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Serena NN, Boschero RA, Santiani MH, Pacce VD, Costa JMDV, Magalhães FBD, Wiedmar C, Alban SM, Soccol CR, Soccol VT. High-performance immune diagnosis of tuberculosis: Use of phage display and synthetic peptide in an optimized experimental design. J Immunol Methods 2022; 503:113242. [PMID: 35182576 DOI: 10.1016/j.jim.2022.113242] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2021] [Revised: 02/11/2022] [Accepted: 02/14/2022] [Indexed: 11/26/2022]
Abstract
Immunoassays are practical and cost-effective approaches suitable for large-scale tuberculosis (TB) screening. This study identified new peptide mimotopes of Mycobacterium tuberculosis and applied them in the serodiagnosis of TB. Thereby, linear (X15, X8CX8) and constrained (LX-4 and LX-8) phage display peptide libraries were screened with purified Immunoglobulin G antibodies from TB-positive patients, and eight mimotopes were selected. The mimotope peptides were screened using the SPOT-synthesis technique followed by immunoblotting. Peptides P.Mt.PD.4 and P.Mt.PD.7 demonstrated the highest binding affinity and were chemically synthesized and used as antigens for enzyme-linked immunosorbent assay (ELISA) assays. Experimental designs were used to optimize the assays and to assess each variable's influence. Peptide P.Mt.PD.7 was differentiated between positive and negative samples and achieved 100% sensitivity and specificity when tested on a 100-sera panel. Therefore, the selected peptide was applied to the ELISA assay as a screening method for diagnosing TB represents a potential tool for helping to combat the disease.
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Affiliation(s)
- Natália Notto Serena
- Graduate Program in Bioprocess Engineering and Biotechnology, Federal University of Paraná, Curitiba, PR, Brazil
| | - Raphael Aparecido Boschero
- Graduate Program in Bioprocess Engineering and Biotechnology, Federal University of Paraná, Curitiba, PR, Brazil
| | - Manuel Hospinal Santiani
- Graduate Program in Bioprocess Engineering and Biotechnology, Federal University of Paraná, Curitiba, PR, Brazil
| | - Violetta Dias Pacce
- Graduate Program in Bioprocess Engineering and Biotechnology, Federal University of Paraná, Curitiba, PR, Brazil
| | | | | | | | - Silvana Maria Alban
- Graduate Program in Bioprocess Engineering and Biotechnology, Federal University of Paraná, Curitiba, PR, Brazil
| | - Carlos Ricardo Soccol
- Graduate Program in Bioprocess Engineering and Biotechnology, Federal University of Paraná, Curitiba, PR, Brazil
| | - Vanete Thomaz Soccol
- Graduate Program in Bioprocess Engineering and Biotechnology, Federal University of Paraná, Curitiba, PR, Brazil.
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2
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Gong Z, Lv X, Li C, Gu Y, Fan X, Sun Q, Tong Y, Zhao F, Xing S, Pei G, Li Q, Xie L, Xie J. Genomic and proteomic portrait of a novel mycobacteriophage SWU2 isolated from China. INFECTION GENETICS AND EVOLUTION 2020; 87:104665. [PMID: 33279716 DOI: 10.1016/j.meegid.2020.104665] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/03/2020] [Revised: 11/22/2020] [Accepted: 12/01/2020] [Indexed: 11/30/2022]
Abstract
Phage therapy, especially combination with antibiotics, was revitalized to control the antibiotics resistance. Mycobacteriophage, the phage of mycobacterium with the most notorious Mycobacterium tuberculosis (M. tuberculosis), was intensively explored. A novel mycobacteriophage SWU2 was isolated from a soil sample collected at Nanchang city, Jiangxi province, China, by using Mycolicibacterium smegmatis (M. smegmatis) mc2 155 as the host. Phage morphology and biology were characterized. Phage structure proteins were analyzed by LC-MS/MS. The putative functions of phage proteins and multi-genome comparison were performed with bioinformatics. The transmission electron microscopy result indicated that this phage belongs to Siphoviridae of Caudovirales. Plaques of SWU2 appeared clear but small. In a one-step growth test, we demonstrated that SWU2 had a latent period of 30 min and a logarithmic phase of 120 min. Among the 76 predicted Open Reading Frames (ORFs), 9 ORFs were identified as phage structure proteins of SWU2. The assembled phage genome size is 50,013 bp, with 62.7% of G + C content. SWU2 genome sequence shares 88% identity with Mycobacterium phages HINdeR and Timshel, differing in substitutions, insertions and deletions in SWU2. Phylogenetic tree revealed that SWU2 is grouped into A7 sub-cluster. There are several substitutions, insertions and deletions in SWU2 genome in comparison with close cousin phages HINdeR and Timshel. The new phage adds another dimension of abundance to the mycobacteriophages.
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Affiliation(s)
- Zhen Gong
- Institute of Modern Biopharmaceuticals, State Key Laboratory Breeding Base of Eco-Environment and Bio-Resource of the Three Gorges Area, Key Laboratory of Eco-environments in Three Gorges Reservoir Region, Ministry of Education, Chongqing Municipal Key Laboratory of Karst Environment, School of Life Sciences, Southwest University, Beibei, Chongqing 400715, China
| | - Xi Lv
- Institute of Modern Biopharmaceuticals, State Key Laboratory Breeding Base of Eco-Environment and Bio-Resource of the Three Gorges Area, Key Laboratory of Eco-environments in Three Gorges Reservoir Region, Ministry of Education, Chongqing Municipal Key Laboratory of Karst Environment, School of Life Sciences, Southwest University, Beibei, Chongqing 400715, China
| | - Chunyan Li
- Institute of Modern Biopharmaceuticals, State Key Laboratory Breeding Base of Eco-Environment and Bio-Resource of the Three Gorges Area, Key Laboratory of Eco-environments in Three Gorges Reservoir Region, Ministry of Education, Chongqing Municipal Key Laboratory of Karst Environment, School of Life Sciences, Southwest University, Beibei, Chongqing 400715, China
| | - Yinzhong Gu
- Institute of Modern Biopharmaceuticals, State Key Laboratory Breeding Base of Eco-Environment and Bio-Resource of the Three Gorges Area, Key Laboratory of Eco-environments in Three Gorges Reservoir Region, Ministry of Education, Chongqing Municipal Key Laboratory of Karst Environment, School of Life Sciences, Southwest University, Beibei, Chongqing 400715, China
| | - Xiangyu Fan
- Institute of Modern Biopharmaceuticals, State Key Laboratory Breeding Base of Eco-Environment and Bio-Resource of the Three Gorges Area, Key Laboratory of Eco-environments in Three Gorges Reservoir Region, Ministry of Education, Chongqing Municipal Key Laboratory of Karst Environment, School of Life Sciences, Southwest University, Beibei, Chongqing 400715, China; School of Biological Science and Technology, University of Jinan, Jinan 250022, China
| | - Qingyu Sun
- Institute of Modern Biopharmaceuticals, State Key Laboratory Breeding Base of Eco-Environment and Bio-Resource of the Three Gorges Area, Key Laboratory of Eco-environments in Three Gorges Reservoir Region, Ministry of Education, Chongqing Municipal Key Laboratory of Karst Environment, School of Life Sciences, Southwest University, Beibei, Chongqing 400715, China
| | - Yigang Tong
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing 100071, China
| | - Feiyang Zhao
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing 100071, China
| | - Shaozhen Xing
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing 100071, China
| | - Guangqian Pei
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing 100071, China
| | - Qiming Li
- Institute of Modern Biopharmaceuticals, State Key Laboratory Breeding Base of Eco-Environment and Bio-Resource of the Three Gorges Area, Key Laboratory of Eco-environments in Three Gorges Reservoir Region, Ministry of Education, Chongqing Municipal Key Laboratory of Karst Environment, School of Life Sciences, Southwest University, Beibei, Chongqing 400715, China
| | - Longxiang Xie
- Institute of Modern Biopharmaceuticals, State Key Laboratory Breeding Base of Eco-Environment and Bio-Resource of the Three Gorges Area, Key Laboratory of Eco-environments in Three Gorges Reservoir Region, Ministry of Education, Chongqing Municipal Key Laboratory of Karst Environment, School of Life Sciences, Southwest University, Beibei, Chongqing 400715, China
| | - Jianping Xie
- Institute of Modern Biopharmaceuticals, State Key Laboratory Breeding Base of Eco-Environment and Bio-Resource of the Three Gorges Area, Key Laboratory of Eco-environments in Three Gorges Reservoir Region, Ministry of Education, Chongqing Municipal Key Laboratory of Karst Environment, School of Life Sciences, Southwest University, Beibei, Chongqing 400715, China.
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3
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Sung KJ, Jabbour Al Maalouf Y, Johns QR, Miller EA, Sikes HD. Functional comparison of paper-based immunoassays based on antibodies and engineered binding proteins. Analyst 2020; 145:2515-2519. [PMID: 32163071 DOI: 10.1039/d0an00299b] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
Binding protein scaffolds, such as rcSso7d, have been investigated for use in diagnostic tests; however, the functional performance of rcSso7d has not yet been studied in comparison to antibodies. Here, we assessed the analyte-binding capabilities of rcSso7d and antibodies on cellulose with samples in buffer and 100% human serum.
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Affiliation(s)
- Ki-Joo Sung
- Department of Chemical Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, USA.
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4
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Zhao N, Kamijo K, Fox PD, Oda H, Morisaki T, Sato Y, Kimura H, Stasevich TJ. A genetically encoded probe for imaging nascent and mature HA-tagged proteins in vivo. Nat Commun 2019; 10:2947. [PMID: 31270320 PMCID: PMC6610143 DOI: 10.1038/s41467-019-10846-1] [Citation(s) in RCA: 53] [Impact Index Per Article: 10.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2018] [Accepted: 05/29/2019] [Indexed: 01/07/2023] Open
Abstract
To expand the toolbox of imaging in living cells, we have engineered a single-chain variable fragment binding the linear HA epitope with high affinity and specificity in vivo. The resulting probe, called the HA frankenbody, can light up in multiple colors HA-tagged nuclear, cytoplasmic, membrane, and mitochondrial proteins in diverse cell types. The HA frankenbody also enables state-of-the-art single-molecule experiments in living cells, which we demonstrate by tracking single HA-tagged histones in U2OS cells and single mRNA translation dynamics in both U2OS cells and neurons. Together with the SunTag, we also track two mRNA species simultaneously to demonstrate comparative single-molecule studies of translation can now be done with genetically encoded tools alone. Finally, we use the HA frankenbody to precisely quantify the expression of HA-tagged proteins in developing zebrafish embryos. The versatility of the HA frankenbody makes it a powerful tool for imaging protein dynamics in vivo.
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Affiliation(s)
- Ning Zhao
- Department of Biochemistry and Molecular Biology, Colorado State University, Fort Collins, CO, 80523, USA
| | - Kouta Kamijo
- Graduate School of Life Science and Technology, Tokyo Institute of Technology, Yokohama, 226-8503, Japan
| | - Philip D Fox
- Department of Biochemistry and Molecular Biology, Colorado State University, Fort Collins, CO, 80523, USA
| | - Haruka Oda
- Cell Biology Center, Institute of Innovative Research, Tokyo Institute of Technology, Yokohama, 226-8503, Japan
| | - Tatsuya Morisaki
- Department of Biochemistry and Molecular Biology, Colorado State University, Fort Collins, CO, 80523, USA
| | - Yuko Sato
- Graduate School of Life Science and Technology, Tokyo Institute of Technology, Yokohama, 226-8503, Japan
- Cell Biology Center, Institute of Innovative Research, Tokyo Institute of Technology, Yokohama, 226-8503, Japan
| | - Hiroshi Kimura
- Graduate School of Life Science and Technology, Tokyo Institute of Technology, Yokohama, 226-8503, Japan
- Cell Biology Center, Institute of Innovative Research, Tokyo Institute of Technology, Yokohama, 226-8503, Japan
- World Research Hub Initiative, Institute of Innovative Research, Tokyo Institute of Technology, Yokohama, 226-8503, Japan
| | - Timothy J Stasevich
- Department of Biochemistry and Molecular Biology, Colorado State University, Fort Collins, CO, 80523, USA.
- World Research Hub Initiative, Institute of Innovative Research, Tokyo Institute of Technology, Yokohama, 226-8503, Japan.
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5
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Paloni JM, Miller EA, Sikes HD, Olsen BD. Improved Ordering in Low Molecular Weight Protein-Polymer Conjugates Through Oligomerization of the Protein Block. Biomacromolecules 2018; 19:3814-3824. [PMID: 30132651 DOI: 10.1021/acs.biomac.8b00928] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Abstract
The self-assembly of protein-polymer conjugates incorporating oligomers of a small, engineered high-affinity binding protein, rcSso7d.SA, is studied to determine the effect of protein oligomerization on nanoscale ordering. Oligomerization enables a systematic increase in the protein molar mass without changing its overall folded structure, leading to a higher driving force for self-assembly into well-ordered structures. Though conjugates of monomeric rcSso7d.SA are found to only exist in disordered states, oligomers of this protein linked to a poly( N-isopropylacrylamide) (PNIPAM) block self-assemble into lamellar nanostructures. Conjugates of trimeric and tetrameric rcSso7d.SA are observed to produce the strongest ordering in concentrated solution, displaying birefringent lamellae at concentrations as low as 40 wt %. In highly concentrated solution, the oligomeric rcSso7d.SA-PNIPAM block copolymers exhibit ordering and domain spacing trends atypical from that of most block copolymers. Fluorescent binding assays indicate that oligomerized protein blocks retain binding functionality and exhibit limits of detection up to three times lower than that of surface-immobilized protein sensors. Therefore, oligomerization of the protein block in these block copolymers serves as an effective method to improve both nanoscale ordering and biosensing capabilities.
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Affiliation(s)
- Justin M Paloni
- Department of Chemical Engineering , Massachusetts Institute of Technology , Cambridge , Massachusetts 02139 , United States
| | - Eric A Miller
- Department of Chemical Engineering , Massachusetts Institute of Technology , Cambridge , Massachusetts 02139 , United States
| | - Hadley D Sikes
- Department of Chemical Engineering , Massachusetts Institute of Technology , Cambridge , Massachusetts 02139 , United States
| | - Bradley D Olsen
- Department of Chemical Engineering , Massachusetts Institute of Technology , Cambridge , Massachusetts 02139 , United States
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6
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Farooq U, Yang Q, Ullah MW, Wang S. Bacterial biosensing: Recent advances in phage-based bioassays and biosensors. Biosens Bioelectron 2018; 118:204-216. [PMID: 30081260 DOI: 10.1016/j.bios.2018.07.058] [Citation(s) in RCA: 79] [Impact Index Per Article: 13.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2018] [Accepted: 07/27/2018] [Indexed: 10/28/2022]
Abstract
In nature, different types of bacteria including pathogenic and beneficial ones exist in different habitats including environment, plants, animals, and humans. Among these, the pathogenic bacteria should be detected at earlier stages of infection; however, the conventional bacterial detection procedures are complex and time-consuming. In contrast, the advanced molecular approaches such as polymerase chain reaction (PCR) and enzyme-linked immunosorbent assay (ELISA) have significantly reduced the detection time; nevertheless, such approaches are not acceptable to a large extent and are mostly laborious and expensive. Therefore, the development of fast, inexpensive, sensitive, and specific approaches for pathogen detection is essential for different applications in food industry, clinical diagnosis, biological defense and counter-terrorism. To this end, the novel sensing approaches involving bacteriophages as recognition elements are receiving immense consideration owing to their high degree of specificity, accuracy, and reduced assay times. Besides, the phages are easily produced and are tolerant to extreme pH, temperature, and organic solvents as compared to antibodies. To date, several phage-based assays and sensors have been developed involving different systems such as quartz crystal microbalance, magnetoelastic platform, surface plasmon resonance, and electrochemical methods. This review highlights different taxonomic species and genera of phages infecting eight common disease-causing bacterial genera. It further overviews the most recent advancements in phage-based sensing assays and sensors. Likewise, it elaborates various whole-phage and phage components-based assays. Overall, this review emphasizes the importance of electrochemical biosensors as simple, reliable, cost-effective, and accurate tools for bacterial detection.
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Affiliation(s)
- Umer Farooq
- Advanced Biomaterials & Tissue Engineering Centre, Huazhong University of Science and Technology, Wuhan 430074, PR China
| | - Qiaoli Yang
- Advanced Biomaterials & Tissue Engineering Centre, Huazhong University of Science and Technology, Wuhan 430074, PR China
| | - Muhammad Wajid Ullah
- Department of Biomedical Engineering, Huazhong University of Science and Technology, Wuhan 430074, PR China
| | - Shenqi Wang
- Advanced Biomaterials & Tissue Engineering Centre, Huazhong University of Science and Technology, Wuhan 430074, PR China.
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7
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Cruz-Teran CA, Tiruthani K, Mischler A, Rao BM. Inefficient Ribosomal Skipping Enables Simultaneous Secretion and Display of Proteins in Saccharomyces cerevisiae. ACS Synth Biol 2017; 6:2096-2107. [PMID: 28805373 PMCID: PMC5905331 DOI: 10.1021/acssynbio.7b00144] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
The need for recombinant expression of soluble protein slows the validation of engineered proteins isolated from combinatorial libraries and limits the number of protein variants evaluated. To overcome this bottleneck, we describe a system for simultaneous cell surface display and soluble secretion of proteins in Saccharomyces cerevisiae based on inefficient ribosomal skipping. Ribosomal skipping mediated by "self-cleaving" 2A peptides produces two proteins from a single open reading frame. Incorporation of the F2A peptide sequence-with ∼50% efficiency of ribosomal skipping-between the protein of interest and the yeast cell wall protein Aga2 results in simultaneous expression of both the solubly secreted protein and the protein-Aga2 fusion that is tethered to the yeast cell surface. We show that binding proteins derived from the Sso7d scaffold and the homodimeric enzyme glucose oxidase can be simultaneously secreted solubly and expressed as yeast cell surface fusions using the F2A-based system. Furthermore, a combinatorial library of Sso7d mutants can be screened to isolate binders with higher affinity for a model target (lysozyme), and the pool of higher affinity binders can be characterized in soluble form. Significantly, we show that both N- and C-terminal fusions to Aga2 can be simultaneously secreted solubly and displayed on the cell surface; this is particularly advantageous because protein functionality can be affected by the specific position of Aga2 in the protein fusion. We expect that the F2A-based yeast surface display and secretion system will be a useful tool for protein engineering and enable efficient characterization of individual clones isolated from combinatorial libraries.
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Affiliation(s)
| | | | - Adam Mischler
- Department of Chemical and Biomolecular Engineering, North Carolina State University, Raleigh, NC
| | - Balaji M. Rao
- Department of Chemical and Biomolecular Engineering, North Carolina State University, Raleigh, NC
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8
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Melander RJ, Zurawski DV, Melander C. Narrow-Spectrum Antibacterial Agents. MEDCHEMCOMM 2017; 9:12-21. [PMID: 29527285 PMCID: PMC5839511 DOI: 10.1039/c7md00528h] [Citation(s) in RCA: 122] [Impact Index Per Article: 17.4] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/17/2017] [Accepted: 11/02/2017] [Indexed: 12/12/2022]
Abstract
While broad spectrum antibiotics play an invaluable role in the treatment of bacterial infections, there are some drawbacks to their use, namely selection for and spread of resistance across multiple bacterial species, and the detrimental effect they can have upon the host microbiome. If the causitive agent of the infection is known, the use of narrow-spectrum antibacterial agents has the potential to mitigate some of these issues. This review outlines the advantages and challenges of narrow-spectrum antibacterial agents, discusses the progress that has been made toward developing diagnostics to enable their use, and describes some of the narrow-spectrum antibacterial agents currently being investigated against some of the most clinically important bacteria including Clostridium difficile, Mycobacterium tuberculosis and several ESKAPE pathogens.
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Affiliation(s)
- Roberta J. Melander
- Department of Chemistry
, North Carolina State University
,
Raleigh
, NC
, USA
.
| | - Daniel V. Zurawski
- Wound Infections Department
, Bacterial Diseases Branch
, Walter Reed Army Institute of Research
,
Silver Spring
, MD
, USA
| | - Christian Melander
- Department of Chemistry
, North Carolina State University
,
Raleigh
, NC
, USA
.
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9
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Imaging Translational and Post-Translational Gene Regulatory Dynamics in Living Cells with Antibody-Based Probes. Trends Genet 2017; 33:322-335. [PMID: 28359585 DOI: 10.1016/j.tig.2017.02.003] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2017] [Revised: 02/25/2017] [Accepted: 02/28/2017] [Indexed: 12/17/2022]
Abstract
Antibody derivatives, such as antibody fragments (Fabs) and single-chain variable fragments (scFvs), are now being used to image traditionally hard-to-see protein subpopulations, including nascent polypeptides being translated and post-translationally modified proteins. This has allowed researchers to directly image and quantify, for the first time, translation initiation and elongation kinetics with single-transcript resolution and the temporal ordering and kinetics of post-translational histone and RNA polymerase II modifications. Here, we review these developments and discuss the strengths and weaknesses of live-cell imaging with antibody-based probes. Further development of these probes will increase their versatility and open new avenues of research for dissecting complex gene regulatory dynamics.
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