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Xu N, Zuo J, Li C, Gao C, Guo M. Reconstruction and Analysis of a Genome-Scale Metabolic Model of Acinetobacter lwoffii. Int J Mol Sci 2024; 25:9321. [PMID: 39273268 DOI: 10.3390/ijms25179321] [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: 06/30/2024] [Revised: 07/31/2024] [Accepted: 08/22/2024] [Indexed: 09/15/2024] Open
Abstract
Acinetobacter lwoffii is widely considered to be a harmful bacterium that is resistant to medicines and disinfectants. A. lwoffii NL1 degrades phenols efficiently and shows promise as an aromatic compound degrader in antibiotic-contaminated environments. To gain a comprehensive understanding of A. lwoffii, the first genome-scale metabolic model of A. lwoffii was constructed using semi-automated and manual methods. The iNX811 model, which includes 811 genes, 1071 metabolites, and 1155 reactions, was validated using 39 unique carbon and nitrogen sources. Genes and metabolites critical for cell growth were analyzed, and 12 essential metabolites (mainly in the biosynthesis and metabolism of glycan, lysine, and cofactors) were identified as antibacterial drug targets. Moreover, to explore the metabolic response to phenols, metabolic flux was simulated by integrating transcriptomics, and the significantly changed metabolism mainly included central carbon metabolism, along with some transport reactions. In addition, the addition of substances that effectively improved phenol degradation was predicted and validated using the model. Overall, the reconstruction and analysis of model iNX811 helped to study the antimicrobial systems and biodegradation behavior of A. lwoffii.
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Affiliation(s)
- Nan Xu
- College of Bioscience and Biotechnology, Yangzhou University, Yangzhou 225009, China
| | - Jiaojiao Zuo
- College of Bioscience and Biotechnology, Yangzhou University, Yangzhou 225009, China
| | - Chenghao Li
- College of Bioscience and Biotechnology, Yangzhou University, Yangzhou 225009, China
| | - Cong Gao
- School of Biotechnology, Jiangnan University, Wuxi 214122, China
| | - Minliang Guo
- College of Bioscience and Biotechnology, Yangzhou University, Yangzhou 225009, China
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2
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Shi Z, Tang Y, Wang Z, Wang M, Zhong Z, Jia J, Chen Y. Characterization of the ADP-β-D-manno-heptose biosynthetic enzymes from two pathogenic Vibrio strains. Appl Microbiol Biotechnol 2024; 108:267. [PMID: 38498053 PMCID: PMC10948575 DOI: 10.1007/s00253-024-13108-3] [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: 10/13/2023] [Revised: 02/24/2024] [Accepted: 03/07/2024] [Indexed: 03/19/2024]
Abstract
ADP-activated β-D-manno-heptoses (ADP-β-D-manno-heptoses) are precursors for the biosynthesis of the inner core of lipopolysaccharide in Gram-negative bacteria. Recently, ADP-D-glycero-β-D-manno-heptose (ADP-D,D-manno-heptose) and its C-6'' epimer, ADP-L-glycero-β-D-manno-heptose (ADP-L,D-manno-heptose), were identified as potent pathogen-associated molecular patterns (PAMPs) that can trigger robust innate immune responses. Although the production of ADP-D,D-manno-heptose has been studied in several different pathogenic Gram-negative bacteria, current knowledge of ADP-β-D-manno-heptose biosynthesis in Vibrio strains remains limited. Here, we characterized the biosynthetic enzymes of ADP-D,D-manno-heptose and the epimerase that converts it to ADP-L,D-manno-heptose from Vibrio cholerae (the causative agent of pandemic cholera) and Vibrio parahaemolyticus (non-cholera pathogen causing vibriosis with clinical manifestations of gastroenteritis and wound infections) in comparison with their isozymes from Escherichia coli. Moreover, we discovered that β-D-mannose 1-phosphate, but not α-D-mannose 1-phosphate, could be activated to its ADP form by the nucleotidyltransferase domains of bifunctional kinase/nucleotidyltransferases HldEVC (from V. cholerae) and HldEVP (from V. parahaemolyticus). Kinetic analyses of the nucleotidyltransferase domains of HldEVC and HldEVP together with the E. coli-derived HldEEC were thus carried out using β-D-mannose 1-phosphate as a mimic sugar substrate. Overall, our works suggest that V. cholerae and V. parahaemolyticus are capable of synthesizing ADP-β-D-manno-heptoses and lay a foundation for further physiological function explorations on manno-heptose metabolism in Vibrio strains. KEY POINTS: • Vibrio strains adopt the same biosynthetic pathway as E. coli in synthesizing ADP-β-D-manno-heptoses. • HldEs from two Vibrio strains and E. coli could activate β-D-mannose 1-phosphate to ADP-β-D-mannose. • Comparable nucleotidyltransfer efficiencies were observed in the kinetic studies of HldEs.
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Affiliation(s)
- Zhaoxiang Shi
- School of Traditional Chinese Materia Medica, Shenyang Pharmaceutical University, Shenyang, 117004, China
| | - Yue Tang
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing, 100101, China
| | | | - Min Wang
- School of Biotechnology and Health Sciences, Wuyi University, Jiangmen, 529020, China
| | - Zijian Zhong
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing, 100101, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Jingming Jia
- School of Traditional Chinese Materia Medica, Shenyang Pharmaceutical University, Shenyang, 117004, China
| | - Yihua Chen
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing, 100101, China.
- University of Chinese Academy of Sciences, Beijing, 100049, China.
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3
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Kaur H, Rode S, Kp S, Mahto JK, Alam MS, Gupta DN, Kar B, Singla J, Kumar P, Sharma AK. Characterization of haloacid dehalogenase superfamily acid phosphatase from Staphylococcus lugdunensis. Arch Biochem Biophys 2024; 753:109888. [PMID: 38232797 DOI: 10.1016/j.abb.2024.109888] [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: 11/10/2023] [Revised: 01/08/2024] [Accepted: 01/09/2024] [Indexed: 01/19/2024]
Abstract
The haloacid dehalogenase superfamily implicated in bacterial pathogenesis comprises different enzymes having roles in many metabolic pathways. Staphylococcus lugdunensis, a Gram-positive bacterium, is an opportunistic human pathogen causing infections in the central nervous system, urinary tract, bones, peritoneum, systemic conditions and cutaneous infection. The haloacid dehalogenase superfamily proteins play a significant role in the pathogenicity of certain bacteria, facilitating invasion, survival, and proliferation within host cells. The genome of S. lugdunensis encodes more than ten proteins belonging to this superfamily. However, none of them have been characterized. The present work reports the characterization of one of the haloacid dehalogenase superfamily proteins (SLHAD1) from Staphylococcus lugdunensis. The functional analysis revealed that SLHAD1 is a metal-dependent acid phosphatase, which catalyzes the dephosphorylation of phosphorylated metabolites of cellular pathways, including glycolysis, gluconeogenesis, nucleotides, and thiamine metabolism. Based on the substrate specificity and genomic analysis, the physiological function of SLHAD1 in thiamine metabolism has been tentatively assigned. The crystal structure of SLHAD1, lacking 49 residues at the C-terminal, was determined at 1.7 Å resolution with a homodimer in the asymmetric unit. It was observed that SLHAD1 exhibited time-dependent cleavage at a specific point, occurring through a self-initiated process. A combination of bioinformatics, biochemical, biophysical, and structural studies explored unique features of SLHAD1. Overall, the study revealed a detailed characterization of a critical enzyme of the human pathogen Staphylococcus lugdunensis, associated with several life-threatening infections.
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Affiliation(s)
- Harry Kaur
- Department of Biosciences and Bioengineering, Indian Institute of Technology Roorkee, Roorkee-247667, India
| | - Surabhi Rode
- Department of Biosciences and Bioengineering, Indian Institute of Technology Roorkee, Roorkee-247667, India
| | - Sandra Kp
- Department of Biosciences and Bioengineering, Indian Institute of Technology Roorkee, Roorkee-247667, India
| | - Jai Krishna Mahto
- Department of Biosciences and Bioengineering, Indian Institute of Technology Roorkee, Roorkee-247667, India
| | - Md Shahid Alam
- Department of Biosciences and Bioengineering, Indian Institute of Technology Roorkee, Roorkee-247667, India
| | - Deena Nath Gupta
- Department of Biosciences and Bioengineering, Indian Institute of Technology Roorkee, Roorkee-247667, India
| | - Bibekananda Kar
- Department of Biosciences and Bioengineering, Indian Institute of Technology Roorkee, Roorkee-247667, India
| | - Jitin Singla
- Department of Biosciences and Bioengineering, Indian Institute of Technology Roorkee, Roorkee-247667, India; Department of Computer Science and Engineering, Indian Institute of Technology Roorkee, Roorkee-247667, India
| | - Pravindra Kumar
- Department of Biosciences and Bioengineering, Indian Institute of Technology Roorkee, Roorkee-247667, India
| | - Ashwani Kumar Sharma
- Department of Biosciences and Bioengineering, Indian Institute of Technology Roorkee, Roorkee-247667, India.
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4
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Lin YH, Tu WC, Urban PL. Kinetic Profiling of Homogeneous and Heterogeneous Biocatalysts in Continuous Flow by Online Mass Spectrometry. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2023; 34:109-118. [PMID: 36515652 DOI: 10.1021/jasms.2c00283] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/17/2023]
Abstract
Enzyme kinetics is normally assessed by performing individual kinetic measurements using batch-type reactors (test tubes, microtiter plates), in which enzymes are mixed with different substrates. Some drawbacks of conventional methods are the large amounts of experimental materials, long analysis times, and limitations of spectrophotometry. Therefore, we have developed a method for facile determination of enzyme kinetics using online flow-based mass spectrometry. A concentration ramp of substrate or product was created by dynamically adjusting flow rates of pumps delivering stock solution of substrate and diluent. Precise kinetic measurements were performed by reaction product quantification and initial rate calculation. In the presence of ascending substrate concentrations, the rate of a target enzyme (penicillinase)-catalyzed hydrolysis was varied. By measuring the reaction product continuously, Michaelis constants (KM) could be calculated. The enzyme kinetic measurements for hydrolysis of penicillins were conducted based on this simple, rapid, and low sample consumption online flow device. In the homogeneous reaction, the KM values for amoxicillin, ampicillin, penicillin G, and penicillin V were 254.9 ± 14.5, 29.2 ± 0.3, 2.6 ± 0.1, and 5.4 ± 0.1 μM, respectively. In the heterogeneous reaction, the KM values for amoxicillin, ampicillin, penicillin G, and penicillin V were 408.9 ± 75.1, 114.4 ± 8.0, 21.8 ± 0.7, and 83.3 ± 4.8 μM, respectively. Apart from enzyme assay, the showcased method for the generation of temporal concentration ramps can be utilized to perform rapid quantity calibrations for mass spectrometric analyses.
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Affiliation(s)
- Yun-Hsuan Lin
- Department of Chemistry, National Tsing Hua University, 101, Section 2, Kuang-Fu Rd., Hsinchu300044, Taiwan
| | - Wei-Chien Tu
- Department of Chemistry, National Tsing Hua University, 101, Section 2, Kuang-Fu Rd., Hsinchu300044, Taiwan
| | - Pawel L Urban
- Department of Chemistry, National Tsing Hua University, 101, Section 2, Kuang-Fu Rd., Hsinchu300044, Taiwan
- Frontier Research Center on Fundamental and Applied Sciences of Matters, National Tsing Hua University, 101, Section 2, Kuang-Fu Rd., Hsinchu300044, Taiwan
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5
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Zheng M, Zheng M, Lupoli TJ. Expanding the Substrate Scope of a Bacterial Nucleotidyltransferase via Allosteric Mutations. ACS Infect Dis 2022; 8:2035-2044. [PMID: 36106727 DOI: 10.1021/acsinfecdis.2c00402] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/29/2023]
Abstract
Bacterial glycoconjugates, such as cell surface polysaccharides and glycoproteins, play important roles in cellular interactions and survival. Enzymes called nucleotidyltransferases use sugar-1-phosphates and nucleoside triphosphates (NTPs) to produce nucleoside diphosphate sugars (NDP-sugars), which serve as building blocks for most glycoconjugates. Research spanning several decades has shown that some bacterial nucleotidyltransferases have broad substrate tolerance and can be exploited to produce a variety of NDP-sugars in vitro. While these enzymes are known to be allosterically regulated by NDP-sugars and their fragments, much work has focused on the effect of active site mutations alone. Here, we show that rational mutations in the allosteric site of the nucleotidyltransferase RmlA lead to expanded substrate tolerance and improvements in catalytic activity that can be explained by subtle changes in quaternary structure and interactions with ligands. These observations will help inform future studies on the directed biosynthesis of diverse bacterial NDP-sugars and downstream glycoconjugates.
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Affiliation(s)
- Maggie Zheng
- Department of Chemistry, New York University, New York, New York 10003, United States
| | - Meng Zheng
- Department of Chemistry, New York University, New York, New York 10003, United States
| | - Tania J Lupoli
- Department of Chemistry, New York University, New York, New York 10003, United States
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Yang S, An X, Gu G, Yan Z, Jiang X, Xu L, Xiao M. Novel dTDP-l-Rhamnose Synthetic Enzymes (RmlABCD) From Saccharothrix syringae CGMCC 4.1716 for One-Pot Four-Enzyme Synthesis of dTDP-l-Rhamnose. Front Microbiol 2021; 12:772839. [PMID: 34819927 PMCID: PMC8606822 DOI: 10.3389/fmicb.2021.772839] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2021] [Accepted: 10/11/2021] [Indexed: 11/13/2022] Open
Abstract
Deoxythymidine diphospho-l-rhamnose (dTDP-l-rhamnose) is used by prokaryotic rhamnosyltransferases as the glycosyl donor for the synthesis of rhamnose-containing polysaccharides and compounds that have potential in pharmaceutical development, so its efficient synthesis has attracted much attention. In this study, we successfully cloned four putative dTDP-l-rhamnose synthesis genes Ss-rmlABCD from Saccharothrix syringae CGMCC 4.1716 and expressed them in Escherichia coli. The recombinant enzymes, Ss-RmlA (glucose-1-phosphate thymidylyltransferase), Ss-RmlB (dTDP-d-glucose 4,6-dehydratase), Ss-RmlC (dTDP-4-keto-6-deoxy-glucose 3,5-epimerase), and Ss-RmlD (dTDP-4-keto-rhamnose reductase), were confirmed to catalyze the sequential formation of dTDP-l-rhamnose from deoxythymidine triphosphate (dTTP) and glucose-1-phosphate (Glc-1-P). Ss-RmlA showed maximal enzyme activity at 37°C and pH 9.0 with 2.5mMMg2+, and the K m and k cat values for dTTP and Glc-1-P were 49.56μM and 5.39s-1, and 117.30μM and 3.46s-1, respectively. Ss-RmlA was promiscuous in the substrate choice and it could use three nucleoside triphosphates (dTTP, dUTP, and UTP) and three sugar-1-Ps (Glc-1-P, GlcNH2-1-P, and GlcN3-1-P) to form nine sugar nucleotides (dTDP-GlcNH2, dTDP-GlcN3, UDP-Glc, UDP-GlcNH2, UDP-GlcN3, dUDP-Glc, dUDP-GlcNH2, and dUDP-GlcN3). Ss-RmlB showed maximal enzyme activity at 50°C and pH 7.5 with 0.02mM NAD+, and the K m and k cat values for dTDP-glucose were 98.60μM and 11.2s-1, respectively. A one-pot four-enzyme reaction system was developed by simultaneously mixing all of the substrates, reagents, and four enzymes Ss-RmlABCD in one pot for the synthesis of dTDP-l-rhamnose and dUDP-l-rhamnose with the maximal yield of 65% and 46%, respectively, under the optimal conditions. dUDP-l-rhamnose was a novel nucleotide-activated rhamnose reported for the first time.
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Affiliation(s)
- Shida Yang
- State Key Laboratory of Microbial Technology, Shandong University, Qingdao, China
| | - Xiaonan An
- State Key Laboratory of Microbial Technology, Shandong University, Qingdao, China
| | - Guofeng Gu
- National Glycoengineering Research Center, Shandong Key Laboratory of Carbohydrate Chemistry and Glycobiology, Shandong University, Qingdao, China
- NMPA Key Laboratory for Quality Research and Evaluation of Carbohydrate-based Medicine Shandong University, Qingdao, China
| | - Zhenxin Yan
- State Key Laboratory of Microbial Technology, Shandong University, Qingdao, China
| | - Xukai Jiang
- National Glycoengineering Research Center, Shandong Key Laboratory of Carbohydrate Chemistry and Glycobiology, Shandong University, Qingdao, China
- NMPA Key Laboratory for Quality Research and Evaluation of Carbohydrate-based Medicine Shandong University, Qingdao, China
| | - Li Xu
- National Glycoengineering Research Center, Shandong Key Laboratory of Carbohydrate Chemistry and Glycobiology, Shandong University, Qingdao, China
- NMPA Key Laboratory for Quality Research and Evaluation of Carbohydrate-based Medicine Shandong University, Qingdao, China
| | - Min Xiao
- State Key Laboratory of Microbial Technology, Shandong University, Qingdao, China
- National Glycoengineering Research Center, Shandong Key Laboratory of Carbohydrate Chemistry and Glycobiology, Shandong University, Qingdao, China
- NMPA Key Laboratory for Quality Research and Evaluation of Carbohydrate-based Medicine Shandong University, Qingdao, China
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7
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Zheng M, Zheng M, Epstein S, Harnagel AP, Kim H, Lupoli TJ. Chemical Biology Tools for Modulating and Visualizing Gram-Negative Bacterial Surface Polysaccharides. ACS Chem Biol 2021; 16:1841-1865. [PMID: 34569792 DOI: 10.1021/acschembio.1c00341] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Abstract
Bacterial cells present a wide diversity of saccharides that decorate the cell surface and help mediate interactions with the environment. Many Gram-negative cells express O-antigens, which are long sugar polymers that makeup the distal portion of lipopolysaccharide (LPS) that constitutes the surface of the outer membrane. This review highlights chemical biology tools that have been developed in recent years to facilitate the modulation of O-antigen synthesis and composition, as well as related bacterial polysaccharide pathways, and the detection of unique glycan sequences. Advances in the biochemistry and structural biology of O-antigen biosynthetic machinery are also described, which provide guidance for the design of novel chemical and biomolecular probes. Many of the tools noted here have not yet been utilized in biological systems and offer researchers the opportunity to investigate the complex sugar architecture of Gram-negative cells.
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Affiliation(s)
- Meng Zheng
- Department of Chemistry, New York University, New York, 10003 New York, United States
| | - Maggie Zheng
- Department of Chemistry, New York University, New York, 10003 New York, United States
| | - Samuel Epstein
- Department of Chemistry, New York University, New York, 10003 New York, United States
| | - Alexa P. Harnagel
- Department of Chemistry, New York University, New York, 10003 New York, United States
| | - Hanee Kim
- Department of Chemistry, New York University, New York, 10003 New York, United States
| | - Tania J. Lupoli
- Department of Chemistry, New York University, New York, 10003 New York, United States
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8
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Taj A, Jia L, Sha S, Wang C, Ullah H, Haris M, Ma X, Ma Y. Functional analysis and enzyme characterization of Mannose-1-phosphate guanylyl transferase (ManB) from Mycobacterium tuberculosis. Res Microbiol 2021; 173:103884. [PMID: 34644596 DOI: 10.1016/j.resmic.2021.103884] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2021] [Revised: 09/29/2021] [Accepted: 10/01/2021] [Indexed: 10/20/2022]
Abstract
Mycobacterium tuberculosis cell wall consist variety of mannose containing glycoconjugates including lipomannan (LM) and lipoarabinomannan (LAM). These lipoglycans are involved in cell wall integrity and play role in virulence of M. tuberculosis by modulating host immune response. GDP-mannose, required for the synthesis of lipoglycans, is catalyzed by enzyme Mannose-1-phosphate guanylyl transferase (ManB). The enzyme with similar function has been studied in variety of species of prokaryotes and eukaryotes. However, biological role of ManB and its enzymatic activity remains uncharacterized in M. tuberculosis. In present study, we elucidated the role of enzyme by constructing manB knockdown strain of M. tuberculosis H37Ra. The manB knockdown decreased the cell growth and also effected the morphology of M. tuberculosis by altering the permeability of cell membrane. These findings provide the understanding on ManB function and suggesting that ManB could be the potential target for novel anti-tuberculosis drug. Furthermore, we also characterized ManB enzyme by establishing 96 well plate colorimetric assay and determined the kinetic properties including initial velocity, optimum temperature, optimum pH and other kinetic parameters. Our established assay will be helpful for further high throughput screening of potential inhibitors against ManB.
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Affiliation(s)
- Ayaz Taj
- Department of Biochemistry and Molecular Biology, Dalian Medical University, 9 W. Lushun South Road, Dalian, 116044, China.
| | - Liqiu Jia
- Department of Biochemistry and Molecular Biology, Dalian Medical University, 9 W. Lushun South Road, Dalian, 116044, China.
| | - Shanshan Sha
- Department of Biochemistry and Molecular Biology, Dalian Medical University, 9 W. Lushun South Road, Dalian, 116044, China.
| | - Chao Wang
- College of Pharmacy, Dalian Medical University, 9 W. Lushun South Road, Dalian, 116044, China.
| | - Hayan Ullah
- Department of Biochemistry and Molecular Biology, Dalian Medical University, 9 W. Lushun South Road, Dalian, 116044, China.
| | - Muhammad Haris
- Department of Biochemistry and Molecular Biology, Dalian Medical University, 9 W. Lushun South Road, Dalian, 116044, China.
| | - Xiaochi Ma
- College of Pharmacy, Dalian Medical University, 9 W. Lushun South Road, Dalian, 116044, China.
| | - Yufang Ma
- Department of Biochemistry and Molecular Biology, Dalian Medical University, 9 W. Lushun South Road, Dalian, 116044, China; Department of Microbiology, Dalian Medical University, 9 W. Lushun South Road, Dalian, 116044, China.
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9
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Kim S, Jo S, Kim MS, Shin DH. A study of inhibitors of d- glycero-β-d- manno-heptose-1-phosphate adenylyltransferase from Burkholderia pseudomallei as a potential antibiotic target. J Enzyme Inhib Med Chem 2021; 36:776-784. [PMID: 33733972 PMCID: PMC7993394 DOI: 10.1080/14756366.2021.1900166] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023] Open
Abstract
d-Glycero-β-d-manno-heptose-1-phosphate adenylyltransferase from Burkholderia pseudomallei (BpHldC) is the fourth enzyme in the ADP‐l‐glycero‐β‐d‐manno‐heptose biosynthesis pathway producing a lipopolysaccharide core. Therefore, BpHldC is an anti-melioidosis target. Three ChemBridge compounds purchased from ChemBridge Corporation (San Diego, CA) were found to have an effective inhibitory activity on BpHldC. Interestingly, ChemBridge 7929959 was the most effective compound due to the presence of the terminal benzyl group. The enzyme kinetic study revealed that most of them show mixed type inhibitory modes against ATP and βG1P. The induced-fit docking indicated that the medium affinity of ChemBridge 7929959 is originated from its benzyl group occupying the substrate-binding pocket of BpHldC. The inhibitory role of terminal aromatic groups was proven with ChemBridge 7570508. Combined with the previous study, ChemBridge 7929959 is found to work as a dual inhibitor against both HldC and HddC. Therefore, three ChemBridge compounds can be developed as a potent anti-melioidosis agent with a novel inhibitory concept.
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Affiliation(s)
- Suwon Kim
- College of Pharmacy and Graduate School of Pharmaceutical Sciences, Ewha W. University, Seoul, Republic of Korea
| | - Seri Jo
- College of Pharmacy and Graduate School of Pharmaceutical Sciences, Ewha W. University, Seoul, Republic of Korea
| | - Mi-Sun Kim
- College of Pharmacy and Graduate School of Pharmaceutical Sciences, Ewha W. University, Seoul, Republic of Korea
| | - Dong Hae Shin
- College of Pharmacy and Graduate School of Pharmaceutical Sciences, Ewha W. University, Seoul, Republic of Korea
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10
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Inhibition of d-glycero-β-d-manno-heptose 1-phosphate adenylyltransferase from Burkholderia pseudomallei by epigallocatechin gallate and myricetin. Biochem J 2021; 478:235-245. [PMID: 33346350 DOI: 10.1042/bcj20200677] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2020] [Revised: 12/10/2020] [Accepted: 12/21/2020] [Indexed: 01/12/2023]
Abstract
Flavonoids play beneficial roles in various human diseases. In this study, a flavonoid library was employed to probe inhibitors of d-glycero-β-d-manno-heptose-1-phosphate adenylyltransferase from Burkholderia pseudomallei (BpHldC) and two flavonoids, epigallocatechin gallate (EGCG) and myricetin, have been discovered. BpHldC is one of the essential enzymes in the ADP-l-glycero-β-d-manno-heptose biosynthesis pathway constructing lipopolysaccharide of B. pseudomallei. Enzyme kinetics study showed that two flavonoids work through different mechanisms to block the catalytic activity of BpHldC. Among them, a docking study of EGCG was performed and the binding mode could explain its competitive inhibitory mode for both ATP and βG1P. Analyses with EGCG homologs could reveal the important functional moieties, too. This study is the first example of uncovering the inhibitory activity of flavonoids against the ADP-l-glycero-β-d-manno-heptose biosynthesis pathway and especially targeting HldC. Since there are no therapeutic agents and vaccines available against melioidosis, EGCG and myricetin can be used as templates to develop antibiotics over B. pseudomallei.
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11
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Qu D, Zhao X, Sun Y, Wu FL, Tao SC. Mycobacterium tuberculosis Thymidylyltransferase RmlA Is Negatively Regulated by Ser/Thr Protein Kinase PknB. Front Microbiol 2021; 12:643951. [PMID: 33868202 PMCID: PMC8044546 DOI: 10.3389/fmicb.2021.643951] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2020] [Accepted: 02/28/2021] [Indexed: 11/13/2022] Open
Abstract
Ser/Thr phosphorylation by serine/threonine protein kinases (STPKs) plays significant roles in molecular regulation, which allows Mycobacteria to adapt their cell wall structure in response to the environment changes. Identifying direct targets of STPKs and determining their activities are therefore critical to revealing their function in Mycobacteria, for example, in cell wall formation and virulence. Herein, we reported that RmlA, a crucial L-rhamnose biosynthesis enzyme, is a substrate of STPK PknB in Mycobacterium tuberculosis (M. tuberculosis). Mass spectrometry analysis revealed that RmlA is phosphorylated at Thr-12, Thr-54, Thr-197, and Thr-12 is located close to the catalytic triad of RmlA. Biochemical and phenotypic analysis of two RmlA mutants, T12A/T12D, showed that their activities were reduced, and cell wall formation was negatively affected. Moreover, virulence of RmlA T12D mutant was attenuated in a macrophage model. Overall, these results provide the first evidence for the role of PknB-dependent RmlA phosphorylation in regulating cell wall formation in Mycobacteria, with significant implications for pathogenicity.
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Affiliation(s)
- Dehui Qu
- Key Laboratory of Molecular Module-Based Breeding of High Yield and Abiotic Resistant Plants in Universities of Shandong, School of Agriculture, Ludong University, Yantai, China.,State Key Laboratory of Microbial Metabolism and School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, China
| | - Xiaohui Zhao
- Key Laboratory of Molecular Module-Based Breeding of High Yield and Abiotic Resistant Plants in Universities of Shandong, School of Agriculture, Ludong University, Yantai, China
| | - Yao Sun
- Key Laboratory of Molecular Module-Based Breeding of High Yield and Abiotic Resistant Plants in Universities of Shandong, School of Agriculture, Ludong University, Yantai, China
| | - Fan-Lin Wu
- Key Laboratory of Molecular Module-Based Breeding of High Yield and Abiotic Resistant Plants in Universities of Shandong, School of Agriculture, Ludong University, Yantai, China
| | - Sheng-Ce Tao
- Key Laboratory of Systems Biomedicine (Ministry of Education), Shanghai Center for Systems Biomedicine, Shanghai Jiao Tong University, Shanghai, China
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12
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Kim S, Jo S, Kim MS, Shin DH. A study of Rose Bengal against a 2-keto-3-deoxy-d- manno-octulosonate cytidylyltransferase as an antibiotic candidate. J Enzyme Inhib Med Chem 2021; 35:1414-1421. [PMID: 32588669 PMCID: PMC7717453 DOI: 10.1080/14756366.2020.1751150] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
Abstract
Frequent occurrences of multi-drug resistance of pathogenic Gram-negative bacteria threaten human beings. The CMP-2-keto-3-deoxy-d-manno-octulosonic acid biosynthesis pathway is one of the new targets for antibiotic design. 2-Keto-3-deoxy-d-manno-octulosonate cytidylyltransferase (KdsB) is the key enzyme in this pathway. KdsB proteins from Burkholderia pseudomallei (Bp), B. thailandensis (Bt), Pseudomonas aeruginosa (Pa), and Chlamydia psittaci (Cp) have been assayed to find inhibitors. Interestingly, Rose Bengal (4,5,6,7-tetrachloro-2′,4′,5′,7′-tetraiodofluorescein) was turned out to be an inhibitor of three KdsBs (BpKdsB, BtKdsB, and PaKdsB) with promising IC50 values and increased thermostability. The inhibitory enzyme kinetics of Rose Bengal revealed that it is competitive with 2-keto-3-deoxy-manno-octulosonic acid (KDO) but non-competitive against cytidine 5′-triphosphate (CTP). Induced-fit docking analysis of PaKdsB revealed that Arg160 and Arg185 together with other interactions in the substrate binding site seemed to play an important role in binding with Rose Bengal. We suggest that Rose Bengal can be used as the scaffold to develop potential antibiotics.
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Affiliation(s)
- Suwon Kim
- Graduate School of Pharmaceutical Sciences, Ewha Woman's University, Seoul, Republic of Korea
| | - Seri Jo
- Graduate School of Pharmaceutical Sciences, Ewha Woman's University, Seoul, Republic of Korea
| | - Mi-Sun Kim
- Graduate School of Pharmaceutical Sciences, Ewha Woman's University, Seoul, Republic of Korea
| | - Dong Hae Shin
- Graduate School of Pharmaceutical Sciences, Ewha Woman's University, Seoul, Republic of Korea
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13
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Kim S, Jo S, Kim MS, Shin DH. A triple-targeting inhibitory activity of Rose Bengal on polysaccharide biosynthesis of Burkholderia pseudomallei. Arch Pharm (Weinheim) 2021; 354:e2000360. [PMID: 33555065 DOI: 10.1002/ardp.202000360] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2020] [Revised: 12/31/2020] [Accepted: 01/15/2021] [Indexed: 11/08/2022]
Abstract
Sugar nucleotidyltransferases (SNTs) participate in various biosynthesis pathways constructing polysaccharides in Gram-negative bacteria. In this study, a triple-targeting inhibitory activity of Rose Bengal against SNTs such as d-glycero-α-d-manno-heptose-1-phosphate guanylyltransferase (HddC), d-glycero-β-d-manno-heptose-1-phosphate adenylyltransferase (HldC), and 3-deoxy-d-manno-oct-2-ulosonic acid cytidylyltransferase (KdsB) from Burkholderia pseudomallei is provided. Rose Bengal effectively suppresses the nucleotidyltransferase activity of the three SNTs, and its IC50 values are 10.42, 0.76, and 5.31 µM, respectively. Interestingly, Rose Bengal inhibits the three enzymes regardless of their primary, secondary, tertiary, and quaternary structural differences. The experimental results indicate that Rose Bengal possesses the plasticity to shape its conformation suitable to interact with the three SNTs. As HddC functions in the formation of capsular polysaccharides and HldC and KdsB produce building blocks to constitute the inner core of lipopolysaccharide, Rose Bengal is a potential candidate to design antibiotics in a new category. In particular, it can be developed as a specific antimelioidosis agent. As the mortality rate of the infected people caused by B. pseudomallei is quite high, there is an urgent need for specific antimelioidosis agents. Therefore, a further study is being carried out with derivatives of Rose Bengal.
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Affiliation(s)
- Suwon Kim
- Department of Pharmacy, College of Pharmacy and Graduate School of Pharmaceutical Sciences, Ewha Womans University, Seoul, Republic of Korea
| | - Seri Jo
- Department of Pharmacy, College of Pharmacy and Graduate School of Pharmaceutical Sciences, Ewha Womans University, Seoul, Republic of Korea
| | - Mi-Sun Kim
- Department of Pharmacy, College of Pharmacy and Graduate School of Pharmaceutical Sciences, Ewha Womans University, Seoul, Republic of Korea
| | - Dong H Shin
- Department of Pharmacy, College of Pharmacy and Graduate School of Pharmaceutical Sciences, Ewha Womans University, Seoul, Republic of Korea
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14
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A severe leakage of intermediates to shunt products in acarbose biosynthesis. Nat Commun 2020; 11:1468. [PMID: 32193369 PMCID: PMC7081202 DOI: 10.1038/s41467-020-15234-8] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2019] [Accepted: 02/23/2020] [Indexed: 11/08/2022] Open
Abstract
The α-glucosidase inhibitor acarbose, produced by Actinoplanes sp. SE50/110, is a well-known drug for the treatment of type 2 diabetes mellitus. However, the largely unexplored biosynthetic mechanism of this compound has impeded further titer improvement. Herein, we uncover that 1-epi-valienol and valienol, accumulated in the fermentation broth at a strikingly high molar ratio to acarbose, are shunt products that are not directly involved in acarbose biosynthesis. Additionally, we find that inefficient biosynthesis of the amino-deoxyhexose moiety plays a role in the formation of these shunt products. Therefore, strategies to minimize the flux to the shunt products and to maximize the supply of the amino-deoxyhexose moiety are implemented, which increase the acarbose titer by 1.2-fold to 7.4 g L−1. This work provides insights into the biosynthesis of the C7-cyclitol moiety and highlights the importance of assessing shunt product accumulation when seeking to improve the titer of microbial pharmaceutical products. Biosynthetic mechanism for the type 2 diabetes treatment drug acarbose is not fully revealed. Here, the authors show that shunt pathways and inefficient amino-deoxyhexose biosynthesis lead to 1-epi-valienol and valienol accumulation, and minimizing the flux to these shunt products can increase acarbose titer in Actinoplanes species.
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15
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Kim S, Kim MS, Jo S, Shin DH. GTP Preference of d-Glycero-α-d- manno-Heptose-1-Phosphate Guanylyltransferase from Yersinia pseudotuberculosis. Int J Mol Sci 2019; 21:ijms21010280. [PMID: 31906195 PMCID: PMC6981941 DOI: 10.3390/ijms21010280] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2019] [Revised: 12/23/2019] [Accepted: 12/24/2019] [Indexed: 12/22/2022] Open
Abstract
d-glycero-α-d-manno-heptose-1-phosphate guanylyltransferase (HddC) is the fourth enzyme synthesizing a building component of lipopolysaccharide (LPS) of Gram-negative bacteria. Since HddC is a potential new target to develop antibiotics, the analysis of the structural and functional relationship of the complex structure will lead to a better idea to design inhibitory compounds. X-ray crystallography and biochemical experiments to elucidate the guanine preference were performed based on the multiple sequence alignment. The crystal structure of HddC from Yersinia pseudotuberculosis (YPT) complexed with guanosine 5′-(β-amino)-diphosphate (GMPPN) has been determined at 1.55 Å resolution. Meanwhile, the mutants revealed their reduced guanine affinity, instead of acquiring noticeable pyrimidine affinity. The complex crystal structure revealed that GMPPN is docked in the catalytic site with the aid of Glu80 positioning on the conserved motif EXXPLGTGGA. In the HddC family, this motif is expected to recruit nucleotides through interacting with bases. The crystal structure shows that oxygen atoms of Glu80 forming two hydrogen bonds play a critical role in interaction with two nitrogen atoms of the guanine base of GMPPN. Interestingly, the binding of GMPPN induced the formation of an oxyanion hole-like conformation on the L(S/A/G)X(S/G) motif and consequently influenced on inducing a conformational shift of the region around Ser55.
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16
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Kim S, Jo S, Kim MS, Shin DH. A Study of a Potent Inhibitor Against a GDP-6-Deoxy-α-d- Manno-Heptose Biosynthesis Pathway as Antibiotic Candidates. Microb Drug Resist 2019; 26:385-390. [PMID: 31613705 DOI: 10.1089/mdr.2019.0144] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022] Open
Abstract
The GDP-6-deoxy-α-d-manno-heptose is a key building block molecule in constructing lipopolysaccharide of Gram-negative bacteria. Therefore, blockage of the biosynthesis pathway of GDP-6-deoxy-α-d-manno-heptose is lethal or increases antibiotics susceptibility to pathogens. In this study, we assayed d-glycero-α-d-manno-heptose-1-phosphate guanylyltransferase (HddC) from Yersinia pseudotuberculosis (Yp) using an efficient assay method supplying its natural substrate. Using the method, 102 chemical compounds were tested to search inhibitory compounds and electrospray ionization mass spectrometry was used to detect the HddC from Y. pseudotuberculosis (YpHddC) reaction product, GDP-d-glycero-α-d-manno-heptose. Interestingly, one promising lead, ethyl 5-({[(5-benzyl-1, 3, 4-oxadiazol-2-yl) thio] acetyl} amino)-4-cyano-3-methyl-2-thiophenecarboxylate (Chembridge 7929959), was discovered. The inhibitory activity of the lead compound against YpHddC has been proven by blocking its nucleotidyltransferase activity transferring the GMP moiety to α-d-mannose-1-phosphate (αM1P). Chembridge 7929959 shows that the half maximal inhibitory concentration (IC50) is 0.222 μM indicating its affinity with αM1P.
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Affiliation(s)
- Suwon Kim
- Department of pharmacy, Graduate School of Pharmaceutical Sciences, Ewha Womans University, Seoul, Republic of Korea
| | - Seri Jo
- Department of pharmacy, Graduate School of Pharmaceutical Sciences, Ewha Womans University, Seoul, Republic of Korea
| | - Mi-Sun Kim
- Department of pharmacy, Graduate School of Pharmaceutical Sciences, Ewha Womans University, Seoul, Republic of Korea
| | - Dong Hae Shin
- Department of pharmacy, Graduate School of Pharmaceutical Sciences, Ewha Womans University, Seoul, Republic of Korea
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Ollinger J, Kumar A, Roberts DM, Bailey MA, Casey A, Parish T. A high-throughput whole cell screen to identify inhibitors of Mycobacterium tuberculosis. PLoS One 2019; 14:e0205479. [PMID: 30650074 PMCID: PMC6334966 DOI: 10.1371/journal.pone.0205479] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2018] [Accepted: 12/04/2018] [Indexed: 12/26/2022] Open
Abstract
Tuberculosis is a disease of global importance for which novel drugs are urgently required. We developed a whole-cell phenotypic screen which can be used to identify inhibitors of Mycobacterium tuberculosis growth. We used recombinant strains of virulent M. tuberculosis which express far-red fluorescent reporters and used fluorescence to monitor growth in vitro. We optimized our high throughput assays using both 96-well and 384-well plates; both formats gave assays which met stringent reproducibility and robustness tests. We screened a compound set of 1105 chemically diverse compounds previously shown to be active against M. tuberculosis and identified primary hits which showed ≥ 90% growth inhibition. We ranked hits and identified three chemical classes of interest-the phenoxyalkylbenzamidazoles, the benzothiophene 1-1 dioxides, and the piperidinamines. These new compound classes may serve as starting points for the development of new series of inhibitors that prevent the growth of M. tuberculosis. This assay can be used for further screening, or could easily be adapted to other strains of M. tuberculosis.
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Affiliation(s)
- Juliane Ollinger
- Infectious Disease Research Institute, Seattle, Washington, United States of America
| | - Anuradha Kumar
- Infectious Disease Research Institute, Seattle, Washington, United States of America
| | - David M. Roberts
- Infectious Disease Research Institute, Seattle, Washington, United States of America
| | - Mai A. Bailey
- Infectious Disease Research Institute, Seattle, Washington, United States of America
| | - Allen Casey
- Infectious Disease Research Institute, Seattle, Washington, United States of America
| | - Tanya Parish
- Infectious Disease Research Institute, Seattle, Washington, United States of America
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18
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Bahia FM, de Almeida GC, de Andrade LP, Campos CG, Queiroz LR, da Silva RLV, Abdelnur PV, Corrêa JR, Bettiga M, Parachin NS. Rhamnolipids production from sucrose by engineered Saccharomyces cerevisiae. Sci Rep 2018; 8:2905. [PMID: 29440668 PMCID: PMC5811566 DOI: 10.1038/s41598-018-21230-2] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2017] [Accepted: 01/31/2018] [Indexed: 11/21/2022] Open
Abstract
Biosurfactants are biological tensioactive agents that can be used in the cosmetic and food industries. Rhamnolipids are glycolipid biosurfactants naturally produced by Pseudomonas aeruginosa and are composed of one or two rhamnose molecules linked to beta-hydroxy fatty acid chains. These compounds are green alternatives to petrochemical surfactants, but their large-scale production is still in its infancy, hindered due to pathogenicity of natural producer, high substrate and purification costs and low yields and productivities. This study, for the first time, aimed at producing mono-rhamnolipids from sucrose by recombinant GRAS Saccharomyces cerevisiae strains. Six enzymes from P. aeruginosa involved in mono-rhamnolipid biosynthesis were functionally expressed in the yeast. Furthermore, its SUC2 invertase gene was disrupted and a sucrose phosphorylase gene from Pelomonas saccharophila was also expressed to reduce the pathway's overall energy requirement. Two strains were constructed aiming to produce mono-rhamnolipids and the pathway's intermediate dTDP-L-rhamnose. Production of both molecules was analyzed by confocal microscopy and mass spectrometry, respectively. These strains displayed, for the first time as a proof of concept, the potential of production of these molecules by a GRAS eukaryotic microorganism from an inexpensive substrate. These constructs show the potential to further improve rhamnolipids production in a yeast-based industrial bioprocess.
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Affiliation(s)
- Frederico Mendonça Bahia
- Department of Molecular Biology, Biological Sciences Institute, University of Brasília (UnB), Campus Darcy Ribeiro, Block K. Postal code: 70.790-900, Brasilia, Federal District, Brazil
| | - Gabriela Carneiro de Almeida
- Catholic University of Brasília (UCB), Advanced Campus Asa Norte, SGAN 916 Block B Avenue W5, Postal code: 70.790-160, Brasilia, Federal District, Brazil
| | - Lorena Pereira de Andrade
- Department of Molecular Biology, Biological Sciences Institute, University of Brasília (UnB), Campus Darcy Ribeiro, Block K. Postal code: 70.790-900, Brasilia, Federal District, Brazil
| | - Christiane Gonçalves Campos
- Brazilian Agricultural Research Corporation, Embrapa Agroenergy, W3 Norte, PqEB, Postal code: 70770-901, Brasília, Federal District, Brazil
- Institute of Chemistry, Federal University of Goiás, Campus Samambaia, Postal code: 74690-900, Goiânia, Goiás, Brazil
| | - Lúcio Rezende Queiroz
- Department of Molecular Biology, Biological Sciences Institute, University of Brasília (UnB), Campus Darcy Ribeiro, Block K. Postal code: 70.790-900, Brasilia, Federal District, Brazil
| | - Rayane Luzia Vieira da Silva
- Catholic University of Brasília (UCB), Advanced Campus Asa Norte, SGAN 916 Block B Avenue W5, Postal code: 70.790-160, Brasilia, Federal District, Brazil
| | - Patrícia Verardi Abdelnur
- Brazilian Agricultural Research Corporation, Embrapa Agroenergy, W3 Norte, PqEB, Postal code: 70770-901, Brasília, Federal District, Brazil
- Institute of Chemistry, Federal University of Goiás, Campus Samambaia, Postal code: 74690-900, Goiânia, Goiás, Brazil
| | - José Raimundo Corrêa
- Department of Molecular Biology, Biological Sciences Institute, University of Brasília (UnB), Campus Darcy Ribeiro, Block K. Postal code: 70.790-900, Brasilia, Federal District, Brazil
| | - Maurizio Bettiga
- Department of Biology and Biological Engineering, Division of Industrial Biotechnology, Chalmers University of Technology, SE-41296, Gothenburg, Sweden
- EviKrets Biobased Processes Consultants, Gibraltarsgatan 40, 41280, Gothenburg, Sweden
| | - Nádia Skorupa Parachin
- Department of Molecular Biology, Biological Sciences Institute, University of Brasília (UnB), Campus Darcy Ribeiro, Block K. Postal code: 70.790-900, Brasilia, Federal District, Brazil.
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19
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Li ZZ, Riegert AS, Goneau MF, Cunningham AM, Vinogradov E, Li J, Schoenhofen IC, Thoden JB, Holden HM, Gilbert M. Characterization of the dTDP-Fuc3N and dTDP-Qui3N biosynthetic pathways in Campylobacter jejuni 81116. Glycobiology 2018; 27:358-369. [PMID: 28096310 DOI: 10.1093/glycob/cww136] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2016] [Accepted: 01/11/2017] [Indexed: 11/12/2022] Open
Abstract
The Gram-negative bacterium Campylobacter jejuni 81116 (Penner serotype HS:6) has a class E lipooligosaccharide (LOS) biosynthesis locus containing 19 genes, which encode for 11 putative glycosyltransferases, 1 lipid A acyltransferase and 7 enzymes thought to be involved in the biosynthesis of dideoxyhexosamine (ddHexN) moieties. Although the LOS outer core structure of C. jejuni 81116 is still unknown, recent mass spectrometry analyses suggest that it contains acetylated forms of two ddHexN residues. For this investigation, five of the genes encoding enzymes reportedly involved in the biosyntheses of these sugar residues were examined, rmlA, rmlB, wlaRA, wlaRB and wlaRG. Specifically, these genes were cloned and expressed in Escherichia coli, and the corresponding enzymes were purified and tested for biochemical activity. Here we present data demonstrating that RmlA functions as a glucose-1-phosphate thymidylyltransferase and that RmlB is a thymidine diphosphate (dTDP)-glucose 4,6-dehydratase. We also show, through nuclear magnetic resonance spectroscopy and mass spectrometry analyses, that WlaRG, when utilized in coupled assays with either WlaRA or WlaRB and dTDP-4-keto-6-deoxyglucose, results in the production of either dTDP-3-amino-3,6-dideoxy-d-galactose (dTDP-Fuc3N) or dTDP-3-amino-3,6-dideoxy-d-glucose (dTDP-Qui3N), respectively. In addition, the X-ray crystallographic structures of the 3,4-ketoisomerases, WlaRA and WlaRB, were determined to 2.14 and 2.0 Å resolutions, respectively. Taken together, the data reported herein demonstrate that C. jejuni 81116 utilizes five enzymes to synthesize dTDP-Fuc3N or dTDP-Qui3N and that WlaRG, an aminotransferase, can function on sugars with differing stereochemistry about their C-4' carbons. Importantly, the data reveal that C. jejuni 81116 has the ability to synthesize two isomeric ddHexN forms.
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Affiliation(s)
- Zack Z Li
- National Research Council Canada, Human Health Therapeutics, 100 Sussex Drive, Ottawa, ON, Canada
| | - Alexander S Riegert
- Department of Biochemistry, University of Wisconsin, 440 Henry Mall, Madison, WI, USA
| | - Marie-France Goneau
- National Research Council Canada, Human Health Therapeutics, 100 Sussex Drive, Ottawa, ON, Canada
| | - Anna M Cunningham
- National Research Council Canada, Human Health Therapeutics, 100 Sussex Drive, Ottawa, ON, Canada
| | - Evgeny Vinogradov
- National Research Council Canada, Human Health Therapeutics, 100 Sussex Drive, Ottawa, ON, Canada
| | - Jianjun Li
- National Research Council Canada, Human Health Therapeutics, 100 Sussex Drive, Ottawa, ON, Canada
| | - Ian C Schoenhofen
- National Research Council Canada, Human Health Therapeutics, 100 Sussex Drive, Ottawa, ON, Canada
| | - James B Thoden
- Department of Biochemistry, University of Wisconsin, 440 Henry Mall, Madison, WI, USA
| | - Hazel M Holden
- Department of Biochemistry, University of Wisconsin, 440 Henry Mall, Madison, WI, USA
| | - Michel Gilbert
- National Research Council Canada, Human Health Therapeutics, 100 Sussex Drive, Ottawa, ON, Canada
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20
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General assay for enzymes in the heptose biosynthesis pathways using electrospray ionization mass spectrometry. Appl Microbiol Biotechnol 2017; 101:4521-4532. [DOI: 10.1007/s00253-017-8148-1] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2016] [Revised: 01/12/2017] [Accepted: 01/25/2017] [Indexed: 10/20/2022]
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21
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Abstract
The cell wall of Mycobacterium tuberculosis is unique in that it differs significantly from those of both Gram-negative and Gram-positive bacteria. The thick, carbohydrate- and lipid-rich cell wall with distinct lipoglycans enables mycobacteria to survive under hostile conditions such as shortage of nutrients and antimicrobial exposure. The key features of this highly complex cell wall are the mycolyl-arabinogalactan-peptidoglycan (mAGP)-based and phosphatidyl-myo-inositol-based macromolecular structures, with the latter possessing potent immunomodulatory properties. These structures are crucial for the growth, viability, and virulence of M. tuberculosis and therefore are often the targets of effective chemotherapeutic agents against tuberculosis. Over the past decade, sophisticated genomic and molecular tools have advanced our understanding of the primary structure and biosynthesis of these macromolecules. The availability of the full genome sequences of various mycobacterial species, including M. tuberculosis, Mycobacterium marinum, and Mycobacterium bovis BCG, have greatly facilitated the identification of large numbers of drug targets and antigens specific to tuberculosis. Techniques to manipulate mycobacteria have also improved extensively; the conditional expression-specialized transduction essentiality test (CESTET) is currently used to determine the essentiality of individual genes. Finally, various biosynthetic assays using either purified proteins or synthetic cell wall acceptors have been developed to study enzyme function. This article focuses on the recent advances in determining the structural details and biosynthesis of arabinogalactan, lipoarabinomannan, and related glycoconjugates.
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22
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A 96-well microtiter plate assay for high-throughput screening of Mycobacterium tuberculosis dTDP-d-glucose 4,6-dehydratase inhibitors. Anal Biochem 2016; 498:53-8. [PMID: 26778528 DOI: 10.1016/j.ab.2016.01.004] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2015] [Revised: 01/05/2016] [Accepted: 01/06/2016] [Indexed: 11/23/2022]
Abstract
Mycobacterium tuberculosis dTDP-d-glucose 4,6-dehydratase (RmlB) is the second enzyme for the biosynthesis of dTDP-l-rhamnose, which is a sugar donor to the synthesis of the cell wall linker, d-N-acetylglucosamine-l-rhamnose. RmlB is essential to mycobacterial growth and is not found in humans; therefore, it is a potential target for developing new anti-tuberculosis drugs. So far, there has been no suitable method for high-throughput screening of RmlB inhibitors. Here, the recombinant M. tuberculosis RmlB was purified and an absorbance-based microtiter plate assay was developed for RmlB activity. It could be used for high-throughput screening of RmlB inhibitors. The kinetic properties of M. tuberculosis RmlB, including optimal pH, optimal temperature, the effect of metal ions, and the kinetic parameters, were determined with this assay. The inhibitory effects of dTTP and dTDP on M. tuberculosis RmlB were also studied with the assay.
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23
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Li S, Wang H, Ma J, Gu G, Chen Z, Guo Z. One-pot four-enzyme synthesis of thymidinediphosphate-l-rhamnose. Chem Commun (Camb) 2016; 52:13995-13998. [DOI: 10.1039/c6cc08366h] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/14/2023]
Abstract
A concise and effective one-pot four-enzyme synthesis of dTDP-Rha, the substrate of rhamnosyltransferases, is described.
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Affiliation(s)
- Siqiang Li
- National Glycoengineering Research Center and Shandong Provincial Key Laboratory of Carbohydrate Chemistry and Glycobiology
- Shandong University
- Jinan 250100
- China
| | - Hong Wang
- National Glycoengineering Research Center and Shandong Provincial Key Laboratory of Carbohydrate Chemistry and Glycobiology
- Shandong University
- Jinan 250100
- China
| | - Juncai Ma
- National Glycoengineering Research Center and Shandong Provincial Key Laboratory of Carbohydrate Chemistry and Glycobiology
- Shandong University
- Jinan 250100
- China
| | - Guofeng Gu
- National Glycoengineering Research Center and Shandong Provincial Key Laboratory of Carbohydrate Chemistry and Glycobiology
- Shandong University
- Jinan 250100
- China
| | - Zonggang Chen
- National Glycoengineering Research Center and Shandong Provincial Key Laboratory of Carbohydrate Chemistry and Glycobiology
- Shandong University
- Jinan 250100
- China
| | - Zhongwu Guo
- Department of Chemistry
- University of Florida
- Gainesville
- USA
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