from an inorganic carbon source. J CO2 UTIL 2022. [DOI: 10.1016/j.jcou.2022.101914] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
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18
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Gardner JM, Walker ME, Boss PK, Jiranek V. The effect of grape juice dilution and complex nutrient addition on oenological fermentation and wine chemical composition. J Food Compost Anal 2022. [DOI: 10.1016/j.jfca.2021.104241] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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19
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Zhao L, Chen Z, Lin S, Wu T, Yu S, Huo YX. In Vitro Biosynthesis of Isobutyraldehyde Through the Establishment of a One-Step Self-Assembly-Based Immobilization Strategy. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2021; 69:14609-14619. [PMID: 34818887 DOI: 10.1021/acs.jafc.1c05387] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/13/2023]
Abstract
The in vitro biosynthesis of high-value compounds has become popular and attractive. The convenient and simple strategy of enzyme immobilization has been significant for continuous and efficient in vitro biosynthesis. On the basis of that, this work established a one-step self-assembly-based immobilization strategy to efficiently biosynthesize isobutyraldehyde in vitro. Isobutyraldehyde is a crucial precursor for the synthesis of foods and spices. The established CipA scaffold-based strategy can express and immobilize enzymes at the same time, and purification requires only one centrifugation step. Structural simulations indicated that this scaffold-dependent self-assembly did not influence the structure or catalytic mechanisms of the isobutyraldehyde production-related enzymes leucine dehydrogenase (LeuDH) and ketoisovalerate decarboxylase (Kivd). Immobilized LeuDH and Kivd displayed a higher conversion capacity and thermal stability than the free enzymes. Batch conversion experiments demonstrated that the recovered immobilized LeuDH and Kivd have similar conversion capacities to the enzymes used in the first round of reaction. The continuous production of isobutyraldehyde was achieved by filling the immobilized enzymes into the column of a constructed device. This study not only expands the application range of self-assembly systems but also provides guidance for the in vitro production of value-added compounds.
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Affiliation(s)
- Luyao Zhao
- Key Laboratory of Molecular Medicine and Biotherapy, School of Life Science, Beijing Institute of Technology, No. 5 South Zhongguancun Street, Haidian District, 100081 Beijing, China
| | - Zhenya Chen
- Key Laboratory of Molecular Medicine and Biotherapy, School of Life Science, Beijing Institute of Technology, No. 5 South Zhongguancun Street, Haidian District, 100081 Beijing, China
| | - Sheng Lin
- Beijing Key Laboratory of Microanalytical Methods and Instrumentation, MOE Key Laboratory of Bioorganic Phosphorus Chemistry and Chemical Biology, Department of Chemistry, Tsinghua University, Haidian District, 100084 Beijing, China
| | - Tong Wu
- Key Laboratory of Molecular Medicine and Biotherapy, School of Life Science, Beijing Institute of Technology, No. 5 South Zhongguancun Street, Haidian District, 100081 Beijing, China
| | - Shengzhu Yu
- Key Laboratory of Molecular Medicine and Biotherapy, School of Life Science, Beijing Institute of Technology, No. 5 South Zhongguancun Street, Haidian District, 100081 Beijing, China
| | - Yi-Xin Huo
- Key Laboratory of Molecular Medicine and Biotherapy, School of Life Science, Beijing Institute of Technology, No. 5 South Zhongguancun Street, Haidian District, 100081 Beijing, China
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20
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Mu Q, Shi Y, Li R, Ma C, Tao Y, Yu B. Production of Propionate by a Sequential Fermentation-Biotransformation Process via l-Threonine. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2021; 69:13895-13903. [PMID: 34757739 DOI: 10.1021/acs.jafc.1c05248] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/13/2023]
Abstract
Bio-based propionate is widely welcome in the food additive industry. The current anaerobic process by Propionibacteria endures low titers and a long fermentation time. In this study, a new route for propionate production from l-threonine was designed. 2-Ketobutyrate, deaminated from l-threonine, is cleaved into propionaldehyde and CO2 and then be oxidized into propionic acid, which is neutralized by ammonia released from the first deamination step. This CoA-independent pathway with only CO2 as a byproduct boosts propionate production from l-threonine with high productivity and purity. The key enzyme for 2-ketobutyrate decarboxylation was selected, and its expression was optimized. The engineered Pseudomonas putida strain, harboring 2-ketoisovalerate decarboxylase from Lactococcus lactis could produce 580 mM (43 g/L) pure propionic acid from 600 mM l-threonine in 24 h in the batch biotransformation process. Furthermore, a high titer of 62 g/L propionic acid with a productivity of 1.07 g/L/h and a molar yield of >0.98 was achieved in the fed-batch pattern. Finally, an efficient sequential fermentation-biotransformation process was demonstrated to produce propionate directly from the fermentation broth containing l-threonine, which further reduces the costs since no l-threonine purification step is required.
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Affiliation(s)
- Qingxuan Mu
- CAS Key Laboratory of Microbial Physiological & Metabolic Engineering, State Key Laboratory of Mycology, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Ya'nan Shi
- CAS Key Laboratory of Microbial Physiological & Metabolic Engineering, State Key Laboratory of Mycology, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Rongshan Li
- CAS Key Laboratory of Microbial Physiological & Metabolic Engineering, State Key Laboratory of Mycology, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China
| | - Chao Ma
- CAS Key Laboratory of Microbial Physiological & Metabolic Engineering, State Key Laboratory of Mycology, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China
| | - Yong Tao
- CAS Key Laboratory of Microbial Physiological & Metabolic Engineering, State Key Laboratory of Mycology, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China
| | - Bo Yu
- CAS Key Laboratory of Microbial Physiological & Metabolic Engineering, State Key Laboratory of Mycology, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China
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21
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Bahls MO, Platz L, Morgado G, Schmidt GW, Panke S. Directed evolution of biofuel-responsive biosensors for automated optimization of branched-chain alcohol biosynthesis. Metab Eng 2021; 69:98-111. [PMID: 34767976 DOI: 10.1016/j.ymben.2021.10.014] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2021] [Revised: 10/21/2021] [Accepted: 10/31/2021] [Indexed: 12/18/2022]
Abstract
The biosynthesis of short-chain alcohols is a carbon-neutral alternative to petroleum-derived production, but strain screening operations are encumbered by laborious analytics. Here, we built, characterized and applied whole cell biosensors by directed evolution of the transcription factor AlkS for screening microbial strain libraries producing industrially relevant alcohols. A selected AlkS variant was applied for in situ product detection in two screening applications concerning key steps in alcohol production. Further, the biosensor strains enabled the implementation of an automated, robotic platform-based workflow with data clustering, which readily allowed the identification of significantly improved strain variants for isopentanol production.
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Affiliation(s)
- Maximilian O Bahls
- Department of Biosystems Science and Engineering, ETH Zurich, Switzerland
| | - Lukas Platz
- Department of Biosystems Science and Engineering, ETH Zurich, Switzerland
| | - Gaspar Morgado
- Department of Biosystems Science and Engineering, ETH Zurich, Switzerland
| | - Gregor W Schmidt
- Department of Biosystems Science and Engineering, ETH Zurich, Switzerland
| | - Sven Panke
- Department of Biosystems Science and Engineering, ETH Zurich, Switzerland.
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22
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Hikage F, Ichioka H, Watanabe M, Umetsu A, Ohguro H, Ida Y. ROCK inhibitors modulate the physical properties and adipogenesis of 3D spheroids of human orbital fibroblasts in different manners. FASEB Bioadv 2021; 3:866-872. [PMID: 34632320 PMCID: PMC8493964 DOI: 10.1096/fba.2021-00037] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2021] [Revised: 07/10/2021] [Accepted: 07/12/2021] [Indexed: 01/01/2023] Open
Abstract
To elucidate the pharmacological effects of Rho-associated coiled-coil containing protein kinase inhibitors (ROCK-is), ripasudil (Rip), Y27632, and KD025, on human orbital fatty tissue, the human orbital fibroblasts (HOFs) were three-dimensional (3D) cultured for 12 days. The effects of ROCK-is on the physical properties of the 3D-cultured HOF spheroids, including their sizes and physical stiffness, their adipogenesis by lipid staining, and the mRNA expression of adipogenesis-related genes, PPARγ and AP2, and extracellular matrix (ECM) including collagen (COL) 1, 4, and 6, and fibronectin were analyzed. A significant increase in the sizes, physical stiffness, lipid staining, and mRNA expression of adipogenesis-related genes, COL4 and COL6, and a decrease in COL1 expression were observed with adipogenesis (DIF+). In the presence of ROCK-is, such DIF+-induced effects were differently modulated as follows: (1) the sizes were not affected or significantly enhanced by Rip, Y27632, or KD025, (2) the physical stiffness was significantly decreased in Rip and Y27632, but was substantially increased in KD025, (3) the lipid staining was further enhanced or significantly suppressed by Rip, Y27632, or KD025, and both PPARγ and AP2 expression were significantly downregulated or upregulated by KD025 or Rip, and (4) Rip upregulated the expression of COL4, Y27632 upregulated the expression of COL1, COL4, and COL6, and KD025 upregulated the expression of COL1 and COL4. This study indicates that ROCK-is significantly and differently modulate physical properties of the 3D HOF spheroids as well as their adipogenesis.
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Affiliation(s)
- Fumihito Hikage
- Departments of OphthalmologySapporo Medical University School of MedicineSapporoJapan
| | - Hanae Ichioka
- Departments of OphthalmologySapporo Medical University School of MedicineSapporoJapan
| | - Megumi Watanabe
- Departments of OphthalmologySapporo Medical University School of MedicineSapporoJapan
| | - Araya Umetsu
- Departments of OphthalmologySapporo Medical University School of MedicineSapporoJapan
| | - Hiroshi Ohguro
- Departments of OphthalmologySapporo Medical University School of MedicineSapporoJapan
| | - Yosuke Ida
- Departments of OphthalmologySapporo Medical University School of MedicineSapporoJapan
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23
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Duran L, López JM, Avalos JL. ¡Viva la mitochondria!: harnessing yeast mitochondria for chemical production. FEMS Yeast Res 2021; 20:5863938. [PMID: 32592388 DOI: 10.1093/femsyr/foaa037] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2020] [Accepted: 06/12/2020] [Indexed: 12/11/2022] Open
Abstract
The mitochondria, often referred to as the powerhouse of the cell, offer a unique physicochemical environment enriched with a distinct set of enzymes, metabolites and cofactors ready to be exploited for metabolic engineering. In this review, we discuss how the mitochondrion has been engineered in the traditional sense of metabolic engineering or completely bypassed for chemical production. We then describe the more recent approach of harnessing the mitochondria to compartmentalize engineered metabolic pathways, including for the production of alcohols, terpenoids, sterols, organic acids and other valuable products. We explain the different mechanisms by which mitochondrial compartmentalization benefits engineered metabolic pathways to boost chemical production. Finally, we discuss the key challenges that need to be overcome to expand the applicability of mitochondrial engineering and reach the full potential of this emerging field.
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Affiliation(s)
- Lisset Duran
- Department of Molecular Biology, Princeton University, Princeton, NJ 08544, USA
| | - José Montaño López
- Department of Chemical and Biological Engineering, Princeton University, Princeton, NJ 08544, USA
| | - José L Avalos
- Department of Molecular Biology, Princeton University, Princeton, NJ 08544, USA
- Department of Chemical and Biological Engineering, Princeton University, Princeton, NJ 08544, USA
- Andlinger Center for Energy and the Environment, Princeton University, Princeton, NJ 08544, USA
- Princeton Environmental Institute, Princeton University, Princeton, NJ 08544, USA
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24
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Feng Y, Zhu J, Wang S, Yu L, He Z, Qian Y, Lu X. Theoretical and Experimental Study of 3-Pentanol Autoignition: Ab Initio Calculation, Shock Tube Experiments, and Kinetic Modeling. J Phys Chem A 2021; 125:5976-5989. [PMID: 34213330 DOI: 10.1021/acs.jpca.1c02713] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
3-Pentanol is a potential alternative fuel or a green fuel additive for modern engines. The H-abstraction reactions from 3-pentanol by H, CH3, HO2, and OH radicals are significant in the 3-pentanol oxidation process. However, corresponding rate constants are forced to rely on either analogy from sec-butanol or estimation from alkanes due to a lack of direct experimental and theoretical study. In this work, stationary points on the potential energy surfaces (PESs) were calculated with the high-level DLPNO-CCSD(T)/CBS(T-Q)//M06-2X/cc-pVTZ method, which is further used to benchmark against the CBS-QB3 method. Then, the high-pressure limit rate constants for target reactions, over a broad range of temperature (400-2000 K), were calculated with the phase-space theory and conventional transition state theory. A comparison was made between the calculated rate constants and the values available in Carbonnier et al. [ Proc. Combust. Inst. 2019, 37(1), 477-484]. The rate constants for the above H-abstraction reactions in the Carbonnier model were updated with the calculated results, followed by a modification based on the computed results of 3-pentanol + HO2 to obtain the revised model. Validation against the shock tube (ST) and the jet-stirred reactor (JSR) measurements from the literature proved the revised model an optimal one. Furthermore, using an ST, ignition delay times (IDTs) for the 3-pentanol/air mixtures were measured spanning a temperature range of 920-1450 K, pressures of 6, 10, and 20 bar, and equivalence ratios of 0.5, 1.0, and 1.5. Generally, IDTs decrease with increasing temperature and reflected shock pressure. Improved predictions to present experimental data were obtained by using the revised model as compared with the Carbonnier model. Finally, sensitivity analysis was conducted using the revised model to gain an in-depth comprehension of the 3-pentanol autoignition.
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Affiliation(s)
- Yuan Feng
- Key Laboratory for Power Machinery and Engineering of M. O. E, Shanghai Jiao Tong University, 200240 Shanghai, P. R. China
| | - Jizhen Zhu
- Key Laboratory for Power Machinery and Engineering of M. O. E, Shanghai Jiao Tong University, 200240 Shanghai, P. R. China
| | - Sixu Wang
- Key Laboratory for Power Machinery and Engineering of M. O. E, Shanghai Jiao Tong University, 200240 Shanghai, P. R. China
| | - Liang Yu
- Key Laboratory for Power Machinery and Engineering of M. O. E, Shanghai Jiao Tong University, 200240 Shanghai, P. R. China
| | - Zhuoyao He
- Key Laboratory for Power Machinery and Engineering of M. O. E, Shanghai Jiao Tong University, 200240 Shanghai, P. R. China
| | - Yong Qian
- Key Laboratory for Power Machinery and Engineering of M. O. E, Shanghai Jiao Tong University, 200240 Shanghai, P. R. China
| | - Xingcai Lu
- Key Laboratory for Power Machinery and Engineering of M. O. E, Shanghai Jiao Tong University, 200240 Shanghai, P. R. China
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25
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Folch PL, Bisschops MM, Weusthuis RA. Metabolic energy conservation for fermentative product formation. Microb Biotechnol 2021; 14:829-858. [PMID: 33438829 PMCID: PMC8085960 DOI: 10.1111/1751-7915.13746] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2020] [Revised: 12/16/2020] [Accepted: 12/21/2020] [Indexed: 12/02/2022] Open
Abstract
Microbial production of bulk chemicals and biofuels from carbohydrates competes with low-cost fossil-based production. To limit production costs, high titres, productivities and especially high yields are required. This necessitates metabolic networks involved in product formation to be redox-neutral and conserve metabolic energy to sustain growth and maintenance. Here, we review the mechanisms available to conserve energy and to prevent unnecessary energy expenditure. First, an overview of ATP production in existing sugar-based fermentation processes is presented. Substrate-level phosphorylation (SLP) and the involved kinase reactions are described. Based on the thermodynamics of these reactions, we explore whether other kinase-catalysed reactions can be applied for SLP. Generation of ion-motive force is another means to conserve metabolic energy. We provide examples how its generation is supported by carbon-carbon double bond reduction, decarboxylation and electron transfer between redox cofactors. In a wider perspective, the relationship between redox potential and energy conservation is discussed. We describe how the energy input required for coenzyme A (CoA) and CO2 binding can be reduced by applying CoA-transferases and transcarboxylases. The transport of sugars and fermentation products may require metabolic energy input, but alternative transport systems can be used to minimize this. Finally, we show that energy contained in glycosidic bonds and the phosphate-phosphate bond of pyrophosphate can be conserved. This review can be used as a reference to design energetically efficient microbial cell factories and enhance product yield.
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Affiliation(s)
- Pauline L. Folch
- Bioprocess EngineeringWageningen University & ResearchPost office box 16Wageningen6700 AAThe Netherlands
| | - Markus M.M. Bisschops
- Bioprocess EngineeringWageningen University & ResearchPost office box 16Wageningen6700 AAThe Netherlands
| | - Ruud A. Weusthuis
- Bioprocess EngineeringWageningen University & ResearchPost office box 16Wageningen6700 AAThe Netherlands
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26
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Seo H, Lee JW, Giannone RJ, Dunlap NJ, Trinh CT. Engineering promiscuity of chloramphenicol acetyltransferase for microbial designer ester biosynthesis. Metab Eng 2021; 66:179-190. [PMID: 33872779 DOI: 10.1016/j.ymben.2021.04.005] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2021] [Revised: 04/06/2021] [Accepted: 04/11/2021] [Indexed: 02/07/2023]
Abstract
Robust and efficient enzymes are essential modules for metabolic engineering and synthetic biology strategies across biological systems to engineer whole-cell biocatalysts. By condensing an acyl-CoA and an alcohol, alcohol acyltransferases (AATs) can serve as interchangeable metabolic modules for microbial biosynthesis of a diverse class of ester molecules with broad applications as flavors, fragrances, solvents, and drop-in biofuels. However, the current lack of robust and efficient AATs significantly limits their compatibility with heterologous precursor pathways and microbial hosts. Through bioprospecting and rational protein engineering, we identified and engineered promiscuity of chloramphenicol acetyltransferases (CATs) from mesophilic prokaryotes to function as robust and efficient AATs compatible with at least 21 alcohol and 8 acyl-CoA substrates for microbial biosynthesis of linear, branched, saturated, unsaturated and/or aromatic esters. By plugging the best engineered CAT (CATec3 Y20F) into the gram-negative mesophilic bacterium Escherichia coli, we demonstrated that the recombinant strain could effectively convert various alcohols into desirable esters, for instance, achieving a titer of 13.9 g/L isoamyl acetate with 95% conversion by fed-batch fermentation. The recombinant E. coli was also capable of simulating the ester profile of roses with high conversion (>97%) and titer (>1 g/L) from fermentable sugars at 37 °C. Likewise, a recombinant gram-positive, cellulolytic, thermophilic bacterium Clostridium thermocellum harboring CATec3 Y20F could produce many of these esters from recalcitrant cellulosic biomass at elevated temperatures (>50 °C) due to the engineered enzyme's remarkable thermostability. Overall, the engineered CATs can serve as a robust and efficient platform for designer ester biosynthesis from renewable and sustainable feedstocks.
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Affiliation(s)
- Hyeongmin Seo
- Department of Chemical and Biomolecular Engineering, The University of Tennessee, Knoxville, TN, USA; Center of Bioenergy Innovation, Oak Ridge National Laboratory, Oak Ridge, TN, USA
| | - Jong-Won Lee
- Bredesen Center for Interdisciplinary Research and Graduate Education, The University of Tennessee, Knoxville, TN, USA; Center of Bioenergy Innovation, Oak Ridge National Laboratory, Oak Ridge, TN, USA
| | - Richard J Giannone
- Center of Bioenergy Innovation, Oak Ridge National Laboratory, Oak Ridge, TN, USA; Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN, 37831, USA
| | - Noah J Dunlap
- Department of Chemical and Biomolecular Engineering, The University of Tennessee, Knoxville, TN, USA
| | - Cong T Trinh
- Department of Chemical and Biomolecular Engineering, The University of Tennessee, Knoxville, TN, USA; Bredesen Center for Interdisciplinary Research and Graduate Education, The University of Tennessee, Knoxville, TN, USA; Center of Bioenergy Innovation, Oak Ridge National Laboratory, Oak Ridge, TN, USA.
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27
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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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28
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Cheng J, Tu W, Luo Z, Gou X, Li Q, Wang D, Zhou J. A High-Efficiency Artificial Synthetic Pathway for 5-Aminovalerate Production From Biobased L-Lysine in Escherichia coli. Front Bioeng Biotechnol 2021; 9:633028. [PMID: 33634090 PMCID: PMC7900509 DOI: 10.3389/fbioe.2021.633028] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2020] [Accepted: 01/20/2021] [Indexed: 12/11/2022] Open
Abstract
Bioproduction of 5-aminovalerate (5AVA) from renewable feedstock can support a sustainable biorefinery process to produce bioplastics, such as nylon 5 and nylon 56. In order to achieve the biobased production of 5AVA, a 2-keto-6-aminocaproate-mediated synthetic pathway was established. Combination of L-Lysine α-oxidase from Scomber japonicus, α-ketoacid decarboxylase from Lactococcus lactis and aldehyde dehydrogenase from Escherichia coli could achieve the biosynthesis of 5AVA from biobased L-Lysine in E. coli. The H2O2 produced by L-Lysine α-oxidase was decomposed by the expression of catalase KatE. Finally, 52.24 g/L of 5AVA were obtained through fed-batch biotransformation. Moreover, homology modeling, molecular docking and molecular dynamic simulation analyses were used to identify mutation sites and propose a possible trait-improvement strategy: the expanded catalytic channel of mutant and more hydrogen bonds formed might be beneficial for the substrates stretch. In summary, we have developed a promising artificial pathway for efficient 5AVA synthesis.
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Affiliation(s)
- Jie Cheng
- Key Laboratory of Meat Processing of Sichuan Province, Key Laboratory of Coarse Cereal Processing, Ministry of Agriculture and Rural Affairs, College of Food and Biological Engineering, Chengdu University, Chengdu, China
| | - Wenying Tu
- Key Laboratory of Meat Processing of Sichuan Province, Key Laboratory of Coarse Cereal Processing, Ministry of Agriculture and Rural Affairs, College of Food and Biological Engineering, Chengdu University, Chengdu, China
| | - Zhou Luo
- Key Laboratory of Meat Processing of Sichuan Province, Key Laboratory of Coarse Cereal Processing, Ministry of Agriculture and Rural Affairs, College of Food and Biological Engineering, Chengdu University, Chengdu, China
| | - Xinghua Gou
- Key Laboratory of Meat Processing of Sichuan Province, Key Laboratory of Coarse Cereal Processing, Ministry of Agriculture and Rural Affairs, College of Food and Biological Engineering, Chengdu University, Chengdu, China
| | - Qiang Li
- Key Laboratory of Meat Processing of Sichuan Province, Key Laboratory of Coarse Cereal Processing, Ministry of Agriculture and Rural Affairs, College of Food and Biological Engineering, Chengdu University, Chengdu, China
| | - Dan Wang
- Department of Chemical Engineering, School of Chemistry and Chemical Engineering, Chongqing University, Chongqing, China
| | - Jingwen Zhou
- National Engineering Laboratory for Cereal Fermentation Technology, Jiangnan University, Wuxi, China
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29
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Hegner R, Neubert K, Kroner C, Holtmann D, Harnisch F. Coupled Electrochemical and Microbial Catalysis for the Production of Polymer Bricks. CHEMSUSCHEM 2020; 13:5295-5300. [PMID: 32658366 PMCID: PMC7590143 DOI: 10.1002/cssc.202001272] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/20/2020] [Revised: 06/29/2020] [Indexed: 06/11/2023]
Abstract
Power-to-X technologies have the potential to pave the way towards a future resource-secure bioeconomy as they enable the exploitation of renewable resources and CO2 . Herein, the coupled electrocatalytic and microbial catalysis of the C5 -polymer precursors mesaconate and 2S-methylsuccinate from CO2 and electric energy by in situ coupling electrochemical and microbial catalysis at 1 L-scale was developed. In the first phase, 6.1±2.5 mm formate was produced by electrochemical CO2 reduction. In the second phase, formate served as the substrate for microbial catalysis by an engineered strain of Methylobacterium extorquens AM-1 producing 7±2 μm and 10±5 μm of mesaconate and 2S-methylsuccinate, respectively. The proof of concept showed an overall conversion efficiency of 0.2 % being 0.4 % of the theoretical maximum.
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Affiliation(s)
- Richard Hegner
- Helmholtz Center for Environmental Research GmbH – UFZDepartment of Environmental MicrobiologyPermoserstraße 1504318LeipzigGermany
| | - Katharina Neubert
- Helmholtz Center for Environmental Research GmbH – UFZDepartment of Environmental MicrobiologyPermoserstraße 1504318LeipzigGermany
| | - Cora Kroner
- DECHEMA Research InstituteIndustrial BiotechnologyTheodor-Heuss-Allee 2560486Frankfurt am MainGermany
| | - Dirk Holtmann
- DECHEMA Research InstituteIndustrial BiotechnologyTheodor-Heuss-Allee 2560486Frankfurt am MainGermany
- Technische Hochschule MittelhessenInstitute of Bioprocess Engineering and Pharmaceutical TechnologyWiesenstraße 1435390GießenGermany
| | - Falk Harnisch
- Helmholtz Center for Environmental Research GmbH – UFZDepartment of Environmental MicrobiologyPermoserstraße 1504318LeipzigGermany
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30
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Bacterial synthesis of C3-C5 diols via extending amino acid catabolism. Proc Natl Acad Sci U S A 2020; 117:19159-19167. [PMID: 32719126 DOI: 10.1073/pnas.2003032117] [Citation(s) in RCA: 31] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022] Open
Abstract
Amino acids are naturally occurring and structurally diverse metabolites in biological system, whose potentials for chemical expansion, however, have not been fully explored. Here, we devise a metabolic platform capable of producing industrially important C3-C5 diols from amino acids. The presented platform combines the natural catabolism of charged amino acids with a catalytically efficient and thermodynamically favorable diol formation pathway, created by expanding the substrate scope of the carboxylic acid reductase toward noncognate ω-hydroxylic acids. Using the established platform as gateways, seven different diol-convertible amino acids are converted to diols including 1,3-propanediol, 1,4-butanediol, and 1,5-pentanediol. Particularly, we afford to optimize the production of 1,4-butanediol and demonstrate the de novo production of 1,5-pentanediol from glucose, with titers reaching 1.41 and 0.97 g l-1, respectively. Our work presents a metabolic platform that enriches the pathway repertoire for nonnatural diols with feedstock flexibility to both sugar and protein hydrolysates.
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31
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Hasegawa S, Jojima T, Suda M, Inui M. Isobutanol production in Corynebacterium glutamicum: Suppressed succinate by-production by pckA inactivation and enhanced productivity via the Entner–Doudoroff pathway. Metab Eng 2020; 59:24-35. [DOI: 10.1016/j.ymben.2020.01.004] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2019] [Revised: 12/24/2019] [Accepted: 01/07/2020] [Indexed: 10/25/2022]
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32
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Gu Y, Ma J, Zhu Y, Xu P. Refactoring Ehrlich Pathway for High-Yield 2-Phenylethanol Production in Yarrowia lipolytica. ACS Synth Biol 2020; 9:623-633. [PMID: 32134637 PMCID: PMC7308069 DOI: 10.1021/acssynbio.9b00468] [Citation(s) in RCA: 32] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2019] [Indexed: 12/16/2022]
Abstract
Efficient microbial synthesis of chemicals requires the coordinated supply of precursors and cofactors to maintain cell growth and product formation. Substrates with different entry points into the metabolic network have different energetic and redox statuses. Generally, substrate cofeeding could bypass the lengthy and highly regulated native metabolism and facilitates high carbon conversion rate. Aiming to efficiently synthesize the high-value rose-smell 2-phenylethanol (2-PE) in Y. lipolytica, we analyzed the stoichiometric constraints of the Ehrlich pathway and identified that the selectivity of the Ehrlich pathway and the availability of 2-oxoglutarate are the rate-limiting factors. Stepwise refactoring of the Ehrlich pathway led us to identify the optimal catalytic modules consisting of l-phenylalanine permease, ketoacid aminotransferase, phenylpyruvate decarboxylase, phenylacetaldehyde reductase, and alcohol dehydrogenase. On the other hand, mitochondrial compartmentalization of 2-oxoglutarate inherently creates a bottleneck for efficient assimilation of l-phenylalanine, which limits 2-PE production. To improve 2-oxoglutarate (aKG) trafficking across the mitochondria membrane, we constructed a cytosolic aKG source pathway by coupling a bacterial aconitase with a native isocitrate dehydrogenase (ylIDP2). Additionally, we also engineered dicarboxylic acid transporters to further improve the 2-oxoglutarate availability. Furthermore, by blocking the precursor-competing pathways and mitigating fatty acid synthesis, the engineered strain produced 2669.54 mg/L of 2-PE in shake flasks, a 4.16-fold increase over the starting strain. The carbon conversion yield reaches 0.702 g/g from l-phenylalanine, 95.0% of the theoretical maximal. The reported work expands our ability to harness the Ehrlich pathway for production of high-value aromatics in oleaginous yeast species.
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Affiliation(s)
- Yang Gu
- Department
of Chemical, Biochemical and Environmental Engineering, University of Maryland, Baltimore County, Baltimore, Maryland 21250, United States
- Key
Laboratory of Carbohydrate Chemistry and Biotechnology, Ministry of
Education, Jiangnan University, Wuxi 214122, China
| | - Jingbo Ma
- Department
of Chemical, Biochemical and Environmental Engineering, University of Maryland, Baltimore County, Baltimore, Maryland 21250, United States
| | - Yonglian Zhu
- Key
Laboratory of Carbohydrate Chemistry and Biotechnology, Ministry of
Education, Jiangnan University, Wuxi 214122, China
| | - Peng Xu
- Department
of Chemical, Biochemical and Environmental Engineering, University of Maryland, Baltimore County, Baltimore, Maryland 21250, United States
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33
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Hammer SK, Zhang Y, Avalos JL. Mitochondrial Compartmentalization Confers Specificity to the 2-Ketoacid Recursive Pathway: Increasing Isopentanol Production in Saccharomyces cerevisiae. ACS Synth Biol 2020; 9:546-555. [PMID: 32049515 DOI: 10.1021/acssynbio.9b00420] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Recursive elongation pathways produce compounds of increasing carbon-chain length with each iterative cycle. Of particular interest are 2-ketoacids derived from recursive elongation, which serve as precursors to a valuable class of advanced biofuels known as branched-chain higher alcohols (BCHAs). Protein engineering has been used to increase the number of iterative elongation cycles completed, yet specific production of longer-chain 2-ketoacids remains difficult to achieve. Here, we show that mitochondrial compartmentalization is an effective strategy to increase specificity of recursive pathways to favor longer-chain products. Using 2-ketoacid elongation as a proof of concept, we show that overexpression of the three elongation enzymes-LEU4, LEU1, and LEU2-in mitochondria of an isobutanol production strain results in a 2.3-fold increase in the isopentanol to isobutanol product ratio relative to overexpressing the same elongation enzymes in the cytosol, and a 31-fold increase relative to wild-type enzyme expression. Reducing the loss of intermediates allows us to further boost isopentanol production to 1.24 ± 0.06 g/L of isopentanol. In this strain, isopentanol accounts for 86% of the total BCHAs produced, while achieving the highest isopentanol titer reported for Saccharomyces cerevisiae. Localizing the elongation enzymes in mitochondria enables the development of strains in which isopentanol constitutes as much as 93% of BCHA production. This work establishes mitochondrial compartmentalization as a new approach to favor high titers and product specificities of larger products from recursive pathways.
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Affiliation(s)
- Sarah K. Hammer
- Department of Chemical and Biological Engineering, Princeton University, Princeton, New Jersey 08544, United States
| | - Yanfei Zhang
- Department of Chemical and Biological Engineering, Princeton University, Princeton, New Jersey 08544, United States
| | - José L. Avalos
- Department of Chemical and Biological Engineering, Princeton University, Princeton, New Jersey 08544, United States
- Andlinger Center for Energy and the Environment, Princeton University, Princeton, New Jersey 08544, United States
- Department of Molecular Biology, Princeton University, Princeton, New Jersey 08544, United States
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Fu L, Zhang J, Si T. Recent advances in high-throughput mass spectrometry that accelerates enzyme engineering for biofuel research. ACTA ACUST UNITED AC 2020. [DOI: 10.1186/s42500-020-0011-8] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
AbstractEnzymes play indispensable roles in producing biofuels, a sustainable and renewable source of transportation fuels. Lacking rational design rules, the development of industrially relevant enzyme catalysts relies heavily on high-throughput screening. However, few universal methods exist to rapidly characterize large-scale enzyme libraries. Therefore, assay development is necessary on an ad hoc basis to link enzyme properties to spectrophotometric signals and often requires the use of surrogate, optically active substrates. On the other hand, mass spectrometry (MS) performs label-free enzyme assays that utilize native substrates and is therefore generally applicable. But the analytical speed of MS is considered rate limiting, mainly due to the use of time-consuming chromatographic separation in traditional MS analysis. Thanks to new instrumentation and sample preparation methods, direct analyte introduction into a mass spectrometer without a prior chromatographic step can be achieved by laser, microfluidics, and acoustics, so that each sample can be analyzed within seconds. Here we review recent advances in MS platforms that improve the throughput of enzyme library screening and discuss how these advances can potentially facilitate biofuel research by providing high sensitivity, selectivity and quantitation that are difficult to obtain using traditional assays. We also highlight the limitations of current MS assays in studying biofuel-related enzymes and propose possible solutions.
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35
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Zhao C, Zhang Y, Li Y. Production of fuels and chemicals from renewable resources using engineered Escherichia coli. Biotechnol Adv 2019; 37:107402. [DOI: 10.1016/j.biotechadv.2019.06.001] [Citation(s) in RCA: 25] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2018] [Revised: 05/23/2019] [Accepted: 06/02/2019] [Indexed: 02/06/2023]
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36
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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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37
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Structure-based Mutational Studies of D-3-hydroxybutyrate Dehydrogenase for Substrate Recognition of Aliphatic Hydroxy Acids with a Variable Length of Carbon Chain. BIOTECHNOL BIOPROC E 2019. [DOI: 10.1007/s12257-019-0135-1] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023]
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38
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Shen S, Zhang X, Li Z. Development of an engineered carbamoyl phosphate synthetase with released sensitivity to feedback inhibition by site-directed mutation and casting error-prone PCR. Enzyme Microb Technol 2019; 129:109354. [PMID: 31307577 DOI: 10.1016/j.enzmictec.2019.05.011] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2019] [Revised: 04/30/2019] [Accepted: 05/26/2019] [Indexed: 12/26/2022]
Abstract
Carbamoyl phosphate synthetase (CPS) is a key enzyme in both pyrimidine and arginine biosynthesis. However, it is inhibited strongly by uridine monophosphate (UMP), which is an intermediate of the de-novo synthesis of pyrimidine nucleoside. In this study, the native carbamoyl phosphate synthetase, from Escherichia coli, was evolved by site-directed mutation and casting error-prone PCR. Compared with the wild-type, the variant N1015 F had released sensitivity to UMP and exhibited 100% of the initial activity in the presence of UMP. Variant K1006A exhibited 0.14-fold improvement in initial activity and kept above 65% of relative activity under the saturated concentration of inhibitor. Structure analysis of variants demonstrated that the reduced sensitivity to inhibitor was largely attributed to the decreased hydrogen bonds, which could reduce the binding affinity with UMP. Also, Phe with large side chain could narrow the binding pocket and generate more steric hindrance. Based on the results in this study, N1015F was an ideal alternative catalyst for the wild-type CPS for pyrimidine biosynthesis.
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Affiliation(s)
- Su Shen
- State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, 130 Meilong Road, Shanghai 200237, China
| | - Xing Zhang
- State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, 130 Meilong Road, Shanghai 200237, China
| | - Zhimin Li
- State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, 130 Meilong Road, Shanghai 200237, China; Shanghai Collaborative Innovation Center for Biomanufacturing Technology, 130 Meilong Road, Shanghai 200237, China.
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Physiological, Genetic, and Transcriptomic Analysis of Alcohol-Induced Delay of Escherichia coli Death. Appl Environ Microbiol 2019; 85:AEM.02113-18. [PMID: 30389772 DOI: 10.1128/aem.02113-18] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2018] [Accepted: 10/27/2018] [Indexed: 11/20/2022] Open
Abstract
When Escherichia coli K-12 is inoculated into rich medium in batch culture, cells experience five phases. While the lag and logarithmic phases are mechanistically fairly well defined, the stationary phase, death phase, and long-term stationary phase are less well understood. Here, we characterize a mechanism of delaying death, a phenomenon we call the "alcohol effect," where the addition of small amounts of certain alcohols prolongs stationary phase for at least 10 days longer than in untreated conditions. We show that the stationary phase is extended when ethanol is added above a minimum threshold concentration. Once ethanol levels fall below a threshold concentration, cells enter the death phase. We also show that the effect is conferred by the addition of straight-chain alcohols 1-propanol, 1-butanol, 1-pentanol, and, to a lesser degree, 1-hexanol. However, methanol, isopropanol, 1-heptanol, and 1-octanol do not delay entry into death phase. Though modulated by RpoS, the alcohol effect does not require RpoS activity or the activities of the AdhE or AdhP alcohol dehydrogenases. Further, we show that ethanol is capable of extending the life span of stationary-phase cultures for non-K-12 E. coli strains and that this effect is caused in part by genes of the glycolate degradation pathway. These data suggest a model where ethanol and other shorter 1-alcohols can serve as signaling molecules, perhaps by modulating patterns of gene expression that normally regulate the transition from stationary phase to death phase.IMPORTANCE In one of the most well-studied organisms in the life sciences, Escherichia coli, we still do not fully understand what causes populations to die. This is largely due to the technological difficulties of studying bacterial cell death. This study provides an avenue to studying how and why E. coli populations, and perhaps other microbes, transition from stationary phase to death phase by exploring how ethanol and other alcohols delay the onset of death. Here, we demonstrate that alcohols are acting as signaling molecules to achieve the delay in death phase. This study not only offers a better understanding of a fundamental process but perhaps also provides a gateway to studying the dynamics between ethanol and microbes in the human gastrointestinal tract.
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Zhang Y, Zhang X, Xiao S, Qi W, Xu J, Yuan Z, Wang Z. Engineering Corynebacterium glutamicum Mutants for 3-Methyl-1-butanol Production. Biochem Genet 2019; 57:443-454. [PMID: 30644007 DOI: 10.1007/s10528-019-09906-4] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2018] [Accepted: 01/04/2019] [Indexed: 11/30/2022]
Abstract
3-Methyl-1-butanol (3MB) is a promising biofuel that can be produced from 2-ketoisocaproate via the common L-leucine biosynthesis pathway. Corynebacterium glutamicum was chosen as a host bacterium because of its strong resistance to isobutanol. In the current study, several strategies were designed to overproduce 3MB in C. glutamicum through a non-fermentation pathway. The engineered C. glutamicum mutant was obtained by silencing the pyruvate dehydrogenase gene complex (aceE) and deleting the lactic dehydrogenase gene (ldh), followed by mutagenesis with diethyl sulfate (DES) and selection with Fmoc-3-4-thiazolyl-L-alanine (FTA). The mutant could produce 659 mg/L of 3MB after 12 h of incubation. To facilitate carbon flux to 3MB biosynthesis, the engineered recombinant was also constructed without branched-chain acid aminotransferase (ilvE) activity by deleting the ilvE gene. This recombinant could produce 697 mg/L of 3MB after 12 h of incubation.
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Affiliation(s)
- Yu Zhang
- Guangzhou Institute of Energy Conversion, Chinese Academy of Sciences, Guangzhou, 510640, China
- CAS Key Laboratory of Renewable Energy, Guangzhou, 510640, China
- Guangdong Provincial Key Laboratory of New and Renewable Energy Research and Development, Guangzhou, 510640, China
| | - Xiaohuan Zhang
- Guangzhou Institute of Energy Conversion, Chinese Academy of Sciences, Guangzhou, 510640, China
- CAS Key Laboratory of Renewable Energy, Guangzhou, 510640, China
- Guangdong Provincial Key Laboratory of New and Renewable Energy Research and Development, Guangzhou, 510640, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Shiyuan Xiao
- Guangzhou Institute of Energy Conversion, Chinese Academy of Sciences, Guangzhou, 510640, China
- CAS Key Laboratory of Renewable Energy, Guangzhou, 510640, China
- Guangdong Provincial Key Laboratory of New and Renewable Energy Research and Development, Guangzhou, 510640, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Wei Qi
- Guangzhou Institute of Energy Conversion, Chinese Academy of Sciences, Guangzhou, 510640, China.
- CAS Key Laboratory of Renewable Energy, Guangzhou, 510640, China.
- Guangdong Provincial Key Laboratory of New and Renewable Energy Research and Development, Guangzhou, 510640, China.
| | - Jingliang Xu
- School of Chemical Engineering and Energy, Zhengzhou University, Zhengzhou, 450001, China.
| | - Zhenhong Yuan
- Guangzhou Institute of Energy Conversion, Chinese Academy of Sciences, Guangzhou, 510640, China
- CAS Key Laboratory of Renewable Energy, Guangzhou, 510640, China
- Guangdong Provincial Key Laboratory of New and Renewable Energy Research and Development, Guangzhou, 510640, China
| | - Zhongming Wang
- Guangzhou Institute of Energy Conversion, Chinese Academy of Sciences, Guangzhou, 510640, China
- CAS Key Laboratory of Renewable Energy, Guangzhou, 510640, China
- Guangdong Provincial Key Laboratory of New and Renewable Energy Research and Development, Guangzhou, 510640, China
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Lee SY, Kim HU, Chae TU, Cho JS, Kim JW, Shin JH, Kim DI, Ko YS, Jang WD, Jang YS. A comprehensive metabolic map for production of bio-based chemicals. Nat Catal 2019. [DOI: 10.1038/s41929-018-0212-4] [Citation(s) in RCA: 282] [Impact Index Per Article: 56.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
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Bai W, Geng W, Wang S, Zhang F. Biosynthesis, regulation, and engineering of microbially produced branched biofuels. BIOTECHNOLOGY FOR BIOFUELS 2019; 12:84. [PMID: 31011367 PMCID: PMC6461809 DOI: 10.1186/s13068-019-1424-9] [Citation(s) in RCA: 27] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/01/2018] [Accepted: 04/03/2019] [Indexed: 05/13/2023]
Abstract
The steadily increasing demand on transportation fuels calls for renewable fuel replacements. This has attracted a growing amount of research to develop advanced biofuels that have similar physical, chemical, and combustion properties with petroleum-derived fossil fuels. Early generations of biofuels, such as ethanol, butanol, and straight-chain fatty acid-derived esters or hydrocarbons suffer from various undesirable properties and can only be blended in limited amounts. Recent research has shifted to the production of branched-chain biofuels that, compared to straight-chain fuels, have higher octane values, better cold flow, and lower cloud points, making them more suitable for existing engines, particularly for diesel and jet engines. This review focuses on several types of branched-chain biofuels and their immediate precursors, including branched short-chain (C4-C8) and long-chain (C15-C19)-alcohols, alkanes, and esters. We discuss their biosynthesis, regulation, and recent efforts in their overproduction by engineered microbes.
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Affiliation(s)
- Wenqin Bai
- Department of Energy, Environmental and Chemical Engineering, Washington University in St. Louis, Saint Louis, MO 63130 USA
| | - Weitao Geng
- Department of Energy, Environmental and Chemical Engineering, Washington University in St. Louis, Saint Louis, MO 63130 USA
| | - Shaojie Wang
- Department of Energy, Environmental and Chemical Engineering, Washington University in St. Louis, Saint Louis, MO 63130 USA
| | - Fuzhong Zhang
- Department of Energy, Environmental and Chemical Engineering, Washington University in St. Louis, Saint Louis, MO 63130 USA
- Division of Biological & Biomedical Sciences, Washington University in St. Louis, Saint Louis, MO 63130 USA
- Institute of Materials Science & Engineering, Washington University in St. Louis, Saint Louis, MO 63130 USA
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Black WB, King E, Wang Y, Jenic A, Rowley AT, Seki K, Luo R, Li H. Engineering a Coenzyme A Detour To Expand the Product Scope and Enhance the Selectivity of the Ehrlich Pathway. ACS Synth Biol 2018; 7:2758-2764. [PMID: 30433765 DOI: 10.1021/acssynbio.8b00358] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The Ehrlich pathway is a major route for the renewable production of higher alcohols. However, the product scope of the Ehrlich pathway is restricted, and the product selectivity is suboptimal. Here, we demonstrate that a Coenzyme A (CoA) detour, which involves conversion of the 2-keto acids into acyl-CoAs, expands the biological toolkit of reaction chemistries available in the Ehrlich pathway to include the gamut of CoA-dependent enzymes. As a proof-of-concept, we demonstrated the first biosynthesis of a tertiary branched-alcohol, pivalcohol, at a level of ∼10 mg/L from glucose in Escherichia coli, using a pivalyl-CoA mutase from Xanthobacter autotrophicus. Furthermore, engineering an enzyme in the CoA detour, the Lactobacillus brevis CoA-acylating aldehyde dehydrogenase, allowed stringent product selectivity. Targeted production of 3-methyl-1-butanol (3-MB) in E. coli mediated by the CoA detour showed a 3-MB:side-product (isobutanol) ratio of >20, an increase over the ratios previously achieved using the conventional Ehrlich pathway.
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Escherichia coli as a host for metabolic engineering. Metab Eng 2018; 50:16-46. [DOI: 10.1016/j.ymben.2018.04.008] [Citation(s) in RCA: 181] [Impact Index Per Article: 30.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2018] [Revised: 04/11/2018] [Accepted: 04/12/2018] [Indexed: 12/21/2022]
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The Applications of Promoter-gene-Engineered Biosensors. SENSORS 2018; 18:s18092823. [PMID: 30150540 PMCID: PMC6164924 DOI: 10.3390/s18092823] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/15/2018] [Revised: 08/16/2018] [Accepted: 08/22/2018] [Indexed: 12/22/2022]
Abstract
A promoter is a small region of a DNA sequence that responds to various transcription factors, which initiates a particular gene expression. The promoter-engineered biosensor can activate or repress gene expression through a transcription factor recognizing specific molecules, such as polyamine, sugars, lactams, amino acids, organic acids, or a redox molecule; however, there are few reported applications of promoter-enhanced biosensors. This review paper highlights the strategies of construction of promoter gene-engineered biosensors with human and bacteria genetic promoter arrays with regard to high-throughput screening (HTS) molecular drugs, the study of the membrane protein’s localization and nucleocytoplasmic shuttling mechanism of regulating factors, enzyme activity, detection of the toxicity of intermediate chemicals, and probing bacteria density to improve value-added product titer. These biosensors’ sensitivity and specificity can be further improved by the proposed approaches of Mn2+ and Mg2+ added random error-prone PCR that is a technique used to generate randomized genomic libraries and site-directed mutagenesis approach, which is applied for the construction of bacteria’s “mutant library”. This is expected to establish a flexible HTS platform (biosensor array) to large-scale screen transcription factor-acting drugs, reduce the toxicity of intermediate compounds, and construct a gene-dynamic regulatory system in “push and pull” mode, in order to effectively regulate the valuable medicinal product production. These proposed novel promoter-engineered biosensors aiding in synthetic genetic circuit construction will maximize the efficiency of the bio-synthesis of medicinal compounds, which will greatly promote the development of microbial metabolic engineering and biomedical science.
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Henritzi S, Fischer M, Grininger M, Oreb M, Boles E. An engineered fatty acid synthase combined with a carboxylic acid reductase enables de novo production of 1-octanol in Saccharomyces cerevisiae. BIOTECHNOLOGY FOR BIOFUELS 2018; 11:150. [PMID: 29881455 PMCID: PMC5984327 DOI: 10.1186/s13068-018-1149-1] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/12/2017] [Accepted: 05/23/2018] [Indexed: 05/05/2023]
Abstract
BACKGROUND The ideal biofuel should not only be a regenerative fuel from renewable feedstocks, but should also be compatible with the existing fuel distribution infrastructure and with normal car engines. As the so-called drop-in biofuel, the fatty alcohol 1-octanol has been described as a valuable substitute for diesel and jet fuels and has already been produced fermentatively from sugars in small amounts with engineered bacteria via reduction of thioesterase-mediated premature release of octanoic acid from fatty acid synthase or via a reversal of the β-oxidation pathway. RESULTS The previously engineered short-chain acyl-CoA producing yeast Fas1R1834K/Fas2 fatty acid synthase variant was expressed together with carboxylic acid reductase from Mycobacterium marinum and phosphopantetheinyl transferase Sfp from Bacillus subtilis in a Saccharomyces cerevisiae Δfas1 Δfas2 Δfaa2 mutant strain. With the involvement of endogenous thioesterases, alcohol dehydrogenases, and aldehyde reductases, the synthesized octanoyl-CoA was converted to 1-octanol up to a titer of 26.0 mg L-1 in a 72-h fermentation. The additional accumulation of 90 mg L-1 octanoic acid in the medium indicated a bottleneck in 1-octanol production. When octanoic acid was supplied externally to the yeast cells, it could be efficiently converted to 1-octanol indicating that re-uptake of octanoic acid across the plasma membrane is not limiting. Additional overexpression of aldehyde reductase Ahr from Escherichia coli nearly completely prevented accumulation of octanoic acid and increased 1-octanol titers up to 49.5 mg L-1. However, in growth tests concentrations even lower than 50.0 mg L-1 turned out to be inhibitory to yeast growth. In situ extraction in a two-phase fermentation with dodecane as second phase did not improve growth, indicating that 1-octanol acts inhibitive before secretion. Furthermore, 1-octanol production was even reduced, which results from extraction of the intermediate octanoic acid to the organic phase, preventing its re-uptake. CONCLUSIONS By providing chain length control via an engineered octanoyl-CoA producing fatty acid synthase, we were able to specifically produce 1-octanol with S. cerevisiae. Before metabolic engineering can be used to further increase product titers and yields, strategies must be developed that cope with the toxic effects of 1-octanol on the yeast cells.
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Affiliation(s)
- Sandra Henritzi
- Faculty of Biological Sciences, Institute of Molecular Bioscience, Goethe University Frankfurt, Max-von-Laue-Str. 9, 60438 Frankfurt, Germany
| | - Manuel Fischer
- Institute of Organic Chemistry and Chemical Biology, Buchmann Institute for Molecular Life Sciences, Cluster of Excellence “Macromolecular Complexes”, Goethe University Frankfurt, Max-von-Laue-Str. 15, 60438 Frankfurt, Germany
| | - Martin Grininger
- Institute of Organic Chemistry and Chemical Biology, Buchmann Institute for Molecular Life Sciences, Cluster of Excellence “Macromolecular Complexes”, Goethe University Frankfurt, Max-von-Laue-Str. 15, 60438 Frankfurt, Germany
| | - Mislav Oreb
- Faculty of Biological Sciences, Institute of Molecular Bioscience, Goethe University Frankfurt, Max-von-Laue-Str. 9, 60438 Frankfurt, Germany
| | - Eckhard Boles
- Faculty of Biological Sciences, Institute of Molecular Bioscience, Goethe University Frankfurt, Max-von-Laue-Str. 9, 60438 Frankfurt, Germany
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Yoshida A, Kosono S, Nishiyama M. Characterization of two 2-isopropylmalate synthase homologs from Thermus thermophilus HB27. Biochem Biophys Res Commun 2018; 501:465-470. [DOI: 10.1016/j.bbrc.2018.05.013] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2018] [Accepted: 05/02/2018] [Indexed: 10/16/2022]
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Profile of James C. Liao. Proc Natl Acad Sci U S A 2018; 115:4807-4809. [DOI: 10.1073/pnas.1805586115] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
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49
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Damodharan D, Sathiyagnanam AP, Rajesh Kumar B, Ganesh KC. Cleaner emissions from a DI diesel engine fueled with waste plastic oil derived from municipal solid waste under the influence of n-pentanol addition, cold EGR, and injection timing. ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH INTERNATIONAL 2018; 25:13611-13625. [PMID: 29497945 DOI: 10.1007/s11356-018-1558-5] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/17/2017] [Accepted: 02/13/2018] [Indexed: 06/08/2023]
Abstract
Urban planning and development is a decisive factor that increases the automobile numbers which leads to increased energy demand across the globe. In order to meet the escalating requirements of energy, it is necessary to find viable alternatives. Waste plastic oil (WPO) is one such alternative which has dual benefits as it reduces the environmental pollution caused by plastic waste and it could possibly meet the energy requirement along with fossil fuels. The study attempted to reduce emissions from a DI diesel engine fueled with WPO using 30% by volume of n-pentanol with fossil diesel (WPO70P30). EGR (10, 20, and 30%) and injection timing modifications were made with the intention to find optimum engine operating conditions. The experimental results indicated that addition of renewable component like n-pentanol had improved the combustion characteristics by igniting WPO more homogeneously producing a higher premixed combustion phase. Smoke density for WPO70P30 was found to be twice lower than that of neat WPO at standard injection timing of 23°CA bTDC at any given EGR rate, NOx emissions were slightly on the higher side about 12% for WPO70P30 blend against WPO at same operating conditions. WPO70P30 showed lowest smoke and carbon monoxide emissions than diesel and WPO while delivering BTE's higher than WPO and closer to diesel at all EGR and injection timings. However NOx and HC emissions increased with n-pentanol addition. The use of EGR reduced NOx emissions but was found to aggravate other emissions. It was concluded WPO70P30 can be favorably used in a DI diesel engine at the engines advanced injection timing for better performance than diesel with a slight penalty in NOx emissions.
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Affiliation(s)
- Dillikannan Damodharan
- Department of Mechanical Engineering, Jeppiaar Engineering College, Chennai, TN, India.
- Department of Mechanical Engineering, Annamalai University, Chidambaram, TN, India.
| | | | - Babu Rajesh Kumar
- Department of Industrial Technology, California State University, Fresno, CA, 93740-8002, USA
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Wang X, He Q, Yang Y, Wang J, Haning K, Hu Y, Wu B, He M, Zhang Y, Bao J, Contreras LM, Yang S. Advances and prospects in metabolic engineering of Zymomonas mobilis. Metab Eng 2018; 50:57-73. [PMID: 29627506 DOI: 10.1016/j.ymben.2018.04.001] [Citation(s) in RCA: 77] [Impact Index Per Article: 12.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2018] [Revised: 03/31/2018] [Accepted: 04/01/2018] [Indexed: 12/22/2022]
Abstract
Biorefinery of biomass-based biofuels and biochemicals by microorganisms is a competitive alternative of traditional petroleum refineries. Zymomonas mobilis is a natural ethanologen with many desirable characteristics, which makes it an ideal industrial microbial biocatalyst for commercial production of desirable bioproducts through metabolic engineering. In this review, we summarize the metabolic engineering progress achieved in Z. mobilis to expand its substrate and product ranges as well as to enhance its robustness against stressful conditions such as inhibitory compounds within the lignocellulosic hydrolysates and slurries. We also discuss a few metabolic engineering strategies that can be applied in Z. mobilis to further develop it as a robust workhorse for economic lignocellulosic bioproducts. In addition, we briefly review the progress of metabolic engineering in Z. mobilis related to the classical synthetic biology cycle of "Design-Build-Test-Learn", as well as the progress and potential to develop Z. mobilis as a model chassis for biorefinery practices in the synthetic biology era.
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Affiliation(s)
- Xia Wang
- Hubei Collaborative Innovation Center for Green Transformation of Bio-resources, Environmental Microbial Technology Center of Hubei Province, Hubei Key Laboratory of Industrial Biotechnology, College of Life Sciences, Hubei University, Wuhan 430062, China.
| | - Qiaoning He
- Hubei Collaborative Innovation Center for Green Transformation of Bio-resources, Environmental Microbial Technology Center of Hubei Province, Hubei Key Laboratory of Industrial Biotechnology, College of Life Sciences, Hubei University, Wuhan 430062, China.
| | - Yongfu Yang
- Hubei Collaborative Innovation Center for Green Transformation of Bio-resources, Environmental Microbial Technology Center of Hubei Province, Hubei Key Laboratory of Industrial Biotechnology, College of Life Sciences, Hubei University, Wuhan 430062, China.
| | - Jingwen Wang
- Hubei Collaborative Innovation Center for Green Transformation of Bio-resources, Environmental Microbial Technology Center of Hubei Province, Hubei Key Laboratory of Industrial Biotechnology, College of Life Sciences, Hubei University, Wuhan 430062, China.
| | - Katie Haning
- Institute for Cellular and Molecular Biology, Department of Chemical Engineering, Cockrell School of Engineering, University of Texas at Austin, Austin, TX, United States.
| | - Yun Hu
- Hubei Collaborative Innovation Center for Green Transformation of Bio-resources, Environmental Microbial Technology Center of Hubei Province, Hubei Key Laboratory of Industrial Biotechnology, College of Life Sciences, Hubei University, Wuhan 430062, China.
| | - Bo Wu
- Key Laboratory of Development and Application of Rural Renewable Energy, Biomass Energy Technology Research Centre, Biogas Institute of Ministry of Agriculture, South Renmin Road, Chengdu 610041, China.
| | - Mingxiong He
- Key Laboratory of Development and Application of Rural Renewable Energy, Biomass Energy Technology Research Centre, Biogas Institute of Ministry of Agriculture, South Renmin Road, Chengdu 610041, China.
| | - Yaoping Zhang
- DOE-Great Lakes Bioenergy Research Center (GLBRC), University of Wisconsin-Madison, Madison, WI, United States.
| | - Jie Bao
- State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, 130 Meilong Road, Shanghai 200237, China.
| | - Lydia M Contreras
- Institute for Cellular and Molecular Biology, Department of Chemical Engineering, Cockrell School of Engineering, University of Texas at Austin, Austin, TX, United States.
| | - Shihui Yang
- Hubei Collaborative Innovation Center for Green Transformation of Bio-resources, Environmental Microbial Technology Center of Hubei Province, Hubei Key Laboratory of Industrial Biotechnology, College of Life Sciences, Hubei University, Wuhan 430062, China.
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