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Tamaru Y, Nakanishi S, Tanaka K, Umetsu M, Nakazawa H, Sugiyama A, Ito T, Shimokawa N, Takagi M. Recent research advances on non-linear phenomena in various biosystems. J Biosci Bioeng 2023:S1389-1723(23)00107-X. [PMID: 37246137 DOI: 10.1016/j.jbiosc.2023.03.012] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2022] [Revised: 03/03/2023] [Accepted: 03/22/2023] [Indexed: 05/30/2023]
Abstract
All biological phenomena can be classified as open, dissipative and non-linear. Moreover, the most typical phenomena are associated with non-linearity, dissipation and openness in biological systems. In this review article, four research topics on non-linear biosystems are described to show the examples from various biological systems. First, membrane dynamics of a lipid bilayer for the cell membrane is described. Since the cell membrane separates the inside of the cell from the outside, self-organizing systems that form spatial patterns on membranes often depend on non-linear dynamics. Second, various data banks based on recent genomics analysis supply the data including vast functional proteins from many organisms and their variable species. Since the proteins existing in nature are only a very small part of the space represented by amino acid sequence, success of mutagenesis-based molecular evolution approach crucially depends on preparing a library with high enrichment of functional proteins. Third, photosynthetic organisms depend on ambient light, the regular and irregular changes of which have a significant impact on photosynthetic processes. The light-driven process proceeds through many redox couples in the cyanobacteria constituting chain of redox reactions. Forth topics focuses on a vertebrate model, the zebrafish, which can help to understand, predict and control the chaos of complex biological systems. In particular, during early developmental stages, developmental differentiation occurs dynamically from a fertilized egg to divided and mature cells. These exciting fields of complexity, chaos, and non-linear science have experienced impressive growth in recent decades. Finally, future directions for non-liner biosystems are presented.
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Affiliation(s)
- Yutaka Tamaru
- Department of Life Sciences, Graduate School of Bioresources, Mie University, 1577 Kurimamachiya, Tsu, Mie 514-8507, Japan.
| | - Shuji Nakanishi
- Research Center for Solar Energy Chemistry, Graduate School of Engineering Science, Osaka University, 1-3 Machikaneyama, Toyonaka, Osaka 560-8531, Japan
| | - Kenya Tanaka
- Research Center for Solar Energy Chemistry, Graduate School of Engineering Science, Osaka University, 1-3 Machikaneyama, Toyonaka, Osaka 560-8531, Japan
| | - Mitsuo Umetsu
- Department of Biomolecular Engineering, Graduate School of Engineering, Tohoku University, 6-6-11 Aramakiazaaoba, Aoba, Sendai, Miyagi 980-8579, Japan
| | - Hikaru Nakazawa
- Department of Biomolecular Engineering, Graduate School of Engineering, Tohoku University, 6-6-11 Aramakiazaaoba, Aoba, Sendai, Miyagi 980-8579, Japan
| | - Aruto Sugiyama
- Department of Biomolecular Engineering, Graduate School of Engineering, Tohoku University, 6-6-11 Aramakiazaaoba, Aoba, Sendai, Miyagi 980-8579, Japan
| | - Tomoyuki Ito
- Department of Biomolecular Engineering, Graduate School of Engineering, Tohoku University, 6-6-11 Aramakiazaaoba, Aoba, Sendai, Miyagi 980-8579, Japan
| | - Naofumi Shimokawa
- School of Materials Science, Japan Advanced Institute of Science and Technology, 1-1 Asahidai, Nomi, Ishikawa 923-1292, Japan
| | - Masahiro Takagi
- School of Materials Science, Japan Advanced Institute of Science and Technology, 1-1 Asahidai, Nomi, Ishikawa 923-1292, Japan
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Ando Y, Nakazawa H, Miura D, Otake M, Umetsu M. Enzymatic ligation of an antibody and arginine 9 peptide for efficient and cell-specific siRNA delivery. Sci Rep 2021; 11:21882. [PMID: 34750461 PMCID: PMC8575896 DOI: 10.1038/s41598-021-01331-1] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2021] [Accepted: 10/18/2021] [Indexed: 01/03/2023] Open
Abstract
A fusion protein comprising an antibody and a cationic peptide, such as arginine-9 (R9), is a candidate molecule for efficient and cell-specific delivery of siRNA into cells in order to reduce the side effects of nucleic acid drugs. However, their expression in bacterial hosts, required for their development, often fails, impeding research progress. In this study, we separately prepared anti-EGFR nanobodies with the K-tag sequence MRHKGS at the C-terminus and R9 with the Q-tag sequence LLQG at the N-terminus, and enzymatically ligated them in vitro by microbial transglutaminase to generate Nanobody-R9, which is not expressed as a fused protein in E. coli. Nanobody-R9 was synthesized at a maximum binding efficiency of 85.1%, without changing the binding affinity of the nanobody for the antigen. Nanobody-R9 successfully delivered siRNA into the cells, and the cellular influx of siRNA increased with increase in the ratio of Nanobody-R9 to siRNA. We further demonstrated that the Nanobody-R9-siRNA complex, at a 30:1 ratio, induced an approximately 58.6% reduction in the amount of target protein due to RNAi in mRNA compared to lipofectamine.
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Affiliation(s)
- Yu Ando
- Department of Biomolecular Engineering, Graduate School of Engineering, Tohoku University, Aoba 6-6-1, Aramaki, Aoba-ku, Sendai, 980-8579, Japan
| | - Hikaru Nakazawa
- Department of Biomolecular Engineering, Graduate School of Engineering, Tohoku University, Aoba 6-6-1, Aramaki, Aoba-ku, Sendai, 980-8579, Japan.
| | - Daisuke Miura
- Department of Biomolecular Engineering, Graduate School of Engineering, Tohoku University, Aoba 6-6-1, Aramaki, Aoba-ku, Sendai, 980-8579, Japan
| | - Maho Otake
- Department of Biomolecular Engineering, Graduate School of Engineering, Tohoku University, Aoba 6-6-1, Aramaki, Aoba-ku, Sendai, 980-8579, Japan
| | - Mitsuo Umetsu
- Department of Biomolecular Engineering, Graduate School of Engineering, Tohoku University, Aoba 6-6-1, Aramaki, Aoba-ku, Sendai, 980-8579, Japan.
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Torres Castillo NE, Melchor-Martínez EM, Ochoa Sierra JS, Ramírez-Torres NM, Sosa-Hernández JE, Iqbal HMN, Parra-Saldívar R. Enzyme mimics in-focus: Redefining the catalytic attributes of artificial enzymes for renewable energy production. Int J Biol Macromol 2021; 179:80-89. [PMID: 33667559 DOI: 10.1016/j.ijbiomac.2021.03.002] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2021] [Revised: 02/19/2021] [Accepted: 03/01/2021] [Indexed: 02/08/2023]
Abstract
Herein, the advantages of enzyme mimetics by redefining the catalytic attributes and implementing artificial enzymes (AEs) for energy-related applications have presented. The intrinsic enzyme-like catalytic characteristics of nanozymes have become a growing area of prime interest in bio-catalysis. The development of AEs has redefined the concept of catalytic activity, opening a wide range of possibilities in biotechnological and energy sectors. Nowadays, power-energy is one of the most valuable resources that enable the development and progress of humanity. Over the last 50 years, fossil fuels' burning has released greenhouse gases and negatively impacted the environment and health. In 2019, around 84% of global primary energy came from coal, oil, and gas. Therefore, a global energy transition to renewable and sustainable energy is urgently needed to generate clean energy as biofuels and biohydrogen. However, to achieve this, the implementation of natural enzymes brings more significant challenges because their practical application is limited by the low operational stability, harsh environmental conditions, and expensive preparation processes. Hence, to accelerate the transition, promising substitutes are AEs, well-defined structures made of organic or inorganic materials that can mimic the catalytic power of natural enzymes. Despite being still in the midst, enzyme mimics overcome the main obstacles for a conventional enzyme. It opens future opportunities to optimize the production of renewable energies with excellent performance, high efficiency, and increasingly competitive prices. Thus, this work is a comprehensive study covering the promising potential of AEs, as biocatalysts, specifically for renewable energy production.
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Affiliation(s)
| | | | | | | | | | - Hafiz M N Iqbal
- Tecnologico de Monterrey, School of Engineering and Sciences, Monterrey 64849, Mexico.
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Singh N, Mathur AS, Gupta RP, Barrow CJ, Tuli DK, Puri M. Enzyme systems of thermophilic anaerobic bacteria for lignocellulosic biomass conversion. Int J Biol Macromol 2020; 168:572-590. [PMID: 33309672 DOI: 10.1016/j.ijbiomac.2020.12.004] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2020] [Revised: 11/30/2020] [Accepted: 12/01/2020] [Indexed: 11/17/2022]
Abstract
Economic production of lignocellulose degrading enzymes for biofuel industries is of considerable interest to the biotechnology community. While these enzymes are widely distributed in fungi, their industrial production from other sources, particularly by thermophilic anaerobic bacteria (growth Topt ≥ 60 °C), is an emerging field. Thermophilic anaerobic bacteria produce a large number of lignocellulolytic enzymes having unique structural features and employ different schemes for biomass degradation, which can be classified into four systems namely; 'free enzyme system', 'cell anchored enzymes', 'complex cellulosome system', and 'multifunctional multimodular enzyme system'. Such enzymes exhibit high specific activity and have a natural ability to withstand harsh bioprocessing conditions. However, achieving a higher production of these thermostable enzymes at current bioprocessing targets is challenging. In this review, the research opportunities for these distinct enzyme systems in the biofuel industry and the associated technological challenges are discussed. The current status of research findings is highlighted along with a detailed description of the categorization of the different enzyme production schemes. It is anticipated that high temperature-based bioprocessing will become an integral part of sustainable bioenergy production in the near future.
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Affiliation(s)
- Nisha Singh
- Centre for Chemistry and Biotechnology, Deakin University, Waurn Ponds, Victoria 3217, Australia; DBT-IOC Centre for Advance Bioenergy Research, Research & Development Centre, Indian Oil Corporation Limited, Sector-13, Faridabad 121007, India
| | - Anshu S Mathur
- DBT-IOC Centre for Advance Bioenergy Research, Research & Development Centre, Indian Oil Corporation Limited, Sector-13, Faridabad 121007, India
| | - Ravi P Gupta
- DBT-IOC Centre for Advance Bioenergy Research, Research & Development Centre, Indian Oil Corporation Limited, Sector-13, Faridabad 121007, India
| | - Colin J Barrow
- Centre for Chemistry and Biotechnology, Deakin University, Waurn Ponds, Victoria 3217, Australia
| | - Deepak K Tuli
- DBT-IOC Centre for Advance Bioenergy Research, Research & Development Centre, Indian Oil Corporation Limited, Sector-13, Faridabad 121007, India
| | - Munish Puri
- Centre for Chemistry and Biotechnology, Deakin University, Waurn Ponds, Victoria 3217, Australia; Medical Biotechnology, Centre for Marine Bioproducts Development, College of Medicine and Public Health, Flinders University, Bedford Park, Adelaide 5042, Australia.
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Ichikawa S, Ogawa S, Nishida A, Kobayashi Y, Kurosawa T, Karita S. Cellulosomes localise on the surface of membrane vesicles from the cellulolytic bacterium Clostridium thermocellum. FEMS Microbiol Lett 2019; 366:5526221. [DOI: 10.1093/femsle/fnz145] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2019] [Accepted: 06/27/2019] [Indexed: 12/21/2022] Open
Abstract
ABSTRACTMembrane vesicles released from bacteria contribute to cell–cell communication by carrying various cargos such as proteins, nucleic acids and signaling molecules. Cellulolytic bacteria have been isolated from many environments, yet the function of membrane vesicles for cellulolytic ability has been rarely described. Here, we show that a Gram-positive cellulolytic bacterium Clostridium thermocellum released membrane vesicles, each approximately 50–300 nm in diameter, into the broth. The observations with immunoelectron microscopy also revealed that cellulosomes, which are carbohydrate-active enzyme complexes that give C. thermocellum high cellulolytic activity, localized on the surface of the membrane vesicles. The membrane vesicles collected by ultracentrifugation maintained the cellulolytic activity. Supplementation with the biosurfactant surfactin or sonication treatment disrupted the membrane vesicles in the exoproteome of C. thermocellum and significantly decreased the degradation activity of the exoproteome for microcrystalline cellulose. However, these did not affect the degradation activity for soluble carboxymethyl cellulose. These results suggest a novel function of membrane vesicles: C. thermocellum releases cellulolytic enzymes on the surface of membrane vesicles to enhance the cellulolytic activity of C. thermocellum for crystalline cellulose.
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Affiliation(s)
- Shunsuke Ichikawa
- Graduate School of Education, Mie University, 1577 Kurimamachiya-cho Tsu, Mie 514-8507, Japan
| | - Satoru Ogawa
- Faculty of Medicine, Mie University, 1577 Kurimamachiya-cho Tsu, Mie 514-8507, Japan
| | - Ayami Nishida
- Graduate School of Education, Mie University, 1577 Kurimamachiya-cho Tsu, Mie 514-8507, Japan
| | - Yuzuki Kobayashi
- Faculty of Education, Mie University, 1577 Kurimamachiya-cho Tsu, Mie 514-8507, Japan
| | - Toshihito Kurosawa
- Advanced Science Research Promotion Center, Mie University, 1577 Kurimamachiya-cho Tsu, Mie 514-8507, Japan
| | - Shuichi Karita
- Graduate School of Bioresources, Mie University, 1577 Kurimamachiya-cho Tsu, Mie 514-8507, Japan
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Changing surface grafting density has an effect on the activity of immobilized xylanase towards natural polysaccharides. Sci Rep 2019; 9:5763. [PMID: 30962508 PMCID: PMC6453946 DOI: 10.1038/s41598-019-42206-w] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2018] [Accepted: 03/25/2019] [Indexed: 12/22/2022] Open
Abstract
Enzymes are involved in various types of biological processes. In many cases, they are part of multi-component machineries where enzymes are localized in close proximity to each-other. In such situations, it is still not clear whether inter-enzyme spacing actually plays a role or if the colocalization of complementary activities is sufficient to explain the efficiency of the system. Here, we focus on the effect of spatial proximity when identical enzymes are immobilized onto a surface. By using an innovative grafting procedure based on the use of two engineered protein fragments, Jo and In, we produce model systems in which enzymes are immobilized at surface densities that can be controlled precisely. The enzyme used is a xylanase that participates to the hydrolysis of plant cell wall polymers. By using a small chromogenic substrate, we first show that the intrinsic activity of the enzymes is fully preserved upon immobilization and does not depend on surface density. However, when using beechwood xylan, a naturally occurring polysaccharide, as substrate, we find that the enzymatic efficiency decreases by 10–60% with the density of grafting. This unexpected result is probably explained through steric hindrance effects at the nanoscale that hinder proper interaction between the enzymes and the polymer. A second effect of enzyme immobilization at high densities is the clear tendency for the system to release preferentially shorter oligosaccharides from beechwood xylan as compared to enzymes in solution.
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Tan L, Tan Z, Feng H, Qiu J. Cellulose as a template to fabricate a cellulase-immobilized composite with high bioactivity and reusability. NEW J CHEM 2018. [DOI: 10.1039/c7nj03271d] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Herein, a new strategy was developed to fabricate an oriented cellulase/chitosan/Fe3O4composite, which possesses extremely high activity, reusability, and stability.
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Affiliation(s)
- Lin Tan
- State Key Laboratory of Advanced Processing and Recycling of Nonferrous Metals
- Lanzhou University of Technology
- Lanzhou 730050
- P. R. China
- College of Petrochemical Technology
| | - Zhaojun Tan
- College of Petrochemical Technology
- Lanzhou University of Technology
- Lanzhou
- P. R. China
| | - Huixia Feng
- State Key Laboratory of Advanced Processing and Recycling of Nonferrous Metals
- Lanzhou University of Technology
- Lanzhou 730050
- P. R. China
- College of Petrochemical Technology
| | - Jianhui Qiu
- Department of Machine Intelligence and Systems Engineering
- Faculty of System Science and Technology
- Akita Prefectural University
- Yurihonjo
- Akita 015-0055
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Vranish JN, Ancona MG, Oh E, Susumu K, Medintz IL. Enhancing coupled enzymatic activity by conjugating one enzyme to a nanoparticle. NANOSCALE 2017; 9:5172-5187. [PMID: 28393943 DOI: 10.1039/c7nr00200a] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/04/2023]
Abstract
Enzymes have long been a prime research target for the commercial production of commodity and specialty chemicals, design of sensing devices, and the development of therapeutics and new chemical processes. Industrial applications for enzymes can potentially be enhanced by enzyme immobilization which often allows for increased enzyme stability, facile product purification, and minimized substrate diffusion times in multienzymatic cascades, but this is usually at the cost of a significant decrease in catalytic rates. Recently, enzyme immobilization has been advanced by the discovery that nanoparticle surfaces are frequently able to enhance the activity of the bound enzyme. Here we extend this observation to a multienzymatic coupled system using semiconductor quantum dots (QDs) as a model nanoparticle material and the prototypical enzyme pair of glucose oxidase (GOX) and horseradish peroxidase (HRP). We first demonstrate that HRP binding to QDs has a significant beneficial effect on enzymatic activity, producing a >2-fold improvement in kcat. We argue that this enhancement is due to affinity of the QD surface for the substrate. Furthermore, we demonstrate that when the ratio of GOX to HRP is adjusted to allow HRP to be the rate-limiting step of the pathway, the QD-induced rate enhancement of HRP can be maintained in a multi-enzyme cascade. Kinetic analysis shows that the underlying processes can be simulated numerically and provide insight into the governing mechanisms. The potential of nanoparticle-based catalytic enhancement is then discussed in the context of multienzyme cascades and synthetic biology.
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Takahara M, Budinova GALG, Nakazawa H, Mori Y, Umetsu M, Kamiya N. Salt-Switchable Artificial Cellulase Regulated by a DNA Aptamer. Biomacromolecules 2016; 17:3356-3362. [PMID: 27602779 DOI: 10.1021/acs.biomac.6b01141] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
A novel artificial cellulase was developed by conjugating a DNA aptamer to an endoglucanase catalytic domain, thereby substituting the natural carbohydrate-binding module. Circular dichroism spectroscopy and adsorption isotherm showed the binding motif of cellulose-binding DNA aptamer (CelApt) was G-quadruplex and stem-loop structures stabilized in the presence of salts, and CelApt binding preferred the amorphous region of the solid cellulose. By introducing the revealed salt-switchable cellulose-binding nature of CelApt into a catalytic domain of a cellulase, we created CelApt-catalytic domain conjugate possessing both controllable adsorption on the solid substrates and equal enzymatic activity to the wild-type cellulase. Thus potential use of a responsive DNA aptamer for biocatalysis at a solid surface was demonstrated.
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Affiliation(s)
- Mari Takahara
- Department of Applied Chemistry, Graduate School of Engineering, Kyushu University , 744 Motooka, Fukuoka 819-0395, Japan
| | | | - Hikaru Nakazawa
- Department of Biomolecular Engineering, Graduate School of Engineering, Tohoku University , 6-6-116 Aoba, Aramaki, Aoba-ku, Sendai 980-8579, Japan
| | - Yutaro Mori
- Biomass Engineering Program, RIKEN , 1-7-22, Suehiro-cho, Tsurumi-ku, Yokohama, Kanagawa 230-0045, Japan
| | - Mitsuo Umetsu
- Department of Biomolecular Engineering, Graduate School of Engineering, Tohoku University , 6-6-116 Aoba, Aramaki, Aoba-ku, Sendai 980-8579, 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 , 744 Motooka, Fukuoka 819-0395, Japan
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Kognole AA, Payne CM. Cello-oligomer-binding dynamics and directionality in family 4 carbohydrate-binding modules. Glycobiology 2015; 25:1100-11. [DOI: 10.1093/glycob/cwv048] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2015] [Accepted: 07/04/2015] [Indexed: 12/11/2022] Open
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C-Terminal-oriented Immobilization of Enzymes Using Sortase A-mediated Technique. Macromol Biosci 2015; 15:1375-80. [DOI: 10.1002/mabi.201500113] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2015] [Revised: 05/29/2015] [Indexed: 11/07/2022]
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