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Li Y, Yang KD, Kong DC, Ye JF. Advances in phage display based nano immunosensors for cholera toxin. Front Immunol 2023; 14:1224397. [PMID: 37781379 PMCID: PMC10534012 DOI: 10.3389/fimmu.2023.1224397] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2023] [Accepted: 08/23/2023] [Indexed: 10/03/2023] Open
Abstract
Cholera, a persistent global public health concern, continues to cause outbreaks in approximately 30 countries and territories this year. The imperative to safeguard water sources and food from Vibrio cholerae, the causative pathogen, remains urgent. The bacterium is mainly disseminated via ingestion of contaminated water or food. Despite the plate method's gold standard status for detection, its time-consuming nature, taking several days to provide results, remains a challenge. The emergence of novel virulence serotypes raises public health concerns, potentially compromising existing detection methods. Hence, exploiting Vibrio cholerae toxin testing holds promise due to its inherent stability. Immunobiosensors, leveraging antibody specificity and sensitivity, present formidable tools for detecting diverse small molecules, encompassing drugs, hormones, toxins, and environmental pollutants. This review explores cholera toxin detection, highlighting phage display-based nano immunosensors' potential. Engineered bacteriophages exhibit exceptional cholera toxin affinity, through specific antibody fragments or mimotopes, enabling precise quantification. This innovative approach promises to reshape cholera toxin detection, offering an alternative to animal-derived methods. Harnessing engineered bacteriophages aligns with ethical detection and emphasizes sensitivity and accuracy, a pivotal stride in the evolution of detection strategies. This review primarily introduces recent advancements in phage display-based nano immunosensors for cholera toxin, encompassing technical aspects, current challenges, and future prospects.
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Affiliation(s)
- Yang Li
- General Surgery Center, First Hospital of Jilin University, Changchun, Jilin, China
- School of Nursing, Jilin University, Changchun, China
| | - Kai-di Yang
- School of Nursing, Jilin University, Changchun, China
| | - De-cai Kong
- General Surgery Center, First Hospital of Jilin University, Changchun, Jilin, China
| | - Jun-feng Ye
- General Surgery Center, First Hospital of Jilin University, Changchun, Jilin, China
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2
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Eighteen distinctive characteristics of life. Heliyon 2023; 9:e13603. [PMID: 37101483 PMCID: PMC10123176 DOI: 10.1016/j.heliyon.2023.e13603] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2022] [Revised: 01/25/2023] [Accepted: 02/06/2023] [Indexed: 02/12/2023] Open
Abstract
A practical approach in the inquiry of life is to contrast living beings with nonliving ones from different perspectives and extract the distinctive features of living beings. We can identify features and mechanisms that truthfully account for the differences between living and nonliving beings by making rigorous logic-based inferences. The set of these differences constitutes the traits or characteristics of life. When the living beings are carefully examined, the apparent characteristics of life are ascertained to be existence, subjectivity, agency, purposiveness and mission orientation, primacy and supremacy, naturality, field phenomenon, locality, transience, transcendence, simplicity, unicity, initiation, information processing, traits, code of conduct, hierarchy and nesting, and the aptitude to vanish. Each feature is described, justified, and explained in detail in this observation-based philosophical article. Among them, an agency with purpose, knowledge, and power is the key feature of life without which the behavior of living beings cannot be explained. These eighteen characteristics constitute a reasonably comprehensive set of features to distinguish living beings from nonliving ones. However, the enigma of life remains.
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Imaging the Infection Cycle of T7 at the Single Virion Level. Int J Mol Sci 2022; 23:ijms231911252. [PMID: 36232552 PMCID: PMC9569847 DOI: 10.3390/ijms231911252] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2022] [Revised: 09/17/2022] [Accepted: 09/21/2022] [Indexed: 11/17/2022] Open
Abstract
T7 phages are E. coli-infecting viruses that find and invade their target with high specificity and efficiency. The exact molecular mechanisms of the T7 infection cycle are yet unclear. As the infection involves mechanical events, single-particle methods are to be employed to alleviate the problems of ensemble averaging. Here we used TIRF microscopy to uncover the spatial dynamics of the target recognition and binding by individual T7 phage particles. In the initial phase, T7 virions bound reversibly to the bacterial membrane via two-dimensional diffusive exploration. Stable bacteriophage anchoring was achieved by tail-fiber complex to receptor binding which could be observed in detail by atomic force microscopy (AFM) under aqueous buffer conditions. The six anchored fibers of a given T7 phage-displayed isotropic spatial orientation. The viral infection led to the onset of an irreversible structural program in the host which occurred in three distinct steps. First, bacterial cell surface roughness, as monitored by AFM, increased progressively. Second, membrane blebs formed on the minute time scale (average ~5 min) as observed by phase-contrast microscopy. Finally, the host cell was lysed in a violent and explosive process that was followed by the quick release and dispersion of the phage progeny. DNA ejection from T7 could be evoked in vitro by photothermal excitation, which revealed that genome release is mechanically controlled to prevent premature delivery of host-lysis genes. The single-particle approach employed here thus provided an unprecedented insight into the details of the complete viral cycle.
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Sweedan A, Cohen Y, Yaron S, Bashouti MY. Binding Capabilities of Different Genetically Engineered pVIII Proteins of the Filamentous M13/Fd Virus and Single-Walled Carbon Nanotubes. NANOMATERIALS 2022; 12:nano12030398. [PMID: 35159743 PMCID: PMC8839290 DOI: 10.3390/nano12030398] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/09/2021] [Revised: 01/20/2022] [Accepted: 01/20/2022] [Indexed: 12/12/2022]
Abstract
Binding functional biomolecules to non-biological materials, such as single-walled carbon nanotubes (SWNTs), is a challenging task with relevance for different applications. However, no one has yet undertaken a comparison of the binding of SWNTs to different recombinant filamentous viruses (phages) bioengineered to contain different binding peptides fused to the virus coat proteins. This is important due to the range of possible binding efficiencies and scenarios that may arise when the protein’s amino acid sequence is modified, since the peptides may alter the virus’s biological properties or they may behave differently when they are in the context of being displayed on the virus coat protein; in addition, non-engineered viruses may non-specifically adsorb to SWNTs. To test these possibilities, we used four recombinant phage templates and the wild type. In the first circumstance, we observed different binding capabilities and biological functional alterations; e.g., some peptides, in the context of viral templates, did not bind to SWNTs, although it was proven that the bare peptide did. The second circumstance was excluded, as the wild-type virus was found to hardly bind to the SWNTs. These results may be relevant to the possible use of the virus as a “SWNT shuttle” in nano-scale self-assembly, particularly since the pIII proteins are free to act as binding-directing agents. Therefore, knowledge of the differences between and efficiencies of SWNT binding templates may help in choosing better binding phages or peptides for possible future applications and industrial mass production.
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Affiliation(s)
- Amro Sweedan
- The Ilse-Katz Institute for Nanoscale Science & Technology, Ben-Gurion University of the Negev, Beer-Sheva 8410501, Israel;
- The Russell Berrie Nanotechnology Institute, Technion-Israel Institute of Technology, Haifa 3200003, Israel
| | - Yachin Cohen
- The Russell Berrie Nanotechnology Institute, Technion-Israel Institute of Technology, Haifa 3200003, Israel
- Department of Chemical Engineering, Technion-Israel Institute of Technology, Haifa 3200003, Israel
- Correspondence: (Y.C.); (S.Y.); (M.Y.B.)
| | - Sima Yaron
- The Russell Berrie Nanotechnology Institute, Technion-Israel Institute of Technology, Haifa 3200003, Israel
- Department of Biotechnology and Food Engineering, Technion-Israel Institute of Technology, Haifa 3200003, Israel
- Correspondence: (Y.C.); (S.Y.); (M.Y.B.)
| | - Muhammad Y. Bashouti
- The Ilse-Katz Institute for Nanoscale Science & Technology, Ben-Gurion University of the Negev, Beer-Sheva 8410501, Israel;
- Jacob Blaustein Institutes for Desert Research, Sede Boqer Campus, Ben-Gurion University of the Negev, Sede Boqer 8499000, Israel
- Correspondence: (Y.C.); (S.Y.); (M.Y.B.)
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Incidence of Phage Capsid Organization on the Resistance to High Energy Proton Beams. APPLIED SCIENCES-BASEL 2022. [DOI: 10.3390/app12030988] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/10/2022]
Abstract
The helical geometry of virus capsid allows simple self-assembly of identical protein subunits with a low request of free energy and a similar spiral path to virus nucleic acid. Consequently, small variations in protein subunits can affect the stability of the entire phage particle. Previously, we observed that rearrangement in the capsid structure of M13 engineered phages affected the resistance to UV-C exposure, while that to H2O2 was mainly ascribable to the amino acids’ sequence of the foreign peptide. Based on these findings, in this work, the resistance to accelerated proton beam exposure (5.0 MeV energy) of the same phage clones was determined at different absorbed doses and dose rates. Then, the number of viral particles able to infect and replicate in the natural host, Escherichia coli F+, was evaluated. By comparing the results with the M13 wild-type vector (pC89), we observed that 12III1 phage clones, with the foreign peptide containing amino acids favorable to carbonylation, exhibited the highest reduction in phage titer associated with a radiation damage (RD) of 35 × 10−3/Gy at 50 dose Gy. On the other hand, P9b phage clones, containing amino acids unfavorable to carbonylation, showed the lowest reduction with an RD of 4.83 × 10−3/Gy at 500 dose Gy. These findings could improve the understanding of the molecular mechanisms underlying the radiation resistance of viruses
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Tong W, Fang H, Xiong H, Wei D, Leng Y, Hu X, Huang X, Xiong Y. Eco-Friendly Fluorescent ELISA Based on Bifunctional Phage for Ultrasensitive Detection of Ochratoxin A in Corn. Foods 2021; 10:2429. [PMID: 34681477 PMCID: PMC8536128 DOI: 10.3390/foods10102429] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2021] [Revised: 10/07/2021] [Accepted: 10/11/2021] [Indexed: 01/21/2023] Open
Abstract
Conventional enzyme-linked immunosorbent assay (ELISA) is commonly used for Ochratoxin A (OTA) screening, but it is limited by low sensitivity and harmful competing antigens of enzyme-OTA conjugates. Herein, a bifunctional M13 bacteriophage with OTA mimotopes fused on the p3 protein and biotin modified on major p8 proteins was introduced as an eco-friendly competing antigen and enzyme container for enhanced sensitivity. Mercaptopropionic acid-modified quantum dots (MPA-QDs), which are extremely sensitive to hydrogen peroxide, were chosen as fluorescent signal transducers that could manifest glucose oxidase-induced fluorescence quenching in the presence of glucose. On these bases, a highly sensitive and eco-friendly fluorescent immunoassay for OTA sensing was developed. Under optimized conditions, the proposed method demonstrates a good linear detection of OTA from 4.8 to 625 pg/mL and a limit of detection (LOD) of 5.39 pg/mL. The LOD is approximately 26-fold lower than that of a conventional horse radish peroxidase (HRP) based ELISA and six-fold lower than that of a GOx-OTA conjugate-based fluorescent ELISA. The proposed method also shows great specificity and accepted accuracy for analyzing OTA in real corn samples. The detection results are highly consistent with those obtained using the ultra-performance liquid chromatography-fluorescence detection method, indicating the high reliability of the proposed method for OTA detection. In conclusion, the proposed method is an excellent OTA screening platform over a conventional ELISA and can be easily extended for sensing other analytes by altering specific mimic peptide sequences in phages.
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Affiliation(s)
- Weipeng Tong
- State Key Laboratory of Food Science and Technology, Nanchang University, Nanchang 330047, China; (W.T.); (H.F.); (H.X.); (D.W.); (X.H.); (Y.X.)
- School of Food Science and Technology, Nanchang University, Nanchang 330047, China
| | - Hao Fang
- State Key Laboratory of Food Science and Technology, Nanchang University, Nanchang 330047, China; (W.T.); (H.F.); (H.X.); (D.W.); (X.H.); (Y.X.)
- School of Food Science and Technology, Nanchang University, Nanchang 330047, China
| | - Hanpeng Xiong
- State Key Laboratory of Food Science and Technology, Nanchang University, Nanchang 330047, China; (W.T.); (H.F.); (H.X.); (D.W.); (X.H.); (Y.X.)
- School of Food Science and Technology, Nanchang University, Nanchang 330047, China
| | - Daixian Wei
- State Key Laboratory of Food Science and Technology, Nanchang University, Nanchang 330047, China; (W.T.); (H.F.); (H.X.); (D.W.); (X.H.); (Y.X.)
- School of Food Science and Technology, Nanchang University, Nanchang 330047, China
| | - Yuankui Leng
- State Key Laboratory of Food Science and Technology, Nanchang University, Nanchang 330047, China; (W.T.); (H.F.); (H.X.); (D.W.); (X.H.); (Y.X.)
- School of Food Science and Technology, Nanchang University, Nanchang 330047, China
| | - Xinyu Hu
- School of Qianhu, Nanchang University, Nanchang 330031, China;
| | - Xiaolin Huang
- State Key Laboratory of Food Science and Technology, Nanchang University, Nanchang 330047, China; (W.T.); (H.F.); (H.X.); (D.W.); (X.H.); (Y.X.)
- School of Food Science and Technology, Nanchang University, Nanchang 330047, China
| | - Yonghua Xiong
- State Key Laboratory of Food Science and Technology, Nanchang University, Nanchang 330047, China; (W.T.); (H.F.); (H.X.); (D.W.); (X.H.); (Y.X.)
- School of Food Science and Technology, Nanchang University, Nanchang 330047, China
- Jiangxi-OAI Joint Research Institute, Nanchang University, Nanchang 330047, China
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7
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Torabi LR, Naghavi NS, Doudi M, Monajemi R. Efficacious antibacterial potency of novel bacteriophages against ESBL-producing Klebsiella pneumoniae isolated from burn wound infections. IRANIAN JOURNAL OF MICROBIOLOGY 2021; 13:678-690. [PMID: 34900166 PMCID: PMC8629815 DOI: 10.18502/ijm.v13i5.7435] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
Abstract
BACKGROUND AND OBJECTIVES Prevalence of extended spectrum β-lactamase (ESBL) leads to the development of antibiotic resistance and mortality in burn patients. One of the alternative strategies for controlling ESBL bacterial infections is clinical trials of bacteriophage therapy. The aim of this study was to isolate and characterize specific bacteriophages against ESBL-producing Klebsiella pneumoniae in patients with burn ulcers. MATERIALS AND METHODS Clinical samples were isolated from the hospitalized patient in burn medical centers, Iran. Biochemical screenings and 16S rRNA gene sequencing were determined. The phages were isolated from municipal sewerage treatment plants, Isfahan, Iran. TEM and FESEM, adsorption velocity, growth curve, host range, and the viability of the phage particles as well as proteomics and enzyme digestion patterns were examined. RESULTS The results showed that Klebsiella pneumoniae Iaufa_lad2 (GenBank accession number: MW836954) was confirmed as an ESBL-producing strain using combined disk method. This bacterium showed significant sensitivity to three phages including PɸBw-Kp1, PɸBw-Kp2, and PɸBw-Kp3. Morphological characterization demonstrated that the phage PɸBw-Kp3 to the Siphoviridae family (lambda-like phages) and both phages PɸBw-Kp1 and ɸBw-Kp2 to the Podoviridae family (T1-like phages). The isolated bacteriophages had a large burst size, thermal and pH viability and efficient adsorption rate to the host cells. CONCLUSION In present study, the efficacy of bacteriophages against ESBL pathogenic bacterium promises a remarkable achievement for phage therapy. It seems that, these isolated bacteriophages, in the form of phage cocktails, had a strong antibacterial impacts and a broad-spectrum strategy against ESBL-producing Klebsiella pneumoniae isolated from burn ulcers.
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Affiliation(s)
| | - Nafiseh Sadat Naghavi
- Department of Microbiology, Falavarjan Branch, Islamic Azad University, Isfahan, Iran
| | - Monir Doudi
- Department of Microbiology, Falavarjan Branch, Islamic Azad University, Isfahan, Iran
| | - Ramesh Monajemi
- Department of Biology, Falavarjan Branch, Islamic Azad University, Isfahan, Iran
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Kim H, Lee JH, Lee JH, Lee BY, Lee BD, Okada K, Ji S, Yoon J, Lee JH, Lee SW. M13 Virus Triboelectricity and Energy Harvesting. NANO LETTERS 2021; 21:6851-6858. [PMID: 34383494 DOI: 10.1021/acs.nanolett.1c01881] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/13/2023]
Abstract
Triboelectrification is a phenomenon that generates electric potential upon contact. Here, we report a viral particle capable of generating triboelectric potential. M13 bacteriophage is exploited to fabricate precisely defined chemical and physical structures. By genetically engineering the charged structures, we observe that more negatively charged phages can generate higher triboelectric potentials and can diffuse the electric charges faster than less negatively charged phages can. The computational results show that the glutamate-engineered phages lower the LUMO energy level so that they can easily accept electrons from other materials upon contact. A phage-based triboelectric nanogenerator is fabricated and it could produce ∼76 V and ∼5.1 μA, enough to power 30 light-emitting diodes upon a mechanical force application. Our biotechnological approach will be useful to understand the electrical behavior of biomaterials, harvest mechanical energy, and provide a novel modality to detect desired viruses in the future.
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Affiliation(s)
- Han Kim
- Department of Applied Science and Technology, University of California, Berkeley, California 94720, United States
- Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720, United States
| | - Ju-Hyuck Lee
- Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720, United States
- Department of Bioengineering, University of California, Berkeley, California 94720, United States
| | - Ju Hun Lee
- Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720, United States
- Department of Bioengineering, University of California, Berkeley, California 94720, United States
| | - Byung Yang Lee
- Department of Mechanical Engineering, Korea University, Seoul 02841, Republic of Korea
| | - Byoung Duk Lee
- Large Display Development Center, Samsung Display Co Ltd, Yongin-si 17113, Republic of Korea
| | - Kento Okada
- Department of Bioengineering, University of California, Berkeley, California 94720, United States
- Department of Materials Science and Engineering, University of California, Berkeley, California 94720, United States
| | - Seungwook Ji
- Department of Applied Science and Technology, University of California, Berkeley, California 94720, United States
- Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720, United States
| | - Jihwan Yoon
- Large Display Development Center, Samsung Display Co Ltd, Yongin-si 17113, Republic of Korea
| | - Jong Hyuk Lee
- Large Display Development Center, Samsung Display Co Ltd, Yongin-si 17113, Republic of Korea
| | - Seung-Wuk Lee
- Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720, United States
- Department of Bioengineering, University of California, Berkeley, California 94720, United States
- Tsinghua-Berkeley Shenzhen Institute, Berkeley, California 94720, United States
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Jayapaul J, Schröder L. Molecular Sensing with Host Systems for Hyperpolarized 129Xe. Molecules 2020; 25:E4627. [PMID: 33050669 PMCID: PMC7587211 DOI: 10.3390/molecules25204627] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2020] [Revised: 09/27/2020] [Accepted: 09/30/2020] [Indexed: 12/12/2022] Open
Abstract
Hyperpolarized noble gases have been used early on in applications for sensitivity enhanced NMR. 129Xe has been explored for various applications because it can be used beyond the gas-driven examination of void spaces. Its solubility in aqueous solutions and its affinity for hydrophobic binding pockets allows "functionalization" through combination with host structures that bind one or multiple gas atoms. Moreover, the transient nature of gas binding in such hosts allows the combination with another signal enhancement technique, namely chemical exchange saturation transfer (CEST). Different systems have been investigated for implementing various types of so-called Xe biosensors where the gas binds to a targeted host to address molecular markers or to sense biophysical parameters. This review summarizes developments in biosensor design and synthesis for achieving molecular sensing with NMR at unprecedented sensitivity. Aspects regarding Xe exchange kinetics and chemical engineering of various classes of hosts for an efficient build-up of the CEST effect will also be discussed as well as the cavity design of host molecules to identify a pool of bound Xe. The concept is presented in the broader context of reporter design with insights from other modalities that are helpful for advancing the field of Xe biosensors.
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Affiliation(s)
| | - Leif Schröder
- Molecular Imaging, Leibniz-Forschungsinstitut für Molekulare Pharmakologie (FMP), 13125 Berlin, Germany;
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CRP-binding bacteriophage as a new element of layer-by-layer assembly carbon nanofiber modified electrodes. Bioelectrochemistry 2020; 136:107629. [PMID: 32818758 DOI: 10.1016/j.bioelechem.2020.107629] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2020] [Revised: 08/02/2020] [Accepted: 08/02/2020] [Indexed: 02/07/2023]
Abstract
Recently, bacteriophage particles have started to be applied as a new biomaterial for developing sensing platforms. They can be used as both a recognition element or/and as building blocks, template/scaffold. In this paper, we studied a bacteriophage selected through phage-display technology. The chosen bacteriophage acted as a building block for creating a carbon nanofiber-based electrode and as a new receptor/binding element that recognizes C-reactive protein (CRP) - one of the markers of inflammatory processes in the human body. The binding efficiency of the selected phage towards CRP is two orders of magnitude higher than in the wild type. We demonstrate that the phage-based sensor is selective against other proteins. Finally, we show that layer-by-layer methods are suitable for deposition of negatively charged phages (wild or CRP-binding) with positively charged carbon nanofibers for electrode surface modification. A three-layered electrode was successfully used for molecular recognition of CRP, and the molecular interactions were studied using electrochemical, biological, and optical methods, including microscopic and spectroscopic analyses.
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Khedkar PH, Patzak A. SARS-CoV-2: What do we know so far? Acta Physiol (Oxf) 2020; 229:e13470. [PMID: 32220035 PMCID: PMC7228362 DOI: 10.1111/apha.13470] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2020] [Revised: 03/22/2020] [Accepted: 03/22/2020] [Indexed: 12/14/2022]
Affiliation(s)
- Pratik H. Khedkar
- Institut für Vegetative PhysiologieCharité – Universitätsmedizin Berlin, corporate member of the Freie Universität Berlin, Humboldt Universität zu Berlin and the Berlin Institute of HealthBerlinGermany
| | - Andreas Patzak
- Institut für Vegetative PhysiologieCharité – Universitätsmedizin Berlin, corporate member of the Freie Universität Berlin, Humboldt Universität zu Berlin and the Berlin Institute of HealthBerlinGermany
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12
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Mori T, Sugita Y. Implicit Micelle Model for Membrane Proteins Using Superellipsoid Approximation. J Chem Theory Comput 2019; 16:711-724. [DOI: 10.1021/acs.jctc.9b00783] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Affiliation(s)
- Takaharu Mori
- Theoretical Molecular Science Laboratory, RIKEN Cluster for Pioneering Research, 2-1 Hirosawa, Wako-shi, Saitama, 351-0198, Japan
| | - Yuji Sugita
- Theoretical Molecular Science Laboratory, RIKEN Cluster for Pioneering Research, 2-1 Hirosawa, Wako-shi, Saitama, 351-0198, Japan
- RIKEN Center for Computational Science, 7-1-26 Minatojima-Minamimachi, Chuo-ku, Kobe, Hyogo 650-0047, Japan
- RIKEN Center for Biosystems Dynamics Research, 7-1-26 Minatojima-Minamimachi, Chuo-ku, Kobe, Hyogo 650-0047, Japan
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13
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14
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Alarcón-Correa M, Günther JP, Troll J, Kadiri VM, Bill J, Fischer P, Rothenstein D. Self-Assembled Phage-Based Colloids for High Localized Enzymatic Activity. ACS NANO 2019; 13:5810-5815. [PMID: 30920792 DOI: 10.1021/acsnano.9b01408] [Citation(s) in RCA: 25] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/24/2023]
Abstract
Catalytically active colloids are model systems for chemical motors and active matter. It is desirable to replace the inorganic catalysts and the toxic fuels that are often used with biocompatible enzymatic reactions. However, compared to inorganic catalysts, enzyme-coated colloids tend to exhibit less activity. Here, we show that the self-assembly of genetically engineered M13 bacteriophages that bind enzymes to magnetic beads ensures high and localized enzymatic activity. These phage-decorated colloids provide a proteinaceous environment for directed enzyme immobilization. The magnetic properties of the colloidal carrier particle permit repeated enzyme recovery from a reaction solution, while the enzymatic activity is retained. Moreover, localizing the phage-based construct with a magnetic field in a microcontainer allows the enzyme-phage-colloids to function as an enzymatic micropump, where the enzymatic reaction generates a fluid flow. This system shows the fastest fluid flow reported to date by a biocompatible enzymatic micropump. In addition, it is functional in complex media including blood, where the enzyme-driven micropump can be powered at the physiological blood-urea concentrations.
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Affiliation(s)
- Mariana Alarcón-Correa
- Max Planck Institute for Intelligent Systems , Heisenbergstrasse 3 , 70569 Stuttgart , Germany
- Institute of Physical Chemistry , University of Stuttgart , Pfaffenwaldring 55 , 70569 Stuttgart , Germany
| | - Jan-Philipp Günther
- Max Planck Institute for Intelligent Systems , Heisenbergstrasse 3 , 70569 Stuttgart , Germany
- Institute of Physical Chemistry , University of Stuttgart , Pfaffenwaldring 55 , 70569 Stuttgart , Germany
| | - Jonas Troll
- Max Planck Institute for Intelligent Systems , Heisenbergstrasse 3 , 70569 Stuttgart , Germany
- Institute of Physical Chemistry , University of Stuttgart , Pfaffenwaldring 55 , 70569 Stuttgart , Germany
| | - Vincent Mauricio Kadiri
- Max Planck Institute for Intelligent Systems , Heisenbergstrasse 3 , 70569 Stuttgart , Germany
- Institute of Physical Chemistry , University of Stuttgart , Pfaffenwaldring 55 , 70569 Stuttgart , Germany
| | - Joachim Bill
- Institute for Materials Science , University of Stuttgart , Heisenbergstrasse 3 , 70569 Stuttgart , Germany
| | - Peer Fischer
- Max Planck Institute for Intelligent Systems , Heisenbergstrasse 3 , 70569 Stuttgart , Germany
- Institute of Physical Chemistry , University of Stuttgart , Pfaffenwaldring 55 , 70569 Stuttgart , Germany
| | - Dirk Rothenstein
- Institute for Materials Science , University of Stuttgart , Heisenbergstrasse 3 , 70569 Stuttgart , Germany
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Sokullu E, Soleymani Abyaneh H, Gauthier MA. Plant/Bacterial Virus-Based Drug Discovery, Drug Delivery, and Therapeutics. Pharmaceutics 2019; 11:E211. [PMID: 31058814 PMCID: PMC6572107 DOI: 10.3390/pharmaceutics11050211] [Citation(s) in RCA: 30] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2019] [Revised: 04/23/2019] [Accepted: 04/25/2019] [Indexed: 02/06/2023] Open
Abstract
Viruses have recently emerged as promising nanomaterials for biotechnological applications. One of the most important applications of viruses is phage display, which has already been employed to identify a broad range of potential therapeutic peptides and antibodies, as well as other biotechnologically relevant polypeptides (including protease inhibitors, minimizing proteins, and cell/organ targeting peptides). Additionally, their high stability, easily modifiable surface, and enormous diversity in shape and size, distinguish viruses from synthetic nanocarriers used for drug delivery. Indeed, several plant and bacterial viruses (e.g., phages) have been investigated and applied as drug carriers. The ability to remove the genetic material within the capsids of some plant viruses and phages produces empty viral-like particles that are replication-deficient and can be loaded with therapeutic agents. This review summarizes the current applications of plant viruses and phages in drug discovery and as drug delivery systems and includes a discussion of the present status of virus-based materials in clinical research, alongside the observed challenges and opportunities.
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Affiliation(s)
- Esen Sokullu
- Institut National de la Recherche Scientifique (INRS), EMT Research Center, Varennes, QC J3X 1S2, Canada.
| | - Hoda Soleymani Abyaneh
- Institut National de la Recherche Scientifique (INRS), EMT Research Center, Varennes, QC J3X 1S2, Canada.
| | - Marc A Gauthier
- Institut National de la Recherche Scientifique (INRS), EMT Research Center, Varennes, QC J3X 1S2, Canada.
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16
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Harada LK, Silva EC, Campos WF, Del Fiol FS, Vila M, Dąbrowska K, Krylov VN, Balcão VM. Biotechnological applications of bacteriophages: State of the art. Microbiol Res 2018; 212-213:38-58. [DOI: 10.1016/j.micres.2018.04.007] [Citation(s) in RCA: 118] [Impact Index Per Article: 19.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2018] [Revised: 04/16/2018] [Accepted: 04/25/2018] [Indexed: 02/06/2023]
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17
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Abstract
Filamentous bacteriophages, also known as filamentous bacterial viruses or Inoviruses, have been studied extensively over the years. They are interesting paradigms in structural molecular biology and offer insight into molecular assembly, a process that remains to be fully understood. In this chapter, an overview on filamentous bacteriophages will be provided. In particular, we review the constituent proteins of filamentous bacteriophage and discuss assembly by examining the structure of the major coat protein at various stages of the process. The minor coat proteins will also be briefly reviewed. Structural information provides key snapshots into the dynamic process of assembly.
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18
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Petrova AB, Herold C, Petrov EP. Conformations and membrane-driven self-organization of rodlike fd virus particles on freestanding lipid membranes. SOFT MATTER 2017; 13:7172-7187. [PMID: 28930355 DOI: 10.1039/c7sm00829e] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/22/2023]
Abstract
Membrane-mediated interactions and aggregation of colloidal particles adsorbed to responsive elastic membranes are challenging problems relevant for understanding the microscopic organization and dynamics of biological membranes. We experimentally study the behavior of rodlike semiflexible fd virus particles electrostatically adsorbed to freestanding cationic lipid membranes and find that their behavior can be controlled by tuning the membrane charge and ionic strength of the surrounding medium. Three distinct interaction regimes of rodlike virus particles with responsive elastic membranes can be observed. (i) A weakly charged freestanding cationic lipid bilayer in a low ionic strength medium represents a gentle quasi-2D substrate preserving the integrity, structure, and mechanical properties of the membrane-bound semiflexible fd virus, which under these conditions is characterized by a monomer length of 884 ± 4 nm and a persistence length of 2.5 ± 0.2 μm, in perfect agreement with its properties in bulk media. (ii) An increase in the membrane charge leads to the membrane-driven collapse of fd virus particles on freestanding lipid bilayers and lipid nanotubes into compact globules. (iii) When the membrane charge is low, and the mutual electrostatic repulsion of membrane-bound virus particles is screened to a considerable degree, membrane-driven self-organization of membrane-bound fd virus particles into long linear tip-to-tip aggregates showing dynamic self-assembly/disassembly and quasi-semiflexible behavior takes place. These observations are in perfect agreement with the results of recent theoretical and simulation studies predicting that membrane-mediated interactions can control the behavior of colloidal particles adsorbed on responsive elastic membranes.
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Affiliation(s)
- Anastasiia B Petrova
- Max Planck Institute of Biochemistry, Department of Cellular and Molecular Biophysics, 82152 Martinsried, Germany.
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19
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El-Shibiny A, El-Sahhar S. Bacteriophages: the possible solution to treat infections caused by pathogenic bacteria. Can J Microbiol 2017; 63:865-879. [PMID: 28863269 DOI: 10.1139/cjm-2017-0030] [Citation(s) in RCA: 41] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
Since their discovery in 1915, bacteriophages have been used to treat bacterial infections in animals and humans because of their unique ability to infect their specific bacterial hosts without affecting other bacterial populations. The research carried out in this field throughout the 20th century, largely in Georgia, part of USSR and Poland, led to the establishment of phage therapy protocols. However, the discovery of penicillin and sulfonamide antibiotics in the Western World during the 1930s was a setback in the advancement of phage therapy. The misuse of antibiotics has reduced their efficacy in controlling pathogens and has led to an increase in the number of antibiotic-resistant bacteria. As an alternative to antibiotics, bacteriophages have become a topic of interest with the emergence of multidrug-resistant bacteria, which are a threat to public health. Recent studies have indicated that bacteriophages can be used indirectly to detect pathogenic bacteria or directly as biocontrol agents. Moreover, they can be used to develop new molecules for clinical applications, vaccine production, drug design, and in the nanomedicine field via phage display.
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Affiliation(s)
- Ayman El-Shibiny
- University of Science and Technology, Zewail City of Science and Technology, Sheikh Zayed District, 12588, Giza, Egypt.,University of Science and Technology, Zewail City of Science and Technology, Sheikh Zayed District, 12588, Giza, Egypt
| | - Salma El-Sahhar
- University of Science and Technology, Zewail City of Science and Technology, Sheikh Zayed District, 12588, Giza, Egypt.,University of Science and Technology, Zewail City of Science and Technology, Sheikh Zayed District, 12588, Giza, Egypt
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20
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The Transmembrane Morphogenesis Protein gp1 of Filamentous Phages Contains Walker A and Walker B Motifs Essential for Phage Assembly. Viruses 2017; 9:v9040073. [PMID: 28397779 PMCID: PMC5408679 DOI: 10.3390/v9040073] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2017] [Revised: 03/29/2017] [Accepted: 04/04/2017] [Indexed: 01/26/2023] Open
Abstract
In contrast to lytic phages, filamentous phages are assembled in the inner membrane and secreted across the bacterial envelope without killing the host. For assembly and extrusion of the phage across the host cell wall, filamentous phages code for membrane-embedded morphogenesis proteins. In the outer membrane of Escherichia coli, the protein gp4 forms a pore-like structure, while gp1 and gp11 form a complex in the inner membrane of the host. By comparing sequences with other filamentous phages, we identified putative Walker A and B motifs in gp1 with a conserved lysine in the Walker A motif (K14), and a glutamic and aspartic acid in the Walker B motif (D88, E89). In this work we demonstrate that both, Walker A and Walker B, are essential for phage production. The crucial role of these key residues suggests that gp1 might be a molecular motor driving phage assembly. We further identified essential residues for the function of the assembly complex. Mutations in three out of six cysteine residues abolish phage production. Similarly, two out of six conserved glycine residues are crucial for gp1 function. We hypothesise that the residues represent molecular hinges allowing domain movement for nucleotide binding and phage assembly.
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21
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Characterization and complete genome sequence analysis of a novel virulent Siphoviridae phage against Staphylococcus aureus isolated from bovine mastitis in Xinjiang, China. Virus Genes 2017; 53:464-476. [DOI: 10.1007/s11262-017-1445-z] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2016] [Accepted: 03/08/2017] [Indexed: 01/23/2023]
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22
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Seo Y, Manivannan S, Kang I, Lee SW, Kim K. Gold dendrites Co-deposited with M13 virus as a biosensor platform for nitrite ions. Biosens Bioelectron 2017; 94:87-93. [PMID: 28262612 DOI: 10.1016/j.bios.2017.02.036] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2016] [Revised: 02/15/2017] [Accepted: 02/22/2017] [Indexed: 11/17/2022]
Abstract
We developed a biosensor for nitrite ion on an electrode surface modified with M13 viruses and gold nanostructures. Gold dendritic nanostructures (Au-DNs) are electrochemically co-deposited from 4E peptides engineered M13 virus (M134E) mixed electrolyte on to the ITO electrode. The M134E could specifically nucleate Au precursor (Gold (III) chloride), which enable the efficient growth of dendritic nanostructures, whereas such dendritic structures were not obtained in the presence of wild-type and Y3E peptides engineered M13 viruses. The structural features of the Au-DNs and their interfacing mechanism with ITO electrode are characterized by SEM, EDX and XRD analyses. The growth of Au-DNs at ITO electrode has been monitored by time dependent SEM study. The M134E induces the formation and plays a crucial role in shaping the dendritic morphology for Au. Biosensor electrode was constructed using Au-DNs modified electrode for nitrite ions and found improved sensitivity relative to the sensor electrode prepared from wild-type M13, Y3E peptides engineered M13 and without M13. Sensor electrode exhibited good selectivity toward target analyte from the possible interferences. Furthermore, 4E native peptides were used as additive to deposit Au nanostructures and it is compared with the structure and reactivity of the Au nanostructures prepared in the presence of M134E. Our novel biosensor fabrication can be extended to other metal and metal oxide nanostructures and its application might be useful to develop novel biosensor electrode for variety of biomolecules.
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Affiliation(s)
- Yeji Seo
- Electrochemistry Laboratory for Sensors & Energy (ELSE), Department of Chemistry, Incheon National University, Incheon 406-772, Republic of Korea
| | - Shanmugam Manivannan
- Electrochemistry Laboratory for Sensors & Energy (ELSE), Department of Chemistry, Incheon National University, Incheon 406-772, Republic of Korea
| | - Inhak Kang
- Electrochemistry Laboratory for Sensors & Energy (ELSE), Department of Chemistry, Incheon National University, Incheon 406-772, Republic of Korea
| | - Seung-Wuk Lee
- Department of Bioengineering, University of California, Berkeley, CA 94720, USA
| | - Kyuwon Kim
- Electrochemistry Laboratory for Sensors & Energy (ELSE), Department of Chemistry, Incheon National University, Incheon 406-772, Republic of Korea.
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23
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Szot-Karpińska K, Golec P, Leśniewski A, Pałys B, Marken F, Niedziółka-Jönsson J, Węgrzyn G, Łoś M. Modified Filamentous Bacteriophage as a Scaffold for Carbon Nanofiber. Bioconjug Chem 2016; 27:2900-2910. [DOI: 10.1021/acs.bioconjchem.6b00555] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Affiliation(s)
- Katarzyna Szot-Karpińska
- Institute
of Physical Chemistry, Polish Academy of Sciences, Kasprzaka 44/52, 01-224 Warszawa, Poland
- Department
of Molecular Biology, University of Gdansk, Wita Stwosza 59, 80-308 Gdansk, Poland
| | - Piotr Golec
- Laboratory
of Molecular Biology (affiliated with the University of Gdansk), Institute of Biochemistry and Biophysics, Polish Academy of Sciences, Wita Stwosza
59, 80-308 Gdansk, Poland
| | - Adam Leśniewski
- Institute
of Physical Chemistry, Polish Academy of Sciences, Kasprzaka 44/52, 01-224 Warszawa, Poland
| | - Barbara Pałys
- Department
of Chemistry, University of Warsaw, Pastuera 1 02-093 Warsaw, Poland
| | - Frank Marken
- Department
of Chemistry, University of Bath, Bath BA2 7AY, United Kingdom
| | - Joanna Niedziółka-Jönsson
- Institute
of Physical Chemistry, Polish Academy of Sciences, Kasprzaka 44/52, 01-224 Warszawa, Poland
| | - Grzegorz Węgrzyn
- Department
of Molecular Biology, University of Gdansk, Wita Stwosza 59, 80-308 Gdansk, Poland
| | - Marcin Łoś
- Institute
of Physical Chemistry, Polish Academy of Sciences, Kasprzaka 44/52, 01-224 Warszawa, Poland
- Department
of Molecular Biology, University of Gdansk, Wita Stwosza 59, 80-308 Gdansk, Poland
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24
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Kim I, Moon JS, Oh JW. Recent advances in M13 bacteriophage-based optical sensing applications. NANO CONVERGENCE 2016; 3:27. [PMID: 28191437 PMCID: PMC5271159 DOI: 10.1186/s40580-016-0087-5] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/05/2016] [Accepted: 10/07/2016] [Indexed: 05/03/2023]
Abstract
Recently, M13 bacteriophage has started to be widely used as a functional nanomaterial for various electrical, chemical, or optical applications, such as battery components, photovoltaic cells, sensors, and optics. In addition, the use of M13 bacteriophage has expanded into novel research, such as exciton transporting. In these applications, the versatility of M13 phage is a result of its nontoxic, self-assembling, and specific binding properties. For these reasons, M13 phage is the most powerful candidate as a receptor for transducing chemical or optical phenomena of various analytes into electrical or optical signal. In this review, we will overview the recent progress in optical sensing applications of M13 phage. The structural and functional characters of M13 phage will be described and the recent results in optical sensing application using fluorescence, surface plasmon resonance, Förster resonance energy transfer, and surface enhanced Raman scattering will be outlined.
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Affiliation(s)
- Inhong Kim
- Research Center for Energy Convergence Technology, Pusan National University, Busan, 46241 Republic of Korea
| | - Jong-Sik Moon
- BK21 Plus Division of Nano Convergence Technology, Pusan National University, Busan, 46241 Republic of Korea
| | - Jin-Woo Oh
- Research Center for Energy Convergence Technology, Pusan National University, Busan, 46241 Republic of Korea
- BK21 Plus Division of Nano Convergence Technology, Pusan National University, Busan, 46241 Republic of Korea
- Department of Nanoenergy Engineering, Pusan National University, Busan, 46241 Republic of Korea
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25
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Bernard JML, Francis MB. Chemical strategies for the covalent modification of filamentous phage. Front Microbiol 2014; 5:734. [PMID: 25566240 PMCID: PMC4274979 DOI: 10.3389/fmicb.2014.00734] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2014] [Accepted: 12/04/2014] [Indexed: 01/16/2023] Open
Abstract
Historically filamentous bacteriophage have been known to be the workhorse of phage display due to their ability to link genotype to phenotype. More recently, the filamentous phage scaffold has proven to be powerful outside the realm of phage display technology in fields such as molecular imaging, cancer research and materials, and vaccine development. The ability of the virion to serve as a platform for a variety of applications heavily relies on the functionalization of the phage coat proteins with a wide variety of functionalities. Genetic modification of the coat proteins has been the most widely used strategy for functionalizing the virion; however, complementary chemical modification strategies can help to diversify the range of materials that can be developed. This review emphasizes the recent advances that have been made in the chemical modification of filamentous phage as well as some of the challenges that are involved in functionalizing the virion.
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Affiliation(s)
- Jenna M L Bernard
- Department of Chemistry, University of California at Berkeley Berkeley, CA, USA ; Materials Sciences Division - Lawrence Berkeley National Laboratories Berkeley, CA, USA
| | - Matthew B Francis
- Department of Chemistry, University of California at Berkeley Berkeley, CA, USA ; Materials Sciences Division - Lawrence Berkeley National Laboratories Berkeley, CA, USA
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26
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Chung WJ, Lee DY, Yoo SY. Chemical modulation of M13 bacteriophage and its functional opportunities for nanomedicine. Int J Nanomedicine 2014; 9:5825-36. [PMID: 25540583 PMCID: PMC4270384 DOI: 10.2147/ijn.s73883] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023] Open
Abstract
M13 bacteriophage (phage) has emerged as an attractive bionanomaterial owing to its genetically tunable surface chemistry and its potential to self-assemble into hierarchical structures. Furthermore, because of its unique nanoscopic structure, phage has been proposed as a model system in soft condensed physics and as a biomimetic building block for structured functional materials. Genetic engineering of phage provides great opportunities to develop novel nanomaterials with functional surface peptide motifs; however, this biological approach is generally limited to peptides containing the 20 natural amino acids. To extend the scope of phage applications, strategies involving chemical modification have been employed to incorporate a wider range of functional groups, including synthetic chemical compounds. In this review, we introduce the design of chemoselective phage functionalization and discuss how such a strategy is combined with genetic engineering for a variety of medical applications, as reported in recent literature.
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Affiliation(s)
- Woo-Jae Chung
- College of Biotechnology and Bioengineering, Sungkyunkwan University, Suwon, Republic of Korea
| | - Doe-Young Lee
- College of Biotechnology and Bioengineering, Sungkyunkwan University, Suwon, Republic of Korea
| | - So Young Yoo
- BIO-IT Foundry Technology Institute, Pusan National University, Busan, Republic of Korea ; Research Institute for Convergence of Biomedical Science and Technology, Pusan National University Yangsan Hospital, Yangsan, Republic of Korea
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27
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Bocklitz T, Kämmer E, Stöckel S, Cialla-May D, Weber K, Zell R, Deckert V, Popp J. Single virus detection by means of atomic force microscopy in combination with advanced image analysis. J Struct Biol 2014; 188:30-8. [PMID: 25196422 DOI: 10.1016/j.jsb.2014.08.008] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2014] [Accepted: 08/25/2014] [Indexed: 11/25/2022]
Abstract
In the present contribution virions of five different virus species, namely Varicella-zoster virus, Porcine teschovirus, Tobacco mosaic virus, Coliphage M13 and Enterobacteria phage PsP3, are investigated using atomic force microscopy (AFM). From the resulting height images quantitative features like maximal height, area and volume of the viruses could be extracted and compared to reference values. Subsequently, these features were accompanied by image moments, which quantify the morphology of the virions. Both types of features could be utilized for an automatic discrimination of the five virus species. The accuracy of this classification model was 96.8%. Thus, a virus detection on a single-particle level using AFM images is possible. Due to the application of advanced image analysis the morphology could be quantified and used for further analysis. Here, an automatic recognition by means of a classification model could be achieved in a reliable and objective manner.
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Affiliation(s)
- Thomas Bocklitz
- Institute of Physical Chemistry and Abbe Center of Photonics, Friedrich Schiller University Jena, Helmholtzweg 4, 07743 Jena, Germany; InfectoGnostics Forschungscampus Jena e.V., Zentrum für Angewandte Forschung, Philosophenweg 7, 07743 Jena, Germany; Leibniz Institute of Photonic Technology, Albert-Einstein-Strasse 9, 07745 Jena, Germany.
| | - Evelyn Kämmer
- Institute of Physical Chemistry and Abbe Center of Photonics, Friedrich Schiller University Jena, Helmholtzweg 4, 07743 Jena, Germany; InfectoGnostics Forschungscampus Jena e.V., Zentrum für Angewandte Forschung, Philosophenweg 7, 07743 Jena, Germany; Leibniz Institute of Photonic Technology, Albert-Einstein-Strasse 9, 07745 Jena, Germany
| | - Stephan Stöckel
- Institute of Physical Chemistry and Abbe Center of Photonics, Friedrich Schiller University Jena, Helmholtzweg 4, 07743 Jena, Germany; InfectoGnostics Forschungscampus Jena e.V., Zentrum für Angewandte Forschung, Philosophenweg 7, 07743 Jena, Germany; Leibniz Institute of Photonic Technology, Albert-Einstein-Strasse 9, 07745 Jena, Germany
| | - Dana Cialla-May
- Institute of Physical Chemistry and Abbe Center of Photonics, Friedrich Schiller University Jena, Helmholtzweg 4, 07743 Jena, Germany; InfectoGnostics Forschungscampus Jena e.V., Zentrum für Angewandte Forschung, Philosophenweg 7, 07743 Jena, Germany; Leibniz Institute of Photonic Technology, Albert-Einstein-Strasse 9, 07745 Jena, Germany
| | - Karina Weber
- Institute of Physical Chemistry and Abbe Center of Photonics, Friedrich Schiller University Jena, Helmholtzweg 4, 07743 Jena, Germany; InfectoGnostics Forschungscampus Jena e.V., Zentrum für Angewandte Forschung, Philosophenweg 7, 07743 Jena, Germany; Leibniz Institute of Photonic Technology, Albert-Einstein-Strasse 9, 07745 Jena, Germany
| | - Roland Zell
- Department of Virology and Antiviral Therapy, Jena University Hospital, Friedrich Schiller University Jena, Hans-Knöll-Strasse 2, 07745 Jena, Germany
| | - Volker Deckert
- Institute of Physical Chemistry and Abbe Center of Photonics, Friedrich Schiller University Jena, Helmholtzweg 4, 07743 Jena, Germany; InfectoGnostics Forschungscampus Jena e.V., Zentrum für Angewandte Forschung, Philosophenweg 7, 07743 Jena, Germany; Leibniz Institute of Photonic Technology, Albert-Einstein-Strasse 9, 07745 Jena, Germany
| | - Jürgen Popp
- Institute of Physical Chemistry and Abbe Center of Photonics, Friedrich Schiller University Jena, Helmholtzweg 4, 07743 Jena, Germany; InfectoGnostics Forschungscampus Jena e.V., Zentrum für Angewandte Forschung, Philosophenweg 7, 07743 Jena, Germany; Leibniz Institute of Photonic Technology, Albert-Einstein-Strasse 9, 07745 Jena, Germany
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28
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Yata T, Lee KY, Dharakul T, Songsivilai S, Bismarck A, Mintz PJ, Hajitou A. Hybrid Nanomaterial Complexes for Advanced Phage-guided Gene Delivery. MOLECULAR THERAPY-NUCLEIC ACIDS 2014; 3:e185. [PMID: 25118171 PMCID: PMC4221597 DOI: 10.1038/mtna.2014.37] [Citation(s) in RCA: 32] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/06/2014] [Accepted: 06/24/2014] [Indexed: 02/07/2023]
Abstract
Developing nanomaterials that are effective, safe, and selective for gene transfer applications is challenging. Bacteriophages (phage), viruses that infect bacteria only, have shown promise for targeted gene transfer applications. Unfortunately, limited progress has been achieved in improving their potential to overcome mammalian cellular barriers. We hypothesized that chemical modification of the bacteriophage capsid could be applied to improve targeted gene delivery by phage vectors into mammalian cells. Here, we introduce a novel hybrid system consisting of two classes of nanomaterial systems, cationic polymers and M13 bacteriophage virus particles genetically engineered to display a tumor-targeting ligand and carry a transgene cassette. We demonstrate that the phage complex with cationic polymers generates positively charged phage and large aggregates that show enhanced cell surface attachment, buffering capacity, and improved transgene expression while retaining cell type specificity. Moreover, phage/polymer complexes carrying a therapeutic gene achieve greater cancer cell killing than phage alone. This new class of hybrid nanomaterial platform can advance targeted gene delivery applications by bacteriophage.
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Affiliation(s)
- Teerapong Yata
- Phage Therapy Group, Department of Medicine, Imperial College London, London, UK
| | - Koon-Yang Lee
- Polymers and Composites Engineering (PaCE) Group, Department of Chemical Engineering, Imperial College London, London, UK
| | - Tararaj Dharakul
- National Nanotechnology Center, National Science and Technology Development Agency, Khlong Luang Pathumthani, Thailand
| | - Sirirurg Songsivilai
- National Nanotechnology Center, National Science and Technology Development Agency, Khlong Luang Pathumthani, Thailand
| | - Alexander Bismarck
- Polymers and Composites Engineering (PaCE) Group, Department of Chemical Engineering, Imperial College London, London, UK
| | - Paul J Mintz
- Department of Surgery and Cancer, Imperial College London, London, UK
| | - Amin Hajitou
- Phage Therapy Group, Department of Medicine, Imperial College London, London, UK
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29
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Wang Y, Wang W, Lv Y, Zheng W, Mi Z, Pei G, An X, Xu X, Han C, Liu J, Zhou C, Tong Y. Characterization and complete genome sequence analysis of novel bacteriophage IME-EFm1 infecting Enterococcus faecium. J Gen Virol 2014; 95:2565-2575. [PMID: 25078302 DOI: 10.1099/vir.0.067553-0] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023] Open
Abstract
We isolated and characterized a novel virulent bacteriophage, IME-EFm1, specifically infecting multidrug-resistant Enterococcus faecium. IME-EFm1 is morphologically similar to members of the family Siphoviridae. It was found capable of lysing a wide range of our E. faecium collections, including two strains resistant to vancomycin. One-step growth tests revealed the host lysis activity of phage IME-EFm1, with a latent time of 30 min and a large burst size of 116 p.f.u. per cell. These biological characteristics suggested that IME-EFm1 has the potential to be used as a therapeutic agent. The complete genome of IME-EFm1 was 42 597 bp, and was linear, with terminally non-redundant dsDNA and a G+C content of 35.2 mol%. The termini of the phage genome were determined with next-generation sequencing and were further confirmed by nuclease digestion analysis. To our knowledge, this is the first report of a complete genome sequence of a bacteriophage infecting E. faecium. IME-EFm1 exhibited a low similarity to other phages in terms of genome organization and structural protein amino acid sequences. The coding region corresponded to 90.7 % of the genome; 70 putative ORFs were deduced and, of these, 29 could be functionally identified based on their homology to previously characterized proteins. A predicted metallo-β-lactamase gene was detected in the genome sequence. The identification of an antibiotic resistance gene emphasizes the necessity for complete genome sequencing of a phage to ensure it is free of any undesirable genes before use as a therapeutic agent against bacterial pathogens.
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Affiliation(s)
- Yahui Wang
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing 100071, PR China.,School of Life Science & Technology, China Pharmaceutical University, 24 Tong Jia Xiang, Nanjing 210009, PR China
| | - Wei Wang
- Anhui Medical University, Hefei 230032, PR China.,State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing 100071, PR China
| | - Yongqiang Lv
- Department of Laboratory, Dalian Beihai Hospital, Dalian Liaoning 116021, PR China
| | - Wangliang Zheng
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing 100071, PR China
| | - Zhiqiang Mi
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing 100071, PR China
| | - Guangqian Pei
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing 100071, PR China
| | - Xiaoping An
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing 100071, PR China
| | - Xiaomeng Xu
- Anhui Medical University, Hefei 230032, PR China.,State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing 100071, PR China
| | - Chuanyin Han
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing 100071, PR China
| | - Jie Liu
- The General Hospital of Beijing Military Command, Beijing 100041, PR China
| | - Changlin Zhou
- School of Life Science & Technology, China Pharmaceutical University, 24 Tong Jia Xiang, Nanjing 210009, PR China
| | - Yigang Tong
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing 100071, PR China
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Marvin DA, Symmons MF, Straus SK. Structure and assembly of filamentous bacteriophages. PROGRESS IN BIOPHYSICS AND MOLECULAR BIOLOGY 2014; 114:80-122. [PMID: 24582831 DOI: 10.1016/j.pbiomolbio.2014.02.003] [Citation(s) in RCA: 85] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/07/2013] [Accepted: 02/09/2014] [Indexed: 12/24/2022]
Abstract
Filamentous bacteriophages are interesting paradigms in structural molecular biology, in part because of the unusual mechanism of filamentous phage assembly. During assembly, several thousand copies of an intracellular DNA-binding protein bind to each copy of the replicating phage DNA, and are then displaced by membrane-spanning phage coat proteins as the nascent phage is extruded through the bacterial plasma membrane. This complicated process takes place without killing the host bacterium. The bacteriophage is a semi-flexible worm-like nucleoprotein filament. The virion comprises a tube of several thousand identical major coat protein subunits around a core of single-stranded circular DNA. Each protein subunit is a polymer of about 50 amino-acid residues, largely arranged in an α-helix. The subunits assemble into a helical sheath, with each subunit oriented at a small angle to the virion axis and interdigitated with neighbouring subunits. A few copies of "minor" phage proteins necessary for infection and/or extrusion of the virion are located at each end of the completed virion. Here we review both the structure of the virion and aspects of its function, such as the way the virion enters the host, multiplies, and exits to prey on further hosts. In particular we focus on our understanding of the way the components of the virion come together during assembly at the membrane. We try to follow a basic rule of empirical science, that one should chose the simplest theoretical explanation for experiments, but be prepared to modify or even abandon this explanation as new experiments add more detail.
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Affiliation(s)
- D A Marvin
- Department of Biochemistry, University of Cambridge, Cambridge CB2 1GA, UK.
| | - M F Symmons
- Department of Biochemistry, University of Cambridge, Cambridge CB2 1GA, UK
| | - S K Straus
- Department of Chemistry, University of British Columbia, 2036 Main Mall, Vancouver, BC V6T 1Z1, Canada.
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Petrova M, Shcherbatova N, Kurakov A, Mindlin S. Genomic characterization and integrative properties of phiSMA6 and phiSMA7, two novel filamentous bacteriophages of Stenotrophomonas maltophilia. Arch Virol 2013; 159:1293-303. [DOI: 10.1007/s00705-013-1882-5] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2013] [Accepted: 09/29/2013] [Indexed: 12/12/2022]
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Schreiber A, Schiller SM. Nanobiotechnology of protein-based compartments: steps toward nanofactories. BIOINSPIRED BIOMIMETIC AND NANOBIOMATERIALS 2013. [DOI: 10.1680/bbn.13.00008] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
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33
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Binding mechanism and electrochemical properties of M13 phage-sulfur composite. PLoS One 2013; 8:e82332. [PMID: 24324560 PMCID: PMC3850111 DOI: 10.1371/journal.pone.0082332] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2013] [Accepted: 10/31/2013] [Indexed: 11/19/2022] Open
Abstract
Self-assembly of nanostructured materials has been proven a powerful technique in material design and synthesis. By phage display screening, M13 phage was found to strongly bind sulfur particles. Fourier transform infrared and X-ray photoelectron spectroscopy measurements indicated that the strong sulfur-binding ability of M13 phage derives from newly generated S-O and C-S bonds. Using this phage assembled sulfur composite in a lithium battery, the first discharge capacity reached 1117 mAh g-1, which is more than twice that of the sulfur only cathode. Besides, the negative polysulfide shuttle effect in a lithium-sulfur battery was significantly suppressed.
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Dong D, Sutaria S, Hwangbo JY, Chen P. A simple and rapid method to isolate purer M13 phage by isoelectric precipitation. Appl Microbiol Biotechnol 2013; 97:8023-9. [PMID: 23807666 DOI: 10.1007/s00253-013-5049-9] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2013] [Revised: 06/06/2013] [Accepted: 06/09/2013] [Indexed: 11/25/2022]
Abstract
M13 virus (phage) has been extensively used in phage display technology and nanomaterial templating. Our research aimed to use M13 phage to template sulfur nanoparticles for making lithium ion batteries. Traditional methods for harvesting M13 phage from Escherichia coli employ polyethylene glycol (PEG)-based precipitation, and the yield is usually measured by plaque counting. With this method, PEG residue is present in the M13 phage pellet and is difficult to eliminate. To resolve this issue, a method based on isoelectric precipitation was introduced and tested. The isoelectric method resulted in the production of purer phage with a higher yield, compared to the traditional PEG-based method. There is no significant variation in infectivity of the phage prepared using isoelectric precipitation, and the dynamic light scattering data indirectly prove that the phage structure is not damaged by pH adjustment. To maximize phage production, a dry-weight yield curve of M13 phage for various culture times was produced. The yield curve is proportional to the growth curve of E. coli. On a 200-mL culture scale, 0.2 g L(-1) M13 phage (dry-weight) was produced by the isoelectric precipitation method.
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Affiliation(s)
- Dexian Dong
- Department of Chemical Engineering, University of Waterloo, 200 University Avenue West, Waterloo, ON, N2L 3G1, Canada.
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Abstract
Since the advent of the electron microscope approximately 70 years ago, bacterial viruses and electron microscopy are inextricably linked. Electron microscopy proved that bacteriophages are particulate and viral in nature, are complex in size and shape, and have intracellular development cycles and assembly pathways. The principal contribution of electron microscopy to bacteriophage research is the technique of negative staining. Over 5500 bacterial viruses have so far been characterized by electron microscopy, making bacteriophages, at least on paper, the largest viral group in existence. Other notable contributions are cryoelectron microcopy and three-dimensional image reconstruction, particle counting, and immunoelectron microscopy. Scanning electron microscopy has had relatively little impact. Transmission electron microscopy has provided the basis for the recognition and establishment of bacteriophage families and is one of the essential criteria to classify novel viruses into families. It allows for instant diagnosis and is thus the fastest diagnostic technique in virology. The most recent major contribution of electron microscopy is the demonstration that the capsid of tailed phages is monophyletic in origin and that structural links exist between some bacteriophages and viruses of vertebrates and archaea. DNA sequencing cannot replace electron microscopy and vice versa.
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Affiliation(s)
- Hans-W Ackermann
- Department of Microbiology, Epidemiology and Infectiology, Faculty of Medicine, Laval University, Quebec, Canada
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36
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Wu Y, Yang H, Shin HJ. Viruses as self-assembled nanocontainers for encapsulation of functional cargoes. KOREAN J CHEM ENG 2013. [DOI: 10.1007/s11814-013-0083-y] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
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37
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Kęsik-Szeloch A, Drulis-Kawa Z, Weber-Dąbrowska B, Kassner J, Majkowska-Skrobek G, Augustyniak D, Lusiak-Szelachowska M, Zaczek M, Górski A, Kropinski AM. Characterising the biology of novel lytic bacteriophages infecting multidrug resistant Klebsiella pneumoniae. Virol J 2013; 10:100. [PMID: 23537199 PMCID: PMC3620542 DOI: 10.1186/1743-422x-10-100] [Citation(s) in RCA: 89] [Impact Index Per Article: 8.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2012] [Accepted: 03/25/2013] [Indexed: 01/21/2023] Open
Abstract
Background Members of the genus Klebsiella are among the leading microbial pathogens associated with nosocomial infection. The increased incidence of antimicrobial resistance in these species has propelled the need for alternate/combination therapeutic regimens to aid clinical treatment. Bacteriophage therapy forms one of these alternate strategies. Methods Electron microscopy, burst size, host range, sensitivity of phage particles to temperature, chloroform, pH, and restriction digestion of phage DNA were used to characterize Klebsiella phages. Results and conclusions Of the 32 isolated phages eight belonged to the family Myoviridae, eight to the Siphoviridae whilst the remaining 16 belonged to the Podoviridae. The host range of these phages was characterised against 254 clinical Enterobacteriaceae strains including multidrug resistant Klebsiella isolates producing extended-spectrum beta-lactamases (ESBLs). Based on their lytic potential, six of the phages were further characterised for burst size, physicochemical properties and sensitivity to restriction endonuclease digestion. In addition, five were fully sequenced. Multiple phage-encoded host resistance mechanisms were identified. The Siphoviridae phage genomes (KP16 and KP36) contained low numbers of host restriction sites similar to the strategy found in T7-like phages (KP32). In addition, phage KP36 encoded its own DNA adenine methyltransferase. The φKMV-like KP34 phage was sensitive to all endonucleases used in this study. Dam methylation of KP34 DNA was detected although this was in the absence of an identifiable phage encoded methyltransferase. The Myoviridae phages KP15 and KP27 both carried Dam and Dcm methyltransferase genes and other anti-restriction mechanisms elucidated in previous studies. No other anti-restriction mechanisms were found, e.g. atypical nucleotides (hmC or glucosyl hmC), although Myoviridae phage KP27 encodes an unknown anti-restriction mechanism that needs further investigation.
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Affiliation(s)
- Agata Kęsik-Szeloch
- Institute of Genetics and Microbiology, University of Wroclaw, Przybyszewskiego 63/77, Wroclaw, Poland
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Zahid M, Kim B, Hussain R, Amin R, Park SH. DNA nanotechnology: a future perspective. NANOSCALE RESEARCH LETTERS 2013; 8:119. [PMID: 23497147 PMCID: PMC3599551 DOI: 10.1186/1556-276x-8-119] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/15/2013] [Accepted: 02/21/2013] [Indexed: 05/05/2023]
Abstract
In addition to its genetic function, DNA is one of the most distinct and smart self-assembling nanomaterials. DNA nanotechnology exploits the predictable self-assembly of DNA oligonucleotides to design and assemble innovative and highly discrete nanostructures. Highly ordered DNA motifs are capable of providing an ultra-fine framework for the next generation of nanofabrications. The majority of these applications are based upon the complementarity of DNA base pairing: adenine with thymine, and guanine with cytosine. DNA provides an intelligent route for the creation of nanoarchitectures with programmable and predictable patterns. DNA strands twist along one helix for a number of bases before switching to the other helix by passing through a crossover junction. The association of two crossovers keeps the helices parallel and holds them tightly together, allowing the assembly of bigger structures. Because of the DNA molecule's unique and novel characteristics, it can easily be applied in a vast variety of multidisciplinary research areas like biomedicine, computer science, nano/optoelectronics, and bionanotechnology.
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Affiliation(s)
- Muniza Zahid
- Interdisciplinary Research Center in Biomedical Materials (IRCBM), COMSATS Institute of Information Technology, Lahore 54000, Pakistan
| | - Byeonghoon Kim
- Department of Physics & SKKU Advanced Institute of Nanotechnology (SAINT), Sungkyunkwan University, Suwon 440-746, South Korea
| | - Rafaqat Hussain
- Ibnu Sina Institute for Fundamental Science Studies, Universiti Teknologi Malaysia, 81310 UTM Skudai, Johor Darul Ta'zim, Malaysia
| | - Rashid Amin
- Interdisciplinary Research Center in Biomedical Materials (IRCBM), COMSATS Institute of Information Technology, Lahore 54000, Pakistan
| | - Sung Ha Park
- Department of Physics & SKKU Advanced Institute of Nanotechnology (SAINT), Sungkyunkwan University, Suwon 440-746, South Korea
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39
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Hathorne AP, Bermudez H. Effects of short elastin-like peptides on filamentous particles and their transition behavior. Biotechnol Bioeng 2013; 110:1822-30. [DOI: 10.1002/bit.24854] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2012] [Revised: 01/08/2013] [Accepted: 01/14/2013] [Indexed: 11/09/2022]
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40
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Henry M, Debarbieux L. Tools from viruses: bacteriophage successes and beyond. Virology 2012; 434:151-61. [PMID: 23063405 DOI: 10.1016/j.virol.2012.09.017] [Citation(s) in RCA: 45] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2012] [Revised: 09/14/2012] [Accepted: 09/20/2012] [Indexed: 01/21/2023]
Abstract
Viruses are ubiquitous and can infect any of the three existing cellular lineages (Archaea, Bacteria and Eukarya). Despite the persisting negative public perception of these entities, scientists learnt how to domesticate some of them. The study of molecular mechanisms essential to the completion of viral cycles has greatly contributed to deciphering fundamental processes in biology. Nowadays, viruses have entered the biotechnological era and numerous applications have already been developed. Viral-derived tools are used to manipulate genetic information, detect, diagnose, control and cure infectious diseases, or even design new structural assemblies. With the recent advances in the field of metagenomics, an overwhelming amount of information on novel viruses has become available. As current tools have been historically developed from a limited number of viruses, the potential of discoveries from new archaeal, bacterial and eukaryotic viruses may be limited only by our understanding of the multiple facets of viral cycles.
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Affiliation(s)
- Marine Henry
- Institut Pasteur, Molecular Biology of the Gene in Extremophiles Unit, Department of Microbiology, F-75015 Paris, France
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41
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Lee JH, Domaille DW, Cha JN. Amplified protein detection and identification through DNA-conjugated M13 bacteriophage. ACS NANO 2012; 6:5621-5626. [PMID: 22587008 DOI: 10.1021/nn301565e] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/31/2023]
Abstract
Sensitive protein detection and accurate identification continues to be in great demand for disease screening in clinical and laboratory settings. For these diagnostics to be of clinical value, it is necessary to develop sensors that have high sensitivity but favorable cost-to-benefit ratios. However, many of these sensing platforms are thermally unstable or require significant materials synthesis, engineering, or fabrication. Recently, we demonstrated that naturally occurring M13 bacteriophage can serve as biological scaffolds for engineering protein diagnostics. These viruses have five copies of the pIII protein, which can bind specifically to target antigens, and thousands of pVIII coat proteins, which can be genetically or chemically modified to react with signal-producing materials, such as plasmon-shifting gold nanoparticles (Au NPs). In this report, we show that DNA-conjugated M13 bacteriophage can act as inexpensive protein sensors that can rapidly induce a color change in the presence of a target protein yet also offer the ability to identify the detected antigen in a separate step. Many copies of a specific DNA oligonucleotide were appended to each virus to create phage-DNA conjugates that can hybridize with DNA-conjugated gold nanoparticles. In the case of a colorimetric positive result, the identity of the antigen can also be easily determined by using a DNA microarray. This saves precious resources by establishing a rapid, quantitative method to first screen for the presence of antigen followed by a highly specific typing assay if necessary.
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Affiliation(s)
- Ju Hun Lee
- Department of Nanoengineering and Materials Science and Engineering Program, University of California, San Diego, 9500 Gilman Drive M/C 0448, La Jolla, California 92093, USA
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42
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Ma Y, Nolte RJM, Cornelissen JJLM. Virus-based nanocarriers for drug delivery. Adv Drug Deliv Rev 2012; 64:811-25. [PMID: 22285585 DOI: 10.1016/j.addr.2012.01.005] [Citation(s) in RCA: 302] [Impact Index Per Article: 25.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2011] [Revised: 01/11/2012] [Accepted: 01/12/2012] [Indexed: 12/28/2022]
Abstract
New nanocarrier platforms based on natural biological building blocks offer great promises in revolutionalizing medicine. The usage of specific protein cage structures: virus-like particles (VLPs) for drug packaging and targetted delivery is summarized here. Versatile chemical and genetic modifications on the outer surfaces and inner cavities of VLPs facilitate the preparation of new materials that could meet the biocompatibility, solubility and high uptake efficiency requirements for drug delivery. A full evaluation on the toxicity, bio-distribution and immunology of these materials are envisaged to boost their application potentials.
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Affiliation(s)
- Yujie Ma
- Group of Biomolecular Nanotechnology, MESA(+) Institute for Nanotechnology, University of Twente, P.O. Box 217, 7500 AE Enschede, The Netherlands
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43
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Abstract
Virtually all studies of structure and assembly of viral filaments have been made on plant and bacterial viruses. Structures have been determined using fiber diffraction methods at high enough resolution to construct reliable molecular models or several of the rigid plant tobamoviruses (related to tobacco mosaic virus, TMV) and the filamentous bacteriophages including Pf1 and fd. Lower-resolution structures have been determined for a number of flexible filamentous plant viruses using fiber diffraction and cryo-electron microscopy. Virions of filamentous viruses have numerous mechanical functions, including cell entry, viral disassembly, viral assembly, and cell exit. The plant viruses, which infect multicellular organisms, also use virions or virion-like assemblies for transport within the host. Plant viruses are generally self-assembling; filamentous bacteriophage assembly is combined with secretion from the host cell, using a complex molecular machine. Tobamoviruses and other plant viruses disassemble concomitantly with translation, by various mechanisms and involving various viral and host assemblies. Plant virus movement within the host also makes use of a variety of viral proteins and modified host assemblies.
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44
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Krupovic M, Prangishvili D, Hendrix RW, Bamford DH. Genomics of bacterial and archaeal viruses: dynamics within the prokaryotic virosphere. Microbiol Mol Biol Rev 2011; 75:610-35. [PMID: 22126996 PMCID: PMC3232739 DOI: 10.1128/mmbr.00011-11] [Citation(s) in RCA: 158] [Impact Index Per Article: 12.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022] Open
Abstract
Prokaryotes, bacteria and archaea, are the most abundant cellular organisms among those sharing the planet Earth with human beings (among others). However, numerous ecological studies have revealed that it is actually prokaryotic viruses that predominate on our planet and outnumber their hosts by at least an order of magnitude. An understanding of how this viral domain is organized and what are the mechanisms governing its evolution is therefore of great interest and importance. The vast majority of characterized prokaryotic viruses belong to the order Caudovirales, double-stranded DNA (dsDNA) bacteriophages with tails. Consequently, these viruses have been studied (and reviewed) extensively from both genomic and functional perspectives. However, albeit numerous, tailed phages represent only a minor fraction of the prokaryotic virus diversity. Therefore, the knowledge which has been generated for this viral system does not offer a comprehensive view of the prokaryotic virosphere. In this review, we discuss all families of bacterial and archaeal viruses that contain more than one characterized member and for which evolutionary conclusions can be attempted by use of comparative genomic analysis. We focus on the molecular mechanisms of their genome evolution as well as on the relationships between different viral groups and plasmids. It becomes clear that evolutionary mechanisms shaping the genomes of prokaryotic viruses vary between different families and depend on the type of the nucleic acid, characteristics of the virion structure, as well as the mode of the life cycle. We also point out that horizontal gene transfer is not equally prevalent in different virus families and is not uniformly unrestricted for diverse viral functions.
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Affiliation(s)
- Mart Krupovic
- Institut Pasteur, Unité Biologie Moléculaire du Gène chez les Extrêmophiles, Département de Microbiologie, 25 rue du Dr. Roux, 75015 Paris, France.
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45
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Lee SY, Lim JS, Harris MT. Synthesis and application of virus-based hybrid nanomaterials. Biotechnol Bioeng 2011; 109:16-30. [DOI: 10.1002/bit.23328] [Citation(s) in RCA: 88] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2011] [Revised: 08/17/2011] [Accepted: 08/31/2011] [Indexed: 12/13/2022]
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46
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Wang T, Kulkarni N, D'Souza GGM, Petrenko VA, Torchilin VP. On the mechanism of targeting of phage fusion protein-modified nanocarriers: only the binding peptide sequence matters. Mol Pharm 2011; 8:1720-8. [PMID: 21675738 DOI: 10.1021/mp200080h] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/23/2023]
Abstract
The integration of pharmaceutical nanocarriers with phage display techniques is emerging as a new paradigm for targeted cancer nanomedicines. We explored the direct use of landscape phage fusion proteins for the self-assembly of phage-derived binding peptides to liposomes for cancer cell targeting. The primary purpose of this study was to elucidate the targeting mechanism with a particular emphasis on the relative contributions of the two motifs that make up the landscape phage fusion protein (a binding peptide and the phage pVIII coat protein) to the targeting efficiency. Using transmission electron microscopy and dynamic light scattering, we confirmed the formation of phage-liposomes. Using FACS analysis, fluorescence microscopy, and fluorescence photospectrometry, we found that liposomes modified with MCF-7-specific phage fusion proteins (MCF-7 binding peptide, DMPGTVLP, fused to the phage PVIII coat protein) provided a strong and specific association with target MCF-7 cancer cells but not with cocultured, nontarget cells including C166-GFP and NIH3T3. The substitution for the binding peptide fused to phage pVIII coat protein abolished the targeting specificity. The addition of free binding peptide, DMPGTVLP, competitively inhibited the interaction of MCF-7-specific phage-liposomes with target MCF-7 cells but showed no reduction of MCF-7-associated plain liposomes. The proteolysis of the binding peptide reduced MCF-7 cell-associated phage-liposomes in a proteinase K (PK) concentration-dependent manner with no effect on the binding of plain liposomes to MCF-7 cells. Overall, only the binding peptide motif was involved in the targeting specificity of phage-liposomes. The presence of phage pVIII coat protein did not interfere with the targeting efficiency.
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Affiliation(s)
- Tao Wang
- Center for Pharmaceutical Biotechnology and Nanomedicine, Northeastern University, Boston, Massachusetts 02115, United States
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47
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Abramov G, Morag O, Goldbourt A. Magic-Angle Spinning NMR of a Class I Filamentous Bacteriophage Virus. J Phys Chem B 2011; 115:9671-80. [DOI: 10.1021/jp2040955] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Gili Abramov
- School of Chemistry, Raymond and Beverly Sackler Faculty of Exact Sciences, Tel Aviv University, Ramat Aviv 69978, Tel Aviv, Israel
| | - Omry Morag
- School of Chemistry, Raymond and Beverly Sackler Faculty of Exact Sciences, Tel Aviv University, Ramat Aviv 69978, Tel Aviv, Israel
| | - Amir Goldbourt
- School of Chemistry, Raymond and Beverly Sackler Faculty of Exact Sciences, Tel Aviv University, Ramat Aviv 69978, Tel Aviv, Israel
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48
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Bacteriophages as twenty-first century antibacterial tools for food and medicine. Appl Microbiol Biotechnol 2011; 90:851-9. [PMID: 21491205 DOI: 10.1007/s00253-011-3227-1] [Citation(s) in RCA: 52] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2010] [Revised: 02/25/2011] [Accepted: 02/27/2011] [Indexed: 01/21/2023]
Abstract
Antibiotic-resistant bacteria are an increasing source of concern in all environments in which these drugs have been used. More stringent regulations have led to a slow but sure decrease in antibiotic use in the food industry worldwide, but have also stimulated the search for alternative antibacterial agents. In medicine, the number of people infected with pan-resistant bacteria is driving research to develop new treatments. Within these contexts, studies on the use of bacteriophages in both medicine and the food industry have recently flourished. This renewed interest has coincided with the demonstration that these viruses are involved in geochemical cycles, revolutionizing our vision of their ecological role on our planet. Bacteriophages have co-evolved with bacteria for billions of years and retain the ability to infect bacteria efficiently. They are undoubtedly one of the best potential sources of new solutions for the management of undesirable bacteria.
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49
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Straus SK, Scott WRP, Schwieters CD, Marvin DA. Consensus structure of Pf1 filamentous bacteriophage from X-ray fibre diffraction and solid-state NMR. EUROPEAN BIOPHYSICS JOURNAL : EBJ 2011; 40:221-34. [PMID: 21082179 PMCID: PMC5545983 DOI: 10.1007/s00249-010-0640-9] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/29/2010] [Revised: 10/24/2010] [Accepted: 10/26/2010] [Indexed: 10/18/2022]
Abstract
Filamentous bacteriophages (filamentous bacterial viruses or Inovirus) are simple and well-characterised macromolecular assemblies that are widely used in molecular biology and biophysics, both as paradigms for studying basic biological questions and as practical tools in areas as diverse as immunology and solid-state physics. The strains fd, M13 and f1 are virtually identical filamentous phages that infect bacteria expressing F-pili, and are sometimes grouped as the Ff phages. For historical reasons fd has often been used for structural studies, but M13 and f1 are more often used for biological experiments. Many other strains have been identified that are genetically quite distinct from Ff and yet have a similar molecular structure and life cycle. One of these, Pf1, gives the highest resolution X-ray fibre diffraction patterns known for filamentous bacteriophage. These diffraction patterns have been used in the past to derive a molecular model for the structure of the phage. Solid-state NMR experiments have been used in separate studies to derive a significantly different model of Pf1. Here we combine previously published X-ray fibre diffraction data and solid-state NMR data to give a consensus structure model for Pf1 filamentous bacteriophage, and we discuss the implications of this model for assembly of the phage at the bacterial membrane.
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Affiliation(s)
- S. K. Straus
- Department of Chemistry, University of British Columbia, Vancouver BC, Canada V6T 1Z1
| | - W. R. P Scott
- Department of Chemistry, University of British Columbia, Vancouver BC, Canada V6T 1Z1
| | - C. D. Schwieters
- Division of Computational Bioscience, Center for Information Technology, National Institutes of Health, Building 12A, Bethesda MD 20892-5624, USA
| | - D. A. Marvin
- Department of Biochemistry, University of Cambridge, Cambridge CB2 1GA, UK
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50
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Abstract
Bacteriophages have been a model system to study assembly processes for over half a century. Formation of infectious phage particles involves specific protein-protein and protein-nucleic acid interactions, as well as large conformational changes of assembly precursors. The sequence and molecular mechanisms of phage assembly have been elucidated by a variety of methods. Differences and similarities of assembly processes in several different groups of bacteriophages are discussed in this review. The general principles of phage assembly are applicable to many macromolecular complexes.
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