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Liu L, Liu S, Hu X, Zhou S, Deng Y. Enhancing the activity and succinyl-CoA specificity of 3-ketoacyl-CoA thiolase Tfu_0875 through rational binding pocket engineering. Synth Syst Biotechnol 2024; 9:558-568. [PMID: 38694995 PMCID: PMC11061225 DOI: 10.1016/j.synbio.2024.04.014] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2024] [Revised: 04/14/2024] [Accepted: 04/16/2024] [Indexed: 05/04/2024] Open
Abstract
The 3-ketoacyl-CoA thiolase is the rate-limiting enzyme for linear dicarboxylic acids production. However, the promiscuous substrate specificity and suboptimal catalytic performance have restricted its application. Here we present both biochemical and structural analyses of a high-efficiency 3-ketoacyl-CoA thiolase Tfu_0875. Notably, Tfu_0875 displayed heightened activity and substrate specificity for succinyl-CoA, a key precursor in adipic acid production. To enhance its performance, a deep learning approach (DLKcat) was employed to identify effective mutants, and a computational strategy, known as the greedy accumulated strategy for protein engineering (GRAPE), was used to accumulate these effective mutants. Among the mutants, Tfu_0875N249W/L163H/E217L exhibited the highest specific activity (320% of wild-type Tfu_0875), the greatest catalytic efficiency (kcat/KM = 1.00 min-1mM-1), the highest succinyl-CoA specificity (KM = 0.59 mM, 28.1% of Tfu_0875) and dramatically reduced substrate binding energy (-30.25 kcal mol-1v.s. -15.94 kcal mol-1). A structural comparison between Tfu_0875N249W/L163H/E217L and the wild type Tfu_0875 revealed that the increased interaction between the enzyme and succinyl-CoA was the primary reason for the enhanced enzyme activity. This interaction facilitated rapid substrate anchoring and stabilization. Furthermore, a reduced binding pocket volume improved substrate specificity by enhancing the complementarity between the binding pocket and the substrate in stereo conformation. Finally, our rationally designed mutant, Tfu_0875N249W/L163H/E217L, increased the adipic acid titer by 1.35-fold compared to the wild type Tfu_0875 in shake flask. The demonstrated enzymatic methods provide a promising enzyme variant for the adipic acid production. The above effective substrate binding pocket engineering strategy can be beneficial for the production of other industrially competitive biobased chemicals when be applied to other thiolases.
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Affiliation(s)
- Lixia Liu
- National Engineering Research Center of Cereal Fermentation and Food Biomanufacturing, Jiangnan University, 1800 Lihu Road, Wuxi, Jiangsu, 214122, China
- Jiangsu Provincial Research Center for Bioactive Product Processing Technology, Jiangnan University, 1800 Lihu Road, Wuxi, Jiangsu, 214122, China
| | - Shuang Liu
- National Engineering Research Center of Cereal Fermentation and Food Biomanufacturing, Jiangnan University, 1800 Lihu Road, Wuxi, Jiangsu, 214122, China
- Jiangsu Provincial Research Center for Bioactive Product Processing Technology, Jiangnan University, 1800 Lihu Road, Wuxi, Jiangsu, 214122, China
| | - Xiangyang Hu
- National Engineering Research Center of Cereal Fermentation and Food Biomanufacturing, Jiangnan University, 1800 Lihu Road, Wuxi, Jiangsu, 214122, China
- Jiangsu Provincial Research Center for Bioactive Product Processing Technology, Jiangnan University, 1800 Lihu Road, Wuxi, Jiangsu, 214122, China
| | - Shenghu Zhou
- National Engineering Research Center of Cereal Fermentation and Food Biomanufacturing, Jiangnan University, 1800 Lihu Road, Wuxi, Jiangsu, 214122, China
- Jiangsu Provincial Research Center for Bioactive Product Processing Technology, Jiangnan University, 1800 Lihu Road, Wuxi, Jiangsu, 214122, China
| | - Yu Deng
- National Engineering Research Center of Cereal Fermentation and Food Biomanufacturing, Jiangnan University, 1800 Lihu Road, Wuxi, Jiangsu, 214122, China
- Jiangsu Provincial Research Center for Bioactive Product Processing Technology, Jiangnan University, 1800 Lihu Road, Wuxi, Jiangsu, 214122, China
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Galis P, Bartosova L, Farkasova V, Bartekova M, Ferenczyova K, Rajtik T. Update on clinical and experimental management of diabetic cardiomyopathy: addressing current and future therapy. Front Endocrinol (Lausanne) 2024; 15:1451100. [PMID: 39140033 PMCID: PMC11319149 DOI: 10.3389/fendo.2024.1451100] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/18/2024] [Accepted: 07/12/2024] [Indexed: 08/15/2024] Open
Abstract
Diabetic cardiomyopathy (DCM) is a severe secondary complication of type 2 diabetes mellitus (T2DM) that is diagnosed as a heart disease occurring in the absence of any previous cardiovascular pathology in diabetic patients. Although it is still lacking an exact definition as it combines aspects of both pathologies - T2DM and heart failure, more evidence comes forward that declares DCM as one complex disease that should be treated separately. It is the ambiguous pathological phenotype, symptoms or biomarkers that makes DCM hard to diagnose and screen for its early onset. This re-view provides an updated look on the novel advances in DCM diagnosis and treatment in the experimental and clinical settings. Management of patients with DCM proposes a challenge by itself and we aim to help navigate and advice clinicians with early screening and pharmacotherapy of DCM.
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Affiliation(s)
- Peter Galis
- Department of Pharmacology and Toxicology, Faculty of Pharmacy, Comenius University Bratislava, Bratislava, Slovakia
| | - Linda Bartosova
- Department of Pharmacology and Toxicology, Faculty of Pharmacy, Comenius University Bratislava, Bratislava, Slovakia
| | - Veronika Farkasova
- Institute for Heart Research, Centre of Experimental Medicine, Slovak Academy of Sciences, Bratislava, Slovakia
| | - Monika Bartekova
- Institute for Heart Research, Centre of Experimental Medicine, Slovak Academy of Sciences, Bratislava, Slovakia
- Institute of Physiology, Faculty of Medicine, Comenius University Bratislava, Bratislava, Slovakia
| | - Kristina Ferenczyova
- Department of Pharmacology and Toxicology, Faculty of Pharmacy, Comenius University Bratislava, Bratislava, Slovakia
- Institute for Heart Research, Centre of Experimental Medicine, Slovak Academy of Sciences, Bratislava, Slovakia
| | - Tomas Rajtik
- Department of Pharmacology and Toxicology, Faculty of Pharmacy, Comenius University Bratislava, Bratislava, Slovakia
- Institute for Heart Research, Centre of Experimental Medicine, Slovak Academy of Sciences, Bratislava, Slovakia
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Wang Z, Fernández-Blanco C, Chen J, Veiga MC, Kennes C. Effect of electron acceptors on product selectivity and carbon flux in carbon chain elongation with Megasphaera hexanoica. THE SCIENCE OF THE TOTAL ENVIRONMENT 2024; 912:169509. [PMID: 38141983 DOI: 10.1016/j.scitotenv.2023.169509] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/06/2023] [Revised: 12/14/2023] [Accepted: 12/17/2023] [Indexed: 12/25/2023]
Abstract
Megasphaera hexanoica is a bacterial strain following the reverse β-oxidation pathway to synthesize caproate (CA) using lactate (LA) as an electron donor (ED) and acetate (AA) or butyrate (BA) as electron acceptors (EA). Differences in the type and concentration of EA lead to distinctions in product distribution and energy bifurcation of carbon fluxes in ED pathways, thereby affecting CA production. In this study, the effect of various ratios of AA, BA, and AA+BA as EA on carbon flux and CA specific titer during the carbon chain elongation in M. hexanoica was explored. The results indicated that the maximum levels of CA were 18.81 mM and 31.48 mM when the molar ratios of LA/AA and LA/BA were 10:1 and 3:1, respectively. Meanwhile, when AA and BA were used as combined EA (LA, AA, and BA molar amounts of 100, 23, and 77 mM), a maximum CA production of 39.45 mM was obtained. Further analysis revealed that the combined EA exhibited a CA production carbon flux of 49 % (4.3 % and 19.5 % higher compared to AA or BA, respectively) and a CA production specific titer of 45.24 mol (80.89 % and 58.51 % higher compared to AA or BA, respectively), indicating that the effective carbon utilization rate and CA production efficiency were greatly improved. Finally, a scaled-up experiment was conducted in a 1.2 L (working volume) automated bioreactor, implying high biomass (optical density at 600 nm or OD600 = 1.809) and a slight decrease in CA production (28.45 mM). A decrease in H2 production (4.11 g/m3) and an increase in CO2 production (0.632 g/m3) demonstrated the appropriate metabolic adaptation of M. hexanoica to environmental changes such as stirring shear.
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Affiliation(s)
- Zeyu Wang
- Chemical Engineering Laboratory, Faculty of Sciences and Interdisciplinary Centre of Chemistry and Biology - Centro Interdisciplinar de Química y Biología (CICA), BIOENGIN group, University of La Coruña (UDC), E-15008 La Coruña, Spain; Key Laboratory of Pollution Exposure and Health Intervention of Zhejiang Province, Interdisciplinary Research Academy, Zhejiang Shuren University, Hangzhou 310015, China
| | - Carla Fernández-Blanco
- Chemical Engineering Laboratory, Faculty of Sciences and Interdisciplinary Centre of Chemistry and Biology - Centro Interdisciplinar de Química y Biología (CICA), BIOENGIN group, University of La Coruña (UDC), E-15008 La Coruña, Spain
| | - Jun Chen
- Key Laboratory of Pollution Exposure and Health Intervention of Zhejiang Province, Interdisciplinary Research Academy, Zhejiang Shuren University, Hangzhou 310015, China
| | - María C Veiga
- Chemical Engineering Laboratory, Faculty of Sciences and Interdisciplinary Centre of Chemistry and Biology - Centro Interdisciplinar de Química y Biología (CICA), BIOENGIN group, University of La Coruña (UDC), E-15008 La Coruña, Spain
| | - Christian Kennes
- Chemical Engineering Laboratory, Faculty of Sciences and Interdisciplinary Centre of Chemistry and Biology - Centro Interdisciplinar de Química y Biología (CICA), BIOENGIN group, University of La Coruña (UDC), E-15008 La Coruña, Spain.
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Abdelrahman SA, Barakat OS, Ahmed MN. Genetic characterization of a novel Salinicola salarius isolate applied for the bioconversion of agro-industrial wastes into polyhydroxybutyrate. Microb Cell Fact 2024; 23:56. [PMID: 38368375 PMCID: PMC10874550 DOI: 10.1186/s12934-024-02326-z] [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: 11/22/2023] [Accepted: 02/05/2024] [Indexed: 02/19/2024] Open
Abstract
BACKGROUND Polyhydroxybutyrate (PHB) has emerged as a promising eco-friendly alternative to traditional petrochemical-based plastics. In the present study, we isolated and characterized a new strain of Salinicola salarius, a halophilic bacterium, from the New Suez Canal in Egypt and characterized exclusively as a potential PHB producer. Further genome analysis of the isolated strain, ES021, was conducted to identify and elucidate the genes involved in PHB production. RESULTS Different PHB-producing marine bacteria were isolated from the New Suez Canal and characterized as PHB producers. Among the 17 bacterial isolates, Salinicola salarius ES021 strain showed the capability to accumulate the highest amount of PHB. Whole genome analysis was implemented to identify the PHB-related genes in Salinicola salarius ES021 strain. Putative genes were identified that can function as phaCAB genes to produce PHB in this strain. These genes include fadA, fabG, and P3W43_16340 (encoding acyl-CoA thioesterase II) for PHB production from glucose. Additionally, phaJ and fadB were identified as key genes involved in PHB production from fatty acids. Optimization of environmental factors such as shaking rate and incubation temperature, resulted in the highest PHB productivity when growing Salinicola salarius ES021 strain at 30°C on a shaker incubator (110 rpm) for 48 h. To maximize PHB production economically, different raw materials i.e., salted whey and sugarcane molasses were examined as cost-effective carbon sources. The PHB productivity increased two-fold (13.34 g/L) when using molasses (5% sucrose) as a fermentation media. This molasses medium was used to upscale PHB production in a 20 L stirred-tank bioreactor yielding a biomass of 25.12 g/L, and PHB of 12.88 g/L. Furthermore, the produced polymer was confirmed as PHB using Fourier-transform infrared spectroscopy (FTIR), gas chromatography-mass spectroscopy (GC-MS), and nuclear magnetic resonance spectroscopy (NMR) analyses. CONCLUSIONS Herein, Salinicola salarius ES021 strain was demonstrated as a robust natural producer of PHB from agro-industrial wastes. The detailed genome characterization of the ES021 strain presented in this study identifies potential PHB-related genes. However, further metabolic engineering is warranted to confirm the gene networks required for PHB production in this strain. Overall, this study contributes to the development of sustainable and cost-effective PHB production strategies.
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Affiliation(s)
- Shymaa A Abdelrahman
- Department of Microbiology, Faculty of Agriculture, Cairo University, El-Gamaa Street, Giza, 12613, Egypt.
| | - Olfat S Barakat
- Department of Microbiology, Faculty of Agriculture, Cairo University, El-Gamaa Street, Giza, 12613, Egypt
| | - Marwa N Ahmed
- Department of Microbiology, Faculty of Agriculture, Cairo University, El-Gamaa Street, Giza, 12613, Egypt
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He S, Bai X, Xu Y. Structural insight into the role of thiolase from Fusobacterium nucleatum. Biochem Biophys Res Commun 2023; 688:149151. [PMID: 37951156 DOI: 10.1016/j.bbrc.2023.149151] [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: 10/12/2023] [Revised: 10/22/2023] [Accepted: 10/23/2023] [Indexed: 11/13/2023]
Abstract
Fusobacterium nucleatum (F. nucleatum) is an anaerobic gram-negative bacterium that was previously thought to be related to the progression of colorectal cancer. In F. nucleatum, thiolase participates in fatty acid metabolism, and it can catalyse the transfer of an acetyl group from acetyl-CoA to another molecule, typically a fatty acid or another molecule in the synthesis of lipids. To gain deeper insight into the molecular mechanism governing the function of thiolase in F. nucleatum (Fn0495), we herein report the structure of Fn0495. The monomer of Fn0495 consists of three subdomains, namely, the N-terminal domain (residues 1-117 and 252-270), the C-terminal domain (residues 273-393), and the loop domain (residues 118-251). Fn0495 shows a unique difference in the charge and structure of the substrate binding pocket compared with homologous proteins. This research found three conserved residues (Cys88, His357, and Cys387) in Fn0495 arranged near a potential substrate binding pocket. In this study, the conformational changes between the covering loop, catalytic cysteine loop, regulatory determinant region, and homologous protein were compared. These results will enhance our understanding of the molecular characteristics and roles of the thiolase family.
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Affiliation(s)
- Shanru He
- Department of Bioengineering, College of Life Science, Dalian Minzu University, Dalian, 116600, Liaoning, China; Key Laboratory of Biotechnology and Bioresources Utilization of Ministry of Education, College of Life Science, Dalian Minzu University, China
| | - Xue Bai
- Department of Bioengineering, College of Life Science, Dalian Minzu University, Dalian, 116600, Liaoning, China; Key Laboratory of Biotechnology and Bioresources Utilization of Ministry of Education, College of Life Science, Dalian Minzu University, China
| | - Yongbin Xu
- Department of Bioengineering, College of Life Science, Dalian Minzu University, Dalian, 116600, Liaoning, China; Key Laboratory of Biotechnology and Bioresources Utilization of Ministry of Education, College of Life Science, Dalian Minzu University, China; CAS Key Laboratory of Separation Science for Analytical Chemistry, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian, 116023, Liaoning, China.
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6
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Singh R, Kundu P, Mishra VK, Singh BK, Bhattacharyya S, Das AK. Crystal structure of FadA2 thiolase from Mycobacterium tuberculosis and prediction of its substrate specificity and membrane-anchoring properties. FEBS J 2023; 290:3997-4022. [PMID: 37026388 DOI: 10.1111/febs.16792] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2022] [Revised: 03/17/2023] [Accepted: 04/05/2023] [Indexed: 04/08/2023]
Abstract
Tuberculosis (TB) is one of the leading causes of human death caused by Mycobacterium tuberculosis (Mtb). Mtb can enter into a long-lasting persistence where it can utilize fatty acids as the carbon source. Hence, fatty acid metabolism pathway enzymes are considered promising and pertinent mycobacterial drug targets. FadA2 (thiolase) is one of the enzymes involved in Mtb's fatty acid metabolism pathway. FadA2 deletion construct (ΔL136-S150) was designed to produce soluble protein. The crystal structure of FadA2 (ΔL136-S150) at 2.9 Å resolution was solved and analysed for membrane-anchoring region. The four catalytic residues of FadA2 are Cys99, His341, His390 and Cys427, and they belong to four loops with characteristic sequence motifs, i.e., CxT, HEAF, GHP and CxA. FadA2 is the only thiolase of Mtb which belongs to the CHH category containing the HEAF motif. Analysing the substrate-binding channel, it has been suggested that FadA2 is involved in the β-oxidation pathway, i.e., the degradative pathway, as the long-chain fatty acid can be accommodated in the channel. The catalysed reaction is favoured by the presence of two oxyanion holes, i.e., OAH1 and OAH2. OAH1 formation is unique in FadA2, formed by the NE2 of His390 present in the GHP motif and NE2 of His341 present in the HEAF motif, whereas OAH2 formation is similar to CNH category thiolase. Sequence and structural comparison with the human trifunctional enzyme (HsTFE-β) suggests the membrane-anchoring region in FadA2. Molecular dynamics simulations of FadA2 with a membrane containing POPE lipid were conducted to understand the role of a long insertion sequence of FadA2 in membrane anchoring.
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Affiliation(s)
- Rashika Singh
- Department of Biotechnology, Indian Institute of Technology Kharagpur, India
| | - Prasun Kundu
- Department of Biotechnology, Indian Institute of Technology Kharagpur, India
| | | | - Bina Kumari Singh
- School of Bioscience, Indian Institute of Technology Kharagpur, India
| | - Sudipta Bhattacharyya
- Department of Bioscience & Bioengineering, Indian Institute of Technology Jodhpur, India
| | - Amit Kumar Das
- Department of Biotechnology, Indian Institute of Technology Kharagpur, India
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Courtney DK, Su Y, Jacobson T, Khana D, Ailiani A, Amador-Noguez D, Pfleger BF. Relative Activities of the β-ketoacyl-CoA and Acyl-CoA Reductases Influence Product Profile and Flux in a Reversed β-Oxidation Pathway. ACS Catal 2023; 13:5914-5925. [PMID: 38094510 PMCID: PMC10718561 DOI: 10.1021/acscatal.3c00379] [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] [Indexed: 03/21/2024]
Abstract
The β-Oxidation pathway, normally involved in the catabolism of fatty acids, can be functionally made to act as a fermentative, iterative, elongation pathway when driven by the activity of a trans-enoyl-CoA reductase. The terminal acyl-CoA reduction to alcohol can occur on substrates with varied chain lengths, leading to a broad distribution of fermentation products in vivo. Tight control of the average chain length and product profile is desirable as chain length greatly influences molecular properties and commercial value. Lacking a termination enzyme with a narrow chain length preference, we sought alternative factors that could influence the product profile and pathway flux in the iterative pathway. In this study, we reconstituted the reversed β-oxidation (R-βox) pathway in vitro with a purified tri-functional complex (FadBA) responsible for the thiolase, enoyl-CoA hydratase and hydroxyacyl-CoA dehydrogenase activities, a trans-enoyl-CoA reductase (TER), and an acyl-CoA reductase (ACR). Using this system, we determined the rate limiting step of the elongation cycle and demonstrated that by controlling the ratio of these three enzymes and the ratio of NADH and NADPH, we can influence the average chain length of the alcohol product profile.
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Affiliation(s)
- Dylan K. Courtney
- Department of Chemical and Biological Engineering, University of Wisconsin – Madison, Madison, WI, USA
| | - Yun Su
- Department of Chemical and Biological Engineering, University of Wisconsin – Madison, Madison, WI, USA
| | - Tyler Jacobson
- Department of Bacteriology, University of Wisconsin – Madison, Madison, WI, USA
| | - Daven Khana
- Department of Bacteriology, University of Wisconsin – Madison, Madison, WI, USA
| | - Aditya Ailiani
- Department of Biomedical Engineering, University of Wisconsin – Madison, Madison, WI, USA
| | | | - Brian F. Pfleger
- Department of Chemical and Biological Engineering, University of Wisconsin – Madison, Madison, WI, USA
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Sreeja S, Shylaja MR, Nazeem PA, Mathew D. Peroxisomal KAT2 (3-ketoacyl-CoA thiolase 2) gene has a key role in gingerol biosynthesis in ginger ( Zingiber officinale Rosc.). JOURNAL OF PLANT BIOCHEMISTRY AND BIOTECHNOLOGY 2023; 32:1-16. [PMID: 36685987 PMCID: PMC9838548 DOI: 10.1007/s13562-022-00825-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 01/29/2022] [Accepted: 12/28/2022] [Indexed: 06/17/2023]
Abstract
Ginger is an important spice crop with medicinal values and gingerols are the most abundant pungent polyphenols present in ginger, responsible for most of its pharmacological properties. The present study focuses on the molecular mechanism of gingerol biosynthesis in ginger using transcriptome analysis. Suppression Subtractive Hybridization (SSH) was done in leaf and rhizome tissues using high gingerol-producing ginger somaclone B3 as the tester and parent cultivar Maran as the driver and generated high-quality leaf and rhizome Expressed Sequence Tags (ESTs). The Blast2GO annotations of the ESTs revealed the involvement of leaf ESTs in secondary metabolite production, identifying the peroxisomal KAT2 gene (Leaf EST 9) for the high gingerol production in ginger. Rhizome ESTs mostly coded for DNA metabolic processes and differential genes for high gingerol production were not observed in rhizomes. In the qRT-PCR analysis, somaclone B3 had shown high chalcone synthase (CHS: rate-limiting gene in gingerol biosynthetic pathway) activity (0.54 fold) in the leaves of rhizome sprouts. The presence of a high gingerol gene in leaf ESTs and high expression of CHS in leaves presumed that the site of synthesis of gingerols in ginger is the leaves. A modified pathway for gingerol/polyketide backbone formation has been constructed explaining the involvement of KAT gene isoforms KAT2 and KAT5 in gingerol/flavonoid biosynthesis, specifically the KAT2 gene which is otherwise thought to be involved mainly in β-oxidation. The results of the present investigations have the potential of utilizing KAT/thiolase superfamily enzymes for protein/metabolic pathway engineering in ginger for large-scale production of gingerols. Supplementary Information The online version contains supplementary material available at 10.1007/s13562-022-00825-x.
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Affiliation(s)
- S. Sreeja
- Centre for Plant Biotechnology and Molecular Biology, College of Agriculture, Kerala Agricultural University, Vellanikkara, Kerala India
| | - M. R. Shylaja
- Centre for Plant Biotechnology and Molecular Biology, College of Agriculture, Kerala Agricultural University, Vellanikkara, Kerala India
| | - P. A. Nazeem
- Centre for Plant Biotechnology and Molecular Biology, College of Agriculture, Kerala Agricultural University, Vellanikkara, Kerala India
| | - Deepu Mathew
- Centre for Plant Biotechnology and Molecular Biology, College of Agriculture, Kerala Agricultural University, Vellanikkara, Kerala India
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Bao Q, Zhi R, Zhou S, Zhao Y, Mao Y, Li G, Deng YU. Claisen condensation reaction mediated pimelate biosynthesis via the reverse adipate-degradation pathway and its isoenzymes. Chembiochem 2022; 23:e202200098. [PMID: 35352865 DOI: 10.1002/cbic.202200098] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2022] [Revised: 03/30/2022] [Indexed: 11/11/2022]
Abstract
Pimelic acid is an important seven-carbon dicarboxylic acid, which is broadly applied in various fields. The industrial production of pimelic acid is mainly through chemical method, which is complicated and environment unfriendly. Herein, we found that pimelic acid could be biosynthesized by the reverse adipate-degradation pathway (RADP), a typical Claisen condensation reaction that could be applied to the arrangement of C-C bond. In order to strengthen the supply of glutaryl-CoA precursor, PA5530 protein was used to transport glutaric acid. Subsequently, we discovered that the enzymes in the BIOZ pathway was isoenzymes with the RADP. By combining the isoenzymes of the two pathways, the titer of pimelic acid reached 36.7 mg·L -1 under the optimal combination, which was increased by 382.9% compared with the control strain B-3. It was also the highest titer of pimelic acid biosynthesized by Claisen condensation reaction, laying foundations for further pimelic acid and its derivatives production.
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Affiliation(s)
- Qingqing Bao
- Jiangnan University, National Engineering Laboratory for Cereal Fermentation Technology (NELCF), CHINA
| | - Rui Zhi
- Jiangnan University, National Engineering Laboratory for Cereal Fermentation Technology (NELCF), CHINA
| | - Shenghu Zhou
- Jiangnan University, National Engineering Laboratory for Cereal Fermentation Technology (NELCF), CHINA
| | - Yunying Zhao
- Jiangnan University, National Engineering Laboratory for Cereal Fermentation Technology (NELCF), CHINA
| | - Yin Mao
- Jiangnan University, National Engineering Laboratory for Cereal Fermentation Technology (NELCF), CHINA
| | - Guohui Li
- Jiangnan University, National Engineering Laboratory for Cereal Fermentation Technology (NELCF), CHINA
| | - Y U Deng
- Jiangnan University, School of biotechnology, 1800 LIHU AVENUE, 214122, WUXI, CHINA
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10
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Park JE, Lee TH, Ham SL, Subedi L, Hong SM, Kim SY, Choi SU, Kim CS, Lee KR. Anticancer and Anti-Neuroinflammatory Constituents Isolated from the Roots of Wasabia japonica. Antioxidants (Basel) 2022; 11:antiox11030482. [PMID: 35326132 PMCID: PMC8944812 DOI: 10.3390/antiox11030482] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2022] [Revised: 02/25/2022] [Accepted: 02/26/2022] [Indexed: 02/06/2023] Open
Abstract
Wasabi (Wasabia japonica (Miq.) Matsum.) is a pungent spice commonly consumed with sushi and sashimi. From the roots of this plant, a new 2-butenolide derivative (1) and 17 previously reported compounds (2–18) were isolated and structurally characterized. Their chemical structures were characterized based on the conventional NMR (1H and 13C, COSY, HSQC, and HMBC) and HRESIMS data analysis. All of these phytochemicals (1–18) were evaluated for their antiproliferative effects on the four human tumor cell lines (A549, SK-OV-3, SK-MEL-2, and MKN-1), for their inhibitory activity on nitric oxide (NO) production in lipopolysaccharide (LPS)-activated BV-2 microglia cells, and for their nerve growth factor (NGF)-releasing effect from C6 glioma cells. Among the isolated compounds, compound 15 showed powerful antiproliferative activities against A549 and SK-MEL-2 cell lines with IC50 values of 2.10 and 9.08 μM, respectively. Moreover, the new compound 1 exhibited moderate NO inhibition activity with IC50 value of 45.3 μM.
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Affiliation(s)
- Jong Eel Park
- School of Pharmacy, Sungkyunkwan University, Suwon 16419, Korea; (J.E.P.); (T.H.L.)
- Korea Environment Corporation, 42 Hwangyeong-ro, Seo-gu, Incheon 22689, Korea
| | - Tae Hyun Lee
- School of Pharmacy, Sungkyunkwan University, Suwon 16419, Korea; (J.E.P.); (T.H.L.)
- Department of Biopharmaceutical Convergence, Sungkyunkwan University, Suwon 16419, Korea;
| | - Song Lim Ham
- Department of Biopharmaceutical Convergence, Sungkyunkwan University, Suwon 16419, Korea;
| | - Lalita Subedi
- Gachon Institute of Pharmaceutical Science, Gachon University, Incheon 21936, Korea; (L.S.); (S.M.H.); (S.Y.K.)
| | - Seong Min Hong
- Gachon Institute of Pharmaceutical Science, Gachon University, Incheon 21936, Korea; (L.S.); (S.M.H.); (S.Y.K.)
| | - Sun Yeou Kim
- Gachon Institute of Pharmaceutical Science, Gachon University, Incheon 21936, Korea; (L.S.); (S.M.H.); (S.Y.K.)
- College of Pharmacy, Gachon University, #191, Hambakmoero, Yeonsu-gu, Incheon 21936, Korea
| | - Sang Un Choi
- Korea Research Institute of Chemical Technology, Daejeon 34114, Korea;
| | - Chung Sub Kim
- School of Pharmacy, Sungkyunkwan University, Suwon 16419, Korea; (J.E.P.); (T.H.L.)
- Department of Biopharmaceutical Convergence, Sungkyunkwan University, Suwon 16419, Korea;
- Correspondence: (C.S.K.); (K.R.L.); Tel.: +82-31-290-7750 (C.S.K.); +82-31-290-7727 (K.R.L.)
| | - Kang Ro Lee
- School of Pharmacy, Sungkyunkwan University, Suwon 16419, Korea; (J.E.P.); (T.H.L.)
- Correspondence: (C.S.K.); (K.R.L.); Tel.: +82-31-290-7750 (C.S.K.); +82-31-290-7727 (K.R.L.)
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11
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Tarasava K, Lee SH, Chen J, Köpke M, Jewett MC, Gonzalez R. Reverse β-oxidation pathways for efficient chemical production. J Ind Microbiol Biotechnol 2022; 49:6537408. [PMID: 35218187 PMCID: PMC9118988 DOI: 10.1093/jimb/kuac003] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2022] [Accepted: 01/25/2022] [Indexed: 12/04/2022]
Abstract
Microbial production of fuels, chemicals, and materials has the potential to reduce greenhouse gas emissions and contribute to a sustainable bioeconomy. While synthetic biology allows readjusting of native metabolic pathways for the synthesis of desired products, often these native pathways do not support maximum efficiency and are affected by complex regulatory mechanisms. A synthetic or engineered pathway that allows modular synthesis of versatile bioproducts with minimal enzyme requirement and regulation while achieving high carbon and energy efficiency could be an alternative solution to address these issues. The reverse β-oxidation (rBOX) pathways enable iterative non-decarboxylative elongation of carbon molecules of varying chain lengths and functional groups with only four core enzymes and no ATP requirement. Here, we describe recent developments in rBOX pathway engineering to produce alcohols and carboxylic acids with diverse functional groups, along with other commercially important molecules such as polyketides. We discuss the application of rBOX beyond the pathway itself by its interfacing with various carbon-utilization pathways and deployment in different organisms, which allows feedstock diversification from sugars to glycerol, carbon dioxide, methane, and other substrates.
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Affiliation(s)
- Katia Tarasava
- Department of Chemical, Biological, and Materials Engineering, University of South Florida, Tampa, FL, USA
| | - Seung Hwan Lee
- Department of Chemical, Biological, and Materials Engineering, University of South Florida, Tampa, FL, USA
| | - Jing Chen
- Department of Chemical, Biological, and Materials Engineering, University of South Florida, Tampa, FL, USA
| | | | - Michael C Jewett
- Department of Chemical and Biological Engineering and Center for Synthetic Biology, Northwestern University, Evanston, IL, USA
| | - Ramon Gonzalez
- Department of Chemical, Biological, and Materials Engineering, University of South Florida, Tampa, FL, USA
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12
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Fu Y, Zhang F, Ma C, Wang W, Liu Z, Chen W, Zhao M, Ma L. Comparative Metabolomics and Lipidomics of Four Juvenoids Application to Scylla paramamosain Hepatopancreas: Implications of Lipid Metabolism During Ovarian Maturation. Front Endocrinol (Lausanne) 2022; 13:886351. [PMID: 35574001 PMCID: PMC9094423 DOI: 10.3389/fendo.2022.886351] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/28/2022] [Accepted: 03/28/2022] [Indexed: 11/13/2022] Open
Abstract
This study was the first to evaluate multiple hormonal manipulations to hepatopancreas over the ovarian development stages of the mud crab, Scylla paramamosain. A total of 1258 metabolites in 75 hepatopancreas explants from five female crabs were induced by juvenile hormone III (JH III), methyl farnesoate (MF), farnesoic acid (FA) and methoprene (Met), as identified from combined metabolomics and lipidomics (LC-MS/MS). 101 significant metabolites and 47 significant pathways were selected and compared for their comprehensive effects to ovarian maturation. While MF played an extensive role in lipid accumulation, JH III and Met shared similar effects, especially in the commonly and significantly elevated triglycerides and lysophospholipids (fold change≥2 and ≤0.5, VIP≥1). The significant upregulation of β-oxidation and key regulators in lipid degradation by FA (P ≤ 0.05) resulted in less lipid accumulation from this treatment, with a shift toward lipid export and energy consumption, unlike the effects of MF, JH III and Met. It was possible that MF and FA played their own unique roles and acted in synergy to modulate lipid metabolism during crab ovarian maturation. Our study yielded insights into the MF-related lipid metabolism in crustacean hepatopancreas for the overall regulation of ovarian maturation, and harbored the potential use of juvenoids to induce reproductive maturity of this economic crab species.
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Affiliation(s)
- Yin Fu
- Key Laboratory of East China Sea Fishery Resources Exploitation, Ministry of Agriculture and Rural Affairs, East China Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Shanghai, China
- College of Fisheries and Life Science, Shanghai Ocean University, Shanghai, China
| | - Fengying Zhang
- Key Laboratory of East China Sea Fishery Resources Exploitation, Ministry of Agriculture and Rural Affairs, East China Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Shanghai, China
- College of Fisheries and Life Science, Shanghai Ocean University, Shanghai, China
| | - Chunyan Ma
- Key Laboratory of East China Sea Fishery Resources Exploitation, Ministry of Agriculture and Rural Affairs, East China Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Shanghai, China
- College of Fisheries and Life Science, Shanghai Ocean University, Shanghai, China
| | - Wei Wang
- Key Laboratory of East China Sea Fishery Resources Exploitation, Ministry of Agriculture and Rural Affairs, East China Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Shanghai, China
| | - Zhiqiang Liu
- Key Laboratory of East China Sea Fishery Resources Exploitation, Ministry of Agriculture and Rural Affairs, East China Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Shanghai, China
| | - Wei Chen
- Key Laboratory of East China Sea Fishery Resources Exploitation, Ministry of Agriculture and Rural Affairs, East China Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Shanghai, China
| | - Ming Zhao
- Key Laboratory of East China Sea Fishery Resources Exploitation, Ministry of Agriculture and Rural Affairs, East China Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Shanghai, China
- *Correspondence: Lingbo Ma, ; Ming Zhao,
| | - Lingbo Ma
- Key Laboratory of East China Sea Fishery Resources Exploitation, Ministry of Agriculture and Rural Affairs, East China Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Shanghai, China
- College of Fisheries and Life Science, Shanghai Ocean University, Shanghai, China
- *Correspondence: Lingbo Ma, ; Ming Zhao,
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13
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Xu YW, Lin P, Zheng SF, Huang W, Lin ZY, Shang-Guan HC, Lin YX, Yao PS, Kang DZ. Acetylation Profiles in the Metabolic Process of Glioma-Associated Seizures. Front Neurol 2021; 12:713293. [PMID: 34664012 PMCID: PMC8519730 DOI: 10.3389/fneur.2021.713293] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2021] [Accepted: 08/13/2021] [Indexed: 11/13/2022] Open
Abstract
Objective: We test the hypothesis that lysine acetylation is involved in the metabolic process of glioma-associated seizures (GAS). Methods: We used label-free mass spectrometry-based quantitative proteomics to quantify dynamic changes of protein acetylation between gliomas with seizure (CA1 group) and gliomas without seizure (CA2 group). Furthermore, differences of acetyltransferase and deacetylase expression between CA1 and CA2 groups were performed by a quantitative proteomic study. We further classified acetylated proteins into groups according to cell component, molecular function, and biological process. In addition, metabolic pathways and protein interaction networks were analyzed. Regulated acetyltransferases and acetylated profiles were validated by PRM and Western blot. Results: We detected 169 downregulated lysine acetylation sites of 134 proteins and 39 upregulated lysine acetylation sites of 35 proteins in glioma with seizures based on acetylome. We detected 407 regulated proteins by proteomics, from which ACAT2 and ACAA2 were the differentially regulated enzymes in the acetylation of GAS. According to the KEGG analysis, the upregulated acetylated proteins within the PPIs were mapped to pathways involved in the TCA cycle, oxidative phosphorylation, biosynthesis of amino acids, and carbon metabolism. The downregulated acetylated proteins within the PPIs were mapped to pathways involved in fatty acid metabolism, oxidative phosphorylation, TCA cycle, and necroptosis. Regulated ACAT2 expression and acetylated profiles were validated by PRM and Western blot. Conclusions: The data support the hypothesis that regulated protein acetylation is involved in the metabolic process of GAS, which may be induced by acetyl-CoA acetyltransferases.
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Affiliation(s)
- Ya-Wen Xu
- Department of Neurosurgery, Neurosurgical Research Institute, The First Affiliated Hospital, Fujian Medical University, Fuzhou, China
| | - Peng Lin
- Department of Pain, The First Affiliated Hospital, Fujian Medical University, Fuzhou, China
| | - Shu-Fa Zheng
- Department of Neurosurgery, Neurosurgical Research Institute, The First Affiliated Hospital, Fujian Medical University, Fuzhou, China
| | - Wen Huang
- Department of Neurosurgery, Neurosurgical Research Institute, The First Affiliated Hospital, Fujian Medical University, Fuzhou, China
| | - Zhang-Ya Lin
- Department of Neurosurgery, Neurosurgical Research Institute, The First Affiliated Hospital, Fujian Medical University, Fuzhou, China
| | - Huang-Cheng Shang-Guan
- Department of Neurosurgery, Neurosurgical Research Institute, The First Affiliated Hospital, Fujian Medical University, Fuzhou, China
| | - Yuan-Xiang Lin
- Department of Neurosurgery, Neurosurgical Research Institute, The First Affiliated Hospital, Fujian Medical University, Fuzhou, China.,Fujian Key Laboratory of Precision Medicine for Cancer, The First Affiliated Hospital, Fujian Medical University, Fuzhou, China
| | - Pei-Sen Yao
- Department of Neurosurgery, Neurosurgical Research Institute, The First Affiliated Hospital, Fujian Medical University, Fuzhou, China
| | - De-Zhi Kang
- Department of Neurosurgery, Neurosurgical Research Institute, The First Affiliated Hospital, Fujian Medical University, Fuzhou, China.,Fujian Key Laboratory of Precision Medicine for Cancer, The First Affiliated Hospital, Fujian Medical University, Fuzhou, China.,Key Laboratory of Radiation Biology of Fujian Higher Education Institutions, The First Affiliated Hospital, Fujian Medical University, Fuzhou, China
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14
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Ding N, Zhou S, Deng Y. Transcription-Factor-based Biosensor Engineering for Applications in Synthetic Biology. ACS Synth Biol 2021; 10:911-922. [PMID: 33899477 DOI: 10.1021/acssynbio.0c00252] [Citation(s) in RCA: 59] [Impact Index Per Article: 19.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
Transcription-factor-based biosensors (TFBs) are often used for metabolite detection, adaptive evolution, and metabolic flux control. However, designing TFBs with superior performance for applications in synthetic biology remains challenging. Specifically, natural TFBs often do not meet real-time detection requirements owing to their slow response times and inappropriate dynamic ranges, detection ranges, sensitivity, and selectivity. Furthermore, designing and optimizing complex dynamic regulation networks is time-consuming and labor-intensive. This Review highlights TFB-based applications and recent engineering strategies ranging from traditional trial-and-error approaches to novel computer-model-based rational design approaches. The limitations of the applications and these engineering strategies are additionally reviewed.
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Affiliation(s)
- Nana Ding
- National Engineering Laboratory for Cereal Fermentation Technology (NELCF), Jiangnan University, 1800 Lihu Road, Wuxi, Jiangsu 214122, China
- Jiangsu Provincial Research Center for Bioactive Product Processing Technology, Jiangnan University, 1800 Lihu Road, Wuxi, Jiangsu 214122, China
| | - Shenghu Zhou
- National Engineering Laboratory for Cereal Fermentation Technology (NELCF), Jiangnan University, 1800 Lihu Road, Wuxi, Jiangsu 214122, China
- Jiangsu Provincial Research Center for Bioactive Product Processing Technology, Jiangnan University, 1800 Lihu Road, Wuxi, Jiangsu 214122, China
| | - Yu Deng
- National Engineering Laboratory for Cereal Fermentation Technology (NELCF), Jiangnan University, 1800 Lihu Road, Wuxi, Jiangsu 214122, China
- Jiangsu Provincial Research Center for Bioactive Product Processing Technology, Jiangnan University, 1800 Lihu Road, Wuxi, Jiangsu 214122, China
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15
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Li HL, Deng RX, Wang W, Liu KQ, Hu HB, Huang XQ, Zhang XH. Biosynthesis and Characterization of Medium-Chain-Length Polyhydroxyalkanoate with an Enriched 3-Hydroxydodecanoate Monomer from a Pseudomonas chlororaphis Cell Factory. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2021; 69:3895-3903. [PMID: 33759523 DOI: 10.1021/acs.jafc.1c00500] [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: 06/12/2023]
Abstract
Polyhydroxyalkanoates (PHAs) have been reported with agricultural and medical applications in virtue of their biodegradable and biocompatible properties. Here, we systematically engineered three modules for the enhanced biosynthesis of medium-chain-length polyhydroxyalkanoate (mcl-PHA) in Pseudomonas chlororaphis HT66. The phzE, fadA, and fadB genes were deleted to block the native phenazine pathway and weaken the fatty acid β-oxidation pathway. Additionally, a PHA depolymerase gene phaZ was knocked out to prevent the degradation of mcl-PHA. Three genes involved in the mcl-PHA biosynthesis pathway were co-overexpressed to increase carbon flux. The engineered strain HT4Δ::C1C2J exhibited an 18.2 g/L cell dry weight with 84.9 wt % of mcl-PHA in a shake-flask culture, and the 3-hydroxydodecanoate (3HDD) monomer was increased to 71.6 mol %. Thermophysical and mechanical properties of mcl-PHA were improved with an enriched ratio of 3HDD. This study demonstrated a rational metabolic engineering approach to enhance the production of mcl-PHA with the enriched dominant monomer and improved material properties.
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Affiliation(s)
- Hui-Ling Li
- State Key Laboratory of Microbial Metabolism, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Ru-Xiang Deng
- State Key Laboratory of Microbial Metabolism, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Wei Wang
- State Key Laboratory of Microbial Metabolism, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Kai-Quan Liu
- State Key Laboratory of Biobased Material and Green Papermaking (LBMP), Qilu University of Technology (Shandong Academy of Sciences), Jinan, Shandong 250353, China
- Key Laboratory of Shandong Microbial Engineering, College of Bioengineering, Qilu University of Technology (Shandong Academy of Sciences), Jinan, Shandong 250353, China
| | - Hong-Bo Hu
- State Key Laboratory of Microbial Metabolism, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai 200240, China
- National Experimental Teaching Center for Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Xian-Qing Huang
- State Key Laboratory of Microbial Metabolism, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Xue-Hong Zhang
- State Key Laboratory of Microbial Metabolism, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai 200240, China
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