1
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Park JE, Patnaik BB, Sang MK, Song DK, Jeong JY, Hong CE, Kim YT, Shin HJ, Ziwei L, Patnaik HH, Hwang HJ, Park SY, Kang SW, Ko JH, Lee JS, Park HS, Jo YH, Han YS, Lee YS. Transcriptome sequencing of the endangered land snail Karaftohelix adamsi from the Island Ulleung: De novo assembly, annotation, valuation of fitness genes and SSR markers. Genes Genomics 2024; 46:851-870. [PMID: 38809491 DOI: 10.1007/s13258-024-01511-z] [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: 06/12/2023] [Accepted: 03/08/2024] [Indexed: 05/30/2024]
Abstract
BACKGROUND The Bradybaenidae snail Karaftohelix adamsi is endemic to Korea, with the species tracked from Island Ulleung in North Gyeongsang Province of South Korea. K. adamsi has been classified under the Endangered Wildlife Class II species of Korea and poses a severe risk of extinction following habitat disturbances. With no available information at the DNA (genome) or mRNA (transcriptome) level for the species, conservation by utilizing informed molecular resources seems difficult. OBJECTIVE In this study, we used the Illumina short-read sequencing and Trinity de novo assembly to draft the reference transcriptome of K. adamsi. RESULTS After assembly, 13,753 unigenes were obtained of which 10,511 were annotated to public databases (a maximum of 10,165 unigenes found homologs in PANM DB). A total of 6,351, 3,535, 358, and 3,407 unigenes were ascribed to the functional categories under KOG, GO, KEGG, and IPS, respectively. The transcripts such as the HSP 70, aquaporin, TLR, and MAPK, among others, were screened as putative functional resources for adaptation. DNA transposons were found to be thickly populated in comparison to retrotransposons in the assembled unigenes. Further, 2,164 SSRs were screened with the promiscuous presence of dinucleotide repeats such as AC/GT and AG/CT. CONCLUSION The transcriptome-guided discovery of molecular resources in K. adamsi will not only serve as a basis for functional genomics studies but also provide sustainable tools to be utilized for the protection of the species in the wild. Moreover, the development of polymorphic SSRs is valuable for the identification of species from newer habitats and cross-species genotyping.
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Affiliation(s)
- Jie Eun Park
- Korea Native Animal Resources Utilization Convergence Research Institute (KNAR), Soonchunhyang University, Asan, Chungnam, 31538, South Korea
- Research Support Center for Bio-Bigdata Analysis and Utilization of Biological Resources, Soonchunhyang University, Chungnam, 31, Asan, South Korea
| | - Bharat Bhusan Patnaik
- Korea Native Animal Resources Utilization Convergence Research Institute (KNAR), Soonchunhyang University, Asan, Chungnam, 31538, South Korea
- Department of Biology, College of Natural Sciences, Soonchunhyang University, Asan, 31538, Chungnam, Korea
- PG Department of Biosciences and Biotechnology, Fakir Mohan University, Nuapadhi, Balasore, Odisha, 756089, India
| | - Min Kyu Sang
- Korea Native Animal Resources Utilization Convergence Research Institute (KNAR), Soonchunhyang University, Asan, Chungnam, 31538, South Korea
- Research Support Center for Bio-Bigdata Analysis and Utilization of Biological Resources, Soonchunhyang University, Chungnam, 31, Asan, South Korea
| | - Dae Kwon Song
- Korea Native Animal Resources Utilization Convergence Research Institute (KNAR), Soonchunhyang University, Asan, Chungnam, 31538, South Korea
- Research Support Center for Bio-Bigdata Analysis and Utilization of Biological Resources, Soonchunhyang University, Chungnam, 31, Asan, South Korea
| | - Jun Yang Jeong
- Korea Native Animal Resources Utilization Convergence Research Institute (KNAR), Soonchunhyang University, Asan, Chungnam, 31538, South Korea
- Department of Biology, College of Natural Sciences, Soonchunhyang University, Asan, 31538, Chungnam, Korea
| | - Chan Eui Hong
- Korea Native Animal Resources Utilization Convergence Research Institute (KNAR), Soonchunhyang University, Asan, Chungnam, 31538, South Korea
- Department of Biology, College of Natural Sciences, Soonchunhyang University, Asan, 31538, Chungnam, Korea
| | - Yong Tae Kim
- Korea Native Animal Resources Utilization Convergence Research Institute (KNAR), Soonchunhyang University, Asan, Chungnam, 31538, South Korea
- Department of Biology, College of Natural Sciences, Soonchunhyang University, Asan, 31538, Chungnam, Korea
| | - Hyeon Jun Shin
- Korea Native Animal Resources Utilization Convergence Research Institute (KNAR), Soonchunhyang University, Asan, Chungnam, 31538, South Korea
- Department of Biology, College of Natural Sciences, Soonchunhyang University, Asan, 31538, Chungnam, Korea
| | - Liu Ziwei
- Korea Native Animal Resources Utilization Convergence Research Institute (KNAR), Soonchunhyang University, Asan, Chungnam, 31538, South Korea
- Department of Biology, College of Natural Sciences, Soonchunhyang University, Asan, 31538, Chungnam, Korea
| | - Hongray Howrelia Patnaik
- Korea Native Animal Resources Utilization Convergence Research Institute (KNAR), Soonchunhyang University, Asan, Chungnam, 31538, South Korea
- PG Department of Zoology, BJB Autonomous College, Bhubaneswar, Odisha, 751014, India
| | - Hee Ju Hwang
- Department of Biology, College of Natural Sciences, Soonchunhyang University, Asan, 31538, Chungnam, Korea
| | - So Young Park
- Biodiversity Research Team, Animal & Plant Research Department, Nakdonggang National Institute of Biological Resources, Sangju, Gyeongbuk, South Korea
| | - Se Won Kang
- Biological Resource Center (BRC), Korea Research Institute of Bioscience and Biotechnology (KRIBB), Jeongeup, Jeonbuk, South Korea
| | - Jung Ho Ko
- Police Science Institute, Korean National Police University, Asan, 31539, Chungnam, Korea
| | - Jun Sang Lee
- Korea Native Animal Resources Utilization Convergence Research Institute (KNAR), Soonchunhyang University, Asan, Chungnam, 31538, South Korea
| | - Hong Seog Park
- Research Institute, GnC BIO Co., LTD, 621-6 Banseok-Dong, Yuseong-Gu, Daejeon, 34069, Korea
| | - Yong Hun Jo
- Korea Native Animal Resources Utilization Convergence Research Institute (KNAR), Soonchunhyang University, Asan, Chungnam, 31538, South Korea
- Department of Biology, College of Natural Sciences, Soonchunhyang University, Asan, 31538, Chungnam, Korea
| | - Yeon Soo Han
- College of Agriculture and Life Science, Chonnam National University, 77 Yongbong-Ro, Buk-Gu, Gwangju, 61186, South Korea
| | - Yong Seok Lee
- Korea Native Animal Resources Utilization Convergence Research Institute (KNAR), Soonchunhyang University, Asan, Chungnam, 31538, South Korea.
- Research Support Center for Bio-Bigdata Analysis and Utilization of Biological Resources, Soonchunhyang University, Chungnam, 31, Asan, South Korea.
- Department of Biology, College of Natural Sciences, Soonchunhyang University, Asan, 31538, Chungnam, Korea.
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2
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Sleight VA. Cell type and gene regulatory network approaches in the evolution of spiralian biomineralisation. Brief Funct Genomics 2023; 22:509-516. [PMID: 37592885 PMCID: PMC10658180 DOI: 10.1093/bfgp/elad033] [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: 05/21/2023] [Revised: 07/10/2023] [Accepted: 07/20/2023] [Indexed: 08/19/2023] Open
Abstract
Biomineralisation is the process by which living organisms produce hard structures such as shells and bone. There are multiple independent origins of biomineralised skeletons across the tree of life. This review gives a glimpse into the diversity of spiralian biominerals and what they can teach us about the evolution of novelty. It discusses different levels of biological organisation that may be informative to understand the evolution of biomineralisation and considers the relationship between skeletal and non-skeletal biominerals. More specifically, this review explores if cell type and gene regulatory network approaches could enhance our understanding of the evolutionary origins of biomineralisation.
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Affiliation(s)
- Victoria A Sleight
- School of Biological Sciences, University of Aberdeen, Aberdeen, United Kingdom
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3
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Clark MS, Hoffman JI, Peck LS, Bargelloni L, Gande D, Havermans C, Meyer B, Patarnello T, Phillips T, Stoof-Leichsenring KR, Vendrami DLJ, Beck A, Collins G, Friedrich MW, Halanych KM, Masello JF, Nagel R, Norén K, Printzen C, Ruiz MB, Wohlrab S, Becker B, Dumack K, Ghaderiardakani F, Glaser K, Heesch S, Held C, John U, Karsten U, Kempf S, Lucassen M, Paijmans A, Schimani K, Wallberg A, Wunder LC, Mock T. Multi-omics for studying and understanding polar life. Nat Commun 2023; 14:7451. [PMID: 37978186 PMCID: PMC10656552 DOI: 10.1038/s41467-023-43209-y] [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: 04/24/2023] [Accepted: 11/02/2023] [Indexed: 11/19/2023] Open
Abstract
Polar ecosystems are experiencing amongst the most rapid rates of regional warming on Earth. Here, we discuss 'omics' approaches to investigate polar biodiversity, including the current state of the art, future perspectives and recommendations. We propose a community road map to generate and more fully exploit multi-omics data from polar organisms. These data are needed for the comprehensive evaluation of polar biodiversity and to reveal how life evolved and adapted to permanently cold environments with extreme seasonality. We argue that concerted action is required to mitigate the impact of warming on polar ecosystems via conservation efforts, to sustainably manage these unique habitats and their ecosystem services, and for the sustainable bioprospecting of novel genes and compounds for societal gain.
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Affiliation(s)
- M S Clark
- British Antarctic Survey, UKRI-NERC, High Cross, Madingley Road, Cambridge, CB3 0ET, UK.
| | - J I Hoffman
- British Antarctic Survey, UKRI-NERC, High Cross, Madingley Road, Cambridge, CB3 0ET, UK.
- Universität Bielefeld, VHF, Konsequenz 45, 33615, Bielefeld, Germany.
| | - L S Peck
- British Antarctic Survey, UKRI-NERC, High Cross, Madingley Road, Cambridge, CB3 0ET, UK.
| | - L Bargelloni
- Department of Comparative Biomedicine and Food Science, Università degli Studi di Padova, Viale dell'Università 16, I-35020, Legnaro, Italy
| | - D Gande
- Microbial Ecophysiology Group, Faculty of Biology/Chemistry & MARUM, University of Bremen, Leobener Straße 3, 28359, Bremen, Germany
| | - C Havermans
- Alfred-Wegener-Institut Helmholtz-Zentrum für Polar- und Meeresforschung, Am Handelshafen 12, 27570, Bremerhaven, Germany
| | - B Meyer
- Alfred-Wegener-Institut Helmholtz-Zentrum für Polar- und Meeresforschung, Am Handelshafen 12, 27570, Bremerhaven, Germany
- Institute for Chemistry and Biology of the Marine Environment, University of Oldenburg, Oldenburg, Germany
- Helmholtz Institute for Functional Marine Biodiversity at the University of Oldenburg (HIFMB), 23129, Oldenburg, Germany
| | - T Patarnello
- Department of Comparative Biomedicine and Food Science, Università degli Studi di Padova, Viale dell'Università 16, I-35020, Legnaro, Italy
| | - T Phillips
- British Antarctic Survey, UKRI-NERC, High Cross, Madingley Road, Cambridge, CB3 0ET, UK
| | - K R Stoof-Leichsenring
- Alfred-Wegener-Institute Helmholtz Centre for Polar and Marine Research, 14473, Potsdam, Germany
| | - D L J Vendrami
- Universität Bielefeld, VHF, Konsequenz 45, 33615, Bielefeld, Germany
| | - A Beck
- Staatliche Naturwissenschaftliche Sammlungen Bayerns, Botanische Staatssammlung München (SNSB-BSM), Menzinger Str. 67, 80638, München, Germany
| | - G Collins
- Senckenberg Biodiversity and Climate Research Centre & Loewe-Centre for Translational Biodiversity Genomics, Senckenberganlage 25, 60325, Frankfurt am Main, Germany
- Manaaki Whenua-Landcare Research, 231 Morrin Road St Johns, Auckland, 1072, New Zealand
| | - M W Friedrich
- Microbial Ecophysiology Group, Faculty of Biology/Chemistry & MARUM, University of Bremen, Leobener Straße 3, 28359, Bremen, Germany
| | - K M Halanych
- Center for Marine Science, University of North Carolina, 5600 Marvin K. Moss Lane, Wilmington, NC, 28409, USA
| | - J F Masello
- Universität Bielefeld, VHF, Konsequenz 45, 33615, Bielefeld, Germany
- Justus-Liebig-Universität Gießen, Giessen, Germany
| | - R Nagel
- Universität Bielefeld, VHF, Konsequenz 45, 33615, Bielefeld, Germany
- School of Biology, University of St Andrews, St Andrews, Fife, KY16 9TH, UK
| | - K Norén
- Department of Zoology, Stockholm University, 106 91, Stockholm, Sweden
| | - C Printzen
- Senckenberg Biodiversity and Climate Research Centre & Loewe-Centre for Translational Biodiversity Genomics, Senckenberganlage 25, 60325, Frankfurt am Main, Germany
- Natural History Museum Frankfurt, Senckenberganlage 25, 60325, Frankfurt am Main, Germany
| | - M B Ruiz
- Alfred-Wegener-Institut Helmholtz-Zentrum für Polar- und Meeresforschung, Am Handelshafen 12, 27570, Bremerhaven, Germany
- Universität Duisburg-Essen, Universitätstrasse 5, 45151, Essen, Germany
| | - S Wohlrab
- Alfred-Wegener-Institut Helmholtz-Zentrum für Polar- und Meeresforschung, Am Handelshafen 12, 27570, Bremerhaven, Germany
- Helmholtz Institute for Functional Marine Biodiversity at the University of Oldenburg (HIFMB), 23129, Oldenburg, Germany
| | - B Becker
- Universität zu Köln, Institut für Pflanzenwissenschaften, Zülpicher Str. 47b, 60674, Köln, Germany
| | - K Dumack
- Universität zu Köln, Terrestrische Ökologie, Zülpicher Str. 47b, 60674, Köln, Germany
| | - F Ghaderiardakani
- Institute for Inorganic and Analytical Chemistry, Friedrich Schiller University Jena, Lessingstraße 8, 07743, Jena, Germany
| | - K Glaser
- Institute of Biological Sciences, Applied Ecology and Phycology, University of Rostock, Albert-Einstein-Straße 3, 18059, Rostock, Germany
| | - S Heesch
- Institute of Biological Sciences, Applied Ecology and Phycology, University of Rostock, Albert-Einstein-Straße 3, 18059, Rostock, Germany
| | - C Held
- Alfred-Wegener-Institut Helmholtz-Zentrum für Polar- und Meeresforschung, Am Handelshafen 12, 27570, Bremerhaven, Germany
| | - U John
- Alfred-Wegener-Institut Helmholtz-Zentrum für Polar- und Meeresforschung, Am Handelshafen 12, 27570, Bremerhaven, Germany
| | - U Karsten
- Institute of Biological Sciences, Applied Ecology and Phycology, University of Rostock, Albert-Einstein-Straße 3, 18059, Rostock, Germany
| | - S Kempf
- Alfred-Wegener-Institut Helmholtz-Zentrum für Polar- und Meeresforschung, Am Handelshafen 12, 27570, Bremerhaven, Germany
| | - M Lucassen
- Alfred-Wegener-Institut Helmholtz-Zentrum für Polar- und Meeresforschung, Am Handelshafen 12, 27570, Bremerhaven, Germany
| | - A Paijmans
- Universität Bielefeld, VHF, Konsequenz 45, 33615, Bielefeld, Germany
| | - K Schimani
- Botanischer Garten und Botanisches Museum Berlin, Freie Universität Berlin, Königin-Luise-Straße 6-8, 14195, Berlin, Germany
| | - A Wallberg
- Department of Medical Biochemistry and Microbiology, Uppsala University, Husargatan 3, 751 23, Uppsala, Sweden
| | - L C Wunder
- Microbial Ecophysiology Group, Faculty of Biology/Chemistry & MARUM, University of Bremen, Leobener Straße 3, 28359, Bremen, Germany
| | - T Mock
- School of Environmental Sciences, University of East Anglia, Norwich Research Park, Norwich, NR4 7TJ, UK.
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4
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Knight BM, Edgar KJ, De Yoreo JJ, Dove PM. Chitosan as a Canvas for Studies of Macromolecular Controls on CaCO 3 Biological Crystallization. Biomacromolecules 2023; 24:1078-1102. [PMID: 36853173 DOI: 10.1021/acs.biomac.2c01394] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/01/2023]
Abstract
A mechanistic understanding of how macromolecules, typically as an organic matrix, nucleate and grow crystals to produce functional biomineral structures remains elusive. Advances in structural biology indicate that polysaccharides (e.g., chitin) and negatively charged proteoglycans (due to carboxyl, sulfate, and phosphate groups) are ubiquitous in biocrystallization settings and play greater roles than currently recognized. This review highlights studies of CaCO3 crystallization onto chitinous materials and demonstrates that a broader understanding of macromolecular controls on mineralization has not emerged. With recent advances in biopolymer chemistry, it is now possible to prepare chitosan-based hydrogels with tailored functional group compositions. By deploying these characterized compounds in hypothesis-based studies of nucleation rate, quantitative relationships between energy barrier to crystallization, macromolecule composition, and solvent structuring can be determined. This foundational knowledge will help researchers understand composition-structure-function controls on mineralization in living systems and tune the designs of new materials for advanced applications.
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Affiliation(s)
- Brenna M Knight
- Department of Chemistry, Virginia Tech, Blacksburg, Virginia 24061, United States
- Department of Geosciences, Virginia Tech, Blacksburg, Virginia 24061, United States
| | - Kevin J Edgar
- Department of Sustainable Biomaterials, Virginia Tech, Blacksburg, Virginia 24061, United States
- Macromolecules Innovation Institute, Virginia Tech, Blacksburg, Virginia 24061, United States
| | - James J De Yoreo
- Department of Materials Science and Engineering, University of Washington, Seattle, Washington 98195, United States
| | - Patricia M Dove
- Department of Chemistry, Virginia Tech, Blacksburg, Virginia 24061, United States
- Macromolecules Innovation Institute, Virginia Tech, Blacksburg, Virginia 24061, United States
- Department of Geosciences, Virginia Tech, Blacksburg, Virginia 24061, United States
- Department of Materials Science and Engineering, Virginia Tech, Blacksburg, Virginia 24061, United States
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5
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Cavallo A, Clark MS, Peck LS, Harper EM, Sleight VA. Evolutionary conservation and divergence of the transcriptional regulation of bivalve shell secretion across life-history stages. ROYAL SOCIETY OPEN SCIENCE 2022; 9:221022. [PMID: 36569229 PMCID: PMC9768464 DOI: 10.1098/rsos.221022] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 08/08/2022] [Accepted: 09/13/2022] [Indexed: 06/17/2023]
Abstract
Adult molluscs produce shells with diverse morphologies and ornamentations, different colour patterns and microstructures. The larval shell, however, is a phenotypically more conserved structure. How do developmental and evolutionary processes generate varying diversity at different life-history stages within a species? Using live imaging, histology, scanning electron microscopy and transcriptomic profiling, we have described shell development in a heteroconchian bivalve, the Antarctic clam, Laternula elliptica, and compared it to adult shell secretion processes in the same species. Adult downstream shell genes, such as those encoding extracellular matrix proteins and biomineralization enzymes, were largely not expressed during shell development. Instead, a development-specific downstream gene repertoire was expressed. Upstream regulatory genes such as transcription factors and signalling molecules were largely conserved between developmental and adult shell secretion. Comparing heteroconchian data with recently reported pteriomorphian larval shell development data suggests that, despite being phenotypically more conserved, the downstream effectors constituting the larval shell 'tool-kit' may be as diverse as that of adults. Overall, our new data suggest that a larval shell formed using development-specific downstream effector genes is a conserved and ancestral feature of the bivalve lineage, and possibly more broadly across the molluscs.
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Affiliation(s)
- Alessandro Cavallo
- Biodiversity, Evolution and Adaptation Team, British Antarctic Survey, Cambridge CB3 0ET, UK
| | - Melody S. Clark
- Biodiversity, Evolution and Adaptation Team, British Antarctic Survey, Cambridge CB3 0ET, UK
| | - Lloyd S. Peck
- Biodiversity, Evolution and Adaptation Team, British Antarctic Survey, Cambridge CB3 0ET, UK
| | - Elizabeth M. Harper
- Department of Earth Sciences, University of Cambridge, Cambridge CB2 1TN, UK
| | - Victoria A. Sleight
- Biodiversity, Evolution and Adaptation Team, British Antarctic Survey, Cambridge CB3 0ET, UK
- Department of Zoology, University of Cambridge, Cambridge CB2 1TN, UK
- School of Biological Sciences, University of Aberdeen, Aberdeen AB24 3FX, UK
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6
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Gilbert PUPA, Bergmann KD, Boekelheide N, Tambutté S, Mass T, Marin F, Adkins JF, Erez J, Gilbert B, Knutson V, Cantine M, Hernández JO, Knoll AH. Biomineralization: Integrating mechanism and evolutionary history. SCIENCE ADVANCES 2022; 8:eabl9653. [PMID: 35263127 PMCID: PMC8906573 DOI: 10.1126/sciadv.abl9653] [Citation(s) in RCA: 62] [Impact Index Per Article: 31.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/05/2023]
Abstract
Calcium carbonate (CaCO3) biomineralizing organisms have played major roles in the history of life and the global carbon cycle during the past 541 Ma. Both marine diversification and mass extinctions reflect physiological responses to environmental changes through time. An integrated understanding of carbonate biomineralization is necessary to illuminate this evolutionary record and to understand how modern organisms will respond to 21st century global change. Biomineralization evolved independently but convergently across phyla, suggesting a unity of mechanism that transcends biological differences. In this review, we combine CaCO3 skeleton formation mechanisms with constraints from evolutionary history, omics, and a meta-analysis of isotopic data to develop a plausible model for CaCO3 biomineralization applicable to all phyla. The model provides a framework for understanding the environmental sensitivity of marine calcifiers, past mass extinctions, and resilience in 21st century acidifying oceans. Thus, it frames questions about the past, present, and future of CaCO3 biomineralizing organisms.
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Affiliation(s)
- Pupa U. P. A. Gilbert
- Departments of Physics, Chemistry, Geoscience, and Materials Science, University of Wisconsin-Madison, Madison, WI 53706, USA
- Chemical Sciences Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
- Corresponding author. (P.U.P.A.G.); (A.H.K.)
| | - Kristin D. Bergmann
- Department of Earth, Atmospheric and Planetary Sciences, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Nicholas Boekelheide
- Department of Earth, Atmospheric and Planetary Sciences, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Sylvie Tambutté
- Centre Scientifique de Monaco, Department of Marine Biology, 98000 Monaco, Principality of Monaco
| | - Tali Mass
- University of Haifa, Marine Biology Department, Mt. Carmel, Haifa 31905, Israel
| | - Frédéric Marin
- Université de Bourgogne–Franche-Comté (UBFC), Laboratoire Biogéosciences, UMR CNRS 6282, Bâtiment des Sciences Gabriel, 21000 Dijon, France
| | - Jess F. Adkins
- Geological and Planetary Sciences, California Institute of Technology, MS 100-23, Pasadena, CA 91125, USA
| | - Jonathan Erez
- The Hebrew University of Jerusalem, Institute of Earth Sciences, Jerusalem 91904, Israel
| | - Benjamin Gilbert
- Energy Geoscience Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
- Department of Earth and Planetary Science, University of California, Berkeley, Berkeley, CA 94720, USA
| | - Vanessa Knutson
- Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, MA 02138, USA
| | - Marjorie Cantine
- Department of Earth, Atmospheric and Planetary Sciences, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
- Goethe-Universität Frankfurt, 60438 Frankfurt am Main, Germany
| | - Javier Ortega Hernández
- Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, MA 02138, USA
| | - Andrew H. Knoll
- Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, MA 02138, USA
- Corresponding author. (P.U.P.A.G.); (A.H.K.)
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7
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Cai J, Tao Z, Chen X, Yi E. Identification and Analysis of Transcriptional Regulatory Networks of Osteosarcoma Microarray Data via Systems Biology. J Oleo Sci 2022; 71:379-386. [PMID: 35236797 DOI: 10.5650/jos.ess21327] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
Osteosarcoma is a relatively uncommon tumor that is defined histologically by malignant cells developing osteoid. Osteosarcomas are mesenchymal cell tumors that cause abnormal bone growth. A combination of genetic, epigenetic, and environmental factors leads mesenchymal stem cells to develop into bone precursor cells, resulting in osteosarcoma. Only tumor suppressor genes, such as p53, Rb, RECQL4, BLM, and WRN, have been detected in inherited family illnesses with an OS susceptibility. These genes, in particular, play an essential role in the development of OS in individuals. In this research, core genes responsible for OS were determined using a microarray and systems biology. 234 genes encoding overexpression and down-regulation were identified, among which 60 were considered as key genes, many of which had known roles in bone growth. Transcriptional regulatory networks were developed with this data and subsequently partitioned to define cis-regulatory modules. Results indicate that several OS-specific genes have strongly conserved the clustering of bone-related cis-regulatory modules, thus promoting the hypothesis that a bone-related gene network is essential for understanding OS biology and may play a role in bone contractility and anomalies.
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Affiliation(s)
- Jun Cai
- Department of Pediatric Orthopedics, Jiangxi Provincial Children's Hospital, Children's Hospital of Nanchang University
| | - Zhiwei Tao
- Department of Bone and Soft Tissue Oncology, Jiangxi Provincial Cancer Hospital, Cancer Hospital of Nanchang University
| | - Xin Chen
- Department of Pediatric Orthopedics, Jiangxi Provincial Children's Hospital, Children's Hospital of Nanchang University
| | - Ende Yi
- Department of Pediatric Orthopedics, Jiangxi Provincial Children's Hospital, Children's Hospital of Nanchang University
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8
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Wall-Palmer D, Mekkes L, Ramos-Silva P, Dämmer LK, Goetze E, Bakker K, Duijm E, Peijnenburg KTCA. The impacts of past, present and future ocean chemistry on predatory planktonic snails. ROYAL SOCIETY OPEN SCIENCE 2021; 8:202265. [PMID: 34386247 PMCID: PMC8334855 DOI: 10.1098/rsos.202265] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/16/2020] [Accepted: 06/23/2021] [Indexed: 06/13/2023]
Abstract
The atlantid heteropods represent the only predatory, aragonite shelled zooplankton. Atlantid shell production is likely to be sensitive to ocean acidification (OA), and yet we know little about their mechanisms of calcification, or their response to changing ocean chemistry. Here, we present the first study into calcification and gene expression effects of short-term OA exposure on juvenile atlantids across three pH scenarios: mid-1960s, ambient and 2050 conditions. Calcification and gene expression indicate a distinct response to each treatment. Shell extension and shell volume were reduced from the mid-1960s to ambient conditions, suggesting that calcification is already limited in today's South Atlantic. However, shell extension increased from ambient to 2050 conditions. Genes involved in protein synthesis were consistently upregulated, whereas genes involved in organismal development were downregulated with decreasing pH. Biomineralization genes were upregulated in the mid-1960s and 2050 conditions, suggesting that any deviation from ambient carbonate chemistry causes stress, resulting in rapid shell growth. We conclude that atlantid calcification is likely to be negatively affected by future OA. However, we also found that plentiful food increased shell extension and shell thickness, and so synergistic factors are likely to impact the resilience of atlantids in an acidifying ocean.
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Affiliation(s)
- Deborah Wall-Palmer
- Plankton Diversity and Evolution, Naturalis Biodiversity Center, Leiden, The Netherlands
| | - Lisette Mekkes
- Plankton Diversity and Evolution, Naturalis Biodiversity Center, Leiden, The Netherlands
- Department of Freshwater and Marine Ecology, Institute for Biodiversity and Ecosystem Dynamics (IBED), University of Amsterdam, Amsterdam, The Netherlands
| | - Paula Ramos-Silva
- Plankton Diversity and Evolution, Naturalis Biodiversity Center, Leiden, The Netherlands
| | - Linda K. Dämmer
- Department of Ocean Systems, Royal Netherlands Institute for Sea Research (NIOZ), Texel, The Netherlands
- Environmental Geology, Department of Geology, Institute of Geosciences, University of Bonn, Bonn, Germany
| | - Erica Goetze
- Department of Oceanography, University of Hawai'i at Mānoa, Honolulu, HI, USA
| | - Karel Bakker
- Department of Ocean Systems, Royal Netherlands Institute for Sea Research (NIOZ), Texel, The Netherlands
| | - Elza Duijm
- Plankton Diversity and Evolution, Naturalis Biodiversity Center, Leiden, The Netherlands
| | - Katja T. C. A. Peijnenburg
- Plankton Diversity and Evolution, Naturalis Biodiversity Center, Leiden, The Netherlands
- Department of Freshwater and Marine Ecology, Institute for Biodiversity and Ecosystem Dynamics (IBED), University of Amsterdam, Amsterdam, The Netherlands
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9
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Ehrlich H, Bailey E, Wysokowski M, Jesionowski T. Forced Biomineralization: A Review. Biomimetics (Basel) 2021; 6:46. [PMID: 34287234 PMCID: PMC8293141 DOI: 10.3390/biomimetics6030046] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2021] [Revised: 05/29/2021] [Accepted: 07/02/2021] [Indexed: 12/31/2022] Open
Abstract
Biologically induced and controlled mineralization of metals promotes the development of protective structures to shield cells from thermal, chemical, and ultraviolet stresses. Metal biomineralization is widely considered to have been relevant for the survival of life in the environmental conditions of ancient terrestrial oceans. Similar behavior is seen among extremophilic biomineralizers today, which have evolved to inhabit a variety of industrial aqueous environments with elevated metal concentrations. As an example of extreme biomineralization, we introduce the category of "forced biomineralization", which we use to refer to the biologically mediated sequestration of dissolved metals and metalloids into minerals. We discuss forced mineralization as it is known to be carried out by a variety of organisms, including polyextremophiles in a range of psychrophilic, thermophilic, anaerobic, alkaliphilic, acidophilic, and halophilic conditions, as well as in environments with very high or toxic metal ion concentrations. While much additional work lies ahead to characterize the various pathways by which these biominerals form, forced biomineralization has been shown to provide insights for the progression of extreme biomimetics, allowing for promising new forays into creating the next generation of composites using organic-templating approaches under biologically extreme laboratory conditions relevant to a wide range of industrial conditions.
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Affiliation(s)
- Hermann Ehrlich
- Institute of Electronic and Sensor Materials, TU Bergakademie Freiberg, 09599 Freiberg, Germany
- Center for Advanced Technology, Adam Mickiewicz University, 61614 Poznan, Poland
- Centre for Climate Change Research, Toronto, ON M4P 1J4, Canada
- ICUBE-University of Toronto Mississauga, Mississauga, ON L5L 1C6, Canada
| | - Elizabeth Bailey
- Department of Astronomy and Astrophysics, University of California, Santa Cruz, CA 95064, USA;
| | - Marcin Wysokowski
- Faculty of Chemical Technology, Institute of Chemical Technology and Engineering, Poznan University of Technology, 60-965 Poznan, Poland
| | - Teofil Jesionowski
- Faculty of Chemical Technology, Institute of Chemical Technology and Engineering, Poznan University of Technology, 60-965 Poznan, Poland
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10
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Caurcel C, Laetsch DR, Challis R, Kumar S, Gharbi K, Blaxter M. MolluscDB: a genome and transcriptome database for molluscs. Philos Trans R Soc Lond B Biol Sci 2021; 376:20200157. [PMID: 33813885 PMCID: PMC8059625 DOI: 10.1098/rstb.2020.0157] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
As sequencing becomes more accessible and affordable, the analysis of genomic and transcriptomic data has become a cornerstone of many research initiatives. Communities with a focus on particular taxa or ecosystems need solutions capable of aggregating genomic resources and serving them in a standardized and analysis-friendly manner. Taxon-focussed resources can be more flexible in addressing the needs of a research community than can universal or general databases. Here, we present MolluscDB, a genome and transcriptome database for molluscs. MolluscDB offers a rich ecosystem of tools, including an Ensembl browser, a BLAST server for homology searches and an HTTP server from which any dataset present in the database can be downloaded. To demonstrate the utility of the database and verify the quality of its data, we imported data from assembled genomes and transcriptomes of 22 species, estimated the phylogeny of Mollusca using single-copy orthologues, explored patterns of gene family size change and interrogated the data for biomineralization-associated enzymes and shell matrix proteins. MolluscDB provides an easy-to-use and openly accessible data resource for the research community. This article is part of the Theo Murphy meeting issue 'Molluscan genomics: broad insights and future directions for a neglected phylum'.
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Affiliation(s)
- Carlos Caurcel
- Institute of Evolutionary Biology, School of Biological Sciences, University of Edinburgh, Edinburgh EH9 3JT, UK
| | - Dominik R Laetsch
- Institute of Evolutionary Biology, School of Biological Sciences, University of Edinburgh, Edinburgh EH9 3JT, UK
| | - Richard Challis
- Institute of Evolutionary Biology, School of Biological Sciences, University of Edinburgh, Edinburgh EH9 3JT, UK.,Tree of Life Programme, Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SA, UK
| | - Sujai Kumar
- Institute of Evolutionary Biology, School of Biological Sciences, University of Edinburgh, Edinburgh EH9 3JT, UK.,Tree of Life Programme, Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SA, UK
| | - Karim Gharbi
- Institute of Evolutionary Biology, School of Biological Sciences, University of Edinburgh, Edinburgh EH9 3JT, UK.,Edinburgh Genomics, School of Biological Sciences, University of Edinburgh, Edinburgh EH9 3JT, UK
| | - Mark Blaxter
- Institute of Evolutionary Biology, School of Biological Sciences, University of Edinburgh, Edinburgh EH9 3JT, UK.,Tree of Life Programme, Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SA, UK
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11
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Collins M, Clark MS, Spicer JI, Truebano M. Transcriptional frontloading contributes to cross-tolerance between stressors. Evol Appl 2021; 14:577-587. [PMID: 33664796 PMCID: PMC7896706 DOI: 10.1111/eva.13142] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2020] [Revised: 09/08/2020] [Accepted: 09/15/2020] [Indexed: 12/01/2022] Open
Abstract
The adaptive value of phenotypic plasticity for performance under single stressors is well documented. However, plasticity may only truly be adaptive in the natural multifactorial environment if it confers resilience to stressors of a different nature, a phenomenon known as cross-tolerance. An understanding of the mechanistic basis of cross-tolerance is essential to aid prediction of species resilience to future environmental change. Here, we identified mechanisms underpinning cross-tolerance between two stressors predicted to increasingly challenge aquatic ecosystems under climate change, chronic warming and hypoxia, in an ecologically-important aquatic invertebrate. Warm acclimation improved hypoxic performance through an adaptive hypometabolic strategy and changes in the expression of hundreds of genes that are important in the response to hypoxia. These 'frontloaded' genes showed a reduced reaction to hypoxia in the warm acclimated compared to the cold acclimated group. Frontloaded genes included stress indicators, immune response and protein synthesis genes that are protective at the cellular level. We conclude that increased constitutive gene expression as a result of warm acclimation reduced the requirement for inducible stress responses to hypoxia. We propose that transcriptional frontloading contributes to cross-tolerance between stressors and may promote fitness of organisms in environments increasingly challenged by multiple anthropogenic threats.
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Affiliation(s)
- Michael Collins
- Marine Biology and Ecology Research Centre, School of Biological and Marine SciencesUniversity of PlymouthPlymouthUK
- British Antarctic SurveyNatural Environment Research CouncilCambridgeUK
| | - Melody S. Clark
- British Antarctic SurveyNatural Environment Research CouncilCambridgeUK
| | - John I. Spicer
- Marine Biology and Ecology Research Centre, School of Biological and Marine SciencesUniversity of PlymouthPlymouthUK
| | - Manuela Truebano
- Marine Biology and Ecology Research Centre, School of Biological and Marine SciencesUniversity of PlymouthPlymouthUK
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12
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McDougall C, Aguilera F, Shokoohmand A, Moase P, Degnan BM. Pearl Sac Gene Expression Profiles Associated With Pearl Attributes in the Silver-Lip Pearl Oyster, Pinctada maxima. Front Genet 2021; 11:597459. [PMID: 33488672 PMCID: PMC7820862 DOI: 10.3389/fgene.2020.597459] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2020] [Accepted: 12/07/2020] [Indexed: 11/21/2022] Open
Abstract
Pearls are highly prized biomineralized gemstones produced by molluscs. The appearance and mineralogy of cultured pearls can vary markedly, greatly affecting their commercial value. To begin to understand the role of pearl sacs—organs that form in host oysters from explanted mantle tissues that surround and synthesize pearls—we undertook transcriptomic analyses to identify genes that are differentially expressed in sacs producing pearls with different surface and structural characteristics. Our results indicate that gene expression profiles correlate with different pearl defects, suggesting that gene regulation in the pearl sac contributes to pearl appearance and quality. For instance, pearl sacs that produced pearls with surface non-lustrous calcification significantly down-regulate genes associated with cilia and microtubule function compared to pearl sacs giving rise to lustrous pearls. These results suggest that gene expression profiling can advance our understanding of processes that control biomineralization, which may be of direct value to the pearl industry, particularly in relation to defects that result in low value pearls.
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Affiliation(s)
- Carmel McDougall
- Centre for Marine Science, School of Biological Sciences, The University of Queensland, St. Lucia, QLD, Australia.,Australian Rivers Institute, Griffith University, Nathan, QLD, Australia
| | - Felipe Aguilera
- Centre for Marine Science, School of Biological Sciences, The University of Queensland, St. Lucia, QLD, Australia
| | - Ali Shokoohmand
- Australian Rivers Institute, Griffith University, Nathan, QLD, Australia
| | - Patrick Moase
- Clipper Pearls and Autore Pearling, Broome, WA, Australia
| | - Bernard M Degnan
- Centre for Marine Science, School of Biological Sciences, The University of Queensland, St. Lucia, QLD, Australia
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13
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Ramsøe A, Clark MS, Sleight VA. Gene network analyses support subfunctionalization hypothesis for duplicated hsp70 genes in the Antarctic clam. Cell Stress Chaperones 2020; 25:1111-1116. [PMID: 32436134 PMCID: PMC7591643 DOI: 10.1007/s12192-020-01118-9] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2020] [Revised: 04/27/2020] [Accepted: 05/04/2020] [Indexed: 12/01/2022] Open
Abstract
A computationally predicted gene regulatory network (GRN), generated from mantle-specific gene expression profiles in the Antarctic clam Laternula elliptica, was interrogated to test the regulation and interaction of duplicated inducible hsp70 paralogues. hsp70A and hsp70B were identified in the GRN with each paralogue falling into unique submodules that were linked together by a single shared second neighbour. Annotations associated with the clusters in each submodule suggested that hsp70A primarily shares regulatory relationships with genes encoding ribosomal proteins, where it may have a role in protecting the ribosome under stress. hsp70B, on the other hand, interacted with a suite of genes involved in signalling pathways, including four transcription factors, cellular response to stress and the cytoskeleton. Given the contrasting submodules and associated annotations of the two hsp70 paralogues, the GRN analysis suggests that each gene is carrying out additional separate functions, as well as being involved in the traditional chaperone heat stress response, and therefore supports the hypothesis that subfunctionalization has occurred after gene duplication. The GRN was specifically produced from experiments investigating biomineralization; however, this study shows the utility of such data for investigating multiple questions concerning gene duplications, interactions and putative functions in a non-model species.
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Affiliation(s)
- Abigail Ramsøe
- BioArCh, Department of Archaeology, University of York, York, YO1 7EP, UK
- Department of Earth Sciences, Natural History Museum, London, SW7 5BD, UK
| | - Melody S Clark
- British Antarctic Survey, Natural Environment Research Council, High Cross, Madingley Road, Cambridge, CB3 0ET, UK.
| | - Victoria A Sleight
- British Antarctic Survey, Natural Environment Research Council, High Cross, Madingley Road, Cambridge, CB3 0ET, UK.
- Department of Zoology, University of Cambridge, Downing Street, Cambridge, CB2 3EJ, UK.
- School of Biological Sciences, University of Aberdeen, Zoology Building, Tillydrone Avenue, Aberdeen, AB24 2TZ, UK.
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14
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Abstract
Much recent marine research has been directed towards understanding the effects of anthropogenic-induced environmental change on marine biodiversity, particularly for those animals with heavily calcified exoskeletons, such as corals, molluscs and urchins. This is because life in our oceans is becoming more challenging for these animals with changes in temperature, pH and salinity. In the future, it will be more energetically expensive to make marine skeletons and the increasingly corrosive conditions in seawater are expected to result in the dissolution of these external skeletons. However, initial predictions of wide-scale sensitivity are changing as we understand more about the mechanisms underpinning skeletal production (biomineralization). These studies demonstrate the complexity of calcification pathways and the cellular responses of animals to these altered conditions. Factors including parental conditioning, phenotypic plasticity and epigenetics can significantly impact the production of skeletons and thus future population success. This understanding is paralleled by an increase in our knowledge of the genes and proteins involved in biomineralization, particularly in some phyla, such as urchins, molluscs and corals. This Review will provide a broad overview of our current understanding of the factors affecting skeletal production in marine invertebrates. It will focus on the molecular mechanisms underpinning biomineralization and how knowledge of these processes affects experimental design and our ability to predict responses to climate change. Understanding marine biomineralization has many tangible benefits in our changing world, including improvements in conservation and aquaculture and exploitation of natural calcified structure design using biomimicry approaches that are aimed at producing novel biocomposites.
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Affiliation(s)
- Melody S Clark
- British Antarctic Survey, Natural Environment Research Council, High Cross, Madingley Road, Cambridge, CB3 0ET, UK
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