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Shi F, Liu K, Chen G, Chang Y, Xue C. Investigation of the Presence of Fibrillin in Sea Cucumber ( Apostichopus japonicus) Body Wall by Utilizing Targeted Proteomics and Visualization Strategies. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2024; 72:8798-8804. [PMID: 38548625 DOI: 10.1021/acs.jafc.4c00046] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/18/2024]
Abstract
Fibrillin is an important structural protein in connective tissues. The presence of fibrillin in sea cucumber Apostichopus japonicus is still poorly understood, which limits our understanding of the role of fibrillin in the A. japonicus microstructure. The aim of this study was to clarify the presence of fibrillin in the sea cucumber A. japonicus body wall. Herein, the presence of fibrillin in sea cucumber A. japonicus was investigated by utilizing targeted proteomics and visualization strategies. The contents of three different isoforms of fibrillin with high abundance in A. japonicus were determined to be 0.96, 2.54, and 0.15 μg/g (wet base), respectively. The amino acid sequence of fibrillin (GeneBank number: PIK56741.1) that started at position 631 and ended at position 921 was selected for cloning and expressing antigen. An anti-A. japonicus fibrillin antibody with a titer greater than 1:64 000 was successfully obtained. It was observed that the distribution of fibrillin in the A. japonicus body wall was scattered and dispersed in the form of fibril bundles at the microscale. It further observed that fibrillin was present near collagen fibrils and some entangled outside the collagen fibrils at the nanoscale. Moreover, the stoichiometry of the most dominant collagen and fibrillin molecules in A. japonicus was determined to be approximately 250:1. These results contribute to an understanding of the role of fibrillin in the sea cucumber microstructure.
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Affiliation(s)
- Feifei Shi
- College of Food Science and Engineering, Ocean University of China, 1299 Sansha Road, Qingdao 266404, China
- College of Food Science, Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Kaimeng Liu
- College of Food Science and Engineering, Ocean University of China, 1299 Sansha Road, Qingdao 266404, China
| | - Guangning Chen
- College of Food Science and Engineering, Ocean University of China, 1299 Sansha Road, Qingdao 266404, China
| | - Yaoguang Chang
- College of Food Science and Engineering, Ocean University of China, 1299 Sansha Road, Qingdao 266404, China
| | - Changhu Xue
- College of Food Science and Engineering, Ocean University of China, 1299 Sansha Road, Qingdao 266404, China
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Candia Carnevali MD, Sugni M, Bonasoro F, Wilkie IC. Mutable Collagenous Tissue: A Concept Generator for Biomimetic Materials and Devices. Mar Drugs 2024; 22:37. [PMID: 38248662 PMCID: PMC10817530 DOI: 10.3390/md22010037] [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: 11/28/2023] [Revised: 12/30/2023] [Accepted: 01/04/2024] [Indexed: 01/23/2024] Open
Abstract
Echinoderms (starfish, sea-urchins and their close relations) possess a unique type of collagenous tissue that is innervated by the motor nervous system and whose mechanical properties, such as tensile strength and elastic stiffness, can be altered in a time frame of seconds. Intensive research on echinoderm 'mutable collagenous tissue' (MCT) began over 50 years ago, and over 20 years ago, MCT first inspired a biomimetic design. MCT, and sea-cucumber dermis in particular, is now a major source of ideas for the development of new mechanically adaptable materials and devices with applications in diverse areas including biomedical science, chemical engineering and robotics. In this review, after an up-to-date account of present knowledge of the structural, physiological and molecular adaptations of MCT and the mechanisms responsible for its variable tensile properties, we focus on MCT as a concept generator surveying biomimetic systems inspired by MCT biology, showing that these include both bio-derived developments (same function, analogous operating principles) and technology-derived developments (same function, different operating principles), and suggest a strategy for the further exploitation of this promising biological resource.
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Affiliation(s)
- M. Daniela Candia Carnevali
- Department of Environmental Science and Policy, University of Milan, 20133 Milan, Italy; (M.D.C.C.); (M.S.); (F.B.)
| | - Michela Sugni
- Department of Environmental Science and Policy, University of Milan, 20133 Milan, Italy; (M.D.C.C.); (M.S.); (F.B.)
| | - Francesco Bonasoro
- Department of Environmental Science and Policy, University of Milan, 20133 Milan, Italy; (M.D.C.C.); (M.S.); (F.B.)
| | - Iain C. Wilkie
- School of Biodiversity, One Health and Veterinary Medicine, University of Glasgow, Glasgow G12 8QQ, UK
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Tamori M, Yamada A. Possible Mechanisms of Stiffness Changes Induced by Stiffeners and Softeners in Catch Connective Tissue of Echinoderms. Mar Drugs 2023; 21:md21030140. [PMID: 36976189 PMCID: PMC10053443 DOI: 10.3390/md21030140] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2023] [Revised: 02/17/2023] [Accepted: 02/21/2023] [Indexed: 02/25/2023] Open
Abstract
The catch connective, or mutable collagenous, tissue of echinoderms changes its mechanical properties in response to stimulation. The body wall dermis of sea cucumbers is a typical catch connective tissue. The dermis assumes three mechanical states: soft, standard, and stiff. Proteins that change the mechanical properties have been purified from the dermis. Tensilin and the novel stiffening factor are involved in the soft to standard and standard to stiff transitions, respectively. Softenin softens the dermis in the standard state. Tensilin and softenin work directly on the extracellular matrix (ECM). This review summarizes the current knowledge regarding such stiffeners and softeners. Attention is also given to the genes of tensilin and its related proteins in echinoderms. In addition, we provide information on the morphological changes of the ECM associated with the stiffness change of the dermis. Ultrastructural study suggests that tensilin induces an increase in the cohesive forces with the lateral fusion of collagen subfibrils in the soft to standard transition, that crossbridge formation between fibrils occurs in both the soft to standard and standard to stiff transitions, and that the bond which accompanies water exudation produces the stiff dermis from the standard state.
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Affiliation(s)
- Masaki Tamori
- School of Life Science and Technology, W3-42, Tokyo Institute of Technology, O-okayama 2-12-1, Meguro-ku, Tokyo 152-8551, Japan
- Correspondence:
| | - Akira Yamada
- National Institute of Information and Communications Technology, 4-2-1, Nukui-Kitamachi, Koganei, Tokyo 184-8795, Japan
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McDonald M, Griffin NP, Howell E, Li D, Harnew-Spradley S, Rodriguez P, Lancaster A, Umutoni F, Besh J, Shelley C. Effects of neurotransmitter receptor antagonists on sea urchin righting behavior and tube foot motility. J Exp Biol 2022; 225:274563. [DOI: 10.1242/jeb.243076] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2021] [Accepted: 02/22/2022] [Indexed: 11/20/2022]
Abstract
Sea urchins, as echinoderms, occupy an interesting position in animal phylogeny in that they are genetically closer to vertebrates than the vast majority of all other invertebrates but have a nervous system that lacks a brain or brain-like structure. Despite this, very little is known about neurobiology of the adult sea urchin, and how the nervous system, is utilized to produced behavior. Here we investigate effects on the righting response of antagonists of ionotropic receptors for the neurotransmitters acetylcholine, GABA, and glycine, and antagonists of metabotropic receptors for the amines dopamine and norepinephrine. Antagonists slowed the righting response in a dose-dependent manner, with a rank order of potency of strychnine>haloperidol>propranolol>bicuculline>hexamethonium, with RT50s (concentrations that slowed righting time by 50%) ranging from 4.3 µM for strychnine to 7.8 mM for hexamethonium. It is also shown that both glycine and adrenergic receptors are needed for actual tube foot movement, and this may explain the slowed righting seen when these receptors are inhibited. Conversely, inhibition of dopamine receptors slowed the righting response but had no effect on tube foot motility, indicating that these receptors play roles more in the neural processing involved in the righting behavior, rather than the actual physical righting. Our results identity the first effects of inhibiting the glycinergic, dopaminergic, and adrenergic neurotransmitter systems in adult sea urchins and distinguish between the ability of sea urchins to right themselves, and the ability of sea urchins to move their tube feet.
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Affiliation(s)
- Morgan McDonald
- Biology Department, The University of the South, Sewanee, TN, 37383, USA
| | | | - Emma Howell
- Biology Department, The University of the South, Sewanee, TN, 37383, USA
| | - Dingchen Li
- Biology Department, The University of the South, Sewanee, TN, 37383, USA
| | | | - Patrick Rodriguez
- Biology Department, The University of the South, Sewanee, TN, 37383, USA
| | - Abigail Lancaster
- Biology Department, The University of the South, Sewanee, TN, 37383, USA
| | - Feza Umutoni
- Biology Department, The University of the South, Sewanee, TN, 37383, USA
| | - Jordan Besh
- Biology Department, The University of the South, Sewanee, TN, 37383, USA
| | - Chris Shelley
- Biology Department, The University of the South, Sewanee, TN, 37383, USA
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Bonneel M, Hennebert E, Aranko AS, Hwang DS, Lefevre M, Pommier V, Wattiez R, Delroisse J, Flammang P. Molecular mechanisms mediating stiffening in the mechanically adaptable connective tissues of sea cucumbers. Matrix Biol 2022; 108:39-54. [DOI: 10.1016/j.matbio.2022.02.006] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2021] [Revised: 01/24/2022] [Accepted: 02/23/2022] [Indexed: 11/25/2022]
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Fassini D, Wilkie IC, Pozzolini M, Ferrario C, Sugni M, Rocha MS, Giovine M, Bonasoro F, Silva TH, Reis RL. Diverse and Productive Source of Biopolymer Inspiration: Marine Collagens. Biomacromolecules 2021; 22:1815-1834. [PMID: 33835787 DOI: 10.1021/acs.biomac.1c00013] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Abstract
Marine biodiversity is expressed through the huge variety of vertebrate and invertebrate species inhabiting intertidal to deep-sea environments. The extraordinary variety of "forms and functions" exhibited by marine animals suggests they are a promising source of bioactive molecules and provides potential inspiration for different biomimetic approaches. This diversity is familiar to biologists and has led to intensive investigation of metabolites, polysaccharides, and other compounds. However, marine collagens are less well-known. This review will provide detailed insight into the diversity of collagens present in marine species in terms of their genetics, structure, properties, and physiology. In the last part of the review the focus will be on the most common marine collagen sources and on the latest advances in the development of innovative materials exploiting, or inspired by, marine collagens.
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Affiliation(s)
- Dario Fassini
- 3B's Research Group, I3Bs - Research Institute on Biomaterials, Biodegradables and Biomimetics, University of Minho, Headquarters of the European Institute of Excellence on Tissue Engineering and Regenerative Medicine, AvePark, Parque de Ciência e Tecnologia, Zona Industrial da Gandra, 4805-017 Barco, Guimarães, Portugal.,ICVS/3B's-PT Government Associate Laboratory, Braga, Guimarães, Portugal
| | - Iain C Wilkie
- Institute of Biodiversity Animal Health & Comparative Medicine, University of Glasgow, Glasgow G12 8QQ, Scotland
| | - Marina Pozzolini
- Department of Earth, Environment and Life Sciences (DISTAV), University of Genova, Via Pastore 3, 16132 Genova, Italy
| | - Cinzia Ferrario
- Dipartimento di Scienze e Politiche Ambientali, Università degli Studi di Milano, Milano, Italy, Center for Complexity & Biosystems, Dipartimento di Fisica, Università degli Studi di Milano, 20122 Milano, Italy
| | - Michela Sugni
- Dipartimento di Scienze e Politiche Ambientali, Università degli Studi di Milano, Milano, Italy, Center for Complexity & Biosystems, Dipartimento di Fisica, Università degli Studi di Milano, 20122 Milano, Italy
| | - Miguel S Rocha
- 3B's Research Group, I3Bs - Research Institute on Biomaterials, Biodegradables and Biomimetics, University of Minho, Headquarters of the European Institute of Excellence on Tissue Engineering and Regenerative Medicine, AvePark, Parque de Ciência e Tecnologia, Zona Industrial da Gandra, 4805-017 Barco, Guimarães, Portugal.,ICVS/3B's-PT Government Associate Laboratory, Braga, Guimarães, Portugal
| | - Marco Giovine
- Department of Earth, Environment and Life Sciences (DISTAV), University of Genova, Via Pastore 3, 16132 Genova, Italy
| | - Francesco Bonasoro
- Dipartimento di Scienze e Politiche Ambientali, Università degli Studi di Milano, Milano, Italy, Center for Complexity & Biosystems, Dipartimento di Fisica, Università degli Studi di Milano, 20122 Milano, Italy
| | - Tiago H Silva
- 3B's Research Group, I3Bs - Research Institute on Biomaterials, Biodegradables and Biomimetics, University of Minho, Headquarters of the European Institute of Excellence on Tissue Engineering and Regenerative Medicine, AvePark, Parque de Ciência e Tecnologia, Zona Industrial da Gandra, 4805-017 Barco, Guimarães, Portugal.,ICVS/3B's-PT Government Associate Laboratory, Braga, Guimarães, Portugal
| | - Rui L Reis
- 3B's Research Group, I3Bs - Research Institute on Biomaterials, Biodegradables and Biomimetics, University of Minho, Headquarters of the European Institute of Excellence on Tissue Engineering and Regenerative Medicine, AvePark, Parque de Ciência e Tecnologia, Zona Industrial da Gandra, 4805-017 Barco, Guimarães, Portugal.,ICVS/3B's-PT Government Associate Laboratory, Braga, Guimarães, Portugal
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Perricone V, Grun TB, Marmo F, Langella C, Candia Carnevali MD. Constructional design of echinoid endoskeleton: main structural components and their potential for biomimetic applications. BIOINSPIRATION & BIOMIMETICS 2020; 16:011001. [PMID: 32927446 DOI: 10.1088/1748-3190/abb86b] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/28/2020] [Accepted: 09/14/2020] [Indexed: 06/11/2023]
Abstract
The endoskeleton of echinoderms (Deuterostomia: Echinodermata) is of mesodermal origin and consists of cells, organic components, as well as an inorganic mineral matrix. The echinoderm skeleton forms a complex lattice-system, which represents a model structure for naturally inspired engineering in terms of construction, mechanical behaviour and functional design. The sea urchin (Echinodermata: Echinoidea) endoskeleton consists of three main structural components: test, dental apparatus and accessory appendages. Although, all parts of the echinoid skeleton consist of the same basic material, their microstructure displays a great potential in meeting several mechanical needs according to a direct and clear structure-function relationship. This versatility has allowed the echinoid skeleton to adapt to different activities such as structural support, defence, feeding, burrowing and cleaning. Although, constrained by energy and resource efficiency, many of the structures found in the echinoid skeleton are optimized in terms of functional performances. Therefore, these structures can be used as role models for bio-inspired solutions in various industrial sectors such as building constructions, robotics, biomedical and material engineering. The present review provides an overview of previous mechanical and biomimetic research on the echinoid endoskeleton, describing the current state of knowledge and providing a reference for future studies.
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Affiliation(s)
- Valentina Perricone
- Dept. of Engineering, University of Campania Luigi Vanvitelli, Aversa, Italy
| | - Tobias B Grun
- Dept. of Invertebrate Paleontology, University of Florida, Florida Museum, Gainesville, Florida, United States of America
| | - Francesco Marmo
- Dept. of Structures for Engineering and Architecture, University of Naples Federico II, Napoli, Italy
| | - Carla Langella
- Dept. of Architecture and Industrial Design, University of Campania Luigi Vanvitelli, Aversa, Italy
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8
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Dolmatov IY, Afanasyev SV, Boyko AV. Molecular mechanisms of fission in echinoderms: Transcriptome analysis. PLoS One 2018; 13:e0195836. [PMID: 29649336 PMCID: PMC5897022 DOI: 10.1371/journal.pone.0195836] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2017] [Accepted: 04/01/2018] [Indexed: 12/11/2022] Open
Abstract
Echinoderms are capable of asexual reproduction by fission. An individual divides into parts due to changes in the strength of connective tissue of the body wall. The structure of connective tissue and the mechanisms of variations in its strength in echinoderms remain poorly studied. An analysis of transcriptomes of individuals during the process of fission provides a new opportunity to understand the mechanisms of connective tissue mutability. In the holothurian Cladolabes schmeltzii, we have found a rather complex organization of connective tissue. Transcripts of genes encoding a wide range of structural proteins of extracellular matrix, as well as various proteases and their inhibitors, have been discovered. All these molecules may constitute a part of the mechanism of connective tissue mutability. According to our data, the extracellular matrix of echinoderms is substantially distinguished from that of vertebrates by the lack of elastin, fibronectins, and tenascins. In case of fission, a large number of genes of transcription factors and components of different signaling pathways are expressed. Products of these genes are probably involved in regulation of asexual reproduction, connective tissue mutability, and preparation of tissues for subsequent regeneration. It has been shown that holothurian tensilins are a special group of tissue inhibitors of metalloproteinases, which has formed within the class Holothuroidea and is absent from other echinoderms. Our data can serve a basis for the further study of the mechanisms of extracellular matrix mutability, as well as the mechanisms responsible for asexual reproduction in echinoderms.
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Affiliation(s)
- Igor Yu. Dolmatov
- A.V. Zhirmunsky Institute of Marine Biology, National Scientific Center of Marine Biology, Far Eastern Branch, Russian Academy of Sciences, Vladivostok, Russia
- Far Eastern Federal University, Vladivostok, Russia
- * E-mail:
| | - Sergey V. Afanasyev
- Sechenov Institute of Evolutionary Physiology and Biochemistry, Saint Petersburg, Russia
| | - Alexey V. Boyko
- A.V. Zhirmunsky Institute of Marine Biology, National Scientific Center of Marine Biology, Far Eastern Branch, Russian Academy of Sciences, Vladivostok, Russia
- Far Eastern Federal University, Vladivostok, Russia
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Goh KL, Holmes DF. Collagenous Extracellular Matrix Biomaterials for Tissue Engineering: Lessons from the Common Sea Urchin Tissue. Int J Mol Sci 2017; 18:ijms18050901. [PMID: 28441344 PMCID: PMC5454814 DOI: 10.3390/ijms18050901] [Citation(s) in RCA: 24] [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] [Received: 01/10/2017] [Revised: 04/05/2017] [Accepted: 04/11/2017] [Indexed: 12/21/2022] Open
Abstract
Scaffolds for tissue engineering application may be made from a collagenous extracellular matrix (ECM) of connective tissues because the ECM can mimic the functions of the target tissue. The primary sources of collagenous ECM material are calf skin and bone. However, these sources are associated with the risk of having bovine spongiform encephalopathy or transmissible spongiform encephalopathy. Alternative sources for collagenous ECM materials may be derived from livestock, e.g., pigs, and from marine animals, e.g., sea urchins. Collagenous ECM of the sea urchin possesses structural features and mechanical properties that are similar to those of mammalian ones. However, even more intriguing is that some tissues such as the ligamentous catch apparatus can exhibit mutability, namely rapid reversible changes in the tissue mechanical properties. These tissues are known as mutable collagenous tissues (MCTs). The mutability of these tissues has been the subject of on-going investigations, covering the biochemistry, structural biology and mechanical properties of the collagenous components. Recent studies point to a nerve-control system for regulating the ECM macromolecules that are involved in the sliding action of collagen fibrils in the MCT. This review discusses the key attributes of the structure and function of the ECM of the sea urchin ligaments that are related to the fibril-fibril sliding action-the focus is on the respective components within the hierarchical architecture of the tissue. In this context, structure refers to size, shape and separation distance of the ECM components while function is associated with mechanical properties e.g., strength and stiffness. For simplicity, the components that address the different length scale from the largest to the smallest are as follows: collagen fibres, collagen fibrils, interfibrillar matrix and collagen molecules. Application of recent theories of stress transfer and fracture mechanisms in fibre reinforced composites to a wide variety of collagen reinforcing (non-mutable) connective tissue, has allowed us to draw general conclusions concerning the mechanical response of the MCT at specific mechanical states, namely the stiff and complaint states. The intent of this review is to provide the latest insights, as well as identify technical challenges and opportunities, that may be useful for developing methods for effective mechanical support when adapting decellularised connective tissues from the sea urchin for tissue engineering or for the design of a synthetic analogue.
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Affiliation(s)
- Kheng Lim Goh
- Newcastle University Singapore, SIT Building at Nanyang Polytechnic, 172A Ang Mo Kio Avenue 8 #05-01, Singapore 567739, Singapore.
- Newcastle University, School of Mechanical & Systems Engineering, Stephenson Building, Claremont Road, Newcastle upon Tyne NE1 7RU, UK.
| | - David F Holmes
- Manchester University, Wellcome Trust Centre for Cell Matrix Research, B.3016 Michael Smith Building, Faculty of Life Sciences, Oxford Road, Manchester M13 9PT, UK.
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Mo J, Prévost SF, Blowes LM, Egertová M, Terrill NJ, Wang W, Elphick MR, Gupta HS. Interfibrillar stiffening of echinoderm mutable collagenous tissue demonstrated at the nanoscale. Proc Natl Acad Sci U S A 2016; 113:E6362-E6371. [PMID: 27708167 PMCID: PMC5081653 DOI: 10.1073/pnas.1609341113] [Citation(s) in RCA: 38] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022] Open
Abstract
The mutable collagenous tissue (MCT) of echinoderms (e.g., sea cucumbers and starfish) is a remarkable example of a biological material that has the unique attribute, among collagenous tissues, of being able to rapidly change its stiffness and extensibility under neural control. However, the mechanisms of MCT have not been characterized at the nanoscale. Using synchrotron small-angle X-ray diffraction to probe time-dependent changes in fibrillar structure during in situ tensile testing of sea cucumber dermis, we investigate the ultrastructural mechanics of MCT by measuring fibril strain at different chemically induced mechanical states. By measuring a variable interfibrillar stiffness (EIF), the mechanism of mutability at the nanoscale can be demonstrated directly. A model of stiffness modulation via enhanced fibrillar recruitment is developed to explain the biophysical mechanisms of MCT. Understanding the mechanisms of MCT quantitatively may have applications in development of new types of mechanically tunable biomaterials.
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Affiliation(s)
- Jingyi Mo
- School of Engineering and Material Science, Queen Mary University of London, London, E1 4NS, United Kingdom
| | - Sylvain F Prévost
- Beamline ID02, European Synchrotron Radiation Facility, Grenoble 38000, France
| | - Liisa M Blowes
- School of Biological and Chemical Sciences, Queen Mary University of London, London, E1 4NS, United Kingdom
| | - Michaela Egertová
- School of Biological and Chemical Sciences, Queen Mary University of London, London, E1 4NS, United Kingdom
| | - Nicholas J Terrill
- Beamline I22, Diamond Light Source, Harwell Science and Innovation Campus, Harwell, OX11 0DE, United Kingdom
| | - Wen Wang
- School of Engineering and Material Science, Queen Mary University of London, London, E1 4NS, United Kingdom; Institute of Bioengineering, Queen Mary University of London, London, E1 4NS, United Kingdom
| | - Maurice R Elphick
- School of Biological and Chemical Sciences, Queen Mary University of London, London, E1 4NS, United Kingdom;
| | - Himadri S Gupta
- School of Engineering and Material Science, Queen Mary University of London, London, E1 4NS, United Kingdom; Institute of Bioengineering, Queen Mary University of London, London, E1 4NS, United Kingdom
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Bronstein O, Kroh A, Haring E. Do genes lie? Mitochondrial capture masks the Red Sea collector urchin's true identity (Echinodermata: Echinoidea: Tripneustes). Mol Phylogenet Evol 2016; 104:1-13. [PMID: 27475495 DOI: 10.1016/j.ympev.2016.07.028] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2016] [Revised: 06/02/2016] [Accepted: 07/25/2016] [Indexed: 10/21/2022]
Abstract
Novel COI and bindin sequences of the Red Sea collector echinoid Tripneustes gratilla elatensis are used to show that (1) discordance between mitochondrial and nuclear loci exists in this echinoid genus, (2) Tripneustes gratilla as currently defined possibly comprises a complex of cryptic species, and (3) Red Sea Tripneustes form a genetically distinct clade in the bindin tree, which diverged from other Tripneustes clades at least 2-4million years ago. Morphological reassessment of T. gratilla elatensis shows perfect congruence between identification based on skeletal features and genetic data based on a nuclear marker sequence. Hence the Red Sea Tripneustes subspecies established by Dafni in 1983 is a distinct biological unit. All T. g. elatensis samples analyzed are highly similar to or share mtDNA haplotypes with Philippine T. g. gratilla, as do representatives from other edge-of-range occurrences. This lack of genetic structure in Indo-Pacific Tripneustes is interpreted as a result of wide-spread mitochondrial introgression. New fossil specimens from the Red Sea area confirm the sympatric occurrence of T. g. elatensis and T. g. gratilla in the northern Red Sea during Late Pleistocene, identifying a possible timing for the introgression. In addition, present-day distribution shows a contact zone in the Southern Red Sea (in the Dahlak Archipelago). T. g. elatensis, is yet another example of a Red Sea taxon historically identified as conspecific with its Indo-Pacific relatives, but which turned out to be a morphologically and genetically distinct endemic taxon, suggesting that the level of endemism in the Red Sea may still be underestimated.
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Affiliation(s)
- Omri Bronstein
- Natural History Museum Vienna, Geological-Paleontological Department, Burgring 7, 1010 Vienna, Austria; Natural History Museum Vienna, Central Research Laboratories, Burgring 7, 1010 Vienna, Austria; The Steinhardt Museum of Natural History and National Research Centre, Tel Aviv University, Israel.
| | - Andreas Kroh
- Natural History Museum Vienna, Geological-Paleontological Department, Burgring 7, 1010 Vienna, Austria.
| | - Elisabeth Haring
- Natural History Museum Vienna, Central Research Laboratories, Burgring 7, 1010 Vienna, Austria; University of Vienna, Department of Integrative Zoology, Vienna, Austria.
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Clouse RM, Linchangco GV, Kerr AM, Reid RW, Janies DA. Phylotranscriptomic analysis uncovers a wealth of tissue inhibitor of metalloproteinases variants in echinoderms. ROYAL SOCIETY OPEN SCIENCE 2015; 2:150377. [PMID: 27017967 PMCID: PMC4807446 DOI: 10.1098/rsos.150377] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/29/2015] [Accepted: 11/06/2015] [Indexed: 06/05/2023]
Abstract
Tissue inhibitors of metalloproteinases (TIMPs) help regulate the extracellular matrix (ECM) in animals, mostly by inhibiting matrix metalloproteinases (MMPs). They are important activators of mutable collagenous tissue (MCT), which have been extensively studied in echinoderms, and the four TIMP copies in humans have been studied for their role in cancer. To understand the evolution of TIMPs, we combined 405 TIMPs from an echinoderm transcriptome dataset built from 41 specimens representing all five classes of echinoderms with variants from protostomes and chordates. We used multiple sequence alignment with various stringencies of alignment quality to cull highly divergent sequences and then conducted phylogenetic analyses using both nucleotide and amino acid sequences. Phylogenetic hypotheses consistently recovered TIMPs as diversifying in the ancestral deuterostome and these early lineages continuing to diversify in echinoderms. The four vertebrate TIMPs diversified from a single copy in the ancestral chordate, all other copies being lost. Consistent with greater MCT needs owing to body wall liquefaction, evisceration, autotomy and reproduction by fission, holothuroids had significantly more TIMPs and higher read depths per contig. Ten cysteine residues, an HPQ binding site and several other residues were conserved in at least 70% of all TIMPs. The conservation of binding sites and the placement of echinoderm TIMPs involved in MCT modification suggest that ECM regulation remains the primary function of TIMP genes, although within this role there are a large number of specialized copies.
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Affiliation(s)
- Ronald M. Clouse
- Department of Bioinformatics and Genomics, University of North Carolina at Charlotte, 9201 University City Boulevard, Charlotte, NC 28223, USA
| | - Gregorio V. Linchangco
- Department of Bioinformatics and Genomics, University of North Carolina at Charlotte, 9201 University City Boulevard, Charlotte, NC 28223, USA
| | - Alexander M. Kerr
- Marine Laboratory, University of Guam, Mangilao, GU 96913, USA
- ARC Centre of Excellence for Coral Reef Studies, James Cook University, Townsville, Queensland 4811, Australia
| | - Robert W. Reid
- Bioinformatics Services Division, North Carolina Research Campus, University of North Carolina at Charlotte, Kannapolis, NC 28081, USA
| | - Daniel A. Janies
- Department of Bioinformatics and Genomics, University of North Carolina at Charlotte, 9201 University City Boulevard, Charlotte, NC 28223, USA
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