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Huang Z, Wang Q, Cao J, Zhou D, Li C. Mechanisms of polyphenols on quality control of aquatic products in storage: A review. Crit Rev Food Sci Nutr 2024; 64:6298-6317. [PMID: 36655433 DOI: 10.1080/10408398.2023.2167803] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023]
Abstract
Aquatic products are easily spoiled during storage due to oxidation, endogenous enzymes, and bacteria. At the same time, compared with synthetic antioxidants, based on the antibacterial and antioxidant mechanism of biological agents, the development of natural, nontoxic, low-temperature, better-effect green biological preservatives is more acceptable to consumers. The type and molecular structure of polyphenols affect their antioxidant and antibacterial effectiveness. This review will describe how they achieve their antioxidant and antibacterial effects. And the recent literature on the mechanism and application of polyphenols in the preservation of aquatic products was updated and summarized. The conclusion is that in aquatic products, polyphenols alleviate lipid oxidation, protein degradation and inhibit the growth and reproduction of microorganisms, so as to achieve the effect of storage quality control. And put forward suggestions on the application of the research results in aquatic products. We hope to provide theoretical support for better exploration of the application of polyphenols and aquatic product storage.
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Affiliation(s)
- Zhiliang Huang
- Hainan Provincial Engineering Research Centre of Aquatic Resources Efficient Utilization in the South China Sea, School of Food Science and Engineering, Hainan University, Haikou, China
| | - Qi Wang
- Hainan Provincial Engineering Research Centre of Aquatic Resources Efficient Utilization in the South China Sea, School of Food Science and Engineering, Hainan University, Haikou, China
| | - Jun Cao
- Hainan Provincial Engineering Research Centre of Aquatic Resources Efficient Utilization in the South China Sea, School of Food Science and Engineering, Hainan University, Haikou, China
| | - Dayong Zhou
- Collaborative Innovation Center of Provincial and Ministerial Co-construction for Marine Food Deep Processing, Dalian Polytechnic University, Dalian, China
| | - Chuan Li
- Hainan Provincial Engineering Research Centre of Aquatic Resources Efficient Utilization in the South China Sea, School of Food Science and Engineering, Hainan University, Haikou, China
- Collaborative Innovation Center of Provincial and Ministerial Co-construction for Marine Food Deep Processing, Dalian Polytechnic University, Dalian, China
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2
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Zhou J, Zhang L, Wang Y, Song W, Huang Y, Mu Y, Schmitz W, Zhang SY, Lin H, Chen HZ, Ye F, Zhang L. The Molecular Basis of Catalysis by SDR Family Members Ketoacyl-ACP Reductase FabG and Enoyl-ACP Reductase FabI in Type-II Fatty Acid Biosynthesis. Angew Chem Int Ed Engl 2023; 62:e202313109. [PMID: 37779101 DOI: 10.1002/anie.202313109] [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: 09/05/2023] [Revised: 09/24/2023] [Accepted: 09/26/2023] [Indexed: 10/03/2023]
Abstract
The short-chain dehydrogenase/reductase (SDR) superfamily members acyl-ACP reductases FabG and FabI are indispensable core enzymatic modules and catalytic orientation controllers in type-II fatty acid biosynthesis. Herein, we report their distinct substrate allosteric recognition and enantioselective reduction mechanisms. FabG achieves allosteric regulation of ACP and NADPH through ACP binding across two adjacent FabG monomers, while FabI follows an irreversible compulsory order of substrate binding in that NADH binding must precede that of ACP on a discrete FabI monomer. Moreover, FabG and FabI utilize a backdoor residue Phe187 or a "rheostat" α8 helix for acyl chain length selection, and their corresponding triad residues Ser142 or Tyr145 recognize the keto- or enoyl-acyl substrates, respectively, facilitating initiation of nucleophilic attack by NAD(P)H. The other two triad residues (Tyr and Lys) mediate subsequent proton transfer and (R)-3-hydroxyacyl- or saturated acyl-ACP production.
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Affiliation(s)
- Jiashen Zhou
- Department of Pharmacology and Chemical Biology, State Key Laboratory of Systems Medicine for Cancer, Shanghai Jiao Tong University School of Medicine, Shanghai, 200025, China
| | - Lin Zhang
- Department of Pharmacology and Chemical Biology, State Key Laboratory of Systems Medicine for Cancer, Shanghai Jiao Tong University School of Medicine, Shanghai, 200025, China
| | - Yiran Wang
- School of Pharmaceutical Science and Technology, Hangzhou Institute for Advanced Study, University of Chinese Academy of Sciences, Hangzhou, 310024, China
- State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, 201203, Shanghai, China
| | - Wenyan Song
- Department of Pharmacology and Chemical Biology, State Key Laboratory of Systems Medicine for Cancer, Shanghai Jiao Tong University School of Medicine, Shanghai, 200025, China
| | - Yuzhou Huang
- Department of Pharmacology and Chemical Biology, State Key Laboratory of Systems Medicine for Cancer, Shanghai Jiao Tong University School of Medicine, Shanghai, 200025, China
| | - Yajuan Mu
- Department of Pharmacology and Chemical Biology, State Key Laboratory of Systems Medicine for Cancer, Shanghai Jiao Tong University School of Medicine, Shanghai, 200025, China
| | - Werner Schmitz
- Department of Biochemistry and Molecular Biology, University of Würzburg, Würzburg, 97074, Germany
| | - Shu-Yu Zhang
- School of Chemistry and Chemical Engineering, Shanghai Jiao Tong University, Shanghai, 200240, China
| | - Houwen Lin
- Research Centre for Marine Drugs, State Key Laboratory of Oncogene and Related Genes, Department of Pharmacy, Ren Ji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, 200127, China
- Institute of Marine Biomedicine, Shenzhen Polytechnic, Shenzhen, 518055, China
| | - Hong-Zhuan Chen
- Institute of Interdisciplinary Integrative Biomedical Research, Shuguang Hospital, Shanghai University of Traditional Chinese Medicine, Shanghai, 201203, China
| | - Fei Ye
- School of Pharmaceutical Science and Technology, Hangzhou Institute for Advanced Study, University of Chinese Academy of Sciences, Hangzhou, 310024, China
| | - Liang Zhang
- Department of Pharmacology and Chemical Biology, State Key Laboratory of Systems Medicine for Cancer, Shanghai Jiao Tong University School of Medicine, Shanghai, 200025, China
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3
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Liu Y, Zhang Y, Kang C, Tian D, Lu H, Xu B, Xia Y, Kashiwagi A, Westermann M, Hoischen C, Xu J, Yomo T. Comparative genomics hints at dispensability of multiple essential genes in two Escherichia coli L-form strains. Biosci Rep 2023; 43:BSR20231227. [PMID: 37819245 PMCID: PMC10600066 DOI: 10.1042/bsr20231227] [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: 07/11/2023] [Revised: 10/09/2023] [Accepted: 10/11/2023] [Indexed: 10/13/2023] Open
Abstract
Despite the critical role of bacterial cell walls in maintaining cell shapes, certain environmental stressors can induce the transition of many bacterial species into a wall-deficient state called L-form. Long-term induced Escherichia coli L-forms lose their rod shape and usually hold significant mutations that affect cell division and growth. Besides this, the genetic background of L-form bacteria is still poorly understood. In the present study, the genomes of two stable L-form strains of E. coli (NC-7 and LWF+) were sequenced and their gene mutation status was determined and compared with their parental strains. Comparative genomic analysis between two L-forms reveals both unique adaptions and common mutated genes, many of which belong to essential gene categories not involved in cell wall biosynthesis, indicating that L-form genetic adaptation impacts crucial metabolic pathways. Missense variants from L-forms and Lenski's long-term evolution experiment (LTEE) were analyzed in parallel using an optimized DeepSequence pipeline to investigate predicted mutation effects (α) on protein functions. We report that the two L-form strains analyzed display a frequency of 6-10% (0% for LTEE) in mutated essential genes where the missense variants have substantial impact on protein functions (α<0.5). This indicates the emergence of different survival strategies in L-forms through changes in essential genes during adaptions to cell wall deficiency. Collectively, our results shed light on the detailed genetic background of two E. coli L-forms and pave the way for further investigations of the gene functions in L-form bacterial models.
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Affiliation(s)
- Yunfei Liu
- Laboratory of Biology and Information Science, School of Life Sciences, East China Normal University, Shanghai 200062, PR China
| | - Yueyue Zhang
- Laboratory of Biology and Information Science, School of Life Sciences, East China Normal University, Shanghai 200062, PR China
| | - Chen Kang
- School of Software Engineering, East China Normal University, Shanghai 200062, PR China
| | - Di Tian
- Laboratory of Biology and Information Science, School of Life Sciences, East China Normal University, Shanghai 200062, PR China
| | - Hui Lu
- Laboratory of Biology and Information Science, School of Life Sciences, East China Normal University, Shanghai 200062, PR China
| | - Boying Xu
- Laboratory of Biology and Information Science, School of Life Sciences, East China Normal University, Shanghai 200062, PR China
- Tongji University Cancer Center, Shanghai Tenth People’s Hospital, School of Medicine, Tongji University, Shanghai 200072, China
| | - Yang Xia
- Laboratory of Biology and Information Science, School of Life Sciences, East China Normal University, Shanghai 200062, PR China
| | - Akiko Kashiwagi
- Faculty of Agriculture and Life Science, Hirosaki University, Hirosaki 036-8561, Japan
| | - Martin Westermann
- Center for Electron Microscopy, Medical Faculty, Friedrich–Schiller–University Jena, Ziegelmühlenweg 1, D-07743 Jena, Germany
| | - Christian Hoischen
- CF Imaging, Leibniz Institute On Aging, Fritz–Lipmann–Institute (FLI), Beutenbergstraße 11, 07745 Jena, Germany
| | - Jian Xu
- Laboratory of Biology and Information Science, School of Life Sciences, East China Normal University, Shanghai 200062, PR China
| | - Tetsuya Yomo
- Laboratory of Biology and Information Science, School of Life Sciences, East China Normal University, Shanghai 200062, PR China
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4
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Sroor FM, Mahrous KF, El-Kader HAMA, Othman AM, Ibrahim NS. Impact of trifluoromethyl and sulfonyl groups on the biological activity of novel aryl-urea derivatives: synthesis, in-vitro, in-silico and SAR studies. Sci Rep 2023; 13:17560. [PMID: 37845243 PMCID: PMC10579241 DOI: 10.1038/s41598-023-44753-9] [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: 05/10/2023] [Accepted: 10/11/2023] [Indexed: 10/18/2023] Open
Abstract
We designed and prepared a novel series of urea derivatives with/without sulfonyl group in their structures to investigate the impact of the sulfonyl group on the biological activity of the evaluated compounds. Antibacterial investigations indicated that derivatives 7, 8, 9, and 11 had the most antibacterial property of all the compounds examined, their minimum inhibitory concentrations (MICs) determined against B. mycoides, E. coli, and C. albicans, with compound 8 being the most active at a MIC value of 4.88 µg/mL. Anti-cancer activity has been tested against eight human cancer cell lines; A549, HCT116, PC3, A431, HePG2, HOS, PACA2 and BJ1. Compounds 7, 8 and 9 emerged IC50 values better than Doxorubicin as a reference drug. Compounds 7 and 8 showed IC50 = 44.4 and 22.4 μM respectively against PACA2 compared to Doxorubicin (IC50 = 52.1 μM). Compound 9 showed IC50 = 17.8, 12.4, and 17.6 μM against HCT116, HePG2, and HOS, respectively. qRT-PCR revealed the down-regulation of PALB2 in compounds 7 and 15 treated PACA2 cells. Also, the down-regulation of BRCA1 and BRCA2 was shown in compound 7 treated PC3 cells. As regard A549 cells, compound 8 decreased the expression level of EGFR and KRAS genes. While compounds 7 and 9 down-regulated TP53 and FASN in HCT116 cells. Molecular docking was done against Escherichia coli enoyl reductase and human Son of sevenless homolog 1 (SOS1) and the results showed the promising inhibition of the studied proteins.
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Affiliation(s)
- Farid M Sroor
- Organometallic and Organometalloid Chemistry Department, National Research Centre, Cairo, 12622, Egypt.
| | - Karima F Mahrous
- Cell Biology Department, National Research Centre, Dokki, 12622, Egypt
| | | | - Abdelmageed M Othman
- Microbial Chemistry Department, Biotechnology Research Institute, National Research Centre, Dokki, 12622, Egypt
| | - Nada S Ibrahim
- Department of Chemistry (Biochemistry Branch), Faculty of Science, Cairo University, Giza, Egypt
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5
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Hasan S, Kayed K, Ghemrawi R, Bataineh NA, Mahgoub RE, Audeh R, Aldulaymi R, Atatreh N, Ghattas MA. Molecular Modelling Study and Antibacterial Evaluation of Diphenylmethane Derivatives as Potential FabI Inhibitors. Molecules 2023; 28:molecules28073000. [PMID: 37049763 PMCID: PMC10095751 DOI: 10.3390/molecules28073000] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2023] [Revised: 03/10/2023] [Accepted: 03/23/2023] [Indexed: 03/30/2023] Open
Abstract
The need for new antibiotics has become a major worldwide challenge as bacterial strains keep developing resistance to the existing drugs at an alarming rate. Enoyl-acyl carrier protein reductases (FabI) play a crucial role in lipids and fatty acid biosynthesis, which are essential for the integrity of the bacterial cell membrane. Our study aimed to discover small FabI inhibitors in continuation to our previously found hit MN02. The process was initially started by conducting a similarity search to the NCI ligand database using MN02 as a query. Accordingly, ten compounds were chosen for the computational assessment and antimicrobial testing. Most of the compounds showed an antibacterial activity against Gram-positive strains, while RK10 exhibited broad-spectrum activity against both Gram-positive and Gram-negative bacteria. All tested compounds were then docked into the saFabI active site followed by 100 ns MD simulations (Molecular Dynamics) and MM-GBSA (Molecular Mechanics with Generalised Born and Surface Area Solvation) calculations in order to understand their fitting and estimate their binding energies. Interestingly, and in line with the experimental data, RK10 was able to exhibit the best fitting with the target catalytic pocket. To sum up, RK10 is a small compound with leadlike characteristics that can indeed act as a promising candidate for the future development of broad-spectrum antibacterial agents.
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Affiliation(s)
- Shaima Hasan
- College of Pharmacy, Al Ain University, Abu Dhabi 64141, United Arab Emirates
| | - Kawthar Kayed
- College of Pharmacy, Al Ain University, Abu Dhabi 64141, United Arab Emirates
- AAU Health and Biomedical Research Center, Al Ain University, Abu Dhabi 64141, United Arab Emirates
| | - Rose Ghemrawi
- College of Pharmacy, Al Ain University, Abu Dhabi 64141, United Arab Emirates
- AAU Health and Biomedical Research Center, Al Ain University, Abu Dhabi 64141, United Arab Emirates
| | - Nezar Al Bataineh
- College of Pharmacy, Al Ain University, Abu Dhabi 64141, United Arab Emirates
- AAU Health and Biomedical Research Center, Al Ain University, Abu Dhabi 64141, United Arab Emirates
| | - Radwa E. Mahgoub
- AAU Health and Biomedical Research Center, Al Ain University, Abu Dhabi 64141, United Arab Emirates
| | - Rola Audeh
- College of Pharmacy, Al Ain University, Abu Dhabi 64141, United Arab Emirates
| | - Raghad Aldulaymi
- AAU Health and Biomedical Research Center, Al Ain University, Abu Dhabi 64141, United Arab Emirates
| | - Noor Atatreh
- College of Pharmacy, Al Ain University, Abu Dhabi 64141, United Arab Emirates
- AAU Health and Biomedical Research Center, Al Ain University, Abu Dhabi 64141, United Arab Emirates
| | - Mohammad A. Ghattas
- College of Pharmacy, Al Ain University, Abu Dhabi 64141, United Arab Emirates
- AAU Health and Biomedical Research Center, Al Ain University, Abu Dhabi 64141, United Arab Emirates
- Correspondence: ; Tel.: +971-26133275
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6
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Dong H, Cronan JE. Unsaturated fatty acid synthesis in Enterococcus faecalis requires a specific enoyl-ACP reductase. Mol Microbiol 2022; 118:541-551. [PMID: 36100979 PMCID: PMC9671860 DOI: 10.1111/mmi.14981] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2022] [Revised: 09/05/2022] [Accepted: 09/06/2022] [Indexed: 01/12/2023]
Abstract
The Enterococcus faecalis genome contains two enoyl-ACP reductases genes, fabK and fabI, which encode proteins having very different structures. Enoyl-ACP reductase catalyzes the last step of the elongation cycle of type II fatty acid synthesis pathway. The fabK gene is located within the large fatty acid synthesis operon whereas fabI is located together with two genes fabN and fabO required for unsaturated fatty acid synthesis. Prior work showed that FabK is weakly expressed due to poor translational initiation and hence virtually all the cellular enoyl ACP reductase activity is that encoded by fabI. Since FabK is a fully functional enzyme, the question is why FabI is an essential enzyme. Why not increase FabK activity? We report that overproduction of FabK is lethal whereas FabI overproduction only slows the growth and is not lethal. In both cases, normal growth is restored by the addition of oleic acid, an unsaturated fatty acid, to the medium indicating that enoyl ACP reductase overproduction disrupts unsaturated fatty acid synthesis. We report that this is due to competition with FabO, a putative 3-ketoacyl-ACP synthase I via FabN, a dehydratase/isomerase providing evidence that the enoyl-ACP reductase must be matched to the unsaturated fatty acid synthetic genes. FabO has been ascribed the same activity as E. coli FabB and we report in vitro evidence that this is the case, whereas FabN is a dehydratase/isomerase, having the activity of E. coli FabA. However, FabN is much larger than FabA, it is a hexamer rather than a dimer like FabA.
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Affiliation(s)
- Huijuan Dong
- Department of MicrobiologyUniversity of Illinois at Urbana‐ChampaignUrbanaIllinoisUSA
| | - John E. Cronan
- Department of MicrobiologyUniversity of Illinois at Urbana‐ChampaignUrbanaIllinoisUSA
- Department of BiochemistryUniversity of Illinois at Urbana‐ChampaignUrbanaIllinoisUSA
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7
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Wang S, Cheng Y, Wang X, Yang Q, Liu W. Tracing of Acyl Carrier Protein-channeled Mitomycin Intermediates in Streptomyces caespitosus Facilitates Characterization of the Biosynthetic Steps for AHBA-GlcN Formation and Processing. J Am Chem Soc 2022; 144:14945-14956. [PMID: 35943208 DOI: 10.1021/jacs.2c06969] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Mitomycins are a family of naturally occurring, potent alkylating agents in which the C member has been clinically used for cancer chemotherapy for over 5 decades. In Streptomyces caespitosus, mitomycins are derived from an N-glycoside composed of a 3-amino-5-hydroxybenzoic acid (AHBA) unit and a d-glucosamine (GlcN) unit; however, how this N-glycoside is formed and rearranged to a mitosane, for example, the compact polycyclic ring system of mitomycin C, remains elusive. Benefiting from the development of a method used to trace the mitomycin intermediates that accumulate on an acyl carrier protein (ACP), we here dissect the enzymatic steps for AHBA-GlcN formation and processing to underlie the mitosane structure. Following the N-glycosylation of AHBA with activated N-acetyl-GlcN, deacetylation occurs on ACP to provide AHBA-GlcN. Then, the sugar portion of this N-glycoside is transformed into a linear aminodiol that terminates with an epoxyethane, yielding an ACP-channeled intermediate that is ready for mitosane formation through crosslinking between the AHBA and linearized sugar units. This transformation is unusual and relies on the functional association of a dihydronicotinamide adenine dinucleotide (phosphate)-dependent protein with a radical S-adenosyl-l-methionine protein. Characterization of these ACP-based enzymatic steps for AHBA-GlcN formation and processing sheds light on the poorly understood biosynthetic pathway of mitomycins.
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Affiliation(s)
- Sili Wang
- State Key Laboratory of Bioorganic and Natural Products Chemistry, Shanghai Institute of Organic Chemistry, University of Chinese Academy of Sciences, 345 Lingling Road, Shanghai 200032, China
| | - Yiyuan Cheng
- State Key Laboratory of Bioorganic and Natural Products Chemistry, Shanghai Institute of Organic Chemistry, University of Chinese Academy of Sciences, 345 Lingling Road, Shanghai 200032, China
| | - Xiaofeng Wang
- School of Chemistry and Materials Science, Hangzhou Institute for Advanced Study, University of Chinese Academy of Sciences, 1 Sub-lane Xiangshan, Hangzhou 310024, China
| | - Qian Yang
- State Key Laboratory of Bioorganic and Natural Products Chemistry, Shanghai Institute of Organic Chemistry, University of Chinese Academy of Sciences, 345 Lingling Road, Shanghai 200032, China
| | - Wen Liu
- State Key Laboratory of Bioorganic and Natural Products Chemistry, Shanghai Institute of Organic Chemistry, University of Chinese Academy of Sciences, 345 Lingling Road, Shanghai 200032, China
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8
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Forquet R, Jiang X, Nasser W, Hommais F, Reverchon S, Meyer S. Mapping the Complex Transcriptional Landscape of the Phytopathogenic Bacterium Dickeya dadantii. mBio 2022; 13:e0052422. [PMID: 35491820 PMCID: PMC9239193 DOI: 10.1128/mbio.00524-22] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2022] [Accepted: 04/07/2022] [Indexed: 11/21/2022] Open
Abstract
Dickeya dadantii is a phytopathogenic bacterium that causes soft rot in a wide range of plant hosts worldwide and a model organism for studying virulence gene regulation. The present study provides a comprehensive and annotated transcriptomic map of D. dadantii obtained by a computational method combining five independent transcriptomic data sets: (i) paired-end RNA sequencing (RNA-seq) data for a precise reconstruction of the RNA landscape; (ii) DNA microarray data providing transcriptional responses to a broad variety of environmental conditions; (iii) long-read Nanopore native RNA-seq data for isoform-level transcriptome validation and determination of transcription termination sites; (iv) differential RNA sequencing (dRNA-seq) data for the precise mapping of transcription start sites; (v) in planta DNA microarray data for a comparison of gene expression profiles between in vitro experiments and the early stages of plant infection. Our results show that transcription units sometimes coincide with predicted operons but are generally longer, most of them comprising internal promoters and terminators that generate alternative transcripts of variable gene composition. We characterize the occurrence of transcriptional read-through at terminators, which might play a basal regulation role and explain the extent of transcription beyond the scale of operons. We finally highlight the presence of noncontiguous operons and excludons in the D. dadantii genome, novel genomic arrangements that might contribute to the basal coordination of transcription. The highlighted transcriptional organization may allow D. dadantii to finely adjust its gene expression program for a rapid adaptation to fast-changing environments. IMPORTANCE This is the first transcriptomic map of a Dickeya species. It may therefore significantly contribute to further progress in the field of phytopathogenicity. It is also one of the first reported applications of long-read Nanopore native RNA-seq in prokaryotes. Our findings yield insights into basal rules of coordination of transcription that might be valid for other bacteria and may raise interest in the field of microbiology in general. In particular, we demonstrate that gene expression is coordinated at the scale of transcription units rather than operons, which are larger functional genomic units capable of generating transcripts with variable gene composition for a fine-tuning of gene expression in response to environmental changes. In line with recent studies, our findings indicate that the canonical operon model is insufficient to explain the complexity of bacterial transcriptomes.
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Affiliation(s)
- Raphaël Forquet
- Université de Lyon, INSA-Lyon, Université Claude Bernard Lyon 1, CNRS UMR5240, Laboratoire de Microbiologie, Adaptation, Pathogénie, Villeurbanne, France
| | - Xuejiao Jiang
- Université de Lyon, INSA-Lyon, Université Claude Bernard Lyon 1, CNRS UMR5240, Laboratoire de Microbiologie, Adaptation, Pathogénie, Villeurbanne, France
| | - William Nasser
- Université de Lyon, INSA-Lyon, Université Claude Bernard Lyon 1, CNRS UMR5240, Laboratoire de Microbiologie, Adaptation, Pathogénie, Villeurbanne, France
| | - Florence Hommais
- Université de Lyon, INSA-Lyon, Université Claude Bernard Lyon 1, CNRS UMR5240, Laboratoire de Microbiologie, Adaptation, Pathogénie, Villeurbanne, France
| | - Sylvie Reverchon
- Université de Lyon, INSA-Lyon, Université Claude Bernard Lyon 1, CNRS UMR5240, Laboratoire de Microbiologie, Adaptation, Pathogénie, Villeurbanne, France
| | - Sam Meyer
- Université de Lyon, INSA-Lyon, Université Claude Bernard Lyon 1, CNRS UMR5240, Laboratoire de Microbiologie, Adaptation, Pathogénie, Villeurbanne, France
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9
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Hopf FSM, Roth CD, de Souza EV, Galina L, Czeczot AM, Machado P, Basso LA, Bizarro CV. Bacterial Enoyl-Reductases: The Ever-Growing List of Fabs, Their Mechanisms and Inhibition. Front Microbiol 2022; 13:891610. [PMID: 35814645 PMCID: PMC9260719 DOI: 10.3389/fmicb.2022.891610] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2022] [Accepted: 05/27/2022] [Indexed: 11/13/2022] Open
Abstract
Enoyl-ACP reductases (ENRs) are enzymes that catalyze the last step of the elongation cycle during fatty acid synthesis. In recent years, new bacterial ENR types were discovered, some of them with structures and mechanisms that differ from the canonical bacterial FabI enzymes. Here, we briefly review the diversity of structural and catalytic properties of the canonical FabI and the new FabK, FabV, FabL, and novel ENRs identified in a soil metagenome study. We also highlight recent efforts to use the newly discovered Fabs as targets for drug development and consider the complex evolutionary history of this diverse set of bacterial ENRs.
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Affiliation(s)
- Fernanda S. M. Hopf
- Centro de Pesquisas em Biologia Molecular e Funcional (CPBMF) and Instituto Nacional de Ciência e Tecnologia em Tuberculose (INCT-TB), Pontifícia Universidade Católica do Rio Grande do Sul (PUCRS), Porto Alegre, Brazil
- Programa de Pós-Graduação em Biologia Celular e Molecular, Pontifícia Universidade Católica do Rio Grande do Sul, Porto Alegre, Brazil
| | - Candida D. Roth
- Centro de Pesquisas em Biologia Molecular e Funcional (CPBMF) and Instituto Nacional de Ciência e Tecnologia em Tuberculose (INCT-TB), Pontifícia Universidade Católica do Rio Grande do Sul (PUCRS), Porto Alegre, Brazil
| | - Eduardo V. de Souza
- Centro de Pesquisas em Biologia Molecular e Funcional (CPBMF) and Instituto Nacional de Ciência e Tecnologia em Tuberculose (INCT-TB), Pontifícia Universidade Católica do Rio Grande do Sul (PUCRS), Porto Alegre, Brazil
- Programa de Pós-Graduação em Biologia Celular e Molecular, Pontifícia Universidade Católica do Rio Grande do Sul, Porto Alegre, Brazil
| | - Luiza Galina
- Centro de Pesquisas em Biologia Molecular e Funcional (CPBMF) and Instituto Nacional de Ciência e Tecnologia em Tuberculose (INCT-TB), Pontifícia Universidade Católica do Rio Grande do Sul (PUCRS), Porto Alegre, Brazil
- Programa de Pós-Graduação em Medicina e Ciências da Saúde, Pontifícia Universidade Católica do Rio Grande do Sul, Porto Alegre, Brazil
| | - Alexia M. Czeczot
- Centro de Pesquisas em Biologia Molecular e Funcional (CPBMF) and Instituto Nacional de Ciência e Tecnologia em Tuberculose (INCT-TB), Pontifícia Universidade Católica do Rio Grande do Sul (PUCRS), Porto Alegre, Brazil
- Programa de Pós-Graduação em Medicina e Ciências da Saúde, Pontifícia Universidade Católica do Rio Grande do Sul, Porto Alegre, Brazil
| | - Pablo Machado
- Centro de Pesquisas em Biologia Molecular e Funcional (CPBMF) and Instituto Nacional de Ciência e Tecnologia em Tuberculose (INCT-TB), Pontifícia Universidade Católica do Rio Grande do Sul (PUCRS), Porto Alegre, Brazil
- Programa de Pós-Graduação em Biologia Celular e Molecular, Pontifícia Universidade Católica do Rio Grande do Sul, Porto Alegre, Brazil
| | - Luiz A. Basso
- Centro de Pesquisas em Biologia Molecular e Funcional (CPBMF) and Instituto Nacional de Ciência e Tecnologia em Tuberculose (INCT-TB), Pontifícia Universidade Católica do Rio Grande do Sul (PUCRS), Porto Alegre, Brazil
- Programa de Pós-Graduação em Biologia Celular e Molecular, Pontifícia Universidade Católica do Rio Grande do Sul, Porto Alegre, Brazil
- Programa de Pós-Graduação em Medicina e Ciências da Saúde, Pontifícia Universidade Católica do Rio Grande do Sul, Porto Alegre, Brazil
| | - Cristiano V. Bizarro
- Centro de Pesquisas em Biologia Molecular e Funcional (CPBMF) and Instituto Nacional de Ciência e Tecnologia em Tuberculose (INCT-TB), Pontifícia Universidade Católica do Rio Grande do Sul (PUCRS), Porto Alegre, Brazil
- Programa de Pós-Graduação em Biologia Celular e Molecular, Pontifícia Universidade Católica do Rio Grande do Sul, Porto Alegre, Brazil
- *Correspondence: Cristiano V. Bizarro,
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10
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Joyner PM, Tran DP, Zenaidee MA, Loo JA. Characterization of protein-ligand binding interactions of enoyl-ACP reductase (FabI) by native MS reveals allosteric effects of coenzymes and the inhibitor triclosan. Protein Sci 2022; 31:568-579. [PMID: 34882866 PMCID: PMC8862436 DOI: 10.1002/pro.4252] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2021] [Revised: 12/06/2021] [Accepted: 12/07/2021] [Indexed: 01/08/2023]
Abstract
The enzyme enoyl-ACP reductase (also called FabI in bacteria) is an essential member of the fatty acid synthase II pathway in plants and bacteria. This enzyme is the target of the antibacterial drug triclosan and has been the subject of extensive studies for the past 20 years. Despite the large number of reports describing the biochemistry of this enzyme, there have been no studies that provided direct observation of the protein and its various ligands. Here we describe the use of native MS to characterize the protein-ligand interactions of FabI with its coenzymes NAD+ and NADH and with the inhibitor triclosan. Measurements of the gas-phase affinities of the enzyme for these ligands yielded values that are in close agreement with solution-phase affinity measurements. Additionally, FabI is a homotetramer and we were able to measure the affinity of each subunit for each coenzyme, which revealed that both coenzymes exhibit a positive homotropic allosteric effect. An allosteric effect was also observed in association with the inhibitor triclosan. These observations provide new insights into this well-studied enzyme and suggest that there may still be gaps in the existing mechanistic models that explain FabI inhibition.
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Affiliation(s)
- P. Matthew Joyner
- Natural Science DivisionPepperdine UniversityMalibuCaliforniaUSA
- Department of Chemistry & BiochemistryUniversity of California‐Los AngelesLos AngelesCaliforniaUSA
| | - Denise P. Tran
- Department of Chemistry & BiochemistryUniversity of California‐Los AngelesLos AngelesCaliforniaUSA
- Sydney Mass SpectrometryThe University of Sydney, Charles Perkins CentreCamperdownNew South WalesAustralia
| | - Muhammad A. Zenaidee
- Department of Chemistry & BiochemistryUniversity of California‐Los AngelesLos AngelesCaliforniaUSA
- Australian Proteome Analysis FacilityMacquarie UniversityMacquarieNew South WalesAustralia
| | - Joseph A. Loo
- Department of Chemistry & BiochemistryUniversity of California‐Los AngelesLos AngelesCaliforniaUSA
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11
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Abstract
Ceragenins are a family of synthetic amphipathic molecules designed to mimic the properties of naturally occurring cationic antimicrobial peptides (CAMPs). Although ceragenins have potent antimicrobial activity, whether their mode of action is similar to that of CAMPs has remained elusive. Here, we reported the results of a comparative study of the bacterial responses to two well-studied CAMPs, LL37 and colistin, and two ceragenins with related structures, CSA13 and CSA131. Using transcriptomic and proteomic analyses, we found that Escherichia coli responded similarly to both CAMPs and ceragenins by inducing a Cpx envelope stress response. However, whereas E. coli exposed to CAMPs increased expression of genes involved in colanic acid biosynthesis, bacteria exposed to ceragenins specifically modulated functions related to phosphate transport, indicating distinct mechanisms of action between these two classes of molecules. Although traditional genetic approaches failed to identify genes that confer high-level resistance to ceragenins, using a Clustered Regularly Interspaced Short Palindromic Repeats interference (CRISPRi) approach we identified E. coli essential genes that when knocked down modify sensitivity to these molecules. Comparison of the essential gene-antibiotic interactions for each of the CAMPs and ceragenins identified both overlapping and distinct dependencies for their antimicrobial activities. Overall, this study indicated that, while some bacterial responses to ceragenins overlap those induced by naturally occurring CAMPs, these synthetic molecules target the bacterial envelope using a distinctive mode of action. IMPORTANCE The development of novel antibiotics is essential because the current arsenal of antimicrobials will soon be ineffective due to the widespread occurrence of antibiotic resistance. The development of naturally occurring cationic antimicrobial peptides (CAMPs) for therapeutics to combat antibiotic resistance has been hampered by high production costs and protease sensitivity, among other factors. The ceragenins are a family of synthetic CAMP mimics that kill a broad spectrum of bacterial species but are less expensive to produce, resistant to proteolytic degradation, and seemingly resistant to the development of high-level resistance. Determining how ceragenins function may identify new essential biological pathways of bacteria that are less prone to the development of resistance and will further our understanding of the design principles for maximizing the effects of synthetic CAMPs.
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12
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Helicobacter pylori FabX contains a [4Fe-4S] cluster essential for unsaturated fatty acid synthesis. Nat Commun 2021; 12:6932. [PMID: 34836944 PMCID: PMC8626469 DOI: 10.1038/s41467-021-27148-0] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2021] [Accepted: 10/29/2021] [Indexed: 11/08/2022] Open
Abstract
Unsaturated fatty acids (UFAs) are essential for functional membrane phospholipids in most bacteria. The bifunctional dehydrogenase/isomerase FabX is an essential UFA biosynthesis enzyme in the widespread human pathogen Helicobacter pylori, a bacterium etiologically related to 95% of gastric cancers. Here, we present the crystal structures of FabX alone and in complexes with an octanoyl-acyl carrier protein (ACP) substrate or with holo-ACP. FabX belongs to the nitronate monooxygenase (NMO) flavoprotein family but contains an atypical [4Fe-4S] cluster absent in all other family members characterized to date. FabX binds ACP via its positively charged α7 helix that interacts with the negatively charged α2 and α3 helices of ACP. We demonstrate that the [4Fe-4S] cluster potentiates FMN oxidation during dehydrogenase catalysis, generating superoxide from an oxygen molecule that is locked in an oxyanion hole between the FMN and the active site residue His182. Both the [4Fe-4S] and FMN cofactors are essential for UFA synthesis, and the superoxide is subsequently excreted by H. pylori as a major resource of peroxide which may contribute to its pathogenic function in the corrosion of gastric mucosa.
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13
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Quantifying the propagation of parametric uncertainty on flux balance analysis. Metab Eng 2021; 69:26-39. [PMID: 34718140 DOI: 10.1016/j.ymben.2021.10.012] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2021] [Revised: 10/21/2021] [Accepted: 10/24/2021] [Indexed: 12/27/2022]
Abstract
Flux balance analysis (FBA) and associated techniques operating on stoichiometric genome-scale metabolic models play a central role in quantifying metabolic flows and constraining feasible phenotypes. At the heart of these methods lie two important assumptions: (i) the biomass precursors and energy requirements neither change in response to growth conditions nor environmental/genetic perturbations, and (ii) metabolite production and consumption rates are equal at all times (i.e., steady-state). Despite the stringency of these two assumptions, FBA has been shown to be surprisingly robust at predicting cellular phenotypes. In this paper, we formally assess the impact of these two assumptions on FBA results by quantifying how uncertainty in biomass reaction coefficients, and departures from steady-state due to temporal fluctuations could propagate to FBA results. In the first case, conditional sampling of parameter space is required to re-weigh the biomass reaction so as the molecular weight remains equal to 1 g mmol-1, and in the second case, metabolite (and elemental) pool conservation must be imposed under temporally varying conditions. Results confirm the importance of enforcing the aforementioned constraints and explain the robustness of FBA biomass yield predictions.
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14
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Zhang F, Li Z, Zhou J, Gu Y, Tan X. Comparative study on fruit development and oil synthesis in two cultivars of Camellia oleifera. BMC PLANT BIOLOGY 2021; 21:348. [PMID: 34301189 PMCID: PMC8299657 DOI: 10.1186/s12870-021-03114-2] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 01/15/2021] [Accepted: 06/22/2021] [Indexed: 06/13/2023]
Abstract
BACKGROUND The oil-tea tree (Camellia oleifera Abel.) is a woody tree species that produces edible oil in the seed. C. oleifera oil has high nutritional value and is also an important raw material for medicine and cosmetics. In China, due to the uncertainty on maturity period and oil synthesis mechanism of many C. oleifera cultivars, growers may harvest fruits prematurely, which could not maximize fruit and oil yields. In this study, our objective was to explore the mechanism and differences of oil synthesis between two Camellia oleifera cultivars for a precise definition of the fruit ripening period and the selection of appropriate cultivars. RESULTS The results showed that 'Huashuo' had smaller fruits and seeds, lower dry seed weight and lower expression levels of fatty acid biosynthesis genes in July. We could not detect the presence of oil and oil bodies in 'Huashuo' seeds until August, and oil and oil bodies were detected in 'Huajin' seeds in July. Moreover, 'Huashuo' seeds were not completely blackened in October with up to 60.38% of water and approximately 37.98% of oil in seed kernels whose oil content was much lower than normal mature seed kernels. The oil bodies in seed endosperm cells of 'Huajin' were always higher than those of 'Huashuo' from July to October. CONCLUSION Our results confirmed that C. oleifera 'Huashuo' fruits matured at a lower rate compared to 'Huajin' fruits and that 'Huajin' seeds entered the oil synthesis period earlier than 'Huashuo' seeds. Moreover, 'Huashuo' fruits did not mature during the Frost's Descent period (October 23-24 each year).
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Affiliation(s)
- Fanhang Zhang
- Key Laboratory of Cultivation and Protection for Non-Wood Forest Trees, Ministry of Education, Central South University of Forestry and Technology, Changsha, 410004 Hunan China
- Centre of Pear Engineering Technology Research, State Key Laboratory of Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University, Nanjing, 210095 Jiangsu China
| | - Ze Li
- Key Laboratory of Cultivation and Protection for Non-Wood Forest Trees, Ministry of Education, Central South University of Forestry and Technology, Changsha, 410004 Hunan China
- Engineering Technology Research Center of Southern Hilly and Mountainous Ecological Non-Wood Forestry Industry of Hunan Province, Central South University of Forestry and Technology, Changsha, 410004 Hunan China
| | - Junqin Zhou
- Key Laboratory of Cultivation and Protection for Non-Wood Forest Trees, Ministry of Education, Central South University of Forestry and Technology, Changsha, 410004 Hunan China
- Engineering Technology Research Center of Southern Hilly and Mountainous Ecological Non-Wood Forestry Industry of Hunan Province, Central South University of Forestry and Technology, Changsha, 410004 Hunan China
| | - Yiyang Gu
- Key Laboratory of Cultivation and Protection for Non-Wood Forest Trees, Ministry of Education, Central South University of Forestry and Technology, Changsha, 410004 Hunan China
- Engineering Technology Research Center of Southern Hilly and Mountainous Ecological Non-Wood Forestry Industry of Hunan Province, Central South University of Forestry and Technology, Changsha, 410004 Hunan China
| | - Xiaofeng Tan
- Key Laboratory of Cultivation and Protection for Non-Wood Forest Trees, Ministry of Education, Central South University of Forestry and Technology, Changsha, 410004 Hunan China
- Engineering Technology Research Center of Southern Hilly and Mountainous Ecological Non-Wood Forestry Industry of Hunan Province, Central South University of Forestry and Technology, Changsha, 410004 Hunan China
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15
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Guest RL, Rutherford ST, Silhavy TJ. Border Control: Regulating LPS Biogenesis. Trends Microbiol 2021; 29:334-345. [PMID: 33036869 PMCID: PMC7969359 DOI: 10.1016/j.tim.2020.09.008] [Citation(s) in RCA: 34] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2020] [Revised: 09/11/2020] [Accepted: 09/14/2020] [Indexed: 12/20/2022]
Abstract
The outer membrane (OM) is a defining feature of Gram-negative bacteria that serves as a permeability barrier and provides rigidity to the cell. Critical to OM function is establishing and maintaining an asymmetrical bilayer structure with phospholipids in the inner leaflet and the complex glycolipid lipopolysaccharide (LPS) in the outer leaflet. Cells ensure this asymmetry by regulating the biogenesis of lipid A, the conserved and essential anchor of LPS. Here we review the consequences of disrupting the regulatory components that control lipid A biogenesis, focusing on the rate-limiting step performed by LpxC. Dissection of these processes provides critical insights into bacterial physiology and potential new targets for antibiotics able to overcome rapidly spreading resistance mechanisms.
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Affiliation(s)
- Randi L Guest
- Department of Molecular Biology, Princeton University, Princeton, NJ, USA
| | - Steven T Rutherford
- Department of Infectious Diseases, Genentech Inc., South San Francisco, CA, USA
| | - Thomas J Silhavy
- Department of Molecular Biology, Princeton University, Princeton, NJ, USA.
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16
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Zheng Y, Dong H, Bai X, Cui H, Li MJ, Wu HY, Zhang K. Effects of lysine 2-hydroxyisobutyrylation on bacterial FabI activity and resistance to triclosan. Biochimie 2021; 182:197-205. [PMID: 33485933 DOI: 10.1016/j.biochi.2021.01.011] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2020] [Revised: 01/14/2021] [Accepted: 01/16/2021] [Indexed: 10/22/2022]
Abstract
Lysine 2-hydroxyisobutyrylation (Khib) is a novel protein posttranslational modification conserved in eukaryotes and prokaryotes. However, the biological significance of Khib remains largely unknown. Here, through screening the proteome-wide Khib modification sites in bacteria using a bioinformatic method, we identified a potential Khib site (K201hib) targeted by de-2-hyroxyisobutyrylase CobB at the substrate-binding site of FabI, an enoyl-acyl carry protein reductase (EnvM or FabI) in fatty acid biosynthesis pathway. First, we confirmed that the previously identified de-2-hyroxyisobutyrylase CobB can remove Khib of FabI in an in vitro experiment. To investigate the biological effects of the Khib on FabI's activity, amino acid substitutes were introduced to the modification sites of the protein of E. coli origin to mimic modified/unmodified status. We found that the mutant mimicking K201hib reduced FabI activity with decreased Michaelis constant (Km) and catalytic turnover number (kcat), while the mutant mimicking the unmodified form and the recombinant wild-type protein treated with CobB exhibited increased activity. However, the dissociation constant (KD) between FabI and NADH was not affected by the mutation mimicking the modification, suggesting that K201hib didn't alter the binding between NADH and FabI. We also found that K201hib tended to increase the resistance of E. coli to triclosan (TCL), a widely-used antibiotics targeting FabI. Taken together, this study identified the regulatory role of Khib on FabI activity and pointed to a novel mechanism related to antibiotic resistance.
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Affiliation(s)
- Yiqiang Zheng
- School of Pharmaceutical Science and Technology, Tianjin University, Tianjin, China
| | - Hanyang Dong
- The Province and Ministry Co-sponsored Collaborative Innovation Center for Medical Epigenetics, Tianjin Key Laboratory of Medical Epigenetics, Key Laboratory of Immune Microenvironment and Disease (Ministry of Education), Department of Biochemistry and Molecular Biology, Tianjin Medical University, Tianjin, 300070, China
| | - Xue Bai
- The Province and Ministry Co-sponsored Collaborative Innovation Center for Medical Epigenetics, Tianjin Key Laboratory of Medical Epigenetics, Key Laboratory of Immune Microenvironment and Disease (Ministry of Education), Department of Biochemistry and Molecular Biology, Tianjin Medical University, Tianjin, 300070, China
| | - Hui Cui
- Department of Pharmacology, Collaborative Innovation Center of Tianjin for Medical Epigenetics, Tianjin Key Laboratory of Medical Epigenetics, School of Basic Medical Sciences, Tianjin Medical University, Tianjin, China
| | - Mulin Jun Li
- Department of Pharmacology, Collaborative Innovation Center of Tianjin for Medical Epigenetics, Tianjin Key Laboratory of Medical Epigenetics, School of Basic Medical Sciences, Tianjin Medical University, Tianjin, China
| | - Hui-Yuan Wu
- School of Pharmaceutical Science and Technology, Tianjin University, Tianjin, China.
| | - Kai Zhang
- The Province and Ministry Co-sponsored Collaborative Innovation Center for Medical Epigenetics, Tianjin Key Laboratory of Medical Epigenetics, Key Laboratory of Immune Microenvironment and Disease (Ministry of Education), Department of Biochemistry and Molecular Biology, Tianjin Medical University, Tianjin, 300070, China.
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17
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Ye Z, Moreb EA, Li S, Lebeau J, Menacho-Melgar R, Munson M, Lynch MD. Escherichia coli Cas1/2 Endonuclease Complex Modifies Self-Targeting CRISPR/Cascade Spacers Reducing Silencing Guide Stability. ACS Synth Biol 2021; 10:29-37. [PMID: 33331764 DOI: 10.1021/acssynbio.0c00398] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
CRISPR-based interference has become common in various applications from genetic circuits to dynamic metabolic control. In E. coli, the native CRISPR Cascade system can be utilized for silencing by deletion of the cas3 nuclease along with expression of guide RNA arrays, where multiple genes can be silenced from a single transcript. We notice the loss of spacer sequences from guide arrays utilized for dynamic silencing. We report that unstable guide arrays are due to expression of the Cas1/2 endonuclease complex. We propose a model wherein basal Cas1/2 endonuclease activity results in the loss of spacers from guide arrays. Subsequently, mutant guide arrays can be amplified through selection. Replacing a constitutive promoter driving Cascade complex expression with a tightly controlled inducible promoter improves guide array stability, while minimizing leaky gene silencing. Additionally, these results demonstrate the potential of Cas1/2 mediated guide deletion as a mechanism to avoid CRISPR based autoimmunity.
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Affiliation(s)
- Zhixia Ye
- Department of Biomedical Engineering, Duke University, Durham, North Carolina 27708, United States
- DMC Biotechnologies, Inc., Durham, North Carolina 27701, United States
| | - Eirik A Moreb
- Department of Biomedical Engineering, Duke University, Durham, North Carolina 27708, United States
| | - Shuai Li
- DMC Biotechnologies, Inc., Durham, North Carolina 27701, United States
- Department of Chemistry, Duke University, Durham, North Carolina 27708, United States
| | - Juliana Lebeau
- Department of Biomedical Engineering, Duke University, Durham, North Carolina 27708, United States
| | - Romel Menacho-Melgar
- Department of Biomedical Engineering, Duke University, Durham, North Carolina 27708, United States
| | - Matthew Munson
- DMC Biotechnologies, Inc., Durham, North Carolina 27701, United States
| | - Michael D Lynch
- Department of Biomedical Engineering, Duke University, Durham, North Carolina 27708, United States
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18
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Shahriar S, Ahsan T, Khan A, Akhteruzzaman S, Shehreen S, Sajib AA. Aspartame, acesulfame K and sucralose- influence on the metabolism of Escherichia coli. Metabol Open 2020; 8:100072. [PMID: 33336183 PMCID: PMC7732866 DOI: 10.1016/j.metop.2020.100072] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2020] [Revised: 11/18/2020] [Accepted: 12/02/2020] [Indexed: 12/13/2022] Open
Abstract
Gut microbes play a crucial role in the maintenance of human health. Components in the diet of the host affect their metabolism and diversity. Here, we investigated the influences of three commonly used non-caloric artificial sweeteners-aspartame, acesulfame K and sucralose-on the growth and metabolism of an omnipresent gut microbe Escherichia coli K-12. Methods: Growth of E. coli in the presence of aspartame, acesulfame K and sucralose in media was assessed and the influences of these artificial sweeteners on metabolism were investigated by relative expression analysis of genes encoding the rate limiting steps of important metabolic pathways as well as their global metabolomic profiles. Results: As a whole, E. coli growth was inhibited by aspartame and induced by acesulfame potassium, while the effect of sucralose on growth was less prominent. Although the expressions of multiple key enzymes that regulate important metabolic pathways were significantly altered by all three sweeteners, acesulfame K caused the most notable changes in this regard. In multivariate analysis with the metabolite profiles, the sucralose-treated cells clustered the closest to the untreated cells, while the acesulfame potassium treated cells were the most distant. These sweeteners affect multiple metabolic pathways in E. coli, which include propanoate, phosphonate, phosphinate and fatty acid metabolism, pentose phosphate pathway, and biosynthesis of several amino acids including lysine and the aromatic amino acids. Similar to the gene expression pattern, acesulfame potassium treated E. coli showed the largest deviation in their metabolite profiles compared to the untreated cells.
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Affiliation(s)
- Shayan Shahriar
- Department of Genetic Engineering & Biotechnology, University of Dhaka, Dhaka, Bangladesh
| | - Tamim Ahsan
- Department of Genetic Engineering & Biotechnology, Bangabandhu Sheikh Mujibur Rahman Maritime University, Dhaka, Bangladesh
| | - Abira Khan
- Department of Genetic Engineering & Biotechnology, University of Dhaka, Dhaka, Bangladesh
| | - Sharif Akhteruzzaman
- Department of Genetic Engineering & Biotechnology, University of Dhaka, Dhaka, Bangladesh
| | - Saadlee Shehreen
- Department of Genetic Engineering & Biotechnology, University of Dhaka, Dhaka, Bangladesh
| | - Abu Ashfaqur Sajib
- Department of Genetic Engineering & Biotechnology, University of Dhaka, Dhaka, Bangladesh
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19
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Rana P, Ghouse SM, Akunuri R, Madhavi YV, Chopra S, Nanduri S. FabI (enoyl acyl carrier protein reductase) - A potential broad spectrum therapeutic target and its inhibitors. Eur J Med Chem 2020; 208:112757. [PMID: 32883635 DOI: 10.1016/j.ejmech.2020.112757] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2020] [Revised: 07/30/2020] [Accepted: 08/11/2020] [Indexed: 12/11/2022]
Abstract
Development of new anti-bacterial agents acting upon underexploited targets and thus evading known mechanisms of resistance is the need of the hour. The highly conserved and distinct bacterial fatty acid biosynthesis pathway (FAS-II), presents a validated and yet relatively underexploited target for drug discovery. FabI and its isoforms (FabL, FabK, FabV and InhA) are essential enoyl-ACP reductases present in several microorganisms. In addition, the components of the FAS-II pathway are distinct from the multi-enzyme FAS-I complex found in mammals. Thus, inhibition of FabI and its isoforms is anticipated to result in broad-spectrum antibacterial activity. Several research groups from industry and academic laboratories have devoted significant efforts to develop effective FabI-targeting antibiotics, which are currently in various stages of clinical development for the treatment of multi-drug resistant bacterial infections. This review summarizes all the natural as well as synthetic inhibitors of gram-positive and gram-negative enoyl ACP reductases (FabI). The knowledge of the reported inhibitors can aid in the development of broad-spectrum antibacterials specifically targeting FabI enzymes from S. aureus, S. epidermidis, B. anthracis, B. cereus, E. coli, P. aeruginosa, P. falciparum and M. tuberculosis.
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Affiliation(s)
- Preeti Rana
- Department of Medicinal Chemistry, National Institute of Pharmaceutical Education and Research (NIPER), Hyderabad, 500 037, India
| | - Shaik Mahammad Ghouse
- Department of Medicinal Chemistry, National Institute of Pharmaceutical Education and Research (NIPER), Hyderabad, 500 037, India
| | - Ravikumar Akunuri
- Department of Medicinal Chemistry, National Institute of Pharmaceutical Education and Research (NIPER), Hyderabad, 500 037, India
| | - Y V Madhavi
- Department of Medicinal Chemistry, National Institute of Pharmaceutical Education and Research (NIPER), Hyderabad, 500 037, India
| | - Sidharth Chopra
- Division of Microbiology, CSIR-Central Drug Research Institute, Sitapur Road, Sector 10, Janakipuram Extension, Lucknow, 226 031, Uttar Pradesh, India.
| | - Srinivas Nanduri
- Department of Medicinal Chemistry, National Institute of Pharmaceutical Education and Research (NIPER), Hyderabad, 500 037, India.
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20
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Yadav S, Mandal H, Saravanan V, Das P, Singh SK. In vitro and in silico analysis of L. donovani enoyl acyl carrier protein reductase - A possible drug target. J Biomol Struct Dyn 2020; 39:6056-6069. [PMID: 32762412 DOI: 10.1080/07391102.2020.1802337] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
The emergence of increased resistance to the available drugs has created a situation that demands to find out more specific molecular drug targets for Leishmaniasis. The enoyl acyl carrier protein reductase (ENR), a regulatory enzyme in type II fatty acid synthesis, was confirmed as a novel drug target and triclosan as its specific inhibitor in many microorganisms. In this study, the triclosan was tested for the leishmanicidal property against Leishmania donovani (L. donovani) and the results of in vitro and ex vivo drug assays on promastigotes and amastigotes showed that triclosan possessed antileishmanial activity with a half minimal inhibitory concentration (IC50) of 30 µM. Consequently, adopting in silico approach, we have tested the triclosan's ability to bind with the L. donovani enoyl acyl carrier protein reductase (LdENR). The 3D structure of LdENR was modelled, triclosan and cofactors were docked in LdENR model and molecular dynamic simulations were performed to observe the protein-ligands interactions, stability, compactness and binding energy calculation of the ligands-LdENR complexes. The observation showed that triclosan stably interacted with LdENR in presence of both the cofactors (NADPH and NADH), however, simulation results favor NADH as a preferred co-factor for LdENR. These results support that the reduction of L. donovani growth in the in vitro and ex vivo drug assays may be due to the interaction of triclosan with LdENR, which should be confirmed through enzymatic assays. The results of this study suggest that LdENR could be a potential drug target and triclosan as a lead for Leishmaniasis.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Shalini Yadav
- Department of Microbiology, Rajendra Memorial Research Institute of Medical Sciences, ICMR, Patna, India
| | - Haraprasad Mandal
- Department of Microbiology, Rajendra Memorial Research Institute of Medical Sciences, ICMR, Patna, India.,Department of Biotechnology, National Institute of Pharmaceutical Education and Research, Hajipur, India
| | - Vijayakumar Saravanan
- Division of Bioinformatics, Rajendra Memorial Research Institute of Medical Sciences, ICMR, Patna, India
| | - Pradeep Das
- Division of Molecular Biology, Rajendra Memorial Research Institute of Medical Sciences (RMRIMS), ICMR, Patna, India
| | - Shubhankar Kumar Singh
- Department of Microbiology, Rajendra Memorial Research Institute of Medical Sciences, ICMR, Patna, India
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21
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About lipid metabolism in Hermetia illucens (L. 1758): on the origin of fatty acids in prepupae. Sci Rep 2020; 10:11916. [PMID: 32680992 PMCID: PMC7368053 DOI: 10.1038/s41598-020-68784-8] [Citation(s) in RCA: 52] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2020] [Accepted: 07/02/2020] [Indexed: 01/09/2023] Open
Abstract
Although increasingly targeted in animal nutrition, black soldier fly larvae or prepupae (BSF, Hermetia illucens L. 1758) require the characterization and modulation of their fatty acid profile to become fully integrated within the feed sector. This improvement will only be possible by the understanding of underlaying biochemical pathways of fatty acid synthesis in BSF. In this study, we hypothesized a labelling of de novo synthesized fatty acids in BSF by the incorporation of deuterated water (D2O) in their feed. Three batches of fifty larvae were reared on two diets with different polyunsaturated fatty acid profiles moistened with 40% of H2O or D2O: chicken feed or 40% of chicken feed and 60% of flax cake. Although the occurrence of D2O in insect feed increased the larval development time and decreased prepupal weight, it was possible to track the biosynthesis of fatty acids through deuterium labelling. Some fatty acids (decanoic, lauric or myristic acid) were exclusively present in their deuterated form while others (palmitic, palmitoleic or oleic acid) were found in two forms (deuterated or not) indicating that BSF can partially produce these fatty acids via biosynthesis pathways and not only by bioaccumulation from the diet. These results suggest the importance of carbohydrates as a source of acetyl-CoA in the constitution of the BSF fatty acid profile but also the potential importance of specific enzymes (e.g. thioesterase II or Δ12 fat2 desaturase) in BSF fatty acid metabolism. Finally, nearly no deuterated polyunsaturated fatty acids were found in BSF fed with deuterium confirming that BSF is not able to produce these types of fatty acids. Despite the high levels of linolenic acid in flax-enriched diets, BSF will simply bioaccumulate around 13% of this fatty acid and will metabolize approximately two-thirds of it into saturated fatty acids as lauric or myristic acid.
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22
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Fage CD, Lathouwers T, Vanmeert M, Gao L, Vrancken K, Lammens E, Weir ANM, Degroote R, Cuppens H, Kosol S, Simpson TJ, Crump MP, Willis CL, Herdewijn P, Lescrinier E, Lavigne R, Anné J, Masschelein J. The Kalimantacin Polyketide Antibiotics Inhibit Fatty Acid Biosynthesis in
Staphylococcus aureus
by Targeting the Enoyl‐Acyl Carrier Protein Binding Site of FabI. Angew Chem Int Ed Engl 2020. [DOI: 10.1002/ange.201915407] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Affiliation(s)
| | - Thomas Lathouwers
- Laboratory of Gene Technology KU Leuven Kasteelpark Arenberg 21, PO Box 2462 3001 Heverlee Belgium
| | - Michiel Vanmeert
- Laboratory for Medicinal Chemistry Rega Institute for Medical Research Herestraat 49, PO Box 1041 3000 Leuven Belgium
| | - Ling‐Jie Gao
- Laboratory for Medicinal Chemistry Rega Institute for Medical Research Herestraat 49, PO Box 1041 3000 Leuven Belgium
| | - Kristof Vrancken
- Laboratory of Molecular Bacteriology Rega Institute for Medical Research Herestraat 49, PO Box 1037 3000 Leuven Belgium
| | - Eveline‐Marie Lammens
- Laboratory of Gene Technology KU Leuven Kasteelpark Arenberg 21, PO Box 2462 3001 Heverlee Belgium
| | - Angus N. M. Weir
- School of Chemistry, Cantock's Close University of Bristol Bristol BS8 1TS UK
| | - Ruben Degroote
- Laboratory of Gene Technology KU Leuven Kasteelpark Arenberg 21, PO Box 2462 3001 Heverlee Belgium
| | - Harry Cuppens
- Department of Human Genetics KU Leuven Herestraat 49 3000 Leuven Belgium
| | - Simone Kosol
- Department of Chemistry University of Warwick Coventry CV4 7AL UK
| | - Thomas J. Simpson
- School of Chemistry, Cantock's Close University of Bristol Bristol BS8 1TS UK
| | - Matthew P. Crump
- School of Chemistry, Cantock's Close University of Bristol Bristol BS8 1TS UK
| | - Christine L. Willis
- School of Chemistry, Cantock's Close University of Bristol Bristol BS8 1TS UK
| | - Piet Herdewijn
- Laboratory for Medicinal Chemistry Rega Institute for Medical Research Herestraat 49, PO Box 1041 3000 Leuven Belgium
| | - Eveline Lescrinier
- Laboratory for Medicinal Chemistry Rega Institute for Medical Research Herestraat 49, PO Box 1041 3000 Leuven Belgium
| | - Rob Lavigne
- Laboratory of Gene Technology KU Leuven Kasteelpark Arenberg 21, PO Box 2462 3001 Heverlee Belgium
| | - Jozef Anné
- Laboratory of Molecular Bacteriology Rega Institute for Medical Research Herestraat 49, PO Box 1037 3000 Leuven Belgium
| | - Joleen Masschelein
- Department of Chemistry University of Warwick Coventry CV4 7AL UK
- Laboratory for Medicinal Chemistry Rega Institute for Medical Research Herestraat 49, PO Box 1041 3000 Leuven Belgium
- Laboratory for Biomolecular Discovery and Engineering KU Leuven Kasteelpark Arenberg 31, box 2438 3001 Heverlee Belgium
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23
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Fage CD, Lathouwers T, Vanmeert M, Gao L, Vrancken K, Lammens E, Weir ANM, Degroote R, Cuppens H, Kosol S, Simpson TJ, Crump MP, Willis CL, Herdewijn P, Lescrinier E, Lavigne R, Anné J, Masschelein J. The Kalimantacin Polyketide Antibiotics Inhibit Fatty Acid Biosynthesis in
Staphylococcus aureus
by Targeting the Enoyl‐Acyl Carrier Protein Binding Site of FabI. Angew Chem Int Ed Engl 2020; 59:10549-10556. [DOI: 10.1002/anie.201915407] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2019] [Revised: 02/17/2020] [Indexed: 01/07/2023]
Affiliation(s)
| | - Thomas Lathouwers
- Laboratory of Gene Technology KU Leuven Kasteelpark Arenberg 21, PO Box 2462 3001 Heverlee Belgium
| | - Michiel Vanmeert
- Laboratory for Medicinal Chemistry Rega Institute for Medical Research Herestraat 49, PO Box 1041 3000 Leuven Belgium
| | - Ling‐Jie Gao
- Laboratory for Medicinal Chemistry Rega Institute for Medical Research Herestraat 49, PO Box 1041 3000 Leuven Belgium
| | - Kristof Vrancken
- Laboratory of Molecular Bacteriology Rega Institute for Medical Research Herestraat 49, PO Box 1037 3000 Leuven Belgium
| | - Eveline‐Marie Lammens
- Laboratory of Gene Technology KU Leuven Kasteelpark Arenberg 21, PO Box 2462 3001 Heverlee Belgium
| | - Angus N. M. Weir
- School of Chemistry, Cantock's Close University of Bristol Bristol BS8 1TS UK
| | - Ruben Degroote
- Laboratory of Gene Technology KU Leuven Kasteelpark Arenberg 21, PO Box 2462 3001 Heverlee Belgium
| | - Harry Cuppens
- Department of Human Genetics KU Leuven Herestraat 49 3000 Leuven Belgium
| | - Simone Kosol
- Department of Chemistry University of Warwick Coventry CV4 7AL UK
| | - Thomas J. Simpson
- School of Chemistry, Cantock's Close University of Bristol Bristol BS8 1TS UK
| | - Matthew P. Crump
- School of Chemistry, Cantock's Close University of Bristol Bristol BS8 1TS UK
| | - Christine L. Willis
- School of Chemistry, Cantock's Close University of Bristol Bristol BS8 1TS UK
| | - Piet Herdewijn
- Laboratory for Medicinal Chemistry Rega Institute for Medical Research Herestraat 49, PO Box 1041 3000 Leuven Belgium
| | - Eveline Lescrinier
- Laboratory for Medicinal Chemistry Rega Institute for Medical Research Herestraat 49, PO Box 1041 3000 Leuven Belgium
| | - Rob Lavigne
- Laboratory of Gene Technology KU Leuven Kasteelpark Arenberg 21, PO Box 2462 3001 Heverlee Belgium
| | - Jozef Anné
- Laboratory of Molecular Bacteriology Rega Institute for Medical Research Herestraat 49, PO Box 1037 3000 Leuven Belgium
| | - Joleen Masschelein
- Department of Chemistry University of Warwick Coventry CV4 7AL UK
- Laboratory for Medicinal Chemistry Rega Institute for Medical Research Herestraat 49, PO Box 1041 3000 Leuven Belgium
- Laboratory for Biomolecular Discovery and Engineering KU Leuven Kasteelpark Arenberg 31, box 2438 3001 Heverlee Belgium
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24
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Kim SH, Khan R, Choi K, Lee SW, Rhee S. A triclosan-resistance protein from the soil metagenome is a novel enoyl-acyl carrier protein reductase: Structure-guided functional analysis. FEBS J 2020; 287:4710-4728. [PMID: 32112503 DOI: 10.1111/febs.15267] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2019] [Revised: 02/05/2020] [Accepted: 02/27/2020] [Indexed: 11/28/2022]
Abstract
The synthetic biocide triclosan targets enoyl-acyl carrier protein reductase(s) (ENR) in bacterial type II fatty acid biosynthesis. Screening and sequence analyses of the triclosan resistome from the soil metagenome identified a variety of triclosan-resistance ENRs. Interestingly, the mode of triclosan resistance by one hypothetical protein was elusive, mainly due to a lack of sequence similarity with other proteins that mediate triclosan resistance. Here, we carried out a structure-based function prediction of the hypothetical protein, herein referred to as FabMG, and in vivo and in vitro functional analyses. The crystal structure of FabMG showed limited structural homology with FabG and FabI, which are also involved in type II fatty acid synthesis. In vivo complementation and in vitro activity assays indicated that FabMG is functionally a FabI-type ENR that employs NADH as a coenzyme. Variations in the sequence and structure of FabMG are likely responsible for inefficient binding of triclosan, resulting in triclosan resistance. These data unravel a previously uncharacterized FabMG, which is prevalent in various microbes in triclosan-contaminated environments and provide mechanistic insight into triclosan resistance.
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Affiliation(s)
- Sang-Hoon Kim
- Department of Agricultural Biotechnology, Seoul National University, Korea
| | - Raees Khan
- Department of Applied Bioscience, Dong-A University, Busan, Korea.,Department of Biological Sciences, National University of Medical Sciences, Rawalpindi, Pakistan
| | - Kihyuck Choi
- Department of Applied Bioscience, Dong-A University, Busan, Korea
| | - Seon-Woo Lee
- Department of Applied Bioscience, Dong-A University, Busan, Korea
| | - Sangkee Rhee
- Department of Agricultural Biotechnology, Seoul National University, Korea.,Research Institute of Agriculture and Life Sciences, Seoul National University, Korea
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25
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Biochemical and Structural Insights Concerning Triclosan Resistance in a Novel YX 7K Type Enoyl-Acyl Carrier Protein Reductase from Soil Metagenome. Sci Rep 2019; 9:15401. [PMID: 31659200 PMCID: PMC6817880 DOI: 10.1038/s41598-019-51895-2] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2019] [Accepted: 10/08/2019] [Indexed: 11/08/2022] Open
Abstract
Enoyl-acyl carrier protein reductase (ENR) catalyzes the last reduction step in the bacterial type II fatty acid biosynthesis cycle. ENRs include FabI, FabL, FabL2, FabK, and FabV. Previously, we reported a unique triclosan (TCL) resistant ENR homolog that was predominant in obligate intracellular pathogenic bacteria and Apicomplexa. Herein, we report the biochemical and structural basis of TCL resistance in this novel ENR. The purified protein revealed NADH-dependent ENR activity and shared similarity to prototypic FabI. Thus, this metagenome-derived ENR was designated FabI2. Unlike other prototypic bacterial ENRs with the YX6K type catalytic domain, FabI2 possessed a unique YX7K type catalytic domain. Computational modeling followed by site-directed mutagenesis revealed that mild resistance (20 µg/ml of minimum inhibitory concentration) of FabI2 to TCL was confined to the relatively less bulky side chain of A128. Substitution of A128 in FabI2 with bulky valine (V128) elevated TCL resistance. Phylogenetic analysis further suggested that the novel FabI2 and prototypical FabI evolved from a common short-chain dehydrogenase reductase family. To our best knowledge, FabI2 is the only known ENR shared by intracellular pathogenic prokaryotes, intracellular pathogenic lower eukaryotes, and a few higher eukaryotes. This suggests that the ENRs of prokaryotes and eukaryotes diverged from a common ancestral ENR of FabI2.
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26
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Wijker RS, Sessions AL, Fuhrer T, Phan M. 2H/ 1H variation in microbial lipids is controlled by NADPH metabolism. Proc Natl Acad Sci U S A 2019; 116:12173-12182. [PMID: 31152138 PMCID: PMC6589753 DOI: 10.1073/pnas.1818372116] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022] Open
Abstract
The hydrogen-isotopic compositions (2H/1H ratios) of lipids in microbial heterotrophs are known to vary enormously, by at least 40% (400‰) relative. This is particularly surprising, given that most C-bound H in their lipids appear to derive from the growth medium water, rather than from organic substrates, implying that the isotopic fractionation between lipids and water is itself highly variable. Changes in the lipid/water fractionation are also strongly correlated with the type of energy metabolism operating in the host. Because lipids are well preserved in the geologic record, there is thus significant potential for using lipid 2H/1H ratios to decipher the metabolism of uncultured microorganisms in both modern and ancient ecosystems. But despite over a decade of research, the precise mechanisms underlying this isotopic variability remain unclear. Differences in the kinetic isotope effects (KIEs) accompanying NADP+ reduction by dehydrogenases and transhydrogenases have been hypothesized as a plausible mechanism. However, this relationship has been difficult to prove because multiple oxidoreductases affect the NADPH pool simultaneously. Here, we cultured five diverse aerobic heterotrophs, plus five Escherichia coli mutants, and used metabolic flux analysis to show that 2H/1H fractionations are highly correlated with fluxes through NADP+-reducing and NADPH-balancing reactions. Mass-balance calculations indicate that the full range of 2H/1H variability in the investigated organisms can be quantitatively explained by varying fluxes, i.e., with constant KIEs for each involved oxidoreductase across all species. This proves that lipid 2H/1H ratios of heterotrophic microbes are quantitatively related to central metabolism and provides a foundation for interpreting 2H/1H ratios of environmental lipids and sedimentary hydrocarbons.
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Affiliation(s)
- Reto S Wijker
- Division of Geological and Planetary Sciences, California Institute of Technology, Pasadena, CA 91125;
| | - Alex L Sessions
- Division of Geological and Planetary Sciences, California Institute of Technology, Pasadena, CA 91125
| | - Tobias Fuhrer
- Institute of Molecular Systems Biology, ETH Zürich, 8093 Zürich, Switzerland
| | - Michelle Phan
- Division of Geological and Planetary Sciences, California Institute of Technology, Pasadena, CA 91125
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27
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Tai L, Li BB, Nie XM, Zhang PP, Hu CH, Zhang L, Liu WT, Li WQ, Chen KM. Calmodulin Is the Fundamental Regulator of NADK-Mediated NAD Signaling in Plants. FRONTIERS IN PLANT SCIENCE 2019; 10:681. [PMID: 31275331 PMCID: PMC6593290 DOI: 10.3389/fpls.2019.00681] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/27/2019] [Accepted: 05/06/2019] [Indexed: 05/02/2023]
Abstract
Calcium (Ca2+) signaling and nicotinamide adenine dinucleotide (NAD) signaling are two basic signal regulation pathways in organisms, playing crucial roles in signal transduction, energy metabolism, stress tolerance, and various developmental processes. Notably, calmodulins (CaMs) and NAD kinases (NADKs) are important hubs for connecting these two types of signaling networks, where CaMs are the unique activators of NADKs. NADK is a key enzyme for NADP (including NADP+ and NADPH) biosynthesis by phosphorylating NAD (including NAD+ and NADH) and therefore, maintains the balance between NAD pool and NADP pool through an allosteric regulation mode. In addition, the two respective derivatives from NAD+ (substrate of NADK) and NADP+ (product of NADK), cyclic ADP-ribose (cADPR) and nicotinic acid adenine dinucleotide phosphate (NAADP), have been considered to be the important messengers for intracellular Ca2+ homeostasis which could finally influence the combination between CaM and NADK, forming a feedback regulation mechanism. In this review article, we briefly summarized the major research advances related to the feedback regulation pathway, which is activated by the interaction of CaM and NADK during plant development and signaling. The theories and fact will lay a solid foundation for further studies related to CaM and NADK and their regulatory mechanisms as well as the NADK-mediated NAD signaling behavior in plant development and response to stress.
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Affiliation(s)
- Li Tai
- State Key Laboratory of Crop Stress Biology in Arid Area/College of Life Sciences, Northwest A&F University, Yangling, China
| | - Bin-Bin Li
- State Key Laboratory of Crop Stress Biology in Arid Area/College of Life Sciences, Northwest A&F University, Yangling, China
| | - Xiu-Min Nie
- State Key Laboratory of Crop Stress Biology in Arid Area/College of Life Sciences, Northwest A&F University, Yangling, China
| | - Peng-Peng Zhang
- State Key Laboratory of Crop Stress Biology in Arid Area/College of Life Sciences, Northwest A&F University, Yangling, China
| | - Chun-Hong Hu
- State Key Laboratory of Crop Stress Biology in Arid Area/College of Life Sciences, Northwest A&F University, Yangling, China
- Department of General Biology, College of Life Science and Agronomy, Zhoukou Normal University, Zhoukou, China
| | - Lu Zhang
- State Key Laboratory of Crop Stress Biology in Arid Area/College of Life Sciences, Northwest A&F University, Yangling, China
| | - Wen-Ting Liu
- State Key Laboratory of Crop Stress Biology in Arid Area/College of Life Sciences, Northwest A&F University, Yangling, China
| | - Wen-Qiang Li
- State Key Laboratory of Crop Stress Biology in Arid Area/College of Life Sciences, Northwest A&F University, Yangling, China
| | - Kun-Ming Chen
- State Key Laboratory of Crop Stress Biology in Arid Area/College of Life Sciences, Northwest A&F University, Yangling, China
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28
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Wu J, Peng L, Dong S, Xia X, Zhao L. Transcriptome analysis of Chelidonium majus elaiosomes and seeds provide insights into fatty acid biosynthesis. PeerJ 2019; 7:e6871. [PMID: 31110927 PMCID: PMC6501766 DOI: 10.7717/peerj.6871] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2018] [Accepted: 03/25/2019] [Indexed: 11/20/2022] Open
Abstract
Background Elaiosomes are specialized fleshy and edible seed appendages dispersed by ants. Lipids are the primary components of elaiosomes. Chelidonium majus is a well-known plant, the seeds of which are dispersed by ants. Previous studies have identified the presence of primary fatty acids in its elaiosomes and seeds. However, the molecular mechanisms underlying fatty acid biosynthesis in elaiosomes remain unknown. Methods In order to gain a comprehensive transcriptional profile of the elaiosomes and seeds of C. majus, and understand the expression patterns of genes associated with fatty acid biosynthesis, four different developmental stages, including the flower-bud (Ch01), flowering (Ch02), young seed (Ch03), and mature seed (Ch04) stages, were chosen to perform whole-transcriptome profiling through the RNA-seq technology (Illumina NGS sequencing). Results A total of 63,064 unigenes were generated from 12 libraries. Of these, 7,323, 258, and 11,540 unigenes were annotated with 25 Cluster of Orthologous Groups, 43 Gene Ontology terms, and 373 Kyoto Encyclopedia of Genes and Genomes pathways, respectively. In addition, 322 genes were involved in lipid transport and metabolism, and 508 genes were involved in the lipid metabolism pathways. A total of 41 significantly differentially expressed genes (DEGs) involved in the lipid metabolism pathways were identified, most of which were upregulated in Ch03 compared to Ch02, indicating that fatty acid biosynthesis primarily occurs during the flowering to the young seed stages. Of the DEGs, acyl-ACP thioesterases, acyl carrier protein desaturase (DESA1), and malonyl CoA-ACP transacylase were involved in palmitic acid synthesis; stearoyl-CoA desaturase and DESA1 were involved in oleic acid synthesis, and acyl-lipid omega-6 desaturase was involved in linoleic acid synthesis.
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Affiliation(s)
- Jiayue Wu
- College of Nature Conservation, Beijing Forestry University, Beijing, China
| | - Linlin Peng
- College of Nature Conservation, Beijing Forestry University, Beijing, China
| | - Shubin Dong
- College of Biological Sciences and Technology, Beijing Forestry University, Beijing, China
| | - Xiaofei Xia
- Beijing Museum of Natural History, Beijing, China
| | - Liangcheng Zhao
- College of Nature Conservation, Beijing Forestry University, Beijing, China.,Museum of Beijing Forestry University, Beijing Forestry University, Beijing, China
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29
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The Continuing Threat of Methicillin-Resistant Staphylococcus aureus. Antibiotics (Basel) 2019; 8:antibiotics8020052. [PMID: 31052511 PMCID: PMC6627156 DOI: 10.3390/antibiotics8020052] [Citation(s) in RCA: 148] [Impact Index Per Article: 29.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2019] [Revised: 04/28/2019] [Accepted: 04/29/2019] [Indexed: 02/06/2023] Open
Abstract
Staphylococcus aureus has been an exceptionally successful pathogen, which is still relevant in modern age-medicine due to its adaptability and tenacity. This bacterium may be a causative agent in a plethora of infections, owing to its abundance (in the environment and in the normal flora) and the variety of virulence factors that it possesses. Methicillin-resistant S. aureus (MRSA) strains—first described in 1961—are characterized by an altered penicillin-binding protein (PBP2a/c) and resistance to all penicillins, cephalosporins, and carbapenems, which makes the β-lactam armamentarium clinically ineffective. The acquisition of additional resistance determinants further complicates their eradication; therefore, MRSA can be considered as the first representative of multidrug-resistant bacteria. Based on 230 references, the aim of this review is to recap the history, the emergence, and clinical features of various MRSA infections (hospital-, community-, and livestock-associated), and to summarize the current advances regarding MRSA screening, typing, and therapeutic options (including lipoglycopeptides, oxazolidinones, anti-MRSA cephalosporins, novel pleuromutilin-, tetracycline- and quinolone-derivatives, daptomycin, fusidic acid, in addition to drug candidates in the development phase), both for an audience of clinical microbiologists and infectious disease specialists.
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30
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Microbial Production of Fatty Acid via Metabolic Engineering and Synthetic Biology. BIOTECHNOL BIOPROC E 2019. [DOI: 10.1007/s12257-018-0374-6] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
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31
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Kang W, Zhu X, Wang Y, Chen L, Duan Y. Transcriptomic and metabolomic analyses reveal that bacteria promote plant defense during infection of soybean cyst nematode in soybean. BMC PLANT BIOLOGY 2018; 18:86. [PMID: 29751738 PMCID: PMC5948838 DOI: 10.1186/s12870-018-1302-9] [Citation(s) in RCA: 37] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/26/2017] [Accepted: 04/30/2018] [Indexed: 05/19/2023]
Abstract
BACKGROUND Soybean cyst nematode (SCN) is the most devastating pathogen of soybean. Our previous study showed that the plant growth-promoting rhizobacterium Bacillus simplex strain Sneb545 promotes soybean resistance to SCN. Here, we conducted a combined metabolomic and transcriptomic analysis to gain information regarding the biological mechanism of defence enhancement against SCN in Sneb545-treated soybean. To this end, we compared the transcriptome and metabolome of Sneb545-treated and non-treated soybeans under SCN infection. RESULTS Transcriptomic analysis showed that 6792 gene transcripts were common in Sneb545-treated and non-treated soybeans. However, Sneb545-treated soybeans showed a higher concentration of various nematicidal metabolites, including 4-vinylphenol, methionine, piperine, and palmitic acid, than non-treated soybeans under SCN infection. CONCLUSIONS Overall, our results validated and expanded the existing models regarding the co-regulation of gene expression and metabolites in plants, indicating the advantage of integrated system-oriented analysis.
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Affiliation(s)
- Wenshu Kang
- Nematology Institute of Northern China, Shenyang Agricultural University, No.120 Dongling Road, Shenyang, 110866 China
| | - Xiaofeng Zhu
- Nematology Institute of Northern China, Shenyang Agricultural University, No.120 Dongling Road, Shenyang, 110866 China
| | - Yuanyuan Wang
- Institute of Biotechnology, Shenyang Agricultural University, No.120 Dongling Road, Shenyang, 110866 China
| | - Lijie Chen
- Nematology Institute of Northern China, Shenyang Agricultural University, No.120 Dongling Road, Shenyang, 110866 China
| | - Yuxi Duan
- Nematology Institute of Northern China, Shenyang Agricultural University, No.120 Dongling Road, Shenyang, 110866 China
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32
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Ren J, Mistry TL, Su PC, Mehboob S, Demissie R, Fung LWM, Ghosh AK, Johnson ME. Determination of absolute configuration and binding efficacy of benzimidazole-based FabI inhibitors through the support of electronic circular dichroism and MM-GBSA techniques. Bioorg Med Chem Lett 2018; 28:2074-2079. [PMID: 29730028 DOI: 10.1016/j.bmcl.2018.04.052] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2018] [Revised: 04/19/2018] [Accepted: 04/20/2018] [Indexed: 01/12/2023]
Abstract
We have previously reported benzimidazole-based compounds to be potent inhibitors of FabI for Francisella tularensis (FtFabI), making them promising antimicrobial hits. Optically active enantiomers exhibit markedly differing affinities toward FtFabI. The IC50 of benzimidazole (-)-1 is ∼100× lower than the (+)-enantiomer, with similar results for the 2 enantiomers. Determining the absolute configuration for these optical compounds and elucidating their binding modes is important for further design. Electronic circular dichroism (ECD) quantum calculations have become important in determining absolute configurations of optical compounds. We determined the absolute configuration of (-)/(+)-1 and (-)/(+)-2 by comparing experimental spectra and theoretical density functional theory (DFT) simulations of ECD spectra at the B3LYP/6-311+G(2d, p) level using Gaussian09. Comparison of experimental and calculated ECD spectra indicates that the S configuration corresponds to the (-)-rotation for both compounds 1 and 2, while the R configuration corresponds to the (+)-rotation. Further, molecular dynamics simulations and MM-GBSA binding energy calculations for these two pairs of enantiomers with FtFabI show much tighter binding MM-GBSA free energies for S-1 and S-2 than for their enantiomers, R-1 and R-2, consistent with the S configuration being the more active one, and with the ECD determination of the S configuration corresponding to (-) and the R configuration corresponding to (+). Thus, our computational studies allow us to assign (-) to (S)- and (+) to (R)- for compounds 1 and 2, and to further evaluate structural changes to improve efficacy.
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Affiliation(s)
- Jinhong Ren
- Center for Biomolecular Sciences, University of Illinois at Chicago, 900 S. Ashland Ave, Chicago, IL 60607, USA
| | - Tina L Mistry
- Center for Biomolecular Sciences, University of Illinois at Chicago, 900 S. Ashland Ave, Chicago, IL 60607, USA
| | - Pin-Chih Su
- Center for Biomolecular Sciences, University of Illinois at Chicago, 900 S. Ashland Ave, Chicago, IL 60607, USA
| | - Shahila Mehboob
- Novalex Therapeutics, Inc., 2242 W Harrison, Chicago, IL 60612, USA
| | - Robel Demissie
- Department of Chemistry, University of Illinois at Chicago, 845 W. Taylor St, Chicago, IL 60607, USA
| | - Leslie Wo-Mei Fung
- Department of Chemistry, University of Illinois at Chicago, 845 W. Taylor St, Chicago, IL 60607, USA
| | - Arun K Ghosh
- Department of Chemistry and Department of Medicinal Chemistry, Purdue University, 560 Oval Drive, West Lafayette, IN 47907, USA
| | - Michael E Johnson
- Center for Biomolecular Sciences, University of Illinois at Chicago, 900 S. Ashland Ave, Chicago, IL 60607, USA; Novalex Therapeutics, Inc., 2242 W Harrison, Chicago, IL 60612, USA.
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Abstract
The outer membrane (OM) bilayer of Gram-negative bacteria is biologically unique in its asymmetrical organization of lipids, with an inner leaflet composed of glycerophospholipids (PLs) and a surface-exposed outer leaflet composed of lipopolysaccharide (LPS). This lipid organization is integral to the OM’s barrier properties. Perturbations of the outer leaflet by antimicrobial peptides or defects in LPS biosynthesis or transport to the OM cause a compensatory flipping of PLs to the outer leaflet. As a result, lipid asymmetry is disrupted and OM integrity is compromised. Recently, we identified an Escherichia coli mutant that exhibits aberrant accumulation of surface PLs accompanied by a cellular increase in LPS production. Remarkably, the observed hyperproduction of LPS is PldA dependent. Here we provide evidence that the fatty acids generated by PldA at the OM are transported into the cytoplasm and simultaneously activated by thioesterification to coenzyme A (CoA) by FadD. The acyl-CoAs produced ultimately inhibit LpxC degradation by FtsH. The increased levels of LpxC, the enzyme that catalyzes the first committed step in LPS biosynthesis, increases the amount of LPS produced. Our data suggest that PldA acts as a sensor for lipid asymmetry in the OM. PldA protects the OM barrier by both degrading mislocalized PLs and generating lipid second messengers that enable long-distance signaling that prompts the cell to restore homeostasis at a distant organelle. The outer membrane of Gram-negative bacteria is an effective permeability barrier that protects the cell from toxic agents, including antibiotics. Barrier defects are often manifested by phospholipids present in the outer leaflet of this membrane that take up space normally occupied by lipopolysaccharide. We have discovered a signaling mechanism that operates across the entire cell envelope used by the cell to detect these outer membrane defects. A phospholipase, PldA, that functions to degrade these mislocalized phospholipids has a second, equally important function as a sensor. The fatty acids produced by hydrolysis of the phospholipids act as second messengers to signal the cell that more lipopolysaccharide is needed. These fatty acids diffuse across the periplasm and are transported into the cytoplasm by a process that attaches coenzyme A. The acyl-CoA molecule produces signals to inhibit the degradation of the critical enzyme LpxC by the ATP-dependent protease FtsH, increasing lipopolysaccharide production.
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34
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Goh EB, Chen Y, Petzold CJ, Keasling JD, Beller HR. Improving methyl ketone production in Escherichia coli by heterologous expression of NADH-dependent FabG. Biotechnol Bioeng 2018; 115:1161-1172. [PMID: 29411856 DOI: 10.1002/bit.26558] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2017] [Revised: 01/22/2018] [Accepted: 01/31/2018] [Indexed: 11/07/2022]
Abstract
We previously engineered Escherichia coli to overproduce medium- to long-chain saturated and monounsaturated methyl ketones, which could potentially be applied as diesel fuel blending agents or in the flavor and fragrance industry. Recent efforts at strain optimization have focused on cofactor balance, as fatty acid-derived pathways face the systematic metabolic challenge of net NADPH consumption (in large part, resulting from the key fatty acid biosynthetic enzyme FabG [β-ketoacyl-ACP reductase]) and net NADH production. In this study, we attempted to mitigate cofactor imbalance by heterologously expressing NADH-dependent, rather than NADPH-dependent, versions of FabG identified in previous studies. Of the four NADH-dependent versions of FabG tested in our previously best-reported methyl ketone-producing strain (EGS1895), the version from Acholeplasma laidlawii (Al_FabG) showed the greatest increase in methyl ketone yield in shake flasks (35-75% higher than for an RFP negative-control strain, depending on sugar loading). An improved strain (EGS2920) attained methyl ketone titers during fed-batch fermentation of 5.4 ± 0.5 g/L, which were, on average, ca. 40% greater than those for the base strain (EGS1895) under fermentation conditions optimized in this study. Shotgun proteomic data for strains EGS2920 and EGS1895 during fed-batch fermentation were consistent with the goal of alleviating NADPH limitation through expression of Al_FabG. For example, relative to strain EGS1895, strain EGS2920 significantly upregulated glucose-6-phosphate isomerase (directing flux into glycolysis rather than the NADPH-producing pentose phosphate pathway) and downregulated MaeB (a NADP+ -dependent malate dehydrogenase). Overall, the results suggest that heterologous expression of NADH-dependent FabG in E. coli may improve sustained production of fatty acid-derived renewable fuels and chemicals.
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Affiliation(s)
- Ee-Been Goh
- Joint BioEnergy Institute (JBEI), Emeryville, California.,Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, California
| | - Yan Chen
- Joint BioEnergy Institute (JBEI), Emeryville, California.,Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, California
| | - Christopher J Petzold
- Joint BioEnergy Institute (JBEI), Emeryville, California.,Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, California
| | - Jay D Keasling
- Joint BioEnergy Institute (JBEI), Emeryville, California.,Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, California.,Departments of Chemical and Biomolecular Engineering and of Bioengineering, University of California, Berkeley, California.,The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Kogle Allee, Hørsholm, Denmark
| | - Harry R Beller
- Joint BioEnergy Institute (JBEI), Emeryville, California.,Earth and Environmental Sciences, Lawrence Berkeley National Laboratory, Berkeley, California
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Wang X, Goh EB, Beller HR. Engineering E. coli for simultaneous glucose-xylose utilization during methyl ketone production. Microb Cell Fact 2018; 17:12. [PMID: 29374483 PMCID: PMC5787283 DOI: 10.1186/s12934-018-0862-6] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2017] [Accepted: 01/19/2018] [Indexed: 11/13/2022] Open
Abstract
Background We previously developed an E. coli strain that overproduces medium-chain methyl ketones for potential use as diesel fuel blending agents or as flavors and fragrances. To date, the strain’s performance has been optimized during growth with glucose. However, lignocellulosic biomass hydrolysates also contain a substantial portion of hemicellulose-derived xylose, which is typically the second most abundant sugar after glucose. Commercialization of the methyl ketone-producing technology would benefit from the increased efficiency resulting from simultaneous, rather than the native sequential (diauxic), utilization of glucose and xylose. Results In this study, genetic manipulations were performed to alleviate carbon catabolite repression in our most efficient methyl ketone-producing strain. A strain engineered for constitutive expression of xylF and xylA (involved in xylose transport and metabolism) showed synchronized glucose and xylose consumption rates. However, this newly acquired capability came at the expense of methyl ketone titer, which decreased fivefold. Further efforts were made to improve methyl ketone production in this strain, and we found that two strategies were effective at enhancing methyl ketone titer: (1) chromosomal deletion of pgi (glucose-6-phosphate isomerase) to increase intracellular NADPH supply and (2) downregulation of CRP (cAMP receptor protein) expression by replacement of the native RBS with an RBS chosen based upon mutant library screening results. Combining these strategies resulted in the most favorable overall phenotypes for simultaneous glucose–xylose consumption without compromising methyl ketone titer at both 1 and 2% total sugar concentrations in shake flasks. Conclusions This work demonstrated a strategy for engineering simultaneous utilization of C6 and C5 sugars in E. coli without sacrificing production of fatty acid-derived compounds. Electronic supplementary material The online version of this article (10.1186/s12934-018-0862-6) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Xi Wang
- Joint BioEnergy Institute (JBEI), 5885 Hollis St., Emeryville, CA, 94608, USA.,Biological Systems & Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA
| | - Ee-Been Goh
- Joint BioEnergy Institute (JBEI), 5885 Hollis St., Emeryville, CA, 94608, USA.,Biological Systems & Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA
| | - Harry R Beller
- Joint BioEnergy Institute (JBEI), 5885 Hollis St., Emeryville, CA, 94608, USA. .,Biological Systems & Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA. .,Earth & Environmental Sciences, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA.
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Li W, Wu H, Li M, San KY. Effect of NADPH availability on free fatty acid production in Escherichia coli. Biotechnol Bioeng 2017; 115:444-452. [PMID: 28976546 DOI: 10.1002/bit.26464] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2017] [Revised: 09/17/2017] [Accepted: 09/25/2017] [Indexed: 11/06/2022]
Abstract
Microbial conversion of renewable carbon sources to free fatty acids has attracted significant attention in recent years. Accumulation of free fatty acids in Escherichia coli by overexpression of an acyl-ACP thioesterase which can break the fatty acid elongation has been well established. Various efforts have been made to increase fatty acid production in E. coli by enhancing the enzymes involved in the fatty acid synthesis cycle or host strain manipulations. The current study focused on the effect of NADPH availability on free fatty acids (FFAs) productivity. There are two reduction steps in the fatty acid elongation cycle which are catalyzed by beta keto-ACP reductase (FabG) and enoyl-ACP reductase (FabI), respectively. It is reported that FabI can use either NADH or NADPH as cofactor, while FabG only uses NADPH in E. coli. Fatty acid production dropped dramatically in the glucose-6-phosphate dehydrogenase (encoded by the zwf gene) deficient strain. Similarly, the pntB (which encodes one of the subunit of proton-translocating membrane bounded transhydrogenase PntAB) and udhA (which encodes the energy dependent cytoplasmic transhydrogenase UdhA) double mutant strain also showed an 88.8% decrease in free fatty acid production. Overexpression of PntAB and NadK restored the fatty acid production capability of these two mutant strains. These results indicated that the availability of NADPH played a very important role in fatty acid production.
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Affiliation(s)
- Wei Li
- Department of Bioengineering, Rice University, Houston, Texas
| | - Hui Wu
- Department of Bioengineering, Rice University, Houston, Texas.,State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, Shanghai, China
| | - Mai Li
- Department of Bioengineering, Rice University, Houston, Texas
| | - Ka-Yiu San
- Department of Bioengineering, Rice University, Houston, Texas.,Department of Chemical & Biomolecular Engineering, Rice University, Houston, Texas
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Khan Z, Rehman A, Nisar MA, Zafar S, Zerr I. Biosorption behavior and proteomic analysis of Escherichia coli P4 under cadmium stress. CHEMOSPHERE 2017; 174:136-147. [PMID: 28161514 DOI: 10.1016/j.chemosphere.2017.01.132] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/13/2016] [Revised: 01/19/2017] [Accepted: 01/26/2017] [Indexed: 06/06/2023]
Abstract
Bacteria develop a variety of adaptations at transcriptomic, metabolomic and proteomic levels in order to survive potentially damaging environmental perturbations. Present study is exploring the fluctuations in proteome of E. coli P4 to knob Cd+2-induced cytotoxicity. An attempt was also made to integrate all these approaches to gain comprehensive insight of Cd+2 stress response in E. coli P4. This study is exposing the altered behavior of various proteins and their underlying metabolic pathways which have previously not been reported with reference to Cd+2 stress such as sulfoquinovose biosynthesis and degradation pathway. Some of the responses studied on all integrated levels followed same dynamics and strategies to conserve energy by down regulating carbohydrate metabolism (depicted by the repression of succinyl-CoA ligase) and growth stasis (down regulation of ftsZ). Moreover, proteomic analysis clearly revealed the affection of Cd+2 stress on various proteins expression including Rrf, MdaB, DapA, GpmA,Cdd, FabI, DsbA, ZnuA and YihW found modulating key cellular metabolic pathways enabling E. coli P4 to withstand Cd+2-induced toxic effects. Furthermore, over-expression of Mn-SOD provided evidence that Cd+2exposure induces superoxide free radicals mediated oxidative stress rather than hydrogen peroxide (H2O2). EnvZ/OmpR -a two component cell envelope regulatory system was observed operating to homeostat the cell's internal environment. Cd+2 bioremediation potential of E. coli P4 and its kinetic and thermodynamic basis were studied by applying different isotherm models which nominated E. coli P4 a good bioresource for green chemistry to eradicate environmental Cd+2.
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Affiliation(s)
- Zaman Khan
- Department of Microbiology and Molecular Genetics, University of the Punjab, Lahore, Pakistan
| | - Abdul Rehman
- Department of Microbiology and Molecular Genetics, University of the Punjab, Lahore, Pakistan.
| | - Muhammad Atif Nisar
- Department of Microbiology, Government College University Faisalabad (GCUF), Faisalabad, Pakistan
| | - Saima Zafar
- Department of Neurology, Clinical Dementia Center and DZNE, Georg-August University, University Medical Center Goettingen (UMG), Robert-Koch-Str. 40, 37075, Goettingen, Germany
| | - Inga Zerr
- Department of Neurology, Clinical Dementia Center and DZNE, Georg-August University, University Medical Center Goettingen (UMG), Robert-Koch-Str. 40, 37075, Goettingen, Germany
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Liu Z, Zhang Y, Jia X, Hu M, Deng Z, Xu Y, Liu T. In Vitro Reconstitution and Optimization of the Entire Pathway to Convert Glucose into Fatty Acid. ACS Synth Biol 2017; 6:701-709. [PMID: 28080041 DOI: 10.1021/acssynbio.6b00348] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
Glucose and fatty acids play essential physiological roles in nearly all living organisms, and the pathway that converts glucose into fatty acid is pivotal to the central metabolic network. We have successfully reconstituted a pathway that converts glucose to fatty acid in vitro using 30 purified proteins. Through systematic titration and optimization of the glycolytic pathway and pyruvate dehydrogenase, we increased the yield of free fatty acid from nondetectable to a level that exceeded 9% of the theoretical yield. We also reconstituted the entire pentose-phosphate pathway of Escherichia coli and established a pentose phosphate-glycolysis hybrid pathway, replacing GAPDH to enhance NADPH availability. Our efforts provide a useful platform for research involving these core biochemical transformations.
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Affiliation(s)
- Zheng Liu
- Department
of Endocrinology, Zhongnan Hospital of Wuhan University, Wuhan 430071, China
| | - Yuchen Zhang
- Key
Laboratory of Combinatorial Biosynthesis and Drug Discovery, Ministry of Education and Wuhan University School of Pharmaceutical Sciences, Wuhan 430071, China
| | - Xiaoge Jia
- Key
Laboratory of Combinatorial Biosynthesis and Drug Discovery, Ministry of Education and Wuhan University School of Pharmaceutical Sciences, Wuhan 430071, China
| | - Mengzhu Hu
- Key
Laboratory of Combinatorial Biosynthesis and Drug Discovery, Ministry of Education and Wuhan University School of Pharmaceutical Sciences, Wuhan 430071, China
| | - Zixin Deng
- Key
Laboratory of Combinatorial Biosynthesis and Drug Discovery, Ministry of Education and Wuhan University School of Pharmaceutical Sciences, Wuhan 430071, China
| | - Yancheng Xu
- Department
of Endocrinology, Zhongnan Hospital of Wuhan University, Wuhan 430071, China
| | - Tiangang Liu
- Key
Laboratory of Combinatorial Biosynthesis and Drug Discovery, Ministry of Education and Wuhan University School of Pharmaceutical Sciences, Wuhan 430071, China
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Enoyl-Acyl Carrier Protein Reductase I (FabI) Is Essential for the Intracellular Growth of Listeria monocytogenes. Infect Immun 2016; 84:3597-3607. [PMID: 27736774 DOI: 10.1128/iai.00647-16] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2016] [Accepted: 10/02/2016] [Indexed: 12/28/2022] Open
Abstract
Enoyl-acyl carrier protein reductase catalyzes the last step in each elongation cycle of type II bacterial fatty acid synthesis and is a key regulatory protein in bacterial fatty acid synthesis. Genes of the facultative intracellular pathogen Listeria monocytogenes encode two functional enoyl-acyl carrier protein isoforms based on their ability to complement the temperature-sensitive growth phenotype of Escherichia coli strain JP1111 [fabI(Ts)]. The FabI isoform was inactivated by the FabI selective inhibitor AFN-1252, but the FabK isoform was not affected by the drug, as expected. Inhibition of FabI by AFN-1252 decreased endogenous fatty acid synthesis by 80% and lowered the growth rate of L. monocytogenes in laboratory medium. Robust exogenous fatty acid incorporation was not detected in L. monocytogenes unless the pathway was partially inactivated by AFN-1252 treatment. However, supplementation with exogenous fatty acids did not restore normal growth in the presence of AFN-1252. FabI inactivation prevented the intracellular growth of L. monocytogenes, showing that neither FabK nor the incorporation of host cellular fatty acids was sufficient to support the intracellular growth of L. monocytogenes Our results show that FabI is the primary enoyl-acyl carrier protein reductase of type II bacterial fatty acid synthesis and is essential for the intracellular growth of L. monocytogenes.
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40
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Heterologous biosynthesis and manipulation of alkanes in Escherichia coli. Metab Eng 2016; 38:19-28. [DOI: 10.1016/j.ymben.2016.06.002] [Citation(s) in RCA: 54] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2016] [Revised: 05/12/2016] [Accepted: 06/03/2016] [Indexed: 12/26/2022]
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Shin KS, Kim S, Lee SK. Improvement of free fatty acid production using a mutant acyl-CoA thioesterase I with high specific activity in Escherichia coli. BIOTECHNOLOGY FOR BIOFUELS 2016; 9:208. [PMID: 27761152 PMCID: PMC5053343 DOI: 10.1186/s13068-016-0622-y] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/05/2016] [Accepted: 09/24/2016] [Indexed: 06/06/2023]
Abstract
BACKGROUND Microbial production of oleochemicals has been actively studied in the last decade. Free fatty acids (FFAs) could be converted into a variety of molecules such as industrial products, consumer products, and fuels. FFAs have been produced in metabolically engineered Escherichia coli cells expressing a signal sequence-deficient acyl-CoA thioesterase I ('TesA). Nonetheless, increasing the expression level of 'TesA seems not to be an appropriate approach to scale up FFA production because a certain ratio of each component including fatty acid synthase and 'TesA is required for optimal production of FFAs. Thus, the catalytic activity of 'TesA should be rationally engineered instead of merely increasing the enzyme expression level to enhance the production of FFAs. RESULTS In this study, we constructed a sensing system with a fusion protein of tetracycline resistance protein and red fluorescent protein (RFP) under the control of a FadR-responsive promoter to select the desired mutants. Fatty acid-dependent growth and RFP expression allowed for selection of FFA-overproducing cells. A 'TesA mutant that produces a twofold greater amount of FFAs was isolated from an error-prone PCR mutant library of E. coli 'TesA. Its kinetic analysis revealed that substitution of Arg64 with Cys64 in the enzyme causes an approximately twofold increase in catalytic activity. CONCLUSIONS Because the expression of 'TesA in E. coli for the production of oleochemicals is almost an indispensable process, the proposed engineering approach has a potential to enhance the production of oleochemicals. The use of the catalytically active mutant 'TesAR64C should accelerate the manufacture of FFA-derived chemicals and fuels.
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Affiliation(s)
- Kwang Soo Shin
- School of Life Sciences, Ulsan National Institute of Science and Technology (UNIST), Ulsan, 44919 Republic of Korea
| | - Sangwoo Kim
- School of Energy and Chemical Engineering, Ulsan National Institute of Science and Technology (UNIST), Ulsan, 44919 Republic of Korea
| | - Sung Kuk Lee
- School of Life Sciences, Ulsan National Institute of Science and Technology (UNIST), Ulsan, 44919 Republic of Korea
- School of Energy and Chemical Engineering, Ulsan National Institute of Science and Technology (UNIST), Ulsan, 44919 Republic of Korea
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Leavitt WD, Flynn TM, Suess MK, Bradley AS. Transhydrogenase and Growth Substrate Influence Lipid Hydrogen Isotope Ratios in Desulfovibrio alaskensis G20. Front Microbiol 2016; 7:918. [PMID: 27445998 PMCID: PMC4916218 DOI: 10.3389/fmicb.2016.00918] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2016] [Accepted: 05/27/2016] [Indexed: 11/19/2022] Open
Abstract
Microbial fatty acids preserve metabolic and environmental information in their hydrogen isotope ratios ((2)H/(1)H). This ratio is influenced by parameters that include the (2)H/(1)H of water in the microbial growth environment, and biosynthetic fractionations between water and lipid. In some microbes, this biosynthetic fractionation has been shown to vary systematically with central energy metabolism, and controls on fatty acid (2)H/(1)H may be linked to the intracellular production of NADPH. We examined the apparent fractionation between media water and the fatty acids produced by Desulfovibrio alaskensis G20. Growth was in batch culture with malate as an electron donor for sulfate respiration, and with pyruvate and fumarate as substrates for fermentation and for sulfate respiration. A larger fractionation was observed as a consequence of respiratory or fermentative growth on pyruvate than growth on fumarate or malate. This difference correlates with opposite apparent flows of electrons through the electron bifurcating/confurcating transhydrogenase NfnAB. When grown on malate or fumarate, mutant strains of D. alaskensis G20 containing transposon disruptions in a copy of nfnAB show different fractionations than the wild type strain. This phenotype is muted during fermentative growth on pyruvate, and it is absent when pyruvate is a substrate for sulfate reduction. All strains and conditions produced similar fatty acid profiles, and the (2)H/(1)H of individual lipids changed in concert with the mass-weighted average. Unsaturated fatty acids were generally depleted in (2)H relative to their saturated homologs, and anteiso-branched fatty acids were generally depleted in (2)H relative to straight-chain fatty acids. Fractionation correlated with growth rate, a pattern that has also been observed in the fractionation of sulfur isotopes during dissimilatory sulfate reduction by sulfate-reducing bacteria.
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Affiliation(s)
- William D. Leavitt
- Department of Earth and Planetary Sciences, Washington University in St. LouisSaint Louis, MO, USA
| | | | - Melanie K. Suess
- Department of Earth and Planetary Sciences, Washington University in St. LouisSaint Louis, MO, USA
| | - Alexander S. Bradley
- Department of Earth and Planetary Sciences, Washington University in St. LouisSaint Louis, MO, USA
- Division of Biology and Biomedical Sciences, Washington University in St. LouisSaint Louis, MO, USA
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Tallorin L, Finzel K, Nguyen QG, Beld J, La Clair JJ, Burkart MD. Trapping of the Enoyl-Acyl Carrier Protein Reductase-Acyl Carrier Protein Interaction. J Am Chem Soc 2016; 138:3962-5. [PMID: 26938266 DOI: 10.1021/jacs.5b13456] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
An ideal target for metabolic engineering, fatty acid biosynthesis remains poorly understood on a molecular level. These carrier protein-dependent pathways require fundamental protein-protein interactions to guide reactivity and processivity, and their control has become one of the major hurdles in successfully adapting these biological machines. Our laboratory has developed methods to prepare acyl carrier proteins (ACPs) loaded with substrate mimetics and cross-linkers to visualize and trap interactions with partner enzymes, and we continue to expand the tools for studying these pathways. We now describe application of the slow-onset, tight-binding inhibitor triclosan to explore the interactions between the type II fatty acid ACP from Escherichia coli, AcpP, and its corresponding enoyl-ACP reductase, FabI. We show that the AcpP-triclosan complex demonstrates nM binding, inhibits in vitro activity, and can be used to isolate FabI in complex proteomes.
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Affiliation(s)
- Lorillee Tallorin
- Department of Chemistry and Biochemistry, University of California, San Diego , 9500 Gilman Drive, La Jolla, California 92093-0358, United States
| | - Kara Finzel
- Department of Chemistry and Biochemistry, University of California, San Diego , 9500 Gilman Drive, La Jolla, California 92093-0358, United States
| | - Quynh G Nguyen
- Department of Chemistry and Biochemistry, University of California, San Diego , 9500 Gilman Drive, La Jolla, California 92093-0358, United States
| | - Joris Beld
- Department of Chemistry and Biochemistry, University of California, San Diego , 9500 Gilman Drive, La Jolla, California 92093-0358, United States
| | - James J La Clair
- Department of Chemistry and Biochemistry, University of California, San Diego , 9500 Gilman Drive, La Jolla, California 92093-0358, United States
| | - Michael D Burkart
- Department of Chemistry and Biochemistry, University of California, San Diego , 9500 Gilman Drive, La Jolla, California 92093-0358, United States
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Crosstalk between the lipopolysaccharide and phospholipid pathways during outer membrane biogenesis in Escherichia coli. Proc Natl Acad Sci U S A 2016; 113:3108-13. [PMID: 26929331 DOI: 10.1073/pnas.1521168113] [Citation(s) in RCA: 51] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023] Open
Abstract
The outer membrane of gram-negative bacteria is composed of phospholipids in the inner leaflet and lipopolysaccharides (LPS) in the outer leaflet. LPS is an endotoxin that elicits a strong immune response from humans, and its biosynthesis is in part regulated via degradation of LpxC (EC 3.5.1.108) and WaaA (EC 2.4.99.12/13) enzymes by the protease FtsH (EC 3.4.24.-). Because the synthetic pathways for both molecules are complex, in addition to being produced in strict ratios, we developed a computational model to interrogate the regulatory mechanisms involved. Our model findings indicate that the catalytic activity of LpxK (EC 2.7.1.130) appears to be dependent on the concentration of unsaturated fatty acids. This is biologically important because it assists in maintaining LPS/phospholipids homeostasis. Further crosstalk between the phospholipid and LPS biosynthetic pathways was revealed by experimental observations that LpxC is additionally regulated by an unidentified protease whose activity is independent of lipid A disaccharide concentration (the feedback source for FtsH-mediated LpxC regulation) but could be induced in vitro by palmitic acid. Further experimental analysis provided evidence on the rationale for WaaA regulation. Overexpression of waaA resulted in increased levels of 3-deoxy-d-manno-oct-2-ulosonic acid (Kdo) sugar in membrane extracts, whereas Kdo and heptose levels were not elevated in LPS. This implies that uncontrolled production of WaaA does not increase the LPS production rate but rather reglycosylates lipid A precursors. Overall, the findings of this work provide previously unidentified insights into the complex biogenesis of the Escherichia coli outer membrane.
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Escherichia coli enoyl-acyl carrier protein reductase (FabI) supports efficient operation of a functional reversal of β-oxidation cycle. Appl Environ Microbiol 2016; 81:1406-16. [PMID: 25527535 DOI: 10.1128/aem.03521-14] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023] Open
Abstract
We recently used a synthetic/bottom-up approach to establish the identity of the four enzymes composing an engineered functional reversal of the -oxidation cycle for fuel and chemical production in Escherichia coli (J. M. Clomburg, J. E. Vick, M. D. Blankschien, M. Rodriguez-Moya, and R. Gonzalez, ACS Synth Biol 1:541–554, 2012, http://dx.doi.org/10.1021/sb3000782).While native enzymes that catalyze the first three steps of the pathway were identified, the identity of the native enzyme(s) acting as the trans-enoyl coenzyme A (CoA) reductase(s) remained unknown, limiting the amount of product that could be synthesized (e.g., 0.34 g/liter butyrate) and requiring the overexpression of a foreign enzyme (the Euglena gracilis trans-enoyl-CoA reductase [EgTER]) to achieve high titers (e.g., 3.4 g/liter butyrate). Here, we examine several native E. coli enzymes hypothesized to catalyze the reduction of enoyl-CoAs to acyl-CoAs. Our results indicate that FabI, the native enoyl-acyl carrier protein (enoyl-ACP) reductase (ENR) from type II fatty acid biosynthesis, possesses sufficient NADH-dependent TER activity to support the efficient operation of a -oxidation reversal. Overexpression of FabI proved as effective as EgTER for the production of butyrate and longer-chain carboxylic acids. Given the essential nature of fabI, we investigated whether bacterial ENRs from other families were able to complement a fabI deletion without promiscuous reduction of crotonyl-CoA. These characteristics from Bacillus subtilis FabL enabled deltaffabI complementation experiments that conclusively established that FabI encodes a native enoyl-CoA reductase activity that supports the β-oxidation reversal in E. coli.
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Tsukuda M, Nakashima N, Miyazaki K. Counterselection method based on conditional silencing of antitoxin genes in Escherichia coli. J Biosci Bioeng 2015; 120:591-5. [DOI: 10.1016/j.jbiosc.2015.03.008] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2015] [Revised: 03/02/2015] [Accepted: 03/12/2015] [Indexed: 01/29/2023]
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Abstract
The pathways in Escherichia coli and (largely by analogy) S. enterica remain the paradigm of bacterial lipid synthetic pathways, although recently considerable diversity among bacteria in the specific areas of lipid synthesis has been demonstrated. The structural biology of the fatty acid synthetic proteins is essentially complete. However, the membrane-bound enzymes of phospholipid synthesis remain recalcitrant to structural analyses. Recent advances in genetic technology have allowed the essentialgenes of lipid synthesis to be tested with rigor, and as expected most genes are essential under standard growth conditions. Conditionally lethal mutants are available in numerous genes, which facilitates physiological analyses. The array of genetic constructs facilitates analysis of the functions of genes from other organisms. Advances in mass spectroscopy have allowed very accurate and detailed analyses of lipid compositions as well as detection of the interactions of lipid biosynthetic proteins with one another and with proteins outside the lipid pathway. The combination of these advances has resulted in use of E. coli and S. enterica for discovery of new antimicrobials targeted to lipid synthesis and in deciphering the molecular actions of known antimicrobials. Finally,roles for bacterial fatty acids other than as membrane lipid structural components have been uncovered. For example, fatty acid synthesis plays major roles in the synthesis of the essential enzyme cofactors, biotin and lipoic acid. Although other roles for bacterial fatty acids, such as synthesis of acyl-homoserine quorum-sensing molecules, are not native to E. coli introduction of the relevant gene(s) synthesis of these foreign molecules readily proceeds and the sophisticated tools available can used to decipher the mechanisms of synthesis of these molecules.
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Ghattas MA, Mansour RA, Atatreh N, Bryce RA. Analysis of Enoyl-Acyl Carrier Protein Reductase Structure and Interactions Yields an Efficient Virtual Screening Approach and Suggests a Potential Allosteric Site. Chem Biol Drug Des 2015; 87:131-42. [PMID: 26259619 DOI: 10.1111/cbdd.12635] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2015] [Revised: 07/14/2015] [Accepted: 07/31/2015] [Indexed: 11/28/2022]
Abstract
Enoyl-acyl carrier protein reductases have an important role in fatty acid biosynthesis and are considered essential for bacterial and protozoal survival. Here, we perform a computational assessment of enoyl-acyl carrier protein reductase structures, providing insights for inhibitor design that we incorporate into a virtual screening approach. Firstly, we analyse 80 crystal structures of 16 different enoyl-acyl carrier protein reductases for their active site characteristics and druggability, finding these sites contain a readily druggable pocket, of varying size and shape. Interestingly, a high affinity, potentially allosteric site was identified for pfFabl. Analysis of the ligand-protein interactions of four enoyl-acyl carrier protein reductases from different micro-organisms (InhA, pfFabl, saFabl and ecFabl), involving 59 available crystal structures, found three commonly shared interactions; constraining these interactions in docking improved enrichment of enoyl-acyl carrier protein reductase virtual screens, by up to 60% in the top 3% of the ranked library. This docking protocol also improved pose prediction, decreasing the root-mean-square deviation to crystallographic pose by up to 75% on average. The binding site analysis and knowledge-based docking protocol presented here can potentially assist in the structure-based design of new enoyl-acyl carrier protein reductase inhibitors.
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Affiliation(s)
- Mohammad A Ghattas
- College of Pharmacy, Al Ain University of Science and Technology, Al Ain, 64141, United Arab Emirates
| | - Ramez A Mansour
- College of Pharmacy, Al Ain University of Science and Technology, Al Ain, 64141, United Arab Emirates
| | - Noor Atatreh
- College of Pharmacy, Al Ain University of Science and Technology, Al Ain, 64141, United Arab Emirates
| | - Richard A Bryce
- Manchester Pharmacy School, University of Manchester, Manchester, M13 9PT, UK
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Narasimha Rao K, Lakshminarasimhan A, Joseph S, Lekshmi SU, Lau MS, Takhi M, Sreenivas K, Nathan S, Yusof R, Abd Rahman N, Ramachandra M, Antony T, Subramanya H. AFN-1252 is a potent inhibitor of enoyl-ACP reductase from Burkholderia pseudomallei--Crystal structure, mode of action, and biological activity. Protein Sci 2015; 24:832-40. [PMID: 25644789 PMCID: PMC4420531 DOI: 10.1002/pro.2655] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2014] [Revised: 01/30/2015] [Accepted: 01/30/2015] [Indexed: 12/20/2022]
Abstract
Melioidosis is a tropical bacterial infection caused by Burkholderia pseudomallei (B. pseudomallei; Bpm), a Gram-negative bacterium. Current therapeutic options are largely limited to trimethoprim-sulfamethoxazole and β-lactam drugs, and the treatment duration is about 4 months. Moreover, resistance has been reported to these drugs. Hence, there is a pressing need to develop new antibiotics for Melioidosis. Inhibition of enoyl-ACP reducatase (FabI), a key enzyme in the fatty acid biosynthesis pathway has shown significant promise for antibacterial drug development. FabI has been identified as the major enoyl-ACP reductase present in B. pseudomallei. In this study, we evaluated AFN-1252, a Staphylococcus aureus FabI inhibitor currently in clinical development, for its potential to bind to BpmFabI enzyme and inhibit B. pseudomallei bacterial growth. AFN-1252 stabilized BpmFabI and inhibited the enzyme activity with an IC50 of 9.6 nM. It showed good antibacterial activity against B. pseudomallei R15 strain, isolated from a melioidosis patient (MIC of 2.35 mg/L). X-ray structure of BpmFabI with AFN-1252 was determined at a resolution of 2.3 Å. Complex of BpmFabI with AFN-1252 formed a symmetrical tetrameric structure with one molecule of AFN-1252 bound to each monomeric subunit. The kinetic and thermal melting studies supported the finding that AFN-1252 can bind to BpmFabI independent of cofactor. The structural and mechanistic insights from these studies might help the rational design and development of new FabI inhibitors.
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Affiliation(s)
- Krishnamurthy Narasimha Rao
- Aurigene Discovery Technologies Ltd, 39-40, KIADB Industrial area, Electronic city Phase IIHosur Road, Bangalore, 560 100, India
| | - Anirudha Lakshminarasimhan
- Aurigene Discovery Technologies Ltd, 39-40, KIADB Industrial area, Electronic city Phase IIHosur Road, Bangalore, 560 100, India
| | - Sarah Joseph
- Aurigene Discovery Technologies Ltd, 39-40, KIADB Industrial area, Electronic city Phase IIHosur Road, Bangalore, 560 100, India
| | - Swathi U Lekshmi
- Aurigene Discovery Technologies Ltd, 39-40, KIADB Industrial area, Electronic city Phase IIHosur Road, Bangalore, 560 100, India
| | - Ming-Seong Lau
- School of Biosciences and Biotechnology, Faculty of Science and Technology, Universiti Kebangsaan Malaysia43600, Bangi, Selangor, Malaysia
| | - Mohammed Takhi
- Aurigene Discovery Technologies LtdBollaram Road, Miyapur, Hyderabad, 500 049, India
| | - Kandepu Sreenivas
- Aurigene Discovery Technologies LtdBollaram Road, Miyapur, Hyderabad, 500 049, India
| | - Sheila Nathan
- School of Biosciences and Biotechnology, Faculty of Science and Technology, Universiti Kebangsaan Malaysia43600, Bangi, Selangor, Malaysia
| | - Rohana Yusof
- Department of Molecular Medicine, Faculty of Medicine, University of Malaya50603, Kuala Lumpur, Malaysia
| | - Noorsaadah Abd Rahman
- Department of Chemistry, Faculty of Science, University of Malaya50603, Kuala Lumpur, Malaysia
| | - Murali Ramachandra
- Aurigene Discovery Technologies Ltd, 39-40, KIADB Industrial area, Electronic city Phase IIHosur Road, Bangalore, 560 100, India
| | - Thomas Antony
- Aurigene Discovery Technologies Ltd, 39-40, KIADB Industrial area, Electronic city Phase IIHosur Road, Bangalore, 560 100, India
| | - Hosahalli Subramanya
- Aurigene Discovery Technologies Ltd, 39-40, KIADB Industrial area, Electronic city Phase IIHosur Road, Bangalore, 560 100, India
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50
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More UA, Joshi SD, Aminabhavi TM, Kulkarni VH, Badiger AM, Lherbet C. Discovery of target based novel pyrrolyl phenoxy derivatives as antimycobacterial agents: An in silico approach. Eur J Med Chem 2015; 94:317-39. [DOI: 10.1016/j.ejmech.2015.03.013] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2014] [Revised: 03/04/2015] [Accepted: 03/05/2015] [Indexed: 11/17/2022]
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