1
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Yan X, Liu X, Zhao C, Chen GQ. Applications of synthetic biology in medical and pharmaceutical fields. Signal Transduct Target Ther 2023; 8:199. [PMID: 37169742 PMCID: PMC10173249 DOI: 10.1038/s41392-023-01440-5] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2022] [Revised: 03/15/2023] [Accepted: 03/24/2023] [Indexed: 05/13/2023] Open
Abstract
Synthetic biology aims to design or assemble existing bioparts or bio-components for useful bioproperties. During the past decades, progresses have been made to build delicate biocircuits, standardized biological building blocks and to develop various genomic/metabolic engineering tools and approaches. Medical and pharmaceutical demands have also pushed the development of synthetic biology, including integration of heterologous pathways into designer cells to efficiently produce medical agents, enhanced yields of natural products in cell growth media to equal or higher than that of the extracts from plants or fungi, constructions of novel genetic circuits for tumor targeting, controllable releases of therapeutic agents in response to specific biomarkers to fight diseases such as diabetes and cancers. Besides, new strategies are developed to treat complex immune diseases, infectious diseases and metabolic disorders that are hard to cure via traditional approaches. In general, synthetic biology brings new capabilities to medical and pharmaceutical researches. This review summarizes the timeline of synthetic biology developments, the past and present of synthetic biology for microbial productions of pharmaceutics, engineered cells equipped with synthetic DNA circuits for diagnosis and therapies, live and auto-assemblied biomaterials for medical treatments, cell-free synthetic biology in medical and pharmaceutical fields, and DNA engineering approaches with potentials for biomedical applications.
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Affiliation(s)
- Xu Yan
- School of Life Sciences, Tsinghua University, 100084, Beijing, China
| | - Xu Liu
- PhaBuilder Biotech Co. Ltd., Shunyi District, Zhaoquan Ying, 101309, Beijing, China
| | - Cuihuan Zhao
- School of Life Sciences, Tsinghua University, 100084, Beijing, China
| | - Guo-Qiang Chen
- School of Life Sciences, Tsinghua University, 100084, Beijing, China.
- Center for Synthetic and Systems Biology, Tsinghua University, 100084, Beijing, China.
- MOE Key Lab for Industrial Biocatalysis, Dept Chemical Engineering, Tsinghua University, 100084, Beijing, China.
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2
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Yoo CH, Yu JK, Seong Y, Choi JK. Microarrays Incorporating Gold Grid Patterns for Protein Quantification. ACS OMEGA 2020; 5:16664-16669. [PMID: 32685833 PMCID: PMC7364605 DOI: 10.1021/acsomega.0c01549] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 04/05/2020] [Accepted: 06/18/2020] [Indexed: 06/11/2023]
Abstract
Protein microarrays are miniaturized two-dimensional arrays, incorporating thousands of immobilized proteins, typically printed in minute amounts on functionalized solid substrates, which can be analyzed in a high-throughput fashion. Irreproducibility of the printing techniques adopted, resulting in inconsistently and nonuniformly deposited microscopic spots, nonuniform signal intensities from the printed microspots, and significantly high background noise are some of the critical issues that affect protein analysis using traditional protein microarrays. To overcome such issues, in this study, we introduced a novel gold grid pattern-based protein microarray. The grid patterns incorporated in our microarray are equivalent to the spots used for protein analysis in conventional protein microarrays. We utilized the signal intensities from the grid patterns acting as spots for quantifying the protein concentration levels. To demonstrate the utility of our novel design concept, we quantified as low as 66.7 ng/mL of bovine serum albumin using our gold grid pattern-based protein microarray. Our grid pattern-based design concept for protein quantification overcame the signal nonuniformity issues and ensured that the dominance of any distorted signal from a single spot did not affect the overall protein quantification results as encountered in conventional protein microarrays.
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Affiliation(s)
- Chang-Hyuk Yoo
- Division
of Life Sciences, College of Life Sciences and Bioengineering, Incheon National University, Incheon 22012, Korea
- Small
Machines Company, Ltd., Daejeon 34012, Korea
| | | | - Yeju Seong
- Small
Machines Company, Ltd., Daejeon 34012, Korea
| | - Jun-Kyu Choi
- Small
Machines Company, Ltd., Daejeon 34012, Korea
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3
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Lee MH, Dong Z, Surh YJ, Choi BY. hYSK1 promotes cancer cell proliferation and migration through negative regulation of p16 INK4a under hypoxic conditions. Oncotarget 2017; 8:89072-89085. [PMID: 29179500 PMCID: PMC5687670 DOI: 10.18632/oncotarget.21654] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2017] [Accepted: 08/27/2017] [Indexed: 11/25/2022] Open
Abstract
The alteration of expression of p16INK4a, a well-known cyclin-dependent kinase inhibitor involved in cell cycle control, in tumors is unclear, especially under hypoxic conditions. To evaluate p16INK4a regulation, we performed a protein microarray analysis. Among 1,800 proteins in the array, we identified hYSK1 as a novel protein that interacts with the tumor suppressor p16INK4a. hYSK1, a member of the Ste20 family of serine/threonine protein kinases, promotes cell migration and tumorigenesis and is activated by oxidative stress. However, the molecular mechanisms underlying the oncogenic potential of hYSK1 remain elusive. Here, we report that hYSK1 interacts with p16INK4a under hypoxic conditions in tumors, where it negatively regulates p16INK4a, enhancing cancer cell migration. Hypoxic stimulation of hYSK1 reduces p16INK4a accumulation through p16 promoter regulation to interact with unphosporylated SP-1 and increases matrix metalloproteinase-2 (MMP-2) expression by activating the MMP-2 promoter associated with cell migration and proliferation.Conversely, knocking down hYSK1 expression activated p16INK4a expression and suppressed MMP-2 expression. Thus, hYSK1 is necessary as a trigger for inactivating p16INK4a and activating MMP-2 during tumor migration, suggesting that hYSK1 is a specific negative regulator of the tumor suppressor p16INK4a and may represent a novel molecular target for reactivation of tumor suppressor genes in humans.
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Affiliation(s)
- Mee-Hyun Lee
- China-US (Henan) Hormel Cancer Institute, Zhengzhou 450008, China
| | - Zigang Dong
- China-US (Henan) Hormel Cancer Institute, Zhengzhou 450008, China.,The Hormel Institute, University of Minnesota, Austin, MN 55912, USA
| | - Young-Joon Surh
- Tumor Microenvironment Global Core Research Center, College of Pharmacy, Seoul National University, Seoul 08826, South Korea.,Research Institute of Pharmaceutical Sciences, College of Pharmacy, Seoul National University, Seoul 08826, South Korea.,Department of Molecular Medicine and Biopharmaceutical Sciences, Graduate School of Convergence Sciences and Technology, Seoul National University, Seoul 08826, South Korea.,Cancer Research Institute, Seoul National University, Seoul 110-744, South Korea
| | - Bu Young Choi
- Department of Pharmaceutical Science & Engineering, Seowon University, Cheongju 28674, South Korea
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4
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Array-on-Array Strategy For Activity-Based Enzyme Profiling. Methods Mol Biol 2016. [PMID: 27873204 DOI: 10.1007/978-1-4939-6584-7_9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register]
Abstract
We describe a novel array on array strategy intended to enhance the throughput of enzymatic activity screening using microarrays. This strategy consists of spotting a first array with large droplets of enzymes with varying concentrations and subsequently spotting a second array with small droplets of fluorogenic substrate on top of the enzyme array. By varying the array on array spotting patterns of different classes of enzyme (e.g., proteases, phosphatases, kinases) and their corresponding fluorogenic substrates, we have the unprecedented ability for testing enzymes and mixed samples in a multiplexed fashion within a single microarray slide. This new approach enables rapid enzyme characterization building upon a one enzyme on one slide droplet-based screening concept previously established.
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5
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Guo X, Deng Y, Zhu C, Cai J, Zhu X, Landry JP, Zheng F, Cheng X, Fei Y. Characterization of protein expression levels with label-free detected reverse phase protein arrays. Anal Biochem 2016; 509:67-72. [PMID: 27372609 DOI: 10.1016/j.ab.2016.06.027] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2016] [Revised: 06/24/2016] [Accepted: 06/27/2016] [Indexed: 01/12/2023]
Abstract
In reverse-phase protein arrays (RPPA), one immobilizes complex samples (e.g., cellular lysate, tissue lysate or serum etc.) on solid supports and performs parallel reactions of antibodies with immobilized protein targets from the complex samples. In this work, we describe a label-free detection of RPPA that enables quantification of RPPA data and thus facilitates comparison of studies performed on different samples and on different solid supports. We applied this detection platform to characterization of phosphoserine aminotransferase (PSAT) expression levels in Acanthamoeba lysates treated with artemether and the results were confirmed by Western blot studies.
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Affiliation(s)
- Xuexue Guo
- Department of Optical Science and Engineering, Shanghai Engineering Research Center for Ultra-Precision Optical Manufacturing, Green Photoelectron Platform, Key Laboratory of Micro and Nano Photonic Structures (Ministry of Education), Fudan University, Shanghai, 200433, China
| | - Yihong Deng
- Department of Medical Microbiology and Parasitology, School of Basic Medical Sciences, Fudan University, Shanghai, 200032, China
| | - Chenggang Zhu
- Department of Optical Science and Engineering, Shanghai Engineering Research Center for Ultra-Precision Optical Manufacturing, Green Photoelectron Platform, Key Laboratory of Micro and Nano Photonic Structures (Ministry of Education), Fudan University, Shanghai, 200433, China
| | - Junlong Cai
- Department of Medical Microbiology and Parasitology, School of Basic Medical Sciences, Fudan University, Shanghai, 200032, China
| | - Xiangdong Zhu
- Department of Physics, University of California, Davis, CA, 95616, USA
| | - James P Landry
- Department of Physics, University of California, Davis, CA, 95616, USA
| | - Fengyun Zheng
- Institutes of Biomedical Science, Fudan University, Shanghai, 200032, China
| | - Xunjia Cheng
- Department of Medical Microbiology and Parasitology, School of Basic Medical Sciences, Fudan University, Shanghai, 200032, China
| | - Yiyan Fei
- Department of Optical Science and Engineering, Shanghai Engineering Research Center for Ultra-Precision Optical Manufacturing, Green Photoelectron Platform, Key Laboratory of Micro and Nano Photonic Structures (Ministry of Education), Fudan University, Shanghai, 200433, China.
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6
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Schumacher S, Muekusch S, Seitz H. Up-to-Date Applications of Microarrays and Their Way to Commercialization. MICROARRAYS (BASEL, SWITZERLAND) 2015; 4:196-213. [PMID: 27600220 PMCID: PMC4996390 DOI: 10.3390/microarrays4020196] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/02/2015] [Revised: 04/01/2015] [Accepted: 04/14/2015] [Indexed: 12/12/2022]
Abstract
This review addresses up-to-date applications of Protein Microarrays. Protein Microarrays play a significant role in basic research as well as in clinical applications and are applicable in a lot of fields, e.g., DNA, proteins and small molecules. Additionally they are on the way to enter clinics in routine diagnostics. Protein Microarrays can be powerful tools to improve healthcare. An overview of basic characteristics to mediate essential knowledge of this technique is given. To reach this goal, some challenges still have to be addressed. A few applications of Protein Microarrays in a medical context are shown. Finally, an outlook, where the potential of Protein Microarrays is depicted and speculations how the future of Protein Microarrays will look like are made.
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Affiliation(s)
- Sarah Schumacher
- Branch Bioanalytics and Bioprocesses, Fraunhofer Institute for Cell Therapy and Immunology, Am Muehlenberg 13, 14476 Potsdam, Germany.
| | - Sandra Muekusch
- Branch Bioanalytics and Bioprocesses, Fraunhofer Institute for Cell Therapy and Immunology, Am Muehlenberg 13, 14476 Potsdam, Germany.
| | - Harald Seitz
- Branch Bioanalytics and Bioprocesses, Fraunhofer Institute for Cell Therapy and Immunology, Am Muehlenberg 13, 14476 Potsdam, Germany.
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7
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Romanov V, Davidoff SN, Miles AR, Grainger DW, Gale BK, Brooks BD. A critical comparison of protein microarray fabrication technologies. Analyst 2015; 139:1303-26. [PMID: 24479125 DOI: 10.1039/c3an01577g] [Citation(s) in RCA: 91] [Impact Index Per Article: 10.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Abstract
Of the diverse analytical tools used in proteomics, protein microarrays possess the greatest potential for providing fundamental information on protein, ligand, analyte, receptor, and antibody affinity-based interactions, binding partners and high-throughput analysis. Microarrays have been used to develop tools for drug screening, disease diagnosis, biochemical pathway mapping, protein-protein interaction analysis, vaccine development, enzyme-substrate profiling, and immuno-profiling. While the promise of the technology is intriguing, it is yet to be realized. Many challenges remain to be addressed to allow these methods to meet technical and research expectations, provide reliable assay answers, and to reliably diversify their capabilities. Critical issues include: (1) inconsistent printed microspot morphologies and uniformities, (2) low signal-to-noise ratios due to factors such as complex surface capture protocols, contamination, and static or no-flow mass transport conditions, (3) inconsistent quantification of captured signal due to spot uniformity issues, (4) non-optimal protocol conditions such as pH, temperature, drying that promote variability in assay kinetics, and lastly (5) poor protein (e.g., antibody) printing, storage, or shelf-life compatibility with common microarray assay fabrication methods, directly related to microarray protocols. Conventional printing approaches, including contact (e.g., quill and solid pin), non-contact (e.g., piezo and inkjet), microfluidics-based, microstamping, lithography, and cell-free protein expression microarrays, have all been used with varying degrees of success with figures of merit often defined arbitrarily without comparisons to standards, or analytical or fiduciary controls. Many microarray performance reports use bench top analyte preparations lacking real-world relevance, akin to "fishing in a barrel", for proof of concept and determinations of figures of merit. This review critiques current protein-based microarray preparation techniques commonly used for analytical and function-based proteomics and their effects on array-based assay performance.
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Affiliation(s)
- Valentin Romanov
- Wasatch Microfluidics, LLC, 825 N. 300 W., Suite C325, Salt Lake City, UT, USA.
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8
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Chepelev N, Chepelev L, Alamgir M, Golshani A. Large-Scale Protein-Protein Interaction Detection Approaches: Past, Present and Future. BIOTECHNOL BIOTEC EQ 2014. [DOI: 10.1080/13102818.2008.10817505] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022] Open
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9
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Matrices for Sensors from Inorganic, Organic, and Biological Nanocomposites. MATERIALS 2011; 4:1483-1518. [PMID: 28824154 PMCID: PMC5448674 DOI: 10.3390/ma4081483] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/19/2011] [Revised: 08/02/2011] [Accepted: 08/11/2011] [Indexed: 12/12/2022]
Abstract
Matrices and sensors resulting from inorganic, organic and biological nanocomposites are presented in this overview. The term nanocomposite designates a solid combination of a matrix and of nanodimensional phases differing in properties from the matrix due to dissimilarities in structure and chemistry. The nanoocomposites chosen for a wide variety of health and environment sensors consist of Anodic Porous Allumina and P450scc, Carbon nanotubes and Conductive Polymers, Langmuir Blodgett Films of Lipases, Laccases, Cytochromes and Rhodopsins, Three-dimensional Nanoporous Materials and Nucleic Acid Programmable Protein Arrays.
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10
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Kassa T, Undesser LP, Hofstetter H, Hofstetter O. Antibody-based multiplex analysis of structurally closely related chiral molecules. Analyst 2011; 136:1113-5. [PMID: 21240425 DOI: 10.1039/c0an00814a] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Four class-specific and stereoselective antibodies were labeled with different fluorophores to enable simultaneous quantification of the enantiomers of phenylalanine and phenyllactic acid. Using fluorescence immunoassays and microarrays, sensitive detection of each analyte was possible even in the presence of a large excess of the other structurally similar molecules.
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Affiliation(s)
- Tigabu Kassa
- Department of Chemistry and Biochemistry, Northern Illinois University, DeKalb, IL 60115, USA
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11
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Stoevesandt O, Vetter M, Kastelic D, Palmer EA, He M, Taussig MJ. Cell free expression put on the spot: advances in repeatable protein arraying from DNA (DAPA). N Biotechnol 2010; 28:282-90. [PMID: 20850573 DOI: 10.1016/j.nbt.2010.09.004] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2010] [Accepted: 09/01/2010] [Indexed: 11/25/2022]
Abstract
We have previously described the 'DNA array to protein array' (DAPA) method for microarraying of proteins expressed by cell-free systems in situ on the array surface. In this technique, a DNA array on one slide acts as the template for generating a protein array on a second slide, mediated by a cell free lysate between the two juxtaposed slides. Here we explore the feature of the repeatability of the technology, in which the same DNA array is reused several times, and use the method to generate a microarray of 116 diverse proteins. The capabilities of DAPA technology in comparison with other protein array methods are discussed.
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Affiliation(s)
- Oda Stoevesandt
- Protein Technology Group, Babraham Bioscience Technologies, Cambridge CB22 3AT, UK.
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12
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Wolf C, Li Q. Tunable two-dimensional array patterning of antibody annuli through microsphere templating. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2010; 26:12068-12074. [PMID: 20462266 DOI: 10.1021/la101212y] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/29/2023]
Abstract
Protein microarrays are of great research interest because of their potential application as biosensors for high-throughput protein and pathogen screening technologies. In this active area, there is a lack of techniques that can result in annulus-shaped protein structures (e.g., for the utilization of curved surfaces for enhanced protein-protein interactions and the detection of antigens). We present a new technique employing colloidal templating to yield large-scale (approximately cm(2)) 2D arrays of antibodies against Escherichia coli K12 and enhanced green fluorescent protein (eGFP) on a versatile glass surface. The antibodies are swept to reside around the templating microspheres during solution drying and physically adsorb onto the glass. After the microspheres are removed, an array of annulus-shaped antibody structures is formed. We demonstrate the preserved antibody structure and functionality by binding the specific antigens and secondary antibodies, respectively, which paves the way for the binding of biomolecules and pathogens such as bacteria and viruses. The structures were investigated via atomic force, confocal, and fluorescence microscopy. Operational factors such as the drying time, temperature, and humidity as well as the presence of surfactants in the antibody solution were tuned to obtain a stable antibody structure.
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Affiliation(s)
- Cornel Wolf
- Max Planck Institute for Polymer Research, Ackermannweg 10, 55128 Mainz, Germany
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13
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Zárate X, Henderson DC, Phillips KC, Lake AD, Galbraith DW. Development of high-yield autofluorescent protein microarrays using hybrid cell-free expression with combined Escherichia coli S30 and wheat germ extracts. Proteome Sci 2010; 8:32. [PMID: 20546627 PMCID: PMC2906421 DOI: 10.1186/1477-5956-8-32] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2009] [Accepted: 06/15/2010] [Indexed: 01/08/2023] Open
Abstract
Background Protein-based microarray platforms offer considerable promise as high-throughput technologies in proteomics. Particular advantages are provided by self-assembling protein microarrays and much interest centers around analysis of eukaryotic proteins and their molecular interactions. Efficient cell-free protein synthesis is paramount for the production of self-assembling protein microarrays, requiring optimal transcription, translation, and protein folding. The Escherichia coli S30 extract demonstrates high translation rates but lacks the protein-folding efficiency of its eukaryotic counterparts derived from rabbit reticulocyte and wheat germ extract. In comparison to E. coli, eukaryotic extracts, on the other hand, exhibit slower translation rates and poor overall protein yields. A cell-free expression system that synthesizes folded eukaryotic proteins in considerable yields would optimize in vitro translation for protein microarray assembly. Results Self-assembling autofluorescent protein microarrays were produced by in situ transcription and translation of chimeric proteins containing a C-terminal Green Fluorescent Protein tag. Proteins were immobilized as array elements using an anti-GFP monoclonal antibody. The amounts of correctly-folded chimeric proteins were quantified by measuring the fluorescence intensity from each array element. During cell-free expression, very little or no fluorescence was observed from GFP-tagged multidomain eukaryotic plant proteins when in vitro translation was performed with E. coli S30 extract. Improvement was seen using wheat germ extract, but fluorescence intensities were still low because of poor protein yields. A hybrid in vitro translation system, combining S30 and wheat germ extracts, produced high levels of correctly-folded proteins for most of the constructs that were tested. Conclusion The results are consistent with the hypothesis that the wheat germ extract enhances the protein folding capabilities of the in vitro system by providing eukaryotic ribosomes and chaperones and, at the same time, the E. coli S30 extract, which includes an ATP regeneration system, translates the polypeptides at high rates. This hybrid cell-free expression system allows the facile production of high-yield protein arrays suitable for downstream assays.
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Affiliation(s)
- Xristo Zárate
- BIO5 Institute, University of Arizona, Tucson, AZ 85721, USA.
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14
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Sobieściak TD, Zielenkiewicz P. Double Selective Synthetic Approach to the N-Functionalized 1,4,7-Triazacyclononane Derivatives: Chelating Compounds for Controllable Protein Orientation. J Org Chem 2010; 75:2069-72. [DOI: 10.1021/jo902504d] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Tomasz D. Sobieściak
- Institute of Biochemistry and Biophysics, Polish Academy of Sciences, Pawińskiego 5a, Warsaw 02-106, Poland
| | - Piotr Zielenkiewicz
- Institute of Biochemistry and Biophysics, Polish Academy of Sciences, Pawińskiego 5a, Warsaw 02-106, Poland
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15
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Dai X, Healy S, Yli-Harja O, Ribeiro AS. Tuning cell differentiation patterns and single cell dynamics by regulating proteins' functionalities in a toggle switch. J Theor Biol 2009; 261:441-8. [PMID: 19712686 DOI: 10.1016/j.jtbi.2009.08.024] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2009] [Revised: 07/29/2009] [Accepted: 08/18/2009] [Indexed: 02/05/2023]
Abstract
We investigate how the regulation of protein multi-functionalities affect the dynamics of a stochastic model of a toggle switch and the differentiation pattern of cell population regulated by the switch. We study the effects of loss of functionality in DNA-binding and repression and the involvement in differentiation pathway choice. First is shown how the patterns of cell differentiation differ, when each of these functionalities is fully non-functional. Next, tuning the fraction of non-functional proteins regarding the ability to bind DNA is shown to allow fine tuning of the switch and cell differentiation pattern dynamics. Finally, biasing the probability of functionality of the two proteins biases the dynamics of the switch and cell differentiation patterns, especially when transcription factors retain the ability to bind DNA but have lost the ability to repress gene expression. Our results suggest that, besides transcriptional and translational levels of regulation, activation of functionalities in multi-functional proteins are an important regulator of gene networks.
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Affiliation(s)
- Xiaofeng Dai
- Computational Systems Biology Research Group, Department of Signal Processing, Tampere University of Technology, Finland
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16
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Stoevesandt O, Taussig MJ, He M. Protein microarrays: high-throughput tools for proteomics. Expert Rev Proteomics 2009; 6:145-57. [PMID: 19385942 PMCID: PMC7105755 DOI: 10.1586/epr.09.2] [Citation(s) in RCA: 116] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
Protein microarrays are versatile tools for parallel, miniaturized screening of binding events involving large numbers of immobilized proteins in a time- and cost-effective manner. They are increasingly applied for high-throughput protein analyses in many research areas, such as protein interactions, expression profiling and target discovery. While conventionally made by the spotting of purified proteins, recent advances in technology have made it possible to produce protein microarrays through in situ cell-free synthesis directly from corresponding DNA arrays. This article reviews recent developments in the generation of protein microarrays and their applications in proteomics and diagnostics.
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Affiliation(s)
- Oda Stoevesandt
- Babraham Bioscience Technologies Ltd., Babraham Research Campus, Cambridge, CB22 3AT, UK.
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17
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Jonkheijm P, Weinrich D, Schröder H, Niemeyer CM, Waldmann H. Chemical strategies for generating protein biochips. Angew Chem Int Ed Engl 2008; 47:9618-47. [PMID: 19025742 DOI: 10.1002/anie.200801711] [Citation(s) in RCA: 510] [Impact Index Per Article: 31.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
Protein biochips are at the heart of many medical and bioanalytical applications. Increasing interest has been focused on surface activation and subsequent functionalization strategies for immobilizing these biomolecules. Different approaches using covalent and noncovalent chemistry are reviewed; particular emphasis is placed on the chemical specificity of protein attachment and on retention of protein function. Strategies for creating protein patterns (as opposed to protein arrays) are also outlined. An outlook on promising and challenging future directions for protein biochip research and applications is also offered.
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Affiliation(s)
- Pascal Jonkheijm
- Department of Chemical Biology, Max Planck Institute of Molecular Physiology and Faculty of Chemistry, Chemical Biology, Technical University of Dortmund, Otto Hahn Strasse 11, 44227 Dortmund, Germany
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18
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Jonkheijm P, Weinrich D, Schröder H, Niemeyer C, Waldmann H. Chemische Verfahren zur Herstellung von Proteinbiochips. Angew Chem Int Ed Engl 2008. [DOI: 10.1002/ange.200801711] [Citation(s) in RCA: 62] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
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19
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Ng JK, Ajikumar PK, Tang YC, Lee JY, Stephanopoulos G, Too HP. Spatially addressable protein array: ssDNA-directed assembly for antibody microarray. Electrophoresis 2007; 28:4638-44. [DOI: 10.1002/elps.200700183] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
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20
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Oishi Y, Yunomura S, Kawahashi Y, Doi N, Takashima H, Baba T, Mori H, Yanagawa H. Escherichia coli proteome chips for detecting protein-protein interactions. Proteomics 2007; 6:6433-6. [PMID: 17109382 DOI: 10.1002/pmic.200600341] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Affiliation(s)
- Yo Oishi
- Department of Biosciences and Informatics, Keio University, Yokohama, Japan
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21
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Uttamchandani M, Liu K, Panicker RC, Yao SQ. Activity-based fingerprinting and inhibitor discovery of cysteine proteases in a microarray. Chem Commun (Camb) 2007:1518-20. [PMID: 17406693 DOI: 10.1039/b702826a] [Citation(s) in RCA: 70] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
A panel of 20 peptide vinyl sulfone probes has been synthesized and used to generate activity-based fingerprinting profiles of cysteine proteases in both gel- and microarray-based formats; the inhibitor fingerprints of representative small molecule inhibitors targeted against 4 cysteine proteases were also obtained, in high-throughput, using the same protein microarray platform.
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Affiliation(s)
- Mahesh Uttamchandani
- Department of Biological Sciences, National University of Singapore, 4 Science Drive 4, 117543, Singapore
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22
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Ptacek J, Snyder M. 14 Yeast Protein Microarrays. J Microbiol Methods 2007. [DOI: 10.1016/s0580-9517(06)36014-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/16/2023]
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23
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Renault NK, Mirotti L, Alcocer MJC. Biotechnologies in new high-throughput food allergy tests: why we need them. Biotechnol Lett 2006; 29:333-9. [PMID: 17160623 DOI: 10.1007/s10529-006-9251-z] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2006] [Revised: 10/30/2006] [Accepted: 10/31/2006] [Indexed: 10/23/2022]
Abstract
The increase in prevalence of food allergies generates a need for more accurate and reliable quantitative allergy testing in order to help diagnosis. In this short review, we briefly outline the history of food allergy testing and extend our comments to current multiplex techniques. Particular emphasis is given to new developments in the protein microarray area, where the use of recent advances in biotechnology has the potential to produce high-throughput devices with improved clinical significance.
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Affiliation(s)
- Neil K Renault
- School of Biosciences, Division of Nutritional Sciences, University of Nottingham, Loughborough, UK
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24
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Creation of a functional heterogeneous vesicle array via DNA controlled surface sorting onto a spotted microarray. Biointerphases 2006; 1:142-5. [DOI: 10.1116/1.2434178] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022] Open
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25
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Abstract
Phosphoproteomics can be defined as the comprehensive study of protein phosphorylation by identification of the phosphoproteins, exact mapping of the phosphorylation sites, quantification of phosphorylation, and eventually, revealing their biological function. Its place in today's research is vitally important to address the most fundamental question - how the phosphorylation events control most, if not all, of the cellular processes in a given organism? Despite the immense importance of phosphorylation, the analysis of phosphoproteins on a proteome-wide scale remains a formidable challenge. Nevertheless, several technologies have been developed, mostly in yeast and mammals, to conduct a large-scale phosphoproteomic study. Some of these technologies have been successfully applied to plants with a few modifications, resulting in documentation of phosphoproteins, phosphorylation site mapping, identification of protein kinase substrates, etc. at the global level. In this review, we summarize in vitro and in vivo approaches for detection and analysis of phosphoproteins including protein kinases and we discuss the importance of phosphoproteomics in understanding plant biology. These approaches along with bioinformatics will help plant researchers to design and apply suitable phosphoproteomic strategies in helping to find answers to their biological questions.
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Affiliation(s)
- Birgit Kersten
- RZPD German Resource Center for Genome Research GmbH, Berlin, Germany
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26
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Dowling VA, Sheehan D. Proteomics as a route to identification of toxicity targets in environmental toxicology. Proteomics 2006; 6:5597-604. [PMID: 16972288 DOI: 10.1002/pmic.200600274] [Citation(s) in RCA: 120] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
Ecotoxicology describes a three-way relationship between ecosystems, chemical pollutants and living organisms. It is predicated on the fact that chemical pollution can exert toxic effects on organisms at the individual and population levels. These toxic effects may provide important information to supplement chemical analysis of environmental samples and aid in assessing the environmental quality of specific ecosystems. Traditionally, effects have been detected by means of biomarkers which, of necessity, were often molecules or processes known to be affected by pollutants. Proteomics provides a means of achieving high-throughput analysis of effects on protein populations and sub-populations with the potential to identify novel biomarkers. This review summarises the main approaches currently used in this area and assesses the potential of proteomics for identification of novel toxicity targets.
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Affiliation(s)
- Vera A Dowling
- Environmental Research Institute and Proteomics Research Group, Department of Biochemistry, University College, Cork, Ireland
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27
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Agostinelli E, Belli F, Tempera G, Mura A, Floris G, Toniolo L, Vavasori A, Fabris S, Momo F, Stevanato R. Polyketone polymer: a new support for direct enzyme immobilization. J Biotechnol 2006; 127:670-8. [PMID: 17007953 DOI: 10.1016/j.jbiotec.2006.08.011] [Citation(s) in RCA: 16] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2006] [Revised: 06/13/2006] [Accepted: 08/01/2006] [Indexed: 10/24/2022]
Abstract
Polyketone polymer -[-CO-CH(2)-CH(2)-](n)-, obtained by copolymerization of ethene and carbon monoxide, is utilized for immobilization of three different enzymes, one peroxidase from horseradish (HRP) and two amine oxidases, from bovine serum (BSAO) and lentil seedlings (LSAO). The easy immobilization procedure is carried out in diluted buffer, at pH 7.0 and 3 degrees C, gently mixing the proteins with the polymer. No bifunctional reagents and spacer arms are required for the immobilization, which occurs exclusively via a large number of hydrogen bonds between the carbonyl groups of the polymer and the -NH groups of the polypeptidic chain. Experiments demonstrate a high linking capacity of polymer for BSAO and an extraordinary strong linkage for LSAO. Moreover, activity measurements demonstrate that immobilized LSAO totally retains the catalytic characteristics of the free enzyme, where only a limited increase of K(M) value is observed. Finally, the HRP-activated polymer is successfully used as active packed bed of an enzymatic reactor for continuous flow conversion and flow injection analysis of hydrogen peroxide containing solutions.
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Affiliation(s)
- E Agostinelli
- Department of Biochemical Sciences A. Rossi Fanelli, University of Rome La Sapienza and CNR, Biology and Molecular Pathology Institutes, Rome, Italy
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28
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Angenendt P, Kreutzberger J, Glökler J, Hoheisel JD. Generation of High Density Protein Microarrays by Cell-free in Situ Expression of Unpurified PCR Products. Mol Cell Proteomics 2006; 5:1658-66. [PMID: 16825183 DOI: 10.1074/mcp.t600024-mcp200] [Citation(s) in RCA: 88] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Due to the success of DNA microarrays and the growing numbers of available protein expression clones, protein microarrays have become more and more popular for the high throughput screening of protein interactions. However, the widespread applicability of protein microarrays is currently hampered by the large effort associated with their production. Apart from the requirement for a protein expression library, expression and purification of the proteins themselves and the lacking stability of many proteins remain the bottleneck. Here we present an approach that allows the generation of high density protein microarrays from unbound DNA template molecules on the chip. It is based on the multiple spotting technique and comprises the deposition of a DNA template in a first spotting step and the transfer of a cell-free transcription and translation mixture on top of the same spot in a second spotting step. Using wild-type green fluorescent protein as a model protein, we demonstrated the time and template dependence of this coupled transcription and translation and showed that enough protein was produced to yield signals that were comparable to 300 microg/ml spotted protein. Plasmids as well as unpurified PCR products can be used as templates, and as little as 35 fg of PCR product ( approximately 22,500 molecules) were sufficient for the detectable expression of full-length wild-type green fluorescent protein in subnanoliter volumes. We showed that both aminopropyltrimethoxysilane and nickel chelate surfaces can be used for capture of the newly synthesized proteins. Surprisingly we observed that nickel chelate-coated slides were binding the newly synthesized proteins in an unspecific manner. Finally we adapted the system to the high throughput expression of libraries by designing a single primer pair for the introduction of the required T7 promoter and demonstrated the in situ expression using 384 randomly chosen clones.
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Affiliation(s)
- Philipp Angenendt
- Functional Genome Analysis, German Cancer Research Center, Im Neuenheimer Feld 580, D-69120 Heidelberg, Germany.
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29
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Oh SJ, Hong BJ, Choi KY, Park JW. Surface Modification for DNA and Protein Microarrays. OMICS-A JOURNAL OF INTEGRATIVE BIOLOGY 2006; 10:327-43. [PMID: 17069511 DOI: 10.1089/omi.2006.10.327] [Citation(s) in RCA: 49] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/02/2023]
Abstract
Microarrays of biomolecules are emerging as powerful tools for genomics, proteomics, and clinical assays, since they make it possible to screen biologically important binding events in a parallel and high throughput fashion. Because the microarrays are fabricated on a solid support, coating of the surface and immobilization strategy of the biomolecules are major issues for successful microarray fabrication. This review deals with both DNA microarrays and protein microarrays, and focuses on the various modification approaches for the two-dimensional surface materials and three-dimensional ones. In addition, the immobilization strategies including adsorption, covalent attachment, physical entrapment, and affinity attachment of the biomolecules are summarized, and advantage and limitation of representative efforts are discussed.
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Affiliation(s)
- Soon Jin Oh
- Department of Biomedical Science and Technology, Institute of Biomedical Science and Technology, Konkuk University, Seoul, Korea.
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30
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Haab BB. Applications of antibody array platforms. Curr Opin Biotechnol 2006; 17:415-21. [PMID: 16837184 DOI: 10.1016/j.copbio.2006.06.013] [Citation(s) in RCA: 148] [Impact Index Per Article: 8.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2006] [Revised: 06/02/2006] [Accepted: 06/30/2006] [Indexed: 12/20/2022]
Abstract
Antibody arrays are valuable for the parallel analysis of multiple proteins in small sample volumes. The earliest and most widely used application of antibody arrays has been to measure multiple protein abundances, using sandwich assays and label-based assays, for biomarker discovery and biological studies. Modifications to these assays have led to studies profiling specific protein post-translational modifications. Additional novel uses include profiling enzyme activities and protein cell-surface expression. Finally, array-based antibody platforms are being used to assist the development and characterization of antibodies. Continued progress in the technology will surely lead to extensions of these applications and the development of new ways of using the methods.
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Affiliation(s)
- Brian B Haab
- Van Andel Research Institute, Grand Rapids, MI 49503, USA.
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31
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Endo Y, Sawasaki T. Cell-free expression systems for eukaryotic protein production. Curr Opin Biotechnol 2006; 17:373-80. [PMID: 16828277 DOI: 10.1016/j.copbio.2006.06.009] [Citation(s) in RCA: 162] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2006] [Revised: 06/01/2006] [Accepted: 06/27/2006] [Indexed: 11/19/2022]
Abstract
Following the success of genome sequencing projects, attention has now turned to studies of the structure and function of proteins. Although cell-based expression systems for protein production have been widely used, they have certain limitations in terms of the quality and quantity of the proteins produced and for high-throughput production. Many of these limitations can be circumvented by the use of cell-free translation systems. Among such systems, the wheat germ based system is of special interest for its eukaryotic nature; it has the significant advantage of producing eukaryotic multidomain proteins in a folded state. Several advances in the use of cell-free expression systems have been made in the past few years and successful applications of these systems to produce proteins for functional and structural biology studies have been reported.
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Affiliation(s)
- Yaeta Endo
- Cell-Free Science and Technology Research Center, Ehime University, Matsuyama, Japan.
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32
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Kumar RA, Clark DS. High-throughput screening of biocatalytic activity: applications in drug discovery. Curr Opin Chem Biol 2006; 10:162-8. [PMID: 16520085 DOI: 10.1016/j.cbpa.2006.02.033] [Citation(s) in RCA: 45] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2006] [Accepted: 02/21/2006] [Indexed: 11/23/2022]
Abstract
Enzymes catalyze a diverse set of reactions that propel life's processes and hence serve as valuable therapeutic targets. High-throughput screening methods have become essential for sifting through large chemical libraries in search of drug candidates, and several sensitive and reliable analytical techniques have been specifically adapted to high-throughput measurements of biocatalytic activity. High-throughput biocatalytic assay platforms thus enable rapid screening against enzymatic targets, and have vast potential to impact various stages of the drug discovery process, including lead identification and optimization, and ADME/Tox assessment. These advances are paving the way for the adoption of high-throughput biocatalytic assays as an indispensable tool for the pharmaceutical industry.
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Affiliation(s)
- R Anand Kumar
- Department of Chemical Engineering, University of California, Berkeley, CA 94720, USA
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33
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Cretich M, Damin F, Pirri G, Chiari M. Protein and peptide arrays: recent trends and new directions. ACTA ACUST UNITED AC 2006; 23:77-88. [PMID: 16527536 DOI: 10.1016/j.bioeng.2006.02.001] [Citation(s) in RCA: 161] [Impact Index Per Article: 8.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2005] [Revised: 02/01/2006] [Accepted: 02/01/2006] [Indexed: 10/24/2022]
Abstract
Microarrays of proteins and peptides make it possible the screening of thousands of binding events in a parallel and high throughput fashion; therefore they are emerging as a powerful tool for proteomics and clinical assays. The complex nature of Proteome, the wide dynamic range of protein concentration in real samples and the critical role of immobilized protein orientation must be taken into account to maximize the utility of protein microarrays. Immobilization strategy and designing of an ideal local chemical environment on the solid surface are both essential for the success of a protein microarray experiment. This review article will focus on protein and peptide arrays highlighting their technical challenges and presenting new directions by means of a set of selected recent applications.
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Affiliation(s)
- Marina Cretich
- Istituto di Chimica del Riconoscimento Molecolare (ICRM) - C.N.R., Via Mario Bianco, 9, 20131 Milano, Italy.
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34
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Wang J, Uttamchandani M, Sun LP, Yao SQ. Activity-based high-throughput profiling of metalloprotease inhibitors using small molecule microarrays. Chem Commun (Camb) 2006:717-9. [PMID: 16465317 DOI: 10.1039/b515278j] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/30/2023]
Abstract
We herein describe a high-throughput small molecule microarray (SMM) method that enables quick and cost-effective identification of potent inhibitors of metalloproteases in an activity-dependent manner, thereby offering a rapid means for inhibitor discovery and profiling.
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Affiliation(s)
- Jun Wang
- Department of Chemistry, National University of Singapore, 3 Science Drive 3, 117543, Singapore
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35
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Uttamchandani M, Wang J, Yao SQ. Protein and small molecule microarrays: powerful tools for high-throughput proteomics. ACTA ACUST UNITED AC 2006; 2:58-68. [PMID: 16880923 DOI: 10.1039/b513935j] [Citation(s) in RCA: 102] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Advances in genomics and proteomics have opened up new possibilities for the rapid functional assignment and global characterization of proteins. Large-scale studies have accelerated this effort by using tools and strategies that enable highly parallel analysis of huge repertoires of biomolecules. Organized assortments of molecules on arrays have furnished a robust platform for rapid screening, lead discovery and molecular characterization. The essential advantage of microarray technology is attributed to the massive throughput attainable, coupled with a highly miniaturized platform--potentially driving discovery both as an analytical and diagnostic tool. The scope of microarrays has in recent years expanded impressively. Virtually every biological component--from diverse small molecules and macromolecules (such as DNA and proteins) to entire living cells--has been harnessed on microarrays in attempts to dissect the bewildering complexity of life. Herein we highlight strategies that address challenges in proteomics using microarrays of immobilized proteins and small molecules. Of specific interest are the techniques involved in stably immobilizing proteins and chemical libraries on slide surfaces as well as novel strategies developed to profile activities of proteins on arrays. As a rapidly maturing technology, microarrays pave the way forward in high-throughput proteomic exploration.
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