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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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2
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Arakawa K, Kono N, Malay AD, Tateishi A, Ifuku N, Masunaga H, Sato R, Tsuchiya K, Ohtoshi R, Pedrazzoli D, Shinohara A, Ito Y, Nakamura H, Tanikawa A, Suzuki Y, Ichikawa T, Fujita S, Fujiwara M, Tomita M, Blamires SJ, Chuah JA, Craig H, Foong CP, Greco G, Guan J, Holland C, Kaplan DL, Sudesh K, Mandal BB, Norma-Rashid Y, Oktaviani NA, Preda RC, Pugno NM, Rajkhowa R, Wang X, Yazawa K, Zheng Z, Numata K. 1000 spider silkomes: Linking sequences to silk physical properties. SCIENCE ADVANCES 2022; 8:eabo6043. [PMID: 36223455 PMCID: PMC9555773 DOI: 10.1126/sciadv.abo6043] [Citation(s) in RCA: 17] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/14/2022] [Accepted: 08/19/2022] [Indexed: 06/16/2023]
Abstract
Spider silks are among the toughest known materials and thus provide models for renewable, biodegradable, and sustainable biopolymers. However, the entirety of their diversity still remains elusive, and silks that exceed the performance limits of industrial fibers are constantly being found. We obtained transcriptome assemblies from 1098 species of spiders to comprehensively catalog silk gene sequences and measured the mechanical, thermal, structural, and hydration properties of the dragline silks of 446 species. The combination of these silk protein genotype-phenotype data revealed essential contributions of multicomponent structures with major ampullate spidroin 1 to 3 paralogs in high-performance dragline silks and numerous amino acid motifs contributing to each of the measured properties. We hope that our global sampling, comprehensive testing, integrated analysis, and open data will provide a solid starting point for future biomaterial designs.
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Affiliation(s)
- Kazuharu Arakawa
- Institute for Advanced Biosciences, Keio University, Tsuruoka, Yamagata 997-0017, Japan
- Faculty of Environment and Information Studies, Keio University, Fujisawa, Kanagawa 252-8520, Japan
- Graduate School of Media and Governance, Keio University, Fujisawa, Kanagawa 252-8520, Japan
- Exploratory Research Center on Life and Living Systems (ExCELLS), National Institutes of Natural Sciences, Okazaki, Aichi 444-8787, Japan
| | - Nobuaki Kono
- Institute for Advanced Biosciences, Keio University, Tsuruoka, Yamagata 997-0017, Japan
- Graduate School of Media and Governance, Keio University, Fujisawa, Kanagawa 252-8520, Japan
| | - Ali D. Malay
- Biomacromolecules Research Team, RIKEN Center for Sustainable Resource Science, Wako, Saitama 351-0198, Japan
| | - Ayaka Tateishi
- Biomacromolecules Research Team, RIKEN Center for Sustainable Resource Science, Wako, Saitama 351-0198, Japan
- Department of Material Chemistry, Kyoto University, Nishikyo, Kyoto 615-8510, Japan
| | - Nao Ifuku
- Biomacromolecules Research Team, RIKEN Center for Sustainable Resource Science, Wako, Saitama 351-0198, Japan
| | - Hiroyasu Masunaga
- Japan Synchrotron Radiation Research Institute, Sayo-gun, Hyogo 679-5198, Japan
| | - Ryota Sato
- Biomacromolecules Research Team, RIKEN Center for Sustainable Resource Science, Wako, Saitama 351-0198, Japan
- Spiber Inc., Tsuruoka, Yamagata 997-0052, Japan
| | - Kousuke Tsuchiya
- Biomacromolecules Research Team, RIKEN Center for Sustainable Resource Science, Wako, Saitama 351-0198, Japan
- Department of Material Chemistry, Kyoto University, Nishikyo, Kyoto 615-8510, Japan
| | - Rintaro Ohtoshi
- Biomacromolecules Research Team, RIKEN Center for Sustainable Resource Science, Wako, Saitama 351-0198, Japan
- Spiber Inc., Tsuruoka, Yamagata 997-0052, Japan
| | | | | | - Yusuke Ito
- Spiber Inc., Tsuruoka, Yamagata 997-0052, Japan
| | - Hiroyuki Nakamura
- Biomacromolecules Research Team, RIKEN Center for Sustainable Resource Science, Wako, Saitama 351-0198, Japan
- Spiber Inc., Tsuruoka, Yamagata 997-0052, Japan
| | - Akio Tanikawa
- Graduate School of Agricultural and Life Sciences, University of Tokyo, Yayoi, Bunkyo, Tokyo 113-8657, Japan
| | - Yuya Suzuki
- Graduate School of Life and Environmental Sciences, University of Tsukuba, Tennodai, Tsukuba, Ibaraki 305-8572, Japan
- The United Graduate School of Agricultural Sciences, Kagoshima University, Korimoto, Kagoshima 890-0065, Japan
| | - Takeaki Ichikawa
- Kokugakuin Kugayama High School, Suginami, Tokyo 168-0082, Japan
| | - Shohei Fujita
- Graduate School of Agriculture, Saga University, Saga 840-8502, Japan
| | - Masayuki Fujiwara
- Institute for Advanced Biosciences, Keio University, Tsuruoka, Yamagata 997-0017, Japan
| | - Masaru Tomita
- Institute for Advanced Biosciences, Keio University, Tsuruoka, Yamagata 997-0017, Japan
- Faculty of Environment and Information Studies, Keio University, Fujisawa, Kanagawa 252-8520, Japan
- Graduate School of Media and Governance, Keio University, Fujisawa, Kanagawa 252-8520, Japan
| | - Sean J. Blamires
- Evolution and Ecology Research Centre, University of New South Wales, Sydney, NSW 2052, Australia
| | - Jo-Ann Chuah
- Biomacromolecules Research Team, RIKEN Center for Sustainable Resource Science, Wako, Saitama 351-0198, Japan
| | - Hamish Craig
- Biomacromolecules Research Team, RIKEN Center for Sustainable Resource Science, Wako, Saitama 351-0198, Japan
- Evolution and Ecology Research Centre, University of New South Wales, Sydney, NSW 2052, Australia
| | - Choon P. Foong
- Biomacromolecules Research Team, RIKEN Center for Sustainable Resource Science, Wako, Saitama 351-0198, Japan
- Department of Material Chemistry, Kyoto University, Nishikyo, Kyoto 615-8510, Japan
| | - Gabriele Greco
- Department of Civil, Environmental and Mechanical Engineering, University of Trento, Via Mesiano 77, I-38123 Trento, Italy
| | - Juan Guan
- Beijing Advanced Innovation Center for Biomedical Engineering, School of Materials Science and Engineering, Beihang University, Beijing 100191, China
| | - Chris Holland
- Natural Materials Group, Department of Materials Science and Engineering, The University of Sheffield, Mappin Street, Sheffield S1 3JD, UK
| | - David L. Kaplan
- Department of Biomedical Engineering, Tufts University, Medford, MA 02155, USA
| | - Kumar Sudesh
- School of Biological Sciences, Universiti Sains Malaysia, 11800 Penang, Malaysia
| | - Biman B. Mandal
- Department of Biosciences and Bioengineering, Indian Institute of Technology Guwahati (IITG), Guwahati, 781 039 Assam, India
- Center for Nanotechnology, IITG, Guwahati, 781 039 Assam, India
- School of Health Sciences and Technology, IITG, Guwahati, 781 039 Assam, India
| | - Y. Norma-Rashid
- Institute of Biological Sciences, Faculty of Science, University of Malaya, 50603 Kuala Lumpur, Malaysia
| | - Nur A. Oktaviani
- Biomacromolecules Research Team, RIKEN Center for Sustainable Resource Science, Wako, Saitama 351-0198, Japan
| | - Rucsanda C. Preda
- Department of Biomedical Engineering, Tufts University, Medford, MA 02155, USA
| | - Nicola M. Pugno
- Department of Civil, Environmental and Mechanical Engineering, University of Trento, Via Mesiano 77, I-38123 Trento, Italy
- School of Engineering and Materials Science, Queen Mary University of London, Mile End Road, E1 4NS London, UK
| | - Rangam Rajkhowa
- Institute for Frontier Materials, Deakin University, Waurn Ponds, VIC 3216, Australia
| | - Xiaoqin Wang
- College of Textile and Clothing Engineering, Soochow University, Suzhou 215123, China
| | - Kenjiro Yazawa
- Biomacromolecules Research Team, RIKEN Center for Sustainable Resource Science, Wako, Saitama 351-0198, Japan
| | - Zhaozhu Zheng
- College of Textile and Clothing Engineering, Soochow University, Suzhou 215123, China
| | - Keiji Numata
- Biomacromolecules Research Team, RIKEN Center for Sustainable Resource Science, Wako, Saitama 351-0198, Japan
- Department of Material Chemistry, Kyoto University, Nishikyo, Kyoto 615-8510, Japan
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3
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Correa-Garhwal SM, Babb PL, Voight BF, Hayashi CY. Golden orb-weaving spider (Trichonephila clavipes) silk genes with sex-biased expression and atypical architectures. G3-GENES GENOMES GENETICS 2021; 11:6044138. [PMID: 33561241 PMCID: PMC8022711 DOI: 10.1093/g3journal/jkaa039] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/02/2020] [Accepted: 12/05/2020] [Indexed: 11/29/2022]
Abstract
Spider silks are renowned for their high-performance mechanical properties. Contributing to these properties are proteins encoded by the spidroin (spider fibroin) gene family. Spidroins have been discovered mostly through cDNA studies of females based on the presence of conserved terminal regions and a repetitive central region. Recently, genome sequencing of the golden orb-web weaver, Trichonephila clavipes, provided a complete picture of spidroin diversity. Here, we refine the annotation of T. clavipes spidroin genes including the reclassification of some as non-spidroins. We rename these non-spidroins as spidroin-like (SpL) genes because they have repetitive sequences and amino acid compositions like spidroins, but entirely lack the archetypal terminal domains of spidroins. Insight into the function of these spidroin and SpL genes was then examined through tissue- and sex-specific gene expression studies. Using qPCR, we show that some silk genes are upregulated in male silk glands compared to females, despite males producing less silk in general. We also find that an enigmatic spidroin that lacks a spidroin C-terminal domain is highly expressed in silk glands, suggesting that spidroins could assemble into fibers without a canonical terminal region. Further, we show that two SpL genes are expressed in silk glands, with one gene highly evolutionarily conserved across species, providing evidence that particular SpL genes are important to silk production. Together, these findings challenge long-standing paradigms regarding the evolutionary and functional significance of the proteins and conserved motifs essential for producing spider silks.
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Affiliation(s)
- Sandra M Correa-Garhwal
- Division of Invertebrate Zoology and Sackler Institute for Comparative Genomics, American Museum of Natural History, New York, NY 10024, USA
| | - Paul L Babb
- Department of Systems Pharmacology and Translational Therapeutics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA.,Department of Genetics, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Benjamin F Voight
- Department of Systems Pharmacology and Translational Therapeutics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA.,Department of Genetics, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA 19104, USA.,Institute for Translational Medicine and Therapeutics, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Cheryl Y Hayashi
- Division of Invertebrate Zoology and Sackler Institute for Comparative Genomics, American Museum of Natural History, New York, NY 10024, USA
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6
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Crews SC, Garcia EL, Spagna JC, Van Dam MH, Esposito LA. The life aquatic with spiders (Araneae): repeated evolution of aquatic habitat association in Dictynidae and allied taxa. Zool J Linn Soc 2019. [DOI: 10.1093/zoolinnean/zlz139] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
Abstract
Despite the dominance of terrestriality in spiders, species across a diverse array of families are associated with aquatic habitats. Many species in the spider family Dictynidae are associated with water, either living near it or, in the case of Argyroneta aquatica, in it. Previous studies have indicated that this association arose once within the family. Here we test the hypothesis of a single origin via the broadest phylogeny of dictynids and related ‘marronoids’ to date, using several taxa that were not previously sampled in molecular analyses to provide the first quantitative test of the hypothesis put forth by Wheeler et al. (2016). We sampled 281 terminal taxa from 14 families, assembling a matrix with 4380 total base pairs of data from most taxa. We also assembled an atlas of morphological traits with potential significance for both ecology and taxonomy. Our resulting trees indicate that an aquatic habitat association has arisen multiple times within dictynids. Dictynidae and the genus Dictyna are polyphyletic and the genera Lathys and Cicurina remain unplaced. A review of aquatic habitat associations in spiders indicates that it occurs in members of at least 21 families. With our morphological atlas, we explore characters that have been implicated in aiding an aquatic lifestyle, which in the past may have caused confusion regarding taxon placement. Our results indicate that not all spiders with traits thought to be useful for aquatic habitat associations occupy such habitats, and that some spider taxa lacking these traits are nonetheless associated with water.
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Affiliation(s)
- Sarah C Crews
- California Academy of Sciences, Department of Entomology, San Francisco, CA, USA
| | - Erika L Garcia
- California Academy of Sciences, Department of Entomology, San Francisco, CA, USA
- San Francisco State University, San Francisco, CA
- Denver Museum of Nature & Science, Department of Zoology, Denver, CO, USA
| | - Joseph C Spagna
- Department of Biology, William Paterson University, Wayne, NJ, USA
| | - Matthew H Van Dam
- California Academy of Sciences, Department of Entomology, San Francisco, CA, USA
| | - Lauren A Esposito
- California Academy of Sciences, Department of Entomology, San Francisco, CA, USA
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7
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Correa-Garhwal SM, Clarke TH, Janssen M, Crevecoeur L, McQuillan BN, Simpson AH, Vink CJ, Hayashi CY. Spidroins and Silk Fibers of Aquatic Spiders. Sci Rep 2019; 9:13656. [PMID: 31541123 PMCID: PMC6754431 DOI: 10.1038/s41598-019-49587-y] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2019] [Accepted: 08/24/2019] [Indexed: 12/21/2022] Open
Abstract
Spiders are commonly found in terrestrial environments and many rely heavily on their silks for fitness related tasks such as reproduction and dispersal. Although rare, a few species occupy aquatic or semi-aquatic habitats and for them, silk-related specializations are also essential to survive in aquatic environments. Most spider silks studied to date are from cob-web and orb-web weaving species, leaving the silks from many other terrestrial spiders as well as water-associated spiders largely undescribed. Here, we characterize silks from three Dictynoidea species: the aquatic spiders Argyroneta aquatica and Desis marina as well as the terrestrial Badumna longinqua. From silk gland RNA-Seq libraries, we report a total of 47 different homologs of the spidroin (spider fibroin) gene family. Some of these 47 spidroins correspond to known spidroin types (aciniform, ampullate, cribellar, pyriform, and tubuliform), while other spidroins represent novel branches of the spidroin gene family. We also report a hydrophobic amino acid motif (GV) that, to date, is found only in the spidroins of aquatic and semi-aquatic spiders. Comparison of spider silk sequences to the silks from other water-associated arthropods, shows that there is a diversity of strategies to function in aquatic environments.
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Affiliation(s)
- Sandra M Correa-Garhwal
- Department of Evolution, Ecology, and Organismal Biology, University of California, Riverside, CA, 92591, USA.
| | - Thomas H Clarke
- Department of Evolution, Ecology, and Organismal Biology, University of California, Riverside, CA, 92591, USA
- J. Craig Venter Institute, Rockville, MD, 28050, USA
| | | | - Luc Crevecoeur
- Limburg Dome for Nature Study, Provincial Nature Center, Genk, 3600, Belgium
| | | | | | - Cor J Vink
- Canterbury Museum, Christchurch, 8013, New Zealand
| | - Cheryl Y Hayashi
- Department of Evolution, Ecology, and Organismal Biology, University of California, Riverside, CA, 92591, USA
- Division of Invertebrate Zoology and Sackler Institute for Comparative Genomics, American Museum of Natural History, New York, NY, 10024, USA
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