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Demay F, Hallier M, Georgeault S, Com E, Cattoir V, Goude R, Gillet R. Simple purification and characterization of soluble and homogenous ABC-F translation factors from Enterococcus faecium. Protein Expr Purif 2023:106325. [PMID: 37354924 DOI: 10.1016/j.pep.2023.106325] [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: 12/05/2022] [Revised: 06/09/2023] [Accepted: 06/16/2023] [Indexed: 06/26/2023]
Abstract
The family of ATP-binding cassette F proteins (ABC-F) is mainly made up of cytosolic proteins involved in regulating protein synthesis, and they are often part of a mechanism that confers resistance to ribosome-targeting antibiotics. The existing literature has emphasized the difficulty of purifying these recombinant proteins because of their very low solubility and stability. Here, we describe a rapid and efficient three-step purification procedure that allows for the production of untagged ABC-F proteins from Enterococcus faecium in the heterologous host Escherichia coli. After four purified ABC-F proteins were produced using this protocol, their biological activities were validated by in vitro experiment. In conclusion, our study provides an invaluable tool for obtaining large amounts of untagged and soluble ABC-F proteins that can then be used for in vitro experiments.
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Affiliation(s)
- Fanny Demay
- Univ. Rennes, CNRS, Institut de Génétique et Développement de Rennes (IGDR) UMR 6290, Rennes, France
| | - Marc Hallier
- Univ. Rennes, CNRS, Institut de Génétique et Développement de Rennes (IGDR) UMR 6290, Rennes, France
| | - Sylvie Georgeault
- Univ. Rennes, CNRS, Institut de Génétique et Développement de Rennes (IGDR) UMR 6290, Rennes, France
| | - Emmanuelle Com
- Univ Rennes, Inserm, EHESP, Irset (Institut de Recherche en Santé, Environnement et Travail) - UMR_S 1085, F-35000, Rennes, France; Univ Rennes, CNRS, Inserm, Biosit UAR 3480 US_S 018, Protim Core Facility, F-35000, Rennes, France
| | - Vincent Cattoir
- Department of Clinical Microbiology, Rennes University Hospital, Rennes, France; Univ. Rennes, Inserm, UMR 1230 BRM, Rennes, France
| | - Renan Goude
- Univ. Rennes, CNRS, Institut de Génétique et Développement de Rennes (IGDR) UMR 6290, Rennes, France
| | - Reynald Gillet
- Univ. Rennes, CNRS, Institut de Génétique et Développement de Rennes (IGDR) UMR 6290, Rennes, France.
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2
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Li F, Lei M, Xie J, Guo S, Li W, Ren X, Wang T, Lin S, Xie Q, Chen X. Discovery and Characteristics of a Novel Antitumor Cyclopeptide Derived from Shark. Bioengineering (Basel) 2023; 10:674. [PMID: 37370606 DOI: 10.3390/bioengineering10060674] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2023] [Revised: 05/20/2023] [Accepted: 05/25/2023] [Indexed: 06/29/2023] Open
Abstract
Peptides pose a challenge in drug development due to their short half-lives in vivo. In this study, we conducted in vitro degradation experiments on SAIF, which is a shark-derived peptide that we previously studied. The degradation fragments were sequenced and a truncated peptide sequence was identified. The truncated peptide was then cloned and expressed via the E. coli system with traceless cloning to form a novel cyclic peptide in vitro oxidation condition via the formation of a disulfide bond between the N- and C-termini, which was named ctSAIF. ctSAIF exhibited high anti-HCC activity and enhanced enzymatic stability in vitro, and retained antitumor activity and good biocompatibility in systemic circulation in a HCC xenograft model. Our study discovered and characterized a novel shark-derived cyclic peptide with antitumor activity, laying a foundation for its further development as an antitumor drug candidate. The study also provided a new solution for peptide drug development.
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Affiliation(s)
- Fu Li
- Department of Cell Biology, College of Life Science and Technology, Jinan University, Guangzhou 510632, China
- National Engineering Research Center of Genetic Medicine, Guangzhou 510632, China
- Guangdong Province Key Laboratory of Bioengineering Medicine, Guangzhou 510632, China
- Guangdong Provincial Biotechnology Drug & Engineering Technology Research Center, Guangzhou 510632, China
| | - Minghua Lei
- Department of Cell Biology, College of Life Science and Technology, Jinan University, Guangzhou 510632, China
- National Engineering Research Center of Genetic Medicine, Guangzhou 510632, China
- Guangdong Province Key Laboratory of Bioengineering Medicine, Guangzhou 510632, China
- Guangdong Provincial Biotechnology Drug & Engineering Technology Research Center, Guangzhou 510632, China
| | - Junye Xie
- Department of Cell Biology, College of Life Science and Technology, Jinan University, Guangzhou 510632, China
- National Engineering Research Center of Genetic Medicine, Guangzhou 510632, China
- Guangdong Province Key Laboratory of Bioengineering Medicine, Guangzhou 510632, China
- Guangdong Provincial Biotechnology Drug & Engineering Technology Research Center, Guangzhou 510632, China
| | - Shujun Guo
- Department of Cell Biology, College of Life Science and Technology, Jinan University, Guangzhou 510632, China
- National Engineering Research Center of Genetic Medicine, Guangzhou 510632, China
- Guangdong Province Key Laboratory of Bioengineering Medicine, Guangzhou 510632, China
- Guangdong Provincial Biotechnology Drug & Engineering Technology Research Center, Guangzhou 510632, China
| | - Weicai Li
- Department of Cell Biology, College of Life Science and Technology, Jinan University, Guangzhou 510632, China
- National Engineering Research Center of Genetic Medicine, Guangzhou 510632, China
- Guangdong Province Key Laboratory of Bioengineering Medicine, Guangzhou 510632, China
- Guangdong Provincial Biotechnology Drug & Engineering Technology Research Center, Guangzhou 510632, China
| | - Xiujuan Ren
- Department of Cell Biology, College of Life Science and Technology, Jinan University, Guangzhou 510632, China
- National Engineering Research Center of Genetic Medicine, Guangzhou 510632, China
- Guangdong Province Key Laboratory of Bioengineering Medicine, Guangzhou 510632, China
- Guangdong Provincial Biotechnology Drug & Engineering Technology Research Center, Guangzhou 510632, China
| | - Teng Wang
- Department of Cell Biology, College of Life Science and Technology, Jinan University, Guangzhou 510632, China
- National Engineering Research Center of Genetic Medicine, Guangzhou 510632, China
- Guangdong Province Key Laboratory of Bioengineering Medicine, Guangzhou 510632, China
- Guangdong Provincial Biotechnology Drug & Engineering Technology Research Center, Guangzhou 510632, China
| | - Songxiong Lin
- Guangzhou Ocean Land Testing Technology Co., Ltd., Guangzhou 511400, China
| | - Qiuling Xie
- Department of Cell Biology, College of Life Science and Technology, Jinan University, Guangzhou 510632, China
- National Engineering Research Center of Genetic Medicine, Guangzhou 510632, China
- Guangdong Province Key Laboratory of Bioengineering Medicine, Guangzhou 510632, China
- Guangdong Provincial Biotechnology Drug & Engineering Technology Research Center, Guangzhou 510632, China
| | - Xiaojia Chen
- Department of Cell Biology, College of Life Science and Technology, Jinan University, Guangzhou 510632, China
- National Engineering Research Center of Genetic Medicine, Guangzhou 510632, China
- Guangdong Province Key Laboratory of Bioengineering Medicine, Guangzhou 510632, China
- Guangdong Provincial Biotechnology Drug & Engineering Technology Research Center, Guangzhou 510632, China
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3
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Impact of Negative Feedbacks on De Novo Pyrimidines Biosynthesis in Escherichia coli. Int J Mol Sci 2023; 24:ijms24054806. [PMID: 36902235 PMCID: PMC10003070 DOI: 10.3390/ijms24054806] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2023] [Revised: 02/25/2023] [Accepted: 02/28/2023] [Indexed: 03/06/2023] Open
Abstract
Earlier studies aimed at investigating the metabolism of endogenous nucleoside triphosphates in synchronous cultures of E. coli cells revealed an auto-oscillatory mode of functioning of the pyrimidine and purine nucleotide biosynthesis system, which the authors associated with the dynamics of cell division. Theoretically, this system has an intrinsic oscillatory potential, since the dynamics of its functioning are controlled through feedback mechanisms. The question of whether the nucleotide biosynthesis system has its own oscillatory circuit is still open. To address this issue, an integral mathematical model of pyrimidine biosynthesis was developed, taking into account all experimentally verified negative feedback in the regulation of enzymatic reactions, the data of which were obtained under in vitro conditions. Analysis of the dynamic modes of the model functioning has shown that in the pyrimidine biosynthesis system, both the steady-state and oscillatory functioning modes can be realized under certain sets of kinetic parameters that fit in the physiological boundaries of the investigated metabolic system. It has been demonstrated that the occurrence of the oscillatory nature of metabolite synthesis depended on the ratio of two parameters: the Hill coefficient, hUMP1-the nonlinearity of the UMP effect on the activity of carbamoyl-phosphate synthetase, and the parameter r characterizing the contribution of the noncompetitive mechanism of UTP inhibition to the regulation of the enzymatic reaction of UMP phosphorylation. Thus, it has been theoretically shown that the E. coli pyrimidine biosynthesis system possesses its own oscillatory circuit whose oscillatory potential depends to a significant degree on the mechanism of regulation of UMP kinase activity.
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Rice AJ, Pesavento RP, Ren J, Youn I, Kwon Y, Ellepola K, Che CT, Johnson ME, Lee H. Identification of Small Molecule Inhibitors against Staphylococcus aureus Dihydroorotase via HTS. Int J Mol Sci 2021; 22:ijms22189984. [PMID: 34576147 PMCID: PMC8467647 DOI: 10.3390/ijms22189984] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2021] [Revised: 09/02/2021] [Accepted: 09/11/2021] [Indexed: 11/16/2022] Open
Abstract
Drug-resistant Staphylococcus aureus is an imminent threat to public health, increasing the importance of drug discovery utilizing unexplored bacterial pathways and enzyme targets. De novo pyrimidine biosynthesis is a specialized, highly conserved pathway implicated in both the survival and virulence of several clinically relevant pathogens. Class I dihydroorotase (DHOase) is a separate and distinct enzyme present in gram positive bacteria (i.e., S. aureus, B. anthracis) that converts carbamoyl-aspartate (Ca-asp) to dihydroorotate (DHO)-an integral step in the de novo pyrimidine biosynthesis pathway. This study sets forth a high-throughput screening (HTS) of 3000 fragment compounds by a colorimetry-based enzymatic assay as a primary screen, identifying small molecule inhibitors of S. aureus DHOase (SaDHOase), followed by hit validation with a direct binding analysis using surface plasmon resonance (SPR). Competition SPR studies of six hit compounds and eight additional analogs with the substrate Ca-asp determined the best compound to be a competitive inhibitor with a KD value of 11 µM, which is 10-fold tighter than Ca-asp. Preliminary structure-activity relationship (SAR) provides the foundation for further structure-based antimicrobial inhibitor design against S. aureus.
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Affiliation(s)
- Amy J. Rice
- Center for Biomolecular Sciences, College of Pharmacy, University of Illinois at Chicago, Chicago, IL 60607, USA; (A.J.R.); (R.P.P.); (J.R.); (Y.K.)
- Department of Pharmaceutical Sciences, College of Pharmacy, University of Illinois at Chicago, Chicago, IL 60612, USA; (I.Y.); (C.-T.C.)
| | - Russell P. Pesavento
- Center for Biomolecular Sciences, College of Pharmacy, University of Illinois at Chicago, Chicago, IL 60607, USA; (A.J.R.); (R.P.P.); (J.R.); (Y.K.)
- Department of Oral Biology, College of Dentistry, University of Illinois at Chicago, Chicago, IL 60607, USA;
| | - Jinhong Ren
- Center for Biomolecular Sciences, College of Pharmacy, University of Illinois at Chicago, Chicago, IL 60607, USA; (A.J.R.); (R.P.P.); (J.R.); (Y.K.)
| | - Isoo Youn
- Department of Pharmaceutical Sciences, College of Pharmacy, University of Illinois at Chicago, Chicago, IL 60612, USA; (I.Y.); (C.-T.C.)
| | - Youngjin Kwon
- Center for Biomolecular Sciences, College of Pharmacy, University of Illinois at Chicago, Chicago, IL 60607, USA; (A.J.R.); (R.P.P.); (J.R.); (Y.K.)
- Biophysics Core at the Research Resource Center, University of Illinois at Chicago, Chicago, IL 60607, USA
| | - Kassapa Ellepola
- Department of Oral Biology, College of Dentistry, University of Illinois at Chicago, Chicago, IL 60607, USA;
| | - Chun-Tao Che
- Department of Pharmaceutical Sciences, College of Pharmacy, University of Illinois at Chicago, Chicago, IL 60612, USA; (I.Y.); (C.-T.C.)
| | - Michael E. Johnson
- Center for Biomolecular Sciences, College of Pharmacy, University of Illinois at Chicago, Chicago, IL 60607, USA; (A.J.R.); (R.P.P.); (J.R.); (Y.K.)
- Department of Pharmaceutical Sciences, College of Pharmacy, University of Illinois at Chicago, Chicago, IL 60612, USA; (I.Y.); (C.-T.C.)
- Correspondence: (M.E.J.); (H.L.); Tel.: +1-312-996-9114 (M.E.J.); +1-312-355-5292 (H.L.)
| | - Hyun Lee
- Center for Biomolecular Sciences, College of Pharmacy, University of Illinois at Chicago, Chicago, IL 60607, USA; (A.J.R.); (R.P.P.); (J.R.); (Y.K.)
- Department of Pharmaceutical Sciences, College of Pharmacy, University of Illinois at Chicago, Chicago, IL 60612, USA; (I.Y.); (C.-T.C.)
- Biophysics Core at the Research Resource Center, University of Illinois at Chicago, Chicago, IL 60607, USA
- Correspondence: (M.E.J.); (H.L.); Tel.: +1-312-996-9114 (M.E.J.); +1-312-355-5292 (H.L.)
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5
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Screening and Molecular Docking of Novel Benzothiazole Derivatives as Potential Antimicrobial Agents. Antibiotics (Basel) 2020; 9:antibiotics9050221. [PMID: 32365587 PMCID: PMC7277330 DOI: 10.3390/antibiotics9050221] [Citation(s) in RCA: 36] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2020] [Revised: 04/26/2020] [Accepted: 04/27/2020] [Indexed: 02/06/2023] Open
Abstract
The burden of antibiotic resistance necessitates a continued search for new antimicrobials. We evaluated the antimicrobial activities of novel benzothiazoles synthesized by our group. Antibacterial activity was evaluated in vitro in Staphylococcus aureus, Bacillus subtilis, and Escherichia coli, while the antifungal activity was tested in Candida albicans and Aspergillus niger, and expressed as the minimum inhibitory concentration (MIC; µg/mL). MIC values of benzothiazole compounds ranged from 25 to 200 µg/mL. Compounds 3 and 4 gave high antibacterial and moderate antifungal activities, while 10 and 12 showed moderate activity against all tested organisms. In addition, some benzothiazole compounds significantly suppressed the activity of Escherichia coli dihydroorotase and inhibited the dimorphic transition of Candida albicans. Moreover, the active benzothiazole compounds induced DNA and protein leakage in Aspergillus niger spores. Molecular interactions of benzothiazole derivatives with dihydroorotase revealed the formation of hydrogen bonds with the active site residues LEU222 or ASN44. Strong hydrophobic interactions of the bulky thiazole and naphthalene rings at the entrance to the active site might interfere with the access of substrates to their binding sites, which results in dihydroorotase inhibition. Thus, inhibition of dihydroorotase might contribute to the observed antimicrobial actions of these compounds.
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6
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Li B, Lv R, Xiao Y, Hu W, Mai Y, Zhang J, Lin L, Hu X. A Novel Nitrite-Base Aerobic Denitrifying Bacterium Acinetobacter sp. YT03 and Its Transcriptome Analysis. Front Microbiol 2019; 10:2580. [PMID: 31803151 PMCID: PMC6872672 DOI: 10.3389/fmicb.2019.02580] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2019] [Accepted: 10/24/2019] [Indexed: 11/21/2022] Open
Abstract
Nitrite in a water environment is very harmful to humans and aquatic animals. A novel aerobic denitrifying bacterium able to utilize NO2--N as the only nitrogen source was isolated for the purpose of removing nitrite from water, which was identified as Acinetobacter sp. and named as YT03. The growth and denitrification activity of strain YT03 was assessed comprehensively. Results showed that the nitrite in water with an initial concentration of 10 mg L–1 could be completely removed within 6 h by strain YT03, and the optimal conditions for strain YT03 to remove nitrite were as follows: sodium succinate as the carbon source, C/N ratio of 16, pH of 6.5, temperature of 30°C, and shaking speed of 250 rpm. An RNA-Seq transcriptome analysis was used to find genes associated with nitrite removal. Compared with the removal of ammonia nitrogen, 47 genes were significantly differentially expressed, including 20 up-regulated and 27 down-regulated genes, mainly involved in the transport process, biosynthetic process, and so on. And among the differentially expressed genes, C4-dicarboxylate transporter (DctA) and nitrate/nitrite transporter (Nrt) might be of importance for the efficient utilization of carbon and nitrogen sources in aerobic nitrite denitrification with sodium succinate by strain YT03.
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Affiliation(s)
- Bin Li
- Guangdong Provincial Key Laboratory of Industrial Surfactant, Guangdong Research Institute of Petrochemical and Fine Chemical Engineering, Guangzhou, China
| | - Ran Lv
- Guangdong Provincial Key Laboratory of Industrial Surfactant, Guangdong Research Institute of Petrochemical and Fine Chemical Engineering, Guangzhou, China
| | - Ying Xiao
- Guangdong Provincial Key Laboratory of Industrial Surfactant, Guangdong Research Institute of Petrochemical and Fine Chemical Engineering, Guangzhou, China
| | - Wei Hu
- Guangdong Provincial Key Laboratory of Industrial Surfactant, Guangdong Research Institute of Petrochemical and Fine Chemical Engineering, Guangzhou, China
| | - Yuliang Mai
- Guangdong Provincial Key Laboratory of Industrial Surfactant, Guangdong Research Institute of Petrochemical and Fine Chemical Engineering, Guangzhou, China
| | - Jingwen Zhang
- Guangdong Provincial Key Laboratory of Industrial Surfactant, Guangdong Research Institute of Petrochemical and Fine Chemical Engineering, Guangzhou, China
| | - Lan Lin
- Guangdong Provincial Key Laboratory of Industrial Surfactant, Guangdong Research Institute of Petrochemical and Fine Chemical Engineering, Guangzhou, China
| | - Xiaoyong Hu
- Guangdong Provincial Key Laboratory of Industrial Surfactant, Guangdong Research Institute of Petrochemical and Fine Chemical Engineering, Guangzhou, China
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7
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An efficient large-scale refolding technique for recovering biologically active recombinant human FGF-21 from inclusion bodies. Int J Biol Macromol 2019; 135:362-372. [PMID: 31129207 DOI: 10.1016/j.ijbiomac.2019.05.167] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2019] [Revised: 05/22/2019] [Accepted: 05/22/2019] [Indexed: 01/15/2023]
Abstract
Fibroblast growth factor 21 (FGF-21) is an important regulator in glycolipid metabolism that is a promising drug candidate for treatment of diabetes and obesity. However, the productivity of recombinant hFGF-21 (rhFGF-21) in Escherichia coli (E. coli) is relatively low, which limits its clinical application. To meet the clinical demand and control the production cost, rhFGF-21 proteins were expressed in inclusion bodies (IBs) form in Rosetta (DE3) by high cell density fermentation in 50-L scale. Hollow fiber membrane filtration technology was used to enrich the bacteria, wash, denature and refold the IBs in the current report. The renatured proteins were purified by two-step affinity chromatography. Authenticity of the purified rhFGF-21 was confirmed by the N-and C-terminal sequence, disulfide bond composition and molecular weight analyses. Results showed that the average target protein and recovery of rhFGF-21 expressed in IBs form of three batches were more than those of the soluble form. Both the rhFGF-21 proteins from the two forms showed equal potency in improving the glucose uptake in HepG2 cells and anti-diabetic effect in db/db mice. In this study, an efficient method for preparation of FGF-21 was established. This novel process provides an important technical basis for the large-scale production of rhFGF-21.
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8
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Zhao X, Liu Z, Liu Z, Meng R, Shi C, Chen X, Bu X, Guo N. Phenotype and RNA-seq-Based transcriptome profiling of Staphylococcus aureus biofilms in response to tea tree oil. Microb Pathog 2018; 123:304-313. [PMID: 30041003 DOI: 10.1016/j.micpath.2018.07.027] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2017] [Revised: 03/06/2018] [Accepted: 07/20/2018] [Indexed: 01/31/2023]
Abstract
Staphylococcus aureus (S. aureus) is a Gram-positive bacterium that causes a wide range of diseases, including food poisoning. Tea tree oil (TTO), an essential oil distilled from Melaleuca alternifolia, is well-known for its antibacterial activities. TTO effectively inhibited all 19 tested strains of S. aureus biofilm and planktonic cells. Phenotype analyses of S. aureus biofilm cells exposed to TTO were performed by biofilm adhesion assays, eDNA detection and PIA release. RNA sequencing (RNA-seq) was used in our study to elucidate the mechanism of TTO as a potential antibacterial agent to evaluate differentially expressed genes (DEGs) and the functional network in S. aureus ATCC 29213 biofilms. TTO significantly changed (greater than a 2- or less than a 2-fold change) the expression of 304 genes in S. aureus contained in biofilms. The levels of genes related to the glycine, serine and threonine metabolism pathway, purine metabolism pathway, pyrimidine metabolism pathway and amino acid biosynthesis pathway were dramatically changed in the biofilm exposed to TTO. Furthermore, the expression changes identified by RNA-seq analysis were verified by real-time RT-PCR. To the best of our knowledge, this research is the first study to report the phenotype and expression profiles of S. aureus in biofilms exposed to TTO.
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Affiliation(s)
- Xingchen Zhao
- Department of Food Quality and Safety, School of Pharmaceutics and Food Science, Tonghua Normal University, 134000, China
| | - Zonghui Liu
- Department of Food Quality and Safety, College of Food Science and Engineering, Jilin University, 130062, China
| | - Zuojia Liu
- State Key Laboratory of Electroanalytical Chemistry, Changchun Institute of Applied Chemistry, Chinese Academy of Sciences, Changchun, Jilin, China
| | - Rizeng Meng
- Jilin Entry-Exit Inspection and Quarantine Bureau, Changchun, 130062, China
| | - Ce Shi
- Department of Food Quality and Safety, College of Food Science and Engineering, Jilin University, 130062, China
| | - Xiangrong Chen
- Department of Food Quality and Safety, College of Food Science and Engineering, Jilin University, 130062, China
| | - Xiujuan Bu
- Department of Food Quality and Safety, College of Food Science and Engineering, Jilin University, 130062, China
| | - Na Guo
- Department of Food Quality and Safety, College of Food Science and Engineering, Jilin University, 130062, China.
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9
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Biochemical characterization of dihydroorotase of Leishmania donovani: Understanding pyrimidine metabolism through its inhibition. Biochimie 2016; 131:45-53. [DOI: 10.1016/j.biochi.2016.09.009] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2016] [Accepted: 09/15/2016] [Indexed: 11/22/2022]
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10
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Ca-asp bound X-ray structure and inhibition of Bacillus anthracis dihydroorotase (DHOase). Bioorg Med Chem 2016; 24:4536-4543. [PMID: 27499369 DOI: 10.1016/j.bmc.2016.07.055] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2016] [Revised: 07/22/2016] [Accepted: 07/25/2016] [Indexed: 01/01/2023]
Abstract
Dihydroorotase (DHOase) is the third enzyme in the de novo pyrimidine synthesis pathway and is responsible for the reversible cyclization of carbamyl-aspartate (Ca-asp) to dihydroorotate (DHO). DHOase is further divided into two classes based on several structural characteristics, one of which is the length of the flexible catalytic loop that interacts with the substrate, Ca-asp, regulating the enzyme activity. Here, we present the crystal structure of Class I Bacillus anthracis DHOase with Ca-asp in the active site, which shows the peptide backbone of glycine in the shorter loop forming the necessary hydrogen bonds with the substrate, in place of the two threonines found in Class II DHOases. Despite the differences in the catalytic loop, the structure confirms that the key interactions between the substrate and active site residues are similar between Class I and Class II DHOase enzymes, which we further validated by mutagenesis studies. B. anthracis DHOase is also a potential antibacterial drug target. In order to identify prospective inhibitors, we performed high-throughput screening against several libraries using a colorimetric enzymatic assay and an orthogonal fluorescence thermal binding assay. Surface plasmon resonance was used for determining binding affinity (KD) and competition analysis with Ca-asp. Our results highlight that the primary difference between Class I and Class II DHOase is the catalytic loop. We also identify several compounds that can potentially be further optimized as potential B. anthracis inhibitors.
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11
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Jones JA, Price E, Miller D, Hevener KE. A simplified protocol for high-yield expression and purification of bacterial topoisomerase I. Protein Expr Purif 2016; 124:32-40. [PMID: 27117979 DOI: 10.1016/j.pep.2016.04.010] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2016] [Revised: 04/21/2016] [Accepted: 04/22/2016] [Indexed: 11/15/2022]
Abstract
Type IA topoisomerases represent promising antibacterial drug targets. Data exists suggesting that the two bacterial type IA topoisomerase enzymes-topoisomerase I and topoisomerase III-share an overlapping biological role. Furthermore, topoisomerase I has been shown to be essential for the survival of certain organisms lacking topoisomerase III. With this in mind, it is plausible that topoisomerase I may represent a potential target for selective antibacterial drug development. As many reported bacterial topoisomerase I purification protocols have either suffered from relatively low yield, numerous steps, or a simple failure to report target protein yield altogether, a high-yield and high-purity bacterial topoisomerase I expression and purification protocol is highly desirable. The goal of this study was therefore to optimize the expression and purification of topoisomerase I from Streptococcus mutans, a clinically relevant organism that plays a significant role in oral and extra-oral infection, in order to quickly and easily attain the requisite quantities of pure target enzyme suitable for use in assay development, compound library screening, and carrying out further structural and biochemical characterization analyses. Herein we report the systematic implementation and analysis of various expression and purification techniques leading to the development and optimization of a rapid and straightforward protocol for the auto-induced expression and two-step, affinity tag purification of Streptococcus mutans topoisomerase I yielding >20 mg/L of enzyme at over 95% purity.
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Affiliation(s)
- Jesse A Jones
- Department of Biomedical and Pharmaceutical Sciences, Idaho State University, 1311 E. Central Drive, Meridian, ID 83642-7991, USA
| | - Emily Price
- Department of Biomedical and Pharmaceutical Sciences, Idaho State University, 1311 E. Central Drive, Meridian, ID 83642-7991, USA
| | - Donovan Miller
- Department of Biomedical and Pharmaceutical Sciences, Idaho State University, 1311 E. Central Drive, Meridian, ID 83642-7991, USA
| | - Kirk E Hevener
- Department of Biomedical and Pharmaceutical Sciences, Idaho State University, 1311 E. Central Drive, Meridian, ID 83642-7991, USA.
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12
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Rice AJ, Woo JK, Khan A, Szypulinski MZ, Johnson ME, Lee H, Lee H. Over-expression, purification, and confirmation of Bacillus anthracis transcriptional regulator NprR. Protein Expr Purif 2015; 125:83-9. [PMID: 26344899 DOI: 10.1016/j.pep.2015.08.030] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2015] [Revised: 08/28/2015] [Accepted: 08/31/2015] [Indexed: 12/21/2022]
Abstract
Quorum sensing (QS) has been recognized as an important biological phenomenon in which bacterial cells communicate and coordinate their gene expression and cellular processes with respect to population density. Bacillus anthracis is the etiological agent of fatal pulmonary anthrax infections, and the NprR/NprX QS system may be involved in its pathogenesis. NprR, renamed as aqsR for anthrax quorum sensing Regulator, is a transcriptional regulator that may control the expression of genes required for proliferation and survival. Currently, there is no protocol reported to over-express and purify B. anthracis AqsR. In this study, we describe cloning, purification, and confirmation of functional full-length B. anthracis AqsR protein. The AqsR gene was cloned into the pQE-30 vector with an HRV 3C protease recognition site between AqsR and the N-terminal His6-tag in order to yield near native AqsR after the His-tag cleavage, leaving only two additional amino acid residues at the N-terminus.
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Affiliation(s)
- Amy J Rice
- Center for Pharmaceutical Biotechnology, University of Illinois at Chicago, 900 S. Ashland, IL 60607, USA; Department of Medicinal Chemistry and Pharmacognosy, University of Illinois at Chicago, 900 S. Ashland, IL 60607, USA
| | - Jerry K Woo
- Center for Pharmaceutical Biotechnology, University of Illinois at Chicago, 900 S. Ashland, IL 60607, USA
| | - Attiya Khan
- Center for Pharmaceutical Biotechnology, University of Illinois at Chicago, 900 S. Ashland, IL 60607, USA
| | - Michael Z Szypulinski
- Center for Pharmaceutical Biotechnology, University of Illinois at Chicago, 900 S. Ashland, IL 60607, USA
| | - Michael E Johnson
- Center for Pharmaceutical Biotechnology, University of Illinois at Chicago, 900 S. Ashland, IL 60607, USA; Department of Medicinal Chemistry and Pharmacognosy, University of Illinois at Chicago, 900 S. Ashland, IL 60607, USA
| | - Hyunwoo Lee
- Center for Pharmaceutical Biotechnology, University of Illinois at Chicago, 900 S. Ashland, IL 60607, USA; Department of Biopharmaceutical Sciences, University of Illinois at Chicago, 900 S. Ashland, IL 60607, USA.
| | - Hyun Lee
- Center for Pharmaceutical Biotechnology, University of Illinois at Chicago, 900 S. Ashland, IL 60607, USA; Department of Medicinal Chemistry and Pharmacognosy, University of Illinois at Chicago, 900 S. Ashland, IL 60607, USA.
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13
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Ramos L, Sinn J, Lehman B, Pfeufer E, Peter K, McNellis T. Erwinia amylovora pyrC
mutant causes fire blight despite pyrimidine auxotrophy. Lett Appl Microbiol 2015; 60:572-9. [DOI: 10.1111/lam.12417] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2014] [Revised: 02/14/2015] [Accepted: 02/24/2015] [Indexed: 12/01/2022]
Affiliation(s)
- L.S. Ramos
- Department of Plant Pathology & Environmental Microbiology; The Pennsylvania State University; University Park PA USA
- Graduate Degree Program in Plant Pathology; Department of Plant Pathology & Environmental Microbiology; The Pennsylvania State University; University Park PA USA
| | - J.P. Sinn
- Department of Plant Pathology & Environmental Microbiology; The Pennsylvania State University; University Park PA USA
| | - B.L. Lehman
- The Pennsylvania State University Fruit Research and Extension Center; Biglerville PA USA
| | - E.E. Pfeufer
- Department of Plant Pathology & Environmental Microbiology; The Pennsylvania State University; University Park PA USA
- Graduate Degree Program in Plant Pathology; Department of Plant Pathology & Environmental Microbiology; The Pennsylvania State University; University Park PA USA
| | - K.A. Peter
- Department of Plant Pathology & Environmental Microbiology; The Pennsylvania State University; University Park PA USA
- The Pennsylvania State University Fruit Research and Extension Center; Biglerville PA USA
| | - T.W. McNellis
- Department of Plant Pathology & Environmental Microbiology; The Pennsylvania State University; University Park PA USA
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14
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Wood DW. New trends and affinity tag designs for recombinant protein purification. Curr Opin Struct Biol 2014; 26:54-61. [DOI: 10.1016/j.sbi.2014.04.006] [Citation(s) in RCA: 88] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2014] [Accepted: 04/24/2014] [Indexed: 01/14/2023]
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