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Markee A, Godfrey RK, Frandsen PB, Weng YM, Triant DA, Kawahara AY. De Novo Long-Read Genome Assembly and Annotation of the Luna Moth (Actias luna) Fully Resolves Repeat-Rich Silk Genes. Genome Biol Evol 2024; 16:evae148. [PMID: 38957923 PMCID: PMC11258402 DOI: 10.1093/gbe/evae148] [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: 03/29/2024] [Revised: 06/18/2024] [Accepted: 06/25/2024] [Indexed: 07/04/2024] Open
Abstract
We present the first long-read de novo assembly and annotation of the luna moth (Actias luna) and provide the full characterization of heavy chain fibroin (h-fibroin), a long and highly repetitive gene (>20 kb) essential in silk fiber production. There are >160,000 described species of moths and butterflies (Lepidoptera), but only within the last 5 years have we begun to recover high-quality annotated whole genomes across the order that capture h-fibroin. Using PacBio HiFi reads, we produce the first high-quality long-read reference genome for this species. The assembled genome has a length of 532 Mb, a contig N50 of 16.8 Mb, an L50 of 14 contigs, and 99.4% completeness (BUSCO). Our annotation using Bombyx mori protein and A. luna RNAseq evidence captured a total of 20,866 genes at 98.9% completeness with 10,267 functionally annotated proteins and a full-length h-fibroin annotation of 2,679 amino acid residues.
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Affiliation(s)
- Amanda Markee
- McGuire Center for Lepidoptera and Biodiversity, Florida Museum of Natural History, University of Florida, Gainesville, FL 32611, USA
| | | | - Paul B Frandsen
- Department of Plant and Wildlife Sciences, Brigham Young University, Provo, UT 84602, USA
| | - Yi-Ming Weng
- McGuire Center for Lepidoptera and Biodiversity, Florida Museum of Natural History, University of Florida, Gainesville, FL 32611, USA
| | - Deborah A Triant
- Department of Biochemistry and Molecular Genetics, University of Virginia, Charlottesville, VA 22908, USA
| | - Akito Y Kawahara
- McGuire Center for Lepidoptera and Biodiversity, Florida Museum of Natural History, University of Florida, Gainesville, FL 32611, USA
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2
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Moreno-Tortolero RO, Luo Y, Parmeggiani F, Skaer N, Walker R, Serpell LC, Holland C, Davis SA. Molecular organization of fibroin heavy chain and mechanism of fibre formation in Bombyx mori. Commun Biol 2024; 7:786. [PMID: 38951579 PMCID: PMC11217467 DOI: 10.1038/s42003-024-06474-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2024] [Accepted: 06/19/2024] [Indexed: 07/03/2024] Open
Abstract
Fibroins' transition from liquid to solid is fundamental to spinning and underpins the impressive native properties of silk. Herein, we establish a fibroin heavy chain fold for the Silk-I polymorph, which could be relevant for other similar proteins, and explains mechanistically the liquid-to-solid transition of this silk, driven by pH reduction and flow stress. Combining spectroscopy and modelling we propose that the liquid Silk-I fibroin heavy chain (FibH) from the silkworm, Bombyx mori, adopts a newly reported β-solenoid structure. Similarly, using rheology we propose that FibH N-terminal domain (NTD) templates reversible higher-order oligomerization driven by pH reduction. Our integrated approach bridges the gap in understanding FibH structure and provides insight into the spatial and temporal hierarchical self-assembly across length scales. Our findings elucidate the complex rheological behaviour of Silk-I, solutions and gels, and the observed liquid crystalline textures within the silk gland. We also find that the NTD undergoes hydrolysis during standard regeneration, explaining key differences between native and regenerated silk feedstocks. In general, in this study we emphasize the unique characteristics of native and native-like silks, offering a fresh perspective on our fundamental understanding of silk-fibre production and applications.
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Affiliation(s)
- Rafael O Moreno-Tortolero
- School of Chemistry, University of Bristol, Cantock's Close, Bristol, BS8 1TS, UK.
- Max Planck-Bristol Centre for Minimal Biology, University of Bristol, Bristol, BS8 1TS, UK.
| | - Yijie Luo
- School of Chemistry, University of Bristol, Cantock's Close, Bristol, BS8 1TS, UK
- School of Biochemistry, University of Bristol, University Walk, Bristol, BS8 1TD, UK
| | - Fabio Parmeggiani
- School of Chemistry, University of Bristol, Cantock's Close, Bristol, BS8 1TS, UK
- School of Biochemistry, University of Bristol, University Walk, Bristol, BS8 1TD, UK
- School of Pharmacy and Pharmaceutical Sciences, Cardiff University, Redwood Building, King Edward VII Ave, Cardiff, CF10 3NB, UK
| | - Nick Skaer
- Orthox Ltd, Milton Park, 66 Innovation Drive, Abingdon, OX14 4RQ, UK
| | - Robert Walker
- Orthox Ltd, Milton Park, 66 Innovation Drive, Abingdon, OX14 4RQ, UK
| | - Louise C Serpell
- Sussex Neuroscience, School of Life Sciences, University of Sussex, Brighton, BN1 9QG, UK
| | - Chris Holland
- Department of Materials Science and Engineering, University of Sheffield, Mappin Street, Sheffield, S1 3JD, UK
| | - Sean A Davis
- School of Chemistry, University of Bristol, Cantock's Close, Bristol, BS8 1TS, UK.
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3
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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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4
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Tang X, Liu H, Wang X, Chang L, Liu Q, Xia Q, Zhao P. BmSLC7A5 is essential for silk protein synthesis and larval development in Bombyx mori. INSECT SCIENCE 2024. [PMID: 38284747 DOI: 10.1111/1744-7917.13314] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/10/2023] [Revised: 11/10/2023] [Accepted: 11/14/2023] [Indexed: 01/30/2024]
Abstract
Insects produce silk to form cocoons, nests, and webs, which are important for their survival and reproduction. However, little is known about the molecular mechanism of silk protein synthesis at the translation level. The solute carrier family 7 (SLC7) genes are involved in activating the target of rapamycin complex 1 (TORC1) signaling pathway and protein translation process, but the physiological roles of SLC7 genes in silk-producing insects have not been reported. Here, we found that amino acid signaling regulates silk protein synthesis and larval development via the L-type amino acid transporter 1 (LAT1; also known as SLC7A5) in Bombyx mori. A total of 12 SLC7 homologs were identified in the silkworm genome, among which BmSLC7A5 was found to be a silk gland-enriched gene and may be involved in leucine transport. Bioinformatics analysis indicated that SLC7A5 displays high homology and a close phylogenetic relationship in silk-producing insects. Subsequently, we found that leucine treatment significantly increased silk protein synthesis by improving the transcription and protein levels of silk genes. Furthermore, systemic and silk gland-specific knockout of BmSLC7A5 led to decreased silk protein synthesis by inhibiting TORC1 signaling, and somatic mutation also resulted in arrested development from the 5th instar to the early pupal stage. Altogether, our study reveals that BmSLC7A5 is involved in regulating silk protein synthesis and larval development by affecting the TORC1 signaling pathway, which provides a new strategy and target for improving silk yield.
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Affiliation(s)
- Xin Tang
- Integrative Science Center of Germplasm Creation in Western China (CHONGQING) Science City, Biological Science Research Center, Southwest University, Chongqing, China
- Chongqing Key Laboratory of Chinese Medicine & Health Science, Chongqing Academy of Chinese Materia Medica, Chongqing College of Traditional Chinese Medicine, Chongqing, China
| | - Huawei Liu
- Integrative Science Center of Germplasm Creation in Western China (CHONGQING) Science City, Biological Science Research Center, Southwest University, Chongqing, China
- Key Laboratory for Germplasm Creation in Upper Reaches of the Yangtze River, Ministry of Agriculture and Rural Affairs, Chongqing, China
| | - Xin Wang
- Integrative Science Center of Germplasm Creation in Western China (CHONGQING) Science City, Biological Science Research Center, Southwest University, Chongqing, China
- Key Laboratory for Germplasm Creation in Upper Reaches of the Yangtze River, Ministry of Agriculture and Rural Affairs, Chongqing, China
| | - Li Chang
- Integrative Science Center of Germplasm Creation in Western China (CHONGQING) Science City, Biological Science Research Center, Southwest University, Chongqing, China
- Key Laboratory for Germplasm Creation in Upper Reaches of the Yangtze River, Ministry of Agriculture and Rural Affairs, Chongqing, China
| | - Qingsong Liu
- Integrative Science Center of Germplasm Creation in Western China (CHONGQING) Science City, Biological Science Research Center, Southwest University, Chongqing, China
- Key Laboratory for Germplasm Creation in Upper Reaches of the Yangtze River, Ministry of Agriculture and Rural Affairs, Chongqing, China
| | - Qingyou Xia
- Integrative Science Center of Germplasm Creation in Western China (CHONGQING) Science City, Biological Science Research Center, Southwest University, Chongqing, China
- Key Laboratory for Germplasm Creation in Upper Reaches of the Yangtze River, Ministry of Agriculture and Rural Affairs, Chongqing, China
| | - Ping Zhao
- Integrative Science Center of Germplasm Creation in Western China (CHONGQING) Science City, Biological Science Research Center, Southwest University, Chongqing, China
- Key Laboratory for Germplasm Creation in Upper Reaches of the Yangtze River, Ministry of Agriculture and Rural Affairs, Chongqing, China
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5
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Li G, Li Y, He C, Wei Y, Cai K, Lu Q, Liu X, Zhu Y, Xu K. The promoting effects of pyriproxyfen on autophagy and apoptosis in silk glands of non-target insect silkworm, Bombyx mori. PESTICIDE BIOCHEMISTRY AND PHYSIOLOGY 2023; 196:105586. [PMID: 37945223 DOI: 10.1016/j.pestbp.2023.105586] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/27/2023] [Revised: 08/12/2023] [Accepted: 08/23/2023] [Indexed: 11/12/2023]
Abstract
Pyriproxyfen is a juvenile hormone analogue. The physiological effects of its low-concentration drift during the process of controlling agricultural and forestry pests on non-target organisms in the ecological environment are unpredictable, especially the effects on organs that play a key role in biological function are worthy of attention. The silk gland is an important organ for silk-secreting insects. Herein, we studied the effects of trace pyriproxyfen on autophagy and apoptosis of the silk gland in the lepidopteran model insect, Bombyx mori (silkworm). After treating fifth instar silkworm larvae with pyriproxyfen for 24 h, we found significant shrinkage, vacuolization, and fragmentation in the posterior silk gland (PSG). In addition, the results of autophagy-related genes of ATG8 and TUNEL assay also demonstrated that autophagy and apoptosis in the PSG of the silkworm was induced by pyriproxyfen. RNA-Seq results showed that pyriproxyfen treatment resulted in the activation of juvenile hormone signaling pathway genes and inhibition of 20-hydroxyecdysone (20E) signaling pathway genes. Among the 1808 significantly differentially expressed genes, 796 were upregulated and 1012 were downregulated. Among them, 30 genes were identified for autophagy-related signaling pathways, such as NOD-like receptor signaling pathway and mTOR signaling pathway, and 30 genes were identified for apoptosis-related signaling pathways, such as P53 signaling pathway and TNF signaling pathway. Further qRT-PCR and in vitro gland culture studies showed that the autophagy-related genes Atg5, Atg6, Atg12, Atg16 and the apoptosis-related genes Aif, Dronc, Dredd, and Caspase1 were responsive to the treatment of pyriproxyfen, with transcription levels up-regulated from 24 to 72 h. In addition, ATG5, ATG6, and Dronc genes had a more direct response to pyriproxyfen treatment. These results suggested that pyriproxyfen treatment could disrupt the hormone regulation in silkworms, promoting autophagy and apoptosis in the PSG. This study provides more evidence for the research on the damage of juvenile hormone analogues to non-target organisms or organs in the environment, and provides reference information for the scientific and rational use of juvenile hormone pesticides.
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Affiliation(s)
- Guoli Li
- College of Agriculture, Guangxi University, Nanning, Guangxi 530004, PR China
| | - Yizhe Li
- College of Agriculture, Guangxi University, Nanning, Guangxi 530004, PR China
| | - Chunhui He
- College of Agriculture, Guangxi University, Nanning, Guangxi 530004, PR China
| | - Yuting Wei
- College of Agriculture, Guangxi University, Nanning, Guangxi 530004, PR China
| | - Kunpei Cai
- College of Agriculture, Guangxi University, Nanning, Guangxi 530004, PR China
| | - Qingyu Lu
- College of Animal Sciences, Zhejiang University, Hangzhou 310058, PR China
| | - Xuebin Liu
- College of Agriculture, Guangxi University, Nanning, Guangxi 530004, PR China
| | - Yizhou Zhu
- College of Agriculture, Guangxi University, Nanning, Guangxi 530004, PR China
| | - Kaizun Xu
- College of Agriculture, Guangxi University, Nanning, Guangxi 530004, PR China; Guangxi Key Laboratory for Agro-Environment and Agric-Product Safety, National Demonstration Center for Experimental Plant Science Education, College of Agriculture, Guangxi University, Nanning, Guangxi 530004, PR China; Sericulture Institute of Guangxi University, Nanning, Guangxi 530004, PR China.
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6
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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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7
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Hotaling S, Wilcox ER, Heckenhauer J, Stewart RJ, Frandsen PB. Highly accurate long reads are crucial for realizing the potential of biodiversity genomics. BMC Genomics 2023; 24:117. [PMID: 36927511 PMCID: PMC10018877 DOI: 10.1186/s12864-023-09193-9] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2022] [Accepted: 02/17/2023] [Indexed: 03/18/2023] Open
Abstract
BACKGROUND Generating the most contiguous, accurate genome assemblies given available sequencing technologies is a long-standing challenge in genome science. With the rise of long-read sequencing, assembly challenges have shifted from merely increasing contiguity to correctly assembling complex, repetitive regions of interest, ideally in a phased manner. At present, researchers largely choose between two types of long read data: longer, but less accurate sequences, or highly accurate, but shorter reads (i.e., >Q20 or 99% accurate). To better understand how these types of long-read data as well as scale of data (i.e., mean length and sequencing depth) influence genome assembly outcomes, we compared genome assemblies for a caddisfly, Hesperophylax magnus, generated with longer, but less accurate, Oxford Nanopore (ONT) R9.4.1 and highly accurate PacBio HiFi (HiFi) data. Next, we expanded this comparison to consider the influence of highly accurate long-read sequence data on genome assemblies across 6750 plant and animal genomes. For this broader comparison, we used HiFi data as a surrogate for highly accurate long-reads broadly as we could identify when they were used from GenBank metadata. RESULTS HiFi reads outperformed ONT reads in all assembly metrics tested for the caddisfly data set and allowed for accurate assembly of the repetitive ~ 20 Kb H-fibroin gene. Across plants and animals, genome assemblies that incorporated HiFi reads were also more contiguous. For plants, the average HiFi assembly was 501% more contiguous (mean contig N50 = 20.5 Mb) than those generated with any other long-read data (mean contig N50 = 4.1 Mb). For animals, HiFi assemblies were 226% more contiguous (mean contig N50 = 20.9 Mb) versus other long-read assemblies (mean contig N50 = 9.3 Mb). In plants, we also found limited evidence that HiFi may offer a unique solution for overcoming genomic complexity that scales with assembly size. CONCLUSIONS Highly accurate long-reads generated with HiFi or analogous technologies represent a key tool for maximizing genome assembly quality for a wide swath of plants and animals. This finding is particularly important when resources only allow for one type of sequencing data to be generated. Ultimately, to realize the promise of biodiversity genomics, we call for greater uptake of highly accurate long-reads in future studies.
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Affiliation(s)
- Scott Hotaling
- Department of Watershed Sciences, Utah State University, Logan, UT, USA.
| | - Edward R Wilcox
- DNA Sequencing Center, Department of Biology, Brigham Young University, Provo, UT, USA
| | - Jacqueline Heckenhauer
- LOEWE Centre for Translational Biodiversity Genomics (LOEWE-TBG), Frankfurt, Germany
- Department of Terrestrial Zoology, Senckenberg Research Institute and Natural History Museum Frankfurt, 60325, Frankfurt, Germany
| | - Russell J Stewart
- Department of Biomedical Engineering, University of Utah, Salt Lake City, UT, USA
| | - Paul B Frandsen
- LOEWE Centre for Translational Biodiversity Genomics (LOEWE-TBG), Frankfurt, Germany.
- Department of Plant and Wildlife Sciences, Brigham Young University, Provo, UT, USA.
- Data Science Lab, Smithsonian Institution, Washington, DC, USA.
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8
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Miserez A, Yu J, Mohammadi P. Protein-Based Biological Materials: Molecular Design and Artificial Production. Chem Rev 2023; 123:2049-2111. [PMID: 36692900 PMCID: PMC9999432 DOI: 10.1021/acs.chemrev.2c00621] [Citation(s) in RCA: 23] [Impact Index Per Article: 23.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2022] [Indexed: 01/25/2023]
Abstract
Polymeric materials produced from fossil fuels have been intimately linked to the development of industrial activities in the 20th century and, consequently, to the transformation of our way of living. While this has brought many benefits, the fabrication and disposal of these materials is bringing enormous sustainable challenges. Thus, materials that are produced in a more sustainable fashion and whose degradation products are harmless to the environment are urgently needed. Natural biopolymers─which can compete with and sometimes surpass the performance of synthetic polymers─provide a great source of inspiration. They are made of natural chemicals, under benign environmental conditions, and their degradation products are harmless. Before these materials can be synthetically replicated, it is essential to elucidate their chemical design and biofabrication. For protein-based materials, this means obtaining the complete sequences of the proteinaceous building blocks, a task that historically took decades of research. Thus, we start this review with a historical perspective on early efforts to obtain the primary sequences of load-bearing proteins, followed by the latest developments in sequencing and proteomic technologies that have greatly accelerated sequencing of extracellular proteins. Next, four main classes of protein materials are presented, namely fibrous materials, bioelastomers exhibiting high reversible deformability, hard bulk materials, and biological adhesives. In each class, we focus on the design at the primary and secondary structure levels and discuss their interplays with the mechanical response. We finally discuss earlier and the latest research to artificially produce protein-based materials using biotechnology and synthetic biology, including current developments by start-up companies to scale-up the production of proteinaceous materials in an economically viable manner.
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Affiliation(s)
- Ali Miserez
- Center
for Sustainable Materials (SusMat), School of Materials Science and
Engineering, Nanyang Technological University
(NTU), Singapore637553
- School
of Biological Sciences, NTU, Singapore637551
| | - Jing Yu
- Center
for Sustainable Materials (SusMat), School of Materials Science and
Engineering, Nanyang Technological University
(NTU), Singapore637553
- Institute
for Digital Molecular Analytics and Science (IDMxS), NTU, 50 Nanyang Avenue, Singapore637553
| | - Pezhman Mohammadi
- VTT
Technical Research Centre of Finland Ltd., Espoo, UusimaaFI-02044, Finland
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9
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Genome sequence and silkomics of the spindle ermine moth, Yponomeuta cagnagella, representing the early diverging lineage of the ditrysian Lepidoptera. Commun Biol 2022; 5:1281. [PMID: 36418465 PMCID: PMC9684489 DOI: 10.1038/s42003-022-04240-9] [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: 02/01/2022] [Accepted: 11/09/2022] [Indexed: 11/24/2022] Open
Abstract
Many lepidopteran species produce silk, cocoons, feeding tubes, or nests for protection from predators and parasites for caterpillars and pupae. Yet, the number of lepidopteran species whose silk composition has been studied in detail is very small, because the genes encoding the major structural silk proteins tend to be large and repetitive, making their assembly and sequence analysis difficult. Here we have analyzed the silk of Yponomeuta cagnagella, which represents one of the early diverging lineages of the ditrysian Lepidoptera thus improving the coverage of the order. To obtain a comprehensive list of the Y. cagnagella silk genes, we sequenced and assembled a draft genome using Oxford Nanopore and Illumina technologies. We used a silk-gland transcriptome and a silk proteome to identify major silk components and verified the tissue specificity of expression of individual genes. A detailed annotation of the major genes and their putative products, including their complete sequences and exon-intron structures is provided. The morphology of silk glands and fibers are also shown. This study fills an important gap in our growing understanding of the structure, evolution, and function of silk genes and provides genomic resources for future studies of the chemical ecology of Yponomeuta species.
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10
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Stewart RJ, Frandsen PB, Pauls SU, Heckenhauer J. Conservation of Three-Dimensional Structure of Lepidoptera and Trichoptera L-Fibroins for 290 Million Years. Molecules 2022; 27:molecules27185945. [PMID: 36144689 PMCID: PMC9504780 DOI: 10.3390/molecules27185945] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2022] [Revised: 09/04/2022] [Accepted: 09/09/2022] [Indexed: 11/23/2022] Open
Abstract
The divergence of sister orders Trichoptera (caddisflies) and Lepidoptera (moths and butterflies) from a silk-spinning ancestor occurred around 290 million years ago. Trichoptera larvae are mainly aquatic, and Lepidoptera larvae are almost entirely terrestrial—distinct habitats that required molecular adaptation of their silk for deployment in water and air, respectively. The major protein components of their silks are heavy chain and light chain fibroins. In an effort to identify molecular changes in L-fibroins that may have contributed to the divergent use of silk in water and air, we used the ColabFold implementation of AlphaFold2 to predict three-dimensional structures of L-fibroins from both orders. A comparison of the structures revealed that despite the ancient divergence, profoundly different habitats, and low sequence conservation, a novel 10-helix core structure was strongly conserved in L-fibroins from both orders. Previously known intra- and intermolecular disulfide linkages were accurately predicted. Structural variations outside of the core may represent molecular changes that contributed to the evolution of insect silks adapted to water or air. The distributions of electrostatic potential, for example, were not conserved and present distinct order-specific surfaces for potential interactions with or modulation by external factors. Additionally, the interactions of L-fibroins with the H-fibroin C-termini are different for these orders; lepidopteran L-fibroins have N-terminal insertions that are not present in trichopteran L-fibroins, which form an unstructured ribbon in isolation but become part of an intermolecular β-sheet when folded with their corresponding H-fibroin C-termini. The results are an example of protein structure prediction from deep sequence data of understudied proteins made possible by AlphaFold2.
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Affiliation(s)
- Russell J. Stewart
- Department of Biomedical Engineering, University of Utah, Salt Lake City, UT 84112, USA
- Correspondence:
| | - Paul B. Frandsen
- Department of Plant and Wildlife Sciences, Brigham Young University, Provo, UT 84062, USA
| | - Steffen U. Pauls
- LOEWE Centre for Translational Biodiversity Genomics (LOEWE-TBG), 60325 Frankfurt, Germany
- Senckenberg Research Institute and Natural History Museum Frankfurt, 60325 Frankfurt, Germany
- Institute for Insect Biotechnology, Justus-Liebig-University, 35392 Gießen, Germany
| | - Jacqueline Heckenhauer
- LOEWE Centre for Translational Biodiversity Genomics (LOEWE-TBG), 60325 Frankfurt, Germany
- Senckenberg Research Institute and Natural History Museum Frankfurt, 60325 Frankfurt, Germany
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11
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Rouhová L, Sehadová H, Pauchová L, Hradilová M, Žurovcová M, Šerý M, Rindoš M, Žurovec M. Using the multi-omics approach to reveal the silk composition in Plectrocnemia conspersa. Front Mol Biosci 2022; 9:945239. [PMID: 36060257 PMCID: PMC9432349 DOI: 10.3389/fmolb.2022.945239] [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: 05/16/2022] [Accepted: 07/19/2022] [Indexed: 11/29/2022] Open
Abstract
Similar to Lepidoptera, the larvae of Trichoptera are also capable of producing silk. Plectrocnemia conspersa, a predatory species belonging to the suborder Annulipalpia, builds massive silken retreats with preycapturing nets. In this study, we describe the silk glands of P. conspersa and use the multi-omics methods to obtain a complete picture of the fiber composition. A combination of silk gland-specific transcriptome and proteomic analyses of the spun-out fibers yielded 27 significant candidates whose full-length sequences and gene structures were retrieved from the publicly available genome database. About one-third of the candidates were completely novel proteins for which there are no described homologs, including a group of five pseudofibroins, proteins with a composition similar to fibroin heavy chain. The rest were homologs of lepidopteran silk proteins, although some had a larger number of paralogs. On the other hand, P. conspersa fibers lacked some proteins that are regular components in moth silk. In summary, the multi-omics approach provides an opportunity to compare the overall composition of silk with other insect species. A sufficient number of such studies will make it possible to distinguish between the basic components of all silks and the proteins that represent the adaptation of the fibers for specific purposes or environments.
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Affiliation(s)
- Lenka Rouhová
- Biology Centre of the Czech Academy of Sciences, Institute of Entomology, Ceske Budejovice, Czechia
- Faculty of Science, University of South Bohemia, Ceske Budejovice, Czechia
| | - Hana Sehadová
- Biology Centre of the Czech Academy of Sciences, Institute of Entomology, Ceske Budejovice, Czechia
- Faculty of Science, University of South Bohemia, Ceske Budejovice, Czechia
| | - Lucie Pauchová
- Biology Centre of the Czech Academy of Sciences, Institute of Entomology, Ceske Budejovice, Czechia
| | - Miluše Hradilová
- Institute of Molecular Genetics, Academy of Sciences of the Czech Republic, Praha, Czechia
| | - Martina Žurovcová
- Biology Centre of the Czech Academy of Sciences, Institute of Entomology, Ceske Budejovice, Czechia
| | - Michal Šerý
- Biology Centre of the Czech Academy of Sciences, Institute of Entomology, Ceske Budejovice, Czechia
| | - Michal Rindoš
- Biology Centre of the Czech Academy of Sciences, Institute of Entomology, Ceske Budejovice, Czechia
- Faculty of Forestry and Wood Sciences, Czech University of Life Sciences Prague, Prague, Czechia
| | - Michal Žurovec
- Biology Centre of the Czech Academy of Sciences, Institute of Entomology, Ceske Budejovice, Czechia
- Faculty of Science, University of South Bohemia, Ceske Budejovice, Czechia
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12
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Kawahara AY, Storer CG, Markee A, Heckenhauer J, Powell A, Plotkin D, Hotaling S, Cleland TP, Dikow RB, Dikow T, Kuranishi RB, Messcher R, Pauls SU, Stewart RJ, Tojo K, Frandsen PB. Long-read HiFi sequencing correctly assembles repetitive heavy fibroin silk genes in new moth and caddisfly genomes. GIGABYTE 2022; 2022:gigabyte64. [PMID: 36824508 PMCID: PMC9693786 DOI: 10.46471/gigabyte.64] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2022] [Accepted: 06/24/2022] [Indexed: 11/09/2022] Open
Abstract
Insect silk is a versatile biomaterial. Lepidoptera and Trichoptera display some of the most diverse uses of silk, with varying strength, adhesive qualities, and elastic properties. Silk fibroin genes are long (>20 Kbp), with many repetitive motifs that make them challenging to sequence. Most research thus far has focused on conserved N- and C-terminal regions of fibroin genes because a full comparison of repetitive regions across taxa has not been possible. Using the PacBio Sequel II system and SMRT sequencing, we generated high fidelity (HiFi) long-read genomic and transcriptomic sequences for the Indianmeal moth (Plodia interpunctella) and genomic sequences for the caddisfly Eubasilissa regina. Both genomes were highly contiguous (N50 = 9.7 Mbp/32.4 Mbp, L50 = 13/11) and complete (BUSCO complete = 99.3%/95.2%), with complete and contiguous recovery of silk heavy fibroin gene sequences. We show that HiFi long-read sequencing is helpful for understanding genes with long, repetitive regions.
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Affiliation(s)
- Akito Y. Kawahara
- McGuire Center for Lepidoptera and Biodiversity, Florida Museum of Natural History, University of Florida, Gainesville, FL 32611, USA
| | - Caroline G. Storer
- McGuire Center for Lepidoptera and Biodiversity, Florida Museum of Natural History, University of Florida, Gainesville, FL 32611, USA
- Pacific Biosciences, 1305 O’Brien Dr., Menlo Park, CA 94025, USA
| | - Amanda Markee
- McGuire Center for Lepidoptera and Biodiversity, Florida Museum of Natural History, University of Florida, Gainesville, FL 32611, USA
- School of Natural Resources and the Environment, University of Florida, Gainesville, FL 32611, USA
| | - Jacqueline Heckenhauer
- LOEWE Centre for Translational Biodiversity Genomics (LOEWE-TBG), Frankfurt 60325, Germany
- Department of Terrestrial Zoology, Senckenberg Research Institute and Natural History Museum Frankfurt, Frankfurt 60325, Germany
| | - Ashlyn Powell
- Department of Plant and Wildlife Sciences, Brigham Young University, Provo, UT 84602, USA
| | - David Plotkin
- McGuire Center for Lepidoptera and Biodiversity, Florida Museum of Natural History, University of Florida, Gainesville, FL 32611, USA
| | - Scott Hotaling
- School of Biological Sciences, Washington State University, Pullman, WA, USA
| | - Timothy P. Cleland
- Museum Conservation Institute, Smithsonian Institution, Suitland, MD 20746, USA
| | - Rebecca B. Dikow
- Data Science Lab, Office of the Chief Information Officer, Smithsonian Institution, Washington, DC 20002, USA
| | - Torsten Dikow
- Department of Entomology, National Museum of Natural History, Smithsonian Institution, Washington, DC, USA
| | - Ryoichi B. Kuranishi
- Graduate School of Science, Chiba University, Chiba 263-8522, Japan
- Kanagawa Institute of Technology, Kanagawa 243-0292, Japan
| | - Rebeccah Messcher
- McGuire Center for Lepidoptera and Biodiversity, Florida Museum of Natural History, University of Florida, Gainesville, FL 32611, USA
| | - Steffen U. Pauls
- LOEWE Centre for Translational Biodiversity Genomics (LOEWE-TBG), Frankfurt 60325, Germany
- Department of Terrestrial Zoology, Senckenberg Research Institute and Natural History Museum Frankfurt, Frankfurt 60325, Germany
- Institute for Insect Biotechnology, Justus-Liebig-University, Gießen 35390, Germany
| | - Russell J. Stewart
- Department of Biomedical Engineering, University of Utah, Salt Lake City, UT 84112, USA
| | - Koji Tojo
- Department of Biology, Shinshu University, Matsumoto, Nagano 390-8621, Japan
| | - Paul B. Frandsen
- Department of Plant and Wildlife Sciences, Brigham Young University, Provo, UT 84602, USA
- Data Science Lab, Office of the Chief Information Officer, Smithsonian Institution, Washington, DC 20002, USA
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13
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Zabelina V, Takasu Y, Sehadova H, Yonemura N, Nakajima K, Sezutsu H, Sery M, Zurovec M, Sehnal F, Tamura T. Mutation in Bombyx mori fibrohexamerin (P25) gene causes reorganization of rough endoplasmic reticulum in posterior silk gland cells and alters morphology of fibroin secretory globules in the silk gland lumen. INSECT BIOCHEMISTRY AND MOLECULAR BIOLOGY 2021; 135:103607. [PMID: 34102294 DOI: 10.1016/j.ibmb.2021.103607] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/14/2021] [Revised: 05/30/2021] [Accepted: 05/31/2021] [Indexed: 06/12/2023]
Abstract
Larvae of many lepidopteran species produce a mixture of secretory proteins, known as silk, for building protective shelters and cocoons. Silk consists of a water-insoluble silk filament core produced in the posterior silk gland (PSG) and a sticky hydrophilic coating produced by the middle silk gland (MSG). In Bombyx mori, the fiber core comprises three proteins: heavy chain fibroin (Fib-H), light chain fibroin (Fib-L) and fibrohexamerin (Fhx, previously referred to as P25). To learn more about the role of Fhx, we used transcription activator-like effector nuclease (TALEN) mutagenesis and prepared a homozygous line with a null mutation in the Fhx gene. Our characterization of cocoon morphology and silk quality showed that the mutation had very little effect. However, a detailed inspection of the secretory cells in the posterior silk gland (PSG) of mid-last-instar mutant larvae revealed temporary changes in the morphology of the endoplasmic reticulum. We also observed a morphological difference in fibroin secretory globules stored in the PSG lumen of Fhx mutants, which suggests that their fibroin complexes have a slightly lower solubility. Finally, we performed an LC-MS-based quantitative proteomic analysis comparing mutant and wild-type (wt) cocoon proteins and found a high abundance of a 16 kDa secretory protein likely involved in fibroin solubility. Overall, our study shows that whilst Fhx is dispensable for silk formation, it contributes to the stability of fibroin complexes during intracellular transport and affects the morphology of fibroin secretory globules in the PSG lumen.
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Affiliation(s)
- Valeriya Zabelina
- National Agriculture and Food Research Organization, 1-2 Owashi, Tsukuba, Ibaraki, 305-8634, Japan; Biology Centre of the Czech Academy of Sciences and Faculty of Sciences, University of South Bohemia, 370 05, České Budějovice, Czech Republic
| | - Yoko Takasu
- National Agriculture and Food Research Organization, 1-2 Owashi, Tsukuba, Ibaraki, 305-8634, Japan
| | - Hana Sehadova
- Biology Centre of the Czech Academy of Sciences and Faculty of Sciences, University of South Bohemia, 370 05, České Budějovice, Czech Republic; Faculty of Science, University of South Bohemia, Branisovska 31, 370 05, Ceske Budejovice, Czech Republic
| | - Naoyuki Yonemura
- National Agriculture and Food Research Organization, 1-2 Owashi, Tsukuba, Ibaraki, 305-8634, Japan
| | - Kenichi Nakajima
- National Agriculture and Food Research Organization, 1-2 Owashi, Tsukuba, Ibaraki, 305-8634, Japan
| | - Hideki Sezutsu
- National Agriculture and Food Research Organization, 1-2 Owashi, Tsukuba, Ibaraki, 305-8634, Japan
| | - Michal Sery
- Biology Centre of the Czech Academy of Sciences and Faculty of Sciences, University of South Bohemia, 370 05, České Budějovice, Czech Republic
| | - Michal Zurovec
- Biology Centre of the Czech Academy of Sciences and Faculty of Sciences, University of South Bohemia, 370 05, České Budějovice, Czech Republic; Faculty of Science, University of South Bohemia, Branisovska 31, 370 05, Ceske Budejovice, Czech Republic.
| | - Frantisek Sehnal
- Biology Centre of the Czech Academy of Sciences and Faculty of Sciences, University of South Bohemia, 370 05, České Budějovice, Czech Republic.
| | - Toshiki Tamura
- Institute of Sericulture, Iikura 1053, 300-0324, Ami-machi, Ibaraki, Japan.
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14
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Xing Y, Thanasirungkul W, Adeel MM, Yu J, Aslam A, Chi DF. Identification and analysis of olfactory genes in Dioryctria abietella based on the antennal transcriptome. COMPARATIVE BIOCHEMISTRY AND PHYSIOLOGY D-GENOMICS & PROTEOMICS 2021; 38:100814. [PMID: 33706113 DOI: 10.1016/j.cbd.2021.100814] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/24/2020] [Revised: 02/09/2021] [Accepted: 02/10/2021] [Indexed: 10/22/2022]
Abstract
The coneworm Dioryctria abietella (Lepidoptera: Pyralidae) is an economy devastating pest that infests many valuable conifer species in the Holarctic regions, such as Pinus koraiensis Siebold and Zucc. The chemosensory system plays a crucial role in the mating, foraging, and ovipositing of this pest, and therefore it is desirable to identify chemosensory molecules for pest control. However, little is known at molecular level about the olfactory mechanisms in D. abietella. In the present study, we first established antennal transcriptomes of D. abietella and identified 132 putative chemosensory genes, including 15 odorant-binding proteins, 18 chemosensory proteins, 65 odorant receptors, 5 sensory neuron membrane proteins, 24 ionotropic receptors, and 5 gustatory receptors. In addition, phylogenetic trees were constructed for chemosensory genes to investigate the orthologs between D. abietella and other species of insects. Furthermore, we also compared the patterns of motifs between OBPs and CSPs using MEME. Additionally, we observed that most of DabiOBPs and DabiCSPs had the antenna-biased expression by quantitative real-time PCR (RT-qPCR), and there was a higher expression of DabiPBP1 and DabiPBP2 in male antennae than in female antennae. The binding sites of DabiPBPs (DabiPBP1, DabiPBP2) and DabiPRs (DabiOR19, DabiOR31) to the sex pheromone were predicted well by three-dimensional docking structure modelling and molecular docking. Our finding supplied a foundation for further research on the binding process of OBPs or CSPs and sensing process of ORs, SNMPs, IRs or GRs in D. abietella.
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Affiliation(s)
- Ya Xing
- Key Laboratory for Sustainable Forest Ecosysttem Management of Ministry of Education, College of Forestry, Northeast Forestry University, Harbin 150040, Heilongjiang, People's Republic of China
| | - Wariya Thanasirungkul
- Key Laboratory for Sustainable Forest Ecosysttem Management of Ministry of Education, College of Forestry, Northeast Forestry University, Harbin 150040, Heilongjiang, People's Republic of China
| | - Muhammad Muzammal Adeel
- Agricultural Bioinformatics Key Laboratory of Hubei Province, Hubei Engineering Technology Research Center of Agricultural Big Data, College of Informatics, Huazhong Agricultural University, Wuhan 430070, Hubei, People's Republic of China
| | - Jia Yu
- Key Laboratory for Sustainable Forest Ecosysttem Management of Ministry of Education, College of Forestry, Northeast Forestry University, Harbin 150040, Heilongjiang, People's Republic of China
| | - Asad Aslam
- Key Laboratory for Sustainable Forest Ecosysttem Management of Ministry of Education, College of Forestry, Northeast Forestry University, Harbin 150040, Heilongjiang, People's Republic of China
| | - De-Fu Chi
- Key Laboratory for Sustainable Forest Ecosysttem Management of Ministry of Education, College of Forestry, Northeast Forestry University, Harbin 150040, Heilongjiang, People's Republic of China.
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15
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Rouhova L, Kludkiewicz B, Sehadova H, Sery M, Kucerova L, Konik P, Zurovec M. Silk of the common clothes moth, Tineola bisselliella, a cosmopolitan pest belonging to the basal ditrysian moth line. INSECT BIOCHEMISTRY AND MOLECULAR BIOLOGY 2021; 130:103527. [PMID: 33476773 DOI: 10.1016/j.ibmb.2021.103527] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/07/2020] [Revised: 01/10/2021] [Accepted: 01/11/2021] [Indexed: 06/12/2023]
Abstract
Many lepidopteran larvae produce silk secretions to build feeding tubes and cocoons that play important protective roles in their lives. Recent research on the silk of bombycoid and pyralid moths has shown that it contains several highly abundant silk components with remarkable mechanical properties. It was also found to contain a number of other proteins of which the functions have yet to be identified. To gain an overview of the silk composition in more primitive lepidopteran species and to identify the core silk components common to most species, we analyzed the cocoon proteins of Tineola bisselliella, which belongs to the basal ditrysian moth line. Using de novo transcriptome sequencing combined with mass spectrometry (MS)-based proteomics, we detected more than 100 secretory proteins in the silk cocoons. Fibroin, sericins, and protease inhibitors were found to be the most abundant proteins, along with several novel candidate silk components. We also verified the tissue and developmental stage specificity of the silk protein expression and characterized the morphology of both the silk glands and silk in T. bisselliella. Our study provides a detailed analysis of silk in the primitive moth, expands the known set of silk-specific genes in Lepidoptera, and helps to elucidate their evolutionary relationships.
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Affiliation(s)
- Lenka Rouhova
- Biology Centre of the Czech Academy of Sciences, Institute of Entomology, Branisovska 31, 370 05, Ceske Budejovice, Czech Republic; Faculty of Sciences, University of South Bohemia, Branisovska 31, 370 05, Ceske Budejovice, Czech Republic
| | - Barbara Kludkiewicz
- Biology Centre of the Czech Academy of Sciences, Institute of Entomology, Branisovska 31, 370 05, Ceske Budejovice, Czech Republic
| | - Hana Sehadova
- Biology Centre of the Czech Academy of Sciences, Institute of Entomology, Branisovska 31, 370 05, Ceske Budejovice, Czech Republic; Faculty of Sciences, University of South Bohemia, Branisovska 31, 370 05, Ceske Budejovice, Czech Republic
| | - Michal Sery
- Biology Centre of the Czech Academy of Sciences, Institute of Entomology, Branisovska 31, 370 05, Ceske Budejovice, Czech Republic
| | - Lucie Kucerova
- Biology Centre of the Czech Academy of Sciences, Institute of Entomology, Branisovska 31, 370 05, Ceske Budejovice, Czech Republic
| | - Peter Konik
- Faculty of Sciences, University of South Bohemia, Branisovska 31, 370 05, Ceske Budejovice, Czech Republic
| | - Michal Zurovec
- Biology Centre of the Czech Academy of Sciences, Institute of Entomology, Branisovska 31, 370 05, Ceske Budejovice, Czech Republic; Faculty of Sciences, University of South Bohemia, Branisovska 31, 370 05, Ceske Budejovice, Czech Republic.
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16
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Davey PA, Power AM, Santos R, Bertemes P, Ladurner P, Palmowski P, Clarke J, Flammang P, Lengerer B, Hennebert E, Rothbächer U, Pjeta R, Wunderer J, Zurovec M, Aldred N. Omics-based molecular analyses of adhesion by aquatic invertebrates. Biol Rev Camb Philos Soc 2021; 96:1051-1075. [PMID: 33594824 DOI: 10.1111/brv.12691] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2020] [Revised: 01/22/2021] [Accepted: 01/26/2021] [Indexed: 12/15/2022]
Abstract
Many aquatic invertebrates are associated with surfaces, using adhesives to attach to the substratum for locomotion, prey capture, reproduction, building or defence. Their intriguing and sophisticated biological glues have been the focus of study for decades. In all but a couple of specific taxa, however, the precise mechanisms by which the bioadhesives stick to surfaces underwater and (in many cases) harden have proved to be elusive. Since the bulk components are known to be based on proteins in most organisms, the opportunities provided by advancing 'omics technologies have revolutionised bioadhesion research. Time-consuming isolation and analysis of single molecules has been either replaced or augmented by the generation of massive data sets that describe the organism's translated genes and proteins. While these new approaches have provided resources and opportunities that have enabled physiological insights and taxonomic comparisons that were not previously possible, they do not provide the complete picture and continued multi-disciplinarity is essential. This review covers the various ways in which 'omics have contributed to our understanding of adhesion by aquatic invertebrates, with new data to illustrate key points. The associated challenges are highlighted and priorities are suggested for future research.
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Affiliation(s)
- Peter A Davey
- School of Natural and Environmental Sciences, Newcastle University, Newcastle upon Tyne, NE1 7RU, U.K
| | - Anne Marie Power
- Ryan Institute, School of Natural Sciences, National University of Ireland Galway, Room 226, Galway, H91 TK33, Ireland
| | - Romana Santos
- Departamento de Biologia Animal, Faculdade de Ciências, Centro de Ciências do Mar e do Ambiente (MARE), Universidade de Lisboa, Lisbon, 1749-016, Portugal
| | - Philip Bertemes
- Institute of Zoology and Center of Molecular Biosciences Innsbruck, University of Innsbruck, Technikerstrasse 25, Innsbruck, 6020, Austria
| | - Peter Ladurner
- Institute of Zoology and Center of Molecular Biosciences Innsbruck, University of Innsbruck, Technikerstrasse 25, Innsbruck, 6020, Austria
| | - Pawel Palmowski
- School of Natural and Environmental Sciences, Newcastle University, Newcastle upon Tyne, NE1 7RU, U.K
| | - Jessica Clarke
- School of Natural and Environmental Sciences, Newcastle University, Newcastle upon Tyne, NE1 7RU, U.K
| | - Patrick Flammang
- Biology of Marine Organisms and Biomimetics Unit, Research Institute for Biosciences, University of Mons, Place du Parc 23, Mons, 7000, Belgium
| | - Birgit Lengerer
- Institute of Zoology and Center of Molecular Biosciences Innsbruck, University of Innsbruck, Technikerstrasse 25, Innsbruck, 6020, Austria
| | - Elise Hennebert
- Laboratory of Cell Biology, Research Institute for Biosciences, University of Mons, Place du Parc 23, Mons, 7000, Belgium
| | - Ute Rothbächer
- Institute of Zoology and Center of Molecular Biosciences Innsbruck, University of Innsbruck, Technikerstrasse 25, Innsbruck, 6020, Austria
| | - Robert Pjeta
- Institute of Zoology and Center of Molecular Biosciences Innsbruck, University of Innsbruck, Technikerstrasse 25, Innsbruck, 6020, Austria
| | - Julia Wunderer
- Institute of Zoology and Center of Molecular Biosciences Innsbruck, University of Innsbruck, Technikerstrasse 25, Innsbruck, 6020, Austria
| | - Michal Zurovec
- Biology Centre of the Czech Academy of Sciences and Faculty of Sciences, University of South Bohemia, České Budějovice, 370 05, Czech Republic
| | - Nick Aldred
- School of Life Sciences, University of Essex, Wivenhoe Park, Colchester, CO4 3SQ, U.K
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17
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Fine structure of the silk spinning system in the caddisworm, Hydatophylax nigrovittatus (Trichoptera: Limnephilidae). Appl Microsc 2020; 50:16. [PMID: 33580455 PMCID: PMC7818296 DOI: 10.1186/s42649-020-00036-5] [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: 06/26/2020] [Accepted: 07/28/2020] [Indexed: 11/10/2022] Open
Abstract
Silk is produced by a variety of insects, but only silk made by terrestrial arthropods has been examined in detail. To fill the gap, this study was designed to understand the silk spinning system of aquatic insect. The larvae of caddis flies, Hydatophylax nigrovittatus produce silk through a pair of labial silk glands and use raw silk to protect themselves in the aquatic environment. The result of this study clearly shows that although silk fibers are made under aquatic conditions, the cellular silk production system is quite similar to that of terrestrial arthropods. Typically, silk production in caddisworm has been achieved by two independent processes in the silk glands. This includes the synthesis of silk fibroin in the posterior region, the production of adhesive glycoproteins in the anterior region, which are ultimately accumulated into functional silk dope and converted to a silk ribbon coated with gluey substances. At the cellular level, each substance of fibroin and glycoprotein is specifically synthesized at different locations, and then transported from the rough ER to the Golgi apparatus as transport vesicles, respectively. Thereafter, the secretory vesicles gradually increase in size by vesicular fusion, forming larger secretory granules containing specific proteins. It was found that these granules eventually migrate to the apical membrane and are exocytosed into the lumen by a mechanism of merocrine secretion.
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18
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Heckenhauer J, Frandsen PB, Gupta DK, Paule J, Prost S, Schell T, Schneider JV, Stewart RJ, Pauls SU. Annotated Draft Genomes of Two Caddisfly Species Plectrocnemia conspersa CURTIS and Hydropsyche tenuis NAVAS (Insecta: Trichoptera). Genome Biol Evol 2019; 11:3445-3451. [PMID: 31774498 PMCID: PMC6916706 DOI: 10.1093/gbe/evz264] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 11/25/2019] [Indexed: 02/06/2023] Open
Abstract
Members of the speciose insect order Trichoptera (caddisflies) provide important ecosystem services, for example, nutrient cycling through breaking down of organic matter. They are also of industrial interest due to their larval silk secretions. These form the basis for their diverse case-making behavior that allows them to exploit a wide range of ecological niches. Only five genomes of this order have been published thus far, with variable qualities regarding contiguity and completeness. A low-cost sequencing strategy, that is, using a single Oxford Nanopore flow cell per individual along with Illumina sequence reads was successfully used to generate high-quality genomes of two Trichoptera species, Plectrocnemia conspersa and Hydropsyche tenuis. Of the de novo assembly methods compared, assembly of low coverage Nanopore reads (∼18×) and subsequent polishing with long reads followed by Illumina short reads (∼80-170× coverage) yielded the highest genome quality both in terms of contiguity and BUSCO completeness. The presented genomes are the shortest to date and extend our knowledge of genome size across caddisfly families. The genomic region that encodes for light (L)-chain fibroin, a protein component of larval caddisfly silk was identified and compared with existing L-fibroin gene clusters. The new genomic resources presented in this paper are among the highest quality Trichoptera genomes and will increase the knowledge of this important insect order by serving as the basis for phylogenomic and comparative genomic studies.
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Affiliation(s)
- Jacqueline Heckenhauer
- LOEWE Centre for Translational Biodiversity Genomics (LOEWE‐TBG), Frankfurt, Germany
- Department of Terrestrial Zoology, Entomology III, Senckenberg Research Institute and Natural History Museum Frankfurt, Frankfurt, Germany
| | - Paul B Frandsen
- LOEWE Centre for Translational Biodiversity Genomics (LOEWE‐TBG), Frankfurt, Germany
- Department of Plant & Wildlife Sciences, Brigham Young University, Provo, UT
- Data Science Lab, Smithsonian Institution, Washington, DC
| | - Deepak K Gupta
- LOEWE Centre for Translational Biodiversity Genomics (LOEWE‐TBG), Frankfurt, Germany
| | - Juraj Paule
- Department of Botany and Molecular Evolution, Senckenberg Research Institute and Natural History Museum Frankfurt, Frankfurt, Germany
| | - Stefan Prost
- LOEWE Centre for Translational Biodiversity Genomics (LOEWE‐TBG), Frankfurt, Germany
- South African National Biodiversity Institute, National Zoological Gardens of South Africa, Pretoria, South Africa
| | - Tilman Schell
- LOEWE Centre for Translational Biodiversity Genomics (LOEWE‐TBG), Frankfurt, Germany
| | - Julio V Schneider
- Department of Terrestrial Zoology, Entomology III, Senckenberg Research Institute and Natural History Museum Frankfurt, Frankfurt, Germany
| | - Russell J Stewart
- Department of Biomedical Engineering, University of Utah, Salt Lake City, UT
| | - Steffen U Pauls
- LOEWE Centre for Translational Biodiversity Genomics (LOEWE‐TBG), Frankfurt, Germany
- Department of Terrestrial Zoology, Entomology III, Senckenberg Research Institute and Natural History Museum Frankfurt, Frankfurt, Germany
- Institute for Insect Biotechnology, Justus-Liebig-University, Gießen, Germany
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19
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Kono N, Nakamura H, Ohtoshi R, Tomita M, Numata K, Arakawa K. The bagworm genome reveals a unique fibroin gene that provides high tensile strength. Commun Biol 2019; 2:148. [PMID: 31044173 PMCID: PMC6488591 DOI: 10.1038/s42003-019-0412-8] [Citation(s) in RCA: 23] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2018] [Accepted: 04/03/2019] [Indexed: 12/30/2022] Open
Abstract
Arthropod silk is known as a versatile tool, and its variability makes it an attractive biomaterial. Eumeta variegata is a bagworm moth (Lepidoptera, Psychidae) that uses silk throughout all life stages. Notably, the bagworm-specific uses of silk include larval development in a bag coated with silk and plant materials and the use of silk attachments to hang pupae. An understanding at the molecular level of bagworm silk, which enables such unique purposes, is an opportunity to expand the possibilities for artificial biomaterial design. However, very little is known about the bagworm fibroin gene and the mechanical properties of bagworm silk. Here, we report the bagworm genome, including a silk fibroin gene. The genome is approximately 700 Mbp in size, and the newly found fibroin gene has a unique repetitive motif. Furthermore, a mechanical property test demonstrates a phylogenetic relationship between the unique motif and tensile strength of bagworm silk.
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Affiliation(s)
- Nobuaki Kono
- Institute for Advanced Biosciences, Keio University, Yamagata, Japan
| | | | | | - Masaru Tomita
- Institute for Advanced Biosciences, Keio University, Yamagata, Japan
| | | | - Kazuharu Arakawa
- Institute for Advanced Biosciences, Keio University, Yamagata, Japan
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J. B, Chanda K, M.M. B. Revisiting the insights and applications of protein engineered hydrogels. MATERIALS SCIENCE & ENGINEERING. C, MATERIALS FOR BIOLOGICAL APPLICATIONS 2019; 95:312-327. [DOI: 10.1016/j.msec.2018.11.002] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/22/2017] [Revised: 09/15/2018] [Accepted: 11/01/2018] [Indexed: 12/19/2022]
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Luo S, Tang M, Frandsen PB, Stewart RJ, Zhou X. The genome of an underwater architect, the caddisfly Stenopsyche tienmushanensis Hwang (Insecta: Trichoptera). Gigascience 2018; 7:5202446. [PMID: 30476205 PMCID: PMC6302954 DOI: 10.1093/gigascience/giy143] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2018] [Accepted: 11/15/2018] [Indexed: 12/18/2022] Open
Abstract
Background Caddisflies (Insecta: Trichoptera) are a highly adapted freshwater group of insects split from a common ancestor with Lepidoptera. They are the most diverse (>16,000 species) of the strictly aquatic insect orders and are widely employed as bio-indicators in water quality assessment and monitoring. Among the numerous adaptations to aquatic habitats, caddisfly larvae use silk and materials from the environment (e.g., stones, sticks, leaf matter) to build composite structures such as fixed retreats and portable cases. Understanding how caddisflies have adapted to aquatic habitats will help explain the evolution and subsequent diversification of the group. Findings We sequenced a retreat-builder caddisfly Stenopsyche tienmushanensis Hwang and assembled a high-quality genome from both Illumina and Pacific Biosciences (PacBio) sequencing. In total, 601.2 M Illumina reads (90.2 Gb) and 16.9 M PacBio subreads (89.0 Gb) were generated. The 451.5 Mb assembled genome has a contig N50 of 1.29 M, has a longest contig of 4.76 Mb, and covers 97.65% of the 1,658 insect single-copy genes as assessed by Benchmarking Universal Single-Copy Orthologs. The genome comprises 36.76% repetitive elements. A total of 14,672 predicted protein-coding genes were identified. The genome revealed gene expansions in specific groups of the cytochrome P450 family and olfactory binding proteins, suggesting potential genomic features associated with pollutant tolerance and mate finding. In addition, the complete gene complex of the highly repetitive H-fibroin, the major protein component of caddisfly larval silk, was assembled. Conclusions We report the draft genome of Stenopsyche tienmushanensis, the highest-quality caddisfly genome so far. The genome information will be an important resource for the study of caddisflies and may shed light on the evolution of aquatic insects.
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Affiliation(s)
- Shiqi Luo
- Beijing Advanced Innovation Center for Food Nutrition and Human Health, College of Plant Protection, China Agricultural University, 2 Yuanmingyuan West Road, Haidian District, Beijing 100193, China
| | - Min Tang
- Beijing Advanced Innovation Center for Food Nutrition and Human Health, College of Plant Protection, China Agricultural University, 2 Yuanmingyuan West Road, Haidian District, Beijing 100193, China
| | - Paul B Frandsen
- Department of Plant and Wildlife Sciences, Brigham Young University, 701 E University Parkway Drive, Provo, UT 84602, USA.,Data Science Lab, Smithsonian Institution, 600 Maryland Ave SW, Washington, DC 20002, USA
| | - Russell J Stewart
- Department of Biomedical Engineering, University of Utah, 20 South 2030 East, Salt Lake City, UT 84112, USA
| | - Xin Zhou
- Beijing Advanced Innovation Center for Food Nutrition and Human Health, College of Plant Protection, China Agricultural University, 2 Yuanmingyuan West Road, Haidian District, Beijing 100193, China
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Ashton NN, Stewart RJ. Aquatic caddisworm silk is solidified by environmental metal ions during the natural fiber-spinning process. FASEB J 2018; 33:572-583. [PMID: 29985645 DOI: 10.1096/fj.201801029r] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Abstract
Aquatic caddisfly larvae (caddisworms) wet-spin fibers to construct composite cases of silk and stone. The silk emerges from labial ducts as a nanofibrous fluid gel, flowing over the stone substrate and making intimate interfacial adhesive contacts before being drawn into tough fibers that rapidly solidify underwater to span gaps in the construction. Divalent metal ions are responsible for the unique mechanical properties of naturally spun silk fibers; however, when and where divalent metal ions are incorporated into the metallofibers and other aspects of the fiber solidification mechanism are poorly understood. To investigate, the elemental composition and secondary structure of silk precursors stored in the silk gland lumen were compared with naturally spun fibers by inductively coupled plasma optical emission spectroscopy and attenuated total reflection Fourier transform infrared spectroscopy. Naturally spun fibers contained near equimolar ratios of Ca2+ to P. In contrast, silk precursors stored in the silk gland lumen contained only traces of Ca2+ and other multivalent metal ions. Ca2+ was also undetectable in anterior lumenal silk using the histochemical Ca2+ indicator, alizarin S red. Addition of Ca2+ to isolated lumenal silk resulted in Ca2+ complexation by H-fibroin phosphoserines (pSs) and a shift in secondary structure from random coils to β-structures, creating infrared spectra in the phosphate and amide I regions nearly equivalent to those found in naturally spun Ca2+-containing silk fibers. Light and electron microscopy within distinct regions of the silk gland suggested that posterior gland silk colloidal complexes transition into a nanofibrous morphology as they pass into the chitin-lined anterior lumen. Altogether, the results suggest that environmental Ca2+ absorbed from natural water triggers silk fiber solidification postdraw by complexing H-fibroin pSs, creating Ca2+-stabilized crystalline β-nanodomains that cross-link and toughen the freshly drawn silk fibers.-Ashton, N. N., Stewart, R. J. Aquatic caddisworm silk is solidified by environmental metal ions during the natural fiber-spinning process.
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Affiliation(s)
- Nicholas N Ashton
- Department of Bioengineering, University of Utah, Salt Lake City, Utah, USA
| | - Russell J Stewart
- Department of Bioengineering, University of Utah, Salt Lake City, Utah, USA
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Herold HM, Scheibel T. Applicability of biotechnologically produced insect silks. ACTA ACUST UNITED AC 2017; 72:365-385. [DOI: 10.1515/znc-2017-0050] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2017] [Accepted: 06/30/2017] [Indexed: 11/15/2022]
Abstract
Abstract
Silks are structural proteins produced by arthropods. Besides the well-known cocoon silk, which is produced by larvae of the silk moth Bombyx mori to undergo metamorphosis inside their silken shelter (and which is also used for textile production by men since millennia), numerous further less known silk-producing animals exist. The ability to produce silk evolved multiple independent times during evolution, and the fact that silk was subject to convergent evolution gave rise to an abundant natural diversity of silk proteins. Silks are used in air, under water, or like honey bee silk in the hydrophobic, waxen environment of the bee hive. The good mechanical properties of insect silk fibres together with their non-toxic, biocompatible, and biodegradable nature renders these materials appealing for both technical and biomedical applications. Although nature provides a great diversity of material properties, the variation in quality inherent in materials from natural sources together with low availability (except from silkworm silk) impeded the development of applications of silks. To overcome these two drawbacks, in recent years, recombinant silks gained more and more interest, as the biotechnological production of silk proteins allows for a scalable production at constant quality. This review summarises recent developments in recombinant silk production as well as technical procedures to process recombinant silk proteins into fibres, films, and hydrogels.
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Affiliation(s)
- Heike M. Herold
- Lehrstuhl Biomaterialien, Fakultät für Ingenieurwissenschaften, Universität Bayreuth , Universitätsstraße 30 , 95440 Bayreuth , Germany
| | - Thomas Scheibel
- Lehrstuhl Biomaterialien, Fakultät für Ingenieurwissenschaften, Universität Bayreuth , Universitätsstraße 30 , 95440 Bayreuth , Germany
- Bayreuther Zentrum für Kolloide und Grenzflächen (BZKG), Universität Bayreuth , Universitätsstraße 30 , 95440 Bayreuth , Germany
- Bayreuther Zentrum für Molekulare Biowissenschaften (BZMB), Universität Bayreuth , Universitätsstraße 30 , 95440 Bayreuth , Germany
- Institut für Bio-Makromoleküle (bio-mac), Universität Bayreuth , Universitätsstraße 30 , 95440 Bayreuth , Germany
- Bayreuther Materialzentrum (BayMAT), Universität Bayreuth , Universitätsstraße 30 , 95440 Bayreuth , Germany
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Tsubota T, Yamamoto K, Mita K, Sezutsu H. Gene expression analysis in the larval silk gland of the eri silkworm Samia ricini. INSECT SCIENCE 2016; 23:791-804. [PMID: 26178074 DOI: 10.1111/1744-7917.12251] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Accepted: 06/23/2015] [Indexed: 06/04/2023]
Abstract
Insects produce silk for a range of purposes. In the Lepidoptera, silk is utilized as a material for cocoon production and serves to protect larvae from adverse environmental conditions or predators. Species in the Saturniidae family produce an especially wide variety of cocoons, for example, large, golden colored cocoons and those with many small holes. Although gene expression in the silk gland of the domestic silkworm (Bombyx mori L.) has been extensively studied, considerably fewer investigations have focused on members of the saturniid family. Here, we established expression sequence tags from the silk gland of the eri silkworm (Samia ricini), a saturniid species, and used these to analyze gene expression. Although we identified the fibroin heavy chain gene in the established library, genes for other major silk proteins, such as fibroin light chain and fibrohexamerin, were absent. This finding is consistent with previous reports that these latter proteins are lacking in saturniid silk. Recently, a series of fibrohexamerin-like genes were identified in the Bombyx genome. We used this information to conduct a detailed analysis of the library established here. This analysis identified putative homologues of these genes. We also found several genes encoding small silk protein molecules that are also present in the silk of other Lepidoptera. Gene expression patterns were compared between eri and domestic silkworm, and both conserved and nonconserved expression patterns were identified for the tested genes. Such differential gene expression might be one of the major causes of the differences in silk properties between these species. We believe that our study can be of value as a basic catalogue for silk gland gene expression, which will yield to the further understanding of silk evolution.
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Affiliation(s)
- Takuya Tsubota
- Transgenic Silkworm Research Unit, National Institute of Agrobiological Sciences, Ibaraki, 305-8634, Japan
| | - Kimiko Yamamoto
- Insect Genome Research Unit, National Institute of Agrobiological Sciences, Ibaraki, 305-8634, Japan
| | - Kazuei Mita
- Insect Genome Research Unit, National Institute of Agrobiological Sciences, Ibaraki, 305-8634, Japan
| | - Hideki Sezutsu
- Transgenic Silkworm Research Unit, National Institute of Agrobiological Sciences, Ibaraki, 305-8634, Japan
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Partlow BP, Applegate MB, Omenetto FG, Kaplan DL. Dityrosine Cross-Linking in Designing Biomaterials. ACS Biomater Sci Eng 2016; 2:2108-2121. [DOI: 10.1021/acsbiomaterials.6b00454] [Citation(s) in RCA: 87] [Impact Index Per Article: 10.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Affiliation(s)
- Benjamin P. Partlow
- Department
of Biomedical Engineering, Tufts University, 4 Colby Street, Medford, Massachusetts 02155, United States
| | - Matthew B. Applegate
- Department
of Biomedical Engineering, Tufts University, 4 Colby Street, Medford, Massachusetts 02155, United States
| | - Fiorenzo G. Omenetto
- Department
of Biomedical Engineering, Tufts University, 4 Colby Street, Medford, Massachusetts 02155, United States
| | - David L. Kaplan
- Department
of Biomedical Engineering, Tufts University, 4 Colby Street, Medford, Massachusetts 02155, United States
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Natural Occurring Silks and Their Analogues as Materials for Nerve Conduits. Int J Mol Sci 2016; 17:ijms17101754. [PMID: 27775616 PMCID: PMC5085779 DOI: 10.3390/ijms17101754] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2016] [Revised: 09/17/2016] [Accepted: 09/28/2016] [Indexed: 01/07/2023] Open
Abstract
Spider silk and its synthetic derivatives have a light weight in combination with good strength and elasticity. Their high cytocompatibility and low immunogenicity make them well suited for biomaterial products such as nerve conduits. Silk proteins slowly degrade enzymatically in vivo, thus allowing for an initial therapeutic effect such as in nerve scaffolding to facilitate endogenous repair processes, and then are removed. Silks are biopolymers naturally produced by many species of arthropods including spiders, caterpillars and mites. The silk fibers are secreted by the labial gland of the larvae of some orders of Holometabola (insects with pupa) or the spinnerets of spiders. The majority of studies using silks for biomedical applications use materials from silkworms or spiders, mostly of the genus Nephila clavipes. Silk is one of the most promising biomaterials with effects not only in nerve regeneration, but in a number of regenerative applications. The development of silks for human biomedical applications is of high scientific and clinical interest. Biomaterials in use for biomedical applications have to meet a number of requirements such as biocompatibility and elicitation of no more than a minor inflammatory response, biodegradability in a reasonable time and specific structural properties. Here we present the current status in the field of silk-based conduit development for nerve repair and discuss current advances with regard to potential clinical transfer of an implantable nerve conduit for enhancement of nerve regeneration.
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Bhagat V, O’Brien E, Zhou J, Becker ML. Caddisfly Inspired Phosphorylated Poly(ester urea)-Based Degradable Bone Adhesives. Biomacromolecules 2016; 17:3016-24. [DOI: 10.1021/acs.biomac.6b00875] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Vrushali Bhagat
- Department of Polymer Science, The University of Akron, Akron, Ohio 44325, United States
| | - Emily O’Brien
- Department of Polymer Science, The University of Akron, Akron, Ohio 44325, United States
| | - Jinjun Zhou
- Department of Polymer Science, The University of Akron, Akron, Ohio 44325, United States
| | - Matthew L. Becker
- Department of Polymer Science, The University of Akron, Akron, Ohio 44325, United States
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Lane DD, Kaur S, Weerasakare GM, Stewart RJ. Toughened hydrogels inspired by aquatic caddisworm silk. SOFT MATTER 2015; 11:6981-6990. [PMID: 26234366 DOI: 10.1039/c5sm01297j] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/04/2023]
Abstract
Aquatic caddisworm silk is a tough adhesive fiber. Part of the toughening mechanism resides in serial, Ca(2+)-phosphate crosslinked nano-domains that comprise H-fibroin, the major structural protein. To mimic the toughening mechanism, a synthetic phosphate-graft-methacrylate prepolymer, as a simple H-fibroin analog, was copolymerized within a covalent elastic network of polyacrylamide. Above a critical phosphate sidechain density, hydrogels equilibrated with Ca(2+) or Zn(2+) ions displayed greatly increased initial stiffness, strain-rate dependent yield behavior, and required 100 times more work to fracture than hydrogels equilibrated with Mg(2+) or Na(+) ions. Conceptually, the enhanced toughness is attributed to energy-dissipating, viscous unfolding of clustered phosphate-metal ion crosslinks at a critical stress. The toughness of the bioinspired hydrogels exceeds the toughness of cartilage and meniscus suggesting potential application as prosthetic biomaterials. The tough hydrogels also provide a simplified model to test hypotheses about caddisworm silk architecture, phosphate metal ion interactions, and mechanochemical toughening mechanisms.
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Affiliation(s)
- Dwight D Lane
- Department of Bioengineering, University of Utah, Salt Lake City, UT 84112, USA.
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Molecular cloning, gene expression analysis, and recombinant protein expression of novel silk proteins from larvae of a retreat-maker caddisfly, Stenopsyche marmorata. Biochem Biophys Res Commun 2015; 464:814-9. [PMID: 26168724 DOI: 10.1016/j.bbrc.2015.07.041] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2015] [Accepted: 07/07/2015] [Indexed: 11/23/2022]
Abstract
Retreat-maker larvae of Stenopsyche marmorata, one of the major caddisfly species in Japan, produce silk threads and adhesives to build food capture nets and protective nests in water. Research on these underwater adhesive silk proteins potentially leads to the development of new functional biofiber materials. Recently, we identified four major S. marmorata silk proteins (Smsps), Smsp-1, Smsp-2, Smsp-3, and Smsp-4 from silk glands of S. marmorata larvae. In this study, we cloned full-length cDNAs of Smsp-2, Smsp-3, and Smsp-4 from the cDNA library of the S. marmorata silk glands to reveal the primary sequences of Smsps. Homology search results of the deduced amino acid sequences indicate that Smsp-2 and Smsp-4 are novel proteins. The Smsp-2 sequence [167 amino acids (aa)] has an array of GYD-rich repeat motifs and two (SX)4E motifs. The Smsp-4 sequence (132 aa) contains a number of GW-rich repeat motifs and three (SX)4E motifs. The Smsp-3 sequence (248 aa) exhibits high homology with fibroin light chain of other caddisflies. Gene expression analysis of Smsps by real-time PCR suggested that the gene expression of Smsp-1 and Smsp-3 was relatively stable throughout the year, whereas that of Smsp-2 and Smsp-4 varied seasonally. Furthermore, Smsps recombinant protein expression was successfully performed in Escherichia coli. The study provides new molecular insights into caddisfly aquatic silk and its potential for future applications.
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Ashton NN, Stewart RJ. Self-recovering caddisfly silk: energy dissipating, Ca(2+)-dependent, double dynamic network fibers. SOFT MATTER 2015; 11:1667-1676. [PMID: 25525713 DOI: 10.1039/c4sm02435d] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/04/2023]
Abstract
Single fibers of the sticky underwater larval silk of the casemaker caddisfly (H. occidentalis) are viscoelastic, display large strain cycle hysteresis, and self-recover 99% of their initial stiffness and strength within 120 min. Mechanical response to cyclical strains suggested viscoelasticity is due to two independent, self-recovering Ca(2+)-crosslinked networks. The networks display distinct pH dependence. The first network is attributed to Ca(2+)-stabilized phosphoserine motifs in H-fibroin, the second to Ca(2+) complexed carboxylate groups in the N-terminus of H-fibroin and a PEVK-like protein. These assignments were corroborated by IR spectroscopy. The results are consolidated into a multi-network model in which reversible rupture of the Ca(2+)-crosslinked domains at a critical stress results in pseudo-plastic deformation. Slow refolding of the domains results in nearly full recovery of fiber length, stiffness, and strength. The fiber toughening, energy dissipation, and recovery mechanisms, are highly adaptive for the high energy aquatic environment of caddisfly larvae.
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Affiliation(s)
- Nicholas N Ashton
- Department of Bioengineering, University of Utah, Salt Lake City, Utah 84112, USA.
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Tszydel M, Zabłotni A, Wojciechowska D, Michalak M, Krucińska I, Szustakiewicz K, Maj M, Jaruszewska A, Strzelecki J. Research on possible medical use of silk produced by caddisfly larvae of Hydropsyche angustipennis (Trichoptera, Insecta). J Mech Behav Biomed Mater 2015; 45:142-53. [PMID: 25723346 DOI: 10.1016/j.jmbbm.2015.02.003] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2014] [Revised: 01/31/2015] [Accepted: 02/01/2015] [Indexed: 11/15/2022]
Abstract
Silk products are used in medicine as biomaterials, and are particularly promising as scaffolds in tissue engineering. To date only silkworm and spider silk medical potential has been evaluated, whereas the possible application of the material spun by caddisflies in wet environment has not been examined. Biomedical application of every natural material requires biocompatibility testing and evaluation of unique microbiological and mechanical properties. This article focuses on silk fibers formed in caddisflies cocoons of Hydropsyche angustipennis (Insecta, Trichoptera) larvae. Preliminary biological evaluation shows that trichopteran silk is not cytotoxic to human cells. Caddisfly silk itself does not possess antiseptic properties and thus sterilization is indispensable for its application in medicine. Among tested methods of sterilization and disinfection only thermal methods (tyndallization and autoclaving) enabled complete eradication of bacteria and gave fully sterile material. Caddisfly silk appeared to be resistant to high temperature. Fully sterile fibers can be stored without a loss of breaking force and tensile strength. Our work shows that trichopteran silk has a significant potential to be used as a biomaterial.
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Affiliation(s)
- M Tszydel
- Department of Ecology and Vertebrate Zoology, Faculty of Biology and Environmental Protection, University of Łódź, 12/16 Banacha Str., 90-237 Łódź, Poland.
| | - A Zabłotni
- Department of General Microbiology, Faculty of Biology and Environmental Protection, University of Łódź, 12/16 Banacha Str., 90-237 Łódź, Poland.
| | - D Wojciechowska
- Department of Material and Commodity Sciences and Textile Metrology, Faculty of Material Technologies and Textile Design, Lodz University of Technology, 116 Żeromskiego Str., 90-543 Łódź, Poland.
| | - M Michalak
- Department of Material and Commodity Sciences and Textile Metrology, Faculty of Material Technologies and Textile Design, Lodz University of Technology, 116 Żeromskiego Str., 90-543 Łódź, Poland.
| | - I Krucińska
- Department of Material and Commodity Sciences and Textile Metrology, Faculty of Material Technologies and Textile Design, Lodz University of Technology, 116 Żeromskiego Str., 90-543 Łódź, Poland
| | - K Szustakiewicz
- Polymer Engineering and Technology Division, Wrocław University of Technology, 27 Wybrzeże Wyspiańskiego Str., 50-370 Wrocław, Poland.
| | - M Maj
- Tissue Engineering Department, L. Rydygier Collegium Medicum in Bydgoszcz, Nicolaus Copernicus University in Toruń, 24 Karłowicza Str., 85-092 Bydgoszcz, Poland.
| | - A Jaruszewska
- Institute of Physics, Nicolaus Copernicus University, 5 Grudziądzka Str., 87-100 Toruń, Poland.
| | - J Strzelecki
- Institute of Physics, Nicolaus Copernicus University, 5 Grudziądzka Str., 87-100 Toruń, Poland.
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Wang CS, Ashton NN, Weiss RB, Stewart RJ. Peroxinectin catalyzed dityrosine crosslinking in the adhesive underwater silk of a casemaker caddisfly larvae, Hysperophylax occidentalis. INSECT BIOCHEMISTRY AND MOLECULAR BIOLOGY 2014; 54:69-79. [PMID: 25220661 DOI: 10.1016/j.ibmb.2014.08.009] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/07/2014] [Revised: 08/26/2014] [Accepted: 08/26/2014] [Indexed: 06/03/2023]
Abstract
Aquatic caddisfly larvae use sticky silk fibers as an adhesive tape to construct protective composite structures under water. Three new silk fiber components were identified by transcriptome and proteome analysis of the silk gland: a heme-peroxidase in the peroxinectin (Pxt) sub-family, a superoxide dismutase 3 (SOD3) that generates the H2O2 substrate of the silk fiber Pxt from environmental reactive oxygen species (eROS), and a novel structural component with sequence similarity to the elastic PEVK region of the muscle protein, titin. All three proteins are co-drawn with fibroins to form silk fibers. The Pxt and SOD3 enzymes retain activity in drawn fibers. In native fibers, Pxt activity and dityrosine crosslinks are co-localized at the boundary of a peripheral layer and the silk fiber core. To our knowledge, dityrosine crosslinks, heme peroxidase, and SOD3 activities have not been previously reported in an insect silk. The PEVK-like protein is homogeneously distributed throughout the fiber core. The results are consolidated into a model in which caddisfly silk Pxt-catalyzed dityrosine crosslinking occurs post-draw using H2O2 generated within the silk fibers by SOD3. The ROS substrate of caddisfly silk SOD3 occurs naturally in aquatic environments, from biotic and abiotic sources. The radially inhomogeneous dityrosine crosslinking and a potential titin-like PEVK protein network have important implications for the mechanical properties of caddifly silk fibers.
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Affiliation(s)
- Ching-Shuen Wang
- Department of Bioengineering, University of Utah, Salt Lake City, UT 84112, USA
| | - Nicholas N Ashton
- Department of Bioengineering, University of Utah, Salt Lake City, UT 84112, USA
| | - Robert B Weiss
- Department of Human Genetics, University of Utah, Salt Lake City, UT 84112, USA
| | - Russell J Stewart
- Department of Bioengineering, University of Utah, Salt Lake City, UT 84112, USA.
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Yang YJ, Jung D, Yang B, Hwang BH, Cha HJ. Aquatic proteins with repetitive motifs provide insights to bioengineering of novel biomaterials. Biotechnol J 2014; 9:1493-502. [DOI: 10.1002/biot.201400070] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2014] [Revised: 06/20/2014] [Accepted: 08/05/2014] [Indexed: 01/20/2023]
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Addison JB, Weber WS, Mou Q, Ashton NN, Stewart RJ, Holland GP, Yarger JL. Reversible assembly of β-sheet nanocrystals within caddisfly silk. Biomacromolecules 2014; 15:1269-75. [PMID: 24576204 DOI: 10.1021/bm401822p] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Nuclear magnetic resonance (NMR) and X-ray diffraction (XRD) experiments reveal the structural importance of divalent cation-phosphate complexes in the formation of β-sheet nanocrystals from phosphorylated serine-rich regions within aquatic silk from caddisfly larvae of the species Hesperophyla consimilis. Wide angle XRD data on native caddisfly silk show that the silk contains a significant crystalline component with a repetitive orthorhombic unit cell aligned along the fiber axis with dimensions of 5.9 Å × 23.2 Å × 17.3 Å. These nanocrystalline domains depend on multivalent cations, which can be removed through chelation with ethylenediaminetetraacetic acid (EDTA). A comparison of wide angle X-ray diffraction data before and after EDTA treatment reveals that the integrated peak area of reflections corresponding to the nanocrystalline regions decreases by 15-25% while that of the amorphous background reflections increases by 20%, indicating a partial loss of crystallinity. (31)P solid-state NMR data on native caddisfly silk also show that the phosphorylated serine-rich motifs transform from a rigid environment to one that is highly mobile and water-solvated after treatment with EDTA. The removal of divalent cations through exchange and chelation has therefore caused a collapse of the β-sheet structure. However, NMR results show that the rigid phosphorus environment is mostly recovered after the silk is re-treated with calcium. The (31)P spin-lattice (T1) relaxation times were measured at 7.6 ± 3.1 and 1 ± 0.5 s for this calcium-recovered sample and the native silk sample, respectively. The shorter (31)P T1 relaxation times measured for the native silk sample are attributed to the presence of paramagnetic iron that is stripped away during EDTA chelation treatment and replaced with diamagnetic calcium.
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Affiliation(s)
- J Bennett Addison
- Department of Chemistry and Biochemistry, Arizona State University , Tempe, Arizona 85287-1604, United States
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Papanicolaou A, Woo A, Brei B, Ma D, Masedunskas A, Gray E, Xiao GG, Cho S, Brockhouse C. Novel aquatic silk genes Simulium (Psilozia) vittatum (Zett) Diptera: Simuliidae. INSECT BIOCHEMISTRY AND MOLECULAR BIOLOGY 2013; 43:1181-1188. [PMID: 24446544 DOI: 10.1016/j.ibmb.2013.09.008] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/03/2023]
Abstract
The silks of arthropods have an elementary role in the natural history of the organisms that spin them, yet they are coded by rapidly evolving genes leading some authors to speculate that silk proteins are non-homologous proteins co-opted multiple times independently for similar functions. However, some general structural patterns are emerging. In this work we identified three major silk gland proteins using a combined biochemical, proteomic, next-generation sequencing and bioinformatic approach. Biochemical characterization determined that they were phosphorylated with multiple isoforms and potentially differential phosphorylation. Structural characterization showed that their structure was more similar to silk proteins from distantly related aquatic Trichopteran species than more closely related terrestrial or aquatic Diptera. Overall, our approach is easily transferable to any non-model species and if used across a larger number of aquatic species, we will be able to better understand the processes involved in linking the secondary structure of silk proteins with their function between in an organisms and its habitat.
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Affiliation(s)
- Alexie Papanicolaou
- CSIRO Ecosystem Sciences, Black Mountain Labs, GPO 1700, Canberra, ACT 2601, Australia.
| | - Angelica Woo
- Biology Department, Creighton University, 2500 California Plaza, Omaha, NE 68131, USA
| | - Brianna Brei
- Biology Department, Creighton University, 2500 California Plaza, Omaha, NE 68131, USA
| | - Danjun Ma
- Entomology Department, University of Georgia, Athens, GA, USA
| | - Andrius Masedunskas
- Biology Department, Creighton University, 2500 California Plaza, Omaha, NE 68131, USA
| | - Elmer Gray
- Entomology Department, University of Georgia, Athens, GA, USA
| | - Gary Guishan Xiao
- Genomics and Functional Proteomics Laboratory, Creighton University Medical Center, Omaha, NE, USA
| | - Soochin Cho
- Biology Department, Creighton University, 2500 California Plaza, Omaha, NE 68131, USA.
| | - Charles Brockhouse
- Biology Department, Creighton University, 2500 California Plaza, Omaha, NE 68131, USA.
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Ashton NN, Roe DR, Weiss RB, Cheatham TE, Stewart RJ. Self-tensioning aquatic caddisfly silk: Ca2+-dependent structure, strength, and load cycle hysteresis. Biomacromolecules 2013; 14:3668-81. [PMID: 24050221 DOI: 10.1021/bm401036z] [Citation(s) in RCA: 52] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
Abstract
Caddisflies are aquatic relatives of silk-spinning terrestrial moths and butterflies. Casemaker larvae spin adhesive silk fibers for underwater construction of protective composite cases. The central region of Hesperophylax sp. H-fibroin contains a repeating pattern of three conserved subrepeats, all of which contain one or more (SX)n motifs with extensively phosphorylated serines. Native silk fibers were highly extensible and displayed a distinct yield point, force plateau, and load cycle hysteresis. FTIR spectroscopy of native silk showed a conformational mix of random coil, β-sheet, and turns. Exchanging multivalent ions with Na(+) EDTA disrupted fiber mechanics, shifted the secondary structure ratios from antiparallel β-sheet toward random coil and turns, and caused the fibers to shorten, swell in diameter, and disrupted fiber birefringence. The EDTA effects were reversed by restoring Ca(2+). Molecular dynamic simulations provided theoretical support for a hypothetical structure in which the (pSX)n motifs may assemble into two- and three-stranded, Ca(2+)-stabilized β-sheets.
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Affiliation(s)
- Nicholas N Ashton
- Departments of †Bioengineering, ‡Medicinal Chemistry, and §Human Genetics, University of Utah , Salt Lake City, Utah 84112, United States
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Samal SK, Dash M, Chiellini F, Kaplan DL, Chiellini E. Silk microgels formed by proteolytic enzyme activity. Acta Biomater 2013; 9:8192-9. [PMID: 23756227 DOI: 10.1016/j.actbio.2013.05.027] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2013] [Revised: 05/05/2013] [Accepted: 05/16/2013] [Indexed: 01/19/2023]
Abstract
The proteolytic enzyme α-chymotrypsin selectively cleaves the amorphous regions of silk fibroin protein (SFP) and allows the crystalline regions to self-assemble into silk microgels (SMGs) at physiological temperature. These microgels consist of lamellar crystals in the micrometer scale, in contrast to the nanometer-scaled crystals in native silkworm fibers. Sodium dodecyl sulfate-polyacrylamide gel electrophoresis and zeta potential results demonstrated that α-chymotrypsin utilized only the non-amorphous domains or segments of the heavy chain of SFP to form negatively charged SMGs. The SMGs were characterized in terms of size, charge, structure, morphology, crystallinity, swelling kinetics, water content and thermal properties. The results suggest that the present technique of preparing SMGs by α-chymotrypsin is simple and efficient, and that the prepared SMGs have useful features for studies related to biomaterial and pharmaceutical needs. This process is also an easy way to obtain the amorphous peptide chains for further study.
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Affiliation(s)
- Sangram K Samal
- BioLab-UdR-INSTM, Via Vecchia Livornese, University of Pisa, Pisa 1291, Italy
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Addison JB, Ashton NN, Weber WS, Stewart RJ, Holland GP, Yarger JL. β-Sheet nanocrystalline domains formed from phosphorylated serine-rich motifs in caddisfly larval silk: a solid state NMR and XRD study. Biomacromolecules 2013; 14:1140-8. [PMID: 23452243 DOI: 10.1021/bm400019d] [Citation(s) in RCA: 49] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Adhesive silks spun by aquatic caddisfly (order Trichoptera) larvae are used to build both intricate protective shelters and food harvesting nets underwater. In this study, we use (13)C and (31)P solid-state NMR and wide angle X-ray diffraction (WAXD) as tools to elucidate molecular protein structure of caddisfly larval silk from the species Hesperophylax consimilis . Caddisfly larval silk is a fibroin protein based biopolymer containing mostly repetitive amino acid motifs. NMR and X-ray results provide strong supporting evidence for a structural model in which phosphorylated serine repeats (pSX)4 complex with divalent cations Ca(2+) and Mg(2+) to form rigid nanocrystalline β-sheet structures in caddisfly silk. (13)C NMR data suggests that both phosphorylated serine and neighboring valine residues exist in a β-sheet conformation while glycine and leucine residues common in GGX repeats likely reside in random coil conformations. Additionally, (31)P chemical shift anisotropy (CSA) analysis indicates that the phosphates on phosphoserine residues are doubly ionized, and are charge-stabilized by divalent cations. Positively charged arginine side chains also likely play a role in charge stabilization. Finally, WAXD results finds that the silk is at least 7-8% crystalline, with β-sheet interplane spacings of 3.7 and 4.5 Å.
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Affiliation(s)
- J Bennett Addison
- Department of Chemistry and Biochemistry, Arizona State University, Tempe, Arizona 85287-1604, USA.
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Yonemura N, Sehnal F, Konik P, Ajimura M, Tamura T, Mita K. Conservation of a pair of serpin 2 genes and their expression in Amphiesmenoptera. INSECT BIOCHEMISTRY AND MOLECULAR BIOLOGY 2012; 42:371-380. [PMID: 22342880 DOI: 10.1016/j.ibmb.2012.01.008] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/11/2011] [Revised: 01/25/2012] [Accepted: 01/28/2012] [Indexed: 05/31/2023]
Abstract
Silk secreted by the larvae of Hydropsyche angustipennis (Trichoptera) contains serpins HaSerp2A and HaSerp2B that are homologous to serpin 2 known from several lepidopterans and some other insects. The gene HaSerp2A is 2684 bp downstream from the HaSerp2B gene. The genes possess identical exon/intron segmentation (9 exons) and their sequences are nearly identical: only 8 out of 1203 nt differ in the coding region, 4 out of 567 nt in the introns and 2 out of 52 nt in 3' UTR. Both genes are highly expressed in the silk glands whereas expression in larval carcass devoid of the silk glands is hard to detect. Translation products of the genes consist of 401 amino acids, are 98.8% identical, and are secreted as 45 kDa proteins into silk. Homologous genes in similar tandem arrangement occur on chromosome 15 of Bombyx mori (Lepidoptera). The upstream gene BmSerp2B is modified in several exons and does not seem to produce functional mRNA. The gene BmSerp2A contains two copies of exon 9, of which only the second one is used. One kind of mRNA does and the other does not include exon 1, which encodes a signal peptide. The mRNA yielding secreted BmSerp2A is expressed in the posterior, and that encoding the cytoplasmic BmSerp2A in the middle silk gland region; both kinds are strongly expressed in the anterior region. The data indicate that (1) A duplication of serpin 2 gene occurred either before Trichoptera and Lepidoptera diverged as separate orders or independently in early phylogeny of either order; (2) In the caddisfly H. angustipennis, both genes are expressed specifically in the silk glands and generate proteins deposited in the silk; (3) Only one gene seems to be functional in B. mori and is expressed in a cytoplasmic and in a secreted forms in diverse organs, including the silk glands.
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Affiliation(s)
- Naoyuki Yonemura
- National Institute of Agrobiological Sciences, Tsukuba, Ibaraki 305 8634, Japan
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Ashton NN, Taggart DS, Stewart RJ. Silk tape nanostructure and silk gland anatomy of trichoptera. Biopolymers 2011; 97:432-45. [PMID: 21953029 DOI: 10.1002/bip.21720] [Citation(s) in RCA: 34] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2011] [Accepted: 09/13/2011] [Indexed: 11/10/2022]
Abstract
Caddisflys (order Trichoptera) construct elaborate protective shelters and food harvesting nets with underwater adhesive silk. The silk fiber resembles a nanostructured tape composed of thousands of nanofibrils (∼ 120 nm) oriented with the major axis of the fiber, which in turn are composed of spherical subunits. Weaker lateral interactions between nanofibrils allow the fiber to conform to surface topography and increase contact area. Highly phosphorylated (pSX)(4) motifs in H-fibroin blocks of positively charged basic residues are conserved across all three suborders of Trichoptera. Electrostatic interactions between the oppositely charged motifs could drive liquid-liquid phase separation of silk fiber precursors into a complex coacervates mesophase. Accessibility of phosphoserine to an anti-phosphoserine antibody is lower in the lumen of the silk gland storage region compared to the nascent fiber formed in the anterior conducting channel. The phosphorylated motifs may serve as a marker for the structural reorganization of the silk precursor mesophase into strongly refringent fibers. The structural change occurring at the transition into the conducting channel makes this region of special interest. Fiber formation from polyampholytic silk proteins in Trichoptera may suggest a new approach to create synthetic silk analogs from water-soluble precursors.
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Affiliation(s)
- Nicholas N Ashton
- Department of Bioengineering, University of Utah, Salt Lake City, UT 84112, USA
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Stewart RJ, Wang CS, Shao H. Complex coacervates as a foundation for synthetic underwater adhesives. Adv Colloid Interface Sci 2011; 167:85-93. [PMID: 21081223 PMCID: PMC3130813 DOI: 10.1016/j.cis.2010.10.009] [Citation(s) in RCA: 212] [Impact Index Per Article: 16.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2010] [Revised: 10/25/2010] [Accepted: 10/27/2010] [Indexed: 10/18/2022]
Abstract
Complex coacervation was proposed to play a role in the formation of the underwater bioadhesive of the Sandcastle worm (Phragmatopoma californica) based on the polyacidic and polybasic nature of the glue proteins and the balance of opposite charges at physiological pH. Morphological studies of the secretory system suggested that the natural process does not involve complex coacervation as commonly defined. The distinction may not be important because electrostatic interactions likely play an important role in the formation of the sandcastle glue. Complex coacervation has also been invoked in the formation of adhesive underwater silk fibers of caddisfly larvae and the adhesive plaques of mussels. A process similar to complex coacervation, that is, condensation and dehydration of biopolyelectrolytes through electrostatic associations, seems plausible for the caddisfly silk. This much is clear, the sandcastle glue complex coacervation model provided a valuable blueprint for the synthesis of a biomimetic, water-borne, underwater adhesive with demonstrated potential for repair of wet tissue.
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Affiliation(s)
- Russell J Stewart
- Department of Bioengineering, University of Utah, Salt Lake City, 84112, United States.
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Collin MA, Edgerly JS, Hayashi CY. Comparison of fibroin cDNAs from webspinning insects: insight into silk formation and function. ZOOLOGY 2011; 114:239-46. [PMID: 21741226 DOI: 10.1016/j.zool.2011.01.004] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2010] [Revised: 01/20/2011] [Accepted: 01/23/2011] [Indexed: 10/18/2022]
Abstract
Embiopterans (webspinning insects) are renowned for their prolific use of silk. These organisms spin silk to construct elaborate networks of tubes in which they live, forage, and reproduce. The silken galleries are essential for protecting these soft-bodied insects from predators and other environmental hazards. Despite the ecological importance of embiopteran silk, very little is known about its constituent proteins. Here, we characterize the silk protein cDNAs from four embiopteran species to better understand the function and evolution of these adaptive molecules. We show that webspinner fibroins (silk proteins) are highly repetitive in sequence and possess several conserved characteristics, despite differences in habitat preferences across species. The most striking similarities are in the codon usage biases of the fibroin genes, particularly in the repetitive regions, as well as sequence conservation of the carboxyl-terminal regions of the fibroins. Based on analyses of the silk genes, we propose hypotheses regarding codon bias and its effect on the translation and replication of these unusual genes. Furthermore, we discuss the significance of specific fibroin motifs to the mechanical and structural characteristics of silk fibers. Lastly, we report that the conservation of webspinner fibroin carboxyl-terminal regions suggests that fiber formation may occur through a mechanism analogous to that found in Lepidoptera. From these results, insight is gained into the tempo and mode of evolution that has shaped embiopteran fibroins.
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Affiliation(s)
- Matthew A Collin
- Department of Biology, University of California, Riverside, CA 92521, USA.
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Stewart RJ, Wang CS. Adaptation of caddisfly larval silks to aquatic habitats by phosphorylation of h-fibroin serines. Biomacromolecules 2010; 11:969-74. [PMID: 20196534 DOI: 10.1021/bm901426d] [Citation(s) in RCA: 88] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Aquatic caddisflies diverged from a silk-spinning ancestor shared with terrestrial moths and butterflies. Caddisfly larva spin adhesive silk underwater to construct protective shelters with adventitiously gathered materials. A repeating (SX)(n) motif conserved in the H-fibroin of several caddisfly species is densely phosphorylated. In total, more than half of the serines in caddisfly silk may be phosphorylated. Major molecular adaptations allowing underwater spinning of an ancestral dry silk appear to have been phosphorylation of serines and the accumulation of basic residues in the silk proteins. The amphoteric nature of the silk proteins could contribute to silk fiber assembly through electrostatic association of phosphorylated blocks with arginine-rich blocks. The presence of Ca(2+) in the caddisfly larval silk proteins suggest phosphorylated serines could contribute to silk fiber periodic substructure through Ca(2+) crossbridging.
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Affiliation(s)
- Russell J Stewart
- Department of Bioengineering, University of Utah, Salt Lake City, Utah 84112, USA.
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Collin MA, Mita K, Sehnal F, Hayashi CY. Molecular evolution of lepidopteran silk proteins: insights from the ghost moth, Hepialus californicus. J Mol Evol 2010; 70:519-29. [PMID: 20458474 PMCID: PMC2876269 DOI: 10.1007/s00239-010-9349-8] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2009] [Accepted: 04/19/2010] [Indexed: 11/24/2022]
Abstract
Silk production has independently evolved in numerous arthropod lineages, such as Lepidoptera, the moths and butterflies. Lepidopteran larvae (caterpillars) synthesize silk proteins in modified salivary glands and spin silk fibers into protective tunnels, escape lines, and pupation cocoons. Molecular sequence data for these proteins are necessary to determine critical features of their function and evolution. To this end, we constructed an expression library from the silk glands of the ghost moth, Hepialus californicus, and characterized light chain fibroin and heavy chain fibroin gene transcripts. The predicted H. californicus silk fibroins share many elements with other lepidopteran and trichopteran fibroins, such as conserved placements of cysteine, aromatic, and polar amino acid residues. Further comparative analyses were performed to determine site-specific signatures of selection and to assess whether fibroin genes are informative as phylogenetic markers. We found that purifying selection has constrained mutation within the fibroins and that light chain fibroin is a promising molecular marker. Thus, by characterizing the H. californicus fibroins, we identified key functional amino acids and gained insight into the evolutionary processes that have shaped these adaptive molecules.
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Affiliation(s)
- Matthew A Collin
- Department of Biology, University of California, Riverside, CA 92521, USA.
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