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Huang H, Chang S, Cui T, Huang M, Qu J, Zhang H, Lu T, Zhang X, Zhou C, Feng Y. An inhibitory mechanism of AasS, an exogenous fatty acid scavenger: Implications for re-sensitization of FAS II antimicrobials. PLoS Pathog 2024; 20:e1012376. [PMID: 39008531 DOI: 10.1371/journal.ppat.1012376] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2024] [Accepted: 06/26/2024] [Indexed: 07/17/2024] Open
Abstract
Antimicrobial resistance is an ongoing "one health" challenge of global concern. The acyl-ACP synthetase (termed AasS) of the zoonotic pathogen Vibrio harveyi recycles exogenous fatty acid (eFA), bypassing the requirement of type II fatty acid synthesis (FAS II), a druggable pathway. A growing body of bacterial AasS-type isoenzymes compromises the clinical efficacy of FAS II-directed antimicrobials, like cerulenin. Very recently, an acyl adenylate mimic, C10-AMS, was proposed as a lead compound against AasS activity. However, the underlying mechanism remains poorly understood. Here we present two high-resolution cryo-EM structures of AasS liganded with C10-AMS inhibitor (2.33 Å) and C10-AMP intermediate (2.19 Å) in addition to its apo form (2.53 Å). Apart from our measurements for C10-AMS' Ki value of around 0.6 μM, structural and functional analyses explained how this inhibitor interacts with AasS enzyme. Unlike an open state of AasS, ready for C10-AMP formation, a closed conformation is trapped by the C10-AMS inhibitor. Tight binding of C10-AMS blocks fatty acyl substrate entry, and therefore inhibits AasS action. Additionally, this intermediate analog C10-AMS appears to be a mixed-type AasS inhibitor. In summary, our results provide proof of principle that inhibiting salvage of eFA by AasS reverses the FAS II bypass. This facilitates the development of next-generation of anti-bacterial therapeutics, esp. the dual therapy consisting of C10-AMS scaffold derivatives combined with certain FAS II inhibitors.
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Affiliation(s)
- Haomin Huang
- Key Laboratory of Multiple Organ Failure, Ministry of Education; Departments of Microbiology and General Intensive Care Unit of the Second Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang, China
| | - Shenghai Chang
- Center of Cryo-Electron Microscopy, Zhejiang University, Hangzhou, Zhejiang, China
| | - Tao Cui
- School of Life Sciences, Northwestern Polytechnical University, Xi'an, Shaanxi, China
| | - Man Huang
- Key Laboratory of Multiple Organ Failure, Ministry of Education; Departments of Microbiology and General Intensive Care Unit of the Second Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang, China
| | - Jiuxin Qu
- Department of Clinical Laboratory, Shenzhen Third People's Hospital, National Clinical Research Center for Infectious Diseases, The Second Affiliated Hospital of Southern University of Science and Technology, Shenzhen, Guangdong, China
| | - Huimin Zhang
- Cancer Center at Illinois, University of Illinois at Urbana-Champaign, Urbana, Illinois, United States of America
| | - Ting Lu
- Department of Bioengineering, University of Illinois at Urbana-Champaign, Urbana, Illinois, United States of America
| | - Xing Zhang
- Center of Cryo-Electron Microscopy, Zhejiang University, Hangzhou, Zhejiang, China
| | - Chun Zhou
- School of Public Health, Zhejiang University School of Medicine, Hangzhou, Zhejiang, China
| | - Youjun Feng
- Key Laboratory of Multiple Organ Failure, Ministry of Education; Departments of Microbiology and General Intensive Care Unit of the Second Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang, China
- Department of Clinical Laboratory, Shenzhen Third People's Hospital, National Clinical Research Center for Infectious Diseases, The Second Affiliated Hospital of Southern University of Science and Technology, Shenzhen, Guangdong, China
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2
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Stanley HM, Trent MS. Loss of YhcB results in overactive fatty acid biosynthesis. mBio 2024; 15:e0079024. [PMID: 38742872 PMCID: PMC11237625 DOI: 10.1128/mbio.00790-24] [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: 03/14/2024] [Accepted: 04/05/2024] [Indexed: 05/16/2024] Open
Abstract
Loss of the Escherichia coli inner membrane protein YhcB results in pleomorphic cell morphology and clear growth defects. Prior work suggested that YhcB was directly involved in cell division or peptidoglycan assembly. We found that loss of YhcB is detrimental in genetic backgrounds in which lipopolysaccharide (LPS) or glycerophospholipid (GPL) synthesis is altered. The growth defect of ΔyhcB could be rescued through inactivation of the Mla pathway, a system responsible for the retrograde transport of GPLs that are mislocalized to the outer leaflet of the outer membrane. Interestingly, this rescue was dependent upon the outer membrane phospholipase PldA that cleaves GPLs at the bacterial surface. Since the freed fatty acids resulting from PldA activity serve as a signal to the cell to increase LPS synthesis, this result suggested that outer membrane lipids are imbalanced in ΔyhcB. Mutations that arose in ΔyhcB populations during two independent suppressor screens were in genes encoding subunits of the acetyl coenzyme A carboxylase complex, which initiates fatty acid biosynthesis (FAB). These mutations fully restored cell morphology and reduced GPL levels, which were increased compared to wild-type bacteria. Growth of ΔyhcB with the FAB-targeting antibiotic cerulenin also increased cellular fitness. Furthermore, genetic manipulation of FAB and lipid biosynthesis showed that decreasing FAB rescued ΔyhcB filamentation, whereas increasing LPS alone could not. Altogether, these results suggest that YhcB may play a pivotal role in regulating FAB and, in turn, impact cell envelope assembly and cell division.IMPORTANCESynthesis of the Gram-negative cell envelope is a dynamic and complex process that entails careful coordination of many biosynthetic pathways. The inner and outer membranes are composed of molecules that are energy intensive to synthesize, and, accordingly, these synthetic pathways are under tight regulation. The robust nature of the Gram-negative outer membrane renders it naturally impermeable to many antibiotics and therefore a target of interest for antimicrobial design. Our data indicate that when the inner membrane protein YhcB is absent in Escherichia coli, the pathway for generating fatty acid substrates needed for all membrane lipid synthesis is dysregulated which leads to increased membrane material. These findings suggest a potentially novel regulatory mechanism for controlling the rate of fatty acid biosynthesis.
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Affiliation(s)
- Hannah M Stanley
- Department of Microbiology, College of Art and Sciences, University of Georgia, Athens, Georgia, USA
| | - M Stephen Trent
- Department of Microbiology, College of Art and Sciences, University of Georgia, Athens, Georgia, USA
- Department of Infectious Diseases, College of Veterinary Medicine, University of Georgia, Athens, Georgia, USA
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3
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Xu X, de Sousa AS, Boram TJ, Jiang W, Lohman JR. Active E. coli heteromeric acetyl-CoA carboxylase forms polymorphic helical tubular filaments. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.05.28.596234. [PMID: 38854064 PMCID: PMC11160672 DOI: 10.1101/2024.05.28.596234] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/11/2024]
Abstract
The Escherichia coli heteromeric acetyl-CoA carboxylase (ACC) has four subunits assumed to form an elusive catalytic complex and are involved in allosteric and transcriptional regulation. The E. coli ACC represents almost all ACCs from pathogenic bacteria making it a key antibiotic development target to fight growing antibiotic resistance. Furthermore, it is a model for cyanobacterial and plant plastid ACCs as biofuel engineering targets. Here we report the catalytic E. coli ACC complex surprisingly forms tubes rather than dispersed particles. The cryo-EM structure reveals key protein-protein interactions underpinning efficient catalysis and how transcriptional regulatory roles are masked during catalysis. Discovering the protein-protein interaction interfaces that facilitate catalysis, allosteric and transcriptional regulation provides new routes to engineering catalytic activity and new targets for drug discovery.
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Affiliation(s)
- Xueyong Xu
- Department of Biological Sciences, Purdue University; West Lafayette, IN 47907 USA
| | - Amanda Silva de Sousa
- Department of Biochemistry and Molecular Biology, Michigan State University; East Lansing, MI 48824 USA
- Department of Biochemistry, Purdue University; West Lafayette, IN 47907 USA
| | - Trevor J. Boram
- Department of Biochemistry, Purdue University; West Lafayette, IN 47907 USA
| | - Wen Jiang
- Department of Biological Sciences, Purdue University; West Lafayette, IN 47907 USA
| | - Jeremy R. Lohman
- Department of Biochemistry and Molecular Biology, Michigan State University; East Lansing, MI 48824 USA
- Department of Biochemistry, Purdue University; West Lafayette, IN 47907 USA
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4
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Shen J, Wu W, Wang K, Wu J, Liu B, Li C, Gong Z, Hong X, Fang H, Zhang X, Xu X. Chloroflexus aurantiacus acetyl-CoA carboxylase evolves fused biotin carboxylase and biotin carboxyl carrier protein to complete carboxylation activity. mBio 2024; 15:e0341423. [PMID: 38572988 PMCID: PMC11077971 DOI: 10.1128/mbio.03414-23] [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: 01/08/2024] [Accepted: 03/13/2024] [Indexed: 04/05/2024] Open
Abstract
Acetyl-CoA carboxylases (ACCs) convert acetyl-CoA to malonyl-CoA, a key step in fatty acid biosynthesis and autotrophic carbon fixation pathways. Three functionally distinct components, biotin carboxylase (BC), biotin carboxyl carrier protein (BCCP), and carboxyltransferase (CT), are either separated or partially fused in different combinations, forming heteromeric ACCs. However, an ACC with fused BC-BCCP and separate CT has not been identified, leaving its catalytic mechanism unclear. Here, we identify two BC isoforms (BC1 and BC2) from Chloroflexus aurantiacus, a filamentous anoxygenic phototroph that employs 3-hydroxypropionate (3-HP) bi-cycle rather than Calvin cycle for autotrophic carbon fixation. We reveal that BC1 possesses fused BC and BCCP domains, where BCCP could be biotinylated by E. coli or C. aurantiacus BirA on Lys553 residue. Crystal structures of BC1 and BC2 at 3.2 Å and 3.0 Å resolutions, respectively, further reveal a tetramer of two BC1-BC homodimers, and a BC2 homodimer, all exhibiting similar BC architectures. The two BC1-BC homodimers are connected by an eight-stranded β-barrel of the partially resolved BCCP domain. Disruption of β-barrel results in dissociation of the tetramer into dimers in solution and decreased biotin carboxylase activity. Biotinylation of the BCCP domain further promotes BC1 and CTβ-CTα interactions to form an enzymatically active ACC, which converts acetyl-CoA to malonyl-CoA in vitro and produces 3-HP via co-expression with a recombinant malonyl-CoA reductase in E. coli cells. This study revealed a heteromeric ACC that evolves fused BC-BCCP but separate CTα and CTβ to complete ACC activity.IMPORTANCEAcetyl-CoA carboxylase (ACC) catalyzes the rate-limiting step in fatty acid biosynthesis and autotrophic carbon fixation pathways across a wide range of organisms, making them attractive targets for drug discovery against various infections and diseases. Although structural studies on homomeric ACCs, which consist of a single protein with three subunits, have revealed the "swing domain model" where the biotin carboxyl carrier protein (BCCP) domain translocates between biotin carboxylase (BC) and carboxyltransferase (CT) active sites to facilitate the reaction, our understanding of the subunit composition and catalytic mechanism in heteromeric ACCs remains limited. Here, we identify a novel ACC from an ancient anoxygenic photosynthetic bacterium Chloroflexus aurantiacus, it evolves fused BC and BCCP domain, but separate CT components to form an enzymatically active ACC, which converts acetyl-CoA to malonyl-CoA in vitro and produces 3-hydroxypropionate (3-HP) via co-expression with recombinant malonyl-CoA reductase in E. coli cells. These findings expand the diversity and molecular evolution of heteromeric ACCs and provide a structural basis for potential applications in 3-HP biosynthesis.
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Affiliation(s)
- Jiejie Shen
- Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Hangzhou Normal University, Hangzhou, China
- Zhejiang Key Laboratory of Medical Epigenetics, Hangzhou Normal University, Hangzhou, China
| | - Wenping Wu
- Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Hangzhou Normal University, Hangzhou, China
- Zhejiang Key Laboratory of Medical Epigenetics, Hangzhou Normal University, Hangzhou, China
| | - Kangle Wang
- Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Hangzhou Normal University, Hangzhou, China
- Zhejiang Key Laboratory of Medical Epigenetics, Hangzhou Normal University, Hangzhou, China
| | - Jingyi Wu
- Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Hangzhou Normal University, Hangzhou, China
- Zhejiang Key Laboratory of Medical Epigenetics, Hangzhou Normal University, Hangzhou, China
| | - Bing Liu
- Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Hangzhou Normal University, Hangzhou, China
- Zhejiang Key Laboratory of Medical Epigenetics, Hangzhou Normal University, Hangzhou, China
| | - Chunyang Li
- Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Hangzhou Normal University, Hangzhou, China
- Zhejiang Key Laboratory of Medical Epigenetics, Hangzhou Normal University, Hangzhou, China
| | - Zijun Gong
- Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Hangzhou Normal University, Hangzhou, China
- Zhejiang Key Laboratory of Medical Epigenetics, Hangzhou Normal University, Hangzhou, China
| | - Xin Hong
- Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Hangzhou Normal University, Hangzhou, China
- Zhejiang Key Laboratory of Medical Epigenetics, Hangzhou Normal University, Hangzhou, China
| | - Han Fang
- Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Hangzhou Normal University, Hangzhou, China
- Zhejiang Key Laboratory of Medical Epigenetics, Hangzhou Normal University, Hangzhou, China
| | - Xingwei Zhang
- The Affiliated Hospital of Hangzhou Normal University, Hangzhou Normal University, Hangzhou, China
| | - Xiaoling Xu
- Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Hangzhou Normal University, Hangzhou, China
- Zhejiang Key Laboratory of Medical Epigenetics, Hangzhou Normal University, Hangzhou, China
- Photosynthesis Research Center, College of Life and Environmental Sciences, Hangzhou Normal University, Hangzhou, China
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5
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Zhao JR, Zuo SQ, Xiao F, Guo FZ, Chen LY, Bi K, Cheng DY, Xu ZN. Advances in biotin biosynthesis and biotechnological production in microorganisms. World J Microbiol Biotechnol 2024; 40:163. [PMID: 38613659 DOI: 10.1007/s11274-024-03971-7] [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: 02/01/2024] [Accepted: 03/28/2024] [Indexed: 04/15/2024]
Abstract
Biotin, also known as vitamin H or B7, acts as a crucial cofactor in the central metabolism processes of fatty acids, amino acids, and carbohydrates. Biotin has important applications in food additives, biomedicine, and other fields. While the ability to synthesize biotin de novo is confined to microorganisms and plants, humans and animals require substantial daily intake, primarily through dietary sources and intestinal microflora. Currently, chemical synthesis stands as the primary method for commercial biotin production, although microbial biotin production offers an environmentally sustainable alternative with promising prospects. This review presents a comprehensive overview of the pathways involved in de novo biotin synthesis in various species of microbes and insights into its regulatory and transport systems. Furthermore, diverse strategies are discussed to improve the biotin production here, including mutation breeding, rational metabolic engineering design, artificial genetic modification, and process optimization. The review also presents the potential strategies for addressing current challenges for industrial-scale bioproduction of biotin in the future. This review is very helpful for exploring efficient and sustainable strategies for large-scale biotin production.
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Affiliation(s)
- Jia-Run Zhao
- Key Laboratory of Biomass Chemical Engineering of Ministry of Education, College of Chemical and Biological Engineering, Zhejiang University, Hangzhou, 310027, China
- Institute of Biological Engineering, College of Chemical and Biological Engineering, Zhejiang University, Hangzhou, 310027, China
| | - Si-Qi Zuo
- Key Laboratory of Biomass Chemical Engineering of Ministry of Education, College of Chemical and Biological Engineering, Zhejiang University, Hangzhou, 310027, China
- Institute of Biological Engineering, College of Chemical and Biological Engineering, Zhejiang University, Hangzhou, 310027, China
| | - Feng Xiao
- Key Laboratory of Biomass Chemical Engineering of Ministry of Education, College of Chemical and Biological Engineering, Zhejiang University, Hangzhou, 310027, China
- Institute of Biological Engineering, College of Chemical and Biological Engineering, Zhejiang University, Hangzhou, 310027, China
- ZJU-Hangzhou Global Scientific and Technological Innovation Center, Zhejiang University, Hangzhou, 310000, China
| | - Feng-Zhu Guo
- Zhejiang Sliver-Elephant Bio-engineering Co., Ltd., Tiantai, 317200, China
| | - Lu-Yi Chen
- Zhejiang Sliver-Elephant Bio-engineering Co., Ltd., Tiantai, 317200, China
| | - Ke Bi
- Key Laboratory of Biomass Chemical Engineering of Ministry of Education, College of Chemical and Biological Engineering, Zhejiang University, Hangzhou, 310027, China
- Institute of Biological Engineering, College of Chemical and Biological Engineering, Zhejiang University, Hangzhou, 310027, China
| | - Dong-Yuan Cheng
- Key Laboratory of Biomass Chemical Engineering of Ministry of Education, College of Chemical and Biological Engineering, Zhejiang University, Hangzhou, 310027, China
- Institute of Biological Engineering, College of Chemical and Biological Engineering, Zhejiang University, Hangzhou, 310027, China
| | - Zhi-Nan Xu
- Key Laboratory of Biomass Chemical Engineering of Ministry of Education, College of Chemical and Biological Engineering, Zhejiang University, Hangzhou, 310027, China.
- Institute of Biological Engineering, College of Chemical and Biological Engineering, Zhejiang University, Hangzhou, 310027, China.
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6
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Cronan JE. Biotin protein ligase as you like it: Either extraordinarily specific or promiscuous protein biotinylation. Proteins 2024; 92:435-448. [PMID: 37997490 PMCID: PMC10932917 DOI: 10.1002/prot.26642] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2023] [Accepted: 11/09/2023] [Indexed: 11/25/2023]
Abstract
Biotin (vitamin H or B7) is a coenzyme essential for all forms of life. Biotin has biological activity only when covalently attached to a few key metabolic enzyme proteins. Most organisms have only one attachment enzyme, biotin protein ligase (BPL), which attaches biotin to all target proteins. The sequences of these proteins and their substrate proteins are strongly conserved throughout biology. Structures of both the biotin ligase- and biotin-acceptor domains of mammals, plants, several bacterial species, and archaea have been determined. These, together with mutational analyses of ligases and their protein substrates, illustrate the exceptional specificity of this protein modification. For example, the Escherichia coli BPL biotinylates only one of the >4000 cellular proteins. Several bifunctional bacterial biotin ligases transcriptionally regulate biotin synthesis and/or transport in concert with biotinylation. The human BPL has been demonstrated to play an important role in that mutations in the BPL encoding gene cause one form of the disease, biotin-responsive multiple carboxylase deficiency. Promiscuous mutant versions of several BPL enzymes release biotinoyl-AMP, the active intermediate of the ligase reaction, to solvent. The released biotinoyl-AMP acts as a chemical biotinylation reagent that modifies lysine residues of neighboring proteins in vivo. This proximity-dependent biotinylation (called BioID) approach has been heavily utilized in cell biology.
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Affiliation(s)
- John E Cronan
- Department of Microbiology, University of Illinois, Urbana, Illinois, USA
- Department of Biochemistry, University of Illinois, Urbana, Illinois, USA
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7
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Gómez Borrego J, Torrent Burgas M. Structural assembly of the bacterial essential interactome. eLife 2024; 13:e94919. [PMID: 38226900 PMCID: PMC10863985 DOI: 10.7554/elife.94919] [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: 11/30/2023] [Accepted: 12/22/2023] [Indexed: 01/17/2024] Open
Abstract
The study of protein interactions in living organisms is fundamental for understanding biological processes and central metabolic pathways. Yet, our knowledge of the bacterial interactome remains limited. Here, we combined gene deletion mutant analysis with deep-learning protein folding using AlphaFold2 to predict the core bacterial essential interactome. We predicted and modeled 1402 interactions between essential proteins in bacteria and generated 146 high-accuracy models. Our analysis reveals previously unknown details about the assembly mechanisms of these complexes, highlighting the importance of specific structural features in their stability and function. Our work provides a framework for predicting the essential interactomes of bacteria and highlight the potential of deep-learning algorithms in advancing our understanding of the complex biology of living organisms. Also, the results presented here offer a promising approach to identify novel antibiotic targets.
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Affiliation(s)
- Jordi Gómez Borrego
- Systems Biology of Infection Lab, Department of Biochemistry and Molecular Biology, Biosciences Faculty, Universitat Autònoma de BarcelonaCerdanyola del VallèsSpain
| | - Marc Torrent Burgas
- Systems Biology of Infection Lab, Department of Biochemistry and Molecular Biology, Biosciences Faculty, Universitat Autònoma de BarcelonaCerdanyola del VallèsSpain
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Chen J, Wang W, Wang L, Wang H, Hu M, Zhou J, Du G, Zeng W. Efficient De Novo Biosynthesis of Curcumin in Escherichia coli by Optimizing Pathway Modules and Increasing the Malonyl-CoA Supply. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2024; 72:566-576. [PMID: 38154088 DOI: 10.1021/acs.jafc.3c07379] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/30/2023]
Abstract
Curcumin is a natural phenylpropanoid compound with various biological activities and is widely used in food and pharmaceuticals. A de novo curcumin biosynthetic pathway was constructed in Escherichia coli BL21(DE3). Optimization of the curcumin biosynthesis module achieved a curcumin titer of 26.8 ± 0.6 mg/L. Regulating the metabolic fluxes of the β-oxidation pathway and fatty acid elongation cycle and blocking the endogenous malonyl-CoA consumption pathway increased the titer to 113.6 ± 7.1 mg/L. Knockout of endogenous curcumin reductase (curA) and intermediate product detoxification by heterologous expression of the solvent-resistant pump (srpB) increased the titer to 137.5 ± 3.0 mg/L. A 5 L pilot-scale fermentation, using a three-stage pH alternation strategy, increased the titer to 696.2 ± 20.9 mg/L, 178.5-fold higher than the highest curcumin titer from de novo biosynthesis previously reported, thereby laying the foundation for efficient biosynthesis of curcumin and its derivatives.
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Affiliation(s)
- Jianbin Chen
- Engineering Research Center of Ministry of Education on Food Synthetic Biotechnology, Jiangnan University, 1800 Lihu Road, Wuxi 214122, Jiangsu, China
- Science Center for Future Foods, Jiangnan University, 1800 Lihu Road, Wuxi 214122, Jiangsu, China
| | - Weigao Wang
- Department of Chemical Engineering, Stanford University, 443 Via Ortega, Stanford, California 94305, United States
| | - Lian Wang
- Engineering Research Center of Ministry of Education on Food Synthetic Biotechnology, Jiangnan University, 1800 Lihu Road, Wuxi 214122, Jiangsu, China
- Science Center for Future Foods, Jiangnan University, 1800 Lihu Road, Wuxi 214122, Jiangsu, China
| | - Huijing Wang
- Engineering Research Center of Ministry of Education on Food Synthetic Biotechnology, Jiangnan University, 1800 Lihu Road, Wuxi 214122, Jiangsu, China
- Science Center for Future Foods, Jiangnan University, 1800 Lihu Road, Wuxi 214122, Jiangsu, China
| | - MingLong Hu
- Engineering Research Center of Ministry of Education on Food Synthetic Biotechnology, Jiangnan University, 1800 Lihu Road, Wuxi 214122, Jiangsu, China
- Science Center for Future Foods, Jiangnan University, 1800 Lihu Road, Wuxi 214122, Jiangsu, China
| | - Jingwen Zhou
- Engineering Research Center of Ministry of Education on Food Synthetic Biotechnology, Jiangnan University, 1800 Lihu Road, Wuxi 214122, Jiangsu, China
- Science Center for Future Foods, Jiangnan University, 1800 Lihu Road, Wuxi 214122, Jiangsu, China
- Jiangsu Province Engineering Research Center of Food Synthetic Biotechnology, Jiangnan University, Wuxi 214122, China
| | - Guocheng Du
- Engineering Research Center of Ministry of Education on Food Synthetic Biotechnology, Jiangnan University, 1800 Lihu Road, Wuxi 214122, Jiangsu, China
- Science Center for Future Foods, Jiangnan University, 1800 Lihu Road, Wuxi 214122, Jiangsu, China
| | - Weizhu Zeng
- Engineering Research Center of Ministry of Education on Food Synthetic Biotechnology, Jiangnan University, 1800 Lihu Road, Wuxi 214122, Jiangsu, China
- Science Center for Future Foods, Jiangnan University, 1800 Lihu Road, Wuxi 214122, Jiangsu, China
- Jiangsu Province Engineering Research Center of Food Synthetic Biotechnology, Jiangnan University, Wuxi 214122, China
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9
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Kim SH, Yun C, Kwon D, Lee YH, Kwak JH, Jung YS. Effect of Isoquercitrin on Free Fatty Acid-Induced Lipid Accumulation in HepG2 Cells. Molecules 2023; 28:molecules28031476. [PMID: 36771140 PMCID: PMC9919102 DOI: 10.3390/molecules28031476] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2023] [Revised: 01/27/2023] [Accepted: 02/01/2023] [Indexed: 02/05/2023] Open
Abstract
Liver metabolic disorders and oxidative stress are crucial factors in the development of nonalcoholic fatty liver disease (NAFLD); however, treatment strategies to combat NAFLD remain poorly established, presenting an important challenge that needs to be addressed. Herein, we aimed to examine the effect of isoquercitrin on lipid accumulation induced by exogenous free fatty acids (FFA) using HepG2 cells and elucidate the underlying molecular mechanism. The cells were exposed to 0.5 mM FFA to induce intracellular lipid accumulation, followed by co-treatment with isoquercitrin to confirm the potential inhibitory effect on FFA-induced lipid production. HepG2 cells exposed to FFA alone exhibited intracellular lipid accumulation, compromised endoplasmic reticulum (ER) stress, and enhanced expression of proteins and genes involved in lipid synthesis; however, co-treatment with isoquercitrin decreased the expression of these molecules in a dose-dependent manner. Furthermore, isoquercitrin could activate AMP-activated protein kinase (AMPK), a key regulatory protein of hepatic fatty acid oxidation, suppressing new lipid production by phosphorylating acetyl-CoA carboxylase (ACC) and inhibiting sterol regulatory element-binding transcription factor 1 (SREBP-1)/fatty acid synthase (FAS) signals. Overall, these findings suggest that isoquercitrin can be employed as a therapeutic agent to improve NAFLD via the regulation of lipid metabolism by targeting the AMPK/ACC and SREBP1/FAS pathways.
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Affiliation(s)
- Sou Hyun Kim
- Department of Pharmacy, College of Pharmacy, Research Institute for Drug Development, Pusan National University, Busan 46241, Republic of Korea
| | - Chawon Yun
- Department of Pharmacy, College of Pharmacy, Research Institute for Drug Development, Pusan National University, Busan 46241, Republic of Korea
| | - Doyoung Kwon
- College of Pharmacy, Jeju Research Institute of Pharmaceutical Sciences, Jeju National University, Jeju 63243, Republic of Korea
| | - Yun-Hee Lee
- College of Pharmacy, Research Institute of Pharmaceutical Sciences, Seoul National University, Seoul 08826, Republic of Korea
| | - Jae-Hwan Kwak
- College of Pharmacy, Chungbuk National University, Cheongju 28160, Republic of Korea
| | - Young-Suk Jung
- Department of Pharmacy, College of Pharmacy, Research Institute for Drug Development, Pusan National University, Busan 46241, Republic of Korea
- Correspondence: ; Tel.: +82-51-5102816
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Medium-Chain-Length Fatty Acid Catabolism in Cupriavidus necator H16: Transcriptome Sequencing Reveals Differences from Long-Chain-Length Fatty Acid β-Oxidation and Involvement of Several Homologous Genes. Appl Environ Microbiol 2023; 89:e0142822. [PMID: 36541797 PMCID: PMC9888253 DOI: 10.1128/aem.01428-22] [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: 12/24/2022] Open
Abstract
The number of genes encoding β-oxidation enzymes in Cupriavidus necator H16 (synonym, Ralstonia eutropha H16) is high, but only the operons A0459-A0464 and A1526-A1531, each encoding four genes for β-oxidation enzymes, were expressed during growth with long-chain-length fatty acids (LCFAs). However, we observed that C. necator ΔA0459-A0464 ΔA1526-A1531 and C. necator H16 showed the same growth behavior during growth with decanoic acid and shorter FAs. The negative effect of the deletion of these two operons increased with an increasing chain length of the utilized FAs. Transcriptome sequencing (RNA-Seq) revealed the expression profiles of genes involved in the catabolism of medium-chain-length fatty acids (MCFAs) in C. necator H16. Operon A0459-A0464 was expressed only during growth with nonanoic acid, whereas operon A1526-A1531 was highly expressed during growth with octanoic and nonanoic acid. The gene clusters B1187-B1192 and B0751-B0759 showed a log2 fold change in expression of up to 4.29 and 4.02, respectively, during growth with octanoic acid and up to 8.82 and 5.50, respectively, with nonanoic acid compared to sodium gluconate-grown cells. Several acyl-CoA ligases catalyze the activation of MCFAs with coenzyme A (CoA), but fadD3 (A3288), involved in activation of LCFAs, was not detected. The expression profiles of C. necator strain ΔA0459-A0464 ΔA1526-A1531 showed that the growth with nonanoic acid resulted in the expression of further β-oxidation enzyme-encoding genes. Additional insights into the transport of FAs in C. necator H16 revealed the complexity and putative involvement of the DegV-like protein encoded by A0463 in the transport of odd-chain-length FAs and of siderophore biosynthesis in the transport mechanism. IMPORTANCE Although Cupriavidus necator H16 has been used in several studies to produce polyhydroxyalkanoates from various lipids, the fatty acid metabolism is poorly understood. The β-oxidation of long-chain-length FAs has been investigated, but the tremendous number of homologous genes encoding β-oxidation enzymes hides the potential for variances in the expressed genes for catabolism of shorter FAs. The catabolism of medium-chain-length FAs and connected pathways has not been investigated yet. As more sustainable substrates such as lipids and the production of fatty acids and fatty acid derivates become more critical with the dependency on fossil-based substances, understanding the complex metabolism in this highly diverse workhorse for biotechnology, C. necator, is inevitable. For further metabolic engineering and construction of production strains, we investigated the metabolism during growth on medium-chain-length FAs by RNA-Seq.
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Liu L, Ma X, Bilal M, Wei L, Tang S, Luo H, Zhao Y, Wang Z, Duan X. Toxicity and inhibition mechanism of gallic acid on physiology and fermentation performance of Escherichia coli. BIORESOUR BIOPROCESS 2022; 9:76. [PMID: 38647760 PMCID: PMC10992115 DOI: 10.1186/s40643-022-00564-w] [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: 04/23/2022] [Accepted: 07/10/2022] [Indexed: 11/10/2022] Open
Abstract
Gallic acid is a natural phenolic acid that has a stress inhibition effect on Escherichia coli. This study by integrates fermentation characteristics and transcriptional analyses to elucidate the physiological mechanism of E. coli 3110 response to gallic acid. Compared with the control (without stress), the cell growth was severely retarded, and irregular cell morphology appeared in the case of high levels of gallic acid stress. The glucose consumption of E. coli was reduced successively with the increase of gallic acid content in the fermentation medium. After 20 h of gallic acid stress, cofactor levels (ATP, NAD+ and NADH) of E. coli 3110 were similarly decreased, indicating a more potent inhibitory effect of gallic acid on E. coli. The transcriptional analysis revealed that gallic acid altered the gene expression profiles related to five notable differentially regulated pathways. The genes related to the two-component system were up-regulated, while the genes associated with ABC-transporter, energy metabolism, carbon metabolism, and fatty acid biosynthesis were down-regulated. This is the first report to comprehensively assess the toxicity of gallic acid on E. coli. This study has implications for the efficient production of phenolic compounds by E. coli and provides new ideas for the study of microbial tolerance to environmental stress and the identification of associated tolerance targets.
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Affiliation(s)
- Lina Liu
- School of Life Science and Food Engineering, Huaiyin Institute of Technology, Huaian, 223003, China.
| | - Xiaolong Ma
- School of Life Science and Food Engineering, Huaiyin Institute of Technology, Huaian, 223003, China
| | - Muhammad Bilal
- School of Life Science and Food Engineering, Huaiyin Institute of Technology, Huaian, 223003, China
| | - Linlin Wei
- School of Life Science and Food Engineering, Huaiyin Institute of Technology, Huaian, 223003, China
| | - Shijie Tang
- School of Life Science and Food Engineering, Huaiyin Institute of Technology, Huaian, 223003, China
| | - Hongzhen Luo
- School of Life Science and Food Engineering, Huaiyin Institute of Technology, Huaian, 223003, China
| | - Yuping Zhao
- School of Life Science and Food Engineering, Huaiyin Institute of Technology, Huaian, 223003, China
| | - Zhaoyu Wang
- School of Life Science and Food Engineering, Huaiyin Institute of Technology, Huaian, 223003, China
| | - Xuguo Duan
- College of Light Industry and Food Engineering, Nanjing Forestry University, Nanjing, 210037, Jiangsu, China
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Wang M, Garneau MG, Poudel AN, Lamm D, Koo AJ, Bates PD, Thelen JJ. Overexpression of pea α-carboxyltransferase in Arabidopsis and camelina increases fatty acid synthesis leading to improved seed oil content. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2022; 110:1035-1046. [PMID: 35220631 DOI: 10.1111/tpj.15721] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/20/2021] [Revised: 02/11/2022] [Accepted: 02/21/2022] [Indexed: 06/14/2023]
Abstract
SUMMARYHeteromeric acetyl‐CoA carboxylase (htACCase) catalyzes the committed step of de novo fatty acid biosynthesis in most plant plastids. Plant htACCase is comprised of four subunits: α‐ and β‐carboxyltransferase (α‐ and β‐CT), biotin carboxylase, and biotin carboxyl carrier protein. Based on in vivo absolute quantification of htACCase subunits, α‐CT is 3‐ to 10‐fold less abundant than its partner subunit β‐CT in developing Arabidopsis seeds [Wilson and Thelen, J. Proteome Res., 2018, 17 (5)]. To test the hypothesis that low expression of α‐CT limits htACCase activity and flux through fatty acid synthesis in planta, we overexpressed Pisum sativum α‐CT, either with or without its C‐terminal non‐catalytic domain, in both Arabidopsis thaliana and Camelina sativa. First‐generation Arabidopsis seed of 35S::Ps α‐CT (n = 25) and 35S::Ps α‐CTΔ406‐875 (n = 47) were on average 14% higher in oil content (% dry weight) than wild type co‐cultivated in a growth chamber. First‐generation camelina seed showed an average 8% increase compared to co‐cultivated wild type. Biochemical analyses confirmed the accumulation of Ps α‐CT and Ps α‐CTΔ406‐875 protein and higher htACCase activity in overexpression lines during early seed development. Overexpressed Ps α‐CT co‐migrated with native At β‐CT during anion exchange chromatography, indicating co‐association. By successfully increasing seed oil content upon heterologous overexpression of α‐CT, we demonstrate how absolute quantitation of in vivo protein complex stoichiometry can be used to guide rational metabolic engineering.
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Affiliation(s)
- Minmin Wang
- Department of Biochemistry, University of Missouri, Columbia, Missouri, 65211, USA
- Christopher S. Bond Life Sciences Center, University of Missouri, Columbia, Missouri, 65211, USA
| | - Matthew G Garneau
- Institute of Biological Chemistry, Washington State University, Pullman, Washington, DC, 99164, USA
| | - Arati N Poudel
- Department of Biochemistry, University of Missouri, Columbia, Missouri, 65211, USA
| | - Daniel Lamm
- Department of Biochemistry, University of Missouri, Columbia, Missouri, 65211, USA
| | - Abraham J Koo
- Department of Biochemistry, University of Missouri, Columbia, Missouri, 65211, USA
| | - Philip D Bates
- Institute of Biological Chemistry, Washington State University, Pullman, Washington, DC, 99164, USA
| | - Jay J Thelen
- Department of Biochemistry, University of Missouri, Columbia, Missouri, 65211, USA
- Christopher S. Bond Life Sciences Center, University of Missouri, Columbia, Missouri, 65211, USA
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Song X, Cronan JE. A conserved and seemingly redundant Escherichia coli biotin biosynthesis gene expressed only during anaerobic growth. Mol Microbiol 2021; 116:1315-1327. [PMID: 34597430 PMCID: PMC8599648 DOI: 10.1111/mmi.14826] [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: 08/23/2021] [Revised: 09/26/2021] [Accepted: 09/27/2021] [Indexed: 11/30/2022]
Abstract
Biotin is an essential metabolic cofactor and de novo biotin biosynthetic pathways are widespread in microorganisms and plants. Biotin synthetic genes are generally found clustered into bio operons to facilitate tight regulation since biotin synthesis is a metabolically expensive process. Dethiobiotin synthetase (DTBS) catalyzes the penultimate step of biotin biosynthesis, the formation of 7,8-diaminononanoate (DAPA). In Escherichia coli, DTBS is encoded by the bio operon gene bioD. Several studies have reported transcriptional activation of ynfK a gene of unknown function, under anaerobic conditions. Alignments of YnfK with BioD have led to suggestions that YnfK has DTBS activity. We report that YnfK is a functional DTBS, although an enzyme of poor activity that is poorly expressed. Supplementation of growth medium with DAPA or substitution of BioD active site residues for the corresponding YnfK residues greatly improved the DTBS activity of YnfK. We confirmed that FNR activates transcriptional level of ynfK during anaerobic growth and identified the FNR binding site of ynfK. The ynfK gene is well conserved in γ-proteobacteria.
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Affiliation(s)
- Xuejiao Song
- Department of Biochemistry, University of Illinois, Urbana, Illinois, USA
| | - John E Cronan
- Department of Biochemistry, University of Illinois, Urbana, Illinois, USA.,Department of Microbiology, University of Illinois, Urbana, Illinois, USA
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