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Guessous G, Blake L, Bui A, Woo Y, Manzanarez G. Disentangling the Web: An Interdisciplinary Review on the Potential and Feasibility of Spider Silk Bioproduction. ACS Biomater Sci Eng 2024; 10:5412-5438. [PMID: 39136701 DOI: 10.1021/acsbiomaterials.4c00145] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 09/10/2024]
Abstract
The remarkable material properties of spider silk, such as its high toughness and tensile strength combined with its low density, make it a highly sought-after material with myriad applications. In addition, the biological nature of spider silk makes it a promising, potentially sustainable alternative to many toxic or petrochemical-derived materials. Therefore, interest in the heterologous production of spider silk proteins has greatly increased over the past few decades, making recombinant spider silk an important frontier in biomanufacturing. This has resulted in a diversity of potential host organisms, a large space for sequence design, and a variety of downstream processing techniques and product applications for spider silk production. Here, we highlight advances in each of these technical aspects as well as white spaces therein, still ripe for further investigation and discovery. Additionally, industry landscaping, patent analyses, and interviews with Key Opinion Leaders help define both the research and industry landscapes. In particular, we found that though textiles dominated the early products proposed by companies, the versatile nature of spider silk has opened up possibilities in other industries, such as high-performance materials in automotive applications or biomedical therapies. While continuing enthusiasm has imbued scientists and investors alike, many technical and business considerations still remain unsolved before spider silk can be democratized as a high-performance product. We provide insights and strategies for overcoming these initial hurdles, and we highlight the importance of collaboration between academia, industry, and policy makers. Linking technical considerations to business and market entry strategies highlights the importance of a holistic approach for the effective scale-up and commercial viability of spider silk bioproduction.
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Affiliation(s)
- Ghita Guessous
- Department of Physics, University of California at San Diego, La Jolla, California 92092, United States
- Research Initiative, Nucleate, 88 Gordon Street #401, Brighton, Massachusetts 02135, United States
| | - Lauren Blake
- Research Initiative, Nucleate, 88 Gordon Street #401, Brighton, Massachusetts 02135, United States
- Department of Biomedical Engineering, Tufts University, Medford, Massachusetts 02155, United States
- Tufts University Center for Cellular Agriculture (TUCCA), Tufts University, Medford, Massachusetts 02155, United States
| | - Anthony Bui
- Research Initiative, Nucleate, 88 Gordon Street #401, Brighton, Massachusetts 02135, United States
- Department of Molecular Medicine, Cornell University, Ithaca, New York 14850, United States
| | - Yelim Woo
- Research Initiative, Nucleate, 88 Gordon Street #401, Brighton, Massachusetts 02135, United States
- Questrom School of Business, Boston University, Boston, Massachusetts 02215, United States
| | - Gabriel Manzanarez
- Research Initiative, Nucleate, 88 Gordon Street #401, Brighton, Massachusetts 02135, United States
- Division of Biological Sciences, University of California at San Diego, La Jolla, California 92092, United States
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2
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Sonavane S, Hassan S, Chatterjee U, Soler L, Holm L, Mollbrink A, Greco G, Fereydouni N, Vinnere Pettersson O, Bunikis I, Churcher A, Lantz H, Johansson J, Reimegård J, Rising A. Origin, structure, and composition of the spider major ampullate silk fiber revealed by genomics, proteomics, and single-cell and spatial transcriptomics. SCIENCE ADVANCES 2024; 10:eadn0597. [PMID: 39141739 PMCID: PMC11323941 DOI: 10.1126/sciadv.adn0597] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/27/2023] [Accepted: 07/15/2024] [Indexed: 08/16/2024]
Abstract
Spiders produce nature's toughest fiber using renewable components at ambient temperatures and with water as solvent, making it highly interesting to replicate for the materials industry. Despite this, much remains to be understood about the bioprocessing and composition of spider silk fibers. Here, we identify 18 proteins that make up the spiders' strongest silk type, the major ampullate fiber. Single-cell RNA sequencing and spatial transcriptomics revealed that the secretory epithelium of the gland harbors six cell types. These cell types are confined to three distinct glandular zones that produce specific combinations of silk proteins. Image analysis of histological sections showed that the secretions from the three zones do not mix, and proteomics analysis revealed that these secretions form layers in the final fiber. Using a multi-omics approach, we provide substantial advancements in the understanding of the structure and function of the major ampullate silk gland as well as of the architecture and composition of the fiber it produces.
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Affiliation(s)
- Sumalata Sonavane
- Department of Animal Biosciences, Swedish University of Agricultural Sciences, Uppsala, Sweden
| | - Sameer Hassan
- Department of Biosciences and Nutrition, Karolinska Institutet, Neo, Huddinge, Sweden
| | - Urmimala Chatterjee
- Department of Biosciences and Nutrition, Karolinska Institutet, Neo, Huddinge, Sweden
| | - Lucile Soler
- National Bioinformatics Infrastructure Sweden (NBIS), Science for Life Laboratory (SciLifeLab), Uppsala University, Uppsala, Sweden
- Department of Medical Biochemistry and Microbiology, Uppsala University, Uppsala, Sweden
| | - Lena Holm
- Department of Animal Biosciences, Swedish University of Agricultural Sciences, Uppsala, Sweden
| | - Annelie Mollbrink
- Department of Gene Technology, KTH Royal Institute of Technology, SciLifeLab, Stockholm, Sweden
| | - Gabriele Greco
- Department of Animal Biosciences, Swedish University of Agricultural Sciences, Uppsala, Sweden
| | - Noah Fereydouni
- Department of Biosciences and Nutrition, Karolinska Institutet, Neo, Huddinge, Sweden
| | - Olga Vinnere Pettersson
- Department of Immunology, Genetics and Pathology, National Genomics Infrastructure, SciLifeLab, Uppsala, Sweden
| | - Ignas Bunikis
- Department of Immunology, Genetics and Pathology, National Genomics Infrastructure, SciLifeLab, Uppsala, Sweden
| | - Allison Churcher
- Department of Molecular Biology, NBIS, SciLifeLab, Umeå University, Umeå, Sweden
| | - Henrik Lantz
- National Bioinformatics Infrastructure Sweden (NBIS), Science for Life Laboratory (SciLifeLab), Uppsala University, Uppsala, Sweden
- Department of Medical Biochemistry and Microbiology, Uppsala University, Uppsala, Sweden
| | - Jan Johansson
- Department of Biosciences and Nutrition, Karolinska Institutet, Neo, Huddinge, Sweden
| | - Johan Reimegård
- National Bioinformatics Infrastructure Sweden (NBIS), Science for Life Laboratory (SciLifeLab), Uppsala University, Uppsala, Sweden
| | - Anna Rising
- Department of Animal Biosciences, Swedish University of Agricultural Sciences, Uppsala, Sweden
- Department of Biosciences and Nutrition, Karolinska Institutet, Neo, Huddinge, Sweden
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3
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Maraldo A, Rnjak-Kovacina J, Marquis C. Tyrosine - a structural glue for hierarchical protein assembly. Trends Biochem Sci 2024; 49:633-648. [PMID: 38653686 DOI: 10.1016/j.tibs.2024.03.014] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2023] [Revised: 03/21/2024] [Accepted: 03/21/2024] [Indexed: 04/25/2024]
Abstract
Protein self-assembly, guided by the interplay of sequence- and environment-dependent liquid-liquid phase separation (LLPS), constitutes a fundamental process in the assembly of numerous intrinsically disordered proteins. Heuristic examination of these proteins has underscored the role of tyrosine residues, evident in their conservation and pivotal involvement in initiating LLPS and subsequent liquid-solid phase transitions (LSPT). The development of tyrosine-templated constructs, designed to mimic their natural counterparts, emerges as a promising strategy for creating adaptive, self-assembling systems with diverse applications. This review explores the central role of tyrosine in orchestrating protein self-assembly, delving into key interactions and examining its potential in innovative applications, including responsive biomaterials and bioengineering.
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Affiliation(s)
- Anton Maraldo
- School of Biotechnology and Biomolecular Sciences, University of New South Wales, Sydney, Australia
| | - Jelena Rnjak-Kovacina
- Graduate School of Biomedical Engineering, University of New South Wales, Sydney, Australia.
| | - Christopher Marquis
- School of Biotechnology and Biomolecular Sciences, University of New South Wales, Sydney, Australia.
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4
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Nakagawa K, Ogino K, Katoh TK, Kono N. Species identification of livefood flightless fly ( Torinido-shoujoubae) through DNA barcoding. Ecol Evol 2024; 14:e11622. [PMID: 38979002 PMCID: PMC11229428 DOI: 10.1002/ece3.11622] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/24/2023] [Revised: 05/28/2024] [Accepted: 06/10/2024] [Indexed: 07/10/2024] Open
Abstract
Torinido-shoujoubae, as it is called in Japanese, is a flightless Drosophila sp. that is sold commercially in Japan. This Drosophila sp. is often used as feeds for model organisms such as reptiles and spiders. There is no scientific name provided for the fruit fly that is known as Torinido-shoujoubae, as well as any historical background or data behind this species. There has been a previous study that was conducted through morphological characteristics analysis of the body as well as the male copulatory organ and has been estimated as Drosophila hydei. The objective of this study was to determine the species of this unidentified fly known as Torinido-shoujoubae based on a molecular evidence with a DNA barcoding. Samples were purchased from four separate suppliers to examine whether there are any differences between them. COI regions were amplified using PCR and the sequenced results were aligned against two databases, NCBI and BOLD. Torinido-shoujoubae samples provided from all suppliers were confirmed to be D. hydei.
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Affiliation(s)
- Koh Nakagawa
- Institute for Advanced Biosciences Keio University Tsuruoka Yamagata Japan
| | - Kaoru Ogino
- Institute for Advanced Biosciences Keio University Tsuruoka Yamagata Japan
- Faculty of Environment and Information Studies Keio University Fujisawa Kanagawa Japan
| | - Takehiro K Katoh
- Department of Biological Sciences Tokyo Metropolitan University Hachioji Tokyo Japan
| | - Nobuaki Kono
- Institute for Advanced Biosciences Keio University Tsuruoka Yamagata Japan
- Faculty of Environment and Information Studies Keio University Fujisawa Kanagawa Japan
- Graduate School of Media and Governance Keio University Fujisawa Kanagawa Japan
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Leyden MR, Michalik P, Baruffaldi L, Mahmood S, Kalani L, Hunt DF, Eirin-Lopez JM, Andrade MC, Shabanowitz J, Ausió J. The protamines of the noble false widow spider Steatoda nobilis provide an example of liquid-liquid phase separation chromatin transitions during spermiogenesis. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.06.04.597381. [PMID: 38895387 PMCID: PMC11185589 DOI: 10.1101/2024.06.04.597381] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/21/2024]
Abstract
While there is extensive information about sperm nuclear basic proteins (SNBP) in vertebrates, there is very little information about Arthropoda by comparison. This paper aims to contribute to filling this gap by analyzing these proteins in the sperm of the noble false widow spider Steatoda nobilis (Order Araneae, Family Theridiidae). To this end, we have developed a protein extraction method that allows the extraction of cysteine-containing protamines suitable for the preparation and analysis of SNBPs from samples where the amount of starting tissue material is limited. We carried out top-down mass spectrometry sequencing and molecular phylogenetic analyses to characterize the protamines of S. nobilis and other spiders. We also used electron microscopy to analyze the chromatin organization of the sperm, and we found it to exhibit liquid-liquid phase spinodal decomposition during the late stages of spermiogenesis. These studies further our knowledge of the distribution of SNBPs within the animal kingdom and provide additional support for a proposed evolutionary origin of many protamines from a histone H1 (H5) replication-independent precursor.
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Affiliation(s)
- Melissa R. Leyden
- Department of Chemistry, University of Virginia, Charlottesville, Virginia 22904, USA
| | - Peter Michalik
- Zoologisches Institut und Museum, Universität Greifswald, Greifswald, Germany
| | - Luciana Baruffaldi
- Department of Biological Sciences, University of Toronto Scarborough, 1265 Military Trail, Toronto, ON, M1C 1A4, Canada
| | - Susheen Mahmood
- Department of Biological Sciences, University of Toronto Scarborough, 1265 Military Trail, Toronto, ON, M1C 1A4, Canada
| | - Ladan Kalani
- Department of Biochemistry and Microbiology, University of Victoria, Victoria BC V8W 2Y2, Canada
| | - Donald F. Hunt
- Department of Chemistry, University of Virginia, Charlottesville, Virginia 22904, USA
| | - Jose Maria Eirin-Lopez
- Environmental Epigenetics Laboratory, Institute of Environment, Florida International University, Miami, Florida, USA
| | - Maydianne C.B. Andrade
- Department of Biological Sciences, University of Toronto Scarborough, 1265 Military Trail, Toronto, ON, M1C 1A4, Canada
| | - Jeffrey Shabanowitz
- Department of Chemistry, University of Virginia, Charlottesville, Virginia 22904, USA
| | - Juan Ausió
- Department of Biochemistry and Microbiology, University of Victoria, Victoria BC V8W 2Y2, Canada
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6
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Ghimire A, Xu L, Liu XQ, Rainey JK. A recombinant chimeric spider pyriform-aciniform silk with highly tunable mechanical performance. Mater Today Bio 2024; 26:101073. [PMID: 38711935 PMCID: PMC11070712 DOI: 10.1016/j.mtbio.2024.101073] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2024] [Revised: 04/11/2024] [Accepted: 04/25/2024] [Indexed: 05/08/2024] Open
Abstract
Spider silks are natural protein-based biomaterials which are renowned for their mechanical properties and hold great promise for applications ranging from high-performance textiles to regenerative medicine. While some spiders can produce several different types of silks, most spider silk types - including pyriform and aciniform silks - are relatively unstudied. Pyriform and aciniform silks have distinct mechanical behavior and physicochemical properties, with materials produced using combinations of these silks currently unexplored. Here, we introduce an engineered chimeric fusion protein consisting of two repeat units of pyriform (Py) silk followed by two repeat units of aciniform (W) silk named Py2W2. This recombinant ∼86.5 kDa protein is amenable to expression and purification from Escherichia coli and exhibits high α-helicity in a fluorinated acid- and alcohol-based solution used to form a dope for wet-spinning. Wet-spinning enables continuous fiber production and post-spin stretching of the wet-spun fibers in air or following submersion in water or ethanol leads to increases in optical anisotropy, consistent with increased molecular alignment along the fiber axis. Mechanical properties of the fibers vary as a function of post-spin stretching condition, with the highest extensibility and strength observed in air-stretched and ethanol-treated fibers, respectively, with mechanics being superior to fibers spun from either constituent protein alone. Notably, the maximum extensibility obtained (∼157 ± 38 %) is of the same magnitude reported for natural flagelliform silks, the class of spider silk most associated with being stretchable. Interestingly, Py2W2 is also water-compatible, unlike its constituent Py2. Fiber-state secondary structure correlates well with the observed mechanical properties, with depleted α-helicity and increased β-sheet content in cases of increased strength. Py2W2 fibers thus provide enhanced materials behavior in terms of their mechanics, tunability, and fiber properties, providing new directions for design and development of biomaterials suitable and tunable for disparate applications.
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Affiliation(s)
- Anupama Ghimire
- Department of Biochemistry & Molecular Biology, Dalhousie University, Halifax, NS, B3H 4R2, Canada
| | - Lingling Xu
- Department of Biochemistry & Molecular Biology, Dalhousie University, Halifax, NS, B3H 4R2, Canada
| | - Xiang-Qin Liu
- Department of Biochemistry & Molecular Biology, Dalhousie University, Halifax, NS, B3H 4R2, Canada
| | - Jan K. Rainey
- Department of Biochemistry & Molecular Biology, Dalhousie University, Halifax, NS, B3H 4R2, Canada
- Department of Chemistry, Dalhousie University, Halifax, NS, B3H 4R2, Canada
- School of Biomedical Engineering, Dalhousie University, Halifax, NS, B3H 4R2, Canada
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7
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Liprandi D, Ramírez M, Schlüter S, Baumgart L, Joel AC, Michalik P, Wolff JO. Hierarchical looping results in extreme extensibility of silk fibre composites produced by Southern house spiders ( Kukulcania hibernalis). Interface Focus 2024; 14:20230071. [PMID: 39081622 PMCID: PMC11286164 DOI: 10.1098/rsfs.2023.0071] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2023] [Revised: 02/26/2024] [Accepted: 04/04/2024] [Indexed: 08/02/2024] Open
Abstract
Spider silk is a tough and versatile biological material combining high tensile strength and extensibility through nanocomposite structure and its nonlinear elastic behaviour. Notably, spiders rarely use single silk fibres in isolation, but instead process them into more complex composites, such as silk fibre bundles, sheets and anchorages, involving a combination of spinneret, leg and body movements. While the material properties of single silk fibres have been extensively studied, the mechanical properties of silk composites and meta-structures are poorly understood and exhibit a hereto largely untapped potential for the bio-inspired design of novel fabrics with outstanding mechanical properties. In this study, we report on the tensile mechanics of the adhesive capture threads of the Southern house spider (Kukulcania hibernalis), which exhibit extreme extensibility, surpassing that of the viscid capture threads of orb weavers by up to tenfold. By combining high-resolution mechanical testing, microscopy and in silico experiments based on a hierarchical modified version of the Fibre Bundle Model, we demonstrate that extreme extensibility is based on a hierarchical loops-on-loops structure combining linear and coiled elements. The stepwise unravelling of the loops leads to the repeated fracture of the connected linear fibres, delaying terminal failure and enhancing energy absorption. This principle could be used to achieve tailored fabrics and materials that are able to sustain high deformation without failure.
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Affiliation(s)
- Daniele Liprandi
- Evolutionary Biomechanics, Zoological Institute and Museum, University of Greifswald, Greifswald, Germany
| | - Martin Ramírez
- Museo Argentino de Ciencias Naturales “Bernardino Rivadavia”, Consejo Nacional de Investigaciones Científicas y Técnicas, Buenos Aires, Argentina
| | - Sascha Schlüter
- Institute of Biology II, RWTH Aachen University, Aachen, Worringerweg52074, Germany
- Institute of Organismic and Molecular Evolution, Johannes Gutenberg-University, Mainz, Germany
| | - Lucas Baumgart
- Institute of Biology II, RWTH Aachen University, Aachen, Worringerweg52074, Germany
| | - Anna-Christin Joel
- Institute of Biology II, RWTH Aachen University, Aachen, Worringerweg52074, Germany
- Institute of Organismic and Molecular Evolution, Johannes Gutenberg-University, Mainz, Germany
| | - Peter Michalik
- Zoological Museum, Zoological Institute and Museum, University of Greifswald, Greifswald, Germany
| | - Jonas O. Wolff
- Evolutionary Biomechanics, Zoological Institute and Museum, University of Greifswald, Greifswald, Germany
- School of Natural Sciences, Macquarie University, Sydney, New South Wales2109, Australia
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8
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Lin B, Xie J, Gao B, He B. Efficient Biosynthetic Fabrication of Spidroins with High Spinning Performance. ADVANCED SCIENCE (WEINHEIM, BADEN-WURTTEMBERG, GERMANY) 2024; 11:e2400128. [PMID: 38520721 PMCID: PMC11165546 DOI: 10.1002/advs.202400128] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/04/2024] [Revised: 03/16/2024] [Indexed: 03/25/2024]
Abstract
The unique 3D structure of spider silk protein (spidroin) determines the excellent mechanical properties of spidroin fiber, but the difficulty of heterologous expression and poor spinning performance of recombinant spider silk protein limit its application. A high-yield low-molecular-weight biomimetic spidroin (Amy-6rep) is obtained by sequence modification, and its excellent spinning performance is verified by electrospinning it for use as a nanogenerator. Amy-6rep increases the highly fibrogenic microcrystalline region in the core repeat region of natural spidroin with limited sequence length and replaces the polyalanine sequence with an amyloid polypeptide through structural similarity. Due to sequence modification, the expression of Amy-6rep increased by ≈200%, and the self-assembly performance of Amy-6rep significantly increased. After electrospinning with Amy-6rep, the nanofibers exhibit good tribopower generation capacity. In this paper, a biomimetic spidroin sequence design with high yield and good spinning performance is reported, and a strategy for electrospinning to produce an artificial nanogenerator is explored.
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Affiliation(s)
- Baoyang Lin
- College of Biotechnology and Pharmaceutical EngineeringSchool of Pharmaceutical SciencesNanjing Tech UniversityNanjing211816China
| | - Jingjun Xie
- College of Biotechnology and Pharmaceutical EngineeringSchool of Pharmaceutical SciencesNanjing Tech UniversityNanjing211816China
| | - Bingbing Gao
- College of Biotechnology and Pharmaceutical EngineeringSchool of Pharmaceutical SciencesNanjing Tech UniversityNanjing211816China
| | - Bingfang He
- College of Biotechnology and Pharmaceutical EngineeringSchool of Pharmaceutical SciencesNanjing Tech UniversityNanjing211816China
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9
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Jiang H, Wang Y, Zhang G, Jia A, Wei Z, Wang Y. Identification and Evolutionary Analysis of the Widely Distributed CAP Superfamily in Spider Venom. Toxins (Basel) 2024; 16:240. [PMID: 38922134 PMCID: PMC11209345 DOI: 10.3390/toxins16060240] [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: 04/05/2024] [Revised: 05/18/2024] [Accepted: 05/22/2024] [Indexed: 06/27/2024] Open
Abstract
Venom plays a crucial role in the defense and predation of venomous animals. Spiders (Araneae) are among the most successful predators and have a fascinating venom composition. Their venom mainly contains disulfide-rich peptides and large proteins. Here, we analyzed spider venom protein families, utilizing transcriptomic and genomic data, and highlighted their similarities and differences. We show that spiders have specific combinations of toxins for better predation and defense, typically comprising a core toxin expressed alongside several auxiliary toxins. Among them, the CAP superfamily is widely distributed and highly expressed in web-building Araneoidea spiders. Our analysis of evolutionary relationships revealed four subfamilies (subA-subD) of the CAP superfamily that differ in structure and potential functions. CAP proteins are composed of a conserved CAP domain and diverse C-terminal domains. CAP subC shares similar domains with the snake ion channel regulator svCRISP proteins, while CAP subD possesses a sequence similar to that of insect venom allergen 5 (Ag5). Furthermore, we show that gene duplication and selective expression lead to increased expression of CAP subD, making it a core member of the CAP superfamily. This study sheds light on the functional diversity of CAP subfamilies and their evolutionary history, which has important implications for fully understanding the composition of spider venom proteins and the core toxin components of web-building spiders.
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Affiliation(s)
- Hongcen Jiang
- Integrative Science Center of Germplasm Creation in Western China (CHONGQING) Science City, Biological Science Research Center, Southwest University, Chongqing 400715, China; (H.J.)
| | - Yiru Wang
- Integrative Science Center of Germplasm Creation in Western China (CHONGQING) Science City, Biological Science Research Center, Southwest University, Chongqing 400715, China; (H.J.)
| | - Guoqing Zhang
- Integrative Science Center of Germplasm Creation in Western China (CHONGQING) Science City, Biological Science Research Center, Southwest University, Chongqing 400715, China; (H.J.)
| | - Anqiang Jia
- Integrative Science Center of Germplasm Creation in Western China (CHONGQING) Science City, Biological Science Research Center, Southwest University, Chongqing 400715, China; (H.J.)
- Yazhouwan National Laboratory, Sanya 572024, China
| | - Zhaoyuan Wei
- Integrative Science Center of Germplasm Creation in Western China (CHONGQING) Science City, Biological Science Research Center, Southwest University, Chongqing 400715, China; (H.J.)
| | - Yi Wang
- Integrative Science Center of Germplasm Creation in Western China (CHONGQING) Science City, Biological Science Research Center, Southwest University, Chongqing 400715, China; (H.J.)
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10
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Lu W, Shi R, Li X, Ma S, Yang D, Shang D, Xia Q. A review on complete silk gene sequencing and de novo assembly of artificial silk. Int J Biol Macromol 2024; 264:130444. [PMID: 38417762 DOI: 10.1016/j.ijbiomac.2024.130444] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/26/2023] [Revised: 02/22/2024] [Accepted: 02/23/2024] [Indexed: 03/01/2024]
Abstract
Silk, especially spider and insect silk, is a highly versatile biomaterial with potential applications in biomedicine, materials science, and biomimetic engineering. The primary structure of silk proteins is the basis for the mechanical properties of silk fibers. Biotechnologies such as single-molecule sequencing have facilitated an increasing number of reports on new silk genes and assembled silk proteins. Therefore, this review aims to provide a comprehensive overview of the recent advances in representative spider and insect silk proteins, focusing on identification methods, sequence characteristics, and de novo design and assembly. The review discusses three identification methods for silk genes: polymerase chain reaction (PCR)-based sequencing, PCR-free cloning and sequencing, and whole-genome sequencing. Moreover, it reveals the main spider and insect silk proteins and their sequences. Subsequent de novo assembly of artificial silk is covered and future research directions in the field of silk proteins, including new silk genes, customizable artificial silk, and the expansion of silk production and applications are discussed. This review provides a basis for the genetic aspects of silk production and the potential applications of artificial silk in material science and biomedical engineering.
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Affiliation(s)
- Wei Lu
- Integrative Science Center of Germplasm Creation in Western China (CHONGQING) Science City, Biological Science Research Center, Southwest University, Chongqing, China
| | - Run Shi
- Integrative Science Center of Germplasm Creation in Western China (CHONGQING) Science City, Biological Science Research Center, Southwest University, Chongqing, China
| | - Xue Li
- Integrative Science Center of Germplasm Creation in Western China (CHONGQING) Science City, Biological Science Research Center, Southwest University, Chongqing, China
| | - Sanyuan Ma
- Integrative Science Center of Germplasm Creation in Western China (CHONGQING) Science City, Biological Science Research Center, Southwest University, Chongqing, China
| | - Daiying Yang
- Integrative Science Center of Germplasm Creation in Western China (CHONGQING) Science City, Biological Science Research Center, Southwest University, Chongqing, China
| | - Deli Shang
- Integrative Science Center of Germplasm Creation in Western China (CHONGQING) Science City, Biological Science Research Center, Southwest University, Chongqing, China
| | - Qingyou Xia
- Integrative Science Center of Germplasm Creation in Western China (CHONGQING) Science City, Biological Science Research Center, Southwest University, Chongqing, China.
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11
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Stadlmayr S, Peter K, Millesi F, Rad A, Wolf S, Mero S, Zehl M, Mentler A, Gusenbauer C, Konnerth J, Schniepp HC, Lichtenegger H, Naghilou A, Radtke C. Comparative Analysis of Various Spider Silks in Regard to Nerve Regeneration: Material Properties and Schwann Cell Response. Adv Healthc Mater 2024; 13:e2302968. [PMID: 38079208 DOI: 10.1002/adhm.202302968] [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: 09/05/2023] [Revised: 11/20/2023] [Indexed: 12/26/2023]
Abstract
Peripheral nerve reconstruction through the employment of nerve guidance conduits with Trichonephila dragline silk as a luminal filling has emerged as an outstanding preclinical alternative to avoid nerve autografts. Yet, it remains unknown whether the outcome is similar for silk fibers harvested from other spider species. This study compares the regenerative potential of dragline silk from two orb-weaving spiders, Trichonephila inaurata and Nuctenea umbratica, as well as the silk of the jumping spider Phidippus regius. Proliferation, migration, and transcriptomic state of Schwann cells seeded on these silks are investigated. In addition, fiber morphology, primary protein structure, and mechanical properties are studied. The results demonstrate that the increased velocity of Schwann cells on Phidippus regius fibers can be primarily attributed to the interplay between the silk's primary protein structure and its mechanical properties. Furthermore, the capacity of silk fibers to trigger cells toward a gene expression profile of a myelinating Schwann cell phenotype is shown. The findings for the first time allow an in-depth comparison of the specific cellular response to various native spider silks and a correlation with the fibers' material properties. This knowledge is essential to open up possibilities for targeted manufacturing of synthetic nervous tissue replacement.
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Affiliation(s)
- Sarah Stadlmayr
- Department of Plastic, Reconstructive and Aesthetic Surgery, Medical University of Vienna, Vienna, 1090, Austria
- Austrian Cluster for Tissue Regeneration, Vienna, Austria
| | - Karolina Peter
- Institute for Physics and Materials Science, University of Natural Resources and Life Sciences, Vienna, 1190, Austria
| | - Flavia Millesi
- Department of Plastic, Reconstructive and Aesthetic Surgery, Medical University of Vienna, Vienna, 1090, Austria
- Austrian Cluster for Tissue Regeneration, Vienna, Austria
| | - Anda Rad
- Department of Plastic, Reconstructive and Aesthetic Surgery, Medical University of Vienna, Vienna, 1090, Austria
| | - Sonja Wolf
- Department of Plastic, Reconstructive and Aesthetic Surgery, Medical University of Vienna, Vienna, 1090, Austria
| | - Sascha Mero
- Department of Plastic, Reconstructive and Aesthetic Surgery, Medical University of Vienna, Vienna, 1090, Austria
| | - Martin Zehl
- Department of Analytical Chemistry, Faculty of Chemistry, University of Vienna, Vienna, 1090, Austria
| | - Axel Mentler
- Institute of Soil Research, University of Natural Resources and Life Sciences, Vienna, 1190, Austria
| | - Claudia Gusenbauer
- Institute of Wood Technology and Renewable Materials, University of Natural Resources and Life Sciences, Tulln an der Donau, 3430, Austria
| | - Johannes Konnerth
- Institute of Wood Technology and Renewable Materials, University of Natural Resources and Life Sciences, Tulln an der Donau, 3430, Austria
| | - Hannes C Schniepp
- Department of Applied Science, William & Mary, Williamsburg, VA, 23185, USA
| | - Helga Lichtenegger
- Institute for Physics and Materials Science, University of Natural Resources and Life Sciences, Vienna, 1190, Austria
| | - Aida Naghilou
- Department of Plastic, Reconstructive and Aesthetic Surgery, Medical University of Vienna, Vienna, 1090, Austria
- Austrian Cluster for Tissue Regeneration, Vienna, Austria
- Medical Systems Biophysics and Bioengineering, Leiden Academic Centre for Drug Research, Leiden University, Leiden, 2333, The Netherlands
| | - Christine Radtke
- Department of Plastic, Reconstructive and Aesthetic Surgery, Medical University of Vienna, Vienna, 1090, Austria
- Austrian Cluster for Tissue Regeneration, Vienna, Austria
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12
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Kato T, Uchida J, Ishii Y, Watanabe G. Aquatic Functional Liquid Crystals: Design, Functionalization, and Molecular Simulation. ADVANCED SCIENCE (WEINHEIM, BADEN-WURTTEMBERG, GERMANY) 2024; 11:e2306529. [PMID: 38126650 PMCID: PMC10885670 DOI: 10.1002/advs.202306529] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/10/2023] [Revised: 11/26/2023] [Indexed: 12/23/2023]
Abstract
Aquatic functional liquid crystals, which are ordered molecular assemblies that work in water environment, are described in this review. Aquatic functional liquid crystals are liquid-crystalline (LC) materials interacting water molecules or aquatic environment. They include aquatic lyotropic liquid crystals and LC based materials that have aquatic interfaces, for example, nanoporous water treatment membranes that are solids preserving LC order. They can remove ions and viruses with nano- and subnano-porous structures. Columnar, smectic, bicontinuous LC structures are used for fabrication of these 1D, 2D, 3D materials. Design and functionalization of aquatic LC sensors based on aqueous/LC interfaces are also described. The ordering transitions of liquid crystals induced by molecular recognition at the aqueous interfaces provide distinct optical responses. Molecular orientation and dynamic behavior of these aquatic functional LC materials are studied by molecular dynamics simulations. The molecular interactions of LC materials and water are key of these investigations. New insights into aquatic functional LC materials contribute to the fields of environment, healthcare, and biotechnology.
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Affiliation(s)
- Takashi Kato
- Department of Chemistry and Biotechnology, School of Engineering, The University of Tokyo, Hongo, Bunkyo-ku, Tokyo, 113-8656, Japan
- Research Initiative for Supra-Materials, Shinshu University, Nagano, 380-8553, Japan
| | - Junya Uchida
- Department of Chemistry and Biotechnology, School of Engineering, The University of Tokyo, Hongo, Bunkyo-ku, Tokyo, 113-8656, Japan
| | - Yoshiki Ishii
- Department of Data Science, School of Frontier Engineering, Kitasato University, Sagamihara, 252-0373, Japan
| | - Go Watanabe
- Department of Data Science, School of Frontier Engineering, Kitasato University, Sagamihara, 252-0373, Japan
- Kanagawa Institute of Industrial Science and Technology (KISTEC), Ebina, 243-0435, Japan
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13
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Wen F, Wang Y, Tu B, Cui L. Superfast Gelation of Spider Silk-Based Artificial Silk Protein. Gels 2024; 10:69. [PMID: 38247791 PMCID: PMC10815891 DOI: 10.3390/gels10010069] [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: 11/20/2023] [Revised: 01/12/2024] [Accepted: 01/15/2024] [Indexed: 01/23/2024] Open
Abstract
Spider silk proteins (spidroins) have garnered attention in biomaterials research due to their ability to self-assemble into hydrogels. However, reported spidroin hydrogels require high protein concentration and prolonged gelation time. Our study engineered an artificial spidroin that exhibits unprecedented rapid self-assembly into hydrogels at physiologically relevant conditions, achieving gelation at a low concentration of 6 mg/mL at 37 °C without external additives. Remarkably, at a 30 mg/mL concentration, our engineered protein forms hydrogels within 30 s, a feature we termed "superfast gelation". This rapid formation is modulated by ions, pH, and temperature, offering versatility in biomedical applications. The hydrogel's capacity to encapsulate proteins and support E. coli growth while inducing RFP expression provides a novel platform for drug delivery and bioengineering applications. Our findings introduce a superfast, highly adaptable, and cytocompatible hydrogel that self-assembles under mild conditions, underscoring the practical implication of rapid gelation in biomedical research and clinical applications.
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Affiliation(s)
- Fan Wen
- CCZU-JITRI Joint Bio-X Lab, School of Pharmacy & School of Biological and Food Engineering, Changzhou University, Changzhou 213164, China; (F.W.); (Y.W.)
| | - Yu Wang
- CCZU-JITRI Joint Bio-X Lab, School of Pharmacy & School of Biological and Food Engineering, Changzhou University, Changzhou 213164, China; (F.W.); (Y.W.)
| | - Bowen Tu
- Pathogenic Biological Laboratory, Changzhou Disease Control and Prevention Centre, Changzhou Medical Centre, Nanjing Medical University, Changzhou 213000, China;
| | - Lun Cui
- CCZU-JITRI Joint Bio-X Lab, School of Pharmacy & School of Biological and Food Engineering, Changzhou University, Changzhou 213164, China; (F.W.); (Y.W.)
- Biomaterials Lab, Changzhou AiRiBio Healthcare Co., Ltd., Changzhou 213164, China
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14
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Matthew SL, Seib FP. Silk Bioconjugates: From Chemistry and Concept to Application. ACS Biomater Sci Eng 2024; 10:12-28. [PMID: 36706352 PMCID: PMC10777352 DOI: 10.1021/acsbiomaterials.2c01116] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2022] [Accepted: 12/09/2022] [Indexed: 01/28/2023]
Abstract
Medical silks have captured global interest. While silk sutures have a long track record in humans, silk bioconjugates are still in preclinical development. This perspective examines key advances in silk bioconjugation, including the fabrication of silk-protein conjugates, bioconjugated silk particles, and bioconjugated substrates to enhance cell-material interactions in two and three dimensions. Many of these systems rely on chemical modification of the silk biopolymer, often using carbodiimide and reactive ester chemistries. However, recent progress in enzyme-mediated and click chemistries has expanded the molecular toolbox to enable biorthogonal, site-specific conjugation in a single step when combined with recombinant silk fibroin tagged with noncanonical amino acids. This perspective outlines key strategies available for chemical modification, compares the resulting silk conjugates to clinical benchmarks, and outlines open questions and areas that require more work. Overall, this assessment highlights a domain of new sunrise capabilities and development opportunities for silk bioconjugates that may ultimately offer new ways of delivering improved healthcare.
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Affiliation(s)
- Saphia
A. L. Matthew
- Strathclyde
Institute of Pharmacy and Biomedical Sciences, University of Strathclyde, 161 Cathedral Street, Glasgow G4 0RE, U.K.
| | - F. Philipp Seib
- Strathclyde
Institute of Pharmacy and Biomedical Sciences, University of Strathclyde, 161 Cathedral Street, Glasgow G4 0RE, U.K.
- Branch
Bioresources, Fraunhofer Institute for Molecular
Biology and Applied Ecology, Ohlebergsweg 12, 35392 Giessen, Germany
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15
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Hovanová V, Hovan A, Humenik M, Sedlák E. Only kosmotrope anions trigger fibrillization of the recombinant core spidroin eADF4(C16) from Araneus diadematus. Protein Sci 2023; 32:e4832. [PMID: 37937854 PMCID: PMC10661072 DOI: 10.1002/pro.4832] [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: 07/18/2023] [Revised: 10/20/2023] [Accepted: 11/05/2023] [Indexed: 11/09/2023]
Abstract
Recombinant core spidroin eADF4(C16) has received increasing attention due to its ability to form micro- and nano-structured scaffolds, which are based on nanofibrils with great potential for biomedical and biotechnological applications. Phosphate anions have been demonstrated to trigger the eADF4(C16) self-assembly into cross-beta fibrils. In the present work, we systematically addressed the effect of nine sodium anions, namely SO4 2- , HPO4 2- (Pi), F- , Cl- , Br- , NO3 - , I- , SCN- , and ClO4 - from the Hofmeister series on the in vitro self-assembly kinetics of eADF4(C16). We show that besides the phosphate anions, only kosmotropic anions such as sulfate and fluoride can initiate the eADF4(C16) fibril formation. Global analysis of the self-assembly kinetics, utilizing the platform AmyloFit, showed the nucleation-based mechanism with a major role of secondary nucleation, surprisingly independent of the type of the kosmotropic anion. The rate constant of the fibril elongation in mixtures of phosphate anions with other studied anions correlated with their kosmotropic or chaotropic position in the Hofmeister series. Our findings suggest an important role of anion hydration in the eADF4(C16) fibrillization process.
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Affiliation(s)
- Veronika Hovanová
- Center for Interdisciplinary Biosciences, Technology and Innovation ParkP.J. Šafárik UniversityKošiceSlovakia
- Department of Biophysics, Faculty of ScienceP.J. Šafárik UniversityKošiceSlovakia
| | - Andrej Hovan
- Department of Biophysics, Faculty of ScienceP.J. Šafárik UniversityKošiceSlovakia
| | - Martin Humenik
- Department of Biomaterials, Faculty of Engineering ScienceUniversity BayreuthBayreuthGermany
| | - Erik Sedlák
- Center for Interdisciplinary Biosciences, Technology and Innovation ParkP.J. Šafárik UniversityKošiceSlovakia
- Department of Biochemistry, Faculty of ScienceP.J. Šafárik UniversityKošiceSlovakia
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16
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Kulkarni S, Wood HM, Hormiga G. Advances in the reconstruction of the spider tree of life: A roadmap for spider systematics and comparative studies. Cladistics 2023; 39:479-532. [PMID: 37787157 DOI: 10.1111/cla.12557] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2022] [Revised: 07/27/2023] [Accepted: 08/17/2023] [Indexed: 10/04/2023] Open
Abstract
In the last decade and a half, advances in genetic sequencing technologies have revolutionized systematics, transforming the field from studying morphological characters or a few genetic markers, to genomic datasets in the phylogenomic era. A plethora of molecular phylogenetic studies on many taxonomic groups have come about, converging on, or refuting prevailing morphology or legacy-marker-based hypotheses about evolutionary affinities. Spider systematics has been no exception to this transformation and the inter-relationships of several groups have now been studied using genomic data. About 51 500 extant spider species have been described, all with a conservative body plan, but innumerable morphological and behavioural peculiarities. Inferring the spider tree of life using morphological data has been a challenging task. Molecular data have corroborated many hypotheses of higher-level relationships, but also resulted in new groups that refute previous hypotheses. In this review, we discuss recent advances in the reconstruction of the spider tree of life and highlight areas where additional effort is needed with potential solutions. We base this review on the most comprehensive spider phylogeny to date, representing 131 of the 132 spider families. To achieve this sampling, we combined six Sanger-based markers with newly generated and publicly available genome-scale datasets. We find that some inferred relationships between major lineages of spiders (such as Austrochiloidea, Palpimanoidea and Synspermiata) are robust across different classes of data. However, several new hypotheses have emerged with different classes of molecular data. We identify and discuss the robust and controversial hypotheses and compile this blueprint to design future studies targeting systematic revisions of these problematic groups. We offer an evolutionary framework to explore comparative questions such as evolution of venoms, silk, webs, morphological traits and reproductive strategies.
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Affiliation(s)
- Siddharth Kulkarni
- Department of Biological Sciences, The George Washington University, 2029 G St. NW, Washington, DC, 20052, USA
- Department of Entomology, National Museum of Natural History, Smithsonian Institution, 1000 Constitution Avenue NW, Washington, DC, 20560, USA
| | - Hannah M Wood
- Department of Entomology, National Museum of Natural History, Smithsonian Institution, 1000 Constitution Avenue NW, Washington, DC, 20560, USA
| | - Gustavo Hormiga
- Department of Biological Sciences, The George Washington University, 2029 G St. NW, Washington, DC, 20052, USA
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17
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Mishina T, Chiu MC, Hashiguchi Y, Oishi S, Sasaki A, Okada R, Uchiyama H, Sasaki T, Sakura M, Takeshima H, Sato T. Massive horizontal gene transfer and the evolution of nematomorph-driven behavioral manipulation of mantids. Curr Biol 2023; 33:4988-4994.e5. [PMID: 37863060 DOI: 10.1016/j.cub.2023.09.052] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2023] [Revised: 08/21/2023] [Accepted: 09/21/2023] [Indexed: 10/22/2023]
Abstract
To complete their life cycle, a wide range of parasites must manipulate the behavior of their hosts.1 This manipulation is a well-known example of the "extended phenotype,2" where genes in one organism have phenotypic effects on another organism. Recent studies have explored the parasite genes responsible for such manipulation of host behavior, including the potential molecular mechanisms.3,4 However, little is known about how parasites have acquired the genes involved in manipulating phylogenetically distinct hosts.4 In a fascinating example of the extended phenotype, nematomorph parasites have evolved the ability to induce their terrestrial insect hosts to enter bodies of water, where the parasite then reproduces. Here, we comprehensively analyzed nematomorphs and their mantid hosts, focusing on the transcriptomic changes associated with host manipulations and sequence similarity between host and parasite genes to test molecular mimicry. The nematomorph's transcriptome changed during host manipulation, whereas no distinct changes were found in mantids. We then discovered numerous possible host-derived genes in nematomorphs, and these genes were frequently up-regulated during host manipulation. Our findings suggest a possible general role of horizontal gene transfer (HGT) in the molecular mechanisms of host manipulation, as well as in the genome evolution of manipulative parasites. The evidence of HGT between multicellular eukaryotes remains scarce but is increasing and, therefore, elucidating its mechanisms will advance our understanding of the enduring influence of HGT on the evolution of the web of life.
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Affiliation(s)
- Tappei Mishina
- Laboratory for Chromosome Segregation, RIKEN Center for Biosystems Dynamics Research (BDR), Kobe 6500047, Japan.
| | - Ming-Chung Chiu
- Department of Biology, Graduate School of Sciences, Kobe University, Kobe 6578501, Japan; Department of Entomology, National Taiwan University, Taipei 50007, Taiwan
| | - Yasuyuki Hashiguchi
- Department of Biology, Faculty of Medicine, Osaka Medical and Pharmaceutical University, Takatsuki 5690801, Japan.
| | - Sayumi Oishi
- Department of Biology, Graduate School of Sciences, Kobe University, Kobe 6578501, Japan
| | - Atsunari Sasaki
- Department of Biology, Graduate School of Sciences, Kobe University, Kobe 6578501, Japan
| | - Ryuichi Okada
- Department of Biology, Graduate School of Sciences, Kobe University, Kobe 6578501, Japan
| | - Hironobu Uchiyama
- NODAI Genome Research Center, Tokyo University of Agriculture, Tokyo 1568502, Japan
| | - Takeshi Sasaki
- Graduate School of Bioresource Development, Tokyo University of Agriculture, Atsugi 2430034, Japan
| | - Midori Sakura
- Department of Biology, Graduate School of Sciences, Kobe University, Kobe 6578501, Japan
| | - Hirohiko Takeshima
- Research Center of Marine Bioresources, Department of Marine Bioscience, Fukui Prefectural University, 49-8-2, Katsumi, Obama, Fukui Prefecture 9170116, Japan
| | - Takuya Sato
- Department of Biology, Graduate School of Sciences, Kobe University, Kobe 6578501, Japan; Center for Ecological Research, Kyoto University, Otsu 5202113, Japan.
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18
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Mi J, Zhou X, Sun R, Han J. Disabling spidroin N-terminal homologs' reverse reaction unveils why its intermolecular disulfide bonds have not evolved for 380 million years. Int J Biol Macromol 2023; 249:125974. [PMID: 37499718 DOI: 10.1016/j.ijbiomac.2023.125974] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2023] [Revised: 07/21/2023] [Accepted: 07/22/2023] [Indexed: 07/29/2023]
Abstract
Spiders, ubiquitous predators known for their powerful silks, rely on spidroins that self-assemble from high-concentration solutions stored in silk glands, which are mediated by the NT and CT domains. CT homodimers containing intermolecular disulfide bonds enhance silk performance, promoting spider survival and reproduction. However, no NT capable of forming such disulfide bonds has been identified. Our study reveals that NT homodimers with sulfur substitution can form under alkaline conditions, shedding light on why spiders have not evolved intermolecular disulfide bonds in the NT module during their 380 million years of evolution. This discovery significantly advances our comprehension of spider evolution and silk spinning mechanisms, while also providing novel insights into protein storage, assembly, as well as the mechanisms and therapeutic strategies for neurodegenerative diseases associated with protein aggregation.
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Affiliation(s)
- Junpeng Mi
- College of Biological Science and Medical Engineering, Donghua University, Shanghai 201620, China
| | - Xingping Zhou
- College of Biological Science and Medical Engineering, Donghua University, Shanghai 201620, China
| | - Rou Sun
- College of Biological Science and Medical Engineering, Donghua University, Shanghai 201620, China
| | - Jiaojiao Han
- Department of Clinical Hematology and osology, Shanghai center for clinical laboratory, Shanghai 200126, China.
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19
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Mu X, Amouzandeh R, Vogts H, Luallen E, Arzani M. A brief review on the mechanisms and approaches of silk spinning-inspired biofabrication. Front Bioeng Biotechnol 2023; 11:1252499. [PMID: 37744248 PMCID: PMC10512026 DOI: 10.3389/fbioe.2023.1252499] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2023] [Accepted: 08/22/2023] [Indexed: 09/26/2023] Open
Abstract
Silk spinning, observed in spiders and insects, exhibits a remarkable biological source of inspiration for advanced polymer fabrications. Because of the systems design, silk spinning represents a holistic and circular approach to sustainable polymer fabrication, characterized by renewable resources, ambient and aqueous processing conditions, and fully recyclable "wastes." Also, silk spinning results in structures that are characterized by the combination of monolithic proteinaceous composition and mechanical strength, as well as demonstrate tunable degradation profiles and minimal immunogenicity, thus making it a viable alternative to most synthetic polymers for the development of advanced biomedical devices. However, the fundamental mechanisms of silk spinning remain incompletely understood, thus impeding the efforts to harness the advantageous properties of silk spinning. Here, we present a concise and timely review of several essential features of silk spinning, including the molecular designs of silk proteins and the solvent cues along the spinning apparatus. The solvent cues, including salt ions, pH, and water content, are suggested to direct the hierarchical assembly of silk proteins and thus play a central role in silk spinning. We also discuss several hypotheses on the roles of solvent cues to provide a relatively comprehensive analysis and to identify the current knowledge gap. We then review the state-of-the-art bioinspired fabrications with silk proteins, including fiber spinning and additive approaches/three-dimensional (3D) printing. An emphasis throughout the article is placed on the universal characteristics of silk spinning developed through millions of years of individual evolution pathways in spiders and silkworms. This review serves as a stepping stone for future research endeavors, facilitating the in vitro recapitulation of silk spinning and advancing the field of bioinspired polymer fabrication.
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Affiliation(s)
- Xuan Mu
- Roy J. Carver Department of Biomedical Engineering, College of Engineering, University of Iowa, Iowa City, IA, United States
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20
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Greco G, Schmuck B, Jalali SK, Pugno NM, Rising A. Influence of experimental methods on the mechanical properties of silk fibers: A systematic literature review and future road map. BIOPHYSICS REVIEWS 2023; 4:031301. [PMID: 38510706 PMCID: PMC10903380 DOI: 10.1063/5.0155552] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/21/2023] [Accepted: 06/20/2023] [Indexed: 03/22/2024]
Abstract
Spider silk fibers are of scientific and industrial interest because of their extraordinary mechanical properties. These properties are normally determined by tensile tests, but the values obtained are dependent on the morphology of the fibers, the test conditions, and the methods by which stress and strain are calculated. Because of this, results from many studies are not directly comparable, which has led to widespread misconceptions in the field. Here, we critically review most of the reports from the past 50 years on spider silk mechanical performance and use artificial spider silk and native silks as models to highlight the effect that different experimental setups have on the fibers' mechanical properties. The results clearly illustrate the importance of carefully evaluating the tensile test methods when comparing the results from different studies. Finally, we suggest a protocol for how to perform tensile tests on silk and biobased fibers.
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Affiliation(s)
| | | | - S. K. Jalali
- Laboratory for Bioinspired, Bionic, Nano, Meta, Materials & Mechanics, Department of Civil, Environmental and Mechanical Engineering, University of Trento, Via Mesiano, 77, 38123 Trento, Italy
| | | | - Anna Rising
- Authors to whom correspondence should be addressed: and
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21
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Heckenhauer J, Stewart RJ, Ríos-Touma B, Powell A, Dorji T, Frandsen PB, Pauls SU. Characterization of the primary structure of the major silk gene, h-fibroin, across caddisfly (Trichoptera) suborders. iScience 2023; 26:107253. [PMID: 37529107 PMCID: PMC10387566 DOI: 10.1016/j.isci.2023.107253] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2023] [Revised: 04/05/2023] [Accepted: 06/27/2023] [Indexed: 08/03/2023] Open
Abstract
Larvae of caddisflies (Trichoptera) produce silk to build various underwater structures allowing them to exploit a wide range of aquatic environments. The silk adheres to various substrates underwater and has high tensile strength, extensibility, and toughness and is of interest as a model for biomimetic adhesives. As a step toward understanding how the properties of underwater silk evolved in Trichoptera, we used genomic data to identify full-length sequences and characterize the primary structure of the major silk protein, h-fibroin, across the order. The h-fibroins have conserved termini and basic motif structure with high variation in repeating modules and variation in the percentage of amino acids, mainly proline. This finding might be linked to differences in mechanical properties related to the different silk usage and sets a starting point for future studies to screen and correlate amino acid motifs and other sequence features with quantifiable silk properties.
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Affiliation(s)
- Jacqueline Heckenhauer
- LOEWE Centre for Translational Biodiversity Genomics (LOEWE-TBG), Frankfurt, Hesse 60325, Germany
- Department of Terrestrial Zoology, Senckenberg Research Institute and Natural History Museum Frankfurt, Frankfurt, Hesse 60325, Germany
| | - Russell J. Stewart
- Department of Biomedical Engineering, University of Utah, Salt Lake City, UT 84112, USA
| | - Blanca Ríos-Touma
- Facultad de Ingenierías y Ciencias Aplicadas, Ingeniería Ambiental, Grupo de Investigación en Biodiversidad, Medio Ambiente y Salud (BIOMAS), Universidad de Las Américas, Quito, EC 170124, Ecuador
| | - Ashlyn Powell
- Department of Plant and Wildlife Science, Brigham Young University, Provo, UT 84602, USA
| | - Tshering Dorji
- Department of Environment and Climate Studies, Royal University of Bhutan, Punakha 13001, Bhutan
| | - Paul B. Frandsen
- LOEWE Centre for Translational Biodiversity Genomics (LOEWE-TBG), Frankfurt, Hesse 60325, Germany
- Department of Plant and Wildlife Science, Brigham Young University, Provo, UT 84602, USA
- Data Science Lab, Smithsonian Institution, Washington, DC 20560, USA
| | - Steffen U. Pauls
- LOEWE Centre for Translational Biodiversity Genomics (LOEWE-TBG), Frankfurt, Hesse 60325, Germany
- Department of Terrestrial Zoology, Senckenberg Research Institute and Natural History Museum Frankfurt, Frankfurt, Hesse 60325, Germany
- Institute for Insect Biotechnology, Justus-Liebig-University, Gießen, Hesse 35392; Germany
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22
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Graham JJ, Keten S. Increase in Charge and Density Improves the Strength and Toughness of Mussel Foot Protein 5 Inspired Protein Materials. ACS Biomater Sci Eng 2023; 9:4662-4672. [PMID: 37417954 DOI: 10.1021/acsbiomaterials.3c00088] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/08/2023]
Abstract
Mussel foot protein 5 (fp5) found in the adhesive byssal plaque of Mediterranean mussel Mytilus galloprovincialis exhibits exceptional underwater adhesion to diverse surfaces to the extent that adhesion strength typically exceeds the cohesive strength of the plaque. While sequence effects such as presence of charged residues, metal ion coordination, and high catechol content have been identified to govern fp5's interaction with surfaces, molecular contributors to its cohesive strength remain to be fully understood. Addressing this issue is critical for designing mussel-inspired sequences for new adhesives and biomaterials enabled by synthetic biology. Here we carry out all-atom molecular dynamics simulations on hydrated model fp5 biopolymer melts to understand how sequence features such as tyrosine and charge content affect packing density and inter-residue and ionic interaction strengths and consequently influence the cohesive strength and toughness. Systematic serine (S) substitutions for lysine (K), arginine (R) and tyrosine (Y) residues reveal that Y to S substitution surprisingly results in improvement of cohesive strength due to densification of the material by removal of steric hindrances, whereas the removal of charge in K and R to S substitutions has a detrimental impact on strength and toughness as it reduces cohesive interactions facilitated by electrostatic interactions. Additionally, melts formed from split fp5 sequences with only C or N terminal halves show distinct mechanical responses that further illustrate the role of charge. Our findings provide new insights for designing materials that could potentially surpass the performance of existing biomolecular and bioinspired adhesives, specifically by tailoring sequences for balancing charge and excluded volume effects.
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Affiliation(s)
- Jacob J Graham
- Northwestern University, Department of Mechanical Engineering, 2145 Sheridan Road, Evanston, Illinois 60208, United States
| | - Sinan Keten
- Northwestern University, Department of Mechanical Engineering, 2145 Sheridan Road, Evanston, Illinois 60208, United States
- Northwestern University, Department of Civil and Environmental Engineering, 2145 Sheridan Road, Evanston, Illinois 60208, United States
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23
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Simmons JR, Gasmi-Seabrook G, Rainey JK. Structural features, intrinsic disorder, and modularity of a pyriform spidroin 1 core repetitive domain. Biochem Cell Biol 2023; 101:271-283. [PMID: 36802452 DOI: 10.1139/bcb-2022-0338] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/23/2023] Open
Abstract
Orb-weaving spiders produce up to seven silk types, each with distinct biological roles, protein compositions, and mechanics. Pyriform (or piriform) silk is composed of pyriform spidroin 1 (PySp1) and is the fibrillar component of attachment discs that attach webs to substrates and to each other. Here, we characterize the 234-residue repeat unit (the "Py unit") from the core repetitive domain of Argiope argentata PySp1. Solution-state nuclear magnetic resonance (NMR) spectroscopy-based backbone chemical shift and dynamics analysis demonstrate a structured core flanked by disordered tails, structuring that is maintained in a tandem protein of two connected Py units, indicative of structural modularity of the Py unit in the context of the repetitive domain. Notably, AlphaFold2 predicts the Py unit structure with low confidence, echoing low confidence and poor agreement to the NMR-derived structure for the Argiope trifasciata aciniform spidroin (AcSp1) repeat unit. Rational truncation, validated through NMR spectroscopy, provided a 144-residue construct retaining the Py unit core fold, enabling near-complete backbone and side chain 1H, 13C, and 15N resonance assignment. A six α-helix globular core is inferred, flanked by regions of intrinsic disorder that would link helical bundles in tandem repeat proteins in a beads-on-a-string architecture.
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Affiliation(s)
- Jeffrey R Simmons
- Department of Biochemistry& Molecular Biology, Dalhousie University, Halifax, NS B3H 4R2, Canada
| | | | - Jan K Rainey
- Department of Biochemistry& Molecular Biology, Dalhousie University, Halifax, NS B3H 4R2, Canada
- Department of Chemistry, Dalhousie University, Halifax, NS B3H 4R2, Canada
- School of Biomedical Engineering, Dalhousie University, Halifax, NS B3H 4R2, Canada
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24
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Fan Z, Wang LY, Xiao L, Tan B, Luo B, Ren TY, Liu N, Zhang ZS, Bai M. Lampshade web spider Ectatosticta davidi chromosome-level genome assembly provides evidence for its phylogenetic position. Commun Biol 2023; 6:748. [PMID: 37463957 PMCID: PMC10354039 DOI: 10.1038/s42003-023-05129-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2022] [Accepted: 07/10/2023] [Indexed: 07/20/2023] Open
Abstract
The spider of Ectatosticta davidi, belonging to the lamp-shade web spider family, Hypochilidae, which is closely related to Hypochilidae and Filistatidae and recovered as sister of the rest Araneomorphs spiders. Here we show the final assembled genome of E. davidi with 2.16 Gb in 15 chromosomes. Then we confirm the evolutionary position of Hypochilidae. Moreover, we find that the GMC gene family exhibit high conservation throughout the evolution of true spiders. We also find that the MaSp genes of E. davidi may represent an early stage of MaSp and MiSp genes in other true spiders, while CrSp shares a common origin with AgSp and PySp but differ from MaSp. Altogether, this study contributes to addressing the limited availability of genomic sequences from Hypochilidae spiders, and provides a valuable resource for investigating the genomic evolution of spiders.
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Affiliation(s)
- Zheng Fan
- Key Laboratory of Zoological Systematics and Evolution, Institute of Zoology, Chinese Academy of Sciences, 100101, Beijing, China
- School of Life Sciences, Southwest University, 400700, Chongqing, China
| | - Lu-Yu Wang
- School of Life Sciences, Southwest University, 400700, Chongqing, China
| | - Lin Xiao
- School of Life Sciences, Southwest University, 400700, Chongqing, China
| | - Bing Tan
- School of Life Sciences, Southwest University, 400700, Chongqing, China
| | - Bin Luo
- School of Life Sciences, Southwest University, 400700, Chongqing, China
| | - Tian-Yu Ren
- School of Life Sciences, Southwest University, 400700, Chongqing, China
| | - Ning Liu
- Key Laboratory of Zoological Systematics and Evolution, Institute of Zoology, Chinese Academy of Sciences, 100101, Beijing, China.
| | - Zhi-Sheng Zhang
- School of Life Sciences, Southwest University, 400700, Chongqing, China.
| | - Ming Bai
- Key Laboratory of Zoological Systematics and Evolution, Institute of Zoology, Chinese Academy of Sciences, 100101, Beijing, China.
- Northeast Asia Biodiversity Research Center, Northeast Forestry University, 150040, Harbin, China.
- University of Chinese Academy of Sciences, 100049, Beijing, China.
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25
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Nakamura H, Kono N, Mori M, Masunaga H, Numata K, Arakawa K. Composition of Minor Ampullate Silk Makes Its Properties Different from Those of Major Ampullate Silk. Biomacromolecules 2023; 24:2042-2051. [PMID: 37002945 DOI: 10.1021/acs.biomac.2c01474] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/03/2023]
Abstract
Spider's minor ampullate silk, or MI-silk, exhibits distinct mechanical properties and water resistance compared to its major ampullate counterpart (MA-silk). The principal protein constituent of MI-silk is known as minor ampullate spidroin, or MiSp, and while its sequence has been deciphered and is thought to underlie the differences in properties with MA-silk, the composition of MI-silk and the relationship between its composition and properties remain elusive. In this study, we set out to investigate the mechanical properties, water resistance, and proteome of MA-silk and MI-silk from Araneus ventricosus and Trichonephila clavata. We also synthesized artificial fibers from major ampullate spidroin, MaSp1 and 2, and MiSp to compare their properties. Our proteomic analysis reveals that the MI-silk of both araneids is composed of MiSp, MaSp1, and spidroin constituting elements (SpiCEs). The absence of MaSp2 in the MI-silk proteome and the comparison of the water resistance of artificial fibers suggest that the presence of MaSp2 is the reason for the disparity in water resistance between MI-silk and MA-silk.
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Affiliation(s)
- Hiroyuki Nakamura
- Institute for Advanced Biosciences, Keio University, Tsuruoka, Yamagata 997-0017, Japan
- Graduate School of Media and Governance, Keio University, 5322 Endo, Fujisawa, Kanagawa 252-0882, Japan
- Spiber Inc., 234-1 Mizukami, Kakuganji, Tsuruoka, Yamagata 997-0052, Japan
| | - Nobuaki Kono
- Institute for Advanced Biosciences, Keio University, Tsuruoka, Yamagata 997-0017, Japan
- Graduate School of Media and Governance, Keio University, 5322 Endo, Fujisawa, Kanagawa 252-0882, Japan
| | - Masaru Mori
- Institute for Advanced Biosciences, Keio University, Tsuruoka, Yamagata 997-0017, Japan
- Graduate School of Media and Governance, Keio University, 5322 Endo, Fujisawa, Kanagawa 252-0882, Japan
| | - Hiroyasu Masunaga
- Japan Synchrotron Radiation Research Institute, 1-1-1, Kouto, Sayo-cho, Sayo-gun, Hyogo 679-5198, Japan
| | - Keiji Numata
- Institute for Advanced Biosciences, Keio University, Tsuruoka, Yamagata 997-0017, Japan
- Biomacromolecules Research Team, RIKEN Center for Sustainable Resource Science, 2-1 Hirosawa, Wako, Saitama 351-0198, Japan
- Department of Material Chemistry, Kyoto University, Katsura, Nishikyo, Kyoto 615-8510, Japan
| | - Kazuharu Arakawa
- Institute for Advanced Biosciences, Keio University, Tsuruoka, Yamagata 997-0017, Japan
- Graduate School of Media and Governance, Keio University, 5322 Endo, Fujisawa, Kanagawa 252-0882, Japan
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