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Ehrlich H, Voronkina A, Tabachniсk K, Kubiak A, Ereskovsky A, Jesionowski T. Silactins and Structural Diversity of Biosilica in Sponges. Biomimetics (Basel) 2024; 9:393. [PMID: 39056834 PMCID: PMC11274843 DOI: 10.3390/biomimetics9070393] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2024] [Revised: 06/23/2024] [Accepted: 06/24/2024] [Indexed: 07/28/2024] Open
Abstract
Sponges (phylum Porifera) were among the first metazoans on Earth, and represent a unique global source of highly structured and diverse biosilica that has been formed and tested over more than 800 million years of evolution. Poriferans are recognized as a unique archive of siliceous multiscaled skeletal constructs with superficial micro-ornamentation patterned by biopolymers. In the present study, spicules and skeletal frameworks of selected representatives of sponges in such classes as Demospongiae, Homoscleromorpha, and Hexactinellida were desilicified using 10% HF with the aim of isolating axial filaments, which resemble the shape and size of the original structures. These filaments were unambiguously identified in all specimens under study as F-actin, using the highly specific indicators iFluor™ 594-Phalloidin, iFluor™ 488-Phalloidin, and iFluor™ 350-Phalloidin. The identification of this kind of F-actins, termed for the first time as silactins, as specific pattern drivers in skeletal constructs of sponges opens the way to the fundamental understanding of their skeletogenesis. Examples illustrating the biomimetic potential of sophisticated poriferan biosilica patterned by silactins are presented and discussed.
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Affiliation(s)
- Hermann Ehrlich
- Center of Advanced Technology, Adam Mickiewicz University, Uniwersytetu Poznańskiego 10, 61-614 Poznan, Poland;
- Faculty of Chemical Technology, Institute of Chemical Technology and Engineering, Poznan University of Technology, Berdychowo 4, 60-965 Poznan, Poland
| | - Alona Voronkina
- Pharmacy Department, National Pirogov Memorial Medical University, Vinnytsya, Pirogov Street 56, 21018 Vinnytsia, Ukraine;
| | - Konstantin Tabachniсk
- International Institute of Biomineralogy GmbH, Am St.-Niclas Schacht 13, 09599 Freiberg, Germany
| | - Anita Kubiak
- Center of Advanced Technology, Adam Mickiewicz University, Uniwersytetu Poznańskiego 10, 61-614 Poznan, Poland;
- Faculty of Chemistry, Adam Mickiewicz University, Uniwersytetu Poznanskiego 8, 61-614 Poznan, Poland
| | - Alexander Ereskovsky
- IMBE, CNRS, IRD, Aix Marseille University, Station Marine d’Endoume, Rue de la Batterie des Lions, 13007 Marseille, France;
| | - Teofil Jesionowski
- Faculty of Chemical Technology, Institute of Chemical Technology and Engineering, Poznan University of Technology, Berdychowo 4, 60-965 Poznan, Poland
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Li Y, He J, Zhang X, Deng X. The draft genome of Nitzschia closterium f. minutissima and transcriptome analysis reveals novel insights into diatom biosilicification. BMC Genomics 2024; 25:560. [PMID: 38840265 PMCID: PMC11151724 DOI: 10.1186/s12864-024-10479-9] [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: 01/16/2024] [Accepted: 05/30/2024] [Indexed: 06/07/2024] Open
Abstract
BACKGROUND Nitzschia closterium f. minutissima is a commonly available diatom that plays important roles in marine aquaculture. It was originally classified as Nitzschia (Bacillariaceae, Bacillariophyta) but is currently regarded as a heterotypic synonym of Phaeodactylum tricornutum. The aim of this study was to obtain the draft genome of the marine microalga N. closterium f. minutissima to understand its phylogenetic placement and evolutionary specialization. Given that the ornate hierarchical silicified cell walls (frustules) of diatoms have immense applications in nanotechnology for biomedical fields, biosensors and optoelectric devices, transcriptomic data were generated by using reference genome-based read mapping to identify significantly differentially expressed genes and elucidate the molecular processes involved in diatom biosilicification. RESULTS In this study, we generated 13.81 Gb of pass reads from the PromethION sequencer. The draft genome of N. closterium f. minutissima has a total length of 29.28 Mb, and contains 28 contigs with an N50 value of 1.23 Mb. The GC content was 48.55%, and approximately 18.36% of the genome assembly contained repeat sequences. Gene annotation revealed 9,132 protein-coding genes. The results of comparative genomic analysis showed that N. closterium f. minutissima was clustered as a sister lineage of Phaeodactylum tricornutum and the divergence time between them was estimated to be approximately 17.2 million years ago (Mya). CAFF analysis demonstrated that 220 gene families that significantly changed were unique to N. closterium f. minutissima and that 154 were specific to P. tricornutum, moreover, only 26 gene families overlapped between these two species. A total of 818 DEGs in response to silicon were identified in N. closterium f. minutissima through RNA sequencing, these genes are involved in various molecular processes such as transcription regulator activity. Several genes encoding proteins, including silicon transporters, heat shock factors, methyltransferases, ankyrin repeat domains, cGMP-mediated signaling pathways-related proteins, cytoskeleton-associated proteins, polyamines, glycoproteins and saturated fatty acids may contribute to the formation of frustules in N. closterium f. minutissima. CONCLUSIONS Here, we described a draft genome of N. closterium f. minutissima and compared it with those of eight other diatoms, which provided new insight into its evolutionary features. Transcriptome analysis to identify DEGs in response to silicon will help to elucidate the underlying molecular mechanism of diatom biosilicification in N. closterium f. minutissima.
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Affiliation(s)
- Yajun Li
- Institute of Tropical Bioscience and Biotechnology, Chinese Academy of Tropical Agricultural Sciences (CATAS) & Key Laboratory of Biology and Genetic Resources of Tropical Crops of Hainan Province, Haikou, 571101, China.
- Hainan Provincial Key Laboratory for Functional Components Research and Utilization of Marine Bioresources, Haikou, 571101, China.
| | - Jinman He
- Institute of Tropical Bioscience and Biotechnology, Chinese Academy of Tropical Agricultural Sciences (CATAS) & Key Laboratory of Biology and Genetic Resources of Tropical Crops of Hainan Province, Haikou, 571101, China
- Hainan Provincial Key Laboratory for Functional Components Research and Utilization of Marine Bioresources, Haikou, 571101, China
| | - Xiuxia Zhang
- Institute of Tropical Bioscience and Biotechnology, Chinese Academy of Tropical Agricultural Sciences (CATAS) & Key Laboratory of Biology and Genetic Resources of Tropical Crops of Hainan Province, Haikou, 571101, China
- Hainan Provincial Key Laboratory for Functional Components Research and Utilization of Marine Bioresources, Haikou, 571101, China
| | - Xiaodong Deng
- Institute of Tropical Bioscience and Biotechnology, Chinese Academy of Tropical Agricultural Sciences (CATAS) & Key Laboratory of Biology and Genetic Resources of Tropical Crops of Hainan Province, Haikou, 571101, China.
- Hainan Provincial Key Laboratory for Functional Components Research and Utilization of Marine Bioresources, Haikou, 571101, China.
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Wang X, Meng X, Dong Y, Song C, Sui F, Lu X, Mei X, Fan Y, Liu Y. Differential protein analysis of saline-alkali promoting the oil accumulation in Nitzschia palea. BIOTECHNOLOGY FOR BIOFUELS AND BIOPRODUCTS 2024; 17:11. [PMID: 38282018 PMCID: PMC10823674 DOI: 10.1186/s13068-023-02451-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/17/2023] [Accepted: 12/16/2023] [Indexed: 01/30/2024]
Abstract
BACKGROUND The increasingly severe salinization of the aquatic environment has led to serious damage to the habitats of aquatic organisms. Benthic diatoms are commonly employed as indicator species for assessing water quality and serve as a reflection of the overall health of the aquatic ecosystem. Nitzschia palea is a common diatom found in freshwater, with high oil content, rapid reproductive rate, and it is a commonly dominant species in various rivers. RESULTS The results showed that after 4 days (d) of saline-alkali stress, the cell density and chlorophyll a content of Nitzschia palea reached their maximum values. Therefore, we selected Nitzschia palea under 4 d stress for Tandem Mass Tag (TMT) quantitative proteomic analysis to explore the molecular adaptation mechanism of freshwater diatoms under saline-alkali stress. Totally, 854 proteins were enriched, of which 439 differentially expressed proteins were identified. Gene ontology (GO), Kyoto Encyclopedia of Genes and Genomes (KEGG), and subcellular fractionation analysis revealed that these proteins were mainly enriched in the photosynthesis pathway, citric acid cycle (TCA cycle), fatty acid synthesis, and glutathione cycle. CONCLUSIONS This study aims to reveal the physiological, biochemical and proteomic mechanisms of salt and alkali tolerance and molecular adaptation of Nitzschia palea under different saline-alkali concentrations. This study showed that Nitzschia palea is one candidate of the environmental friendly, renewable bioenergy microalgae. Meantime, Nitzschia palea reveals for the proteome of the freshwater and provides the basis, it became a model algal species for freshwater diatoms.
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Affiliation(s)
- Xintong Wang
- College of Life Sciences and Technology, Harbin Normal University, Harbin, China
| | - Xianghong Meng
- College of Life Sciences and Technology, Harbin Normal University, Harbin, China
| | - Yanlong Dong
- College of Life Sciences and Technology, Harbin Normal University, Harbin, China
| | - Chunhua Song
- College of Life Sciences and Technology, Harbin Normal University, Harbin, China
| | - Fengyang Sui
- College of Life Sciences and Technology, Harbin Normal University, Harbin, China
| | - Xinxin Lu
- College of Life Sciences and Technology, Harbin Normal University, Harbin, China
| | - Xiaoxue Mei
- College of Life Sciences and Technology, Harbin Normal University, Harbin, China
| | - Yawen Fan
- College of Life Sciences and Technology, Harbin Normal University, Harbin, China.
- Key Laboratory of Biodiversity of Aquatic Organisms, Harbin Normal University, Harbin, China.
| | - Yan Liu
- College of Life Sciences and Technology, Harbin Normal University, Harbin, China.
- Key Laboratory of Biodiversity of Aquatic Organisms, Harbin Normal University, Harbin, China.
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Zepernick BN, Niknejad DJ, Stark GF, Truchon AR, Martin RM, Rossignol KL, Paerl HW, Wilhelm SW. Morphological, physiological, and transcriptional responses of the freshwater diatom Fragilaria crotonensis to elevated pH conditions. Front Microbiol 2022; 13:1044464. [PMID: 36504786 PMCID: PMC9732472 DOI: 10.3389/fmicb.2022.1044464] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2022] [Accepted: 11/07/2022] [Indexed: 11/27/2022] Open
Abstract
Harmful algal blooms (HABs) caused by the toxin-producing cyanobacteria Microcystis spp., can increase water column pH. While the effect(s) of these basified conditions on the bloom formers are a high research priority, how these pH shifts affect other biota remains understudied. Recently, it was shown these high pH levels decrease growth and Si deposition rates in the freshwater diatom Fragilaria crotonensis and natural Lake Erie (Canada-US) diatom populations. However, the physiological mechanisms and transcriptional responses of diatoms associated with these observations remain to be documented. Here, we examined F. crotonensis with a set of morphological, physiological, and transcriptomic tools to identify cellular responses to high pH. We suggest 2 potential mechanisms that may contribute to morphological and physiological pH effects observed in F. crotonensis. Moreover, we identified a significant upregulation of mobile genetic elements in the F. crotonensis genome which appear to be an extreme transcriptional response to this abiotic stress to enhance cellular evolution rates-a process we have termed "genomic roulette." We discuss the ecological and biogeochemical effects high pH conditions impose on fresh waters and suggest a means by which freshwater diatoms such as F. crotonensis may evade high pH stress to survive in a "basified" future.
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Affiliation(s)
| | - David J. Niknejad
- Department of Microbiology, University of Tennessee, Knoxville, TN, United States
| | - Gwendolyn F. Stark
- Department of Microbiology, University of Tennessee, Knoxville, TN, United States
| | - Alexander R. Truchon
- Department of Microbiology, University of Tennessee, Knoxville, TN, United States
| | - Robbie M. Martin
- Department of Microbiology, University of Tennessee, Knoxville, TN, United States
| | - Karen L. Rossignol
- Institute of Marine Sciences, University of North Carolina at Chapel Hill, Morehead City, NC, United States
| | - Hans W. Paerl
- Institute of Marine Sciences, University of North Carolina at Chapel Hill, Morehead City, NC, United States
| | - Steven W. Wilhelm
- Department of Microbiology, University of Tennessee, Knoxville, TN, United States
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Fattorini N, Maier UG. Targeting motifs in frustule-associated proteins from the centric diatom Thalassiosira pseudonana. FRONTIERS IN PLANT SCIENCE 2022; 13:1006072. [PMID: 36388477 PMCID: PMC9650480 DOI: 10.3389/fpls.2022.1006072] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/28/2022] [Accepted: 09/05/2022] [Indexed: 06/16/2023]
Abstract
The frustule of diatoms has an exceptional structure composed of inorganic and organic molecules. In the organic fraction, protein families were identified whose members are expected to have a complex cellular targeting to their final location within the frustule. Here we investigated for frustule-targeting signals two representatives of the cingulin family, the proteins CinY2 and CinW2; beside an already known, classical signal peptide, we have identified further regions involved in cellular targeting. By using these regions as a search criteria we were able to identify two new frustule proteins. In addition, we showed that the temporal regulation of the gene expression determines the final location of one cingulin. Our results therefore point to a sophisticated cellular and extracellular targeting of frustule components to build the fascinating frustule structure of a diatom.
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Affiliation(s)
- Neri Fattorini
- Department of Biology, Laboratory for Cell Biology Philipps-University Marburg, Marburg, Germany
| | - Uwe G. Maier
- Department of Biology, Laboratory for Cell Biology Philipps-University Marburg, Marburg, Germany
- Center for Synthetic Microbiology (SYNMIKRO), Philipps-University Marburg, Marburg, Germany
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6
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Ehrlich H, Luczak M, Ziganshin R, Mikšík I, Wysokowski M, Simon P, Baranowska‐Bosiacka I, Kupnicka P, Ereskovsky A, Galli R, Dyshlovoy S, Fischer J, Tabachnick KR, Petrenko I, Jesionowski T, Lubkowska A, Figlerowicz M, Ivanenko VN, Summers AP. Arrested in Glass: Actin within Sophisticated Architectures of Biosilica in Sponges. ADVANCED SCIENCE (WEINHEIM, BADEN-WURTTEMBERG, GERMANY) 2022; 9:e2105059. [PMID: 35156333 PMCID: PMC9009123 DOI: 10.1002/advs.202105059] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/23/2021] [Revised: 01/25/2022] [Indexed: 06/14/2023]
Abstract
Actin is a fundamental member of an ancient superfamily of structural intracellular proteins and plays a crucial role in cytoskeleton dynamics, ciliogenesis, phagocytosis, and force generation in both prokaryotes and eukaryotes. It is shown that actin has another function in metazoans: patterning biosilica deposition, a role that has spanned over 500 million years. Species of glass sponges (Hexactinellida) and demosponges (Demospongiae), representatives of the first metazoans, with a broad diversity of skeletal structures with hierarchical architecture unchanged since the late Precambrian, are studied. By etching their skeletons, organic templates dominated by individual F-actin filaments, including branched fibers and the longest, thickest actin fiber bundles ever reported, are isolated. It is proposed that these actin-rich filaments are not the primary site of biosilicification, but this highly sophisticated and multi-scale form of biomineralization in metazoans is ptterned.
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Affiliation(s)
- Hermann Ehrlich
- Institute of Electronic and Sensor MaterialsTU Bergakademie FreibergFreiberg09599Germany
- Center for Advanced TechnologyAdam Mickiewicz UniversityPoznan61614Poland
| | - Magdalena Luczak
- Institute of Bioorganic ChemistryPolish Academy of SciencesPoznan61704Poland
| | - Rustam Ziganshin
- Institute of Bioorganic ChemistryRussian Academy of SciencesMoscow142290Russian Federation
| | - Ivan Mikšík
- Institute of PhysiologyThe Czech Academy of SciencesPrague142 20Czech Republic
| | - Marcin Wysokowski
- Institute of Electronic and Sensor MaterialsTU Bergakademie FreibergFreiberg09599Germany
- Faculty of Chemical TechnologyInstitute of Chemical Technology and EngineeringPoznan University of TechnologyPoznan60965Poland
| | - Paul Simon
- Max Planck Institute for Chemical Physics of SolidsDresden01187Germany
| | - Irena Baranowska‐Bosiacka
- Department of Biochemistry and Medical ChemistryPomeranian Medical University in SzczecinSzczecin70111Poland
| | - Patrycja Kupnicka
- Department of Biochemistry and Medical ChemistryPomeranian Medical University in SzczecinSzczecin70111Poland
| | - Alexander Ereskovsky
- Institut Méditerranéen de Biodiversité et d'Ecologie (IMBE)CNRSIRDAix Marseille UniversitéMarseille13003France
- Biological FacultySt. Petersburg State UniversitySt. Petersburg199034Russian Federation
- Koltzov Institute of Developmental Biology of Russian Academy of SciencesMoscow119334Russian Federation
| | - Roberta Galli
- Clinical Sensoring and MonitoringDepartment of Anesthesiology and Intensive Care MedicineTU DresdenDresden01307Germany
| | - Sergey Dyshlovoy
- Laboratory of Experimental OncologyUniversity Medical Center Hamburg‐EppendorfHamburg20251Germany
- Laboratory of PharmacologyA.V. Zhirmunsky National Scientific Center of Marine BiologyFar Eastern BranchRussian Academy of SciencesVladivostok690041Russian Federation
| | - Jonas Fischer
- Institute of Electronic and Sensor MaterialsTU Bergakademie FreibergFreiberg09599Germany
| | | | - Iaroslav Petrenko
- Institute of Electronic and Sensor MaterialsTU Bergakademie FreibergFreiberg09599Germany
| | - Teofil Jesionowski
- Faculty of Chemical TechnologyInstitute of Chemical Technology and EngineeringPoznan University of TechnologyPoznan60965Poland
| | - Anna Lubkowska
- Department of Functional Diagnostics and Physical MedicineFaculty of Health SciencesPomeranian Medical University in SzczecinSzczecin71210Poland
| | - Marek Figlerowicz
- Institute of Bioorganic ChemistryPolish Academy of SciencesPoznan61704Poland
| | - Viatcheslav N. Ivanenko
- Department of Invertebrate ZoologyBiological FacultyLomonosov Moscow State UniversityMoscow119991Russian Federation
| | - Adam P. Summers
- Department of BiologyFriday Harbor LabsUniversity of WashingtonFriday HarborWA98195USA
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7
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Machado M, Vaz MGMV, Bromke MA, Rosa RM, Covell L, Souza LPD, Rocha DI, Martins MA, Araújo WL, Szymański J, Nunes-Nesi A. Metabolic stability of freshwater Nitzschia palea strains under silicon stress associated with triacylglycerol accumulation. ALGAL RES 2021. [DOI: 10.1016/j.algal.2021.102554] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
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Osuna-Cruz CM, Bilcke G, Vancaester E, De Decker S, Bones AM, Winge P, Poulsen N, Bulankova P, Verhelst B, Audoor S, Belisova D, Pargana A, Russo M, Stock F, Cirri E, Brembu T, Pohnert G, Piganeau G, Ferrante MI, Mock T, Sterck L, Sabbe K, De Veylder L, Vyverman W, Vandepoele K. The Seminavis robusta genome provides insights into the evolutionary adaptations of benthic diatoms. Nat Commun 2020; 11:3320. [PMID: 32620776 PMCID: PMC7335047 DOI: 10.1038/s41467-020-17191-8] [Citation(s) in RCA: 31] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2020] [Accepted: 06/12/2020] [Indexed: 12/15/2022] Open
Abstract
Benthic diatoms are the main primary producers in shallow freshwater and coastal environments, fulfilling important ecological functions such as nutrient cycling and sediment stabilization. However, little is known about their evolutionary adaptations to these highly structured but heterogeneous environments. Here, we report a reference genome for the marine biofilm-forming diatom Seminavis robusta, showing that gene family expansions are responsible for a quarter of all 36,254 protein-coding genes. Tandem duplications play a key role in extending the repertoire of specific gene functions, including light and oxygen sensing, which are probably central for its adaptation to benthic habitats. Genes differentially expressed during interactions with bacteria are strongly conserved in other benthic diatoms while many species-specific genes are strongly upregulated during sexual reproduction. Combined with re-sequencing data from 48 strains, our results offer insights into the genetic diversity and gene functions in benthic diatoms.
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Affiliation(s)
- Cristina Maria Osuna-Cruz
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Technologiepark 71, 9052, Ghent, Belgium
- VIB Center for Plant Systems Biology, Technologiepark 71, 9052, Ghent, Belgium
- Bioinformatics Institute Ghent, Ghent University, Technologiepark 71, 9052, Ghent, Belgium
| | - Gust Bilcke
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Technologiepark 71, 9052, Ghent, Belgium
- VIB Center for Plant Systems Biology, Technologiepark 71, 9052, Ghent, Belgium
- Protistology and Aquatic Ecology, Department of Biology, Ghent University, 9000, Ghent, Belgium
- Department of Applied Mathematics, Computer Science and Statistics, Ghent University, 9000, Ghent, Belgium
| | - Emmelien Vancaester
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Technologiepark 71, 9052, Ghent, Belgium
- VIB Center for Plant Systems Biology, Technologiepark 71, 9052, Ghent, Belgium
- Bioinformatics Institute Ghent, Ghent University, Technologiepark 71, 9052, Ghent, Belgium
| | - Sam De Decker
- Protistology and Aquatic Ecology, Department of Biology, Ghent University, 9000, Ghent, Belgium
| | - Atle M Bones
- Cell Molecular Biology and Genomics Group, Department of Biology, Norwegian University of Science and Technology, 7491, Trondheim, Norway
| | - Per Winge
- Cell Molecular Biology and Genomics Group, Department of Biology, Norwegian University of Science and Technology, 7491, Trondheim, Norway
| | - Nicole Poulsen
- B CUBE Center for Molecular Bioengineering, Technical University of Dresden, Tatzberg 41, 01307, Dresden, Germany
| | - Petra Bulankova
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Technologiepark 71, 9052, Ghent, Belgium
- VIB Center for Plant Systems Biology, Technologiepark 71, 9052, Ghent, Belgium
| | - Bram Verhelst
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Technologiepark 71, 9052, Ghent, Belgium
- VIB Center for Plant Systems Biology, Technologiepark 71, 9052, Ghent, Belgium
| | - Sien Audoor
- Protistology and Aquatic Ecology, Department of Biology, Ghent University, 9000, Ghent, Belgium
| | - Darja Belisova
- Protistology and Aquatic Ecology, Department of Biology, Ghent University, 9000, Ghent, Belgium
| | - Aikaterini Pargana
- Protistology and Aquatic Ecology, Department of Biology, Ghent University, 9000, Ghent, Belgium
| | - Monia Russo
- Integrative Marine Ecology, Stazione Zoologica Anton Dohrn, Villa Comunale, Naples, Italy
| | - Frederike Stock
- Protistology and Aquatic Ecology, Department of Biology, Ghent University, 9000, Ghent, Belgium
| | - Emilio Cirri
- Friedrich Schiller University Jena, Institute of Inorganic and Analytical Chemistry, Lessingstrasse 8, 07745, Jena, Germany
| | - Tore Brembu
- Cell Molecular Biology and Genomics Group, Department of Biology, Norwegian University of Science and Technology, 7491, Trondheim, Norway
| | - Georg Pohnert
- Friedrich Schiller University Jena, Institute of Inorganic and Analytical Chemistry, Lessingstrasse 8, 07745, Jena, Germany
| | - Gwenael Piganeau
- Sorbonne Université, CNRS, UMR 7232 Biologie Intégrative des Organismes Marins BIOM, Observatoire Océanologique, F-66650, Banyuls-sur-Mer, France
| | | | - Thomas Mock
- School of Environmental Sciences, University of East Anglia, Norwich Research Park, Norwich, NR4 7TJ, UK
| | - Lieven Sterck
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Technologiepark 71, 9052, Ghent, Belgium
- VIB Center for Plant Systems Biology, Technologiepark 71, 9052, Ghent, Belgium
| | - Koen Sabbe
- Protistology and Aquatic Ecology, Department of Biology, Ghent University, 9000, Ghent, Belgium
| | - Lieven De Veylder
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Technologiepark 71, 9052, Ghent, Belgium
- VIB Center for Plant Systems Biology, Technologiepark 71, 9052, Ghent, Belgium
| | - Wim Vyverman
- Protistology and Aquatic Ecology, Department of Biology, Ghent University, 9000, Ghent, Belgium
| | - Klaas Vandepoele
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Technologiepark 71, 9052, Ghent, Belgium.
- VIB Center for Plant Systems Biology, Technologiepark 71, 9052, Ghent, Belgium.
- Bioinformatics Institute Ghent, Ghent University, Technologiepark 71, 9052, Ghent, Belgium.
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Fu H, Wang P, Wu X, Zhou X, Ji G, Shen Y, Gao Y, Li QQ, Liang J. Distinct genome‐wide alternative polyadenylation during the response to silicon availability in the marine diatom
Thalassiosira pseudonana. THE PLANT JOURNAL 2019; 99:67-80. [PMID: 30844106 DOI: 10.1111/tpj.14309] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/22/2018] [Revised: 02/15/2019] [Accepted: 02/27/2019] [Indexed: 05/28/2023]
Affiliation(s)
- Haihui Fu
- Key Laboratory of the Ministry of Education for Coastal and Wetland Ecosystems College of the Environment and Ecology Xiamen University Xiamen Fujian 361102 China
| | - Peng Wang
- School of Life Sciences Xiamen University Xiamen Fujian 361102 China
| | - Xiaohui Wu
- Department of Automation Xiamen University Xiamen Fujian 361005 China
| | - Xiaoxuan Zhou
- Key Laboratory of the Ministry of Education for Coastal and Wetland Ecosystems College of the Environment and Ecology Xiamen University Xiamen Fujian 361102 China
| | - Guoli Ji
- Department of Automation Xiamen University Xiamen Fujian 361005 China
| | - Yingjia Shen
- Key Laboratory of the Ministry of Education for Coastal and Wetland Ecosystems College of the Environment and Ecology Xiamen University Xiamen Fujian 361102 China
| | - Yahui Gao
- School of Life Sciences Xiamen University Xiamen Fujian 361102 China
| | - Qingshun Q. Li
- Key Laboratory of the Ministry of Education for Coastal and Wetland Ecosystems College of the Environment and Ecology Xiamen University Xiamen Fujian 361102 China
- Graduate College of Biomedical Sciences Western University of Health Sciences Pomona CA 91766 USA
| | - Junrong Liang
- School of Life Sciences Xiamen University Xiamen Fujian 361102 China
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10
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Bretherton L, Hillhouse J, Bacosa H, Setta S, Genzer J, Kamalanathan M, Finkel ZV, Quigg A. Growth dynamics and domoic acid production of Pseudo-nitzschia sp. in response to oil and dispersant exposure. HARMFUL ALGAE 2019; 86:55-63. [PMID: 31358277 DOI: 10.1016/j.hal.2019.05.008] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/22/2019] [Revised: 05/09/2019] [Accepted: 05/13/2019] [Indexed: 06/10/2023]
Abstract
The diatom genus Pseudo-nitzschia is a common component of phytoplankton communities in the Gulf of Mexico and is potentially toxic as some species produce the potent neurotoxin domoic acid. The impact of oil and chemical dispersants on Pseudo-nitzschia spp. and domoic acid production have not yet been studied; preliminary findings from a mesocosm experiment suggest this genus may be particularly resilient. A toxicological study was conducted using a colony of Pseudo-nitzschia sp. isolated from a station off the coast of Louisiana in the Gulf of Mexico. The cultures were exposed to a water accommodated fraction (WAF) of oil and a diluted chemically enhanced WAF (DCEWAF) which was a mix of oil and dispersant (20:1). Exposure to WAF induced a lag phase but did not inhibit growth rates once in exponential growth. Cultures grown in DCEWAF did not experience a lag phase but had significantly lower growth rates than the Control and WAF cultures. The cellular quota of domoic acid was higher in cultures treated with DCEWAF and WAF relative to their control values, and half of the domoic acid had leaked out of the cells into the surrounding seawater in the DCEWAF cultures while all the domoic acid remained inside the cells in WAF-treated cultures. These results suggest that the presence of oil could lead to toxic blooms, but that the application of dispersant could decrease bioaccumulation of domoic acid through the food web.
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Affiliation(s)
- Laura Bretherton
- Department of Marine Biology, Texas A&M University at Galveston, Galveston, TX, 77554, USA.
| | - Jessica Hillhouse
- Department of Marine Biology, Texas A&M University at Galveston, Galveston, TX, 77554, USA
| | - Hernando Bacosa
- Department of Marine Biology, Texas A&M University at Galveston, Galveston, TX, 77554, USA
| | - Samantha Setta
- Department of Marine Biology, Texas A&M University at Galveston, Galveston, TX, 77554, USA
| | - Jennifer Genzer
- Department of Marine Biology, Texas A&M University at Galveston, Galveston, TX, 77554, USA
| | - Manoj Kamalanathan
- Department of Marine Biology, Texas A&M University at Galveston, Galveston, TX, 77554, USA
| | - Zoe V Finkel
- Department of Oceanography, Dalhousie University, Halifax, NS, B3H 4R2, Canada
| | - Antonietta Quigg
- Department of Marine Biology, Texas A&M University at Galveston, Galveston, TX, 77554, USA; Department of Oceanography, Texas A&M University, College Station, TX, 77843 USA
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11
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Polyamines in Microalgae: Something Borrowed, Something New. Mar Drugs 2018; 17:md17010001. [PMID: 30577419 PMCID: PMC6356823 DOI: 10.3390/md17010001] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2018] [Revised: 12/14/2018] [Accepted: 12/17/2018] [Indexed: 01/13/2023] Open
Abstract
Microalgae of different evolutionary origins are typically found in rivers, lakes, and oceans, providing more than 45% of global primary production. They provide not only a food source for animals, but also affect microbial ecosystems through symbioses with microorganisms or secretion of some metabolites. Derived from amino acids, polyamines are present in almost all types of organisms, where they play important roles in maintaining physiological functions or against stress. Microalgae can produce a variety of distinct polyamines, and the polyamine content is important to meet the physiological needs of microalgae and may also affect other species in the environment. In addition, some polyamines produced by microalgae have medical or nanotechnological applications. Previous studies on several types of microalgae have indicated that the putative polyamine metabolic pathways may be as complicated as the genomes of these organisms, which contain genes originating from plants, animals, and even bacteria. There are also several novel polyamine synthetic routes in microalgae. Understanding the nature of polyamines in microalgae will not only improve our knowledge of microalgal physiology and ecological function, but also provide valuable information for biotechnological applications.
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12
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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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13
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Pawolski D, Heintze C, Mey I, Steinem C, Kröger N. Reconstituting the formation of hierarchically porous silica patterns using diatom biomolecules. J Struct Biol 2018; 204:64-74. [DOI: 10.1016/j.jsb.2018.07.005] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2018] [Revised: 07/06/2018] [Accepted: 07/07/2018] [Indexed: 11/15/2022]
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14
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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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15
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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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16
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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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17
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Longworth J, Wu D, Huete-Ortega M, Wright PC, Vaidyanathan S. Proteome response of Phaeodactylum tricornutum, during lipid accumulation induced by nitrogen depletion. ALGAL RES 2016; 18:213-224. [PMID: 27812494 PMCID: PMC5070409 DOI: 10.1016/j.algal.2016.06.015] [Citation(s) in RCA: 73] [Impact Index Per Article: 9.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2015] [Revised: 05/08/2016] [Accepted: 06/14/2016] [Indexed: 11/26/2022]
Abstract
Nitrogen stress is a common strategy employed to stimulate lipid accumulation in microalgae, a biofuel feedstock of topical interest. Although widely investigated, the underlying mechanism of this strategy is still poorly understood. We examined the proteome response of lipid accumulation in the model diatom, Phaeodactylum tricornutum (CCAP 1055/1), at an earlier stage of exposure to selective nitrogen exclusion than previously investigated, and at a time point when changes would reflect lipid accumulation more than carbohydrate accumulation. In total 1043 proteins were confidently identified (≥ 2 unique peptides) with 645 significant (p < 0.05) changes observed, in the LC-MS/MS based iTRAQ investigation. Analysis of significant changes in KEGG pathways and individual proteins showed that under nitrogen starvation P. tricornutum reorganizes its proteome in favour of nitrogen scavenging and reduced lipid degradation whilst rearranging the central energy metabolism that deprioritizes photosynthetic pathways. By doing this, this species appears to increase nitrogen availability inside the cell and limit its use to the pathways where it is needed most. Compared to previously published proteomic analysis of nitrogen starvation in Chlamydomonas reinhardtii, central energy metabolism and photosynthesis appear to be affected more in the diatom, whilst the green algae appears to invest its energy in reorganizing respiration and the cellular organization pathways.
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18
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Karakostis K, Costa C, Zito F, Brümmer F, Matranga V. Characterization of an Alpha Type Carbonic Anhydrase from Paracentrotus lividus Sea Urchin Embryos. MARINE BIOTECHNOLOGY (NEW YORK, N.Y.) 2016; 18:384-395. [PMID: 27230618 DOI: 10.1007/s10126-016-9701-0] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/05/2015] [Accepted: 02/10/2016] [Indexed: 06/05/2023]
Abstract
Carbonic anhydrases (CA) are zinc metalloenzymes that catalyze the reversible hydration of carbon dioxide to bicarbonate. In the sea urchin, CA has a role in the formation of the calcitic skeleton during embryo development. Here, we report a newly identified mRNA sequence from embryos of the sea urchin Paracentrotus lividus, referred to as Pl-can. The complete coding sequence was identified with the aid of both EST databases and experimental procedures. Pl-CAN is a 447 aa-long protein, with an estimated molecular mass of 48.5 kDa and an isoelectric point of 6.83. The in silico study of functional domains showed, in addition to the alpha type CA-specific domain, the presence of an unexpected glycine-rich region at the N-terminal of the molecule. This is not found in any other species described so far, but probably it is restricted to the sea urchins. The phylogenetic analysis indicated that Pl-CAN is evolutionarily closer to human among chordates than to other species. The putative role(s) of the identified domains is discussed. The Pl-can temporal and spatial expression profiles, analyzed throughout embryo development by comparative qPCR and whole-mount in situ hybridization (WMISH), showed that Pl-can mRNA is specifically expressed in the primary mesenchyme cells (PMC) of the embryo and levels increase along with the growth of the embryonic skeleton, reaching a peak at the pluteus stage. A recombinant fusion protein was produced in E. coli and used to raise specific antibodies in mice recognized the endogenous Pl-CAN by Western blot in embryo extracts from gastrula and pluteus.
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Affiliation(s)
- Konstantinos Karakostis
- Institute of Biomedicine and Molecular Immunology "A. Monroy", National Research Council, Via Ugo La Malfa, 153-90146, Palermo, Italy
- Institute for Biomaterials and Biomolecular Systems, University of Stuttgart, Stuttgart, Germany
- INSERM - UMR 1162, Institute de Génétique Moléculaire, Hôpital St. Louis, 27 rue Juliette Dodu, 75010, Paris, France
| | - Caterina Costa
- Institute of Biomedicine and Molecular Immunology "A. Monroy", National Research Council, Via Ugo La Malfa, 153-90146, Palermo, Italy.
| | - Francesca Zito
- Institute of Biomedicine and Molecular Immunology "A. Monroy", National Research Council, Via Ugo La Malfa, 153-90146, Palermo, Italy
| | - Franz Brümmer
- Institute for Biomaterials and Biomolecular Systems, University of Stuttgart, Stuttgart, Germany
| | - Valeria Matranga
- Institute of Biomedicine and Molecular Immunology "A. Monroy", National Research Council, Via Ugo La Malfa, 153-90146, Palermo, Italy
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19
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Kotzsch A, Pawolski D, Milentyev A, Shevchenko A, Scheffel A, Poulsen N, Shevchenko A, Kröger N. Biochemical Composition and Assembly of Biosilica-associated Insoluble Organic Matrices from the Diatom Thalassiosira pseudonana. J Biol Chem 2016; 291:4982-97. [PMID: 26710847 PMCID: PMC4777836 DOI: 10.1074/jbc.m115.706440] [Citation(s) in RCA: 51] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2015] [Revised: 12/23/2015] [Indexed: 11/06/2022] Open
Abstract
The nano- and micropatterned biosilica cell walls of diatoms are remarkable examples of biological morphogenesis and possess highly interesting material properties. Only recently has it been demonstrated that biosilica-associated organic structures with specific nanopatterns (termed insoluble organic matrices) are general components of diatom biosilica. The model diatom Thalassiosira pseudonana contains three types of insoluble organic matrices: chitin meshworks, organic microrings, and organic microplates, the latter being described in the present study for the first time. To date, little is known about the molecular composition, intracellular assembly, and biological functions of organic matrices. Here we have performed structural and functional analyses of the organic microrings and organic microplates from T. pseudonana. Proteomics analysis yielded seven proteins of unknown function (termed SiMat proteins) together with five known silica biomineralization proteins (four cingulins and one silaffin). The location of SiMat1-GFP in the insoluble organic microrings and the similarity of tyrosine- and lysine-rich functional domains identifies this protein as a new member of the cingulin protein family. Mass spectrometric analysis indicates that most of the lysine residues of cingulins and the other insoluble organic matrix proteins are post-translationally modified by short polyamine groups, which are known to enhance the silica formation activity of proteins. Studies with recombinant cingulins (rCinY2 and rCinW2) demonstrate that acidic conditions (pH 5.5) trigger the assembly of mixed cingulin aggregates that have silica formation activity. Our results suggest an important role for cingulins in the biogenesis of organic microrings and support the hypothesis that this type of insoluble organic matrix functions in biosilica morphogenesis.
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Affiliation(s)
| | | | - Alexander Milentyev
- the Max-Planck-Institute of Molecular Cell Biology and Genetics, 01307 Dresden, Germany, and
| | - Anna Shevchenko
- the Max-Planck-Institute of Molecular Cell Biology and Genetics, 01307 Dresden, Germany, and
| | - André Scheffel
- the Max-Planck-Institute of Plant Physiology, 14476 Potsdam, Germany
| | | | - Andrej Shevchenko
- the Max-Planck-Institute of Molecular Cell Biology and Genetics, 01307 Dresden, Germany, and
| | - Nils Kröger
- From the B CUBE Center for Molecular Bioengineering and the Department of Chemistry and Food Chemistry, Technische Universität Dresden, 01307 Dresden, Germany,
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20
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Muhseen ZT, Xiong Q, Chen Z, Ge F. Proteomics studies on stress responses in diatoms. Proteomics 2015; 15:3943-53. [PMID: 26364674 DOI: 10.1002/pmic.201500165] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2015] [Revised: 08/09/2015] [Accepted: 09/09/2015] [Indexed: 01/09/2023]
Abstract
Diatoms are a highly diverse group of eukaryotic phytoplankton that are distributed throughout marine and freshwater environments and are believed to be responsible for approximately 40% of the total marine primary productivity. The ecological success of diatoms suggests that they have developed a range of strategies to cope with various biotic and abiotic stress factors. It is of great interest to understand the adaptive responses of diatoms to different stresses in the marine environment. Proteomic technologies have been applied to the adaptive responses of marine diatoms under different growth conditions in recent years such as nitrogen starvation, iron limitation and phosphorus deficiency. These studies have provided clues to elucidate the sophisticated sensing mechanisms that control their adaptive responses. Although only a very limited number of proteomic studies were conducted in diatoms, the obtained data have led to a better understanding of the biochemical processes that contribute to their ecological success. This review presents the current status of proteomic studies of diatom stress responses and discusses the novel developments and applications for the analysis of protein post-translational modification in diatoms. The potential future application of proteomics could contribute to a better understanding of the physiological mechanisms underlying diatom acclimation to a given stress and the acquisition of an enhanced diatom stress tolerance. Future challenges and research opportunities in the proteomics studies of diatoms are also discussed.
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Affiliation(s)
- Ziyad Tariq Muhseen
- Key Laboratory of Algal Biology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, P. R. China.,University of Chinese Academy of Sciences, Beijing, P. R. China
| | - Qian Xiong
- Key Laboratory of Algal Biology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, P. R. China
| | - Zhuo Chen
- Key Laboratory of Algal Biology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, P. R. China
| | - Feng Ge
- Key Laboratory of Algal Biology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, P. R. China
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21
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Lechner CC, Becker CFW. Silaffins in Silica Biomineralization and Biomimetic Silica Precipitation. Mar Drugs 2015; 13:5297-333. [PMID: 26295401 PMCID: PMC4557024 DOI: 10.3390/md13085297] [Citation(s) in RCA: 67] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2015] [Revised: 07/17/2015] [Accepted: 07/20/2015] [Indexed: 12/05/2022] Open
Abstract
Biomineralization processes leading to complex solid structures of inorganic material in biological systems are constantly gaining attention in biotechnology and biomedical research. An outstanding example for biomineral morphogenesis is the formation of highly elaborate, nano-patterned silica shells by diatoms. Among the organic macromolecules that have been closely linked to the tightly controlled precipitation of silica in diatoms, silaffins play an extraordinary role. These peptides typically occur as complex posttranslationally modified variants and are directly involved in the silica deposition process in diatoms. However, even in vitro silaffin-based peptides alone, with and without posttranslational modifications, can efficiently mediate biomimetic silica precipitation leading to silica material with different properties as well as with encapsulated cargo molecules of a large size range. In this review, the biomineralization process of silica in diatoms is summarized with a specific focus on silaffins and their in vitro silica precipitation properties. Applications in the area of bio- and nanotechnology as well as in diagnostics and therapy are discussed.
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Affiliation(s)
- Carolin C Lechner
- Swiss Federal Institute of Technology in Lausanne (EPFL), Fondation Sandoz Chair in Biophysical Chemistry of Macromolecules, 1015 Lausanne, Switzerland.
| | - Christian F W Becker
- Institute of Biological Chemistry, Department of Chemistry, University of Vienna, Währinger Straße 38, 1090 Vienna, Austria.
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22
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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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23
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Liu T, Huang C, Shen C, Shi J. Isolation and Analysis of Cell Wall Proteome in Elsholtzia splendens Roots Using ITRAQ with LC-ESI-MS/MS. Appl Biochem Biotechnol 2015; 176:1174-94. [PMID: 25926012 DOI: 10.1007/s12010-015-1638-7] [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: 11/28/2014] [Accepted: 04/21/2015] [Indexed: 11/26/2022]
Abstract
Cell wall proteins (CWPs) are a prime site for signal perception and defense responses to environmental stresses. To gain further insights into CWPs and their molecular function, traditional techniques (e.g., two-dimensional gel electrophoresis) may be ineffective for special proteins. Elsholtzia splendens is a copper-tolerant plant species that grow on copper deposits. In this study, a fourplex isobaric tag was used for relative and absolute quantitation with liquid chromatography-tandem mass spectrometry approach to analyze the root CWPs of E. splendens. A total of 479 unique proteins were identified, including 121 novel proteins. Approximately 80.79 % of the proteins were extracted in the CaCl2 fraction, 16.08 % were detected in the NaCl fraction, and 3.13 % were identified in both fractions. The identified proteins have been involved in various processes, including cell wall remodeling, signal transduction, defense, and carbohydrate metabolism, thereby indicating a complex regulatory network in the apoplast of E. splendens roots. This study presents the first large-scale analysis of CWPs in metal-tolerant plants, which may be of paramount importance to understand the molecular functions and metabolic pathways in the root cell wall of copper-tolerant plants.
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Affiliation(s)
- Tingting Liu
- Institute of Environmental Science and Technology, College of Environmental and Resource Sciences, Zhejiang University, Hangzhou, 310058, People's Republic of China
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24
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Kitching M, Ramani M, Marsili E. Fungal biosynthesis of gold nanoparticles: mechanism and scale up. Microb Biotechnol 2014. [PMID: 25154648 DOI: 10.1111/1751–7915.12151] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022] Open
Abstract
Gold nanoparticles (AuNPs) are a widespread research tool because of their oxidation resistance, biocompatibility and stability. Chemical methods for AuNP synthesis often produce toxic residues that raise environmental concern. On the other hand, the biological synthesis of AuNPs in viable microorganisms and their cell-free extracts is an environmentally friendly and low-cost process. In general, fungi tolerate higher metal concentrations than bacteria and secrete abundant extracellular redox proteins to reduce soluble metal ions to their insoluble form and eventually to nanocrystals. Fungi harbour untapped biological diversity and may provide novel metal reductases for metal detoxification and bioreduction. A thorough understanding of the biosynthetic mechanism of AuNPs in fungi is needed to reduce the time of biosynthesis and to scale up the AuNP production process. In this review, we describe the known mechanisms for AuNP biosynthesis in viable fungi and fungal protein extracts and discuss the most suitable bioreactors for industrial AuNP biosynthesis.
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Affiliation(s)
- Michael Kitching
- School of Biotechnology, Dublin City University, Dublin, Dublin 9, Ireland
| | - Meghana Ramani
- Center for Materials science and Nano Devices, Department of Physics, SRM University, Kattankulathur, India
| | - Enrico Marsili
- Marine and Environmental Sensing Technology Hub, Dublin City University, Dublin, Dublin 9, Ireland.,Singapore Centre on Environmental Life Sciences Engineering, Nanyang Technological University, 60 Nanyang Drive, Singapore, 637551, Singapore
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25
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Kitching M, Ramani M, Marsili E. Fungal biosynthesis of gold nanoparticles: mechanism and scale up. Microb Biotechnol 2014; 8:904-17. [PMID: 25154648 PMCID: PMC4621444 DOI: 10.1111/1751-7915.12151] [Citation(s) in RCA: 147] [Impact Index Per Article: 14.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2014] [Revised: 07/12/2014] [Accepted: 07/17/2014] [Indexed: 11/26/2022] Open
Abstract
Gold nanoparticles (AuNPs) are a widespread research tool because of their oxidation resistance, biocompatibility and stability. Chemical methods for AuNP synthesis often produce toxic residues that raise environmental concern. On the other hand, the biological synthesis of AuNPs in viable microorganisms and their cell-free extracts is an environmentally friendly and low-cost process. In general, fungi tolerate higher metal concentrations than bacteria and secrete abundant extracellular redox proteins to reduce soluble metal ions to their insoluble form and eventually to nanocrystals. Fungi harbour untapped biological diversity and may provide novel metal reductases for metal detoxification and bioreduction. A thorough understanding of the biosynthetic mechanism of AuNPs in fungi is needed to reduce the time of biosynthesis and to scale up the AuNP production process. In this review, we describe the known mechanisms for AuNP biosynthesis in viable fungi and fungal protein extracts and discuss the most suitable bioreactors for industrial AuNP biosynthesis.
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Affiliation(s)
- Michael Kitching
- School of Biotechnology, Dublin City University, Dublin, Dublin 9, Ireland
| | - Meghana Ramani
- Center for Materials science and Nano Devices, Department of Physics, SRM University, Kattankulathur, India
| | - Enrico Marsili
- Marine and Environmental Sensing Technology Hub, Dublin City University, Dublin, Dublin 9, Ireland.,Singapore Centre on Environmental Life Sciences Engineering, Nanyang Technological University, 60 Nanyang Drive, Singapore, 637551, Singapore
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26
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Xu B, Luo CS, Liang JR, Chen DD, Zhuo WH, Gao YH, Chen CP, Song SS. Cellular metabolic responses of the marine diatom Pseudo-nitzschia multiseries associated with cell wall formation. Mar Genomics 2014; 16:29-38. [DOI: 10.1016/j.margen.2013.12.005] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2013] [Revised: 12/18/2013] [Accepted: 12/18/2013] [Indexed: 10/25/2022]
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27
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Wong DM, Nguyen TT, Franz AK. Ethylenediaminetetraacetic acid (EDTA) enhances intracellular lipid staining with Nile red in microalgae Tetraselmis suecica. ALGAL RES 2014. [DOI: 10.1016/j.algal.2014.08.002] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
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28
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Chen Z, Yang MK, Li CY, Wang Y, Zhang J, Wang DB, Zhang XE, Ge F. Phosphoproteomic analysis provides novel insights into stress responses in Phaeodactylum tricornutum, a model diatom. J Proteome Res 2014; 13:2511-23. [PMID: 24712722 DOI: 10.1021/pr401290u] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Protein phosphorylation on serine, threonine, and tyrosine (Ser/Thr/Tyr) is well established as a key regulatory posttranslational modification used in signal transduction to control cell growth, proliferation, and stress responses. However, little is known about its extent and function in diatoms. Phaeodactylum tricornutum is a unicellular marine diatom that has been used as a model organism for research on diatom molecular biology. Although more than 1000 protein kinases and phosphatases with specificity for Ser/Thr/Tyr residues have been predicted in P. tricornutum, no phosphorylation event has so far been revealed by classical biochemical approaches. Here, we performed a global phosphoproteomic analysis combining protein/peptide fractionation, TiO(2) enrichment, and LC-MS/MS analyses. In total, we identified 264 unique phosphopeptides, including 434 in vivo phosphorylated sites on 245 phosphoproteins. The phosphorylated proteins were implicated in the regulation of diverse biological processes, including signaling, metabolic pathways, and stress responses. Six identified phosphoproteins were further validated by Western blotting using phospho-specific antibodies. The functions of these proteins are discussed in the context of signal transduction networks in P. tricornutum. Our results advance the current understanding of diatom biology and will be useful for elucidating the phosphor-relay signaling networks in this model diatom.
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Affiliation(s)
- Zhuo Chen
- State Key Laboratory of Virology, Wuhan Institute of Virology, Chinese Academy of Sciences , Wuhan 430071, China
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29
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Du C, Liang JR, Chen DD, Xu B, Zhuo WH, Gao YH, Chen CP, Bowler C, Zhang W. iTRAQ-based proteomic analysis of the metabolism mechanism associated with silicon response in the marine diatom Thalassiosira pseudonana. J Proteome Res 2014; 13:720-34. [PMID: 24372006 DOI: 10.1021/pr400803w] [Citation(s) in RCA: 36] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Silicon is a critical element for diatom growth; however our understanding of the molecular mechanisms involved in intracellular silicon responses are limited. In this study, an iTRAQ-LC-MS/MS quantitative proteomic approach was coupled with an established synchrony technique to reveal the global metabolic silicon-response in the model diatom Thalassiosira pseudonana subject to silicon starvation and readdition. Four samples, which corresponded to the time of silicon starvation, girdle band synthesis, valve formation, and right after daughter cell separation (0, 1, 5, 7 h), were collected for the proteomic analysis. The results indicated that a total of 1,831 proteins, representing 16% of the predicted proteins encoded by the T. pseudonana genome, could be identified. Of the identified proteins, 165 were defined as being differentially expressed proteins, and these proteins could be linked to multiple biochemical pathways. In particular, a number of proteins related to silicon transport, cell wall synthesis, and cell-cycle progress could be identified. In addition, other proteins that are potentially involved in amino acid synthesis, protein metabolism, and energy generation may have roles in the cellular response to silicon. Our findings provide a range of valuable information that will be of use for further studies of this important physiological response that is unique to diatoms.
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Affiliation(s)
- Chao Du
- School of Life Sciences, Xiamen University , Xiamen 361005, China
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30
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Poulsen N, Scheffel A, Sheppard VC, Chesley PM, Kröger N. Pentalysine clusters mediate silica targeting of silaffins in Thalassiosira pseudonana. J Biol Chem 2013; 288:20100-9. [PMID: 23720751 DOI: 10.1074/jbc.m113.469379] [Citation(s) in RCA: 53] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
The biological formation of inorganic materials (biomineralization) often occurs in specialized intracellular vesicles. Prominent examples are diatoms, a group of single-celled eukaryotic microalgae that produce their SiO2 (silica)-based cell walls within intracellular silica deposition vesicles (SDVs). SDVs contain protein-based organic matrices that control silica formation, resulting in species specifically nanopatterned biosilica, an organic-inorganic composite material. So far no information is available regarding the molecular mechanisms of SDV biogenesis. Here we have investigated by fluorescence microscopy and subcellular membrane fractionation the intracellular transport of silaffin Sil3. Silaffins are a group of phosphoproteins constituting the main components of the organic matrix of diatom biosilica. We demonstrate that the N-terminal signal peptide of Sil3 mediates import into a specific subregion of the endoplasmic reticulum. Additional segments from the mature part of Sil3 are required to reach post-endoplasmic reticulum compartments. Further transport of Sil3 and incorporation into the biosilica (silica targeting) require protein segments that contain a high density of modified lysine residues and phosphoserines. Silica targeting of Sil3 is not dependent on a particular peptide sequence, yet a lysine-rich 12-14-amino acid peptide motif (pentalysine cluster), which is conserved in all silaffins, strongly promotes silica targeting. The results of the present work provide the first insight into the molecular mechanisms for biogenesis of mineral-forming vesicles from an eukaryotic organism.
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31
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Petrova DP, Khabudaev KV, Marchenkov AM, Galachyants YP, Kalyuzhnaya OV, Zakharova YR, Likhoshvai EV, Grachev MA. Aquaporin-like protein of the diatom Synedra acus. DOKL BIOCHEM BIOPHYS 2013; 448:5-8. [PMID: 23478976 DOI: 10.1134/s160767291301002x] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2012] [Indexed: 01/18/2023]
Affiliation(s)
- D P Petrova
- Russian Academy of Sciences, ul. Ulan-Batorskaya 3, Irkutsk, Russia
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Santos J, Almeida SFP, Figueira E. Cadmium chelation by frustulins: a novel metal tolerance mechanism in Nitzschia palea (Kützing) W. Smith. ECOTOXICOLOGY (LONDON, ENGLAND) 2013; 22:166-173. [PMID: 23124677 DOI: 10.1007/s10646-012-1013-1] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Accepted: 10/25/2012] [Indexed: 06/01/2023]
Abstract
The ubiquity of diatom distribution, species richness, short generation time, and specific sensitivity to several environmental stressors such as metals, make diatoms particularly useful for scientific studies. Anthropogenic activities have increased the concentration of metals in air, soil and water. Due to their toxicity and persistent character, the effects of metals on organisms have been extensively studied. In this work, the association of cadmium to different extracellular molecules of Nitzschia palea cells was investigated. Cells were grown in the absence and presence (0.2 mg l(-1)) of cadmium in Chu no. 10 medium. Extracellular polysaccharides were extracted, and subsamples were used for polysaccharide and Cd determination. The frustules were broken mechanically under liquid nitrogen and the intracellular and frustule fractions separated. Frustulins, a protein family found on the outmost frustule layer, constituting a protection coating to environmental stress, were extracted. In each fraction proteins were quantified by the BCA method and separated by gel electrophoresis (SDS-PAGE). Cadmium associated to each fraction was quantified by Inductively Coupled Plasma Mass Spectrometry (ICP-MS) analysis. Exposure of Nitzschia palea to cadmium decreased extracellular polysaccharides by 52.8 % and increased 6 times the amount of frustulins. Cadmium was mostly retained extracellularly: 85.4 % was bound to the frustulin fraction, and 11.1 % to polysaccharides. The ability of Nitzschia palea to increase the production of frustulins due to the presence of Cd, the extracellular location of this frustulin coating and the ability of these proteins to bind Cd, suggests a new cellular defense mechanism to metals unknown until now.
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Affiliation(s)
- José Santos
- Biology Department, and CBC (Centro de Biologia Celular), University of Aveiro, Campus Universitário de Santiago, 3810-193, Aveiro, Portugal
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33
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Bertrand EM, Allen AE. Influence of vitamin B auxotrophy on nitrogen metabolism in eukaryotic phytoplankton. Front Microbiol 2012; 3:375. [PMID: 23091473 PMCID: PMC3476827 DOI: 10.3389/fmicb.2012.00375] [Citation(s) in RCA: 53] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2012] [Accepted: 10/02/2012] [Indexed: 01/22/2023] Open
Abstract
While nitrogen availability is known to limit primary production in large parts of the ocean, vitamin starvation amongst eukaryotic phytoplankton is becoming increasingly recognized as an oceanographically relevant phenomenon. Cobalamin (B(12)) and thiamine (B(1)) auxotrophy are widespread throughout eukaryotic phytoplankton, with over 50% of cultured isolates requiring B(12) and 20% requiring B(1). The frequency of vitamin auxotrophy in harmful algal bloom species is even higher. Instances of colimitation between nitrogen and B vitamins have been observed in marine environments, and interactions between these nutrients have been shown to impact phytoplankton species composition. This review surveys available data, including relevant gene expression patterns, to evaluate the potential for interactive effects of nitrogen and vitamin B(12) and B(1) starvation in eukaryotic phytoplankton. B(12) plays essential roles in amino acid and one-carbon metabolism, while B(1) is important for primary carbohydrate and amino acid metabolism and likely useful as an anti-oxidant. Here we will focus on three potential metabolic interconnections between vitamin, nitrogen, and sulfur metabolism that may have ramifications for the role of vitamin and nitrogen scarcities in driving ocean productivity and species composition. These include: (1) B(12), B(1), and N starvation impacts on osmolyte and antioxidant production, (2) B(12) and B(1) starvation impacts on polyamine biosynthesis, and (3) influence of B(12) and B(1) starvation on the diatom urea cycle and amino acid recycling through impacts on the citric acid cycle. We evaluate evidence for these interconnections and identify oceanographic contexts in which each may impact rates of primary production and phytoplankton community composition. Major implications include that B(12) and B(1) deprivation may impair the ability of phytoplankton to recover from nitrogen starvation and that changes in vitamin and nitrogen availability may synergistically impact harmful algal bloom formation.
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Affiliation(s)
- Erin M Bertrand
- Department of Microbial and Environmental Genomics, J. Craig Venter Institute San Diego, CA, USA
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Shrestha RP, Tesson B, Norden-Krichmar T, Federowicz S, Hildebrand M, Allen AE. Whole transcriptome analysis of the silicon response of the diatom Thalassiosira pseudonana. BMC Genomics 2012; 13:499. [PMID: 22994549 PMCID: PMC3478156 DOI: 10.1186/1471-2164-13-499] [Citation(s) in RCA: 92] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2012] [Accepted: 09/14/2012] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Silicon plays important biological roles, but the mechanisms of cellular responses to silicon are poorly understood. We report the first analysis of cell cycle arrest and recovery from silicon starvation in the diatom Thalassiosira pseudonana using whole genome microarrays. RESULTS Three known responses to silicon were examined, 1) silicified cell wall synthesis, 2) recovery from silicon starvation, and 3) co-regulation with silicon transporter (SIT) genes. In terms of diatom cell wall formation, thus far only cell surface proteins and proteins tightly associated with silica have been characterized. Our analysis has identified new genes potentially involved in silica formation, and other genes potentially involved in signaling, trafficking, protein degradation, glycosylation and transport, which provides a larger-scale picture of the processes involved. During silicon starvation, an overrepresentation of transcription and translation related genes were up-regulated, indicating that T. pseudonana is poised to rapidly recover from silicon starvation and resume cell cycle progression upon silicon replenishment. This is in contrast to other types of limitation, and provides the first molecular data explaining the well-established environmental response of diatoms to grow as blooms and to out-compete other classes of microalgae for growth. Comparison of our data with a previous diatom cell cycle analysis indicates that assignment of the cell cycle specific stage of particular cyclins and cyclin dependent kinases should be re-evaluated. Finally, genes co-varying in expression with the SITs enabled identification of a new class of diatom-specific proteins containing a unique domain, and a putative silicon efflux protein. CONCLUSIONS Analysis of the T. pseudonana microarray data has provided a wealth of new genes to investigate previously uncharacterized cellular phenomenon related to silicon metabolism, silicon's interaction with cellular components, and environmental responses to silicon.
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Affiliation(s)
- Roshan Prakash Shrestha
- Scripps Institution of Oceanography, University of California, San Diego, California 92037, USA
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35
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Otzen D. The role of proteins in biosilicification. SCIENTIFICA 2012; 2012:867562. [PMID: 24278750 PMCID: PMC3820600 DOI: 10.6064/2012/867562] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/29/2012] [Accepted: 09/24/2012] [Indexed: 05/19/2023]
Abstract
Although the use of silicon dioxide (silica) as a constituent of living organisms is mainly restricted to diatoms and sponges, the ways in which this process is controlled by nature continue to inspire and fascinate. Both diatoms and sponges carry out biosilificiation using an organic matrix but they adopt very different strategies. Diatoms use small and heavily modified peptides called silaffins, where the most characteristic feature is a modulation of charge by attaching long chain polyamines (LCPAs) to lysine groups. Free LCPAs can also cooperate with silaffins. Sponges use the enzyme silicatein which is homologous to the cysteine protease cathepsin. Both classes of proteins form higher-order structures which act both as structural templates and mechanistic catalysts for the polycondensation reaction. In both cases, additional proteins are continuously being discovered which modulate the process further. This paper concentrates on the role of these proteins in the biosilification process as well as in various applications, highlighting areas where focus on specific protein properties may provide further insight. The field of biosilification is a crossroads of different disciplines, where insight into the energetics and mechanisms of molecular self-assembly combine with fundamental biology, complex multicomponent colloidal systems, and an impressive array of potential technological applications.
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Affiliation(s)
- Daniel Otzen
- Interdisciplinary Nanoscience Center (iNANO), Center for Insoluble Protein Structures (inSPIN), and Department of Molecular Biology and Genetics, Aarhus University, Gustav Wieds Vej 14, 8000 Aarhus C, Denmark
- *Daniel Otzen:
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Norici A, Bazzoni AM, Pugnetti A, Raven JA, Giordano M. Impact of irradiance on the C allocation in the coastal marine diatom Skeletonema marinoi Sarno and Zingone. PLANT, CELL & ENVIRONMENT 2011; 34:1666-77. [PMID: 21707652 DOI: 10.1111/j.1365-3040.2011.02362.x] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/24/2023]
Abstract
Elemental stoichiometry and organic composition were investigated in an Adriatic strain of Skeletonema marinoi, cultured at 25 [low light (LL)] and 250 [high light (HL)]µmol photon m⁻² s⁻¹. Inorganic carbon acquisition, fixation and allocation, and silicic acid and orthophosphate uptake were also studied. The C:P ratio was below the Redfield ratio, especially at LL. In HL cells, N quota was halved, C quota was similar, silica quota was lower, growth rate and long-term net primary productivity were almost doubled, relative to LL cells. The HL:LL cell quota ratios were 6 for lipid, 0.5 for protein and 0.4 for carbohydrate. Phosphoenolpyruvate carboxylase (PEPc) and glutamine synthetase (GS) activities were unaffected by the growth irradiance; phosphoenolpyruvate carboxykinase (PEPck) was 2.5-fold more active in LL cells. This suggests that in S. marinoi, C₄ photosynthesis is unlikely, PEPc is anaplerotic and PEPck may be involved in the conversion of lipid C to carbohydrates, especially in LL cells. Because about 50% of the cost for the production of an HL cell is caused by lipid biosynthesis, we propose that the preferential allocation of C to lipid at HL takes advantage of the relatively high volume-based energy content of lipids, in an organism that reduces its size at each vegetative cell division.
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Affiliation(s)
- Alessandra Norici
- Laboratorio di Fisiologia delle Alghe, Dipartimento di Scienze del Mare, Università Politecnica delle Marche, Via Brecce Bianche, 60131 Ancona, Italy
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Alverson AJ, Beszteri B, Julius ML, Theriot EC. The model marine diatom Thalassiosira pseudonana likely descended from a freshwater ancestor in the genus Cyclotella. BMC Evol Biol 2011; 11:125. [PMID: 21569560 PMCID: PMC3121624 DOI: 10.1186/1471-2148-11-125] [Citation(s) in RCA: 46] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2010] [Accepted: 05/14/2011] [Indexed: 11/25/2022] Open
Abstract
Background Publication of the first diatom genome, that of Thalassiosira pseudonana, established it as a model species for experimental and genomic studies of diatoms. Virtually every ensuing study has treated T. pseudonana as a marine diatom, with genomic and experimental data valued for their insights into the ecology and evolution of diatoms in the world's oceans. Results The natural distribution of T. pseudonana spans both marine and fresh waters, and phylogenetic analyses of morphological and molecular datasets show that, 1) T. pseudonana marks an early divergence in a major freshwater radiation by diatoms, and 2) as a species, T. pseudonana is likely ancestrally freshwater. Marine strains therefore represent recent recolonizations of higher salinity habitats. In addition, the combination of a relatively nondescript form and a convoluted taxonomic history has introduced some confusion about the identity of T. pseudonana and, by extension, its phylogeny and ecology. We resolve these issues and use phylogenetic criteria to show that T. pseudonana is more appropriately classified by its original name, Cyclotella nana. Cyclotella contains a mix of marine and freshwater species and so more accurately conveys the complexities of the phylogenetic and natural histories of T. pseudonana. Conclusions The multitude of physical barriers that likely must be overcome for diatoms to successfully colonize freshwaters suggests that the physiological traits of T. pseudonana, and the genes underlying those traits, might differ from those of strictly marine diatoms. The freshwater ancestry of T. pseudonana might therefore confound generalizations about the physiological and metabolic properties of marine diatoms. The freshwater component of T. pseudonana's history merits careful consideration in the interpretation of experimental data collected for this important model species.
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Affiliation(s)
- Andrew J Alverson
- Department of Biology, Indiana University, 1001 East Third Street, Bloomington, IN 47405, USA.
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Bridoux MC, Annenkov VV, Menzel H, Keil RG, Ingalls AE. A new liquid chromatography/electrospray ionization mass spectrometry method for the analysis of underivatized aliphatic long-chain polyamines: application to diatom-rich sediments. RAPID COMMUNICATIONS IN MASS SPECTROMETRY : RCM 2011; 25:877-888. [PMID: 21416524 DOI: 10.1002/rcm.4931] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/16/2010] [Revised: 01/04/2011] [Accepted: 01/05/2011] [Indexed: 05/30/2023]
Abstract
Natural polyamines are found in all three domains of life and long-chain polyamines (LCPAs) play a special role in silicifying organisms such as diatoms and sponges where they are actively involved in the complex formation and nanopatterning of siliceous structures. With chain lengths extending up to 20 N-methylated propylamine repeat units, diatom LCPAs constitute the longest natural polyamines. Mixtures of natural LCPAs are typically purified in bulk using ion-exchange, size-exclusion and dialysis and then analyzed either by direct infusion mass spectrometry or by MALDI-TOF. Here, we describe a novel ion-pairing liquid chromatographic method that allows baseline separation, detection and structural elucidation of underivatized aliphatic methylated and non-methylated LCPAs with a wide range of chain lengths. Complete separation of synthetic mixtures of LCPA species differing by either a propylamine or an N-methylpropylamine unit is achievable using this method and chromatographic separation of natural, diatom frustule bound LCPAs extracted from sediment core samples is greatly improved. Using electrospray ionization mass spectrometry (ESI-MS), we detected singly [M+H](+) and multiply [M+nH](n+) charged protonated ions. The abundance of multiply charged LCPA species increased linearly as a function of LCPA chain length (N) and multiprotonated ions [M+nH](n+) were more abundant for longer chain polyamines. The abundance of multiply charged LCPAs along with the concomitant disappearance of the singly charged protonated molecular ion significantly increases the complexity of the MS spectra, justifying the need for good chromatographic separation of complex LCPA mixtures. This analytical procedure will likely constitute a powerful tool for the characterization, quantification, as well as the purification of individual LCPAs in natural and synthetic samples for studies of silica precipitation as well as nitrogen and carbon isotopic analysis used in paleoceanographic studies.
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Affiliation(s)
- Maxime C Bridoux
- School of Oceanography, Box 355351, University of Washington, Seattle, WA 98195, USA
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Patwardhan SV. Biomimetic and bioinspired silica: recent developments and applications. Chem Commun (Camb) 2011; 47:7567-82. [PMID: 21479320 DOI: 10.1039/c0cc05648k] [Citation(s) in RCA: 144] [Impact Index Per Article: 11.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
In a previous review of biological and bioinspired silica formation (S. V. Patwardhan et al., Chem. Commun., 2005, 1113 [ref. 1]), we have identified and discussed the roles that organic molecules (additives) play in silica formation in vitro. Tremendous progress has been made in this field since and this review attempts to capture, with selected examples from the literature, the key advances in synthesising and controlling properties of silica-based materials using bioinspired approaches, i.e. conditions of near-neutral pH, all aqueous environments and room temperature. One important reason to investigate biosilicifying systems is to be able to develop novel materials and/or technologies suitable for a wide range of applications. Therefore, this review will also focus on applications arising from research on biological and bioinspired silica. A range of applications such as in the areas of sensors, coatings, hybrid materials, catalysis and biocatalysis and drug delivery have started appearing. Furthermore, scale-up of this technology suitable for large-scale manufacturing has proven the potential of biologically inspired synthesis.
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Affiliation(s)
- Siddharth V Patwardhan
- Department of Chemical and Process Engineering, University of Strathclyde, 75 Montrose Street, Glasgow G1 1XJ, UK.
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40
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Carvalho RN, Lettieri T. Proteomic analysis of the marine diatom Thalassiosira pseudonana upon exposure to benzo(a)pyrene. BMC Genomics 2011; 12:159. [PMID: 21435224 PMCID: PMC3076255 DOI: 10.1186/1471-2164-12-159] [Citation(s) in RCA: 50] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2010] [Accepted: 03/24/2011] [Indexed: 02/05/2023] Open
Abstract
Background Polycyclic aromatic hydrocarbons (PAHs) are environmental pollutants ubiquitously distributed. They are generated by incomplete combustion of organic materials such as wood or fossil fuels. Due to their carcinogenic, mutagenic effects and to their wide distribution in the environment, these pollutants pose many concerns to researchers and regulators. In our laboratories we investigated the effect of benzo(a)pyrene (BaP) exposure in the marine diatom Thalassiosira pseudonana, which has become an important model organism in aquatic toxicology studies. Results In order to investigate the mechanism of action of PAHs, we exposed the diatoms for 24 h to 36.45 μg/L of BaP which inhibits the growth by about 30%, and analysed the relative protein expression profile by a quantitative proteomics approach based on iTRAQ labels. The proteomics profile analysis showed that around 10% of the identified proteins were regulated and one fourth of them confirmed the gene expression changes seen by DNA microarray. Particularly interesting was the down regulation of the Silicon transporter 1 (SIT1), an enzyme that is responsible for the uptake of silicon from the media into the diatom cells. Regulation of SIT1 upon BaP treatment was also confirmed at the gene expression level. Conclusions The potential use of the regulated proteins found in this study as early indicators of environmental exposure to PAHs is discussed. In particular, SIT1 is considered a promising biomarker and SIT1 expression changes were confirmed also when the diatoms were exposed to field samples, e.g. marine surface sediments contaminated by PAHs.
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Affiliation(s)
- Raquel N Carvalho
- European Commission - Joint Research Centre, Institute for Environment and Sustainability, Rural, Water, and Ecosystem Resources Unit, T.P. 270, Via E. Fermi 2749, 21027 Ispra, VA, Italy
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Nanopatterned protein microrings from a diatom that direct silica morphogenesis. Proc Natl Acad Sci U S A 2011; 108:3175-80. [PMID: 21300899 DOI: 10.1073/pnas.1012842108] [Citation(s) in RCA: 115] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Diatoms are eukaryotic microalgae that produce species-specifically structured cell walls made of SiO(2) (silica). Formation of the intricate silica structures of diatoms is regarded as a paradigm for biomolecule-controlled self-assembly of three-dimensional, nano- to microscale-patterned inorganic materials. Silica formation involves long-chain polyamines and phosphoproteins (silaffins and silacidins), which are readily soluble in water, and spontaneously form dynamic supramolecular assemblies that accelerate silica deposition and influence silica morphogenesis in vitro. However, synthesis of diatom-like silica structure in vitro has not yet been accomplished, indicating that additional components are required. Here we describe the discovery and intracellular location of six novel proteins (cingulins) that are integral components of a silica-forming organic matrix (microrings) in the diatom Thalassiosira pseudonana. The cingulin-containing microrings are specifically associated with girdle bands, which constitute a substantial part of diatom biosilica. Remarkably, the microrings exhibit protein-based nanopatterns that closely resemble characteristic features of the girdle band silica nanopatterns. Upon the addition of silicic acid the microrings become rapidly mineralized in vitro generating nanopatterned silica replicas of the microring structures. A silica-forming organic matrix with characteristic nanopatterns was also discovered in the diatom Coscinodiscus wailesii, which suggests that preassembled protein-based templates might be general components of the cellular machinery for silica morphogenesis in diatoms. These data provide fundamentally new insight into the molecular mechanisms of biological silica morphogenesis, and may lead to the development of self-assembled 3D mineral forming protein scaffolds with designed nanopatterns for a host of applications in nanotechnology.
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Carvalho RN, Burchardt AD, Sena F, Mariani G, Mueller A, Bopp SK, Umlauf G, Lettieri T. Gene biomarkers in diatom Thalassiosira pseudonana exposed to polycyclic aromatic hydrocarbons from contaminated marine surface sediments. AQUATIC TOXICOLOGY (AMSTERDAM, NETHERLANDS) 2011; 101:244-253. [PMID: 21087797 DOI: 10.1016/j.aquatox.2010.10.004] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/11/2010] [Revised: 09/28/2010] [Accepted: 10/09/2010] [Indexed: 05/30/2023]
Abstract
Marine diatoms have a key role in the global carbon fixation and therefore in the ecosystem. We used Thalassiosira pseudonana as a model organism to assess the effects of exposure to environmental pollutants at the gene expression level. Diatoms were exposed to polycyclic aromatic hydrocarbons mixture (PAH) from surface sediments collected at a highly PAH contaminated area of the Mediterranean Sea (Genoa, Italy), due to intense industrial and harbor activities. The gene expression data for exposure to the sediment-derived PAH mixture was compared with gene expression data for in vitro exposure to specific polycyclic aromatic hydrocarbons. The data shows that genes involved in stress response, silica uptake, and metabolism were regulated both upon exposure to the sediment-derived PAH mixture and to the single component. Complementary monitoring of silica in the diatom cultures provide further evidence of a reduced cellular uptake of silica as an end-point for benzo[a]pyrene exposure that could be linked with the reduced gene and protein expression of the silicon transporter protein. However some genes showed differences in regulation indicating that mixtures of structurally related chemical compounds can elicit a slightly different gene expression response compared to that of a single component. The paper provides indications on the specific pathways affected by PAH exposure and shows that selected genes (silicon transporter, and silaffin 3) involved in silica uptake and metabolism could be suitable molecular biomarkers of exposure to PAHs.
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Affiliation(s)
- Raquel N Carvalho
- European Commission-Joint Research Centre, Institute for Environment and Sustainability, Ispra (VA), Italy
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Rynearson TA, Palenik B. Learning to read the oceans genomics of marine phytoplankton. ADVANCES IN MARINE BIOLOGY 2011; 60:1-39. [PMID: 21962749 DOI: 10.1016/b978-0-12-385529-9.00001-9] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/25/2023]
Abstract
The phytoplankton are key members of marine ecosystems, generating about half of global primary productivity, supporting valuable fisheries and regulating global biogeochemical cycles. Marine phytoplankton are phylogenetically diverse and are comprised of both prokaryotic and eukaryotic species. In the last decade, new insights have been gained into the ecology and evolution of these important organisms through whole genome sequencing projects and more recently, through both transcriptomics and targeted metagenomics approaches. Sequenced genomes of cyanobacteria are generally small, ranging in size from 1.8 to 9 million base pairs (Mbp). Eukaryotic genomes, in general, have a much larger size range and those that have been sequenced range from 12 to 57 Mbp. Whole genome sequencing projects have revealed key features of the evolutionary history of marine phytoplankton, their varied responses to environmental stress, their ability to scavenge and store nutrients and their unique ability to form elaborate cellular coverings. We have begun to learn how to read the 'language' of marine phytoplankton, as written in their DNA. Here, we review the ecological and evolutionary insights gained from whole genome sequencing projects, illustrate how these genomes are yielding information on marine natural products and informing nanotechnology as well as make suggestions for future directions in the field of marine phytoplankton genomics.
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Affiliation(s)
- Tatiana A Rynearson
- Graduate School of Oceanography, University of Rhode Island, Narragansett, RI, USA.
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Abstract
Diatom inspired bio-hybrids offer new possibilities for the synthesis of nanostructured materials and the development of nanomedicine.
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Affiliation(s)
- Nadine Nassif
- Chimie de la matière condensée de Paris
- CNRS
- UPMC
- 75231 Paris Cedex 05
- France
| | - Jacques Livage
- Chimie de la matière condensée de Paris
- CNRS
- UPMC
- 75231 Paris Cedex 05
- France
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SCOTT K. 3D elemental and structural analysis of biological specimens using electrons and ions. J Microsc 2010; 242:86-93. [DOI: 10.1111/j.1365-2818.2010.03444.x] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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Ehrlich H, Demadis KD, Pokrovsky OS, Koutsoukos PG. Modern Views on Desilicification: Biosilica and Abiotic Silica Dissolution in Natural and Artificial Environments. Chem Rev 2010; 110:4656-89. [DOI: 10.1021/cr900334y] [Citation(s) in RCA: 177] [Impact Index Per Article: 12.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Hermann Ehrlich
- Institute of Bioanalytical Chemistry, Dresden University of Technology, D-01069 Dresden, Germany, Crystal Engineering, Growth and Design Laboratory, Department of Chemistry, University of Crete, Voutes Campus, GR-71003 Heraklion, Crete, Greece, Laboratory of Mechanisms and Transfer in Geology, Observatory Midi-Pyrenees (OMP), UMR 5563, CNRS, 14 Avenue Edouard Belin, 31400 Toulouse, France, and FORTH-ICEHT and Laboratory of Inorganic and Analytical Chemistry, Department of Chemical Engineering, University
| | - Konstantinos D. Demadis
- Institute of Bioanalytical Chemistry, Dresden University of Technology, D-01069 Dresden, Germany, Crystal Engineering, Growth and Design Laboratory, Department of Chemistry, University of Crete, Voutes Campus, GR-71003 Heraklion, Crete, Greece, Laboratory of Mechanisms and Transfer in Geology, Observatory Midi-Pyrenees (OMP), UMR 5563, CNRS, 14 Avenue Edouard Belin, 31400 Toulouse, France, and FORTH-ICEHT and Laboratory of Inorganic and Analytical Chemistry, Department of Chemical Engineering, University
| | - Oleg S. Pokrovsky
- Institute of Bioanalytical Chemistry, Dresden University of Technology, D-01069 Dresden, Germany, Crystal Engineering, Growth and Design Laboratory, Department of Chemistry, University of Crete, Voutes Campus, GR-71003 Heraklion, Crete, Greece, Laboratory of Mechanisms and Transfer in Geology, Observatory Midi-Pyrenees (OMP), UMR 5563, CNRS, 14 Avenue Edouard Belin, 31400 Toulouse, France, and FORTH-ICEHT and Laboratory of Inorganic and Analytical Chemistry, Department of Chemical Engineering, University
| | - Petros G. Koutsoukos
- Institute of Bioanalytical Chemistry, Dresden University of Technology, D-01069 Dresden, Germany, Crystal Engineering, Growth and Design Laboratory, Department of Chemistry, University of Crete, Voutes Campus, GR-71003 Heraklion, Crete, Greece, Laboratory of Mechanisms and Transfer in Geology, Observatory Midi-Pyrenees (OMP), UMR 5563, CNRS, 14 Avenue Edouard Belin, 31400 Toulouse, France, and FORTH-ICEHT and Laboratory of Inorganic and Analytical Chemistry, Department of Chemical Engineering, University
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Heintzelman MB, Enriquez ME. Myosin diversity in the diatom Phaeodactylum tricornutum. Cytoskeleton (Hoboken) 2010; 67:142-51. [PMID: 20217677 DOI: 10.1002/cm.20431] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Abstract
This report describes the domain architecture of ten myosins cloned from the pennate diatom Phaeodactylum tricornutum. Several of the P. tricornutum myosins show similarity to myosins from the centric diatom Thalassiosira pseudonana as well as to one myosin from the oomycete Phytophthora ramorum. The P. tricornutum myosins, ranging in size from 126 kDa to over 250 kDa, all possess the canonical head, neck and tail domains common to most myosins, though variations in each of these domains is evident. Among the features distinguishing several of the diatom myosin head domains are N-terminal SH3-like domains, variations in or near the P-loop and Loop 1 regions close to the nucleotide binding pocket, and extended converter domains. Variations in the length of the neck domain or lever arm, defined by the light chain-binding IQ motifs, are apparent with the different diatom myosins predicted to contain from one to nine IQ motifs. Protein domains found within the P. tricornutum myosin tails include regions of coiled-coil structure, ankyrin repeats, CBS domain pairs, a PB1 domain, a kinase domain and a FYVE-finger motif. As many of these features have never before been characterized in myosins of any type, it is likely that these new diatom myosins will expand the repertoire of known myosin behaviors.
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Affiliation(s)
- Matthew B Heintzelman
- Program in Cell Biology and Biochemistry, Department of Biology, Bucknell University, Lewisburg, PA 17837, USA.
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Brunner E, Richthammer P, Ehrlich H, Paasch S, Simon P, Ueberlein S, van Pée KH. Chitin-based organic networks: an integral part of cell wall biosilica in the diatom Thalassiosira pseudonana. Angew Chem Int Ed Engl 2010; 48:9724-7. [PMID: 19924754 DOI: 10.1002/anie.200905028] [Citation(s) in RCA: 203] [Impact Index Per Article: 14.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Affiliation(s)
- Eike Brunner
- FR Chemie und Lebensmittelchemie, TU Dresden, 01069 Dresden, Germany.
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Sheppard V, Poulsen N, Kröger N. Characterization of an endoplasmic reticulum-associated silaffin kinase from the diatom Thalassiosira pseudonana. J Biol Chem 2010; 285:1166-76. [PMID: 19889629 PMCID: PMC2801245 DOI: 10.1074/jbc.m109.039529] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2009] [Revised: 11/02/2009] [Indexed: 11/06/2022] Open
Abstract
The formation of SiO(2)-based cell walls by diatoms (a large group of unicellular microalgae) is a well established model system for the study of molecular mechanisms of biological mineral morphogenesis (biomineralization). Diatom biomineralization involves highly phosphorylated proteins (silaffins and silacidins), analogous to other biomineralization systems, which also depend on diverse sets of phosphoproteins (e.g. mammalian teeth and bone, mollusk shells, and sponge silica). The phosphate moieties on biomineralization proteins play an essential role in mineral formation, yet the kinases catalyzing the phosphorylation of these proteins have remained poorly characterized. Recent functional genomics studies on the diatom Thalassiosira pseudonana have revealed >100 proteins potentially involved in diatom silica formation. Here we have characterized the biochemical properties and biological function of one of these proteins, tpSTK1. Multiple tpSTK1-like proteins are encoded in diatom genomes, all of which exhibit low but significant sequence similarity to kinases from other organisms. We show that tpSTK1 has serine/threonine kinase activity capable of phosphorylating silaffins but not silacidins. Cell biological and biochemical analysis demonstrated that tpSTK1 is an abundant component of the lumen of the endoplasmic reticulum. The present study provides the first molecular structure of a kinase that appears to catalyze phosphorylation of biomineral forming proteins in vivo.
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Affiliation(s)
| | | | - Nils Kröger
- From the Schools of Chemistry and Biochemistry
- Materials Science and Engineering, and
- Biology, Georgia Institute of Technology, Atlanta, Georgia 30332-0400
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Sapriel G, Quinet M, Heijde M, Jourdren L, Tanty V, Luo G, Le Crom S, Lopez PJ. Genome-wide transcriptome analyses of silicon metabolism in Phaeodactylum tricornutum reveal the multilevel regulation of silicic acid transporters. PLoS One 2009; 4:e7458. [PMID: 19829693 PMCID: PMC2758714 DOI: 10.1371/journal.pone.0007458] [Citation(s) in RCA: 65] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2009] [Accepted: 09/21/2009] [Indexed: 12/26/2022] Open
Abstract
Background Diatoms are largely responsible for production of biogenic silica in the global ocean. However, in surface seawater, Si(OH)4 can be a major limiting factor for diatom productivity. Analyzing at the global scale the genes networks involved in Si transport and metabolism is critical in order to elucidate Si biomineralization, and to understand diatoms contribution to biogeochemical cycles. Methodology/Principal Findings Using whole genome expression analyses we evaluated the transcriptional response to Si availability for the model species Phaeodactylum tricornutum. Among the differentially regulated genes we found genes involved in glutamine-nitrogen pathways, encoding putative extracellular matrix components, or involved in iron regulation. Some of these compounds may be good candidates for intracellular intermediates involved in silicic acid storage and/or intracellular transport, which are very important processes that remain mysterious in diatoms. Expression analyses and localization studies gave the first picture of the spatial distribution of a silicic acid transporter in a diatom model species, and support the existence of transcriptional and post-transcriptional regulations. Conclusions/Significance Our global analyses revealed that about one fourth of the differentially expressed genes are organized in clusters, underlying a possible evolution of P. tricornutum genome, and perhaps other pennate diatoms, toward a better optimization of its response to variable environmental stimuli. High fitness and adaptation of diatoms to various Si levels in marine environments might arise in part by global regulations from gene (expression level) to genomic (organization in clusters, dosage compensation by gene duplication), and by post-transcriptional regulation and spatial distribution of SIT proteins.
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Affiliation(s)
- Guillaume Sapriel
- Biomineralization and Morphogenesis Group, CNRS UMR-8186, Ecole Normale Supérieure, Paris, France
| | - Michelle Quinet
- Biomineralization and Morphogenesis Group, CNRS UMR-8186, Ecole Normale Supérieure, Paris, France
| | - Marc Heijde
- Biomineralization and Morphogenesis Group, CNRS UMR-8186, Ecole Normale Supérieure, Paris, France
| | - Laurent Jourdren
- Ecole Normale Supérieure, IFR36, Plate-forme Transcriptome, Paris, France
| | - Véronique Tanty
- Ecole Normale Supérieure, IFR36, Plate-forme Transcriptome, Paris, France
| | - Guangzuo Luo
- Biomineralization and Morphogenesis Group, CNRS UMR-8186, Ecole Normale Supérieure, Paris, France
| | - Stéphane Le Crom
- Ecole Normale Supérieure, IFR36, Plate-forme Transcriptome, Paris, France
| | - Pascal Jean Lopez
- Biomineralization and Morphogenesis Group, CNRS UMR-8186, Ecole Normale Supérieure, Paris, France
- * E-mail:
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