1
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Guo Z, Chen M, Ouyang W, Lin C, He M. Fine particle contents in sediment drive silica transport and deposition to the estuary in the turbid river basin. WATER RESEARCH 2024; 255:121464. [PMID: 38492311 DOI: 10.1016/j.watres.2024.121464] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/26/2023] [Revised: 03/11/2024] [Accepted: 03/12/2024] [Indexed: 03/18/2024]
Abstract
Changes in riverine sediment transport are an important part of land-sea geochemical cycling and further impact geochemical element fluxes in turbid rivers. However, as a vital nutrient element supporting primary productivity, silica mobilization from drainage in turbid rivers is overlooked. The turbid Yellow River has a strong ability to adsorb reactive silica, thereby exerting a substantial impact on the estuarine deposition of silica. Through an integration of monitoring databases, field sampling and historical hydrological data, we concluded that riverine fine particles control the exchangeable silica in the river and its estuary under soil erosion. Indoor simulation further revealed that the adsorbed content of exchangeable silica (ex-Si) in fine sediment constituted 35 % of total sediment matter. In addition, the transport of phosphorus and ex-Si was jointly regulated by fine sediment in global fluvial sediment transport, thereby exerting additional influence on the trophic structure of estuarine ecosystems. Against the backdrop of sediment budget deficit in the estuary, the heightened content of fine particles is depleting the silica storage from estuarine sediments.
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Affiliation(s)
- Zewei Guo
- State Key Laboratory of Water Environment Simulation, School of Environment, Beijing Normal University, Beijing 100875, PR China
| | - Ming Chen
- State Key Laboratory of Water Environment Simulation, School of Environment, Beijing Normal University, Beijing 100875, PR China
| | - Wei Ouyang
- State Key Laboratory of Water Environment Simulation, School of Environment, Beijing Normal University, Beijing 100875, PR China; Advanced Interdisciplinary Institute of Environment and Ecology, Beijing Normal University, Zhuhai, 519087, PR China.
| | - Chunye Lin
- State Key Laboratory of Water Environment Simulation, School of Environment, Beijing Normal University, Beijing 100875, PR China
| | - Mengchang He
- State Key Laboratory of Water Environment Simulation, School of Environment, Beijing Normal University, Beijing 100875, PR China
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2
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Bryłka K, Pinseel E, Roberts WR, Ruck EC, Conley DJ, Alverson AJ. Gene Duplication, Shifting Selection, and Dosage Balance of Silicon Transporter Proteins in Marine and Freshwater Diatoms. Genome Biol Evol 2023; 15:evad212. [PMID: 37996067 PMCID: PMC10700740 DOI: 10.1093/gbe/evad212] [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: 07/06/2023] [Revised: 09/15/2023] [Accepted: 11/17/2023] [Indexed: 11/25/2023] Open
Abstract
Numerous factors shape the evolution of protein-coding genes, including shifts in the strength or type of selection following gene duplications or changes in the environment. Diatoms and other silicifying organisms use a family of silicon transporters (SITs) to import dissolved silicon from the environment. Freshwaters contain higher silicon levels than oceans, and marine diatoms have more efficient uptake kinetics and less silicon in their cell walls, making them better competitors for a scarce resource. We compiled SITs from 37 diatom genomes to characterize shifts in selection following gene duplications and marine-freshwater transitions. A deep gene duplication, which coincided with a whole-genome duplication, gave rise to two gene lineages. One of them (SIT1-2) is present in multiple copies in most species and is known to actively import silicon. These SITs have evolved under strong purifying selection that was relaxed in freshwater taxa. Episodic diversifying selection was detected but not associated with gene duplications or habitat shifts. In contrast, genes in the second SIT lineage (SIT3) were present in just half the species, the result of multiple losses. Despite conservation of SIT3 in some lineages for the past 90-100 million years, repeated losses, relaxed selection, and low expression highlighted the dispensability of SIT3, consistent with a model of deterioration and eventual loss due to relaxed selection on SIT3 expression. The extensive but relatively balanced history of duplications and losses, together with paralog-specific expression patterns, suggest diatoms continuously balance gene dosage and expression dynamics to optimize silicon transport across major environmental gradients.
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Affiliation(s)
| | - Eveline Pinseel
- Department of Biological Sciences, University of Arkansas, Fayetteville, AR, USA
| | - Wade R Roberts
- Department of Biological Sciences, University of Arkansas, Fayetteville, AR, USA
| | - Elizabeth C Ruck
- Department of Biological Sciences, University of Arkansas, Fayetteville, AR, USA
| | | | - Andrew J Alverson
- Department of Biological Sciences, University of Arkansas, Fayetteville, AR, USA
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3
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Ban H, Sato S, Yoshikawa S, Yamada K, Nakamura Y, Ichinomiya M, Sato N, Blanc-Mathieu R, Endo H, Kuwata A, Ogata H. Genome analysis of Parmales, the sister group of diatoms, reveals the evolutionary specialization of diatoms from phago-mixotrophs to photoautotrophs. Commun Biol 2023; 6:697. [PMID: 37420035 PMCID: PMC10328945 DOI: 10.1038/s42003-023-05002-x] [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: 10/13/2022] [Accepted: 05/31/2023] [Indexed: 07/09/2023] Open
Abstract
The order Parmales (class Bolidophyceae) is a minor group of pico-sized eukaryotic marine phytoplankton that contains species with cells surrounded by silica plates. Previous studies revealed that Parmales is a member of ochrophytes and sister to diatoms (phylum Bacillariophyta), the most successful phytoplankton group in the modern ocean. Therefore, parmalean genomes can serve as a reference to elucidate both the evolutionary events that differentiated these two lineages and the genomic basis for the ecological success of diatoms vs. the more cryptic lifestyle of parmaleans. Here, we compare the genomes of eight parmaleans and five diatoms to explore their physiological and evolutionary differences. Parmaleans are predicted to be phago-mixotrophs. By contrast, diatoms have lost genes related to phagocytosis, indicating the ecological specialization from phago-mixotrophy to photoautotrophy in their early evolution. Furthermore, diatoms show significant enrichment in gene sets involved in nutrient uptake and metabolism, including iron and silica, in comparison with parmaleans. Overall, our results suggest a strong evolutionary link between the loss of phago-mixotrophy and specialization to a silicified photoautotrophic life stage early in diatom evolution after diverging from the Parmales lineage.
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Affiliation(s)
- Hiroki Ban
- Bioinformatics Center, Institute for Chemical Research, Kyoto University, Gokasho, Uji, Kyoto, 611-0011, Japan
| | - Shinya Sato
- Department of Marine Science and Technology, Fukui Prefectural University, 1-1 Gakuen-cho, Obama City, Fukui, 917-0003, Japan
| | - Shinya Yoshikawa
- Department of Marine Science and Technology, Fukui Prefectural University, 1-1 Gakuen-cho, Obama City, Fukui, 917-0003, Japan
| | - Kazumasa Yamada
- Department of Marine Science and Technology, Fukui Prefectural University, 1-1 Gakuen-cho, Obama City, Fukui, 917-0003, Japan
| | - Yoji Nakamura
- Bioinformatics and Biosciences Division, Fisheries Stock Assessment Center, Fisheries Resources Institute, Japan Fisheries Research and Education Agency, 2-12-4 Fuku-ura, Kanazawa, Yokohama, Kanagawa, 236-8648, Japan
| | - Mutsuo Ichinomiya
- Prefectural University of Kumamoto, 3-1-100 Tsukide, Kumamoto, 862-8502, Japan
| | - Naoki Sato
- Graduate School of Arts and Sciences, University of Tokyo, Komaba, Meguro-ku, Tokyo, 153-8902, Japan
| | - Romain Blanc-Mathieu
- Bioinformatics Center, Institute for Chemical Research, Kyoto University, Gokasho, Uji, Kyoto, 611-0011, Japan
- Laboratoire de Physiologie Cellulaire & Végétale, CEA, Univ. Grenoble Alpes, CNRS, INRA, IRIG, Grenoble, France
| | - Hisashi Endo
- Bioinformatics Center, Institute for Chemical Research, Kyoto University, Gokasho, Uji, Kyoto, 611-0011, Japan
| | - Akira Kuwata
- Shiogama field station, Fisheries Resources Institute, Japan Fisheries Research and Education Agency, 3-27-5 Shinhama-cho, Shiogama, Miyagi, Japan.
| | - Hiroyuki Ogata
- Bioinformatics Center, Institute for Chemical Research, Kyoto University, Gokasho, Uji, Kyoto, 611-0011, Japan.
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4
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Ratcliffe S, Meyer EM, Walker CE, Knight M, McNair HM, Matson PG, Iglesias-Rodriguez D, Brzezinski M, Langer G, Sadekov A, Greaves M, Brownlee C, Curnow P, Taylor AR, Wheeler GL. Characterization of the molecular mechanisms of silicon uptake in coccolithophores. Environ Microbiol 2023; 25:315-330. [PMID: 36397254 PMCID: PMC10098502 DOI: 10.1111/1462-2920.16280] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2022] [Accepted: 11/05/2022] [Indexed: 11/19/2022]
Abstract
Coccolithophores are an important group of calcifying marine phytoplankton. Although coccolithophores are not silicified, some species exhibit a requirement for Si in the calcification process. These species also possess a novel protein (SITL) that resembles the SIT family of Si transporters found in diatoms. However, the nature of Si transport in coccolithophores is not yet known, making it difficult to determine the wider role of Si in coccolithophore biology. Here, we show that coccolithophore SITLs act as Na+ -coupled Si transporters when expressed in heterologous systems and exhibit similar characteristics to diatom SITs. We find that CbSITL from Coccolithus braarudii is transcriptionally regulated by Si availability and is expressed in environmental coccolithophore populations. However, the Si requirement of C. braarudii and other coccolithophores is very low, with transport rates of exogenous Si below the level of detection in sensitive assays of Si transport. As coccoliths contain only low levels of Si, we propose that Si acts to support the calcification process, rather than forming a structural component of the coccolith itself. Si is therefore acting as a micronutrient in coccolithophores and natural populations are only likely to experience Si limitation in circumstances where dissolved silicon (DSi) is depleted to extreme levels.
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Affiliation(s)
| | - Erin M Meyer
- Department of Biology and Marine Biology, University of North Carolina Wilmington, Wilmington, North Carolina, USA
| | - Charlotte E Walker
- Marine Biological Association, The Laboratory, Citadel Hill, Plymouth, UK
| | - Michael Knight
- School of Ocean and Earth Science, University of Southampton, Southampton, UK
| | - Heather M McNair
- Department of Ecology Evolution and Marine Biology and the Marine Science Institute, University of California, Santa Barbara, California, USA
- Graduate School of Oceanography, University of Rhode Island, Narragansett, Rhode Island, USA
| | - Paul G Matson
- Department of Ecology Evolution and Marine Biology and the Marine Science Institute, University of California, Santa Barbara, California, USA
- Environmental Sciences Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee, USA
| | - Debora Iglesias-Rodriguez
- Department of Ecology Evolution and Marine Biology and the Marine Science Institute, University of California, Santa Barbara, California, USA
| | - Mark Brzezinski
- Department of Ecology Evolution and Marine Biology and the Marine Science Institute, University of California, Santa Barbara, California, USA
- Graduate School of Oceanography, University of Rhode Island, Narragansett, Rhode Island, USA
- Environmental Sciences Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee, USA
| | - Gerald Langer
- Marine Biological Association, The Laboratory, Citadel Hill, Plymouth, UK
| | - Aleksey Sadekov
- ARC Centre of Excellence for Coral Reef Studies, Ocean Graduate School, University of Western Australia, Crawley, Western Australia, Australia
| | - Mervyn Greaves
- The Godwin Laboratory for Palaeoclimate Research, Department of Earth Sciences, University of Cambridge, Cambridge, UK
| | - Colin Brownlee
- Marine Biological Association, The Laboratory, Citadel Hill, Plymouth, UK
| | - Paul Curnow
- School of Biochemistry, University of Bristol, Bristol, UK
| | - Alison R Taylor
- Department of Biology and Marine Biology, University of North Carolina Wilmington, Wilmington, North Carolina, USA
| | - Glen L Wheeler
- Marine Biological Association, The Laboratory, Citadel Hill, Plymouth, UK
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5
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Brownlee C, Helliwell KE, Meeda Y, McLachlan D, Murphy EA, Wheeler GL. Regulation and integration of membrane transport in marine diatoms. Semin Cell Dev Biol 2023; 134:79-89. [PMID: 35305902 DOI: 10.1016/j.semcdb.2022.03.006] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2021] [Revised: 02/18/2022] [Accepted: 03/04/2022] [Indexed: 12/27/2022]
Abstract
Diatoms represent one of the most successful groups of marine phytoplankton and are major contributors to ocean biogeochemical cycling. They have colonized marine, freshwater and ice environments and inhabit all regions of the World's oceans, from poles to tropics. Their success is underpinned by a remarkable ability to regulate their growth and metabolism during nutrient limitation and to respond rapidly when nutrients are available. This requires precise regulation of membrane transport and nutrient acquisition mechanisms, integration of nutrient sensing mechanisms and coordination of different transport pathways. This review outlines transport mechanisms involved in acquisition of key nutrients (N, C, P, Si, Fe) by marine diatoms, illustrating their complexity, sophistication and multiple levels of control.
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Affiliation(s)
- Colin Brownlee
- Marine Biological Association, The Laboratory, Citadel Hill, Plymouth PL1 2PB, UK; School of Ocean and Earth Sciences, University of Southampton, Southampton SO14 3ZH, UK
| | - Katherine E Helliwell
- Marine Biological Association, The Laboratory, Citadel Hill, Plymouth PL1 2PB, UK; Biosciences, College of Life and Environmental Sciences, University of Exeter, Exeter EX4 4QD, UK
| | - Yasmin Meeda
- Marine Biological Association, The Laboratory, Citadel Hill, Plymouth PL1 2PB, UK
| | - Deirdre McLachlan
- Marine Biological Association, The Laboratory, Citadel Hill, Plymouth PL1 2PB, UK; School of Biological Sciences, University of Bristol, Bristol BS8 1TQ, UK
| | - Eleanor A Murphy
- Marine Biological Association, The Laboratory, Citadel Hill, Plymouth PL1 2PB, UK
| | - Glen L Wheeler
- Marine Biological Association, The Laboratory, Citadel Hill, Plymouth PL1 2PB, UK
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6
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Knight MJ, Hardy BJ, Wheeler GL, Curnow P. Computational modelling of diatom silicic acid transporters predicts a conserved fold with implications for their function and evolution. BIOCHIMICA ET BIOPHYSICA ACTA. BIOMEMBRANES 2023; 1865:184056. [PMID: 36191629 DOI: 10.1016/j.bbamem.2022.184056] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/12/2022] [Revised: 09/16/2022] [Accepted: 09/20/2022] [Indexed: 11/27/2022]
Abstract
Diatoms are an important group of algae that can produce intricate silicified cell walls (frustules). The complex process of silicification involves a set of enigmatic integral membrane proteins that are thought to actively transport the soluble precursor of biosilica, dissolved silicic acid. Full-length silicic acid transporters are found widely across the diatoms while homologous shorter proteins have now been identified in a range of other organisms. It has been suggested that modern silicic acid transporters arose from the union of such partial sequences. Here, we present a computational study of the silicic acid transporters and related transporter-like sequences to help understand the structure, function and evolution of this class of membrane protein. The AlphaFold software predicts that all of the protein sequences studied here share a common fold in the membrane domain which is entirely different from the predicted folds of non-homologous silicic acid transporters from plants. Substrate docking reveals how conserved polar residues could interact with silicic acid at a central solvent-accessible binding site, consistent with an alternating access mechanism of transport. The structural conservation between these proteins supports a model where modern silicon transporters evolved from smaller ancestral proteins by gene fusion.
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Affiliation(s)
| | | | | | - Paul Curnow
- School of Biochemistry, University of Bristol, UK.
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7
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Maniscalco MA, Brzezinski MA, Lampe RH, Cohen NR, McNair HM, Ellis KA, Brown M, Till CP, Twining BS, Bruland KW, Marchetti A, Thamatrakoln K. Diminished carbon and nitrate assimilation drive changes in diatom elemental stoichiometry independent of silicification in an iron-limited assemblage. ISME COMMUNICATIONS 2022; 2:57. [PMID: 37938259 PMCID: PMC9723790 DOI: 10.1038/s43705-022-00136-1] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/09/2021] [Revised: 05/12/2022] [Accepted: 06/09/2022] [Indexed: 06/17/2023]
Abstract
In the California Current Ecosystem, upwelled water low in dissolved iron (Fe) can limit phytoplankton growth, altering the elemental stoichiometry of the particulate matter and dissolved macronutrients. Iron-limited diatoms can increase biogenic silica (bSi) content >2-fold relative to that of particulate organic carbon (C) and nitrogen (N), which has implications for carbon export efficiency given the ballasted nature of the silica-based diatom cell wall. Understanding the molecular and physiological drivers of this altered cellular stoichiometry would foster a predictive understanding of how low Fe affects diatom carbon export. In an artificial upwelling experiment, water from 96 m depth was incubated shipboard and left untreated or amended with dissolved Fe or the Fe-binding siderophore desferrioxamine-B (+DFB) to induce Fe-limitation. After 120 h, diatoms dominated the communities in all treatments and displayed hallmark signatures of Fe-limitation in the +DFB treatment, including elevated particulate Si:C and Si:N ratios. Single-cell, taxon-resolved measurements revealed no increase in bSi content during Fe-limitation despite higher transcript abundance of silicon transporters and silicanin-1. Based on these findings we posit that the observed increase in bSi relative to C and N was primarily due to reductions in C fixation and N assimilation, driven by lower transcript expression of key Fe-dependent genes.
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Affiliation(s)
- Michael A Maniscalco
- Marine Science Institute and The Department of Ecology Evolution and Marine Biology, University of California, Santa Barbara, CA, USA.
| | - Mark A Brzezinski
- Marine Science Institute and The Department of Ecology Evolution and Marine Biology, University of California, Santa Barbara, CA, USA
| | - Robert H Lampe
- Integrative Oceanography Division, Scripps Institution of Oceanography, University of California, San Diego, La Jolla, CA, USA
| | - Natalie R Cohen
- Skidaway Institute of Oceanography, University of Georgia, Savannah, GA, USA
| | - Heather M McNair
- University of Rhode Island, Graduate School of Oceanography, Narragansett, RI, USA
| | - Kelsey A Ellis
- Department of Earth, Marine and Environmental Sciences, University of North Carolina at Chapel Hill, Chapel Hill, USA
| | | | - Claire P Till
- Chemistry Department, California State Polytechnic University, Humboldt, Arcata, CA, USA
| | | | - Kenneth W Bruland
- Department of Ocean Sciences, University of California, Santa Cruz, CA, USA
| | - Adrian Marchetti
- Department of Earth, Marine and Environmental Sciences, University of North Carolina at Chapel Hill, Chapel Hill, USA
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8
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Kamikawa R, Mochizuki T, Sakamoto M, Tanizawa Y, Nakayama T, Onuma R, Cenci U, Moog D, Speak S, Sarkozi K, Toseland A, van Oosterhout C, Oyama K, Kato M, Kume K, Kayama M, Azuma T, Ishii KI, Miyashita H, Henrissat B, Lombard V, Win J, Kamoun S, Kashiyama Y, Mayama S, Miyagishima SY, Tanifuji G, Mock T, Nakamura Y. Genome evolution of a nonparasitic secondary heterotroph, the diatom Nitzschia putrida. SCIENCE ADVANCES 2022; 8:eabi5075. [PMID: 35486731 PMCID: PMC9054022 DOI: 10.1126/sciadv.abi5075] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 03/15/2021] [Accepted: 03/16/2022] [Indexed: 06/14/2023]
Abstract
Secondary loss of photosynthesis is observed across almost all plastid-bearing branches of the eukaryotic tree of life. However, genome-based insights into the transition from a phototroph into a secondary heterotroph have so far only been revealed for parasitic species. Free-living organisms can yield unique insights into the evolutionary consequence of the loss of photosynthesis, as the parasitic lifestyle requires specific adaptations to host environments. Here, we report on the diploid genome of the free-living diatom Nitzschia putrida (35 Mbp), a nonphotosynthetic osmotroph whose photosynthetic relatives contribute ca. 40% of net oceanic primary production. Comparative analyses with photosynthetic diatoms and heterotrophic algae with parasitic lifestyle revealed that a combination of gene loss, the accumulation of genes involved in organic carbon degradation, a unique secretome, and the rapid divergence of conserved gene families involved in cell wall and extracellular metabolism appear to have facilitated the lifestyle of a free-living secondary heterotroph.
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Affiliation(s)
- Ryoma Kamikawa
- Graduate School of Agriculture, Kyoto University, Kyoto 606-8502, Japan
| | - Takako Mochizuki
- Department of Informatics, National Institute of Genetics, Research Organization of Information and Systems, Shizuoka 411-8540, Japan
| | - Mika Sakamoto
- Department of Informatics, National Institute of Genetics, Research Organization of Information and Systems, Shizuoka 411-8540, Japan
| | - Yasuhiro Tanizawa
- Department of Informatics, National Institute of Genetics, Research Organization of Information and Systems, Shizuoka 411-8540, Japan
| | - Takuro Nakayama
- Graduate School of Life Sciences, Tohoku University, Sendai 980-8578, Japan
| | - Ryo Onuma
- Department of Gene Function and Phenomics, National Institute of Genetics, Shizuoka 411-8540, Japan
| | - Ugo Cenci
- Université de Lille, CNRS, UMR 8576 – UGSF – Unité de Glycobiologie Structurale et Fonctionnelle, F-59000 Lille, France
| | - Daniel Moog
- Laboratory for Cell Biology, Philipps University Marburg, Karl-von-Frisch-Str. 8
- SYNMIKRO Research Center, Hans-Meerwein-Str. 6, 35032, Marburg, Germany
| | - Samuel Speak
- School of Environmental Sciences, University of East Anglia, Norwich Research Park, Norwich, UK
| | - Krisztina Sarkozi
- School of Environmental Sciences, University of East Anglia, Norwich Research Park, Norwich, UK
| | - Andrew Toseland
- School of Environmental Sciences, University of East Anglia, Norwich Research Park, Norwich, UK
| | - Cock van Oosterhout
- School of Environmental Sciences, University of East Anglia, Norwich Research Park, Norwich, UK
| | - Kaori Oyama
- Graduate School of Humanities and Sciences, Ochanomizu University, Tokyo, Japan
| | - Misako Kato
- Graduate School of Humanities and Sciences, Ochanomizu University, Tokyo, Japan
| | - Keitaro Kume
- Department of Clinical Medicine, Faculty of Medicine, University of Tsukuba, Ibaraki 305-8572, Japan
| | - Motoki Kayama
- Graduate School of Human and Environmental Studies, Kyoto University, Kyoto 606-8501, Japan
| | - Tomonori Azuma
- Graduate School of Human and Environmental Studies, Kyoto University, Kyoto 606-8501, Japan
| | - Ken-ichiro Ishii
- Graduate School of Human and Environmental Studies, Kyoto University, Kyoto 606-8501, Japan
| | - Hideaki Miyashita
- Graduate School of Human and Environmental Studies, Kyoto University, Kyoto 606-8501, Japan
| | - Bernard Henrissat
- Architecture et Fonction des Macromolécules Biologiques (AFMB), CNRS, Université Aix-Marseille, 163 Avenue de Luminy, 13288 Marseille, France
- INRA, USC 1408 AFMB, 13288 Marseille, France
- Department of Biological Sciences, King Abdulaziz University, Jeddah 21589, Saudi Arabia
| | - Vincent Lombard
- Architecture et Fonction des Macromolécules Biologiques (AFMB), CNRS, Université Aix-Marseille, 163 Avenue de Luminy, 13288 Marseille, France
- INRA, USC 1408 AFMB, 13288 Marseille, France
| | - Joe Win
- The Sainsbury Laboratory, University of East Anglia, Norwich Research Park, Norwich, UK
| | - Sophien Kamoun
- The Sainsbury Laboratory, University of East Anglia, Norwich Research Park, Norwich, UK
| | - Yuichiro Kashiyama
- Graduate School of Engineering, Fukui University of Technology, Fukui, Japan
| | - Shigeki Mayama
- Advanced Support Center for Science Teachers, Tokyo Gakugei University, Koganei, Tokyo, Japan
| | - Shin-ya Miyagishima
- Department of Gene Function and Phenomics, National Institute of Genetics, Shizuoka 411-8540, Japan
| | - Goro Tanifuji
- Department of Zoology, National Museum of Nature and Science, Tsukuba 305-0005, Japan
| | - Thomas Mock
- School of Environmental Sciences, University of East Anglia, Norwich Research Park, Norwich, UK
| | - Yasukazu Nakamura
- Department of Informatics, National Institute of Genetics, Research Organization of Information and Systems, Shizuoka 411-8540, Japan
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9
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Reid A, Buchanan F, Julius M, Walsh PJ. A review on diatom biosilicification and their adaptive ability to uptake other metals into their frustules for potential application in bone repair. J Mater Chem B 2021; 9:6728-6737. [PMID: 34346480 DOI: 10.1039/d1tb00322d] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Diatoms are unicellular eukaryotic algae that have a distinctive siliceous cell wall (frustule) with unique architectures. The nanotopography of the frustule is perfectly replicated between generations, offering a source of highly intricate and identical silica microparticles. In recent years, the ability to alter their cell wall chemistry both in terms of functionalisation with organic moieties or by incorporation of the metal ions in their frustules has increased interest in their utility for catalysis technologies, and semiconductor and biomedical applications. Herein we review the fundamental biological mechanisms in which diatoms produce their frustule and their ability to substitute different metal ions in their frustule fabrication process. The review focuses on the potential of diatom frustules as a naturally derived biomaterial in bone tissue engineering applications and how their cell walls, comprising biogenic silica, could either partially or fully incorporate other bone therapeutic metal ions, e.g., titanium or calcium, into their frustule. The use of diatom frustules in bone repair also potentially offers a 'greener', more environmentally friendly, biomaterial as they can naturally synthesise oxides of silicon and other metals into their frustules under ambient conditions at a relatively neutral pH. This process would negate the use of harsh organic chemicals and high-temperature processing conditions, often used in the fabrication of silica based biomaterials, e.g., bioactive glass.
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Affiliation(s)
- A Reid
- School of Chemistry & Chemical Engineering, Queen's University, Belfast, UK.
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10
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Mini-Review: Potential of Diatom-Derived Silica for Biomedical Applications. APPLIED SCIENCES-BASEL 2021. [DOI: 10.3390/app11104533] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
Diatoms are unicellular eukaryotic microalgae widely distributed in aquatic environments, possessing a porous silica cell wall known as frustule. Diatom frustules are considered as a sustainable source for several industrial applications because of their high biocompatibility and the easiness of surface functionalisation, which make frustules suitable for regenerative medicine and as drug carriers. Frustules are made of hydrated silica, and can be extracted and purified both from living and fossil diatoms using acid treatments or high temperatures. Biosilica frustules have proved to be suitable for biomedical applications, but, unfortunately, they are not officially recognised as safe by governmental food and medical agencies yet. In the present review, we highlight the frustule formation process, the most common purification techniques, as well as advantages and bottlenecks related to the employment of diatom-derived silica for medical purposes, suggesting possible solutions for a large-scale biosilica production.
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11
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Lei Q, Guo J, Kong F, Cao J, Wang L, Zhu W, Brinker CJ. Bioinspired Cell Silicification: From Extracellular to Intracellular. J Am Chem Soc 2021; 143:6305-6322. [PMID: 33826324 DOI: 10.1021/jacs.1c00814] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
In nature, biosilicification directs the formation of elaborate amorphous silica exoskeletons that provide diatoms mechanically strong, chemically inert, non-decomposable silica armor conferring chemical and thermal stability as well as resistance to microbial attack, without changing the optical transparency or adversely effecting nutrient and waste exchange required for growth. These extraordinary silica/cell biocomposites have inspired decades of biomimetic research aimed at replication of diatoms' hierarchically organized exoskeletons, immobilization of cells or living organisms within silica matrices and coatings to protect them against harmful external stresses, genetic re-programming of cellular functions by virtue of physico-chemical confinement within silica, cellular integration into devices, and endowment of cells with non-native, abiotic properties through facile silica functionalization. In this Perspective, we focus our discussions on the development and concomitant challenges of bioinspired cell silicification ranging from "cells encapsulated within 3D silica matrices" and "cells encapsulated within 2D silica shells" to extra- and intracellular silica replication, wherein all biomolecular interfaces are encased within nanoscopic layers of amorphous silica. We highlight notable examples of advances in the science and technology of biosilicification and consider challenges to advancing the field, where we propose cellular "mineralization" with arbitrary nanoparticle exoskeletons as a generalizable means to impart limitless abiotic properties and functions to cells, and, based on the interchangeability of water and silicic acid and analogies between amorphous ice and amorphous silica, we consider "freezing" cells within amorphous silica as an alternative to cryo-preservation.
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Affiliation(s)
- Qi Lei
- MOE International Joint Research Laboratory on Synthetic Biology and Medicines, School of Biology and Biological Engineering, South China University of Technology, Guangzhou 510006, P. R. China
| | - Jimin Guo
- Center for Micro-Engineered Materials, Department of Chemical and Biological Engineering, The University of New Mexico, Albuquerque, New Mexico 87131, United States.,Department of Internal Medicine, Molecular Medicine, The University of New Mexico, Albuquerque, New Mexico 87131, United States
| | - Fanhui Kong
- MOE International Joint Research Laboratory on Synthetic Biology and Medicines, School of Biology and Biological Engineering, South China University of Technology, Guangzhou 510006, P. R. China
| | - Jiangfan Cao
- MOE International Joint Research Laboratory on Synthetic Biology and Medicines, School of Biology and Biological Engineering, South China University of Technology, Guangzhou 510006, P. R. China
| | - Lu Wang
- Department of Biochemistry and Molecular Biology, University of New Mexico, Albuquerque, New Mexico 87131, United States
| | - Wei Zhu
- MOE International Joint Research Laboratory on Synthetic Biology and Medicines, School of Biology and Biological Engineering, South China University of Technology, Guangzhou 510006, P. R. China
| | - C Jeffrey Brinker
- Center for Micro-Engineered Materials, Department of Chemical and Biological Engineering, The University of New Mexico, Albuquerque, New Mexico 87131, United States
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12
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Annenkov VV, Gordon R, Zelinskiy SN, Danilovtseva EN. The Probable Mechanism for Silicon Capture by Diatom Algae: Assimilation of Polycarbonic Acids with Diatoms-Is Endocytosis a Key Stage in Building of Siliceous Frustules? JOURNAL OF PHYCOLOGY 2020; 56:1729-1737. [PMID: 32767752 DOI: 10.1111/jpy.13062] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/23/2020] [Accepted: 07/28/2020] [Indexed: 06/11/2023]
Abstract
Many organisms including unicellular (diatoms, radiolaria, and chrysophytes), higher plants (rice and horsetail) and animals (sponges) use silica as a main part of skeletons. The bioavailable form of silicon is silicic acid and the mechanism of silicic acid penetration into living cells is still an enigma. Macropinocytosis was assumed as a key stage of the silicon capture by diatoms but assimilation of monomeric silicic acid by this way requires enormous amounts of water to be passed through the cell. We hypothesized that silicon can be captured by diatoms via endocytosis in the form of partially condensed silicic acid (oligosilicates) whose formation on the diatom surface was supposed. Oligosilicates are negatively charged nanoparticles and similar to coils of poly(acrylic acid) (PAA). We have synthesized fluorescent tagged PAA as well as several neutral and positively charged polymers. Cultivation of the diatom Ulnaria ferefusiformis in the presence of these polymers showed that only PAA is able to penetrate into siliceous frustules. The presence of PAA in the frustules was confirmed with chromatography and PAA causes various aberrations of the valve morphology. Growth of U. ferefusiformis and two other diatoms in the presence of tri- and tetracarbonic fluorescent tagged acids points to the ability of diatoms to recognize substances that bear four acidic groups and to include them into siliceous frustules. Thus, partial condensation of silicic acid is a plausible first stage of silicon assimilation.
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Affiliation(s)
- Vadim V Annenkov
- Limnological Institute of Siberian Branch of the Russian Academy of Sciences, 3, Ulan-Bator Str., Irkutsk, 664033, Russia
| | - Richard Gordon
- Gulf Specimen Marine Laboratory & Aquarium, 222 Clark Drive, Panacea, Florida, 32346, USA
- C.S. Mott Center for Human Growth &, Development Department of Obstetrics & Gynecology, Wayne State University, 275 E. Hancock, Detroit, Michigan, 48201, USA
| | - Stanislav N Zelinskiy
- Limnological Institute of Siberian Branch of the Russian Academy of Sciences, 3, Ulan-Bator Str., Irkutsk, 664033, Russia
| | - Elena N Danilovtseva
- Limnological Institute of Siberian Branch of the Russian Academy of Sciences, 3, Ulan-Bator Str., Irkutsk, 664033, Russia
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13
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Maldonado M, López-Acosta M, Beazley L, Kenchington E, Koutsouveli V, Riesgo A. Cooperation between passive and active silicon transporters clarifies the ecophysiology and evolution of biosilicification in sponges. SCIENCE ADVANCES 2020; 6:eaba9322. [PMID: 32832609 PMCID: PMC7439455 DOI: 10.1126/sciadv.aba9322] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/16/2020] [Accepted: 05/22/2020] [Indexed: 06/11/2023]
Abstract
The biological utilization of dissolved silicon (DSi) influences ocean ecology and biogeochemistry. In the deep sea, hexactinellid sponges are major DSi consumers that remain poorly understood. Their DSi consumption departs from the Michaelis-Menten kinetics of shallow-water demosponges and appears particularly maladapted to incorporating DSi from the modest concentrations typical of the modern ocean. Why did sponges not adapt to the shrinking DSi availability that followed diatom expansion some 100 to 65 million years ago? We propose that sponges incorporate DSi combining passive (aquaglyceroporins) and active (ArsB) transporters, while only active transporters (SITs) operate in diatoms and choanoflagellates. Evolution of greater silicon transport efficiency appears constrained by the additional role of aquaglyceroporins in transporting essential metalloids other than silicon. We discuss the possibility that lower energy costs may have driven replacement of ancestral SITs by less efficient aquaglyceroporins, and discuss the functional implications of conservation of aquaglyceroporin-mediated DSi utilization in vertebrates.
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Affiliation(s)
- M. Maldonado
- Department of Marine Ecology, Center for Advanced Studies of Blanes (CEAB-CSIC), Acceso Cala St. Francesc 14, Blanes 17300, Girona, Spain
| | - M. López-Acosta
- Department of Marine Ecology, Center for Advanced Studies of Blanes (CEAB-CSIC), Acceso Cala St. Francesc 14, Blanes 17300, Girona, Spain
| | - L. Beazley
- Department of Fisheries and Oceans, Bedford Institute of Oceanography, 1 Challenger Dr., Dartmouth, NS, Canada
| | - E. Kenchington
- Department of Fisheries and Oceans, Bedford Institute of Oceanography, 1 Challenger Dr., Dartmouth, NS, Canada
| | - V. Koutsouveli
- Department of Life Sciences, The Natural History Museum of London, Cromwell Road, SW7 5BD London, UK
| | - A. Riesgo
- Department of Life Sciences, The Natural History Museum of London, Cromwell Road, SW7 5BD London, UK
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14
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Thangaraj S, Giordano M, Sun J. Comparative Proteomic Analysis Reveals New Insights Into the Common and Specific Metabolic Regulation of the Diatom Skeletonema dohrnii to the Silicate and Temperature Availability. FRONTIERS IN PLANT SCIENCE 2020; 11:578915. [PMID: 33224167 PMCID: PMC7674209 DOI: 10.3389/fpls.2020.578915] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/01/2020] [Accepted: 09/28/2020] [Indexed: 05/12/2023]
Abstract
Silicate (Si) and temperature are essential drivers for diatom growth and development in the ocean. Response of diatoms to these particular stress has been investigated; however, their common and specific responses to regulate intracellular development and growth are not known. Here, we investigated the combination of physiological characteristics and comparative proteomics of the diatom Skeletonema dohrnii grown in silicate- and temperature-limited conditions. Results show that cell carbon and lipid quotas were higher at lower-temperature cells, whereas cellular phosphate was higher in cells grown with lower Si. In silicate-limited cells, nitrate transporters were downregulated and resulted in lower nitrate assimilation, whereas the phosphate transporters and its assimilation were reduced in lower-temperature conditions. In photosynthesis, lower silicate caused impact in the linear electron flow and NADPH production, whereas cycling electron transport and ATP production were affected by the lower temperature. Concerning cell cycle, imbalances in the translation process were observed in lower-silicate cells, whereas impact in the transcription mechanism was observed in lower-temperature cells. However, proteins associated with carbon fixation and photorespiration were downregulated in both stress conditions, while the carbohydrate and lipid synthesis proteins were upregulated. Our results showed new insights into the common and specific responses on the proteome and physiology of S. dohrnii to silicate and temperature limitation, providing particular nutrient (Si)- and temperature-dependent mechanisms in diatoms.
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Affiliation(s)
- Satheeswaran Thangaraj
- College of Marine Science and Technology, China University of Geosciences (Wuhan), Wuhan, China
| | - Mario Giordano
- Dipartimento di Scienze della Vita e dell’Ambiente, Università Politecnica delle Marche, Ancona, Italy
| | - Jun Sun
- College of Marine Science and Technology, China University of Geosciences (Wuhan), Wuhan, China
- *Correspondence: Jun Sun,
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15
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Johnson LK, Alexander H, Brown CT. Re-assembly, quality evaluation, and annotation of 678 microbial eukaryotic reference transcriptomes. Gigascience 2019; 8:5241890. [PMID: 30544207 PMCID: PMC6481552 DOI: 10.1093/gigascience/giy158] [Citation(s) in RCA: 47] [Impact Index Per Article: 9.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2018] [Revised: 09/18/2018] [Accepted: 11/29/2018] [Indexed: 12/18/2022] Open
Abstract
BACKGROUND De novo transcriptome assemblies are required prior to analyzing RNA sequencing data from a species without an existing reference genome or transcriptome. Despite the prevalence of transcriptomic studies, the effects of using different workflows, or "pipelines," on the resulting assemblies are poorly understood. Here, a pipeline was programmatically automated and used to assemble and annotate raw transcriptomic short-read data collected as part of the Marine Microbial Eukaryotic Transcriptome Sequencing Project. The resulting transcriptome assemblies were evaluated and compared against assemblies that were previously generated with a different pipeline developed by the National Center for Genome Research. RESULTS New transcriptome assemblies contained the majority of previous contigs as well as new content. On average, 7.8% of the annotated contigs in the new assemblies were novel gene names not found in the previous assemblies. Taxonomic trends were observed in the assembly metrics. Assemblies from the Dinoflagellata showed a higher number of contigs and unique k-mers than transcriptomes from other phyla, while assemblies from Ciliophora had a lower percentage of open reading frames compared to other phyla. CONCLUSIONS Given current bioinformatics approaches, there is no single "best" reference transcriptome for a particular set of raw data. As the optimum transcriptome is a moving target, improving (or not) with new tools and approaches, automated and programmable pipelines are invaluable for managing the computationally intensive tasks required for re-processing large sets of samples with revised pipelines and ensuring a common evaluation workflow is applied to all samples. Thus, re-assembling existing data with new tools using automated and programmable pipelines may yield more accurate identification of taxon-specific trends across samples in addition to novel and useful products for the community.
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Affiliation(s)
- Lisa K Johnson
- Department of Population Health, and Reproduction, School of Veterinary Medicine, University of California Davis, One Shields Ave, Davis, CA 95616, USA.,Molecular, Cellular, and Integrative Physiology Graduate Group, University of California Davis, One Shields Ave, Davis, CA 95616, USA
| | - Harriet Alexander
- Department of Population Health, and Reproduction, School of Veterinary Medicine, University of California Davis, One Shields Ave, Davis, CA 95616, USA.,Biology Department, Woods Hole Oceanographic Institution, Woods Hole, MA 02543, USA
| | - C Titus Brown
- Department of Population Health, and Reproduction, School of Veterinary Medicine, University of California Davis, One Shields Ave, Davis, CA 95616, USA.,Molecular, Cellular, and Integrative Physiology Graduate Group, University of California Davis, One Shields Ave, Davis, CA 95616, USA.,Genome Center, University of California Davis, 451 Health Sciences Dr, Davis, CA 95616, USA
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16
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Durak GM, Laumann M, Wolf SLP, Pawar A, Gebauer D, Böttcher T. Pseudo-Biomineralization: Complex Mineral Structures Shaped by Microbes. ACS Biomater Sci Eng 2019; 5:5088-5096. [DOI: 10.1021/acsbiomaterials.9b00387] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
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17
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Zhang Y, Lin X, Shi X, Lin L, Luo H, Li L, Lin S. Metatranscriptomic Signatures Associated With Phytoplankton Regime Shift From Diatom Dominance to a Dinoflagellate Bloom. Front Microbiol 2019; 10:590. [PMID: 30967855 PMCID: PMC6439486 DOI: 10.3389/fmicb.2019.00590] [Citation(s) in RCA: 38] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2018] [Accepted: 03/07/2019] [Indexed: 12/19/2022] Open
Abstract
Diatoms and dinoflagellates dominate coastal marine phytoplankton communities as major players of marine biogeochemical cycles and their seasonal succession often leads to harmful algal blooms (HABs). What regulates their respective dominances and the development of the HABs remains elusive. Here we conducted time-sequential metatranscriptomic profiling on a natural assemblage that evolved from diatom dominance to a dinoflagellate bloom to interrogate the underlying major metabolic and ecological drivers. Data reveals similarity between diatoms and dinoflagellates in exhibiting high capacities of energy production, nutrient acquisition, and stress protection in their respective dominance stages. The diatom-to-dinoflagellate succession coincided with an increase in turbidity and sharp declines in silicate and phosphate availability, concomitant with the transcriptomic shift from expression of silicate uptake and urea utilization genes in diatoms to that of genes for light harvesting, diversified phosphorus acquisition and autophagy-based internal nutrient recycling in dinoflagellates. Furthermore, the diatom-dominant community featured strong potential to carbohydrate metabolism and a strikingly high expression of trypsin potentially promoting frustule building. In contrast, the dinoflagellate bloom featured elevated expression of xanthorhodopsin, and antimicrobial defensin genes, indicating potential importance of energy harnessing and microbial defense in bloom development. This study sheds light on mechanisms potentially governing diatom- and dinoflagellate-dominance and regulating bloom development in the natural environment and raises new questions to be addressed in future studies.
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Affiliation(s)
- Yaqun Zhang
- State Key Laboratory of Marine Environmental Science, College of Ocean and Earth Sciences, Xiamen University, Xiamen, China
| | - Xin Lin
- State Key Laboratory of Marine Environmental Science, College of Ocean and Earth Sciences, Xiamen University, Xiamen, China
| | - Xinguo Shi
- State Key Laboratory of Marine Environmental Science, College of Ocean and Earth Sciences, Xiamen University, Xiamen, China.,College of Biological Science and Engineering, Fuzhou University, Fuzhou, China
| | - Lingxiao Lin
- State Key Laboratory of Marine Environmental Science, College of Ocean and Earth Sciences, Xiamen University, Xiamen, China
| | - Hao Luo
- State Key Laboratory of Marine Environmental Science, College of Ocean and Earth Sciences, Xiamen University, Xiamen, China
| | - Ling Li
- State Key Laboratory of Marine Environmental Science, College of Ocean and Earth Sciences, Xiamen University, Xiamen, China
| | - Senjie Lin
- State Key Laboratory of Marine Environmental Science, College of Ocean and Earth Sciences, Xiamen University, Xiamen, China.,Department of Marine Sciences, University of Connecticut, Groton, CT, United States
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18
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Götz W, Tobiasch E, Witzleben S, Schulze M. Effects of Silicon Compounds on Biomineralization, Osteogenesis, and Hard Tissue Formation. Pharmaceutics 2019; 11:E117. [PMID: 30871062 PMCID: PMC6471146 DOI: 10.3390/pharmaceutics11030117] [Citation(s) in RCA: 78] [Impact Index Per Article: 15.6] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2019] [Revised: 02/25/2019] [Accepted: 03/03/2019] [Indexed: 12/19/2022] Open
Abstract
Bioinspired stem cell-based hard tissue engineering includes numerous aspects: The synthesis and fabrication of appropriate scaffold materials, their analytical characterization, and guided osteogenesis using the sustained release of osteoinducing and/or osteoconducting drugs for mesenchymal stem cell differentiation, growth, and proliferation. Here, the effect of silicon- and silicate-containing materials on osteogenesis at the molecular level has been a particular focus within the last decade. This review summarizes recently published scientific results, including material developments and analysis, with a special focus on silicon hybrid bone composites. First, the sources, bioavailability, and functions of silicon on various tissues are discussed. The second focus is on the effects of calcium-silicate biomineralization and corresponding analytical methods in investigating osteogenesis and bone formation. Finally, recent developments in the manufacturing of Si-containing scaffolds are discussed, including in vitro and in vivo studies, as well as recently filed patents that focus on the influence of silicon on hard tissue formation.
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Affiliation(s)
- Werner Götz
- Department of Orthodontics, Oral Biology Laboratory, School of Dentistry, Rheinische Wilhelms University of Bonn, Welschnonnenstr. 17, D-53111 Bonn, Germany.
| | - Edda Tobiasch
- Department of Natural Sciences, Bonn-Rhine-Sieg University of Applied Sciences, D-53359 Rheinbach, Germany.
| | - Steffen Witzleben
- Department of Natural Sciences, Bonn-Rhine-Sieg University of Applied Sciences, D-53359 Rheinbach, Germany.
| | - Margit Schulze
- Department of Natural Sciences, Bonn-Rhine-Sieg University of Applied Sciences, D-53359 Rheinbach, Germany.
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19
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Marchenkov AM, Petrova DP, Morozov AA, Zakharova YR, Grachev MA, Bondar AA. A family of silicon transporter structural genes in a pennate diatom Synedra ulna subsp. danica (Kütz.) Skabitsch. PLoS One 2018; 13:e0203161. [PMID: 30157241 PMCID: PMC6114903 DOI: 10.1371/journal.pone.0203161] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2018] [Accepted: 08/15/2018] [Indexed: 11/19/2022] Open
Abstract
Silicon transporters (SIT) are the proteins, which capture silicic acid in the aquatic environment and direct it across the plasmalemma to the cytoplasm of diatoms. Diatoms utilize silicic acid to build species-specific ornamented exoskeletons and make a significant contribution to the global silica cycle, estimated at 240 ±40 Tmol a year. Recently SaSIT genes of the freshwater araphid pennate diatom Synedra acus subsp. radians are found to be present in the genome as a cluster of two structural genes (SaSIT-TD and SaSIT-TRI) encoding several concatenated copies of a SIT protein each. These structural genes could potentially be transformed into "mature" SIT proteins by means of posttranslational proteolytic cleavage. In the present study, we discovered three similar structural SuSIT genes in the genome of a closely related freshwater diatom Synedra ulna subsp. danica. Structural gene SuSIT1 is identical to structural gene SuSIT2, and the two are connected by a non-coding nucleotide DNA sequence. All the putative "mature" SITs contain conserved amino acid motifs, which are believed to be important in silicon transport. The data obtained suggest that the predicted "mature" SIT proteins may be the minimal units necessary for the transport of silicon is S. ulna subsp. danica. The comparative analysis of all available multi-SITs has allowed us to detect two conservative motifs YQXDXVYL and DXDID, located between the "mature" proteins. Aspartic acid-rich DXDID motif can, in our opinion, serve as a proteolysis site during the multi-SIT cleavage. The narrow distribution of the distances between CMLD and DXDID motifs can serve as additional evidence to the conservation of their function.
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Affiliation(s)
- Artyom M. Marchenkov
- Department of Cell Ultrastructure, Limnological Institute, Siberian Branch of the Russian Academy of Sciences, Irkutsk, Russia
| | - Darya P. Petrova
- Department of Cell Ultrastructure, Limnological Institute, Siberian Branch of the Russian Academy of Sciences, Irkutsk, Russia
| | - Alexey A. Morozov
- Department of Cell Ultrastructure, Limnological Institute, Siberian Branch of the Russian Academy of Sciences, Irkutsk, Russia
| | - Yulia R. Zakharova
- Department of Cell Ultrastructure, Limnological Institute, Siberian Branch of the Russian Academy of Sciences, Irkutsk, Russia
| | - Michael A. Grachev
- Department of Cell Ultrastructure, Limnological Institute, Siberian Branch of the Russian Academy of Sciences, Irkutsk, Russia
| | - Alexander A. Bondar
- Genomics Core Facility, Institute of Chemical Biology and Fundamental Medicine, Siberian Branch of the Russian Academy of Sciences, Novosibirsk, Russia
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20
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Ji N, Lin L, Li L, Yu L, Zhang Y, Luo H, Li M, Shi X, Wang DZ, Lin S. Metatranscriptome analysis reveals environmental and diel regulation of a Heterosigma akashiwo
(raphidophyceae) bloom. Environ Microbiol 2018; 20:1078-1094. [DOI: 10.1111/1462-2920.14045] [Citation(s) in RCA: 35] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2017] [Accepted: 01/09/2018] [Indexed: 11/29/2022]
Affiliation(s)
- Nanjing Ji
- State Key Laboratory of Marine Environmental Science and College of Ocean and Earth Sciences; Xiamen University; Xiamen Fujian 361102 China
- Department of Marine Sciences; University of Connecticut; Groton CT 06340 USA
| | - Lingxiao Lin
- State Key Laboratory of Marine Environmental Science and College of Ocean and Earth Sciences; Xiamen University; Xiamen Fujian 361102 China
| | - Ling Li
- State Key Laboratory of Marine Environmental Science and College of Ocean and Earth Sciences; Xiamen University; Xiamen Fujian 361102 China
| | - Liying Yu
- State Key Laboratory of Marine Environmental Science and College of Ocean and Earth Sciences; Xiamen University; Xiamen Fujian 361102 China
| | - Yaqun Zhang
- State Key Laboratory of Marine Environmental Science and College of Ocean and Earth Sciences; Xiamen University; Xiamen Fujian 361102 China
| | - Hao Luo
- State Key Laboratory of Marine Environmental Science and College of Ocean and Earth Sciences; Xiamen University; Xiamen Fujian 361102 China
| | - Meizhen Li
- State Key Laboratory of Marine Environmental Science and College of Ocean and Earth Sciences; Xiamen University; Xiamen Fujian 361102 China
| | - Xinguo Shi
- State Key Laboratory of Marine Environmental Science and College of Ocean and Earth Sciences; Xiamen University; Xiamen Fujian 361102 China
| | - Da-Zhi Wang
- State Key Laboratory of Marine Environmental Science and College of Ocean and Earth Sciences; Xiamen University; Xiamen Fujian 361102 China
| | - Senjie Lin
- State Key Laboratory of Marine Environmental Science and College of Ocean and Earth Sciences; Xiamen University; Xiamen Fujian 361102 China
- Department of Marine Sciences; University of Connecticut; Groton CT 06340 USA
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21
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De Tommasi E, Gielis J, Rogato A. Diatom Frustule Morphogenesis and Function: a Multidisciplinary Survey. Mar Genomics 2017; 35:1-18. [PMID: 28734733 DOI: 10.1016/j.margen.2017.07.001] [Citation(s) in RCA: 46] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2017] [Revised: 07/05/2017] [Accepted: 07/06/2017] [Indexed: 01/08/2023]
Abstract
Diatoms represent the major component of phytoplankton and are responsible for about 20-25% of global primary production. Hundreds of millions of years of evolution led to tens of thousands of species differing in dimensions and morphologies. In particular, diatom porous silica cell walls, the frustules, are characterized by an extraordinary, species-specific diversity. It is of great interest, among the marine biologists and geneticists community, to shed light on the origin and evolutionary advantage of this variability of dimensions, geometries and pore distributions. In the present article the main reported data related to frustule morphogenesis and functionalities with contributions from fundamental biology, genetics, mathematics, geometry and physics are reviewed.
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Affiliation(s)
- Edoardo De Tommasi
- Institute for Microelectronics and Microsystems, CNR, Via P. Castellino 111, 80131 Naples, Italy
| | - Johan Gielis
- University of Antwerp, Department of Bioscience Engineering, Groenenborgerlaan 171, 2020 Antwerp, Belgium
| | - Alessandra Rogato
- Institute of Biosciences and BioResources, CNR, Via P. Castellino 111, 80131 Naples, Italy; Stazione Zoologica Anton Dohrn, Department of Integrative Marine Ecology, Villa Comunale 1, 80121 Naples, Italy.
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22
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Brembu T, Chauton MS, Winge P, Bones AM, Vadstein O. Dynamic responses to silicon in Thalasiossira pseudonana - Identification, characterisation and classification of signature genes and their corresponding protein motifs. Sci Rep 2017; 7:4865. [PMID: 28687794 PMCID: PMC5501833 DOI: 10.1038/s41598-017-04921-0] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2017] [Accepted: 05/22/2017] [Indexed: 11/10/2022] Open
Abstract
The diatom cell wall, or frustule, is a highly complex, three-dimensional structure consisting of nanopatterned silica as well as proteins and other organic components. While some key components have been identified, knowledge on frustule biosynthesis is still fragmented. The model diatom Thalassiosira pseudonana was subjected to silicon (Si) shift-up and shift-down situations. Cellular and molecular signatures, dynamic changes and co-regulated clusters representing the hallmarks of cellular and molecular responses to changing Si availabilities were characterised. Ten new proteins with silaffin-like motifs, two kinases and a novel family of putatively frustule-associated transmembrane proteins induced by Si shift-up with a possible role in frustule biosynthesis were identified. A separate cluster analysis performed on all significantly regulated silaffin-like proteins (SFLPs), as well as silaffin-like motifs, resulted in the classification of silaffins, cingulins and SFLPs into distinct clusters. A majority of the genes in the Si-responsive clusters are highly divergent, but positive selection does not seem to be the driver behind this variability. This study provides a high-resolution map over transcriptional responses to changes in Si availability in T. pseudonana. Hallmark Si-responsive genes are identified, characteristic motifs and domains are classified, and taxonomic and evolutionary implications outlined and discussed.
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Affiliation(s)
- Tore Brembu
- NTNU Norwegian University of Science and Technology, Departments of Biology, N-7491, Trondheim, Norway.
| | | | - Per Winge
- NTNU Norwegian University of Science and Technology, Departments of Biology, N-7491, Trondheim, Norway
| | - Atle M Bones
- NTNU Norwegian University of Science and Technology, Departments of Biology, N-7491, Trondheim, Norway
| | - Olav Vadstein
- Biotechnology and Food Science, N-7491, Trondheim, Norway
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