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Tesson B, Genet MJ, Fernandez V, Degand S, Rouxhet PG, Martin-Jézéquel V. Surface Chemical Composition of Diatoms. Chembiochem 2009; 10:2011-24. [DOI: 10.1002/cbic.200800811] [Citation(s) in RCA: 71] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
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52
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From biominerals to biomaterials: the role of biomolecule–mineral interactions. Biochem Soc Trans 2009; 37:687-91. [DOI: 10.1042/bst0370687] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Abstract
Interactions between inorganic materials and biomolecules at the molecular level, although complex, are commonplace. Examples include biominerals, which are, in most cases, facilitated by and in contact with biomolecules; implantable biomaterials; and food and drug handling. The effectiveness of these functional materials is dependent on the interfacial properties, i.e. the extent of molecular level ‘association’ with biomolecules. The present article gives information on biomolecule–inorganic material interactions and illustrates our current understanding using selected examples. The examples include (i) mechanism of biointegration: the role of surface chemistry and protein adsorption, (ii) towards improved aluminium-containing materials, and (iii) understanding the bioinorganic interface: experiment and modelling. A wide range of experimental techniques (microscopic, spectroscopic, particle sizing, thermal methods and solution methods) are used by the research group to study interactions between (bio)molecules and molecular and colloidal species that are coupled with computational simulation studies to gain as much information as possible on the molecular-scale interactions. Our goal is to uncover the mechanisms underpinning any interactions and to identify ‘rules’ or ‘guiding principles’ that could be used to explain and hence predict behaviour for a wide range of (bio)molecule–mineral systems.
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53
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Durkin CA, Mock T, Armbrust EV. Chitin in diatoms and its association with the cell wall. EUKARYOTIC CELL 2009; 8:1038-50. [PMID: 19429777 PMCID: PMC2708456 DOI: 10.1128/ec.00079-09] [Citation(s) in RCA: 94] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/08/2009] [Accepted: 04/24/2009] [Indexed: 11/20/2022]
Abstract
Chitin is a globally abundant polymer widely distributed throughout eukaryotes that has been well characterized in only a few lineages. Diatoms are members of the eukaryotic lineage of stramenopiles. Of the hundreds of diatom genera, two produce long fibers of chitin that extrude through their cell walls of silica. We identify and describe here genes encoding putative chitin synthases in a variety of additional diatom genera, indicating that the ability to produce chitin is more widespread and likely plays a more central role in diatom biology than previously considered. Diatom chitin synthases fall into four phylogenetic clades. Protein domain predictions and differential gene expression patterns provide evidence that chitin synthases have multiple functions within a diatom cell. Thalassiosira pseudonana possesses six genes encoding three types of chitin synthases. Transcript abundance of the gene encoding one of these chitin synthase types increases when cells resume division after short-term silicic acid starvation and during short-term limitation by silicic acid or iron, two nutrient conditions connected in the environment and known to affect the cell wall. During long-term silicic acid starvation transcript abundance of this gene and one additional chitin synthase gene increased at the same time a chitin-binding lectin localized to the girdle band region of the cell wall. Together, these results suggest that the ability to produce chitin is more widespread in diatoms than previously thought and that a subset of the chitin produced by diatoms is associated with the cell wall.
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Affiliation(s)
- Colleen A Durkin
- School of Oceanography, University of Washington, Seattle, Washington 98195, USA.
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Scott K, Ritchie NWM. Analysis of 3D elemental mapping artefacts in biological specimens using Monte Carlo simulation. J Microsc 2009; 233:331-9. [PMID: 19220700 DOI: 10.1111/j.1365-2818.2009.03124.x] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
In this paper, we present Monte Carlo simulation results demonstrating the feasibility of using the focused ion beam based X-ray microanalysis technique (FIB-EDS) for the 3D elemental analysis of biological samples. In this study, we used a marine diatom Thalassiosira pseudonana as our model organism and NISTMonte for the Monte Carlo simulations. We explored several beam energies commonly used for the X-ray microanalysis to examine their effects on the resulting 3D elemental volume of the model organism. We also performed a preliminary study on the sensitivity of X-ray analysis for detecting nanoparticles in the model. For the conditions considered in this work, we show that the X-ray mapping performed using the 5 keV beam energy results in 3D elemental distributions that closely reflect the elemental distributions in the original model. At 5 keV, the depth resolution of the X-ray maps is about 250 nm for the model organism. We also show that the nanoparticles that are 50 nm in diameter or greater are easily located. Although much work is still needed in generating more accurate biological models and simulating experimental conditions relevant to these samples, our results indicate that FIB-EDS is a promising technique for the 3D elemental analysis of some biological specimens.
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Affiliation(s)
- K Scott
- National Institute of Standards and Technology, 100 Bureau Drive, Gaithersburg, MD 20899, USA.
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55
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Light-dependent transcriptional regulation of genes of biogeochemical interest in the diploid and haploid life cycle stages of Emiliania huxleyi. Appl Environ Microbiol 2009; 75:3366-9. [PMID: 19304825 DOI: 10.1128/aem.02737-08] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
The expression of genes of biogeochemical interest in calcifying and noncalcifying life stages of the coccolithophore Emiliania huxleyi was investigated. Transcripts potentially involved in calcification were tested through a light-dark cycle. These transcripts were more abundant in calcifying cells and were upregulated in the light. Their application as potential candidates for in situ biogeochemical proxies is also suggested.
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56
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3D imaging of diatoms with ion-abrasion scanning electron microscopy. J Struct Biol 2009; 166:316-28. [PMID: 19269330 DOI: 10.1016/j.jsb.2009.02.014] [Citation(s) in RCA: 42] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2008] [Revised: 02/23/2009] [Accepted: 02/25/2009] [Indexed: 11/22/2022]
Abstract
Ion-abrasion scanning electron microscopy (IASEM) takes advantage of focused ion beams to abrade thin sections from the surface of bulk specimens, coupled with SEM to image the surface of each section, enabling 3D reconstructions of subcellular architecture at approximately 30nm resolution. Here, we report the first application of IASEM for imaging a biomineralizing organism, the marine diatom Thalassiosira pseudonana. Diatoms have highly patterned silica-based cell wall structures that are unique models for the study and application of directed nanomaterials synthesis by biological systems. Our study provides new insights into the architecture and assembly principles of both the "hard" (siliceous) and "soft" (organic) components of the cell. From 3D reconstructions of developmentally synchronized diatoms captured at different stages, we show that both micro- and nanoscale siliceous structures can be visualized at specific stages in their formation. We show that not only are structures visualized in a whole-cell context, but demonstrate that fragile, early-stage structures are visible, and that this can be combined with elemental mapping in the exposed slice. We demonstrate that the 3D architectures of silica structures, and the cellular components that mediate their creation and positioning can be visualized simultaneously, providing new opportunities to study and manipulate mineral nanostructures in a genetically tractable system.
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Thamatrakoln K, Kustka AB. When to say when: can excessive drinking explain silicon uptake in diatoms? Bioessays 2009; 31:322-7. [DOI: 10.1002/bies.200800185] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
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Vartanian M, Desclés J, Quinet M, Douady S, Lopez PJ. Plasticity and robustness of pattern formation in the model diatom Phaeodactylum tricornutum. THE NEW PHYTOLOGIST 2009; 182:429-442. [PMID: 19210721 DOI: 10.1111/j.1469-8137.2009.02769.x] [Citation(s) in RCA: 35] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/27/2023]
Abstract
Understanding the morphogenesis of mineralized structures found in shells, bones, teeth, spicules and plant cell walls is difficult because of the complexities underlying biomineralization, and the requirement of accurate models for pattern formation. Here, we investigated the spatial and temporal development of siliceous structures found in a model diatom species, Phaeodactylum tricornutum, for which the entire genome has been sequenced and transformation is routine. Analyses of pattern formation revealed that the process of silicification starts from a 'pi-like' structure that controls the spatial organization of a sternum upon which regular instabilities are initiated and developed. Detailed analyses also demonstrate that morphogenesis of silica is nonuniform. We also tested the sensitivity of pattern formation to perturbation of proton pumps, and found that selective inhibitors of H(+)-V-ATPases affect silica biomineralization both quantitatively and qualitatively. Morphometric analyses of valves purified from isogenic populations of cells show that the morphometric noise of several traits is under exquisite regulation, explaining why the overall valve pattern is reproducibly maintained. Altogether our analyses demonstrate that silica morphogenesis is a robust but nonuniform process, and allow us to propose a model for the dynamic growth of materials within a spatially controlled geometry.
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Affiliation(s)
- Mathieu Vartanian
- Biomineralization and Morphogenesis Group, CNRS UMR 8186, Ecole Normale Supérieure, 46 rue d'Ulm, 75230 Paris Cedex 05, France
| | - Julien Desclés
- Biomineralization and Morphogenesis Group, CNRS UMR 8186, Ecole Normale Supérieure, 46 rue d'Ulm, 75230 Paris Cedex 05, France
| | - Michelle Quinet
- Biomineralization and Morphogenesis Group, CNRS UMR 8186, Ecole Normale Supérieure, 46 rue d'Ulm, 75230 Paris Cedex 05, France
| | - Stéphane Douady
- Laboratoire Matière et Systèmes Complexes (MSC), UMR 7057 CNRS & Université Paris-Diderot, 10 rue Alice Domon et Léonie Duquet, 75205 Paris Cedex 13, France
| | - Pascal J Lopez
- Biomineralization and Morphogenesis Group, CNRS UMR 8186, Ecole Normale Supérieure, 46 rue d'Ulm, 75230 Paris Cedex 05, France
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Abstract
Marine eukaryotic photosynthesis is dominated by a diverse group of unicellular organisms collectively called microalgae. Microalgae include cells derived from a primary endosymbiotic event (similar to land plants) and cells derived from subsequent secondary and/or tertiary endosymbiotic events. These latter cells are chimeras of several genomes and dominate primary production in the marine environment. Two consequences of multiple endosymbiotic events include complex targeting mechanisms to allow nuclear-encoded proteins to be imported into the plastid and coordination of enzymes, potentially from disparate originator cells, to form complete metabolic pathways. In this review, we discuss the forces that shaped the genomes of marine microalgae and then discuss some of the metabolic consequences of such a complex evolutionary history. We focus our metabolic discussion on carbon, nitrogen, and iron. We then discuss biomineralization and new evidence for programmed cell death in microalgae. We conclude with a short summary on advances in genetic manipulation of microalgae and thoughts on the future directions of marine algal genomics.
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Affiliation(s)
- Micaela S Parker
- School of Oceanography, University of Washington, Seattle, Washington 98195, USA.
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Bonucci E. Calcification and silicification: a comparative survey of the early stages of biomineralization. J Bone Miner Metab 2009; 27:255-64. [PMID: 19301088 DOI: 10.1007/s00774-009-0061-y] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/30/2008] [Accepted: 10/23/2008] [Indexed: 10/21/2022]
Abstract
Most of the studies on biomineralization have focused on calcification and silicification, the two systems that predominate in nature in the construction of skeletal or integumental hard tissues. They have, however, been studied separately, as if they were completely distinct processes, in spite of their several points of contact, especially as far as the organic-inorganic relationships during the early mineralization stages are concerned. A very tight association of the inorganic substance with organic macromolecules, in fact, initially characterizes both systems. Although the mechanism of biomineralization remains elusive, a number of old and new findings, which have been taken into account in this review, support the view that, both in calcification and in silicification, genetically controlled organic macromolecules induce the formation of composite, organic-inorganic nanoparticles, behave as templates for the subsequent assemblage of the nanoparticles into micro- to macroarchitectures of complex pattern, and, eventually, are mostly reabsorbed. There are still many gaps left in our knowledge of this process. Comparative studies of the two biomineralization systems may help to fill them.
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Affiliation(s)
- Ermanno Bonucci
- Department of Experimental Medicine, Sapienza University of Rome, Policlinico Umberto I, Viale Regina Elena 324, 00161 Rome, Italy.
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An overview of silica in biology: its chemistry and recent technological advances. PROGRESS IN MOLECULAR AND SUBCELLULAR BIOLOGY 2009; 47:295-313. [PMID: 19198783 DOI: 10.1007/978-3-540-88552-8_13] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Biomineralisation is widespread in the biological world and occurs in bacteria, single-celled protists, plants, invertebrates and vertebrates. Minerals formed in the biological environment often show unusual physical properties (e.g. strength, degree of hydration) and often have structures that exhibit order on many length scales. Biosilica, found in single cell organisms through to higher plants and primitive animals (sponges), is formed from an environment that is undersaturated with respect to silicon and under conditions of around neutral pH and low temperature, ca. 4-40 degrees C. Formation of the mineral may occur intra- or extra-cellularly, and specific biochemical locations for mineral deposition that include lipids, proteins and carbohydrates are known. In most cases, the formation of the mineral phase is linked to cellular processes, understanding of which could lead to the design of new materials for biomedical, optical and other applications. This Chapter briefly describes the occurrence of silica in biology including known roles for the mineral phase, the chemistry of the material, the associated biomolecules and some recent applications of this knowledge in materials chemistry.The terminology which is used in this and other contributions within this volume is as follows: Si: the chemical symbol for the element and the generic term used when the nature of the specific silicon compound is not known. Si(OH) ( 4 ): orthosilicic acid, the fundamental building block used in the formation of silicas. SiO ( 2 ) x nH ( 2 ) O or SiO ( 2-x ) (OH) ( 2x ) x 2H ( 2 ) O: amorphous, hydrated, polymerised material. Oligomerisation: the formation of dimers and small oligomers from orthosilicic acid by removal of water. For example, 2Si(OH)(4) <--> (HO)(3)Si-O-Si(OH)(3) + H(2)O Polymerisation: the mutual condensation of silicic acid to give molecularly coherent units of increasing size. Organosilicon compound: must contain silicon covalently bonded to carbon within a distinct chemical species Silane: a compound having silicon atom(s) and organic chemical groups often connected through an oxygen linkage; e.g. tetrethoxy or tetramethoxysilane Silanol: hydroxyl group bonded to silicon atom Silicate: a chemically specific ion having negative charge (e.g. [Formula: see text]), term also used to describe salts (e.g. sodium silicate Na(2)SiO(3)) Opal: the term used to describe the gem-stone and often used to describe the type of amorphous silica produced by biological organisms. The two are similar in structure at the molecular level (disordered or amorphous), but at higher levels of structural organisation are distinct from one another.
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Affiliation(s)
- Nils Kröger
- School of Chemistry & Biochemistry, Georgia Institute of Technology, Atlanta, Georgia 30332-0400
- School of Materials Science & Engineering, Georgia Institute of Technology, Atlanta, Georgia 30332-0400
- School of Biology, Georgia Institute of Technology, Atlanta, Georgia 30332-0400; ,
| | - Nicole Poulsen
- School of Chemistry & Biochemistry, Georgia Institute of Technology, Atlanta, Georgia 30332-0400
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63
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Gillard J, Devos V, Huysman MJJ, De Veylder L, D'Hondt S, Martens C, Vanormelingen P, Vannerum K, Sabbe K, Chepurnov VA, Inzé D, Vuylsteke M, Vyverman W. Physiological and transcriptomic evidence for a close coupling between chloroplast ontogeny and cell cycle progression in the pennate diatom Seminavis robusta. PLANT PHYSIOLOGY 2008; 148:1394-411. [PMID: 18820084 PMCID: PMC2577256 DOI: 10.1104/pp.108.122176] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/29/2008] [Accepted: 09/18/2008] [Indexed: 05/18/2023]
Abstract
Despite the growing interest in diatom genomics, detailed time series of gene expression in relation to key cellular processes are still lacking. Here, we investigated the relationships between the cell cycle and chloroplast development in the pennate diatom Seminavis robusta. This diatom possesses two chloroplasts with a well-orchestrated developmental cycle, common to many pennate diatoms. By assessing the effects of induced cell cycle arrest with microscopy and flow cytometry, we found that division and reorganization of the chloroplasts are initiated only after S-phase progression. Next, we quantified the expression of the S. robusta FtsZ homolog to address the division status of chloroplasts during synchronized growth and monitored microscopically their dynamics in relation to nuclear division and silicon deposition. We show that chloroplasts divide and relocate during the S/G2 phase, after which a girdle band is deposited to accommodate cell growth. Synchronized cultures of two genotypes were subsequently used for a cDNA-amplified fragment length polymorphism-based genome-wide transcript profiling, in which 917 reproducibly modulated transcripts were identified. We observed that genes involved in pigment biosynthesis and coding for light-harvesting proteins were up-regulated during G2/M phase and cell separation. Light and cell cycle progression were both found to affect fucoxanthin-chlorophyll a/c-binding protein expression and accumulation of fucoxanthin cell content. Because chloroplasts elongate at the stage of cytokinesis, cell cycle-modulated photosynthetic gene expression and synthesis of pigments in concert with cell division might balance chloroplast growth, which confirms that chloroplast biogenesis in S. robusta is tightly regulated.
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Affiliation(s)
- Jeroen Gillard
- Laboratory of Protistology and Aquatic Ecology, Department of Biology, Ghent University, B-9000 Gent, Belgium.
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64
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Affiliation(s)
- Mark Hildebrand
- Marine Biology Research Division, Scripps Institution of Oceanography, University of California, San Diego, La Jolla, California 92093-0202
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65
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Belton DJ, Patwardhan SV, Annenkov VV, Danilovtseva EN, Perry CC. From biosilicification to tailored materials: optimizing hydrophobic domains and resistance to protonation of polyamines. Proc Natl Acad Sci U S A 2008; 105:5963-8. [PMID: 18420819 PMCID: PMC2329702 DOI: 10.1073/pnas.0710809105] [Citation(s) in RCA: 88] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2007] [Indexed: 11/18/2022] Open
Abstract
Considerable research has been directed toward identifying the mechanisms involved in biosilicification to understand and possibly mimic the process for the production of superior silica-based materials while simultaneously minimizing pollution and energy costs. Molecules isolated from diatoms and, most recently sponges, thought to be key to this process contain polyamines with a propylamine backbone and variable levels of methylation. In a chemical approach to understanding the role of amine (especially propylamine) structures in silicification we have explored three key structural features: (i) the degree of polymerization, (ii) the level of amine methylation, and (iii) the size of the amine chain spacers. In this article, we show that there are two factors critical to their function: the ability of the amines to produce microemulsions and the presence of charged and uncharged amine groups within a molecule, with the latter feature helping to catalyze silicic acid condensation by a proton donor/acceptor mechanism. The understanding of amine-silicate interactions obtained from this study has enabled the controlled preparation of hollow and nonporous siliceous materials under mild conditions (circumneutral pH, room temperature, and in all aqueous systems) possibly compatible with the conditions used by biosystems. The "rules" identified from our study were further used predictively to modulate the activity of a given amine. We believe that the outcomes of the present contribution will form the basis for an approach to controlling the growth of inorganic materials by using tailor-made organic molecules.
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Affiliation(s)
- David J. Belton
- *School of Science and Technology, Nottingham Trent University, Clifton Lane, Nottingham NG11 8NS, United Kingdom; and
| | - Siddharth V. Patwardhan
- *School of Science and Technology, Nottingham Trent University, Clifton Lane, Nottingham NG11 8NS, United Kingdom; and
| | - Vadim V. Annenkov
- Limnological Institute of Siberian Branch of Russian Academy of Sciences, 3, Ulan-Batorskaya Street, P.O. Box 4199, Irkutsk 664033, Russia
| | - Elena N. Danilovtseva
- Limnological Institute of Siberian Branch of Russian Academy of Sciences, 3, Ulan-Batorskaya Street, P.O. Box 4199, Irkutsk 664033, Russia
| | - Carole C. Perry
- *School of Science and Technology, Nottingham Trent University, Clifton Lane, Nottingham NG11 8NS, United Kingdom; and
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Petrova DP, Bedoshvili YD, Shelukhina IV, Samukov VV, Korneva ES, Vereshagin AL, Popkova TP, Karpyshev NN, Lebedeva DV, Klimenkov IV, Likhoshway YV, Grachev MA. Detection of the silicic acid transport protein in the freshwater diatom Synedra acus by immunoblotting and immunoelectron microscopy. DOKL BIOCHEM BIOPHYS 2008; 417:295-8. [PMID: 18274442 DOI: 10.1134/s1607672907060014] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
Affiliation(s)
- D P Petrova
- Limnological Institute, Siberian Division, Russian Academy of Sciences, ul. Ulan-Batorskaya 3, Irkutsk 664033, Russia
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Wenzl S, Hett R, Richthammer P, Sumper M. Silacidins: highly acidic phosphopeptides from diatom shells assist in silica precipitation in vitro. Angew Chem Int Ed Engl 2008; 47:1729-32. [PMID: 18203228 DOI: 10.1002/anie.200704994] [Citation(s) in RCA: 118] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
Affiliation(s)
- Stephan Wenzl
- Lehrstuhl Biochemie I, Universität Regensburg, 93040 Regensburg, Germany
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68
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Wenzl S, Hett R, Richthammer P, Sumper M. Silacidins: Highly Acidic Phosphopeptides from Diatom Shells Assist in Silica Precipitation In Vitro. Angew Chem Int Ed Engl 2008. [DOI: 10.1002/ange.200704994] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
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69
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Mock T, Samanta MP, Iverson V, Berthiaume C, Robison M, Holtermann K, Durkin C, BonDurant SS, Richmond K, Rodesch M, Kallas T, Huttlin EL, Cerrina F, Sussman MR, Armbrust EV. Whole-genome expression profiling of the marine diatom Thalassiosira pseudonana identifies genes involved in silicon bioprocesses. Proc Natl Acad Sci U S A 2008; 105:1579-84. [PMID: 18212125 PMCID: PMC2234187 DOI: 10.1073/pnas.0707946105] [Citation(s) in RCA: 204] [Impact Index Per Article: 12.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2007] [Indexed: 11/18/2022] Open
Abstract
Formation of complex inorganic structures is widespread in nature. Diatoms create intricately patterned cell walls of inorganic silicon that are a biomimetic model for design and generation of three-dimensional silica nanostructures. To date, only relatively simple silica structures can be generated in vitro through manipulation of known diatom phosphoproteins (silaffins) and long-chain polyamines. Here, we report the use of genome-wide transcriptome analyses of the marine diatom Thalassiosira pseudonana to identify additional candidate gene products involved in the biological manipulation of silicon. Whole-genome oligonucleotide tiling arrays and tandem mass spectrometry identified transcripts for >8,000 genes, approximately 3,000 of which were not previously described and included noncoding and antisense RNAs. Gene-specific expression profiles detected a set of 75 genes induced only under low concentrations of silicon but not under low concentrations of nitrogen or iron, alkaline pH, or low temperatures. Most of these induced gene products were predicted to contain secretory signals and/or transmembrane domains but displayed no homology to known proteins. Over half of these genes were newly discovered, identified only through the use of tiling arrays. Unexpectedly, a common set of 84 genes were induced by both silicon and iron limitations, suggesting that biological manipulation of silicon may share pathways in common with iron or, alternatively, that iron may serve as a required cofactor for silicon processes. These results provide insights into the transcriptional and translational basis for the biological generation of elaborate silicon nanostructures by these ecologically important microbes.
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Affiliation(s)
- Thomas Mock
- *School of Oceanography, University of Washington, Box 357940, Seattle, WA 98195
| | | | - Vaughn Iverson
- *School of Oceanography, University of Washington, Box 357940, Seattle, WA 98195
| | - Chris Berthiaume
- *School of Oceanography, University of Washington, Box 357940, Seattle, WA 98195
| | - Matthew Robison
- Biotechnology Center, University of Wisconsin, Madison, WI 53706
| | - Karie Holtermann
- *School of Oceanography, University of Washington, Box 357940, Seattle, WA 98195
| | - Colleen Durkin
- *School of Oceanography, University of Washington, Box 357940, Seattle, WA 98195
| | | | - Kathryn Richmond
- Biotechnology Center, University of Wisconsin, Madison, WI 53706
| | - Matthew Rodesch
- Biotechnology Center, University of Wisconsin, Madison, WI 53706
| | - Toivo Kallas
- Department of Biology and Microbiology, University of Wisconsin, Oshkosh, WI 54901; and
| | | | - Francesco Cerrina
- Biotechnology Center, University of Wisconsin, Madison, WI 53706
- Electrical and Computer Engineering, University of Wisconsin, Madison, WI 53706
| | - Michael R. Sussman
- Biotechnology Center, University of Wisconsin, Madison, WI 53706
- Departments of Biochemistry and
| | - E. Virginia Armbrust
- *School of Oceanography, University of Washington, Box 357940, Seattle, WA 98195
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Misumi O, Yoshida Y, Nishida K, Fujiwara T, Sakajiri T, Hirooka S, Nishimura Y, Kuroiwa T. Genome analysis and its significance in four unicellular algae, Cyanidioschyzon [corrected] merolae, Ostreococcus tauri, Chlamydomonas reinhardtii, and Thalassiosira pseudonana. JOURNAL OF PLANT RESEARCH 2008; 121:3-17. [PMID: 18074102 DOI: 10.1007/s10265-007-0133-9] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/05/2007] [Accepted: 10/30/2007] [Indexed: 05/19/2023]
Abstract
Algae play a more important role than land plants in the maintenance of the global environment and productivity. Progress in genome analyses of these organisms means that we can now obtain information on algal genomes, global annotation and gene expression. The full genome information for several algae has already been analyzed. Whole genomes of the red alga Cyanidioschyzon [corrected] merolae, the green algae Ostreococcus tauri and Chlamydomonas reinhardtii, and the diatom Thalassiosira pseudonana have been sequenced. Genome composition and the features of cells among the four algae were compared. Each alga maintains basic genes as photosynthetic eukaryotes and possesses additional gene groups to represent their particular characteristics. This review discusses and introduces the latest research that makes the best use of the particular features of each organism and the significance of genome analysis to study biological phenomena. In particular, examples of post-genome studies of organelle multiplication in C. merolae based on analyzed genome information are presented.
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Affiliation(s)
- Osami Misumi
- Department of Life Science, Graduate School of Science, Rikkyo University, Tokyo 171-8501, Japan
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Crookes-Goodson WJ, Slocik JM, Naik RR. Bio-directed synthesis and assembly of nanomaterials. Chem Soc Rev 2008; 37:2403-12. [DOI: 10.1039/b702825n] [Citation(s) in RCA: 161] [Impact Index Per Article: 10.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
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72
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Davis AK, Palenik B. Characterization of a modular, cell-surface protein and identification of a new gene family in the diatom Thalassiosira pseudonana. Protist 2007; 159:195-207. [PMID: 18162437 DOI: 10.1016/j.protis.2007.09.006] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2007] [Accepted: 09/29/2007] [Indexed: 11/17/2022]
Abstract
We report the characterization of a cell-surface protein isolated from copper-stressed cells of the centric diatom Thalassiosira pseudonana Hasle and Heimdal (CCMP 1335). This protein has an apparent molecular weight of 100kDa and is highly acidic. The 100kDa protein (p100) sequence is comprised almost entirely of a novel domain termed TpRCR for T. pseudonana repetitive cysteine-rich domain, that is repeated 8 times and that contains conserved aromatic, acidic, and potential metal-binding amino acids. The analysis of the T. pseudonana genome suggests that p100 belongs to a large family of modular proteins that consist of a variable number of TpRCR domain repeats. Based on cell surface biotinylation and antibody data, p100 appears to migrate more rapidly with SDS-PAGE when extracted from cells exposed to high levels of copper; however, the discovery of a large family of TpRCR domain-containing proteins leaves open the possibility that the antibody may be cross-reacting with members of this protein family that are responding differently to copper. The response of the gene encoding p100 at the mRNA level during synchronized progression through the normal cell cycle is similar to previously characterized genes in T. pseudonana encoding cell wall proteins called silaffins.
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Affiliation(s)
- Aubrey K Davis
- Scripps Institution of Oceanography, University of California-San Diego, La Jolla, CA 92093-0202, USA
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73
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Desclés J, Vartanian M, El Harrak A, Quinet M, Bremond N, Sapriel G, Bibette J, Lopez PJ. New tools for labeling silica in living diatoms. THE NEW PHYTOLOGIST 2007; 177:822-829. [PMID: 18069957 DOI: 10.1111/j.1469-8137.2007.02303.x] [Citation(s) in RCA: 44] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/25/2023]
Abstract
Silicon biomineralization is a widespread mechanism found in several kingdoms that concerns both unicellular and multicellular organisms. As a result of genomic and molecular tools, diatoms have emerged as a good model for biomineralization studies and have provided most of the current knowledge on this process. However, the number of techniques available to study its dynamics at the cellular level is still rather limited. Here, new probes were developed specifically to label the pre-existing or the newly synthesized silica frustule of several diatoms species. It is shown that the LysoTracker Yellow HCK-123, which can be used to visualize silica frustules with common filter sets, presents an enhanced signal-to-noise ratio and allows details of the frustules to be imaged without of the use of ionophores. It is also demonstrated that methoxysilane derivatives can be coupled to fluorescein-5-isothiocyanate (FITC) to preferentially label the silica components of living cells. The coupling of labeling procedures might help to address the challenging question of the process of frustule exocytosis.
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Affiliation(s)
- Julien Desclés
- Laboratoire Biologie Moléculaire des Organismes Photosynthétiques CNRS UMR-8186, Ecole Normale Supérieure, 46 rue d'Ulm, 75005 Paris, France
| | - Mathieu Vartanian
- Laboratoire Biologie Moléculaire des Organismes Photosynthétiques CNRS UMR-8186, Ecole Normale Supérieure, 46 rue d'Ulm, 75005 Paris, France
| | - Abdeslam El Harrak
- Laboratoire Colloïdes et Matériaux Divisés, ESPCI, 10 rue Vauquelin, 75005 Paris, France
| | - Michelle Quinet
- Laboratoire Biologie Moléculaire des Organismes Photosynthétiques CNRS UMR-8186, Ecole Normale Supérieure, 46 rue d'Ulm, 75005 Paris, France
| | - Nicolas Bremond
- Laboratoire Colloïdes et Matériaux Divisés, ESPCI, 10 rue Vauquelin, 75005 Paris, France
| | - Guillaume Sapriel
- Laboratoire Biologie Moléculaire des Organismes Photosynthétiques CNRS UMR-8186, Ecole Normale Supérieure, 46 rue d'Ulm, 75005 Paris, France
| | - Jérome Bibette
- Laboratoire Colloïdes et Matériaux Divisés, ESPCI, 10 rue Vauquelin, 75005 Paris, France
| | - Pascal J Lopez
- Laboratoire Biologie Moléculaire des Organismes Photosynthétiques CNRS UMR-8186, Ecole Normale Supérieure, 46 rue d'Ulm, 75005 Paris, France
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74
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Kröger N. Prescribing diatom morphology: toward genetic engineering of biological nanomaterials. Curr Opin Chem Biol 2007; 11:662-9. [PMID: 17991447 DOI: 10.1016/j.cbpa.2007.10.009] [Citation(s) in RCA: 69] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2007] [Accepted: 10/08/2007] [Indexed: 10/22/2022]
Abstract
The formation of inorganic materials with complex form is a widespread biological phenomenon (biomineralization). Among the most spectacular examples of biomineralization is the production by diatoms (a group of eukaryotic microalgae) of intricately nanopatterned to micropatterned cell walls made of silica (SiO2). Understanding the molecular mechanisms of diatom silica biomineralization is not only a fundamental biological problem, but also of great interest in materials engineering, as the biological self-assembly of three-dimensional (3D) inorganic nanomaterials has no man-made analog. Recently, insight into the molecular mechanism of diatom silica formation has been obtained by structural and functional analysis of biomolecules that are involved in this process. Furthermore, the rapid development of diatom molecular genetics has provided new tools for investigating the silica forming machinery of diatoms and for manipulating silica biogenesis. This has opened the door for the production, through genetic engineering, of unique 3D nanomaterials with designed structures and functionalities.
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Affiliation(s)
- Nils Kröger
- School of Chemistry & Biochemistry, Georgia Institute of Technology, Atlanta, GA 30332-0400, USA.
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75
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Zhou F, Li S, Vo CD, Yuan JJ, Chai S, Gao Q, Armes SP, Lu C, Cheng S. Biomimetic deposition of silica templated by a cationic polyamine-containing microgel. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2007; 23:9737-44. [PMID: 17685562 DOI: 10.1021/la700715t] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/16/2023]
Abstract
We report using poly(acrylamide-co-2-(dimethylamino)ethyl methacrylate, methyl chloride quaternized) cationic microgels as a porous colloidal template for biomimetic in situ silica mineralization, allowing the well-controlled synthesis of submicrometer-sized hybrid microgel--silica particles and porous silica particles by subsequent calcination. The microgels were prepared by inverse emulsion polymerization in the presence of a bisacrylamide cross-linker. Silica deposition was achieved by simply stirring an aqueous mixture of the microgel particles and tetramethyl orthosilicate (TMOS) at 20 degrees C for 30 min. No experimental evidence was found for nontemplated silica, which indicated that silica deposition occurred exclusively within the cationic microgel template particles. The resulting microgel-silica hybrid particles were characterized by electron microscopy, dynamic light scattering, FT-IR spectroscopy, 1H NMR and solid-state 29Si magic angle spinning NMR spectroscopy, thermogravimetry, aqueous electrophoresis, and surface area measurements. Aqueous electrophoresis studies confirmed that the hybrid microgel-silica particles had positive zeta potentials over a wide pH range and isoelectric points could be tuned by varying the synthesis conditions. This suggests that these particles could form complexes with DNA for improved gene delivery. The porosity of the calcined silica particles could be controlled by varying the amount of TMOS, suggesting potential encapsulation/controlled release applications.
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Affiliation(s)
- Fen Zhou
- Faculty of Materials Sciences and Engineering, Hubei University, Wuhan 430062, China
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76
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MANURUNG AGNESIMELDA, PRATIWI ALBERTARIKA, SYAH DAHRUL, SUHARTONO MAGGYTHENAWIDJAJA. Isolation and Characterization of Silaffin that Catalyze Biosilica Formation from Marine Diatom Chaetoceros gracilis. HAYATI JOURNAL OF BIOSCIENCES 2007. [DOI: 10.4308/hjb.14.3.119] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022] Open
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77
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Bopp SK, Lettieri T. Gene regulation in the marine diatom Thalassiosira pseudonana upon exposure to polycyclic aromatic hydrocarbons (PAHs). Gene 2007; 396:293-302. [PMID: 17540515 DOI: 10.1016/j.gene.2007.03.013] [Citation(s) in RCA: 58] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2006] [Revised: 03/23/2007] [Accepted: 03/23/2007] [Indexed: 11/20/2022]
Abstract
Diatoms are eukaryotic algae, which can be found worldwide in oceans and freshwaters. These organisms are ecologically relevant due to their key role in the global carbon cycle, contributing to about 25% to the global primary production [Falciatore, A., Bowler, C., 2002. Revealing the molecular secrets of marine diatoms. Annu. Rev. Plant Biol. 53, 109-130]. We investigated the effects of three polycyclic aromatic hydrocarbons (PAHs, pyrene, fluoranthene, and benzo[a]pyrene), either as single compound or as mixture, at molecular level. Dose-response curves for growth inhibition were determined and four concentrations eliciting from "no effect" up to a severe growth inhibition were chosen for further investigation to detect alterations at gene expression level by Real-Time PCR. Among the eight selected genes, two were strongly influenced by the PAH treatment. lacsA, which is involved in the fatty acid metabolism, was found to be strongly up-regulated by all single PAHs, as well as by the mixture. sil3, involved in the formation of the silica shell, was repressed by a factor up to three even at low PAH concentrations not eliciting any growth inhibition. For other genes, involved e.g. in photosynthesis, a slight down-regulation was detected. Based on the effects at gene expression level it can be assumed that PAHs impair the fatty acid metabolism and silica shell formation.
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Affiliation(s)
- Stephanie K Bopp
- European Commission -- DG Joint Research Centre, Institute for Environment and Sustainability, Rural, Water, and Ecosystem Resources Unit, T.P. 300, Via E. Fermi 1, 21020 Ispra (VA), Italy
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78
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Affiliation(s)
- Martin T Croft
- Department of Plant Sciences, University of Cambridge, Cambridge CB2 3EA, United Kingdom.
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79
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Thamatrakoln K, Hildebrand M. Analysis of Thalassiosira pseudonana silicon transporters indicates distinct regulatory levels and transport activity through the cell cycle. EUKARYOTIC CELL 2007; 6:271-9. [PMID: 17172435 PMCID: PMC1797941 DOI: 10.1128/ec.00235-06] [Citation(s) in RCA: 56] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/18/2006] [Accepted: 12/06/2006] [Indexed: 12/31/2022]
Abstract
An analysis of the expression and activity of silicon transporters (SITs) was done on synchronously growing cultures of the diatom Thalassiosira pseudonana to provide insight into the role these proteins play in cellular silicon metabolism during the cell cycle. The first SIT-specific polyclonal peptide antibody was generated and used in the immunoblot analysis of whole-cell protein lysates to monitor SIT protein levels during synchronized progression through the cell cycle. Peaks in SIT protein levels correlated with active periods of silica incorporation into cell wall substructures. Quantitative real-time PCR on each of the three distinct SIT genes (TpSIT1, TpSIT2, and TpSIT3) showed that mRNA levels for the most highly expressed SIT genes peaked during the S phase of the cell cycle, a period prior to maximal silicon uptake and during which cell wall silicification does not occur. Variations in protein and mRNA levels did not correlate, suggesting that a significant regulatory step of SITs is at the translational or posttranslational level. Surge uptake rates also did not correlate with SIT protein levels, suggesting that SIT activity is internally controlled by the rate of silica incorporation. This is the first study to characterize SIT mRNA and protein expression and cellular uptake kinetics during the course of the cell cycle and cell wall synthesis, and it provides novel insight into SIT regulation.
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Affiliation(s)
- Kimberlee Thamatrakoln
- Marine Biology Research Division, Scripps Institution of Oceanography, 9500 Gilman Dr., MC 0202, La Jolla, CA 92093-0202, USA
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