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Lai XH, Zhao LF, Chen XM, Ren Y. Rapid Identification and Characterization of Francisella by Molecular Biology and Other Techniques. Open Microbiol J 2016; 10:64-77. [PMID: 27335619 PMCID: PMC4899538 DOI: 10.2174/1874285801610010064] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2015] [Revised: 10/20/2015] [Accepted: 10/22/2015] [Indexed: 11/22/2022] Open
Abstract
Francisella tularensis is the causative pathogen of tularemia and a
Tier 1 bioterror agent on the CDC list. Considering the fact that some
subpopulation of the F. tularensis strains is more virulent, more
significantly associated with mortality, and therefore poses more threat to
humans, rapid identification and characterization of this subpopulation strains
is of invaluable importance. This review summarizes the up-to-date developments
of assays for mainly detecting and characterizing F. tularensis and a
touch of caveats of some of the assays.
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Affiliation(s)
- Xin-He Lai
- Institute of Inflammation & Diseases, The First Affiliated Hospital of Wenzhou Medical University, Wenzhou, China; Institute of Translational Medicine, The First Affiliated Hospital of Wenzhou Medical University, Wenzhou, China
| | - Long-Fei Zhao
- College of Life Sciences, Key Laboratory of Plant-Microbe Interactions of Henan, Shangqiu Normal University, Shangqiu, Henan, 476000, PR China
| | - Xiao-Ming Chen
- Institute of Inflammation & Diseases, The First Affiliated Hospital of Wenzhou Medical University, Wenzhou, China; Institute of Translational Medicine, The First Affiliated Hospital of Wenzhou Medical University, Wenzhou, China ; Department of Pediatric Surgery, The First Affiliated Hospital of Wenzhou Medical University, Wenzhou, China
| | - Yi Ren
- Institute of Inflammation & Diseases, The First Affiliated Hospital of Wenzhou Medical University, Wenzhou, China; Department of Biomedical Sciences, Florida State University College of Medicine, Tallahassee, FL, USA
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Chen YS, Li HR, Zhang W, Hua ZD, Lin XH, Lin MQ, Huang WS, Huang LP, Yu XL, Xu NL, Lin M, Xie BS, Shen XN, Xie JF, Wang Y, Huang M, Wu YA, Hu XL. Development of a bead-based suspension array for the detection of pathogens in acute respiratory tract infections. Exp Biol Med (Maywood) 2016; 241:1551-8. [PMID: 27190247 DOI: 10.1177/1535370216647128] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2016] [Accepted: 04/06/2016] [Indexed: 01/15/2023] Open
Abstract
We developed a high-throughput bead-based suspension array for simultaneous detection of 20 respiratory tract pathogens in clinical specimens. Pathogen-specific genes were amplified and hybridized to probes coupled to carboxyl-encoded microspheres. Fluorescence intensities generated via the binding of phycoerythrin-conjugated streptavidin with biotin-labeled targets were measured by the Luminex 100 bead-based suspension array system. The bead-based suspension array detected bacteria in a significantly higher number of samples compared to the conventional culture. There was no significant difference in the detection rate of atypical pathogensatypical pathogens or viruses between the bead-based suspension array and real-time PCR. This technology can play a significant role in screening patients with pneumonia.
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Affiliation(s)
- Yu-Sheng Chen
- Department of Respiratory and Critical Care Medicine, Fujian Provicial Hospital, Fujian Provincial Medical College, Fujian Medical University, Fuzhou 350001, China
| | - Hong-Ru Li
- Department of Respiratory and Critical Care Medicine, Fujian Provicial Hospital, Fujian Provincial Medical College, Fujian Medical University, Fuzhou 350001, China
| | - Wei Zhang
- Department of Respiratory and Critical Care Medicine, Fujian Provicial Hospital, Fujian Provincial Medical College, Fujian Medical University, Fuzhou 350001, China
| | - Zhi-Dan Hua
- Department of Respiratory and Critical Care Medicine, Fujian Provicial Hospital, Fujian Provincial Medical College, Fujian Medical University, Fuzhou 350001, China
| | - Xiao-Hong Lin
- Department of Respiratory and Critical Care Medicine, Fujian Provicial Hospital, Fujian Provincial Medical College, Fujian Medical University, Fuzhou 350001, China
| | - Meng-Qing Lin
- Department of Respiratory and Critical Care Medicine, Fujian Provicial Hospital, Fujian Provincial Medical College, Fujian Medical University, Fuzhou 350001, China
| | - Wen-Sen Huang
- Department of Respiratory and Critical Care Medicine, Fujian Provicial Hospital, Fujian Provincial Medical College, Fujian Medical University, Fuzhou 350001, China
| | - Li-Ping Huang
- Department of Respiratory and Critical Care Medicine, Fujian Provicial Hospital, Fujian Provincial Medical College, Fujian Medical University, Fuzhou 350001, China
| | - Xiao-Li Yu
- Department of Respiratory and Critical Care Medicine, Fujian Provicial Hospital, Fujian Provincial Medical College, Fujian Medical University, Fuzhou 350001, China
| | - Neng-Luan Xu
- Department of Respiratory and Critical Care Medicine, Fujian Provicial Hospital, Fujian Provincial Medical College, Fujian Medical University, Fuzhou 350001, China
| | - Ming Lin
- Department of Respiratory and Critical Care Medicine, Fujian Provicial Hospital, Fujian Provincial Medical College, Fujian Medical University, Fuzhou 350001, China
| | - Bao-Song Xie
- Department of Respiratory and Critical Care Medicine, Fujian Provicial Hospital, Fujian Provincial Medical College, Fujian Medical University, Fuzhou 350001, China
| | - Xiao-Na Shen
- Department of Viral Diseases, Fujian Center for Disease Control and Prevention, Fuzhou 350001, China
| | - Jian-Feng Xie
- Department of Viral Diseases, Fujian Center for Disease Control and Prevention, Fuzhou 350001, China
| | - Yi Wang
- Shanghai Tellgen Life Science Co. Ltd, Shanghai 201203,China
| | - Meng Huang
- Department of Viral Diseases, Fujian Center for Disease Control and Prevention, Fuzhou 350001, China
| | - Yan-An Wu
- Clinical Microbiology Laboratory, Fujian Provincial Hospital, Fuzhou 350001, China
| | - Xin-Lan Hu
- Clinical Microbiology Laboratory, Fujian Provincial Hospital, Fuzhou 350001, China
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Pan X, Smith CE, Zhang J, McCabe KA, Fu J, Bell CE. A Structure-Activity Analysis for Probing the Mechanism of Processive Double-Stranded DNA Digestion by λ Exonuclease Trimers. Biochemistry 2016; 54:6139-48. [PMID: 26361255 DOI: 10.1021/acs.biochem.5b00707] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
Abstract
λ exonuclease (λexo) is an ATP-independent 5'-to-3' exonuclease that binds to double-stranded DNA (dsDNA) ends and processively digests the 5'-strand into mononucleotides. The crystal structure of λexo revealed that the enzyme forms a ring-shaped homotrimer with a central funnel-shaped channel for tracking along the DNA. On the basis of this structure, it was proposed that dsDNA enters the open end of the channel, the 5'-strand is digested at one of the three active sites, and the 3'-strand passes through the narrow end of the channel to emerge out the back. This model was largely confirmed by the structure of the λexo-DNA complex, which further revealed that the enzyme unwinds the DNA by 2 bp prior to cleavage, to thread the 5'-end of the DNA into the active site. On the basis of this structure, an "electrostatic ratchet" model was proposed, in which the enzyme uses a hydrophobic wedge to insert into the base pairs to unwind the DNA, a two-metal mechanism for nucleotide hydrolysis, a positively charged pocket to bind to the terminal 5'-phosphate generated after each round of cleavage, and an arginine residue (Arg-45) to bind to the minor groove of the downstream end of the DNA. To test this model, in this study we have determined the effects of 11 structure-based mutations in λexo on DNA binding and exonuclease activities in vitro, and on DNA recombination in vivo. The results are largely consistent with the model for the mechanism that was proposed on the basis of the structure and provide new insights into the roles of particular residues of the protein in promoting the reaction. In particular, a key role for Arg-45 in DNA binding is revealed.
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Affiliation(s)
| | | | | | | | - Jun Fu
- Shandong University-Helmholtz Institute of Biotechnology, State Key Laboratory of Microbial Technology, School of Life Science, Shandong University , Shanda Nanlu 27, 250100 Jinan, People's Republic of China
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Silvestri EE, Perkins SD, Rice EW, Stone H, Schaefer FW. Review of processing and analytical methods for Francisella tularensis in soil and water. ANN MICROBIOL 2015. [DOI: 10.1007/s13213-015-1144-8] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022] Open
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Huynh HTT, Gotthard G, Terras J, Aboudharam G, Drancourt M, Chabrière E. Surface plasmon resonance imaging of pathogens: the Yersinia pestis paradigm. BMC Res Notes 2015; 8:259. [PMID: 26105071 PMCID: PMC4479326 DOI: 10.1186/s13104-015-1236-3] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2014] [Accepted: 06/17/2015] [Indexed: 11/26/2022] Open
Abstract
Background Yersinia pestis, causing deadly plague, is classified as a group A bioterrorism bacterium. Some recent DNA-based methods were used for detection of bioterrorism agents. Results Y. pestis was used as a model organism to develop an immunosensor based on surface plasmon resonance imaging (SPRi) using monoclonal antibody against Y. pestis F1 antigen. The experimental approach included step-by-step detection of Y. pestis membrane proteins, lysed bacteria, intact bacteria, mock-infected powder and mock-infected clinical specimens. SPRi detected on average 106 intact Y. pestis organisms in buffer, in mock-infected powder and in a 1:4 mixture with HEL cells. Conclusions This study offers the proof-of-concept of the SPRi-based detection of a human pathogen in both environmental and clinical specimens.
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Affiliation(s)
- Hong T T Huynh
- Faculté de médecine, Unité de Recherche sur les Maladies Infectieuses et Tropicales Emergentes (URMITE), UMR CNRS 7278, IRD 198, INSERM 1095, 27, Boulevard Jean Moulin-Cedex 5, Marseille, France.
| | - Guillaume Gotthard
- Faculté de médecine, Unité de Recherche sur les Maladies Infectieuses et Tropicales Emergentes (URMITE), UMR CNRS 7278, IRD 198, INSERM 1095, 27, Boulevard Jean Moulin-Cedex 5, Marseille, France.
| | - Jérome Terras
- Faculté de médecine, Unité de Recherche sur les Maladies Infectieuses et Tropicales Emergentes (URMITE), UMR CNRS 7278, IRD 198, INSERM 1095, 27, Boulevard Jean Moulin-Cedex 5, Marseille, France.
| | - Gérard Aboudharam
- Faculté de médecine, Unité de Recherche sur les Maladies Infectieuses et Tropicales Emergentes (URMITE), UMR CNRS 7278, IRD 198, INSERM 1095, 27, Boulevard Jean Moulin-Cedex 5, Marseille, France.
| | - Michel Drancourt
- Faculté de médecine, Unité de Recherche sur les Maladies Infectieuses et Tropicales Emergentes (URMITE), UMR CNRS 7278, IRD 198, INSERM 1095, 27, Boulevard Jean Moulin-Cedex 5, Marseille, France.
| | - Eric Chabrière
- Faculté de médecine, Unité de Recherche sur les Maladies Infectieuses et Tropicales Emergentes (URMITE), UMR CNRS 7278, IRD 198, INSERM 1095, 27, Boulevard Jean Moulin-Cedex 5, Marseille, France.
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Pan X, Yan J, Patel A, Wysocki VH, Bell CE. Mutant poisoning demonstrates a nonsequential mechanism for digestion of double-stranded DNA by λ exonuclease trimers. Biochemistry 2015; 54:942-51. [PMID: 25531139 DOI: 10.1021/bi501431w] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
Abstract
λ Exonuclease (λexo) is a highly processive 5'-3' exonuclease that binds double-stranded DNA (dsDNA) ends and digests the 5'-strand into mononucleotides. The enzyme forms a toroidal homotrimer with a central tapered channel for tracking along the DNA. During catalysis, dsDNA enters the open end of the channel, and the 5'-strand is digested at one of the three active sites. It is currently not known if λexo uses a sequential mechanism, in which the DNA moves from one active site to the next around the trimer for each round of catalysis or a nonsequential mechanism, in which the DNA locks onto a single active site for multiple rounds. To understand how λexo uses its three active sites, we used a mutant poisoning approach, in which a 6xHis-tagged K131A inactive mutant of λexo was mixed with untagged wild type (WT) to form hybrid trimers. Nickel-spin pull-down analysis confirmed complete subunit exchange after 1 h at 37 °C. Exonuclease assays revealed an approximately linear decrease in activity with increasing fraction of mutant, as expected for a nonsequential mechanism. By fitting the observed rates of digestion to a simple mathematical model, the individual rates of the two hybrid species of trimer were determined. This analysis showed that trimers containing only one or two WT subunits contribute significantly to the observed activity, in further agreement with a nonsequential mechanism. Finally, purification of hybrid trimer mixtures by Ni-spin chromatography, to remove the contribution from fully WT trimers, also resulted in significant levels of activity, again consistent with a nonsequential mechanism.
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Affiliation(s)
- Xinlei Pan
- Ohio State Biochemistry Program, ‡Department of Molecular and Cellular Biochemistry, and §Department of Chemistry and Biochemistry, The Ohio State University , Columbus, Ohio 43210, United States
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Weis A, Liang F, Gao J, Barnard RT, Corrie S. RNA and DNA Diagnostics on Microspheres: Current and Emerging Methods. RNA TECHNOLOGIES 2015. [DOI: 10.1007/978-3-319-17305-4_10] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/01/2023]
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