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Abdul Rahman A, Mohd Isa IL, Tofail SAM, Bartlomiej L, Rodriguez BJ, Biggs MJ, Pandit A. Modification of Living Diatom, Thalassiosira weissflogii, with a Calcium Precursor through a Calcium Uptake Mechanism: A Next Generation Biomaterial for Advanced Delivery Systems. ACS APPLIED BIO MATERIALS 2024; 7:4102-4115. [PMID: 38758756 DOI: 10.1021/acsabm.4c00431] [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] [Indexed: 05/19/2024]
Abstract
The diatom's frustule, characterized by its rugged and porous exterior, exhibits a remarkable biomimetic morphology attributable to its highly ordered pores, extensive surface area, and unique architecture. Despite these advantages, the toxicity and nonbiodegradable nature of silica-based organisms pose a significant challenge when attempting to utilize these organisms as nanotopographically functionalized microparticles in the realm of biomedicine. In this study, we addressed this limitation by modulating the chemical composition of diatom microparticles by modulating the active silica metabolic uptake mechanism while maintaining their intricate three-dimensional architecture through calcium incorporation into living diatoms. Here, the diatom Thalassiosira weissflogii was chemically modified to replace its silica composition with a biodegradable calcium template, while simultaneously preserving the unique three-dimensional (3D) frustule structure with hierarchical patterns of pores and nanoscale architectural features, which was evident by the deposition of calcium as calcium carbonate. Calcium hydroxide is incorporated into the exoskeleton through the active mechanism of calcium uptake via a carbon-concentrating mechanism, without altering the microstructure. Our findings suggest that calcium-modified diatoms hold potential as a nature-inspired delivery system for immunotherapy through antibody-specific binding.
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Affiliation(s)
- Asrizal Abdul Rahman
- CÚRAM, SFI Research Centre for Medical Devices, University of Galway, Galway H91 W2TY, Ireland
| | - Isma Liza Mohd Isa
- CÚRAM, SFI Research Centre for Medical Devices, University of Galway, Galway H91 W2TY, Ireland
- Department of Anatomy, Faculty of Medicine, Universiti Kebangsaan Malaysia, 56000 Cheras, Kuala Lumpur, Malaysia
| | - Syed A M Tofail
- Materials and Surface Science Institute, University of Limerick, Limerick V94 T9PX, Ireland
| | - Lukasz Bartlomiej
- Conway Institute of Biomolecular and Biomedical Research and School of Physics, University College Dublin, Dublin 4, Ireland
| | - Brian J Rodriguez
- Conway Institute of Biomolecular and Biomedical Research and School of Physics, University College Dublin, Dublin 4, Ireland
| | - Manus J Biggs
- CÚRAM, SFI Research Centre for Medical Devices, University of Galway, Galway H91 W2TY, Ireland
| | - Abhay Pandit
- CÚRAM, SFI Research Centre for Medical Devices, University of Galway, Galway H91 W2TY, Ireland
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Frleta Matas R, Radman S, Čagalj M, Šimat V. Influence of Nutrient Deprivation on the Antioxidant Capacity and Chemical Profile of Two Diatoms from Genus Chaetoceros. Mar Drugs 2024; 22:96. [PMID: 38393067 PMCID: PMC10890447 DOI: 10.3390/md22020096] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2024] [Revised: 02/13/2024] [Accepted: 02/17/2024] [Indexed: 02/25/2024] Open
Abstract
The limited availability of phosphate, nitrogen and silicon in the growth media affects the growth, cellular processes, and metabolism of diatoms. Silicon deficiency primarily affects diatom morphology, while phosphate deficiency reduces the production of nucleic acids and phospholipids. Differences in pigment and protein composition are mainly due to nitrogen deficiency. In this study, Chaetoceros socialis and Chaetoceros costatus were cultured under phosphate, nitrogen, and silicon deprivation conditions. The diatom biomass was collected during the stationary growth phase and extracted with 70% ethanol under ultrasonication. The chemical profiles of the extracts were analyzed by high-performance liquid chromatography with high-resolution mass spectrometry with electrospray ionisation (UHPLC-ESI-HRMS), while the antioxidant capacity was determined by 2,2-diphenyl-1-picrylhydrazyl (DPPH) radical scavenging and oxygen radical absorbance capacity (ORAC) assays. Pigments, fatty acids, sterols, and derivatives were detected in both species. The total phenolic content in the extracts ranged from 46.25 ± 1.08 to 89.38 ± 6.21 mg of gallic acid equivalent (GAE)/L and from 29.58 ± 1.08 to 54.17 ± 1.18 mg GAE/L. for C. costatus and C. socialis, respectively. Antioxidant activity was higher in C. costatus extracts, especially those obtained from nitrogen-deprived media. The results of this study contribute to the existing knowledge and the ongoing efforts to overcome application and commercialization barriers of microalgae for wide-ranging potential in different industries.
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Affiliation(s)
- Roberta Frleta Matas
- Center of Excellence for Science and Technology-Integration of Mediterranean Region (STIM), Faculty of Science, University of Split, Rudera Boškovića 35, 21000 Split, Croatia;
| | - Sanja Radman
- Department of Food Technology and Biotechnology, Faculty of Chemistry and Technology, University of Split, Ruđera Boškovića 35, 21000 Split, Croatia
| | - Martina Čagalj
- University Department of Marine Studies, University of Split, Rudera Boškovića 37, 21000 Split, Croatia;
| | - Vida Šimat
- University Department of Marine Studies, University of Split, Rudera Boškovića 37, 21000 Split, Croatia;
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Brunson JK, Thukral M, Ryan JP, Anderson CR, Kolody BC, James C, Chavez FP, Leaw CP, Rabines AJ, Venepally P, Zheng H, Kudela RM, Smith GJ, Moore BS, Allen AE. Molecular Forecasting of Domoic Acid during a Pervasive Toxic Diatom Bloom. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.11.02.565333. [PMID: 37961417 PMCID: PMC10635071 DOI: 10.1101/2023.11.02.565333] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/15/2023]
Abstract
In 2015, the largest recorded harmful algal bloom (HAB) occurred in the Northeast Pacific, causing nearly 100 million dollars in damages to fisheries and killing many protected marine mammals. Dominated by the toxic diatom Pseudo-nitzschia australis , this bloom produced high levels of the neurotoxin domoic acid (DA). Through molecular and transcriptional characterization of 52 near-weekly phytoplankton net-tow samples collected at a bloom hotspot in Monterey Bay, California, we identified active transcription of known DA biosynthesis ( dab ) genes from the three identified toxigenic species, including P. australis as the primary origin of toxicity. Elevated expression of silicon transporters ( sit1 ) during the bloom supports the previously hypothesized role of dissolved silica (Si) exhaustion in contributing to bloom physiology and toxicity. We find that co-expression of the dabA and sit1 genes serves as a robust predictor of DA one week in advance, potentially enabling the forecasting of DA-producing HABs. We additionally present evidence that low levels of iron could have co-limited the diatom population along with low Si. Iron limitation represents a previously unrecognized driver of both toxin production and ecological success of the low iron adapted Pseudo-nitzschia genus during the 2015 bloom, and increasing pervasiveness of iron limitation may fuel the escalating magnitude and frequency of toxic Pseudo-nitzschia blooms globally. Our results advance understanding of bloom physiology underlying toxin production, bloom prediction, and the impact of global change on toxic blooms. Significance Pseudo-nitzschia diatoms form oceanic harmful algal blooms that threaten human health through production of the neurotoxin domoic acid (DA). DA biosynthetic gene expression is hypothesized to control DA production in the environment, yet what regulates expression of these genes is yet to be discovered. In this study, we uncovered expression of DA biosynthesis genes by multiple toxigenic Pseudo-nitzschia species during an economically impactful bloom along the North American West Coast, and identified genes that predict DA in advance of its production. We discovered that iron and silica co-limitation restrained the bloom and likely promoted toxin production. This work suggests that increasing iron limitation due to global change may play a previously unrecognized role in driving bloom frequency and toxicity.
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Poulsen N, Kröger N. Thalassiosira pseudonana (Cyclotella nana) (Hustedt) Hasle et Heimdal (Bacillariophyceae): A genetically tractable model organism for studying diatom biology, including biological silica formation. JOURNAL OF PHYCOLOGY 2023; 59:809-817. [PMID: 37424141 DOI: 10.1111/jpy.13362] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/14/2023] [Accepted: 06/15/2023] [Indexed: 07/11/2023]
Abstract
In 2004, Thalassiosira pseudonana was the first eukaryotic marine alga to have its genome sequenced. Since then, this species has quickly emerged as a valuable model species for investigating the molecular underpinnings of essentially all aspects of diatom life, particularly bio-morphogenesis of the cell wall. An important prerequisite for the model status of T. pseudonana is the ongoing development of increasingly precise tools to study the function of gene networks and their encoded proteins in vivo. Here, we briefly review the current toolbox for genetic manipulation, highlight specific examples of its application in studying diatom metabolism, and provide a peek into the role of diatoms in the emerging field of silica biotechnology.
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Affiliation(s)
- Nicole Poulsen
- B CUBE - Center for Molecular Bioengineering, Technische Universität Dresden, Dresden, Germany
| | - Nils Kröger
- B CUBE - Center for Molecular Bioengineering, Technische Universität Dresden, Dresden, Germany
- Cluster of Excellence Physics of Life, Technische Universität Dresden, Dresden, Germany
- Faculty of Chemistry and Food Chemistry, Technische Universität Dresden, Dresden, Germany
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Wang L, Sun Y, Zhang R, Pan K, Li Y, Wang R, Zhang L, Zhou C, Li J, Li Y, Zhu B, Han J. Enhancement of hemostatic properties of Cyclotella cryptica frustule through genetic manipulation. BIOTECHNOLOGY FOR BIOFUELS AND BIOPRODUCTS 2023; 16:136. [PMID: 37710352 PMCID: PMC10503012 DOI: 10.1186/s13068-023-02389-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/15/2023] [Accepted: 09/01/2023] [Indexed: 09/16/2023]
Abstract
BACKGROUND The silicified cell wall of diatoms, also known as frustule, shows huge potential as an outstanding bio-nanomaterial for hemostatic applications due to its high hemostatic efficiency, good biocompatibility, and ready availability. As the architectural features of the frustule determine its hemostatic performance, it is of great interest to develop an effective method to modify the frustule morphology into desired patterns to further improve hemostatic efficiency. RESULTS In this study, the gene encoding Silicalemma Associated Protein 2 (a silicalemma-spanning protein) of Cyclotella cryptica (CcSAP2) was identified as a key gene in frustule morphogenesis. Thus, it was overexpressed and knocked down, respectively. The frustule of the overexpress lines showed no obvious alteration in morphology compared to the wild type (WT), while the size, specific surface area (BET), pore volume, and pore diameter of the knockdown strains changed greatly. Particularly, the knockdown frustules achieved a more pronounced coagulation effect and in vivo hemostatic performance than the WT strains. Such observations suggested that silicalemma proteins are ideal genetic encoding targets for manipulating frustule morphology associated hemostatic properties. Furthermore, the Mantel test was adopted to identify the key morphologies associated with C. cryptica bleeding control. Finally, based on our results and recent advances, the mechanism of frustule morphogenesis was discussed. CONCLUSION This study explores a new strategy for enhancing the hemostatic efficiency of the frustule based on genetic morphology modification and may provide insights into a better understanding of the frustule morphogenesis mechanism.
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Affiliation(s)
- Lulu Wang
- Key Laboratory of Mariculture, Ministry of Education, Ocean University of China, Qingdao, 266003, China
| | - Yan Sun
- College of Food and Pharmaceutical Sciences, Ningbo University, Ningbo, 315200, China
| | - Ruihao Zhang
- Key Laboratory of Mariculture, Ministry of Education, Ocean University of China, Qingdao, 266003, China
| | - Kehou Pan
- Key Laboratory of Mariculture, Ministry of Education, Ocean University of China, Qingdao, 266003, China
- Laoshan Laboratory, Qingdao, 266237, China
| | - Yuhang Li
- Department of Marine Organism Taxonomy and Phylogeny, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, 266071, China
| | - Ruibing Wang
- State Key Laboratory of Quality Research in Chinese Medicine, Institute of Chinese Medical Sciences, University of Macau, Macau, 999078, China
| | - Lin Zhang
- Key Laboratory of Applied Marine Biotechnology, School of Marine Sciences, Ningbo University, Ningbo, 315200, China
| | - Chengxu Zhou
- College of Food and Pharmaceutical Sciences, Ningbo University, Ningbo, 315200, China
| | - Jian Li
- School of Biological and Chemical Engineering, Panzhihua University, Panzhihua, 617000, China
| | - Yun Li
- Key Laboratory of Mariculture, Ministry of Education, Ocean University of China, Qingdao, 266003, China
| | - Baohua Zhu
- Key Laboratory of Mariculture, Ministry of Education, Ocean University of China, Qingdao, 266003, China
| | - Jichang Han
- College of Food and Pharmaceutical Sciences, Ningbo University, Ningbo, 315200, China.
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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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7
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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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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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The molecular basis for pore pattern morphogenesis in diatom silica. Proc Natl Acad Sci U S A 2022; 119:e2211549119. [PMID: 36459651 PMCID: PMC9894196 DOI: 10.1073/pnas.2211549119] [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: 12/04/2022] Open
Abstract
Biomineral-forming organisms produce inorganic materials with complex, genetically encoded morphologies that are unmatched by current synthetic chemistry. It is poorly understood which genes are involved in biomineral morphogenesis and how the encoded proteins guide this process. We addressed these questions using diatoms, which are paradigms for the self-assembly of hierarchically meso- and macroporous silica under mild reaction conditions. Proteomics analysis of the intracellular organelle for silica biosynthesis led to the identification of new biomineralization proteins. Three of these, coined dAnk1-3, contain a common protein-protein interaction domain (ankyrin repeats), indicating a role in coordinating assembly of the silica biomineralization machinery. Knocking out individual dank genes led to aberrations in silica biogenesis that are consistent with liquid-liquid phase separation as underlying mechanism for pore pattern morphogenesis. Our work provides an unprecedented path for the synthesis of tailored mesoporous silica materials using synthetic biology.
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10
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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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11
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Abstract
Biomass and lipid production by the marine centric diatom Thalassiosira pseudonana were characterized in media based on palm oil mill effluent (POME) as a source of key nutrients. The optimal medium comprised 20% by volume POME, 80 µM Na2SiO3, and 35 g NaCl L−1 in water at pH ~7.7. In 15-day batch cultures (16:8 h/h light–dark cycle; 200 µmol photons m−2 s−1, 26 ± 1 °C) bubbled continuously with air mixed with CO2 (2.5% by vol), the peak concentration of dry biomass was 869 ± 14 mg L−1 corresponding to a productivity of ~58 mg L−1 day−1. The neutral lipid content of the biomass was 46.2 ± 1.1% by dry weight. The main components of the esterified lipids were palmitoleic acid methyl ester (31.6% w/w) and myristic acid methyl ester (16.8% w/w). The final biomass concentration and the lipid content were affected by the light–dark cycle. Continuous (24 h light) illumination at the above-specified irradiance reduced biomass productivity to ~54 mg L−1 day−1 and lipid content to 38.1%.
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12
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Gal A. Dense intracellular ion pools in unicellular organisms. J Struct Biol 2021; 213:107807. [PMID: 34740781 DOI: 10.1016/j.jsb.2021.107807] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2021] [Revised: 10/28/2021] [Accepted: 10/30/2021] [Indexed: 10/19/2022]
Abstract
Uptake and concentration of inorganic ions are part of the complex cellular processes required for cell homeostasis, as well as for mineral formation by organisms. These ion transport mechanisms include distinct cellular compartments and chemical phases that play various roles in the physiology of organisms. Here, the prominent cases of dense ion pools in unicellular organisms are briefly reviewed. The specific observations that were reported for different organisms are consolidated into a wide perspective that emphasizes general traits. It is suggested that the intracellular ion pools can be divided into three types: a high cytoplasmic concentration, a labile storage compartment that hosts dense ion-rich phases, and a mineral-forming compartment in which a stable long-lived structure is formed. Recently, many labile pools were identified in various organisms using advanced techniques, bringing many new questions about their possible roles in the formation of the stable mineralized structures.
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Affiliation(s)
- Assaf Gal
- Department of Plant and Environmental Sciences, Weizmann Institute of Science, Rehovot, Israel.
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13
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Coskun D, Deshmukh R, Shivaraj SM, Isenring P, Bélanger RR. Lsi2: A black box in plant silicon transport. PLANT AND SOIL 2021; 466:1-20. [PMID: 34720209 PMCID: PMC8550040 DOI: 10.1007/s11104-021-05061-1] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/13/2021] [Accepted: 06/22/2021] [Indexed: 05/12/2023]
Abstract
BACKGROUND Silicon (Si) is widely considered a non-essential but beneficial element for higher plants, providing broad protection against various environmental stresses (both biotic and abiotic), particularly in species that can readily absorb the element. Two plasma-membrane proteins are known to coordinate the radial transport of Si (in the form of Si(OH)4) from soil to xylem within roots: the influx channel Lsi1 and the efflux transporter Lsi2. From a structural and mechanistic perspective, much more is known about Lsi1 (a member of the NIP-III subgroup of the Major Intrinsic Proteins) compared to Lsi2 (a putative Si(OH)4/H+ antiporter, with some homology to bacterial anion transporters). SCOPE Here, we critically review the current state of understanding regarding the physiological role and molecular characteristics of Lsi2. We demonstrate that the structure-function relationship of Lsi2 is largely uncharted and that the standing transport model requires much better supportive evidence. We also provide (to our knowledge) the most current and extensive phylogenetic analysis of Lsi2 from all fully sequenced higher-plant genomes. We end by suggesting research directions and hypotheses to elucidate the properties of Lsi2. CONCLUSIONS Given that Lsi2 is proposed to mediate xylem Si loading and thus root-to-shoot translocation and biosilicification, it is imperative that the field of Si transport focus its efforts on a better understanding of this important topic. With this review, we aim to stimulate and advance research in the field of Si transport and thus better exploit Si to improve crop resilience and agricultural output. SUPPLEMENTARY INFORMATION The online version contains supplementary material available at 10.1007/s11104-021-05061-1.
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Affiliation(s)
- Devrim Coskun
- Département de Phytologie, Faculté Des Sciences de L’Agriculture Et de L’Alimentation (FSAA), Université Laval, Québec, Québec Canada
| | - Rupesh Deshmukh
- National Agri-Food Biotechnology Institute (NABI), Mohali, India
| | - S. M. Shivaraj
- National Agri-Food Biotechnology Institute (NABI), Mohali, India
- CSIR-National Chemical Laboratory, Pune, India
| | - Paul Isenring
- Département de Médecine, Faculté de Médecine, Université Laval, Québec, Québec Canada
| | - Richard R. Bélanger
- Département de Phytologie, Faculté Des Sciences de L’Agriculture Et de L’Alimentation (FSAA), Université Laval, Québec, Québec Canada
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14
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Thamatrakoln K. Diatom Ecophysiology: Crossing Signals on the Road to Recovery from Nutrient Deprivation. Curr Biol 2021; 31:R253-R254. [PMID: 33689725 DOI: 10.1016/j.cub.2021.01.016] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022]
Abstract
A new study reveals that phosphorus-limited diatoms employ a rapid calcium-based signaling pathway upon phosphorus resupply. This response leads to enhanced nitrogen uptake and assimilation, setting the stage for recovery from nutrient deprivation.
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Affiliation(s)
- Kimberlee Thamatrakoln
- Department of Marine and Coastal Sciences, Rutgers, The State University of New Jersey, New Brunswick, NJ 08901, USA.
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15
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Physical, Chemical, and Genetic Techniques for Diatom Frustule Modification: Applications in Nanotechnology. APPLIED SCIENCES-BASEL 2020. [DOI: 10.3390/app10238738] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
Diatom frustules represent one of the most complex examples of micro- and nano-structured materials found in nature, being the result of a biomineralization process refined through tens of milions of years of evolution. They are constituted by an intricate, ordered porous silica matrix which recently found several applications in optoelectronics, sensing, solar light harvesting, filtering, and drug delivery, to name a few. The possibility to modify the composition and the structure of frustules can further broaden the range of potential applications, adding new functions and active features to the material. In the present work the most remarkable physical and chemical techniques aimed at frustule modification are reviewed, also examining the most recent genetic techniques developed for its controlled morphological mutation.
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16
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Saxena A, Prakash K, Phogat S, Singh PK, Tiwari A. Inductively coupled plasma nanosilica based growth method for enhanced biomass production in marine diatom algae. BIORESOURCE TECHNOLOGY 2020; 314:123747. [PMID: 32629376 DOI: 10.1016/j.biortech.2020.123747] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/07/2020] [Revised: 06/22/2020] [Accepted: 06/23/2020] [Indexed: 06/11/2023]
Abstract
This work reports a novel solution-based method to trigger the growth of diatoms for enhanced biomass production, which can efficiently stimulate their applications in nutraceuticals, aquaculture and wastewater remediation. The optimization for the growth of three marine diatoms species was performed using inductively coupled plasma (ICP) synthesized nanosilica which can be a cost-effective and productive method for biomass production. The exponential growth phase was achieved in 14 days with high biomass productivity compared to F/2-Si Media [Chaetoceros sp. (125 ± 3 & 750 ± 3 mgL-1day-1); Skeletonema sp., (185.3 ± 2.63 & 562.5 ± 3.96 mgL-1day-1) and Thalassiosira sp. (312.5 ± 2.51 & 433.5 ± 1.80 mgL-1day-1)] along with a sharp rise of 50-100 fold increment in pigmentation. This work opens up an avenue with novel insights to trigger the growth of diatoms on large scale leading to their better exploitation towards biotechnological applications.
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Affiliation(s)
- Abhishek Saxena
- Diatom Research Laboratory, Amity Institute of Biotechnology, Amity University, Noida, Uttar Pradesh 201 313, India
| | - Kunal Prakash
- Department of Chemistry, Kirori Mal College, University of Delhi, Delhi 110007, India
| | - Sakshi Phogat
- Diatom Research Laboratory, Amity Institute of Biotechnology, Amity University, Noida, Uttar Pradesh 201 313, India
| | - Pankaj Kumar Singh
- Diatom Research Laboratory, Amity Institute of Biotechnology, Amity University, Noida, Uttar Pradesh 201 313, India
| | - Archana Tiwari
- Diatom Research Laboratory, Amity Institute of Biotechnology, Amity University, Noida, Uttar Pradesh 201 313, India.
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17
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Kumar S, Rechav K, Kaplan-Ashiri I, Gal A. Imaging and quantifying homeostatic levels of intracellular silicon in diatoms. SCIENCE ADVANCES 2020; 6:6/42/eaaz7554. [PMID: 33067244 PMCID: PMC7567585 DOI: 10.1126/sciadv.aaz7554] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/17/2019] [Accepted: 08/28/2020] [Indexed: 05/21/2023]
Abstract
Diatoms are an abundant group of microalgae, known for their ability to form an intricate cell wall made of silica. Silicon levels in seawater are in the micromolar range, making it a challenge for diatoms to supply the rapid intracellular silicification process with the needed flux of soluble silicon. Here, we use three-dimensional cryo-electron microscopy and spectroscopy to quantitatively analyze, at submicrometer spatial resolution and sensitivity in the millimolar range, intracellular silicon in diatom cells. Our results show that the internal silicon concentration inside the cell is ~150 mM in average, three orders of magnitude higher than the external environment. The cellular silicon content is not compartmentalized, but rather unevenly distributed throughout the cell. Unexpectedly, under silicon starvation, the internal silicon pool is not depleted, reminiscent of a constitutive metabolite. Our spatially resolved approach to analyze intracellular silicon opens avenues to investigate this homeostatic trait of diatoms.
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Affiliation(s)
- Santosh Kumar
- Department of Plant and Environmental Sciences, Weizmann Institute of Science, Rehovot, Israel
| | - Katya Rechav
- Department of Chemical Research Support, Weizmann Institute of Science, Rehovot, Israel
| | - Ifat Kaplan-Ashiri
- Department of Chemical Research Support, Weizmann Institute of Science, Rehovot, Israel
| | - Assaf Gal
- Department of Plant and Environmental Sciences, Weizmann Institute of Science, Rehovot, Israel.
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18
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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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19
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Falciatore A, Jaubert M, Bouly JP, Bailleul B, Mock T. Diatom Molecular Research Comes of Age: Model Species for Studying Phytoplankton Biology and Diversity. THE PLANT CELL 2020; 32:547-572. [PMID: 31852772 PMCID: PMC7054031 DOI: 10.1105/tpc.19.00158] [Citation(s) in RCA: 56] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/12/2019] [Revised: 10/18/2019] [Accepted: 12/13/2019] [Indexed: 05/08/2023]
Abstract
Diatoms are the world's most diverse group of algae, comprising at least 100,000 species. Contributing ∼20% of annual global carbon fixation, they underpin major aquatic food webs and drive global biogeochemical cycles. Over the past two decades, Thalassiosira pseudonana and Phaeodactylum tricornutum have become the most important model systems for diatom molecular research, ranging from cell biology to ecophysiology, due to their rapid growth rates, small genomes, and the cumulative wealth of associated genetic resources. To explore the evolutionary divergence of diatoms, additional model species are emerging, such as Fragilariopsis cylindrus and Pseudo-nitzschia multistriata Here, we describe how functional genomics and reverse genetics have contributed to our understanding of this important class of microalgae in the context of evolution, cell biology, and metabolic adaptations. Our review will also highlight promising areas of investigation into the diversity of these photosynthetic organisms, including the discovery of new molecular pathways governing the life of secondary plastid-bearing organisms in aquatic environments.
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Affiliation(s)
- Angela Falciatore
- Institut de Biologie Physico-Chimique, Laboratory of Chloroplast Biology and Light Sensing in Microalgae, UMR7141 Centre National de la Recherche Scientifique (CNRS), Sorbonne Université, 75005 Paris, France
- Institut de Biologie Paris-Seine, Laboratory of Computational and Quantitative Biology, UMR7238 Sorbonne Université, 75005 Paris, France
| | - Marianne Jaubert
- Institut de Biologie Physico-Chimique, Laboratory of Chloroplast Biology and Light Sensing in Microalgae, UMR7141 Centre National de la Recherche Scientifique (CNRS), Sorbonne Université, 75005 Paris, France
- Institut de Biologie Paris-Seine, Laboratory of Computational and Quantitative Biology, UMR7238 Sorbonne Université, 75005 Paris, France
| | - Jean-Pierre Bouly
- Institut de Biologie Physico-Chimique, Laboratory of Chloroplast Biology and Light Sensing in Microalgae, UMR7141 Centre National de la Recherche Scientifique (CNRS), Sorbonne Université, 75005 Paris, France
- Institut de Biologie Paris-Seine, Laboratory of Computational and Quantitative Biology, UMR7238 Sorbonne Université, 75005 Paris, France
| | - Benjamin Bailleul
- Institut de Biologie Physico-Chimique, Laboratory of Chloroplast Biology and Light Sensing in Microalgae, UMR7141 Centre National de la Recherche Scientifique (CNRS), Sorbonne Université, 75005 Paris, France
| | - Thomas Mock
- School of Environmental Sciences, University of East Anglia, Norwich Research Park, Norwich NR4 7TJ, United Kingdom
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20
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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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21
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Di Dato V, Di Costanzo F, Barbarinaldi R, Perna A, Ianora A, Romano G. Unveiling the presence of biosynthetic pathways for bioactive compounds in the Thalassiosira rotula transcriptome. Sci Rep 2019; 9:9893. [PMID: 31289324 PMCID: PMC6616357 DOI: 10.1038/s41598-019-46276-8] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2018] [Accepted: 06/26/2019] [Indexed: 12/02/2022] Open
Abstract
Diatoms are phytoplankton eukaryotic microalgae that are widely distributed in the world’s oceans and are responsible for 20–25% of total carbon fixation on the planet. Using transcriptome sequencing here we show for the first time that the ubiquitous diatom Thalassiosira rotula expresses biosynthetic pathways that potentially lead to the synthesis of interesting secondary metabolites with pharmaceutical applications such as polyketides, prostaglandins and secologanin. We also show that these pathways are differentially expressed in conditions of silica depletion in comparison with standard growth conditions.
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Affiliation(s)
- Valeria Di Dato
- Stazione Zoologica Anton Dohrn Napoli, Department of Marine Biotechnology, Villa Comunale, 80121, Napoli, Italy.
| | - Federica Di Costanzo
- Stazione Zoologica Anton Dohrn Napoli, Department of Marine Biotechnology, Villa Comunale, 80121, Napoli, Italy
| | - Roberta Barbarinaldi
- Stazione Zoologica Anton Dohrn Napoli, Department of Marine Biotechnology, Villa Comunale, 80121, Napoli, Italy
| | - Anna Perna
- Stazione Zoologica Anton Dohrn Napoli, Department of Marine Biotechnology, Villa Comunale, 80121, Napoli, Italy
| | - Adrianna Ianora
- Stazione Zoologica Anton Dohrn Napoli, Department of Marine Biotechnology, Villa Comunale, 80121, Napoli, Italy
| | - Giovanna Romano
- Stazione Zoologica Anton Dohrn Napoli, Department of Marine Biotechnology, Villa Comunale, 80121, Napoli, Italy
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22
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Orefice I, Musella M, Smerilli A, Sansone C, Chandrasekaran R, Corato F, Brunet C. Role of nutrient concentrations and water movement on diatom's productivity in culture. Sci Rep 2019; 9:1479. [PMID: 30728371 PMCID: PMC6365584 DOI: 10.1038/s41598-018-37611-6] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2018] [Accepted: 12/10/2018] [Indexed: 02/06/2023] Open
Abstract
Microalgal growth maximization is becoming a duty for enhancing the biotechnological fate of these photosynthetic microorganisms. This study, based on an extensive set of data, aims to revisit diatom’s cultivation in laboratory with the objective to increase growth rate and biomass production. We investigated the growth ability and resource requirements of the coastal diatom Skeletonema marinoi Sarno & Zingone grown in laboratory in the conventional f/2 medium with aeration and in two modified conditions: (i) the same medium with water movement inside and (ii) an enriched medium with the same water movement. Results revealed that, by doubling the concentration of phosphate, silicate, microelements and vitamins, growth rate was successfully enhanced, preventing phosphate or silicate limitation in the f/2 culture medium. Yet, irrespective of the media (f/2 or enriched one), water movement induced an increase of growth efficiency compared to aeration, affecting nutrients’ requirement and consumption by diatoms. This study is an important step for enhancing diatom biomass production, reducing its cost, as required in the blue biotechnology context.
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Affiliation(s)
- Ida Orefice
- Stazione Zoologica Anton Dohrn, Istituto Nazionale di Biologia, Ecologia e Biotecnologie Marine, Villa comunale, 80121, Napoli, Italy
| | - Margherita Musella
- Stazione Zoologica Anton Dohrn, Istituto Nazionale di Biologia, Ecologia e Biotecnologie Marine, Villa comunale, 80121, Napoli, Italy
| | - Arianna Smerilli
- Stazione Zoologica Anton Dohrn, Istituto Nazionale di Biologia, Ecologia e Biotecnologie Marine, Villa comunale, 80121, Napoli, Italy
| | - Clementina Sansone
- Stazione Zoologica Anton Dohrn, Istituto Nazionale di Biologia, Ecologia e Biotecnologie Marine, Villa comunale, 80121, Napoli, Italy
| | - Raghu Chandrasekaran
- Stazione Zoologica Anton Dohrn, Istituto Nazionale di Biologia, Ecologia e Biotecnologie Marine, Villa comunale, 80121, Napoli, Italy.,CAS in Marine Biology, Faculty of Marine Sciences, Annamalai University, Parangipettai, 608502, Tamil Nadu, India
| | - Federico Corato
- Stazione Zoologica Anton Dohrn, Istituto Nazionale di Biologia, Ecologia e Biotecnologie Marine, Villa comunale, 80121, Napoli, Italy
| | - Christophe Brunet
- Stazione Zoologica Anton Dohrn, Istituto Nazionale di Biologia, Ecologia e Biotecnologie Marine, Villa comunale, 80121, Napoli, Italy.
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23
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Chen XH, Li YY, Zhang H, Liu JL, Xie ZX, Lin L, Wang DZ. Quantitative Proteomics Reveals Common and Specific Responses of a Marine Diatom Thalassiosira pseudonana to Different Macronutrient Deficiencies. Front Microbiol 2018; 9:2761. [PMID: 30487787 PMCID: PMC6246746 DOI: 10.3389/fmicb.2018.02761] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2018] [Accepted: 10/29/2018] [Indexed: 11/13/2022] Open
Abstract
Macronutrients such as nitrogen (N), phosphorus (P), and silicon (Si) are essential for the productivity and distribution of diatoms in the ocean. Responses of diatoms to a particular macronutrient deficiency have been investigated, however, we know little about their common or specific responses to different macronutrients. Here, we investigated the physiology and quantitative proteomics of a diatom Thalassiosira pseudonana grown in nutrient-replete, N-, P-, and Si-deficient conditions. Cell growth was ceased in all macronutrient deficient conditions while cell volume and cellular C content under P- and Si-deficiencies increased. Contents of chlorophyll a, protein and cellular N decreased in both N- and P-deficient cells but chlorophyll a and cellular N increased in the Si-deficient cells. Cellular P content increased under N- and Si-deficiencies. Proteins involved in carbon fixation and photorespiration were down-regulated under all macronutrient deficiencies while neutral lipid synthesis and carbohydrate accumulation were enhanced. Photosynthesis, chlorophyll biosynthesis, and protein biosynthesis were down-regulated in both N- and P-deficient cells, while Si transporters, light-harvesting complex proteins, chloroplastic ATP synthase, plastid transcription and protein synthesis were up-regulated in the Si-deficient cells. Our results provided insights into the common and specific responses of T. pseudonana to different macronutrient deficiencies and identified specific proteins potentially indicating a particular macronutrient deficiency.
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Affiliation(s)
- Xiao-Huang Chen
- State Key Laboratory of Marine Environmental Science, College of the Environment and Ecology, Xiamen University, Xiamen, China
| | - Yuan-Yuan Li
- State Key Laboratory of Marine Environmental Science, College of the Environment and Ecology, Xiamen University, Xiamen, China
| | - Hao Zhang
- State Key Laboratory of Marine Environmental Science, College of the Environment and Ecology, Xiamen University, Xiamen, China
| | - Jiu-Ling Liu
- State Key Laboratory of Marine Environmental Science, College of the Environment and Ecology, Xiamen University, Xiamen, China
| | - Zhang-Xian Xie
- State Key Laboratory of Marine Environmental Science, College of the Environment and Ecology, Xiamen University, Xiamen, China
| | - Lin Lin
- State Key Laboratory of Marine Environmental Science, College of the Environment and Ecology, Xiamen University, Xiamen, China
| | - Da-Zhi Wang
- State Key Laboratory of Marine Environmental Science, College of the Environment and Ecology, Xiamen University, Xiamen, China.,Key Laboratory of Marine Ecology and Environmental Sciences, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, China
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24
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Ikehata K, Zhao Y, Kulkarni HV, Li Y, Snyder SA, Ishida KP, Anderson MA. Water Recovery from Advanced Water Purification Facility Reverse Osmosis Concentrate by Photobiological Treatment Followed by Secondary Reverse Osmosis. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2018; 52:8588-8595. [PMID: 29916696 DOI: 10.1021/acs.est.8b00951] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/21/2023]
Abstract
Reverse osmosis (RO)-based desalination and advanced water purification facilities have inherent challenges associated with concentrate management and disposal. Although enhanced permeate recovery and concentrate minimization are desired, membrane scaling due to inorganic constituents, such as silica, calcium, phosphate, and iron, hinders the process. To solve this problem, a new diatom-based photobiological process has been developed to remove these scaling constituents by biological uptake and precipitation. In this study, RO concentrate samples were collected from a full-scale advanced water reclamation facility in California and were treated in 3.8 and 57 L photobioreactors inoculated with a brackish water diatom Pseudostaurosira trainorii PEWL001 using light-emitting diode bulbs or natural sunlight as a light source. The photobiological treatment removed 95% of reactive silica and 64% of calcium and enabled additional water recovery using a secondary RO at a recovery rate up to 66%. This represents 95% overall recovery, including 85% recovery in the primary RO unit. In addition to the scaling constituents, the photobiological treatment removed 12 pharmaceuticals and personal care products, as well as N-nitrosodimethylamine, from RO concentrate samples primarily via photolysis. This novel approach has a strong potential for application to brackish water desalination and advanced water purification in arid and semiarid areas.
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Affiliation(s)
- Keisuke Ikehata
- Pacific Advanced Civil Engineering, Inc. , Fountain Valley , California 92708 , United States
| | - Yuanyuan Zhao
- Pacific Advanced Civil Engineering, Inc. , Fountain Valley , California 92708 , United States
| | - Harshad V Kulkarni
- Pacific Advanced Civil Engineering, Inc. , Fountain Valley , California 92708 , United States
| | - Yuan Li
- Pacific Advanced Civil Engineering, Inc. , Fountain Valley , California 92708 , United States
| | - Shane A Snyder
- Department of Chemical and Environmental Engineering , University of Arizona , Tucson , Arizona 85721 , United States
| | - Kenneth P Ishida
- Orange County Water District , Fountain Valley , California 92708 , United States
| | - Michael A Anderson
- Department of Environmental Sciences , University of California , Riverside , California 92521 , United States
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25
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Abbriano R, Vardar N, Yee D, Hildebrand M. Manipulation of a glycolytic regulator alters growth and carbon partitioning in the marine diatom Thalassiosira pseudonana. ALGAL RES 2018. [DOI: 10.1016/j.algal.2018.03.018] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/17/2022]
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26
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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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27
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Olmez T, Yuca E, Eyupoglu E, Catalak HB, Sahin O, Seker UOS. Autonomous Synthesis of Fluorescent Silica Biodots Using Engineered Fusion Proteins. ACS OMEGA 2018; 3:585-594. [PMID: 30023783 PMCID: PMC6044564 DOI: 10.1021/acsomega.7b01769] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/10/2017] [Accepted: 01/03/2018] [Indexed: 06/08/2023]
Abstract
Formation of biological materials is a well-controlled process that is orchestrated by biomolecules such as proteins. Proteins can control the nucleation and mineralization of biomaterials, thereby forming the hard tissues of biological organisms, such as bones, teeth, and shells. In this study, the design and implementation of multifunctional designer proteins are demonstrated for fluorescent silica micro/nanoparticle synthesis. The R5 motif of silaffin polypeptide, which is known for its silicification capability, was fused genetically into three spectrally distinct fluorescent proteins with the intention of forming modified fluorescent proteins. The bifunctional R5 peptide domain served as a tag to provide silica synthesis at ambient conditions. Three functional fusion constructs have been prepared, including GFPmut3-R5, Venus YFP-R5, and mCherry-R5. Recombinant fluorescent proteins were purified using silica-binding peptide tag through silica gel resin. Purified proteins were tested for their binding affinity to silica using quartz crystal microbalance with dissipation monitoring to make sure they can interact strong enough with the silica surfaces. Later, engineered fluorescent proteins were used to synthesize silica nano/microparticles using silica precursor materials. Synthesized silica particles were investigated for their fluorescence properties, including time-resolved fluorescence. Additionally, elemental analysis of the particles was carried out using electron energy loss spectroscopy and energy-filtered transmission electron microscopy. Last, they were tested for their biocompatibility. In this study, we aimed to provide a biomimetic route to synthesize fluorescent silica nanoparticles. Recombinant fluorescent proteins-directed silica nanoparticles synthesis offers a one-step, reliable method to produce fluorescent particles both for biomaterial applications and other nanotechnology applications.
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Affiliation(s)
- Tolga
T. Olmez
- UNAM-National
Nanotechnology Research Center,
Institute of Materials Science and Nanotechnology, and Department of
Molecular Biology and Genetics, Faculty of Science, Bilkent University, Ankara 06800, Turkey
| | - Esra Yuca
- UNAM-National
Nanotechnology Research Center,
Institute of Materials Science and Nanotechnology, and Department of
Molecular Biology and Genetics, Faculty of Science, Bilkent University, Ankara 06800, Turkey
- Department
of Molecular Biology and Genetics, Faculty of Arts and Science, Yildiz Technical University, Istanbul 34210, Turkey
| | - Erol Eyupoglu
- UNAM-National
Nanotechnology Research Center,
Institute of Materials Science and Nanotechnology, and Department of
Molecular Biology and Genetics, Faculty of Science, Bilkent University, Ankara 06800, Turkey
| | - Hazal B. Catalak
- UNAM-National
Nanotechnology Research Center,
Institute of Materials Science and Nanotechnology, and Department of
Molecular Biology and Genetics, Faculty of Science, Bilkent University, Ankara 06800, Turkey
| | - Ozgur Sahin
- UNAM-National
Nanotechnology Research Center,
Institute of Materials Science and Nanotechnology, and Department of
Molecular Biology and Genetics, Faculty of Science, Bilkent University, Ankara 06800, Turkey
| | - Urartu Ozgur Safak Seker
- UNAM-National
Nanotechnology Research Center,
Institute of Materials Science and Nanotechnology, and Department of
Molecular Biology and Genetics, Faculty of Science, Bilkent University, Ankara 06800, Turkey
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28
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Casabianca S, Penna A, Capellacci S, Cangiotti M, Ottaviani MF. Silicification process in diatom algae using different silicon chemical sources: Colloidal silicic acid interactions at cell surface. Colloids Surf B Biointerfaces 2018; 161:620-627. [DOI: 10.1016/j.colsurfb.2017.11.032] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2017] [Revised: 11/10/2017] [Accepted: 11/13/2017] [Indexed: 11/29/2022]
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29
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Steinrücken P, Mjøs SA, Prestegard SK, Erga SR. Enhancing EPA Content in an Arctic Diatom: A Factorial Design Study to Evaluate Interactive Effects of Growth Factors. FRONTIERS IN PLANT SCIENCE 2018; 9:491. [PMID: 29755487 PMCID: PMC5932356 DOI: 10.3389/fpls.2018.00491] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/24/2018] [Accepted: 04/03/2018] [Indexed: 05/20/2023]
Abstract
Microalgae with a high content of the omega-3 polyunsaturated fatty acids (PUFAs), eicosapentaenoic acid (EPA), and docosahexaenoic acid (DHA) are of great demand for microalgae-based technologies. An Arctic strain of the diatom Attheya septentrionalis was shown in previous experiments to increase its EPA content from 3.0 to 4.6% of dry weight (DW) in the nutrient-replete exponential phase and nutrient-depleted stationary phase, respectively. In the present study, a factorial-design experiment was used, to investigate this effect in more detail and in combination with varying salinities and irradiances. A mathematical model revealed that both growth phase and salinity, alone and in combination, influenced the EPA content significantly. Maximum EPA values of 7.1% DW were obtained at a salinity of 22 and after 5 days in stationary phase, and might be related to a decreased silica content, an accumulation of storage lipids containing EPA, or both. However, growth rates were lower for low salinity (0.54 and 0.57 d-1) than high salinity (0.77 and 0.98 d-1) cultures.
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Affiliation(s)
- Pia Steinrücken
- Department of Biological Sciences, University of Bergen, Bergen, Norway
- *Correspondence: Pia Steinrücken
| | - Svein A. Mjøs
- Department of Chemistry, University of Bergen, Bergen, Norway
| | | | - Svein R. Erga
- Department of Biological Sciences, University of Bergen, Bergen, Norway
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30
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Leung PTY, Yi AX, Ip JCH, Mak SST, Leung KMY. Photosynthetic and transcriptional responses of the marine diatom Thalassiosira pseudonana to the combined effect of temperature stress and copper exposure. MARINE POLLUTION BULLETIN 2017; 124:938-945. [PMID: 28365019 DOI: 10.1016/j.marpolbul.2017.03.038] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/27/2016] [Revised: 03/16/2017] [Accepted: 03/18/2017] [Indexed: 06/07/2023]
Abstract
A 96-h exposure experiment was conducted to elucidate the toxicity responses of the marine diatom Thalassiosira pseudonana upon exposure to different temperatures and copper (Cu) concentrations. Three Cu treatments (seawater control; 200μg/L Cu, EC50 for the yield at 25°C; and 1000μg/L Cu, EC50 for growth inhibition at 25°C) were conducted against four temperatures (10°C, 15°C, 25°C and 30°C). Growth rate and photosynthetic responses showed a significant interacting thermal-chemical effect with strong synergistic responses observed at 30°C treatments. Expression of heat shock protein (hsp) was positively modulated by increasing temperatures. Hsp 90, hsp90-2 and sit1 (related to silica shell formation) were highly expressed at 30°C under 1000μg/L Cu, while the genes encoding light harvesting proteins (3HfcpA and 3HfcpB) and silaffin precursor sil3 were significantly up-regulated at 15°C under 200μg/L Cu. Our results indicated an increase Cu toxicity to T. pseudonana under high temperature and Cu dose.
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Affiliation(s)
- Priscilla T Y Leung
- The Swire Institute of Marine Science and School of Biological Sciences, The University of Hong Kong, Pokfulam, Hong Kong, China; State Key Laboratory in Marine Pollution, City University of Hong Kong, Tat Chee Avenue, Kowloon, Hong Kong, China.
| | - Andy Xianliang Yi
- The Swire Institute of Marine Science and School of Biological Sciences, The University of Hong Kong, Pokfulam, Hong Kong, China
| | - Jack C H Ip
- The Swire Institute of Marine Science and School of Biological Sciences, The University of Hong Kong, Pokfulam, Hong Kong, China
| | - Sarah S T Mak
- The Swire Institute of Marine Science and School of Biological Sciences, The University of Hong Kong, Pokfulam, Hong Kong, China; Centre for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, Denmark
| | - Kenneth M Y Leung
- The Swire Institute of Marine Science and School of Biological Sciences, The University of Hong Kong, Pokfulam, Hong Kong, China; State Key Laboratory in Marine Pollution, City University of Hong Kong, Tat Chee Avenue, Kowloon, Hong Kong, China.
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31
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Kirkham AR, Richthammer P, Schmidt K, Wustmann M, Maeda Y, Hedrich R, Brunner E, Tanaka T, van Pée KH, Falciatore A, Mock T. A role for the cell-wall protein silacidin in cell size of the diatom Thalassiosira pseudonana. THE ISME JOURNAL 2017; 11:2452-2464. [PMID: 28731468 PMCID: PMC5649158 DOI: 10.1038/ismej.2017.100] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/24/2016] [Revised: 04/28/2017] [Accepted: 05/19/2017] [Indexed: 01/06/2023]
Abstract
Diatoms contribute 20% of global primary production and form the basis of many marine food webs. Although their species diversity correlates with broad diversity in cell size, there is also an intraspecific cell-size plasticity owing to sexual reproduction and varying environmental conditions. However, despite the ecological significance of the diatom cell size for food-web structure and global biogeochemical cycles, our knowledge about genes underpinning the size of diatom cells remains elusive. Here, a combination of reverse genetics, experimental evolution and comparative RNA-sequencing analyses enabled us to identify a previously unknown genetic control of cell size in the diatom Thalassiosira pseudonana. In particular, the targeted deregulation of the expression of the cell-wall protein silacidin caused a significant increase in valve diameter. Remarkably, the natural downregulation of the silacidin gene transcript due to experimental evolution under low temperature also correlated with cell-size increase. Our data give first evidence for a genetically controlled regulation of cell size in T. pseudonana and possibly other centric diatoms as they also encode the silacidin gene in their genomes.
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Affiliation(s)
- Amy R Kirkham
- School of Environmental Sciences, University of East Anglia, Norwich Research Park, Norwich, UK
| | | | - Katrin Schmidt
- School of Environmental Sciences, University of East Anglia, Norwich Research Park, Norwich, UK
| | | | - Yoshiaki Maeda
- Tokyo University of Agriculture and Technology, Tokyo, Japan
| | - René Hedrich
- Allgemeine Biochemie, TU Dresden, Dresden, Germany
| | - Eike Brunner
- Allgemeine Biochemie, TU Dresden, Dresden, Germany
| | - Tsuyoshi Tanaka
- Tokyo University of Agriculture and Technology, Tokyo, Japan
| | | | - Angela Falciatore
- Sorbonne Universités, UPMC, Institut de Biologie Paris-Seine, CNRS, Laboratoire de Biologie Computationnelle et Quantitative, Paris, France
| | - Thomas Mock
- School of Environmental Sciences, University of East Anglia, Norwich Research Park, Norwich, UK
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32
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Tesson B, Lerch SJL, Hildebrand M. Characterization of a New Protein Family Associated With the Silica Deposition Vesicle Membrane Enables Genetic Manipulation of Diatom Silica. Sci Rep 2017; 7:13457. [PMID: 29044150 PMCID: PMC5647440 DOI: 10.1038/s41598-017-13613-8] [Citation(s) in RCA: 41] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2017] [Accepted: 09/25/2017] [Indexed: 01/27/2023] Open
Abstract
Diatoms are known for their intricate, silicified cell walls (frustules). Silica polymerization occurs in a compartment called the silica deposition vesicle (SDV) and it was proposed that the cytoskeleton influences silica patterning through the SDV membrane (silicalemma) via interactions with transmembrane proteins. In this work we identify a family of proteins associated with the silicalemma, named SAPs for Silicalemma Associated Proteins. The T. pseudonana SAPs (TpSAPs) are characterized by their motif organization; each contains a transmembrane domain, serine rich region and a conserved cytoplasmic domain. Fluorescent tagging demonstrated that two of the TpSAPs were localized to the silicalemma and that the intralumenal region of TpSAP3 remained embedded in the silica while the cytoplasmic region was cleaved. Knockdown lines of TpSAP1 and 3 displayed malformed valves; which confirmed their roles in frustule morphogenesis. This study provides the first demonstration of altering silica structure through manipulation of a single gene.
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Affiliation(s)
- Benoit Tesson
- Marine Biology Research Division, Scripps Institution of Oceanography, University of California San Diego, La Jolla, California, United States of America.
| | - Sarah J L Lerch
- Marine Biology Research Division, Scripps Institution of Oceanography, University of California San Diego, La Jolla, California, United States of America
| | - Mark Hildebrand
- Marine Biology Research Division, Scripps Institution of Oceanography, University of California San Diego, La Jolla, California, United States of America.
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33
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Shrestha RP, Hildebrand M. Development of a silicon limitation inducible expression system for recombinant protein production in the centric diatoms Thalassiosira pseudonana and Cyclotella cryptica. Microb Cell Fact 2017; 16:145. [PMID: 28818078 PMCID: PMC5561644 DOI: 10.1186/s12934-017-0760-3] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2017] [Accepted: 08/10/2017] [Indexed: 01/03/2023] Open
Abstract
Background An inducible promoter for recombinant protein expression provides substantial benefits because under induction conditions cellular energy and metabolic capability can be directed into protein synthesis. The most widely used inducible promoter for diatoms is for nitrate reductase, however, nitrogen metabolism is tied into diverse aspects of cellular function, and the induction response is not necessarily robust. Silicon limitation offers a means to eliminate energy and metabolic flux into cell division processes, with little other detrimental effect on cellular function, and a protein expression system that works under those conditions could be advantageous. Results In this study, we evaluate a number of promoters for recombinant protein expression induced by silicon limitation and repressed by the presence of silicon in the diatoms Thalassiosira pseudonana and Cyclotella cryptica. In addition to silicon limitation, we describe additional strategies to elevate recombinant protein expression level, including inclusion of the 5′ fragment of the coding region of the native gene and reducing carbon flow into ancillary processes of pigment synthesis and formation of photosynthetic storage products. We achieved yields of eGFP to 1.8% of total soluble protein in C. cryptica, which is about 3.6-fold higher than that obtained with chloroplast expression and ninefold higher than nuclear expression in another well-established algal system. Conclusions Our studies demonstrate that the combination of inducible promoter and other strategies can result in robust expression of recombinant protein in a nuclear-based expression system in diatoms under silicon limited conditions, separating the protein expression regime from growth processes and improving overall recombinant protein yields. Electronic supplementary material The online version of this article (doi:10.1186/s12934-017-0760-3) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Roshan P Shrestha
- Scripps Institution of Oceanography, University of California San Diego, La Jolla, CA, USA
| | - Mark Hildebrand
- Scripps Institution of Oceanography, University of California San Diego, La Jolla, CA, USA.
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34
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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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35
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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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36
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Ozkan A, Rorrer GL. Effects of light intensity on the selectivity of lipid and chitin nanofiber production during photobioreactor cultivation of the marine diatom Cyclotella sp. ALGAL RES 2017. [DOI: 10.1016/j.algal.2017.04.032] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
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37
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Thompson SEM, Coates JC. Surface sensing and stress-signalling in Ulva and fouling diatoms - potential targets for antifouling: a review. BIOFOULING 2017; 33:410-432. [PMID: 28508711 DOI: 10.1080/08927014.2017.1319473] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/20/2016] [Accepted: 04/11/2017] [Indexed: 06/07/2023]
Abstract
Understanding the underlying signalling pathways that enable fouling algae to sense and respond to surfaces is essential in the design of environmentally friendly coatings. Both the green alga Ulva and diverse diatoms are important ecologically and economically as they are persistent biofoulers. Ulva spores exhibit rapid secretion, allowing them to adhere quickly and permanently to a ship, whilst diatoms secrete an abundance of extracellular polymeric substances (EPS), which are highly adaptable to different environmental conditions. There is evidence, now supported by molecular data, for complex calcium and nitric oxide (NO) signalling pathways in both Ulva and diatoms being involved in surface sensing and/or adhesion. Moreover, adaptation to stress has profound effects on the biofouling capability of both types of organism. Targets for future antifouling coatings based on surface sensing are discussed, with an emphasis on pursuing NO-releasing coatings as a potentially universal antifouling strategy.
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Affiliation(s)
| | - Juliet C Coates
- a School of Biosciences , University of Birmingham , Birmingham , UK
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38
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Expression of Histophilus somni IbpA DR2 protective antigen in the diatom Thalassiosira pseudonana. Appl Microbiol Biotechnol 2017; 101:5313-5324. [PMID: 28405704 PMCID: PMC5486823 DOI: 10.1007/s00253-017-8267-8] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2017] [Revised: 03/15/2017] [Accepted: 03/27/2017] [Indexed: 01/08/2023]
Abstract
Increasing demand for the low-cost production of valuable proteins has stimulated development of novel expression systems. Many challenges faced by existing technology may be overcome by using unicellular microalgae as an expression platform due to their ability to be cultivated rapidly, inexpensively, and in large scale. Diatoms are a particularly productive type of unicellular algae showing promise as production organisms. Here, we report the development of an expression system in the diatom Thalassiosira pseudonana by expressing the protective IbpA DR2 antigen from Histophilus somni for the production of a vaccine against bovine respiratory disease. The utilization of diatoms with their typically silicified cell walls permitted development of silicon-responsive transcription elements to induce protein expression. Specifically, we demonstrate that transcription elements from the silicon transporter gene SIT1 are sufficient to drive high levels of IbpA DR2 expression during silicon limitation and growth arrest. These culture conditions eliminate the flux of cellular resources into cell division processes, yet do not limit protein expression. In addition to improving protein expression levels by molecular manipulations, yield was dramatically increased through cultivation enhancement including elevated light and CO2 supplementation. We substantially increased recombinant protein production over starting levels to 1.2% of the total sodium dodecyl sulfate-extractable protein in T. pseudonana, which was sufficient to conduct preliminary immunization trials in mice. Mice exposed to 5 μg of diatom-expressed DR2 in whole or sonicated cells (without protein purification) exhibited a modest immune response without the addition of adjuvant.
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39
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Effects of chrysolaminarin synthase knockdown in the diatom Thalassiosira pseudonana: Implications of reduced carbohydrate storage relative to green algae. ALGAL RES 2017. [DOI: 10.1016/j.algal.2017.01.010] [Citation(s) in RCA: 52] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
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40
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Chiriboga N. OG, Rorrer GL. Control of chitin nanofiber production by the lipid‐producing diatom Cyclotella Sp. through fed‐batch addition of dissolved silicon and nitrate in a bubble‐column photobioreactor. Biotechnol Prog 2017; 33:407-415. [DOI: 10.1002/btpr.2445] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2016] [Revised: 01/30/2017] [Indexed: 01/18/2023]
Affiliation(s)
- Omar G. Chiriboga N.
- School of Chemical, Biological, and Environmental EngineeringOregon State UniversityCorvallis OR97331
| | - Gregory L. Rorrer
- School of Chemical, Biological, and Environmental EngineeringOregon State UniversityCorvallis OR97331
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41
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Davis A, Abbriano R, Smith SR, Hildebrand M. Clarification of Photorespiratory Processes and the Role of Malic Enzyme in Diatoms. Protist 2016; 168:134-153. [PMID: 28104538 DOI: 10.1016/j.protis.2016.10.005] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2016] [Revised: 10/03/2016] [Accepted: 10/08/2016] [Indexed: 11/20/2022]
Abstract
Evidence suggests that diatom photorespiratory metabolism is distinct from other photosynthetic eukaryotes in that there may be at least two routes for the metabolism of the photorespiratory metabolite glycolate. One occurs primarily in the mitochondria and is similar to the C2 photorespiratory pathway, and the other processes glycolate through the peroxisomal glyoxylate cycle. Genomic analysis has identified the presence of key genes required for glycolate oxidation, the glyoxylate cycle, and malate metabolism, however, predictions of intracellular localization can be ambiguous and require verification. This knowledge gap leads to uncertainties surrounding how these individual pathways operate, either together or independently, to process photorespiratory intermediates under different environmental conditions. Here, we combine in silico sequence analysis, in vivo protein localization techniques and gene expression patterns to investigate key enzymes potentially involved in photorespiratory metabolism in the model diatom Thalassiosira pseudonana. We demonstrate the peroxisomal localization of isocitrate lyase and the mitochondrial localization of malic enzyme and a glycolate oxidase. Based on these analyses, we propose an updated model for photorespiratory metabolism in T. pseudonana, as well as a mechanism by which C2 photorespiratory metabolism and its associated pathways may operate during silicon starvation and growth arrest.
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Affiliation(s)
- Aubrey Davis
- Marine Biology Research Division, Scripps Institution of Oceanography, UC San Diego, La Jolla, CA, U.S.A
| | - Raffaela Abbriano
- Marine Biology Research Division, Scripps Institution of Oceanography, UC San Diego, La Jolla, CA, U.S.A
| | - Sarah R Smith
- Integrative Oceanography Division, Scripps Institution of Oceanography, UC San Diego, La Jolla, CA, U.S.A.; J. Craig Venter Institute, La Jolla, CA, U.S.A
| | - Mark Hildebrand
- Marine Biology Research Division, Scripps Institution of Oceanography, UC San Diego, La Jolla, CA, U.S.A..
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42
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Marron AO, Ratcliffe S, Wheeler GL, Goldstein RE, King N, Not F, de Vargas C, Richter DJ. The Evolution of Silicon Transport in Eukaryotes. Mol Biol Evol 2016; 33:3226-3248. [PMID: 27729397 PMCID: PMC5100055 DOI: 10.1093/molbev/msw209] [Citation(s) in RCA: 51] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023] Open
Abstract
Biosilicification (the formation of biological structures from silica) occurs in diverse eukaryotic lineages, plays a major role in global biogeochemical cycles, and has significant biotechnological applications. Silicon (Si) uptake is crucial for biosilicification, yet the evolutionary history of the transporters involved remains poorly known. Recent evidence suggests that the SIT family of Si transporters, initially identified in diatoms, may be widely distributed, with an extended family of related transporters (SIT-Ls) present in some nonsilicified organisms. Here, we identify SITs and SIT-Ls in a range of eukaryotes, including major silicified lineages (radiolarians and chrysophytes) and also bacterial SIT-Ls. Our evidence suggests that the symmetrical 10-transmembrane-domain SIT structure has independently evolved multiple times via duplication and fusion of 5-transmembrane-domain SIT-Ls. We also identify a second gene family, similar to the active Si transporter Lsi2, that is broadly distributed amongst siliceous and nonsiliceous eukaryotes. Our analyses resolve a distinct group of Lsi2-like genes, including plant and diatom Si-responsive genes, and sequences unique to siliceous sponges and choanoflagellates. The SIT/SIT-L and Lsi2 transporter families likely contribute to biosilicification in diverse lineages, indicating an ancient role for Si transport in eukaryotes. We propose that these Si transporters may have arisen initially to prevent Si toxicity in the high Si Precambrian oceans, with subsequent biologically induced reductions in Si concentrations of Phanerozoic seas leading to widespread losses of SIT, SIT-L, and Lsi2-like genes in diverse lineages. Thus, the origin and diversification of two independent Si transporter families both drove and were driven by ancient ocean Si levels.
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Affiliation(s)
- Alan O Marron
- Department of Applied Mathematics and Theoretical Physics, Centre for Mathematical Sciences, University of Cambridge, Cambridge, United Kingdom .,Department of Zoology, University of Cambridge, Cambridge, United Kingdom
| | - Sarah Ratcliffe
- School of Biochemistry, Biomedical Sciences Building, University of Bristol, University Walk, Bristol, United Kingdom
| | - Glen L Wheeler
- Marine Biological Association, The Laboratory, Citadel Hill, Plymouth, Devon, United Kingdom
| | - Raymond E Goldstein
- Department of Applied Mathematics and Theoretical Physics, Centre for Mathematical Sciences, University of Cambridge, Cambridge, United Kingdom
| | - Nicole King
- Howard Hughes Medical Institute and Department of Molecular and Cell Biology, University of California, Berkeley, CA
| | - Fabrice Not
- CNRS, UMR 7144, Station Biologique de Roscoff, Place Georges Teissier, Roscoff, France.,Sorbonne Universités, Université Pierre et Marie Curie (UPMC) Paris 06, UMR 7144, Station Biologique de Roscoff, Place Georges Teissier, Roscoff, France
| | - Colomban de Vargas
- CNRS, UMR 7144, Station Biologique de Roscoff, Place Georges Teissier, Roscoff, France.,Sorbonne Universités, Université Pierre et Marie Curie (UPMC) Paris 06, UMR 7144, Station Biologique de Roscoff, Place Georges Teissier, Roscoff, France
| | - Daniel J Richter
- Howard Hughes Medical Institute and Department of Molecular and Cell Biology, University of California, Berkeley, CA.,CNRS, UMR 7144, Station Biologique de Roscoff, Place Georges Teissier, Roscoff, France.,Sorbonne Universités, Université Pierre et Marie Curie (UPMC) Paris 06, UMR 7144, Station Biologique de Roscoff, Place Georges Teissier, Roscoff, France
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43
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Durkin CA, Koester JA, Bender SJ, Armbrust EV. The evolution of silicon transporters in diatoms. JOURNAL OF PHYCOLOGY 2016; 52:716-731. [PMID: 27335204 PMCID: PMC5129515 DOI: 10.1111/jpy.12441] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/19/2016] [Accepted: 05/21/2016] [Indexed: 05/06/2023]
Abstract
Diatoms are highly productive single-celled algae that form an intricately patterned silica cell wall after every cell division. They take up and utilize silicic acid from seawater via silicon transporter (SIT) proteins. This study examined the evolution of the SIT gene family to identify potential genetic adaptations that enable diatoms to thrive in the modern ocean. By searching for sequence homologs in available databases, the diversity of organisms found to encode SITs increased substantially and included all major diatom lineages and other algal protists. A bacterial-encoded gene with homology to SIT sequences was also identified, suggesting that a lateral gene transfer event occurred between bacterial and protist lineages. In diatoms, the SIT genes diverged and diversified to produce five distinct clades. The most basal SIT clades were widely distributed across diatom lineages, while the more derived clades were lineage-specific, which together produced a distinct repertoire of SIT types among major diatom lineages. Differences in the predicted protein functional domains encoded among SIT clades suggest that the divergence of clades resulted in functional diversification among SITs. Both laboratory cultures and natural communities changed transcription of each SIT clade in response to experimental or environmental growth conditions, with distinct transcriptional patterns observed among clades. Together, these data suggest that the diversification of SITs within diatoms led to specialized adaptations among diatoms lineages, and perhaps their dominant ability to take up silicic acid from seawater in diverse environmental conditions.
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Affiliation(s)
- Colleen A. Durkin
- Moss Landing Marine Laboratories8272 Moss Landing RoadMoss LandingCalifornia95039USA
| | - Julie A. Koester
- Department of Biology and Marine BiologyUniversity of North Carolina WilmingtonWilmingtonNorth Carolina28403USA
| | - Sara J. Bender
- Marine Chemistry and GeochemistryWoods Hole Oceanographic InstitutionWoods HoleMassachusetts02543USA
- Present address: The Gordon and Betty Moore FoundationPalo AltoCalifornia94304USA
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44
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Goncalves EC, Wilkie AC, Kirst M, Rathinasabapathi B. Metabolic regulation of triacylglycerol accumulation in the green algae: identification of potential targets for engineering to improve oil yield. PLANT BIOTECHNOLOGY JOURNAL 2016; 14:1649-60. [PMID: 26801206 PMCID: PMC5066758 DOI: 10.1111/pbi.12523] [Citation(s) in RCA: 63] [Impact Index Per Article: 7.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/30/2015] [Revised: 11/13/2015] [Accepted: 11/25/2015] [Indexed: 05/03/2023]
Abstract
The great need for more sustainable alternatives to fossil fuels has increased our research interests in algal biofuels. Microalgal cells, characterized by high photosynthetic efficiency and rapid cell division, are an excellent source of neutral lipids as potential fuel stocks. Various stress factors, especially nutrient-starvation conditions, induce an increased formation of lipid bodies filled with triacylglycerol in these cells. Here we review our knowledge base on glycerolipid synthesis in the green algae with an emphasis on recent studies on carbon flux, redistribution of lipids under nutrient-limiting conditions and its regulation. We discuss the contributions and limitations of classical and novel approaches used to elucidate the algal triacylglycerol biosynthetic pathway and its regulatory network in green algae. Also discussed are gaps in knowledge and suggestions for much needed research both on the biology of triacylglycerol accumulation and possible avenues to engineer improved algal strains.
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Affiliation(s)
- Elton C Goncalves
- Plant Molecular and Cellular Biology Program, Horticultural Sciences Department, Institute of Food and Agricultural Sciences, University of Florida, Gainesville, FL, USA
| | - Ann C Wilkie
- Soil and Water Science Department, Institute of Food and Agricultural Sciences, University of Florida, Gainesville, FL, USA
| | - Matias Kirst
- School of Forestry, University of Florida, Gainesville, FL, USA
| | - Bala Rathinasabapathi
- Plant Molecular and Cellular Biology Program, Horticultural Sciences Department, Institute of Food and Agricultural Sciences, University of Florida, Gainesville, FL, USA
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45
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Knight MJ, Senior L, Nancolas B, Ratcliffe S, Curnow P. Direct evidence of the molecular basis for biological silicon transport. Nat Commun 2016; 7:11926. [PMID: 27305972 PMCID: PMC4912633 DOI: 10.1038/ncomms11926] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2015] [Accepted: 05/11/2016] [Indexed: 12/19/2022] Open
Abstract
Diatoms are an important group of eukaryotic algae with a curious evolutionary innovation: they sheath themselves in a cell wall made largely of silica. The cellular machinery responsible for silicification includes a family of membrane permeases that recognize and actively transport the soluble precursor of biosilica, silicic acid. However, the molecular basis of silicic acid transport remains obscure. Here, we identify experimentally tractable diatom silicic acid transporter (SIT) homologues and study their structure and function in vitro, enabled by the development of a new fluorescence method for studying substrate transport kinetics. We show that recombinant SITs are Na+/silicic acid symporters with a 1:1 protein: substrate stoichiometry and KM for silicic acid of 20 μM. Protein mutagenesis supports the long-standing hypothesis that four conserved GXQ amino acid motifs are important in SIT function. This marks a step towards a detailed understanding of silicon transport with implications for biogeochemistry and bioinspired materials. Diatoms sheath themselves in a self-made casing of silica, which requires the function of silicic acid transporters. Here, the authors identify versions of these transporters that are experimentally tractable, and develop a fluorescence method to study silicic acid transport in vitro.
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Affiliation(s)
- Michael J Knight
- School of Biochemistry, University of Bristol, Bristol BS8 1TD, UK
| | - Laura Senior
- School of Biochemistry, University of Bristol, Bristol BS8 1TD, UK
| | - Bethany Nancolas
- School of Biochemistry, University of Bristol, Bristol BS8 1TD, UK
| | - Sarah Ratcliffe
- School of Biochemistry, University of Bristol, Bristol BS8 1TD, UK
| | - Paul Curnow
- School of Biochemistry, University of Bristol, Bristol BS8 1TD, UK.,BrisSynBio, Life Sciences Building, Tyndall Avenue, Bristol BS8 1TQ, UK
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46
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Smith SR, Glé C, Abbriano RM, Traller JC, Davis A, Trentacoste E, Vernet M, Allen AE, Hildebrand M. Transcript level coordination of carbon pathways during silicon starvation-induced lipid accumulation in the diatom Thalassiosira pseudonana. THE NEW PHYTOLOGIST 2016; 210:890-904. [PMID: 26844818 PMCID: PMC5067629 DOI: 10.1111/nph.13843] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/10/2015] [Accepted: 12/03/2015] [Indexed: 05/06/2023]
Abstract
Diatoms are one of the most productive and successful photosynthetic taxa on Earth and possess attributes such as rapid growth rates and production of lipids, making them candidate sources of renewable fuels. Despite their significance, few details of the mechanisms used to regulate growth and carbon metabolism are currently known, hindering metabolic engineering approaches to enhance productivity. To characterize the transcript level component of metabolic regulation, genome-wide changes in transcript abundance were documented in the model diatom Thalassiosira pseudonana on a time-course of silicon starvation. Growth, cell cycle progression, chloroplast replication, fatty acid composition, pigmentation, and photosynthetic parameters were characterized alongside lipid accumulation. Extensive coordination of large suites of genes was observed, highlighting the existence of clusters of coregulated genes as a key feature of global gene regulation in T. pseudonana. The identity of key enzymes for carbon metabolic pathway inputs (photosynthesis) and outputs (growth and storage) reveals these clusters are organized to synchronize these processes. Coordinated transcript level responses to silicon starvation are probably driven by signals linked to cell cycle progression and shifts in photophysiology. A mechanistic understanding of how this is accomplished will aid efforts to engineer metabolism for development of algal-derived biofuels.
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Affiliation(s)
- Sarah R. Smith
- Scripps Institution of OceanographyUC San Diego9500 Gilman DriveLa JollaCA92093USA
- J. Craig Venter Institute4120 Capricorn LaneLa JollaCA92037USA
| | - Corine Glé
- Scripps Institution of OceanographyUC San Diego9500 Gilman DriveLa JollaCA92093USA
| | - Raffaela M. Abbriano
- Scripps Institution of OceanographyUC San Diego9500 Gilman DriveLa JollaCA92093USA
| | - Jesse C. Traller
- Scripps Institution of OceanographyUC San Diego9500 Gilman DriveLa JollaCA92093USA
| | - Aubrey Davis
- Scripps Institution of OceanographyUC San Diego9500 Gilman DriveLa JollaCA92093USA
| | - Emily Trentacoste
- Scripps Institution of OceanographyUC San Diego9500 Gilman DriveLa JollaCA92093USA
| | - Maria Vernet
- Scripps Institution of OceanographyUC San Diego9500 Gilman DriveLa JollaCA92093USA
| | - Andrew E. Allen
- Scripps Institution of OceanographyUC San Diego9500 Gilman DriveLa JollaCA92093USA
- J. Craig Venter Institute4120 Capricorn LaneLa JollaCA92037USA
| | - Mark Hildebrand
- Scripps Institution of OceanographyUC San Diego9500 Gilman DriveLa JollaCA92093USA
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47
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Hopes A, Nekrasov V, Kamoun S, Mock T. Editing of the urease gene by CRISPR-Cas in the diatom Thalassiosira pseudonana. PLANT METHODS 2016; 12:49. [PMID: 27904648 PMCID: PMC5121945 DOI: 10.1186/s13007-016-0148-0] [Citation(s) in RCA: 81] [Impact Index Per Article: 10.1] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/20/2016] [Accepted: 11/10/2016] [Indexed: 05/18/2023]
Abstract
BACKGROUND CRISPR-Cas is a recent and powerful addition to the molecular toolbox which allows programmable genome editing. It has been used to modify genes in a wide variety of organisms, but only two alga to date. Here we present a methodology to edit the genome of Thalassiosira pseudonana, a model centric diatom with both ecological significance and high biotechnological potential, using CRISPR-Cas. RESULTS A single construct was assembled using Golden Gate cloning. Two sgRNAs were used to introduce a precise 37 nt deletion early in the coding region of the urease gene. A high percentage of bi-allelic mutations (≤61.5%) were observed in clones with the CRISPR-Cas construct. Growth of bi-allelic mutants in urea led to a significant reduction in growth rate and cell size compared to growth in nitrate. CONCLUSIONS CRISPR-Cas can precisely and efficiently edit the genome of T. pseudonana. The use of Golden Gate cloning to assemble CRISPR-Cas constructs gives additional flexibility to the CRISPR-Cas method and facilitates modifications to target alternative genes or species.
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Affiliation(s)
- Amanda Hopes
- School of Environmental Sciences, University of East Anglia, Norwich Research Park, Norwich, NR4 7TJ UK
| | - Vladimir Nekrasov
- The Sainsbury Laboratory, Norwich Research Park, Norwich, NR4 7UH UK
| | - Sophien Kamoun
- The Sainsbury Laboratory, Norwich Research Park, Norwich, NR4 7UH UK
| | - Thomas Mock
- School of Environmental Sciences, University of East Anglia, Norwich Research Park, Norwich, NR4 7TJ UK
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48
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Traller JC, Cokus SJ, Lopez DA, Gaidarenko O, Smith SR, McCrow JP, Gallaher SD, Podell S, Thompson M, Cook O, Morselli M, Jaroszewicz A, Allen EE, Allen AE, Merchant SS, Pellegrini M, Hildebrand M. Genome and methylome of the oleaginous diatom Cyclotella cryptica reveal genetic flexibility toward a high lipid phenotype. BIOTECHNOLOGY FOR BIOFUELS 2016; 9:258. [PMID: 27933100 PMCID: PMC5124317 DOI: 10.1186/s13068-016-0670-3] [Citation(s) in RCA: 58] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/08/2016] [Accepted: 11/15/2016] [Indexed: 05/08/2023]
Abstract
BACKGROUND Improvement in the performance of eukaryotic microalgae for biofuel and bioproduct production is largely dependent on characterization of metabolic mechanisms within the cell. The marine diatom Cyclotella cryptica, which was originally identified in the Aquatic Species Program, is a promising strain of microalgae for large-scale production of biofuel and bioproducts, such as omega-3 fatty acids. RESULTS We sequenced the nuclear genome and methylome of this oleaginous diatom to identify the genetic traits that enable substantial accumulation of triacylglycerol. The genome is comprised of highly methylated repetitive sequence, which does not significantly change under silicon starved lipid induction, and data further suggests the primary role of DNA methylation is to suppress DNA transposition. Annotation of pivotal glycolytic, lipid metabolism, and carbohydrate degradation processes reveal an expanded enzyme repertoire in C. cryptica that would allow for an increased metabolic capacity toward triacylglycerol production. Identification of previously unidentified genes, including those involved in carbon transport and chitin metabolism, provide potential targets for genetic manipulation of carbon flux to further increase its lipid phenotype. New genetic tools were developed, bringing this organism on a par with other microalgae in terms of genetic manipulation and characterization approaches. CONCLUSIONS Functional annotation and detailed cross-species comparison of key carbon rich processes in C. cryptica highlights the importance of enzymatic subcellular compartmentation for regulation of carbon flux, which is often overlooked in photosynthetic microeukaryotes. The availability of the genome sequence, as well as advanced genetic manipulation tools enable further development of this organism for deployment in large-scale production systems.
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Affiliation(s)
- Jesse C. Traller
- Scripps Institution of Oceanography, University California San Diego, 9500 Gilman Drive, La Jolla, CA 92093-0202 USA
| | - Shawn J. Cokus
- Institute for Genomics and Proteomics, University of California, Los Angeles, CA 90095 USA
| | - David A. Lopez
- Institute for Genomics and Proteomics, University of California, Los Angeles, CA 90095 USA
| | - Olga Gaidarenko
- Scripps Institution of Oceanography, University California San Diego, 9500 Gilman Drive, La Jolla, CA 92093-0202 USA
| | - Sarah R. Smith
- Scripps Institution of Oceanography, University California San Diego, 9500 Gilman Drive, La Jolla, CA 92093-0202 USA
- J. Craig Venter Institute, 4120 Capricorn Lane, La Jolla, CA 92037 USA
| | - John P. McCrow
- J. Craig Venter Institute, 4120 Capricorn Lane, La Jolla, CA 92037 USA
| | - Sean D. Gallaher
- Institute for Genomics and Proteomics, University of California, Los Angeles, CA 90095 USA
- Department of Chemistry and Biochemistry, University of California, Los Angeles, CA 90095 USA
| | - Sheila Podell
- Scripps Institution of Oceanography, University California San Diego, 9500 Gilman Drive, La Jolla, CA 92093-0202 USA
| | - Michael Thompson
- Institute for Genomics and Proteomics, University of California, Los Angeles, CA 90095 USA
| | - Orna Cook
- Scripps Institution of Oceanography, University California San Diego, 9500 Gilman Drive, La Jolla, CA 92093-0202 USA
| | - Marco Morselli
- Institute for Genomics and Proteomics, University of California, Los Angeles, CA 90095 USA
| | - Artur Jaroszewicz
- Institute for Genomics and Proteomics, University of California, Los Angeles, CA 90095 USA
| | - Eric E. Allen
- Scripps Institution of Oceanography, University California San Diego, 9500 Gilman Drive, La Jolla, CA 92093-0202 USA
| | - Andrew E. Allen
- Scripps Institution of Oceanography, University California San Diego, 9500 Gilman Drive, La Jolla, CA 92093-0202 USA
- J. Craig Venter Institute, 4120 Capricorn Lane, La Jolla, CA 92037 USA
| | - Sabeeha S. Merchant
- Department of Chemistry and Biochemistry, University of California, Los Angeles, CA 90095 USA
| | - Matteo Pellegrini
- Institute for Genomics and Proteomics, University of California, Los Angeles, CA 90095 USA
| | - Mark Hildebrand
- Scripps Institution of Oceanography, University California San Diego, 9500 Gilman Drive, La Jolla, CA 92093-0202 USA
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Pommerrenig B, Diehn TA, Bienert GP. Metalloido-porins: Essentiality of Nodulin 26-like intrinsic proteins in metalloid transport. PLANT SCIENCE : AN INTERNATIONAL JOURNAL OF EXPERIMENTAL PLANT BIOLOGY 2015; 238:212-27. [PMID: 26259189 DOI: 10.1016/j.plantsci.2015.06.002] [Citation(s) in RCA: 83] [Impact Index Per Article: 9.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/27/2015] [Revised: 05/30/2015] [Accepted: 06/01/2015] [Indexed: 05/08/2023]
Abstract
Metalloids are a group of physiologically important elements ranging from the essential to the highly toxic. Arsenic, antimony, germanium, and tellurium are highly toxic to plants themselves and to consumers of metalloid-contaminated plants. Boron, silicon, and selenium fulfill essential or beneficial functions in plants. However, when present at high concentrations, boron and selenium cause toxicity symptoms that are detrimental to plant fitness and yield. Consequently, all plants require efficient membrane transport systems to control the uptake and extrusion of metalloids into or out of the plant and their distribution within the plant body. Several Nodulin 26-like intrinsic proteins (NIPs) that belong to the aquaporin plant water channel protein family facilitate the diffusion of uncharged metalloid species. Genetic, physiological, and molecular evidence is that NIPs from primitive to higher plants not only transport all environmentally important metalloids, but that these proteins have a major role in the uptake, translocation, and extrusion of metalloids in plants. As most of the metalloid-permeable NIP aquaporins are impermeable or are poorly permeable to water, these NIP channel proteins should be considered as physiologically essential metalloido-porins.
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Affiliation(s)
- Benjamin Pommerrenig
- Metalloid Transport Group, Department of Physiology and Cell Biology, Leibniz Institute of Plant Genetics and Crop Plant Research, Corrensstrasse 3, D-06466 Gatersleben, Germany.
| | - Till Arvid Diehn
- Metalloid Transport Group, Department of Physiology and Cell Biology, Leibniz Institute of Plant Genetics and Crop Plant Research, Corrensstrasse 3, D-06466 Gatersleben, Germany.
| | - Gerd Patrick Bienert
- Metalloid Transport Group, Department of Physiology and Cell Biology, Leibniz Institute of Plant Genetics and Crop Plant Research, Corrensstrasse 3, D-06466 Gatersleben, Germany.
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50
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Hildebrand M, Lerch SJL. Diatom silica biomineralization: Parallel development of approaches and understanding. Semin Cell Dev Biol 2015; 46:27-35. [PMID: 26256954 DOI: 10.1016/j.semcdb.2015.06.007] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2015] [Revised: 06/03/2015] [Accepted: 06/28/2015] [Indexed: 10/23/2022]
Abstract
Diatom silica cell walls present an intriguing application of biomineralization in a single celled organism. The ability of diatoms to make an enormous variety of silica structures on the nano- to micro-scale is unparalleled in nature. The process is a whole-cell endeavor, involving diverse cellular components that coordinate "bottom up" and "top down" structure formation processes to reproducibly convert genetic information into physical structure. The study of silicification has been similarly all encompassing, involving the application of diverse analytical techniques to examine different aspects of the process. This review highlights the application of different approaches used to study silicification and the insights they have provided, and documents the progress that has been made. The current status offers the possibility of major breakthroughs in our understanding, by enabling a more widespread identification of genes involved, and direct testing of the role these genes play by genetic manipulation.
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Affiliation(s)
- Mark Hildebrand
- Marine Biology Research Division, Scripps Institution of Oceanography, University of California, San Diego, USA.
| | - Sarah J L Lerch
- Marine Biology Research Division, Scripps Institution of Oceanography, University of California, San Diego, USA
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