1
|
Goodheart JA, Rio RA, Taraporevala NF, Fiorenza RA, Barnes SR, Morrill K, Jacob MAC, Whitesel C, Masterson P, Batzel GO, Johnston HT, Ramirez MD, Katz PS, Lyons DC. A chromosome-level genome for the nudibranch gastropod Berghia stephanieae helps parse clade-specific gene expression in novel and conserved phenotypes. BMC Biol 2024; 22:9. [PMID: 38233809 PMCID: PMC10795318 DOI: 10.1186/s12915-024-01814-3] [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: 08/07/2023] [Accepted: 01/03/2024] [Indexed: 01/19/2024] Open
Abstract
BACKGROUND How novel phenotypes originate from conserved genes, processes, and tissues remains a major question in biology. Research that sets out to answer this question often focuses on the conserved genes and processes involved, an approach that explicitly excludes the impact of genetic elements that may be classified as clade-specific, even though many of these genes are known to be important for many novel, or clade-restricted, phenotypes. This is especially true for understudied phyla such as mollusks, where limited genomic and functional biology resources for members of this phylum have long hindered assessments of genetic homology and function. To address this gap, we constructed a chromosome-level genome for the gastropod Berghia stephanieae (Valdés, 2005) to investigate the expression of clade-specific genes across both novel and conserved tissue types in this species. RESULTS The final assembled and filtered Berghia genome is comparable to other high-quality mollusk genomes in terms of size (1.05 Gb) and number of predicted genes (24,960 genes) and is highly contiguous. The proportion of upregulated, clade-specific genes varied across tissues, but with no clear trend between the proportion of clade-specific genes and the novelty of the tissue. However, more complex tissue like the brain had the highest total number of upregulated, clade-specific genes, though the ratio of upregulated clade-specific genes to the total number of upregulated genes was low. CONCLUSIONS Our results, when combined with previous research on the impact of novel genes on phenotypic evolution, highlight the fact that the complexity of the novel tissue or behavior, the type of novelty, and the developmental timing of evolutionary modifications will all influence how novel and conserved genes interact to generate diversity.
Collapse
Affiliation(s)
- Jessica A Goodheart
- Division of Invertebrate Zoology, American Museum of Natural History, New York, NY, USA.
- Scripps Institution of Oceanography, University of California San Diego, La Jolla, CA, USA.
| | - Robin A Rio
- Bioengineering Department, Stanford University, Stanford, CA, USA
| | - Neville F Taraporevala
- Scripps Institution of Oceanography, University of California San Diego, La Jolla, CA, USA
- Department of Wildland Resources, Utah State University, Logan, UT, USA
| | - Rose A Fiorenza
- Scripps Institution of Oceanography, University of California San Diego, La Jolla, CA, USA
| | - Seth R Barnes
- Scripps Institution of Oceanography, University of California San Diego, La Jolla, CA, USA
| | - Kevin Morrill
- Scripps Institution of Oceanography, University of California San Diego, La Jolla, CA, USA
| | - Mark Allan C Jacob
- Scripps Institution of Oceanography, University of California San Diego, La Jolla, CA, USA
| | - Carl Whitesel
- Scripps Institution of Oceanography, University of California San Diego, La Jolla, CA, USA
| | - Park Masterson
- Scripps Institution of Oceanography, University of California San Diego, La Jolla, CA, USA
| | - Grant O Batzel
- Scripps Institution of Oceanography, University of California San Diego, La Jolla, CA, USA
| | - Hereroa T Johnston
- Scripps Institution of Oceanography, University of California San Diego, La Jolla, CA, USA
| | - M Desmond Ramirez
- Department of Biology, University of Massachusetts Amherst, Amherst, MA, USA
- Institute of Neuroscience, University of Oregon, Eugene, OR, USA
| | - Paul S Katz
- Department of Biology, University of Massachusetts Amherst, Amherst, MA, USA
| | - Deirdre C Lyons
- Scripps Institution of Oceanography, University of California San Diego, La Jolla, CA, USA.
| |
Collapse
|
2
|
Xavier JC, Golikov AV, Queirós JP, Perales-Raya C, Rosas-Luis R, Abreu J, Bello G, Bustamante P, Capaz JC, Dimkovikj VH, González AF, Guímaro H, Guerra-Marrero A, Gomes-Pereira JN, Hernández-Urcera J, Kubodera T, Laptikhovsky V, Lefkaditou E, Lishchenko F, Luna A, Liu B, Pierce GJ, Pissarra V, Reveillac E, Romanov EV, Rosa R, Roscian M, Rose-Mann L, Rouget I, Sánchez P, Sánchez-Márquez A, Seixas S, Souquet L, Varela J, Vidal EAG, Cherel Y. The significance of cephalopod beaks as a research tool: An update. Front Physiol 2022; 13:1038064. [PMID: 36467695 PMCID: PMC9716703 DOI: 10.3389/fphys.2022.1038064] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2022] [Accepted: 10/25/2022] [Indexed: 11/17/2022] Open
Abstract
The use of cephalopod beaks in ecological and population dynamics studies has allowed major advances of our knowledge on the role of cephalopods in marine ecosystems in the last 60 years. Since the 1960's, with the pioneering research by Malcolm Clarke and colleagues, cephalopod beaks (also named jaws or mandibles) have been described to species level and their measurements have been shown to be related to cephalopod body size and mass, which permitted important information to be obtained on numerous biological and ecological aspects of cephalopods in marine ecosystems. In the last decade, a range of new techniques has been applied to cephalopod beaks, permitting new kinds of insight into cephalopod biology and ecology. The workshop on cephalopod beaks of the Cephalopod International Advisory Council Conference (Sesimbra, Portugal) in 2022 aimed to review the most recent scientific developments in this field and to identify future challenges, particularly in relation to taxonomy, age, growth, chemical composition (i.e., DNA, proteomics, stable isotopes, trace elements) and physical (i.e., structural) analyses. In terms of taxonomy, new techniques (e.g., 3D geometric morphometrics) for identifying cephalopods from their beaks are being developed with promising results, although the need for experts and reference collections of cephalopod beaks will continue. The use of beak microstructure for age and growth studies has been validated. Stable isotope analyses on beaks have proven to be an excellent technique to get valuable information on the ecology of cephalopods (namely habitat and trophic position). Trace element analyses is also possible using beaks, where concentrations are significantly lower than in other tissues (e.g., muscle, digestive gland, gills). Extracting DNA from beaks was only possible in one study so far. Protein analyses can also be made using cephalopod beaks. Future challenges in research using cephalopod beaks are also discussed.
Collapse
Affiliation(s)
- José C. Xavier
- Department of Life Sciences, Marine and Environmental Sciences Centre/ ARNET–Aquatic Research Network, University of Coimbra, Coimbra, Portugal
- British Antarctic Survey, Natural Environment Research Council, Cambridge, United Kingdom
| | | | - José P. Queirós
- Department of Life Sciences, Marine and Environmental Sciences Centre/ ARNET–Aquatic Research Network, University of Coimbra, Coimbra, Portugal
- British Antarctic Survey, Natural Environment Research Council, Cambridge, United Kingdom
| | | | | | - José Abreu
- Department of Life Sciences, Marine and Environmental Sciences Centre/ ARNET–Aquatic Research Network, University of Coimbra, Coimbra, Portugal
- British Antarctic Survey, Natural Environment Research Council, Cambridge, United Kingdom
| | | | - Paco Bustamante
- Littoral Environnement et Sociétés (LIENSs), UMR 7266 CNRS-La Rochelle Université, La Rochelle, France
- Institut Universitaire de France (IUF), Paris, France
| | - Juan C. Capaz
- Center of Marine Sciences, University of Algarve, Campus de Gambelas, Faro, Portugal
| | - Valerie H. Dimkovikj
- Department of Marine Science, Coastal Carolina University, Conway, SC, United States
| | | | - Hugo Guímaro
- Department of Life Sciences, Marine and Environmental Sciences Centre/ ARNET–Aquatic Research Network, University of Coimbra, Coimbra, Portugal
- British Antarctic Survey, Natural Environment Research Council, Cambridge, United Kingdom
| | - Airam Guerra-Marrero
- IU-ECOAQUA, University of Las Palmas de Gran Canaria, Edf. Ciencias Básicas, Campus de Tafira, Las Palmas de Gran Canaria, Spain
| | | | | | | | - Vladimir Laptikhovsky
- Centre for Environment, Fisheries and Aquaculture Science (CEFAS), Lowestoft, United Kingdom
| | | | - Fedor Lishchenko
- Laboratory for Ecology and Morphology of Marine Invertebrates, A.N. Severtsov Institute of Ecology and Evolution of the Russian Academy of Sciences, Moscow, Russia
| | - Amanda Luna
- Department of Ecology and Animal Biology, Faculty of Marine Sciences, University of Vigo, Vigo, Spain
| | - Bilin Liu
- College of Marine Sciences, Shanghai Ocean University, Shanghai, China
| | | | - Vasco Pissarra
- MARE—Marine and Environmental Sciences Centre/ARNET–Aquatic Research Network, Laboratório Marítimo da Guia, Faculdade de Ciências, Universidade de Lisboa, Cascais, Portugal
| | - Elodie Reveillac
- Littoral Environnement et Sociétés (LIENSs), UMR 7266 CNRS-La Rochelle Université, La Rochelle, France
| | - Evgeny V. Romanov
- Centre Technique de Recherche et de Valorisation des Milieux Aquatiques (CITEB), Le Port, Île de la Réunion, France
| | - Rui Rosa
- MARE—Marine and Environmental Sciences Centre/ARNET–Aquatic Research Network, Laboratório Marítimo da Guia, Faculdade de Ciências, Universidade de Lisboa, Cascais, Portugal
| | - Marjorie Roscian
- Centre de Recherche en Paléontologie-Paris (CR2P), CNRS, Sorbonne Université, Paris, France
| | - Lisa Rose-Mann
- University of South Florida, College of Marine Science, St. Petersburg, FL, United States
| | - Isabelle Rouget
- Centre de Recherche en Paléontologie-Paris (CR2P), CNRS, Sorbonne Université, Paris, France
| | - Pilar Sánchez
- Institut de Ciènces del Mar, CSIC, Psg. Marítim de la Barceloneta, Barcelona, Spain
| | | | - Sónia Seixas
- Department of Life Sciences, Marine and Environmental Sciences Centre/ ARNET–Aquatic Research Network, University of Coimbra, Coimbra, Portugal
- Universidade Aberta, Rua Escola Politécnica, Lisboa, Portugal
| | - Louise Souquet
- Department of Mechanical Engineering, Faculty of Engineering Science, University College London, London, United Kingdom
| | - Jaquelino Varela
- MARE—Marine and Environmental Sciences Centre/ARNET–Aquatic Research Network, Laboratório Marítimo da Guia, Faculdade de Ciências, Universidade de Lisboa, Cascais, Portugal
| | - Erica A. G. Vidal
- Center for Marine Studies—Federal University of Parana (UFPR), Pontal do Paraná, PR, Brazil
| | - Yves Cherel
- Centre d’Etudes Biologiques de Chizé, UMR 7372 du CNRS-La Rochelle Université, Villiers-en-Bois, France
| |
Collapse
|
3
|
Rodrigo AP, Lopes A, Pereira R, Anjo SI, Manadas B, Grosso AR, Baptista PV, Fernandes AR, Costa PM. Endogenous Fluorescent Proteins in the Mucus of an Intertidal Polychaeta: Clues for Biotechnology. Mar Drugs 2022; 20:md20040224. [PMID: 35447897 PMCID: PMC9028460 DOI: 10.3390/md20040224] [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: 02/25/2022] [Revised: 03/23/2022] [Accepted: 03/23/2022] [Indexed: 02/04/2023] Open
Abstract
The vast ocean holds many unexplored organisms with unique adaptive features that enable them to thrive in their environment. The secretion of fluorescent proteins is one of them, with reports on the presence of such compounds in marine annelids being scarce. The intertidal Eulalia sp. is an example. The worm secretes copious amounts of mucus, that when purified and concentrated extracts, yield strong fluorescence under UV light. Emission has two main maxima, at 400 nm and at 500 nm, with the latter responsible for the blue–greenish fluorescence. Combining proteomics and transcriptomics techniques, we identified ubiquitin, peroxiredoxin, and 14-3-3 protein as key elements in the mucus. Fluorescence was found to be mainly modulated by redox status and pH, being consistently upheld in extracts prepared in Tris-HCl buffer with reducing agent at pH 7 and excited at 330 nm. One of the proteins associated with the fluorescent signal was localized in secretory cells in the pharynx. The results indicate that the secretion of fluorescent proteinaceous complexes can be an important defense against UV for this dweller. Additionally, the internalization of fluorescent complexes by ovarian cancer cells and modulation of fluorescence of redox status bears important considerations for biotechnological application of mucus components as markers.
Collapse
Affiliation(s)
- Ana P. Rodrigo
- UCIBIO—Applied Molecular Biosciences Unit, Department of Life Sciences, NOVA School of Science and Technology, Universidade NOVA de Lisboa, 2829-516 Caparica, Portugal; (A.L.); (R.P.); (A.R.G.); (P.V.B.); (A.R.F.)
- Associate Laboratory i4HB, Institute for Health and Bioeconomy, NOVA School of Science and Technology, Universidade NOVA de Lisboa, 2829-516 Caparica, Portugal
- Correspondence: (A.P.R.); (P.M.C.); Tel.: +351-212-948-300 (A.P.R. & P.M.C.)
| | - Ana Lopes
- UCIBIO—Applied Molecular Biosciences Unit, Department of Life Sciences, NOVA School of Science and Technology, Universidade NOVA de Lisboa, 2829-516 Caparica, Portugal; (A.L.); (R.P.); (A.R.G.); (P.V.B.); (A.R.F.)
| | - Ricardo Pereira
- UCIBIO—Applied Molecular Biosciences Unit, Department of Life Sciences, NOVA School of Science and Technology, Universidade NOVA de Lisboa, 2829-516 Caparica, Portugal; (A.L.); (R.P.); (A.R.G.); (P.V.B.); (A.R.F.)
| | - Sandra I. Anjo
- Center for Neuroscience and Cell Biology, University of Coimbra, Parque Tecnológico de Cantanhede, Núcleo 04, Lote 8, 3060-197 Cantanhede, Portugal; (S.I.A.); (B.M.)
| | - Bruno Manadas
- Center for Neuroscience and Cell Biology, University of Coimbra, Parque Tecnológico de Cantanhede, Núcleo 04, Lote 8, 3060-197 Cantanhede, Portugal; (S.I.A.); (B.M.)
| | - Ana R. Grosso
- UCIBIO—Applied Molecular Biosciences Unit, Department of Life Sciences, NOVA School of Science and Technology, Universidade NOVA de Lisboa, 2829-516 Caparica, Portugal; (A.L.); (R.P.); (A.R.G.); (P.V.B.); (A.R.F.)
- Associate Laboratory i4HB, Institute for Health and Bioeconomy, NOVA School of Science and Technology, Universidade NOVA de Lisboa, 2829-516 Caparica, Portugal
| | - Pedro V. Baptista
- UCIBIO—Applied Molecular Biosciences Unit, Department of Life Sciences, NOVA School of Science and Technology, Universidade NOVA de Lisboa, 2829-516 Caparica, Portugal; (A.L.); (R.P.); (A.R.G.); (P.V.B.); (A.R.F.)
- Associate Laboratory i4HB, Institute for Health and Bioeconomy, NOVA School of Science and Technology, Universidade NOVA de Lisboa, 2829-516 Caparica, Portugal
| | - Alexandra R. Fernandes
- UCIBIO—Applied Molecular Biosciences Unit, Department of Life Sciences, NOVA School of Science and Technology, Universidade NOVA de Lisboa, 2829-516 Caparica, Portugal; (A.L.); (R.P.); (A.R.G.); (P.V.B.); (A.R.F.)
- Associate Laboratory i4HB, Institute for Health and Bioeconomy, NOVA School of Science and Technology, Universidade NOVA de Lisboa, 2829-516 Caparica, Portugal
| | - Pedro M. Costa
- UCIBIO—Applied Molecular Biosciences Unit, Department of Life Sciences, NOVA School of Science and Technology, Universidade NOVA de Lisboa, 2829-516 Caparica, Portugal; (A.L.); (R.P.); (A.R.G.); (P.V.B.); (A.R.F.)
- Associate Laboratory i4HB, Institute for Health and Bioeconomy, NOVA School of Science and Technology, Universidade NOVA de Lisboa, 2829-516 Caparica, Portugal
- Correspondence: (A.P.R.); (P.M.C.); Tel.: +351-212-948-300 (A.P.R. & P.M.C.)
| |
Collapse
|
4
|
Lutz TM, Kimna C, Casini A, Lieleg O. Bio-based and bio-inspired adhesives from animals and plants for biomedical applications. Mater Today Bio 2022; 13:100203. [PMID: 35079700 PMCID: PMC8777159 DOI: 10.1016/j.mtbio.2022.100203] [Citation(s) in RCA: 15] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2021] [Revised: 01/08/2022] [Accepted: 01/08/2022] [Indexed: 01/01/2023] Open
Abstract
With the "many-headed" slime mold Physarum polycelphalum having been voted the unicellular organism of the year 2021 by the German Society of Protozoology, we are reminded that a large part of nature's huge variety of life forms is easily overlooked - both by the general public and researchers alike. Indeed, whereas several animals such as mussels or spiders have already inspired many scientists to create novel materials with glue-like properties, there is much more to discover in the flora and fauna. Here, we provide an overview of naturally occurring slimy substances with adhesive properties and categorize them in terms of the main chemical motifs that convey their stickiness, i.e., carbohydrate-, protein-, and glycoprotein-based biological glues. Furthermore, we highlight selected recent developments in the area of material design and functionalization that aim at making use of such biological compounds for novel applications in medicine - either by conjugating adhesive motifs found in nature to biological or synthetic macromolecules or by synthetically creating (multi-)functional materials, which combine adhesive properties with additional, problem-specific (and sometimes tunable) features.
Collapse
Affiliation(s)
- Theresa M. Lutz
- School of Engineering and Design, Department of Materials Engineering, Technical University of Munich, Boltzmannstraße 15, Garching, 85748, Germany
- Center for Protein Assemblies, Technical University of Munich, Ernst-Otto-Fischer Str. 8, Garching, 85748, Germany
| | - Ceren Kimna
- School of Engineering and Design, Department of Materials Engineering, Technical University of Munich, Boltzmannstraße 15, Garching, 85748, Germany
- Center for Protein Assemblies, Technical University of Munich, Ernst-Otto-Fischer Str. 8, Garching, 85748, Germany
| | - Angela Casini
- Chair of Medicinal and Bioinorganic Chemistry, Department of Chemistry, Technical University of Munich, Lichtenbergstraße 4, Garching, 85748, Germany
| | - Oliver Lieleg
- School of Engineering and Design, Department of Materials Engineering, Technical University of Munich, Boltzmannstraße 15, Garching, 85748, Germany
- Center for Protein Assemblies, Technical University of Munich, Ernst-Otto-Fischer Str. 8, Garching, 85748, Germany
| |
Collapse
|
5
|
Sanchez G, Fernández-Álvarez FÁ, Taite M, Sugimoto C, Jolly J, Simakov O, Marlétaz F, Allcock L, Rokhsar DS. Phylogenomics illuminates the evolution of bobtail and bottletail squid (order Sepiolida). Commun Biol 2021; 4:819. [PMID: 34188187 PMCID: PMC8241861 DOI: 10.1038/s42003-021-02348-y] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2020] [Accepted: 05/13/2021] [Indexed: 11/09/2022] Open
Abstract
Bobtail and bottletail squid are small cephalopods with striking anti-predatory defensive mechanisms, bioluminescence, and complex morphology; that inhabit nektobenthic and pelagic environments around the world's oceans. Yet, the evolution and diversification of these animals remain unclear. Here, we used shallow genome sequencing of thirty-two bobtail and bottletail squids to estimate their evolutionary relationships and divergence time. Our phylogenetic analyses show that each of Sepiadariidae, Sepiolidae, and the three subfamilies of the Sepiolidae are monophyletic. We found that the ancestor of the Sepiolinae very likely possessed a bilobed light organ with bacteriogenic luminescence. Sepiolinae forms a sister group to Rossinae and Heteroteuthinae, and split into Indo-Pacific and Atlantic-Mediterranean lineages. The origin of these lineages coincides with the end of the Tethys Sea and the separation of these regions during the Eocene and the beginning of the Oligocene. We demonstrated that sepiolids radiated after the Late Cretaceous and that major biogeographic events might have shaped their distribution and speciation.
Collapse
Affiliation(s)
- Gustavo Sanchez
- Graduate School of Integrated Science for Life, Hiroshima University, Higashi Hiroshima, Hiroshima, Japan.,Molecular Genetics Unit, Okinawa Institute of Science and Technology Graduate University, Onna, Okinawa, Japan
| | | | - Morag Taite
- Ryan Institute and School of Natural Sciences, National University of Ireland Galway, Galway, Ireland, UK
| | - Chikatoshi Sugimoto
- Molecular Genetics Unit, Okinawa Institute of Science and Technology Graduate University, Onna, Okinawa, Japan
| | - Jeffrey Jolly
- Molecular Genetics Unit, Okinawa Institute of Science and Technology Graduate University, Onna, Okinawa, Japan
| | - Oleg Simakov
- Department of Molecular Evolution and Development, University of Vienna, Vienna, Austria
| | - Ferdinand Marlétaz
- Department of Genetics, Evolution and Environment, Centre for Life's Origins and Evolution, University College London, London, UK
| | - Louise Allcock
- Ryan Institute and School of Natural Sciences, National University of Ireland Galway, Galway, Ireland, UK
| | - Daniel S Rokhsar
- Molecular Genetics Unit, Okinawa Institute of Science and Technology Graduate University, Onna, Okinawa, Japan. .,Department of Molecular and Cell Biology, Life Sciences Addition #3200, Berkeley, CA, USA. .,Chan-Zuckerberg BioHub, San Francisco, CA, USA.
| |
Collapse
|
6
|
Pales Espinosa E, Allam B. High spatial resolution mapping of the mucosal proteome of the gills of Crassostrea virginica: implication in particle processing. J Exp Biol 2021; 224:jeb.233361. [PMID: 33431594 DOI: 10.1242/jeb.233361] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2020] [Accepted: 01/06/2021] [Indexed: 11/20/2022]
Abstract
In the oyster Crassostrea virginica, the organization of the gill allows bidirectional particle transport where a dorsal gill tract directs particles meant to be ingested while a ventral tract collects particles intended to be rejected as pseudofeces. Previous studies showed that the transport of particles in both tracts is mediated by mucus. Consequently, we hypothesized that the nature and/or the quantity of mucosal proteins present in each tract is likely to be different. Using endoscopy-aided micro-sampling of mucus from each tract followed by multidimensional protein identification technologies, and in situ hybridization, a high spatial resolution mapping of the oyster gill proteome was generated. Results showed the presence in gill mucus of a wide range of molecules involved in non-self recognition and interactions with microbes. Mucus composition was different between the two tracts, with mucus from the ventral tract shown to be rich in mucin-like proteins, providing an explanation of its high viscosity, while mucus from the dorsal tract was found to be enriched in mannose-binding proteins, known to be involved in food particle binding and selection. Overall, this study generated high-resolution proteomes for C. virginica gill mucus and demonstrated that the contrasting functions of the two pathways present on oyster gills are associated with significant differences in their protein makeup.
Collapse
Affiliation(s)
| | - Bassem Allam
- School of Marine and Atmospheric Sciences, Stony Brook University, Stony Brook, NY 11794-5000, USA
| |
Collapse
|
7
|
Caruana NJ, Strugnell JM, Finn J, Faou P, Plummer KM, Cooke IR. Quantitative Proteomic Analysis of the Slime and Ventral Mantle Glands of the Striped Pyjama Squid ( Sepioloidea lineolata). J Proteome Res 2020; 19:1491-1501. [PMID: 32091901 DOI: 10.1021/acs.jproteome.9b00738] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2023]
Abstract
Cephalopods are known to produce an extensive range of secretions including ink, mucus, and venom. Sepiadariidae, a family of small, benthic bobtail squids, are notable for the high volume of viscous slime they emit when stressed. One species, Sepioloidea lineolata (striped pyjama squid), is covered with glands along the perimeter of the ventral mantle, and these structures are hypothesized to be the source of its slime. Using label-free quantitative proteomics, we analyzed five tissue types (dorsal and ventral mantle muscle, dorsal and ventral epithelium, and ventral mantle glands) and the slime from four individuals. In doing so, we were able to determine the relationship between the slime and the tissues as well as highlight proteins that were specifically identified within the slime and ventral mantle glands. A total of 28 proteins were identified to be highly enriched in slime, and these were composed of peptidases and protease inhibitors. Seven of these proteins contained predicted signal peptides, indicating classical secretion, with four proteins having no identifiable domains or similarity to any known proteins. The ventral mantle glands also appear to be the tissue with the closest overall proteomic composition to the slime; therefore, it is likely that the slime originates, at least in part, from these glands.
Collapse
Affiliation(s)
- Nikeisha J Caruana
- Department of Ecology, Environment and Evolution, La Trobe University, Melbourne, Victoria 3086, Australia
| | - Jan M Strugnell
- Department of Ecology, Environment and Evolution, La Trobe University, Melbourne, Victoria 3086, Australia.,Centre for Sustainable Tropical Fisheries and Aquaculture, James Cook University, Townsville, Queensland 4811, Australia
| | - Julian Finn
- Sciences, Museums Victoria, Carlton, Victoria 3053, Australia
| | - Pierre Faou
- Department of Biochemistry and Genetics, La Trobe Institute for Molecular Science, La Trobe University, Melbourne, Victoria 3086, Australia
| | - Kim M Plummer
- Department of Animal, Plant and Soil Sciences, AgriBio, La Trobe University, Melbourne, Victoria 3086, Australia
| | - Ira R Cooke
- Department of Biochemistry and Genetics, La Trobe Institute for Molecular Science, La Trobe University, Melbourne, Victoria 3086, Australia.,Department of Molecular and Cell Biology, James Cook University, Townsville, Queensland 4811, Australia
| |
Collapse
|
8
|
Discovery of Novel Crustacean and Cephalopod Flaviviruses: Insights into the Evolution and Circulation of Flaviviruses between Marine Invertebrate and Vertebrate Hosts. J Virol 2019; 93:JVI.00432-19. [PMID: 31068424 DOI: 10.1128/jvi.00432-19] [Citation(s) in RCA: 32] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2019] [Accepted: 04/23/2019] [Indexed: 12/21/2022] Open
Abstract
Most described flaviviruses (family Flaviviridae) are disease-causing pathogens of vertebrates maintained in zoonotic cycles between mosquitoes or ticks and vertebrate hosts. Poor sampling of flaviviruses outside vector-borne flaviviruses such as Zika virus and dengue virus has presented a narrow understanding of flavivirus diversity and evolution. In this study, we discovered three crustacean flaviviruses (Gammarus chevreuxi flavivirus, Gammarus pulex flavivirus, and Crangon crangon flavivirus) and two cephalopod flaviviruses (Southern Pygmy squid flavivirus and Firefly squid flavivirus). Bayesian and maximum likelihood phylogenetic methods demonstrate that crustacean flaviviruses form a well-supported clade and share a more closely related ancestor with terrestrial vector-borne flaviviruses than with classical insect-specific flaviviruses. In addition, we identify variants of Wenzhou shark flavivirus in multiple gazami crab (Portunus trituberculatus) populations, with active replication supported by evidence of an active RNA interference response. This suggests that Wenzhou shark flavivirus moves horizontally between sharks and gazami crabs in ocean ecosystems. Analyses of the mono- and dinucleotide composition of marine flaviviruses compared to that of flaviviruses with known host status suggest that some marine flaviviruses share a nucleotide bias similar to that of vector-borne flaviviruses. Furthermore, we identify crustacean flavivirus endogenous viral elements that are closely related to elements of terrestrial vector-borne flaviviruses. Taken together, these data provide evidence of flaviviruses circulating between marine vertebrates and invertebrates, expand our understanding of flavivirus host range, and offer potential insights into the evolution and emergence of terrestrial vector-borne flaviviruses.IMPORTANCE Some flaviviruses are known to cause disease in vertebrates and are typically transmitted by blood-feeding arthropods such as ticks and mosquitoes. While an ever-increasing number of insect-specific flaviviruses have been described, we have a narrow understanding of flavivirus incidence and evolution. To expand this understanding, we discovered a number of novel flaviviruses that infect a range of crustaceans and cephalopod hosts. Phylogenetic analyses of these novel marine flaviviruses suggest that crustacean flaviviruses share a close ancestor to all terrestrial vector-borne flaviviruses, and squid flaviviruses are the most divergent of all known flaviviruses to date. Additionally, our results indicate horizontal transmission of a marine flavivirus between crabs and sharks. Taken together, these data suggest that flaviviruses move horizontally between invertebrates and vertebrates in ocean ecosystems. This study demonstrates that flavivirus invertebrate-vertebrate host associations have arisen in flaviviruses at least twice and may potentially provide insights into the emergence or origin of terrestrial vector-borne flaviviruses.
Collapse
|
9
|
Caruana NJ, Strugnell JM, Faou P, Finn J, Cooke IR. Comparative Proteomic Analysis of Slime from the Striped Pyjama Squid, Sepioloidea lineolata, and the Southern Bottletail Squid, Sepiadarium austrinum (Cephalopoda: Sepiadariidae). J Proteome Res 2019; 18:890-899. [PMID: 30628786 DOI: 10.1021/acs.jproteome.8b00569] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Sepioloidea lineolata, the striped pyjama squid (family Sepiadariidae), is a small species of benthic bobtail squid distributed along the Southern Indo-Pacific coast of Australia. Like other sepiadariid squids, it is known to secrete large volumes of viscous slime when stressed. In order to identify key proteins involved in the function of sepiadariid slimes, we compared the slime proteome of Sepioloidea lineolata with that of a closely related species, Sepiadarium austrinum. Of the 550 protein groups identified in Sepioloidea lineolata slime, 321 had orthologs in Sepiadarium austrinum, and the abundance of these (iBAQ) was highly correlated between species. Both slimes were dominated by a small number of abundant proteins, and several of these were short secreted proteins with no homologues outside the class Cephalopoda. No mucins were identified within either species' slime, suggesting that it is structurally distinct from mucin polymer-based gels found in many vertebrate and echinoderm secretions. The extent of N-glycosylation in the slime of Sepioloidea lineolata was also studied via glycan cleavage with Peptide: N-glycosidase F (PNGase-F). Although very few (four) proteins showed strong evidence of N-glycosylation, we found that treatment with PNGase-F led to a slight increase in peptide identification rates compared with controls.
Collapse
Affiliation(s)
- Nikeisha J Caruana
- Department of Ecology, Environment and Evolution , La Trobe University , Melbourne , VIC 3086 , Australia
| | - Jan M Strugnell
- Department of Ecology, Environment and Evolution , La Trobe University , Melbourne , VIC 3086 , Australia.,Centre for Sustainable Tropical Fisheries and Aquaculture , James Cook University , Townsville , QLD 4811 , Australia
| | - Pierre Faou
- Department of Biochemistry and Genetics, La Trobe Institute for Molecular Science , La Trobe University , Melbourne , VIC 3086 , Australia
| | - Julian Finn
- Sciences , Museums Victoria , Carlton , VIC 3053 , Australia
| | - Ira R Cooke
- Department of Biochemistry and Genetics, La Trobe Institute for Molecular Science , La Trobe University , Melbourne , VIC 3086 , Australia.,Department of Molecular and Cell Biology , James Cook University , Townsville , QLD 4811 , Australia
| |
Collapse
|
10
|
Fingerhut LCHW, Strugnell JM, Faou P, Labiaga ÁR, Zhang J, Cooke IR. Shotgun Proteomics Analysis of Saliva and Salivary Gland Tissue from the Common Octopus Octopus vulgaris. J Proteome Res 2018; 17:3866-3876. [PMID: 30220204 DOI: 10.1021/acs.jproteome.8b00525] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
The salivary apparatus of the common octopus ( Octopus vulgaris) has been the subject of biochemical study for over a century. A combination of bioassays, behavioral studies and molecular analysis on O. vulgaris and related species suggests that its proteome should contain a mixture of highly potent neurotoxins and degradative proteins. However, a lack of genomic and transcriptomic data has meant that the amino acid sequences of these proteins remain almost entirely unknown. To address this, we assembled the posterior salivary gland transcriptome of O. vulgaris and combined it with high resolution mass spectrometry data from the posterior and anterior salivary glands of two adults, the posterior salivary glands of six paralarvae and the saliva from a single adult. We identified a total of 2810 protein groups from across this range of salivary tissues and age classes, including 84 with homology to known venom protein families. Additionally, we found 21 short secreted cysteine rich protein groups of which 12 were specific to cephalopods. By combining protein expression data with phylogenetic analysis we demonstrate that serine proteases expanded dramatically within the cephalopod lineage and that cephalopod specific proteins are strongly associated with the salivary apparatus.
Collapse
Affiliation(s)
- Legana C H W Fingerhut
- Department of Molecular and Cell Biology , James Cook University , Townsville , Queensland 4811 , Australia
| | - Jan M Strugnell
- Centre for Sustainable Tropical Fisheries and Aquaculture, College of Science and Engineering , James Cook University , Townsville , Queensland 4811 , Australia.,Department of Ecology, Environment and Evolution, School of Life Sciences , La Trobe University , Melbourne , Victoria 3086 , Australia
| | - Pierre Faou
- Department of Biochemistry and Genetics, La Trobe Institute for Molecular Science , La Trobe University , Melbourne , Victoria 3086 , Australia
| | - Álvaro Roura Labiaga
- Department of Ecology and Marine Biodiversity , Instituto de Investigaciones Marinas de Vigo (IIM-CSIC) , Vigo 36208 , Spain
| | - Jia Zhang
- Department of Molecular and Cell Biology , James Cook University , Townsville , Queensland 4811 , Australia
| | - Ira R Cooke
- Department of Molecular and Cell Biology , James Cook University , Townsville , Queensland 4811 , Australia.,Department of Biochemistry and Genetics, La Trobe Institute for Molecular Science , La Trobe University , Melbourne , Victoria 3086 , Australia
| |
Collapse
|
11
|
Guglielmetti C, Manfredi M, Brusadore S, Sciuto S, Esposito G, Ubaldi PG, Magnani L, Gili S, Marengo E, Acutis PL, Mazza M. Two-dimensional gel and shotgun proteomics approaches to distinguish fresh and frozen-thawed curled octopus (Eledone cirrhosa). J Proteomics 2018; 186:1-7. [PMID: 30055322 DOI: 10.1016/j.jprot.2018.07.017] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2018] [Revised: 07/20/2018] [Accepted: 07/24/2018] [Indexed: 02/07/2023]
Abstract
The substitution and sale of frozen-thawed fish labeled as fresh is a widespread, difficult to unmask commercial fraud and a potential risk for consumer health. Proteomics could help to identify markers for the rapid screening of food samples and the identification of frozen-thawed seafood. Using two-dimensional electrophoresis (2-DE) and high-resolution liquid chromatography tandem mass spectrometry (LC-MS/MS), we identified biomarkers that are able to discriminate between fresh and frozen-thawed tissue samples of curled octopus (Eledone cirrhosa). The 2-DE analysis showed a significant reduction in two protein spots (molecular weight of 45-50 kDa, isoelectric point of 6.5-7) identified as transgelin. At shotgun analysis, nine proteins resulted modulated and transgelin was confirmed as down-regulated, making it a potentially useful marker for differentiating between fresh and frozen-thawed fish product samples. BIOLOGICAL SIGNIFICANCE This work, based on two different proteomics approaches, investigated differentially expressed proteins in the tentacles of the curled octopus (E. cirrhosa) after freezing-thawing processes. We were able to characterize the proteome of the tentacles, increasing our knowledge on this species, and a common down-regulated protein was identified by 2-DE and shotgun analysis, a calponin-like protein called transgelin, suggesting a potential use as a marker to distinguish different states of conservation in this species.
Collapse
Affiliation(s)
- Chiara Guglielmetti
- S.C. Neuroscienze con annesso CEA- S.S. Genetica ed Immunobiochimica - Istituto Zooprofilattico Sperimentale del Piemonte, Liguria e Valle d'Aosta, Torino, Italy.
| | - Marcello Manfredi
- Dipartimento di Scienze ed Innovazione Tecnologica, Università del Piemonte Orientale, Alessandria, Italy; ISALIT, Spin-off dell'Università del Piemonte Orientale, Novara, Italy.
| | - Sonia Brusadore
- S.C. Neuroscienze con annesso CEA- S.S. Genetica ed Immunobiochimica - Istituto Zooprofilattico Sperimentale del Piemonte, Liguria e Valle d'Aosta, Torino, Italy.
| | - Simona Sciuto
- S.C. Neuroscienze con annesso CEA- S.S. Genetica ed Immunobiochimica - Istituto Zooprofilattico Sperimentale del Piemonte, Liguria e Valle d'Aosta, Torino, Italy.
| | - Giovanna Esposito
- S.C. Neuroscienze con annesso CEA- S.S. Genetica ed Immunobiochimica - Istituto Zooprofilattico Sperimentale del Piemonte, Liguria e Valle d'Aosta, Torino, Italy.
| | | | - Luca Magnani
- Esselunga Centro distribuzione, Biandrate, Italy.
| | - Stefano Gili
- Azienda Sanitaria Locale "Città di Torino", Torino, Italy.
| | - Emilio Marengo
- Dipartimento di Scienze ed Innovazione Tecnologica, Università del Piemonte Orientale, Alessandria, Italy.
| | - Pier Luigi Acutis
- S.C. Neuroscienze con annesso CEA- S.S. Genetica ed Immunobiochimica - Istituto Zooprofilattico Sperimentale del Piemonte, Liguria e Valle d'Aosta, Torino, Italy.
| | - Maria Mazza
- S.C. Neuroscienze con annesso CEA- S.S. Genetica ed Immunobiochimica - Istituto Zooprofilattico Sperimentale del Piemonte, Liguria e Valle d'Aosta, Torino, Italy.
| |
Collapse
|
12
|
Zhang M, Faou P, Maier AG, Rug M. Plasmodium falciparum exported protein PFE60 influences Maurer’s clefts architecture and virulence complex composition. Int J Parasitol 2018; 48:83-95. [DOI: 10.1016/j.ijpara.2017.09.003] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2017] [Revised: 08/20/2017] [Accepted: 09/06/2017] [Indexed: 11/30/2022]
|
13
|
Proffitt JM, Glenn J, Cesnik AJ, Jadhav A, Shortreed MR, Smith LM, Kavanagh K, Cox LA, Olivier M. Proteomics in non-human primates: utilizing RNA-Seq data to improve protein identification by mass spectrometry in vervet monkeys. BMC Genomics 2017; 18:877. [PMID: 29132314 PMCID: PMC5683380 DOI: 10.1186/s12864-017-4279-0] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2017] [Accepted: 11/03/2017] [Indexed: 01/05/2023] Open
Abstract
Background Shotgun proteomics utilizes a database search strategy to compare detected mass spectra to a library of theoretical spectra derived from reference genome information. As such, the robustness of proteomics results is contingent upon the completeness and accuracy of the gene annotation in the reference genome. For animal models of disease where genomic annotation is incomplete, such as non-human primates, proteogenomic methods can improve the detection of proteins by incorporating transcriptional data from RNA-Seq to improve proteomics search databases used for peptide spectral matching. Customized search databases derived from RNA-Seq data are capable of identifying unannotated genetic and splice variants while simultaneously reducing the number of comparisons to only those transcripts actively expressed in the tissue. Results We collected RNA-Seq and proteomic data from 10 vervet monkey liver samples and used the RNA-Seq data to curate sample-specific search databases which were analyzed in the program Morpheus. We compared these results against those from a search database generated from the reference vervet genome. A total of 284 previously unannotated splice junctions were predicted by the RNA-Seq data, 92 of which were confirmed by peptide spectral matches. More than half (53/92) of these unannotated splice variants had orthologs in other non-human primates, suggesting that failure to match these peptides in the reference analyses likely arose from incomplete gene model information. The sample-specific databases also identified 101 unique peptides containing single amino acid substitutions which were missed by the reference database. Because the sample-specific searches were restricted to actively expressed transcripts, the search databases were smaller, more computationally efficient, and identified more peptides at the empirically derived 1 % false discovery rate. Conclusion Proteogenomic approaches are ideally suited to facilitate the discovery and annotation of proteins in less widely studies animal models such as non-human primates. We expect that these approaches will help to improve existing genome annotations of non-human primate species such as vervet. Electronic supplementary material The online version of this article (doi: 10.1186/s12864-017-4279-0) contains supplementary material, which is available to authorized users.
Collapse
Affiliation(s)
- J Michael Proffitt
- Department of Genetics, Texas Biomedical Research Institute, San Antonio, Texas, USA
| | - Jeremy Glenn
- Department of Genetics, Texas Biomedical Research Institute, San Antonio, Texas, USA
| | - Anthony J Cesnik
- Department of Chemistry, University of Wisconsin, Madison, Wisconsin, USA
| | - Avinash Jadhav
- Department of Genetics, Texas Biomedical Research Institute, San Antonio, Texas, USA.,Current address: Department of Internal Medicine, Section of Molecular Medicine, Wake Forest School of Medicine, NRC Building, G-55, Winston-Salem, North Carolina, 27157, USA
| | | | - Lloyd M Smith
- Department of Chemistry, University of Wisconsin, Madison, Wisconsin, USA.,Genome Center of Wisconsin, University of Wisconsin, Madison, Wisconsin, USA
| | - Kylie Kavanagh
- Department of Pathology and Comparative Medicine, Wake Forest School of Medicine, Winston-Salem, North Carolina, USA
| | - Laura A Cox
- Department of Genetics, Texas Biomedical Research Institute, San Antonio, Texas, USA.,Southwest National Primate Research Center, Texas Biomedical Research Institute, San Antonio, Texas, USA
| | - Michael Olivier
- Department of Genetics, Texas Biomedical Research Institute, San Antonio, Texas, USA. .,Southwest National Primate Research Center, Texas Biomedical Research Institute, San Antonio, Texas, USA. .,Current address: Department of Internal Medicine, Section of Molecular Medicine, Wake Forest School of Medicine, NRC Building, G-55, Winston-Salem, North Carolina, 27157, USA.
| |
Collapse
|
14
|
D'Lima NG, Khitun A, Rosenbloom AD, Yuan P, Gassaway BM, Barber KW, Rinehart J, Slavoff SA. Comparative Proteomics Enables Identification of Nonannotated Cold Shock Proteins in E. coli. J Proteome Res 2017; 16:3722-3731. [PMID: 28861998 PMCID: PMC5647875 DOI: 10.1021/acs.jproteome.7b00419] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
![]()
Recent advances in mass spectrometry-based
proteomics have revealed
translation of previously nonannotated microproteins from thousands
of small open reading frames (smORFs) in prokaryotic and eukaryotic
genomes. Facile methods to determine cellular functions of these newly
discovered microproteins are now needed. Here, we couple semiquantitative
comparative proteomics with whole-genome database searching to identify
two nonannotated, homologous cold shock-regulated microproteins in Escherichia coli K12 substr. MG1655, as well as two
additional constitutively expressed microproteins. We apply molecular
genetic approaches to confirm expression of these cold shock proteins
(YmcF and YnfQ) at reduced temperatures and identify the noncanonical
ATT start codons that initiate their translation. These proteins are
conserved in related Gram-negative bacteria and are predicted to be
structured, which, in combination with their cold shock upregulation,
suggests that they are likely to have biological roles in the cell.
These results reveal that previously unknown factors are involved
in the response of E. coli to lowered
temperatures and suggest that further nonannotated, stress-regulated E. coli microproteins may remain to be found. More
broadly, comparative proteomics may enable discovery of regulated,
and therefore potentially functional, products of smORF translation
across many different organisms and conditions.
Collapse
Affiliation(s)
- Nadia G D'Lima
- Department of Chemistry, Yale University , New Haven, Connecticut 06520, United States.,Chemical Biology Institute, Yale University , West Haven, Connecticut 06516, United States
| | - Alexandra Khitun
- Department of Chemistry, Yale University , New Haven, Connecticut 06520, United States.,Chemical Biology Institute, Yale University , West Haven, Connecticut 06516, United States
| | - Aaron D Rosenbloom
- Department of Chemistry, Yale University , New Haven, Connecticut 06520, United States
| | - Peijia Yuan
- Department of Chemistry, Yale University , New Haven, Connecticut 06520, United States.,Chemical Biology Institute, Yale University , West Haven, Connecticut 06516, United States
| | - Brandon M Gassaway
- Department of Cellular and Molecular Physiology, Yale University , New Haven, Connecticut 06520, United States.,Systems Biology Institute, Yale University , West Haven, Connecticut 06511, United States
| | - Karl W Barber
- Department of Cellular and Molecular Physiology, Yale University , New Haven, Connecticut 06520, United States.,Systems Biology Institute, Yale University , West Haven, Connecticut 06511, United States
| | - Jesse Rinehart
- Department of Cellular and Molecular Physiology, Yale University , New Haven, Connecticut 06520, United States.,Systems Biology Institute, Yale University , West Haven, Connecticut 06511, United States
| | - Sarah A Slavoff
- Department of Chemistry, Yale University , New Haven, Connecticut 06520, United States.,Chemical Biology Institute, Yale University , West Haven, Connecticut 06516, United States.,Department of Molecular Biophysics and Biochemistry, Yale University , New Haven, Connecticut 06529, United States
| |
Collapse
|