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Garibyan M, Hoffman T, Makaske T, Do SK, Wu Y, Williams BA, March AR, Cho N, Pedroncelli N, Lima RE, Soto J, Jackson B, Santoso JW, Khademhosseini A, Thomson M, Li S, McCain ML, Morsut L. Engineering programmable material-to-cell pathways via synthetic notch receptors to spatially control differentiation in multicellular constructs. Nat Commun 2024; 15:5891. [PMID: 39003263 PMCID: PMC11246427 DOI: 10.1038/s41467-024-50126-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2023] [Accepted: 07/02/2024] [Indexed: 07/15/2024] Open
Abstract
Synthetic Notch (synNotch) receptors are genetically encoded, modular synthetic receptors that enable mammalian cells to detect environmental signals and respond by activating user-prescribed transcriptional programs. Although some materials have been modified to present synNotch ligands with coarse spatial control, applications in tissue engineering generally require extracellular matrix (ECM)-derived scaffolds and/or finer spatial positioning of multiple ligands. Thus, we develop here a suite of materials that activate synNotch receptors for generalizable engineering of material-to-cell signaling. We genetically and chemically fuse functional synNotch ligands to ECM proteins and ECM-derived materials. We also generate tissues with microscale precision over four distinct reporter phenotypes by culturing cells with two orthogonal synNotch programs on surfaces microcontact-printed with two synNotch ligands. Finally, we showcase applications in tissue engineering by co-transdifferentiating fibroblasts into skeletal muscle or endothelial cell precursors in user-defined micropatterns. These technologies provide avenues for spatially controlling cellular phenotypes in mammalian tissues.
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Affiliation(s)
- Mher Garibyan
- Department of Stem Cell Biology and Regenerative Medicine, Keck School of Medicine of USC, University of Southern California, Los Angeles, CA, USA
- Eli and Edythe Broad Center, University of Southern California, Los Angeles, CA, 90033, USA
- Alfred E. Mann Department of Biomedical Engineering, USC Viterbi School of Engineering, University of Southern California, Los Angeles, CA, USA
| | - Tyler Hoffman
- Department of Bioengineering, University of California Los Angeles, Los Angeles, CA, USA
| | - Thijs Makaske
- Department of Stem Cell Biology and Regenerative Medicine, Keck School of Medicine of USC, University of Southern California, Los Angeles, CA, USA
- Eli and Edythe Broad Center, University of Southern California, Los Angeles, CA, 90033, USA
- Utrecht University in the lab of Prof. Dr. Lukas Kapitein, Los Angeles, CA, 90024, USA
| | - Stephanie K Do
- Alfred E. Mann Department of Biomedical Engineering, USC Viterbi School of Engineering, University of Southern California, Los Angeles, CA, USA
| | - Yifan Wu
- Department of Bioengineering, University of California Los Angeles, Los Angeles, CA, USA
| | - Brian A Williams
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA, USA
| | - Alexander R March
- Department of Stem Cell Biology and Regenerative Medicine, Keck School of Medicine of USC, University of Southern California, Los Angeles, CA, USA
- Eli and Edythe Broad Center, University of Southern California, Los Angeles, CA, 90033, USA
| | - Nathan Cho
- Alfred E. Mann Department of Biomedical Engineering, USC Viterbi School of Engineering, University of Southern California, Los Angeles, CA, USA
| | - Nicolas Pedroncelli
- Department of Bioengineering, University of California Los Angeles, Los Angeles, CA, USA
| | - Ricardo Espinosa Lima
- Department of Bioengineering, University of California Los Angeles, Los Angeles, CA, USA
| | - Jennifer Soto
- Department of Bioengineering, University of California Los Angeles, Los Angeles, CA, USA
| | - Brooke Jackson
- Department of Bioengineering, University of California Los Angeles, Los Angeles, CA, USA
| | - Jeffrey W Santoso
- Alfred E. Mann Department of Biomedical Engineering, USC Viterbi School of Engineering, University of Southern California, Los Angeles, CA, USA
| | - Ali Khademhosseini
- Department of Bioengineering, University of California Los Angeles, Los Angeles, CA, USA
- Terasaki Institute for Biomedical Innovation (TIBI), Los Angeles, CA, 90024, USA
| | - Matt Thomson
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA, USA
| | - Song Li
- Department of Bioengineering, University of California Los Angeles, Los Angeles, CA, USA
- Broad Stem Cell Center, University of California, Los Angeles, Los Angeles, CA, 90095, USA
- Jonsson Comprehensive Cancer Center, University of California, Los Angeles, Los Angeles, CA, 90095, USA
| | - Megan L McCain
- Department of Stem Cell Biology and Regenerative Medicine, Keck School of Medicine of USC, University of Southern California, Los Angeles, CA, USA.
- Alfred E. Mann Department of Biomedical Engineering, USC Viterbi School of Engineering, University of Southern California, Los Angeles, CA, USA.
| | - Leonardo Morsut
- Department of Stem Cell Biology and Regenerative Medicine, Keck School of Medicine of USC, University of Southern California, Los Angeles, CA, USA.
- Eli and Edythe Broad Center, University of Southern California, Los Angeles, CA, 90033, USA.
- Alfred E. Mann Department of Biomedical Engineering, USC Viterbi School of Engineering, University of Southern California, Los Angeles, CA, USA.
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van der Ven AM, Gyamfi H, Suttisansanee U, Ahmad MS, Su Z, Taylor RM, Poole A, Chiorean S, Daub E, Urquhart T, Honek JF. Molecular Engineering of E. coli Bacterioferritin: A Versatile Nanodimensional Protein Cage. Molecules 2023; 28:4663. [PMID: 37375226 DOI: 10.3390/molecules28124663] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2023] [Revised: 05/23/2023] [Accepted: 06/05/2023] [Indexed: 06/29/2023] Open
Abstract
Currently, intense interest is focused on the discovery and application of new multisubunit cage proteins and spherical virus capsids to the fields of bionanotechnology, drug delivery, and diagnostic imaging as their internal cavities can serve as hosts for fluorophores or bioactive molecular cargo. Bacterioferritin is unusual in the ferritin protein superfamily of iron-storage cage proteins in that it contains twelve heme cofactors and is homomeric. The goal of the present study is to expand the capabilities of ferritins by developing new approaches to molecular cargo encapsulation employing bacterioferritin. Two strategies were explored to control the encapsulation of a diverse range of molecular guests compared to random entrapment, a predominant strategy employed in this area. The first was the inclusion of histidine-tag peptide fusion sequences within the internal cavity of bacterioferritin. This approach allowed for the successful and controlled encapsulation of a fluorescent dye, a protein (fluorescently labeled streptavidin), or a 5 nm gold nanoparticle. The second strategy, termed the heme-dependent cassette strategy, involved the substitution of the native heme with heme analogs attached to (i) fluorescent dyes or (ii) nickel-nitrilotriacetate (NTA) groups (which allowed for controllable encapsulation of a histidine-tagged green fluorescent protein). An in silico docking approach identified several small molecules able to replace the heme and capable of controlling the quaternary structure of the protein. A transglutaminase-based chemoenzymatic approach to surface modification of this cage protein was also accomplished, allowing for future nanoparticle targeting. This research presents novel strategies to control a diverse set of molecular encapsulations and adds a further level of sophistication to internal protein cavity engineering.
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Affiliation(s)
- Anton M van der Ven
- Department of Chemistry, University of Waterloo, Waterloo, ON N2L 3G1, Canada
| | - Hawa Gyamfi
- Department of Chemistry, University of Waterloo, Waterloo, ON N2L 3G1, Canada
| | | | - Muhammad S Ahmad
- Department of Chemistry, University of Waterloo, Waterloo, ON N2L 3G1, Canada
| | - Zhengding Su
- Department of Chemistry, University of Waterloo, Waterloo, ON N2L 3G1, Canada
| | - Robert M Taylor
- Department of Chemistry, University of Waterloo, Waterloo, ON N2L 3G1, Canada
| | - Amanda Poole
- Department of Chemistry, University of Waterloo, Waterloo, ON N2L 3G1, Canada
| | - Sorina Chiorean
- Department of Chemistry, University of Waterloo, Waterloo, ON N2L 3G1, Canada
| | - Elisabeth Daub
- Department of Chemistry, University of Waterloo, Waterloo, ON N2L 3G1, Canada
| | - Taylor Urquhart
- Department of Chemistry, University of Waterloo, Waterloo, ON N2L 3G1, Canada
| | - John F Honek
- Department of Chemistry, University of Waterloo, Waterloo, ON N2L 3G1, Canada
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3
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Garibyan M, Hoffman T, Makaske T, Do S, March AR, Cho N, Pedroncelli N, Lima RE, Soto J, Jackson B, Khademhosseini A, Li S, McCain M, Morsut L. Engineering Programmable Material-To-Cell Pathways Via Synthetic Notch Receptors To Spatially Control Cellular Phenotypes In Multi-Cellular Constructs. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.05.19.541497. [PMID: 37293089 PMCID: PMC10245658 DOI: 10.1101/2023.05.19.541497] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
Synthetic Notch (synNotch) receptors are modular synthetic components that are genetically engineered into mammalian cells to detect signals presented by neighboring cells and respond by activating prescribed transcriptional programs. To date, synNotch has been used to program therapeutic cells and pattern morphogenesis in multicellular systems. However, cell-presented ligands have limited versatility for applications that require spatial precision, such as tissue engineering. To address this, we developed a suite of materials to activate synNotch receptors and serve as generalizable platforms for generating user-defined material-to-cell signaling pathways. First, we demonstrate that synNotch ligands, such as GFP, can be conjugated to cell- generated ECM proteins via genetic engineering of fibronectin produced by fibroblasts. We then used enzymatic or click chemistry to covalently link synNotch ligands to gelatin polymers to activate synNotch receptors in cells grown on or within a hydrogel. To achieve microscale control over synNotch activation in cell monolayers, we microcontact printed synNotch ligands onto a surface. We also patterned tissues comprising cells with up to three distinct phenotypes by engineering cells with two distinct synthetic pathways and culturing them on surfaces microfluidically patterned with two synNotch ligands. We showcase this technology by co-transdifferentiating fibroblasts into skeletal muscle or endothelial cell precursors in user-defined spatial patterns towards the engineering of muscle tissue with prescribed vascular networks. Collectively, this suite of approaches extends the synNotch toolkit and provides novel avenues for spatially controlling cellular phenotypes in mammalian multicellular systems, with many broad applications in developmental biology, synthetic morphogenesis, human tissue modeling, and regenerative medicine.
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4
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Rocha RA, Speight RE, Scott C. Engineering Enzyme Properties for Improved Biocatalytic Processes in Batch and Continuous Flow. Org Process Res Dev 2022. [DOI: 10.1021/acs.oprd.1c00424] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Affiliation(s)
- Raquel A. Rocha
- School of Biology and Environmental Science, Faculty of Science, Queensland University of Technology, Brisbane, Queensland 4000, Australia
- CSIRO Synthetic Biology Future Science Platform, CSIRO Land & Water, Black Mountain Science and Innovation Park, Canberra, ACT 2601, Australia
| | - Robert E. Speight
- School of Biology and Environmental Science, Faculty of Science, Queensland University of Technology, Brisbane, Queensland 4000, Australia
- ARC Centre of Excellence in Synthetic Biology, Queensland University of Technology, Brisbane, Queensland 4000, Australia
| | - Colin Scott
- CSIRO Synthetic Biology Future Science Platform, CSIRO Land & Water, Black Mountain Science and Innovation Park, Canberra, ACT 2601, Australia
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Zhang X, Shao W, Chen B, Wang M. Cross-linking of carbonic anhydrase and formate dehydrogenase based on amino acid specific recognition: Conversion of carbon dioxide to formic acid. Enzyme Microb Technol 2021; 146:109763. [PMID: 33812561 DOI: 10.1016/j.enzmictec.2021.109763] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2020] [Revised: 01/15/2021] [Accepted: 01/25/2021] [Indexed: 10/22/2022]
Abstract
Inspired by the cascades performed in vivo, the assembly of multiple enzymes in vitro has strongly moved into the focus of researchers in the field of biocatalysis. In this study, a new, mild and accurate enzyme cross-linking method is revealed. Microbial transglutaminase (MTG) acts as a "cross-linking medium" by identifying the amide group of the glutamine and the primary amine group of lysine in the artificial peptide tags specifically to form an iso-peptide bond. Here, carbonic anhydrase (CA) and formate dehydrogenase (FDH) with different peptide tags that can be recognized by MTG were linked together to obtain different proportions of cross-linked enzymes for efficient conversion of greenhouse gas carbon dioxide to formic acid. After cross-linking, we obtained "one-to-one" and "one-to-more" cross-linked enzyme aggregates. There is a minor residual loss of the two enzymes, the remaining enzyme activity of CA is more than 93%, and the remaining enzyme activity of FDH is more than 84%. In particular, the overall catalytic efficiency of the cross-linked enzyme is increased by 5.8 times compared with free enzymes and the thermal stability of FDH at different temperatures is improved. The applied strategy demonstrates the potential application of MTG in multi-enzyme assembly and synthetic biology.
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Affiliation(s)
- Xiaonan Zhang
- National Energy R&D Center for Biorefinery, Beijing University of Chemical Technology, Beijing, 100029, PR China
| | - Wenxuan Shao
- National Energy R&D Center for Biorefinery, Beijing University of Chemical Technology, Beijing, 100029, PR China
| | - Biqiang Chen
- National Energy R&D Center for Biorefinery, Beijing University of Chemical Technology, Beijing, 100029, PR China.
| | - Meng Wang
- National Energy R&D Center for Biorefinery, Beijing University of Chemical Technology, Beijing, 100029, PR China
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6
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Park J, Lee S, Kim Y, Yoo TH. Methods to generate site-specific conjugates of antibody and protein. Bioorg Med Chem 2021; 30:115946. [DOI: 10.1016/j.bmc.2020.115946] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2020] [Revised: 12/07/2020] [Accepted: 12/09/2020] [Indexed: 02/07/2023]
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7
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Deweid L, Avrutina O, Kolmar H. Microbial transglutaminase for biotechnological and biomedical engineering. Biol Chem 2019; 400:257-274. [PMID: 30291779 DOI: 10.1515/hsz-2018-0335] [Citation(s) in RCA: 23] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2018] [Accepted: 09/04/2018] [Indexed: 12/17/2022]
Abstract
Research on bacterial transglutaminase dates back to 1989, when the enzyme has been isolated from Streptomyces mobaraensis. Initially discovered during an extensive screening campaign to reduce costs in food manufacturing, it quickly appeared as a robust and versatile tool for biotechnological and pharmaceutical applications due to its excellent activity and simple handling. While pioneering attempts to make use of its extraordinary cross-linking ability resulted in heterogeneous polymers, currently it is applied to site-specifically ligate diverse biomolecules yielding precisely modified hybrid constructs comprising two or more components. This review covers the extensive and rapidly growing field of microbial transglutaminase-mediated bioconjugation with the focus on pharmaceutical research. In addition, engineering of the enzyme by directed evolution and rational design is highlighted. Moreover, cumbersome drawbacks of this technique mainly caused by the enzyme's substrate indiscrimination are discussed as well as the ways to bypass these limitations.
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Affiliation(s)
- Lukas Deweid
- Institute for Organic Chemistry and Biochemistry, Technische Universität Darmstadt, Alarich-Weiss-Straße 4, D-64287 Darmstadt, Germany
| | - Olga Avrutina
- Institute for Organic Chemistry and Biochemistry, Technische Universität Darmstadt, Alarich-Weiss-Straße 4, D-64287 Darmstadt, Germany
| | - Harald Kolmar
- Institute for Organic Chemistry and Biochemistry, Technische Universität Darmstadt, Alarich-Weiss-Straße 4, D-64287 Darmstadt, Germany
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8
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Li J, Wu S, Kim E, Yan K, Liu H, Liu C, Dong H, Qu X, Shi X, Shen J, Bentley WE, Payne GF. Electrobiofabrication: electrically based fabrication with biologically derived materials. Biofabrication 2019; 11:032002. [PMID: 30759423 PMCID: PMC7025432 DOI: 10.1088/1758-5090/ab06ea] [Citation(s) in RCA: 26] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
While conventional material fabrication methods focus on form and strength to achieve function, the fabrication of material systems for emerging life science applications will need to satisfy a more subtle set of requirements. A common goal for biofabrication is to recapitulate complex biological contexts (e.g. tissue) for applications that range from animal-on-a-chip to regenerative medicine. In these cases, the material systems will need to: (i) present appropriate surface functionalities over a hierarchy of length scales (e.g. molecular features that enable cell adhesion and topographical features that guide differentiation); (ii) provide a suite of mechanobiological cues that promote the emergence of native-like tissue form and function; and (iii) organize structure to control cellular ingress and molecular transport, to enable the development of an interconnected cellular community that is engaged in cell signaling. And these requirements are not likely to be static but will vary over time and space, which will require capabilities of the material systems to dynamically respond, adapt, heal and reconfigure. Here, we review recent advances in the use of electrically based fabrication methods to build material systems from biological macromolecules (e.g. chitosan, alginate, collagen and silk). Electrical signals are especially convenient for fabrication because they can be controllably imposed to promote the electrophoresis, alignment, self-assembly and functionalization of macromolecules to generate hierarchically organized material systems. Importantly, this electrically based fabrication with biologically derived materials (i.e. electrobiofabrication) is complementary to existing methods (photolithographic and printing), and enables access to the biotechnology toolbox (e.g. enzymatic-assembly and protein engineering, and gene expression) to offer exquisite control of structure and function. We envision that electrobiofabrication will emerge as an important platform technology for organizing soft matter into dynamic material systems that mimic biology's complexity of structure and versatility of function.
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Affiliation(s)
- Jinyang Li
- Institute for Bioscience and Biotechnology Research, University of Maryland, College Park, United States of America
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Jin M, Chen Z, Wang Z, Huang J, Chang Z, Gao H. Separation of two microbial transglutaminase isomers from Streptomyces mobaraensis using pH-mediated cation exchange chromatography and their characterization. J Chromatogr B Analyt Technol Biomed Life Sci 2018; 1097-1098:111-118. [PMID: 30218918 DOI: 10.1016/j.jchromb.2018.09.003] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2018] [Revised: 08/04/2018] [Accepted: 09/02/2018] [Indexed: 11/29/2022]
Abstract
Microbial transglutaminase (MTGase) derived from Streptomyces mobaraensis has been widely used in the food, biotechnology and medicine fields. The lot-to-lot consistency and product stability of MTGase must be ensured. The structure and charge variants of MTGase can influence its bioactivity. In this study, MTGase isomers (MTG I1 and MTG I2) were found during the separation of MTGase by pH-mediated cation-exchange chromatography. MTG I1 and MTG I2 had the same molecular weight and N-terminal amino acid sequences, but they showed charge heterogeneity. The affinity of MTG I2 for substrates was higher than that of MTG I1, and the thermal stability and the acid-base tolerance of MTG I1 were significantly higher than that of MTG I2. Therefore, the ratio of MTG I1/MTG I2 was positively correlated with the stability of MTGase. The buffer pH and the ionic strength of the eluent had significant effects on the separation of MTG I1 and MTG I2, and the elution gradient steepness and column load showed little effect on the separation of the MTG I1 and MTG I2 peaks. We built a stable and repeatable separation method for MTG I1 and MTG I2. MTG I1 could transform into MTG I2, but MTG I2 was unable to transform into MTG I1, making the transformation of MTG I1 to MTG I2 was irreversible. When MTG I2 was removed from the MTGase, a portion of the MTG I1 could transform into MTG I2. Therefore, one way to increase the stability of MTGase was to reduce the transformation of MTG I1 to MTG I2.
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Affiliation(s)
- Mingfei Jin
- School of Life Sciences, East China Normal University, 500 Dongchuan Road, Shanghai 200241, China.
| | - Zhongshan Chen
- School of Life Sciences, East China Normal University, 500 Dongchuan Road, Shanghai 200241, China
| | - Zhizhen Wang
- Guangdong Guangya High School, No. 1 Xiwan Road, Guangzhou 510160, China
| | - Jing Huang
- School of Life Sciences, East China Normal University, 500 Dongchuan Road, Shanghai 200241, China.
| | - Zhongyi Chang
- School of Life Sciences, East China Normal University, 500 Dongchuan Road, Shanghai 200241, China.
| | - Hongliang Gao
- School of Life Sciences, East China Normal University, 500 Dongchuan Road, Shanghai 200241, China.
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10
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Liu Y, Wu HC, Bhokisham N, Li J, Hong KL, Quan DN, Tsao CY, Bentley WE, Payne GF. Biofabricating Functional Soft Matter Using Protein Engineering to Enable Enzymatic Assembly. Bioconjug Chem 2018; 29:1809-1822. [PMID: 29745651 PMCID: PMC7045599 DOI: 10.1021/acs.bioconjchem.8b00197] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
Abstract
Biology often provides the inspiration for functional soft matter, but biology can do more: it can provide the raw materials and mechanisms for hierarchical assembly. Biology uses polymers to perform various functions, and biologically derived polymers can serve as sustainable, self-assembling, and high-performance materials platforms for life-science applications. Biology employs enzymes for site-specific reactions that are used to both disassemble and assemble biopolymers both to and from component parts. By exploiting protein engineering methodologies, proteins can be modified to make them more susceptible to biology's native enzymatic activities. They can be engineered with fusion tags that provide (short sequences of amino acids at the C- and/or N- termini) that provide the accessible residues for the assembling enzymes to recognize and react with. This "biobased" fabrication not only allows biology's nanoscale components (i.e., proteins) to be engineered, but also provides the means to organize these components into the hierarchical structures that are prevalent in life.
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Affiliation(s)
| | - Hsuan-Chen Wu
- Department of Biochemical Science and Technology , National Taiwan University , Taipei City , Taiwan
| | | | | | - Kai-Lin Hong
- Department of Biochemical Science and Technology , National Taiwan University , Taipei City , Taiwan
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Nagamune T. Biomolecular engineering for nanobio/bionanotechnology. NANO CONVERGENCE 2017; 4:9. [PMID: 28491487 PMCID: PMC5401866 DOI: 10.1186/s40580-017-0103-4] [Citation(s) in RCA: 52] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/17/2017] [Accepted: 03/29/2017] [Indexed: 05/02/2023]
Abstract
Biomolecular engineering can be used to purposefully manipulate biomolecules, such as peptides, proteins, nucleic acids and lipids, within the framework of the relations among their structures, functions and properties, as well as their applicability to such areas as developing novel biomaterials, biosensing, bioimaging, and clinical diagnostics and therapeutics. Nanotechnology can also be used to design and tune the sizes, shapes, properties and functionality of nanomaterials. As such, there are considerable overlaps between nanotechnology and biomolecular engineering, in that both are concerned with the structure and behavior of materials on the nanometer scale or smaller. Therefore, in combination with nanotechnology, biomolecular engineering is expected to open up new fields of nanobio/bionanotechnology and to contribute to the development of novel nanobiomaterials, nanobiodevices and nanobiosystems. This review highlights recent studies using engineered biological molecules (e.g., oligonucleotides, peptides, proteins, enzymes, polysaccharides, lipids, biological cofactors and ligands) combined with functional nanomaterials in nanobio/bionanotechnology applications, including therapeutics, diagnostics, biosensing, bioanalysis and biocatalysts. Furthermore, this review focuses on five areas of recent advances in biomolecular engineering: (a) nucleic acid engineering, (b) gene engineering, (c) protein engineering, (d) chemical and enzymatic conjugation technologies, and (e) linker engineering. Precisely engineered nanobiomaterials, nanobiodevices and nanobiosystems are anticipated to emerge as next-generation platforms for bioelectronics, biosensors, biocatalysts, molecular imaging modalities, biological actuators, and biomedical applications.
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Affiliation(s)
- Teruyuki Nagamune
- Department of Chemistry and Biotechnology, Graduate School of Engineering, The University of Tokyo, Tokyo, Japan
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12
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Tatsukawa H, Liu HH, Oba S, Kamiya N, Nakanishi Y, Hitomi K. FRET-based detection of isozyme-specific activities of transglutaminases. Amino Acids 2016; 49:615-623. [PMID: 27586957 DOI: 10.1007/s00726-016-2322-0] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2016] [Accepted: 08/25/2016] [Indexed: 01/07/2023]
Abstract
Transglutaminases (TGs) comprise a protein family in which the members catalyze the formation of isopeptide bonds between glutamine and lysine residues in various proteins. Expression studies on its three major members, FXIII, TG1, and TG2, have been performed in a relatively large number of mammalian tissues in comparison with those on the other isozymes. We previously identified a highly reactive substrate peptide, including glutamine, for each isozyme from a phage display library and developed a method for detecting isozyme-specific activities by incorporating a labeled substrate peptide into lysine residues of proteins. Here, we describe genetically encoded Förster resonance energy transfer (FRET)-based probes composed of each fluorescence protein (Cerulean and EVenus) fused with substrate peptides. The probe pairs, designated as Trac-MTG (His-CerΔ11-LQ/EV-K-His) containing linker and substrate peptide sequence for microbial TG (MTG), increased the EVenus:Cerulean fluorescence intensity ratio by more than 1.5-fold. Furthermore, we demonstrated that Trac-TG1 (His-CerΔ11-K5) and Trac-TG2 (His-CerΔ11-T26) containing substrate peptide sequence for mammalian TGs successfully detected the isozyme-specific activity of TG1 and TG2, respectively. In this study, we developed a rapid and convenient experimental system for measuring the isozyme-specific activity of TGs. The application of these probes for analyses in cells and tissues will be helpful for elucidating the physiological and pathological functions of TGs.
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Affiliation(s)
- Hideki Tatsukawa
- Cellular Biochemistry Lab., Department of Basic Medicinal Sciences, Graduate School of Pharmaceutical Sciences, Nagoya University, Furo-cho, Chikusa, Nagoya, 464-0814, Japan.
| | - Hong Hong Liu
- Cellular Biochemistry Lab., Department of Basic Medicinal Sciences, Graduate School of Pharmaceutical Sciences, Nagoya University, Furo-cho, Chikusa, Nagoya, 464-0814, Japan
| | - Shota Oba
- Cellular Biochemistry Lab., Department of Basic Medicinal Sciences, Graduate School of Pharmaceutical Sciences, Nagoya University, Furo-cho, Chikusa, Nagoya, 464-0814, Japan
| | - Noriho Kamiya
- Department of Applied Chemistry, Graduate School of Engineering, Kyushu University, 744 Motooka, Fukuoka, 819-0395, Japan.,Division of Biotechnology, Center for Future Chemistry, Kyushu University, Fukuoka, 819-0388, Japan
| | - Yoichi Nakanishi
- Department of Biological Mechanisms and Functions, Graduate School of Bioagricultural Sciences, Nagoya University, Nagoya, Japan
| | - Kiyotaka Hitomi
- Cellular Biochemistry Lab., Department of Basic Medicinal Sciences, Graduate School of Pharmaceutical Sciences, Nagoya University, Furo-cho, Chikusa, Nagoya, 464-0814, Japan
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13
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DIVERSE System: De Novo Creation of Peptide Tags for Non-enzymatic Covalent Labeling by In Vitro Evolution for Protein Imaging Inside Living Cells. ACTA ACUST UNITED AC 2016; 22:1671-9. [PMID: 26687484 DOI: 10.1016/j.chembiol.2015.10.016] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2015] [Revised: 10/10/2015] [Accepted: 10/15/2015] [Indexed: 10/22/2022]
Abstract
Polypeptide-tag/small-molecule pairs for specific cellular protein labeling are useful for visualizing cellular proteins and controlling their activity. Here, we report the development of an in vitro evolution-based (poly)peptide tag identification system named the DIVERSE (Directed In Vitro Evolution of Reactive peptide tags via Sequential Enrichment) system. In this system, an extremely diverse (10(14)) library of peptide tags, displayed by covalent attachment to their encoding cDNAs, is continuously prepared from the DNA library in a one-pot approach. Using this system, we demonstrated de novo creation of non-enzymatically covalent-labeling peptide tags for a synthetic small-molecule target from a random peptide library. Protein labeling with these tags was applicable to N- and C-terminal fusions, multiple different proteins and fluorophores, and intracellular labeling. The DIVERSE system can be used not only for the de novo creation of polypeptide tags but also sequence optimization of existing polypeptide tags from extremely diverse libraries.
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Liu Y, Wu HC, Chhuan M, Terrell JL, Tsao CY, Bentley WE, Payne GF. Functionalizing Soft Matter for Molecular Communication. ACS Biomater Sci Eng 2015; 1:320-328. [PMID: 26501127 PMCID: PMC4603720 DOI: 10.1021/ab500160e] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2014] [Accepted: 03/26/2015] [Indexed: 11/28/2022]
Abstract
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The
information age was enabled by advances in microfabrication
and communication theory that allowed information to be processed
by electrons and transmitted by electromagnetic radiation. Despite
immense capabilities, microelectronics has limited abilities to access
and participate in the molecular-based communication that characterizes
our biological world. Here, we use biological materials and methods
to create components and fabricate devices to perform simple molecular
communication functions based on bacterial quorum sensing (QS). Components
were created by protein engineering to generate a multidomain fusion
protein capable of sending a molecular QS signal, and by synthetic
biology to engineer E. coli to receive and report
this QS signal. The device matrix was formed using stimuli-responsive
hydrogel-forming biopolymers (alginate and gelatin). Assembly of the
components within the device matrix was achieved by physically entrapping
the cell-based components, and covalently conjugating the protein-based
components using the enzyme microbial transglutaminase. We demonstrate
simple devices that can send or receive a molecular QS signal to/from
the surrounding medium, and a two-component device in which one component
generates the signal (i.e., issues a command) that is acted upon by
the second component. These studies illustrate the broad potential
of biofabrication to generate molecular communication devices.
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Affiliation(s)
- Yi Liu
- Institute for Bioscience and Biotechnology Research and Fischell Department of Bioengineering, University of Maryland , College Park, Maryland 20742, United States
| | - Hsuan-Chen Wu
- Institute for Bioscience and Biotechnology Research and Fischell Department of Bioengineering, University of Maryland , College Park, Maryland 20742, United States
| | - Melanie Chhuan
- Institute for Bioscience and Biotechnology Research and Fischell Department of Bioengineering, University of Maryland , College Park, Maryland 20742, United States
| | - Jessica L Terrell
- Institute for Bioscience and Biotechnology Research and Fischell Department of Bioengineering, University of Maryland , College Park, Maryland 20742, United States
| | - Chen-Yu Tsao
- Institute for Bioscience and Biotechnology Research and Fischell Department of Bioengineering, University of Maryland , College Park, Maryland 20742, United States
| | - William E Bentley
- Institute for Bioscience and Biotechnology Research and Fischell Department of Bioengineering, University of Maryland , College Park, Maryland 20742, United States
| | - Gregory F Payne
- Institute for Bioscience and Biotechnology Research and Fischell Department of Bioengineering, University of Maryland , College Park, Maryland 20742, United States
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15
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Chitosan to Connect Biology to Electronics: Fabricating the Bio-Device Interface and Communicating Across This Interface. Polymers (Basel) 2014. [DOI: 10.3390/polym7010001] [Citation(s) in RCA: 73] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022] Open
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16
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Minamihata K, Goto M, Kamiya N. Site-specific conjugation of an antibody-binding protein catalyzed by horseradish peroxidase creates a multivalent protein conjugate with high affinity to IgG. Biotechnol J 2014; 10:222-6. [DOI: 10.1002/biot.201400512] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2014] [Revised: 10/15/2014] [Accepted: 11/03/2014] [Indexed: 11/08/2022]
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Abstract
Tissue transglutaminase (transglutaminase 2) is a multifunctional enzyme with many interesting properties resulting in versatile roles in both physiology and pathophysiology. Herein, the particular involvement of the enzyme in human diseases will be outlined with special emphasis on its role in cancer and in tissue interactions with biomaterials. Despite recent progress in unraveling the different cellular functions of transglutaminase 2, several questions remain. Transglutaminase 2 features in both confirmed and some still ambiguous roles within pathological conditions, raising interest in developing inhibitors and imaging probes which target this enzyme. One important prerequisite for identifying and characterizing such molecular tools are reliable assay methods to measure the enzymatic activity. This digest Letter will provide clarification about the various assay methods described to date, accompanied by a discussion of recent progress in the development of inhibitors and imaging probes targeting transglutaminase 2.
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Affiliation(s)
- Pavel Strop
- Rinat-Pfizer Inc., 230 East Grand Avenue, South San Francisco, California 94080, United States
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19
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Lee JH, Song E, Lee SG, Kim BG. High-throughput screening for transglutaminase activities using recombinant fluorescent proteins. Biotechnol Bioeng 2013; 110:2865-73. [PMID: 23740563 DOI: 10.1002/bit.24970] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2013] [Revised: 04/28/2013] [Accepted: 05/28/2013] [Indexed: 01/20/2023]
Abstract
Since detailed evaluation of specific transglutaminases (TGs) from various species requires identification of their substrate specificities, rapid substrate screening method by measurement of their relative activities is in great demand. Here, a novel evaluation method of TG activity was developed using two recombinant fluorescent proteins (FPs), that is, eYFP and DsRed, tagged with TG substrate peptides. By cross-linking the two FPs based on the tagged target peptide sequences at their C-terminus, the expression of co-transformed TG allows quenching of the yellow fluorescence intensities. It was shown that the degree of in vivo fluorescent quenching by the TG activity agrees well with its in vitro reaction data, suggesting that this system can be used to identify relative substrate specificity of TGs for target peptide sequences. Using this method, the lysine substrates of TGs from Bacillus species (BTG) were evaluated, and the newly selected pentapeptide, KTKTN showed almost the same reactivity with the well-known hexa-lysine (K₆) substrate for BTG reaction.
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Affiliation(s)
- Jae-Hun Lee
- Interdisciplinary Program for Biochemical Engineering and Biotechnology, Seoul National University, Kwanak-Gu, Seoul, South Korea; Institute of Bioengineering, Seoul National University, Kwanak-Gu, Seoul, South Korea
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Cheng Y, Liu Y, Liba BD, Ghodssi R, Rubloff GW, Bentley WE, Payne GF. Biofabricating the Bio-Device Interface Using Biological Materials and Mechanisms. Biofabrication 2013. [DOI: 10.1016/b978-1-4557-2852-7.00012-3] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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21
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22
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Mori Y, Goto M, Kamiya N. Transglutaminase-mediated internal protein labeling with a designed peptide loop. Biochem Biophys Res Commun 2011; 410:829-33. [PMID: 21703236 DOI: 10.1016/j.bbrc.2011.06.073] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2011] [Accepted: 06/09/2011] [Indexed: 10/18/2022]
Abstract
Post-translational internal protein labeling was explored through the insertion of a 13-mer peptidyl loop specifically recognized by microbial transglutaminase (MTG). The peptidyl loop included one lysine residue (abbreviated as the K-loop), and was designed and inserted into two different regions of the protein bacterial alkaline phosphatase (BAP). MTG-mediated selective labeling of a lysine residue in the K-loop was achieved with a functional Gln-donor substrate. Internal protein labeling in the vicinity of the active site of BAP (residues 91-93) markedly decreased the activity of the enzyme. Conversely, insertion of the K-loop at a site distal from the active site (residues 219-221) afforded site-specific and covalent internal protein labeling without impairing the activity of the enzyme.
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Affiliation(s)
- Yutaro Mori
- Department of Applied Chemistry, Graduate School of Engineering, Kyushu University, 744 Moto-oka, Fukuoka 819-0395, Japan
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23
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Kamiya N, Abe H. New fluorescent substrates of microbial transglutaminase and its application to peptide tag-directed covalent protein labeling. Methods Mol Biol 2011; 751:81-94. [PMID: 21674327 DOI: 10.1007/978-1-61779-151-2_7] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
Transglutaminase (TGase) is an enzyme that catalyzes the post-translational covalent cross-linking of Gln- and Lys-containing peptides and/or proteins according to its substrate specificity. We have recently designed a variety of Gln-donor fluorescent substrates of microbial transglutaminase (MTG) from Streptomyces mobaraensis and evaluated their potential use in MTG-mediated covalent protein labeling. The newly designed substrates are based on the relatively broad substrate recognition of MTG for the substitution of the N-terminal group of a conventional TGase substrate, benzyloxycarbonyl-L-glutaminylglycine (Z-QG). It is revealed that MTG is capable of accepting a diverse range of fluorophores in place of the N-terminal moiety of Z-QG when linked via a suitable linker. Here, we show the potential utility of a new fluorescent substrate for peptide tag-directed covalent protein labeling by employing fluorescein-4-isothiocyanate-β-Ala-QG as a model Gln-donor substrate for MTG.
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Affiliation(s)
- Noriho Kamiya
- Department of Applied Chemistry, Graduate School of Engineering, Kyushu University, Fukuoka, Japan.
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24
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Abstract
Most of the bacterial cytochrome P450 s require two kinds of electron transfer proteins, ferredoxin and ferredoxin reductase, and thus P450 s do not show catalytic activity by themselves. A microbial transglutaminase-mediated site-specific cross-linking enables the formation of fusion P450 protein with a branched structure, which is generated from a genetic fusion protein of P450-ferredoxin reductase and ferredoxin, an interactive nanoscale protein structure. This fusion P450 system is self-sufficient due to intramolecular electron transfer, which means the system does not require additional electron-transferring proteins. Because some components of bacterial cytochrome P450 system are interchangeable, this self-sufficient system can be applied to non-natural combination of P450 and electron transfer proteins from different species of bacteria.
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Affiliation(s)
- Hidehiko Hirakawa
- Department of Bioengineering, Graduate School of Engineering, Center for NanoBio Integration, The University of Tokyo, Tokyo 113-8656, Japan
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25
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Minamihata K, Goto M, Kamiya N. Site-Specific Protein Cross-Linking by Peroxidase-Catalyzed Activation of a Tyrosine-Containing Peptide Tag. Bioconjug Chem 2010; 22:74-81. [DOI: 10.1021/bc1003982] [Citation(s) in RCA: 57] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Kosuke Minamihata
- Department of Applied Chemistry, Graduate School of Engineering, and Center for Future Chemistry, Kyushu University
| | - Masahiro Goto
- Department of Applied Chemistry, Graduate School of Engineering, and Center for Future Chemistry, Kyushu University
| | - Noriho Kamiya
- Department of Applied Chemistry, Graduate School of Engineering, and Center for Future Chemistry, Kyushu University
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26
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Liu Y, Kim E, Ghodssi R, Rubloff GW, Culver JN, Bentley WE, Payne GF. Biofabrication to build the biology–device interface. Biofabrication 2010; 2:022002. [DOI: 10.1088/1758-5082/2/2/022002] [Citation(s) in RCA: 78] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
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27
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Büttner K, Marx C, Hertel T, Pietzsch M. Optimierung einer rekombinanten mikrobiellen Transglutaminase. CHEM-ING-TECH 2010. [DOI: 10.1002/cite.200900104] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
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28
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Tsukiji S, Nagamune T. Sortase-mediated ligation: a gift from Gram-positive bacteria to protein engineering. Chembiochem 2009; 10:787-98. [PMID: 19199328 DOI: 10.1002/cbic.200800724] [Citation(s) in RCA: 163] [Impact Index Per Article: 10.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/30/2023]
Affiliation(s)
- Shinya Tsukiji
- Department of Chemistry and Biotechnology, School of Engineering, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-8656, Japan
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29
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Plagmann I, Chalaris A, Kruglov AA, Nedospasov S, Rosenstiel P, Rose-John S, Scheller J. Transglutaminase-catalyzed covalent multimerization of Camelidae anti-human TNF single domain antibodies improves neutralizing activity. J Biotechnol 2009; 142:170-8. [PMID: 19439388 DOI: 10.1016/j.jbiotec.2009.04.002] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2009] [Revised: 03/23/2009] [Accepted: 04/03/2009] [Indexed: 11/29/2022]
Abstract
Tumor necrosis factor (TNF) plays an important role in chronic inflammatory disorders, such as Rheumatoid Arthritis and Crohn's disease. Recently, monoclonal Camelidae variable heavy-chain domain-only antibodies (V(H)H) were developed to antagonize the action of human TNF (hTNF). Here, we show that hTNF-V(H)H does not interfere with hTNF trimerization, but competes with hTNF for hTNF-receptor binding. Moreover, we describe posttranslational dimerization and multimerization of hTNF-V(H)H molecules in vitro catalyzed by microbial transglutaminases (MTG). The ribonuclease S-tag-peptide was shown to act as a peptidyl substrate in covalent protein cross-linking reactions catalyzed by MTG from Streptomyces mobaraensis. The S-tag sequence was C-terminally fused to the hTNF-V(H)H and the fusion protein was expressed and purified from Escherichia coli culture supernatants. hTNF-V(H)H-S-tag fusion proteins were efficiently dimerized and multimerized by MTG whereas hTNF-V(H)H was not susceptible to protein cross-linking. Cell cytotoxicity assays, using hTNF as apoptosis inducing cytokine, revealed that dimerized and multimerized hTNF-V(H)H proteins were much more active than the monomeric hTNF-V(H)H. We hypothesize that improved inhibition by dimeric and multimeric single chain hTNF-V(H)H proteins is caused by avidity effects.
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Affiliation(s)
- Ingo Plagmann
- Department of Biochemistry, Christian-Albrechts-Universität zu Kiel, Olshausenstrasse 40, D-24098 Kiel, Germany
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30
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Yang X, Shi XW, Liu Y, Bentley WE, Payne GF. Orthogonal enzymatic reactions for the assembly of proteins at electrode addresses. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2009; 25:338-44. [PMID: 19115870 DOI: 10.1021/la802618q] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/05/2023]
Abstract
The ability to interface proteins to device surfaces is important for a range of applications. Here, we enlist the unique capabilities of enzymes and biologically derived polymers to assemble target proteins to electrode addresses. First, the stimuli-responsive aminopolysaccharide chitosan is directed to assemble at the electrode address in response to electrode-imposed signals. The electrodeposited chitosan film serves as the biodevice interface for subsequent protein assembly. Next, tyrosinase is used to catalyze grafting of a protein or peptide tether to the chitosan film. Finally, microbial transglutaminase (mTG) catalyzes the assembly of target proteins to the tether. mTG covalently links proteins through their glutamine (Gln) and lysine (Lys) residues. Since Gln and Lys residues of globular proteins are often inaccessible to mTG, we engineered our target proteins to have fusion tags with added Gln or Lys residues. This assembly method employs the electrical signal to confer spatial selectivity (during chitosan electrodeposition) and employs the enzymes to confer chemical selectivity (i.e., amino acid residue selectivity). Further, this method is mild, since no reactive reagents or protection steps are required, and all steps are performed in aqueous solution. These results demonstrate the potential for employing biological materials and mechanisms to biofabricate the biodevice interface.
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Affiliation(s)
- Xiaohua Yang
- Center for Biosystems Research, University of Maryland Biotechnology Institute, 5115 Plant Sciences Building, College Park, Maryland 20742, USA
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31
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Kamiya N, Abe H, Goto M, Tsuji Y, Jikuya H. Fluorescent substrates for covalent protein labeling catalyzed by microbial transglutaminase. Org Biomol Chem 2009; 7:3407-12. [DOI: 10.1039/b904046c] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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32
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Transglutaminases and their substrates in biology and human diseases: 50 years of growing. Amino Acids 2008; 36:599-614. [DOI: 10.1007/s00726-008-0124-8] [Citation(s) in RCA: 46] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2008] [Accepted: 05/15/2008] [Indexed: 12/19/2022]
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33
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Site-specific modification and PEGylation of pharmaceutical proteins mediated by transglutaminase. Adv Drug Deliv Rev 2008; 60:13-28. [PMID: 17916398 DOI: 10.1016/j.addr.2007.06.015] [Citation(s) in RCA: 205] [Impact Index Per Article: 12.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2007] [Accepted: 06/26/2007] [Indexed: 11/23/2022]
Abstract
Transglutaminase (TGase, E.C. 2.3.2.13) catalyzes acyl transfer reactions between the gamma-carboxamide groups of protein-bound glutamine (Gln) residues, which serve as acyl donors, and primary amines, resulting in the formation of new gamma-amides of glutamic acid and ammonia. By using an amino-derivative of poly(ethylene glycol) (PEG-NH(2)) as substrate for the enzymatic reaction with TGase it is possible to covalently bind the PEG polymer to proteins of pharmaceutical interest. In our laboratory, we have conducted experiments aimed to modify proteins of known structure using TGase and, surprisingly, we were able to obtain site-specific modification or PEGylation of protein-bound Gln residue(s) in the protein substrates. For example, in apomyoglobin (apoMb, myoglobin devoid of heme) only Gln91 was modified and in human growth hormone only Gln40 and Gln141, despite these proteins having many more Gln residues. Moreover, we noticed that these proteins suffered highly selective limited proteolysis phenomena at the same chain regions being attacked by TGase. We have analysed also the results of other published experiments of TGase-mediated modification or PEGylation of several proteins in terms of protein structure and dynamics, among them alpha-lactalbumin and interleukin-2, as well as disordered proteins. A noteworthy correlation was observed between chain regions of high temperature factor (B-factor) determined crystallographically and sites of TGase attack and limited proteolysis, thus emphasizing the role of chain mobility or local unfolding in dictating site-specific enzymatic modification. We propose that enhanced chain flexibility favors limited enzymatic reactions on polypeptide substrates by TGases and proteases, as well as by other enzymes involved in a number of site-specific post-translational modifications of proteins, such as phosphorylation and glycosylation. Therefore, it is possible to predict the site(s) of TGase-mediated modification and PEGylation of a therapeutic protein on the basis of its structure and dynamics and, consequently, the likely effects of modifications on the functional properties of the protein.
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Kamiya N, Doi S, Tanaka Y, Ichinose H, Goto M. Functional immobilization of recombinant alkaline phosphatases bearing a glutamyl donor substrate peptide of microbial transglutaminase. J Biosci Bioeng 2007; 104:195-9. [DOI: 10.1263/jbb.104.195] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2007] [Accepted: 06/18/2007] [Indexed: 11/17/2022]
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35
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Yi H, Wu LQ, Bentley WE, Ghodssi R, Rubloff GW, Culver JN, Payne GF. Biofabrication with Chitosan. Biomacromolecules 2005; 6:2881-94. [PMID: 16283704 DOI: 10.1021/bm050410l] [Citation(s) in RCA: 438] [Impact Index Per Article: 23.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
The traditional motivation for integrating biological components into microfabricated devices has been to create biosensors that meld the molecular recognition capabilities of biology with the signal processing capabilities of electronic devices. However, a different motivation is emerging; biological components are being explored to radically change how fabrication is achieved at the micro- and nanoscales. Here we review biofabrication, the use of biological materials for fabrication, and focus on three specific biofabrication approaches: directed assembly, where localized external stimuli are employed to guide assembly; enzymatic assembly, where selective biocatalysts are enlisted to build macromolecular structure; and self-assembly, where information internal to the biological material guides its own assembly. Also reviewed are recent results with the aminopolysaccharide chitosan, a material that offers a combination of properties uniquely suited for biofabrication. In particular, chitosan can be directed to assemble in response to locally applied electrical signals, and the chitosan backbone provides sites that can be employed for the assembly of proteins, nucleic acids, and virus particles.
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Affiliation(s)
- Hyunmin Yi
- Center for Biosystems Research, University of Maryland Biotechnology Institute, 5115 Plant Sciences Building, College Park, Maryland 20742, USA
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36
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Tominaga J, Kamiya N, Doi S, Ichinose H, Maruyama T, Goto M. Design of a Specific Peptide Tag that Affords Covalent and Site-Specific Enzyme Immobilization Catalyzed by Microbial Transglutaminase. Biomacromolecules 2005; 6:2299-304. [PMID: 16004475 DOI: 10.1021/bm050193o] [Citation(s) in RCA: 42] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Transglutaminase-mediated site-specific and covalent immobilization of an enzyme to chemically modified agarose was explored. Using Escherichia coli alkaline phosphatase (AP) as a model, two designed specific peptide tags containing a reactive lysine (Lys) residue with different length Gly-Ser linkers for microbial transglutaminase (MTG) were genetically attached to N- or C-termini. For solid support, agarose gel beads were chemically modified with beta-casein to display reactive glutamine (Gln) residues on the support surface. Recombinant APs were enzymatically and covalently immobilized to casein-grafted agarose beads. Immobilization by MTG markedly depended on either the position or the length of the peptide tags incorporated to AP, suggesting steric constraint upon enzymatic immobilization. Enzymatically immobilized AP showed comparable catalytic turnover (k(cat)) to the soluble counterpart and comparable operational stability with chemically immobilized AP. These results indicate that attachment of a suitable specific peptide tag to the right position of a target protein is crucial for MTG-mediated formulation of highly active immobilized proteins.
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Affiliation(s)
- Jo Tominaga
- Department of Applied Chemistry, Graduate School of Engineering, Kyushu University, 6-10-1 Hakozaki, Fukuoka 812-8581, Japan
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Tanaka T, Kamiya N, Nagamune T. N-terminal glycine-specific protein conjugation catalyzed by microbial transglutaminase. FEBS Lett 2005; 579:2092-6. [PMID: 15811324 DOI: 10.1016/j.febslet.2005.02.064] [Citation(s) in RCA: 62] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2004] [Revised: 02/16/2005] [Accepted: 02/25/2005] [Indexed: 11/30/2022]
Abstract
Here, we report the N-terminal glycine (Gly) residue of a target protein can be a candidate primary amine for site-specific protein conjugation catalyzed by microbial transglutaminase (MTG) from Streptomyces mobaraensis. Gly5-enhanced green fluorescent protein (EGFP) (EGFP with five additional Gly residues at its N-terminus) was cross-linked with Myc-dihydrofolate reductase (DHFR) (DHFR with the myc epitope sequence at its N-terminus) to yield DHFR-EGFP heterodimers. The reactivities of additional peptidyl linkers were investigated and the results obtained suggested that at least three additional Gly residues at the N-terminus were required to yield the EGFP-DHFR heterodimeric form. Site-directed mutagenesis analysis revealed marked preference of MTG for amino acids adjacent to the N-terminal Gly residue involved in the protein conjugation. In addition, peptide-protein conjugation was demonstrated by MTG-catalyzed N-terminal Gly-specific modification of a target protein with the myc epitope peptide.
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Affiliation(s)
- Tsutomu Tanaka
- Department of Chemistry and Biotechnology, School of Engineering, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-8656, Japan
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Kamiya N, Doi S, Tominaga J, Ichinose H, Goto M. Transglutaminase-Mediated Protein Immobilization to Casein Nanolayers Created on a Plastic Surface. Biomacromolecules 2004; 6:35-8. [PMID: 15638501 DOI: 10.1021/bm0494895] [Citation(s) in RCA: 33] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
An enzymatic method for covalent and site-specific immobilization of recombinant proteins on a plastic surface was explored. Using Escherichia coli alkaline phosphatase (AP) with a specific peptide tag (MKHKGS) genetically incorporated at the N-terminus as a model (NK-AP), microbial transglutaminase (MTG)-mediated protein immobilization was demonstrated. To generate a reactive surface for MTG, a 96-well polystyrene microtiter plate was physically coated with casein, a good MTG substrate. Successful immobilization of recombinant AP to the nanolayer of casein on the surface of the microtiter plate was verified by the detection of enzymatic activity. Since little activity was observed when wild-type AP was used, immobilization of NK-AP was likely directed by the specific peptide tag. When polymeric casein prepared by MTG was used as a matrix on the plate, the loading capacity of AP was increased about 2-fold compared to when casein was used as the matrix. Transglutaminase-mediated site-specific posttranslational modification of proteins offers one way of generating a variety of protein-based solid formulations for biotechnological applications.
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Affiliation(s)
- Noriho Kamiya
- Department of Applied Chemistry, Graduate School of Engineering, Kyushu University, 6-10-1 Hakozaki, Fukuoka, Japan.
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39
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Takazawa T, Kamiya N, Ueda H, Nagamune T. Enzymatic labeling of a single chain variable fragment of an antibody with alkaline phosphatase by microbial transglutaminase. Biotechnol Bioeng 2004; 86:399-404. [PMID: 15112292 DOI: 10.1002/bit.20019] [Citation(s) in RCA: 41] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Abstract
Functional cross-linking of a single chain Fv fragment of anti-hen egg-white lysozyme antibody (scFv) and alkaline phosphatase (AP) was explored using microbial transglutaminase (MTG) from Streptomyces mobaraensis. A specific peptidyl linker for MTG was genetically fused to the N-terminus of each protein and the resultant proteins were obtained separately by bacterial expression. The recombinant peptide-tagged scFv and AP were site-specifically cross-linked by MTG through the extra peptidyl linkers in vitro, which mainly yielded the heterodimer (i.e., scFv-AP conjugate). The enzymatic cross-linking reaction had little influence on either the antigen-binding ability of the scFv moiety or the enzymatic activity of the AP moiety of the conjugate, allowing use within an enzyme-linked immunosorbent assay. The results obtained suggest that the enzymatic approach with MTG facilitates the posttranslational construction of functional fusion proteins.
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Affiliation(s)
- Takeshi Takazawa
- Department of Chemistry and Biotechnology, School of Engineering, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-8656, Japan
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An enzymatic strategy for site-specific immobilization of functional proteins using microbial transglutaminase. Enzyme Microb Technol 2004. [DOI: 10.1016/j.enzmictec.2004.08.014] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
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41
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