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  • 1
    Language: English
    In: Journal of Zoological Systematics and Evolutionary Research, May, 2011, Vol.49, p.111(9)
    Description: To authenticate to the full-text of this article, please visit this link: http://dx.doi.org/10.1111/j.1439-0469.2010.00608.x Byline: Elham Schokraie (1), Agnes Hotz-Wagenblatt (1), Uwe Warnken (1), Marcus Frohme (2), Thomas Dandekar (3), Ralph O. Schill (4), Martina Schnolzer (1) Keywords: Tardigrades; heat shock proteins; Hsp60 (chaperonin); Hsp40 (DnaJ); Hsp70 (DnaK); Hsp90; small heat shock proteins; nucleotide exchange factors; co-chaperones; high throughput proteomics Abstract: Abstract The eutardigrade Milnesium tardigradum can undergo cryptobiosis and can survive extreme environmental conditions. However, the survival mechanisms of tardigrades are still poorly understood. Heat shock proteins (Hsps) as an important subgroup of chaperones which protect proteins from irreversible aggregation and degradation might play an important role in anhydrobiosis. In this report, we therefore investigated Hsps in tardigrades in the active versus the anhydrobiotic state employing proteomics techniques. Protein lysates from tardigrades in both states were separated by one-dimensional gel electrophoresis, in-gel digested with trypsin and tryptic peptides were analyzed by high sensitive nanoLC-ESI-MS/MS on a LTQ-Orbitrap mass spectrometer. This study indicates the presence of Hsps of the major chaperone families Hsp40, Hsp60, Hsp70, Hsp90, small Hsps and furthermore nucleotide exchange factors and co-chaperones in Milnesium tardigradum. A comparative analysis of the identified Hsps in both states was performed by calculating the exponentially modified protein abundance index. Abstract (German): Zusammenfassung Untersuchung von Hitzeschock-Proteinen bei Tardigraden im aktiven gegenuber anhydrobiotischen Zustand mit Hilfe von Proteomics-Techniken Tardigraden haben die au[sz]ergewohnliche Fahigkeit, extreme Stress-Bedingungen zu uberleben, indem sie Kryptobiose eingehen. Dabei andern sie ihre Korperform, ziehen sich zusammen und bilden ein Tonnchen, in dem keinerlei Metabolismus mehr nachweisbar ist. Obwohl Tardigraden seit ca. 300 Jahren bekannt sind, sind die molekularen Mechanismen wahrend der Kryptobiose aufgrund fehlender fundamentaler Untersuchungen noch unklar. Eine wichtige Proteinklasse, die beim Uberleben der Tardigraden wahrend der Stress-Situation moglicherweise eine gro[sz]e Rolle spielt, sind die Hitzeschockproteine. Hitzeschockproteine (Stressproteine, Hsps) sind ubiquitare, hoch konservierte Chaperone, die die Aufrechterhaltung der Proteine in ihrer funktionellen Konfirmation bewirken, indem sie ihre Aggregation verhindern. Wahrend die Anwesenheit der Hitzeschockproteine in der Zelle unter normalen Bedingungen erforderlich ist, ist ihre Aktivitat bei Hitze oder in Stress-Situationen zum Uberleben absolut notwendig. In unserer Studie haben wir die Hitzeschockproteine in Milnesium tardigradum unter Verwendung von Proteomics-Techniken identifiziert. Dazu wurde die eindimensionale Gelelektrophorese gefolgt von der hochsensitiven Analyse der nach Trypsin-Verdau erhaltenen Peptide durch nanoLC-ESI-MS/MS auf einem LTQ-Orbitrap-Massenspektrometer eingesetzt. Proteine aus diversen Hitzeschock-Proteinfamilien Hsp40, Hsp60, Hsp70 und Hsp90 sowie kleine Hitzeschockproteine (Hsp20) und zusatzlich Co-Chaperone wie GrpE konnten durch MS/MS Analyse und Datenbank-Suche gegen die NCBInr- sowie eine neu zusammengestellte Proteindatenbank aus EST-Sequenzen von Milnesium tardigradum nachgewiesen werden. Au[sz]erdem konnten durch eine semiquantitative Methode die identifizierten Hitzeschockproteine in Tardigraden im aktiven und anhydrobiotischen Zustand verglichen werden. Author Affiliation: (1)Functional Proteome Analysis, German Cancer Research Center, Heidelberg (2)Department of Molecular Biology and Functional Genomics, University of Applied Sciences Wildau, Wildau (3)Department of Bioinformatics, University of Wurzburg, Wurzburg (4)Department of Zoology, University of Stuttgart, Stuttgart, Germany Article History: Accepted on 1 October 2010 Article note: Corresponding author: Martina Schnolzer (m.schnoelzer@dkfz.de)
    Keywords: Trypsin -- Investigations ; Trypsin -- Analysis ; Proteins -- Investigations ; Proteins -- Analysis ; Heat Shock Proteins -- Investigations ; Heat Shock Proteins -- Analysis ; Cancer Research -- Investigations ; Cancer Research -- Analysis ; Proteomics -- Investigations ; Proteomics -- Analysis ; Universities And Colleges -- Investigations ; Universities And Colleges -- Analysis
    ISSN: 0947-5745
    Source: Cengage Learning, Inc.
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  • 2
    Language: English
    In: 2012, Vol.7(9), p.e45682
    Description: Tardigrades have fascinated researchers for more than 300 years because of their extraordinary capability to undergo cryptobiosis and survive extreme environmental conditions. However, the survival mechanisms of tardigrades are still poorly understood mainly due to the absence of detailed knowledge about the proteome and genome of these organisms. Our study was intended to provide a basis for the functional characterization of expressed proteins in different states of tardigrades. High-throughput, high-accuracy proteomics in combination with a newly developed tardigrade specific protein database resulted in the identification of more than 3000 proteins in three different states: early embryonic state and adult animals in active and anhydrobiotic state. This comprehensive proteome resource includes protein families such as chaperones, antioxidants, ribosomal proteins, cytoskeletal proteins, transporters, protein channels, nutrient reservoirs, and developmental proteins. A comparative analysis of protein families in the different states was performed by calculating the exponentially modified protein abundance index which classifies proteins in major and minor components. This is the first step to analyzing the proteins involved in early embryonic development, and furthermore proteins which might play an important role in the transition into the anhydrobiotic state.
    Keywords: Research Article ; Biology ; Biochemistry
    E-ISSN: 1932-6203
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  • 3
    Language: English
    In: PLoS ONE, 2010, Vol.5(3), p.e9502
    Description: Tardigrades are small, multicellular invertebrates which are able to survive times of unfavourable environmental conditions using their well-known capability to undergo cryptobiosis at any stage of their life cycle. Milnesium tardigradum has become a powerful model system for the analysis of cryptobiosis. While some genetic information is already available for Milnesium tardigradum the proteome is still to be discovered. ; Here we present to the best of our knowledge the first comprehensive study of on the protein level. To establish a proteome reference map we developed optimized protocols for protein extraction from tardigrades in the active state and for separation of proteins by high resolution two-dimensional gel electrophoresis. Since only limited sequence information of on the genome and gene expression level is available to date in public databases we initiated in parallel a tardigrade EST sequencing project to allow for protein identification by electrospray ionization tandem mass spectrometry. 271 out of 606 analyzed protein spots could be identified by searching against the publicly available NCBInr database as well as our newly established tardigrade protein database corresponding to 144 unique proteins. Another 150 spots could be identified in the tardigrade clustered EST database corresponding to 36 unique contigs and ESTs. Proteins with annotated function were further categorized in more detail by their molecular function, biological process and cellular component. For the proteins of unknown function more information could be obtained by performing a protein domain annotation analysis. Our results include proteins like protein member of different heat shock protein families and LEA group 3, which might play important roles in surviving extreme conditions. ; The proteome reference map of provides the basis for further studies in order to identify and characterize the biochemical mechanisms of tolerance to extreme desiccation. The optimized proteomics workflow will enable application of sensitive quantification techniques to detect differences in protein expression, which are characteristic of the active and anhydrobiotic states of tardigrades.
    Keywords: Research Article ; Biochemistry -- Protein Chemistry ; Biotechnology -- Protein Chemistry And Proteomics ; Chemical Biology -- Protein Chemistry And Proteomics
    E-ISSN: 1932-6203
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  • 4
    Language: English
    In: Biogerontology, 2010, Vol.11(3), pp.321-334
    Description: Mitochondria being the major source and target of reactive oxygen species (ROS) play a crucial role during ageing. We analyzed ageing and calorie restriction (CR)-induced changes in abundance of rat liver mitochondrial proteins to understand key aspects behind the age-retarding mechanism of CR. The combination of blue-native (BN) gel system with fluorescence Difference Gel Electrophoresis (DIGE) facilitated an efficient analysis of soluble and membrane proteins, existing as monomers or multi-protein assemblies. Changes in abundance of specific key subunits of respiratory chain complexes I, IV and V, critical for activity and/or assembly of the complexes were identified. CR lowered complex I assembly and complex IV activity, which is discussed as a molecular mechanism to minimize ROS production at mitochondria. Notably, the antioxidant system was found to be least affected. The GSH:GSSG couple could be depicted as a rapid mean to handle the fluctuations in ROS levels led by reversible metabolic shifts. We evaluated the relative significance of ROS generation against quenching. We also observed parallel and unidirectional changes as effect of ageing and CR, in subunits of ATP synthase, cytochrome P450 and glutathione S-transferase. This is the first report on such ‘putatively hormetic’ ageing-analogous effects of CR, besides the age-retarding ones.
    Keywords: Ageing ; Antioxidants ; Calorie restriction ; DIGE ; Proteomics ; Mitochondria
    ISSN: 1389-5729
    E-ISSN: 1573-6768
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  • 5
    Language: English
    In: Journal of Zoological Systematics and Evolutionary Research, 05/2011, Vol.49, supplement s1, pp.111-119
    Description: The eutardigrade Milnesium tardigradum can undergo cryptobiosis and can survive extreme environmental conditions. However, the survival mechanisms of tardigrades are still poorly understood. Heat shock proteins (Hsps) as an important subgroup of chaperones which protect proteins from irreversible aggregation and degradation might play an important role in anhydrobiosis. In this report, we therefore investigated Hsps in tardigrades in the active versus the anhydrobiotic state employing proteomics techniques. Protein lysates from tardigrades in both states were separated by one-dimensional gel electrophoresis, in-gel digested with trypsin and tryptic peptides were analyzed by high sensitive nanoLC-ESI-MS/MS on a LTQ-Orbitrap mass spectrometer. This study indicates the presence of Hsps of the major chaperone families Hsp40, Hsp60, Hsp70, Hsp90, small Hsps and furthermore nucleotide exchange factors and co-chaperones in Milnesium tardigradum. A comparative analysis of the identified Hsps in both states was performed by calculating the exponentially modified protein abundance index.Original Abstract: Tardigraden haben die ausergewohnliche Faehigkeit, extreme Stress-Bedingungen zu ueberleben, indem sie Kryptobiose eingehen. Dabei aendern sie ihre Korperform, ziehen sich zusammen und bilden ein Tonnchen, in dem keinerlei Metabolismus mehr nachweisbar ist. Obwohl Tardigraden seit ca. 300 Jahren bekannt sind, sind die molekularen Mechanismen waehrend der Kryptobiose aufgrund fehlender fundamentaler Untersuchungen noch unklar. Eine wichtige Proteinklasse, die beim Ueberleben der Tardigraden waehrend der Stress-Situation moglicherweise eine grose Rolle spielt, sind die Hitzeschockproteine. Hitzeschockproteine (Stressproteine, Hsps) sind ubiquitaere, hoch konservierte Chaperone, die die Aufrechterhaltung der Proteine in ihrer funktionellen Konfirmation bewirken, indem sie ihre Aggregation verhindern. Waehrend die Anwesenheit der Hitzeschockproteine in der Zelle unter normalen Bedingungen erforderlich ist, ist ihre Aktivitaet bei Hitze oder in Stress-Situationen zum Ueberleben absolut notwendig. In unserer Studie haben wir die Hitzeschockproteine in Milnesium tardigradum unter Verwendung von Proteomics-Techniken identifiziert. Dazu wurde die eindimensionale Gelelektrophorese gefolgt von der hochsensitiven Analyse der nach Trypsin-Verdau erhaltenen Peptide durch nanoLC-ESI-MS/MS auf einem LTQ-Orbitrap-Massenspektrometer eingesetzt. Proteine aus diversen Hitzeschock-Proteinfamilien Hsp40, Hsp60, Hsp70 und Hsp90 sowie kleine Hitzeschockproteine (Hsp20) und zusaetzlich Co-Chaperone wie GrpE konnten durch MS/MS Analyse und Datenbank-Suche gegen die NCBInr- sowie eine neu zusammengestellte Proteindatenbank aus EST-Sequenzen von Milnesium tardigradum nachgewiesen werden. Auserdem konnten durch eine semiquantitative Methode die identifizierten Hitzeschockproteine in Tardigraden im aktiven und anhydrobiotischen Zustand verglichen werden.
    Keywords: Proteins ; Heat Shock ; Peptides ; Environmental Conditions ; Nucleotides ; Milnesium Tardigradum ; Population Structure;
    ISSN: Journal of Zoological Systematics and Evolutionary Research
    E-ISSN: 09475745
    E-ISSN: 14390469
    Source: Wiley (via CrossRef)
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  • 6
    Language: English
    In: Bioinformatics and Biology Insights, April 23, 2012, p.69(28)
    Description: Tardigrades have unique stress-adaptations that allow them to survive extremes of cold, heat, radiation and vacuum. To study this, encoded protein clusters and pathways from an ongoing transcriptome study on the tardigrade Milnesium tardigradum were analyzed using bioinformatics tools and compared to expressed sequence tags (ESTs) from Hypsibius dujardini, revealing major pathways involved in resistance against extreme environmental conditions. ESTs are available on the Tardigrade Workbench along with software and databank updates. Our analysis reveals that RNA stability motifs for M. tardigradum are different from typical motifs known from higher animals. M. tardigradum and H. dujardini protein clusters and conserved domains imply metabolic storage pathways for glycogen, glycolipids and specific secondary metabolism as well as stress response pathways (including heat shock proteins, bmh2, and specific repair pathways). Redox-, DNA-, stress- and protein protection pathways complement specific repair capabilities to achieve the strong robustness of M. tardigradum. These pathways are partly conserved in other animals and their manipulation could boost stress adaptation even in human cells. However, the unique combination of resistance and repair pathways make tardigrades and M. tardigradum in particular so highly stress resistant. Keywords: RNA, expressed sequence tag, cluster, protein family, adaptation, tardigrada, transcriptome
    Keywords: Glycogen -- Physiological Aspects ; Nuclear Radiation -- Physiological Aspects ; Anopheles -- Physiological Aspects ; Radiation (Physics) -- Physiological Aspects ; Software -- Physiological Aspects ; Proteins -- Physiological Aspects ; Rna -- Physiological Aspects ; Heat Shock Proteins -- Physiological Aspects ; Plant Lipids -- Physiological Aspects ; Polysaccharides -- Physiological Aspects ; Cells (Biology) -- Physiological Aspects ; Dna -- Physiological Aspects ; Wildlife Conservation -- Physiological Aspects ; Glucose Metabolism -- Physiological Aspects
    ISSN: 1177-9322
    Source: Cengage Learning, Inc.
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  • 7
    Language: English
    In: Bioinformatics and Biology Insights, April 23, 2012, p.69(28)
    Description: Tardigrades have unique stress-adaptations that allow them to survive extremes of cold, heat, radiation and vacuum. To study this, encoded protein clusters and pathways from an ongoing transcriptome study on the tardigrade Milnesium tardigradum were analyzed using bioinformatics tools and compared to expressed sequence tags (ESTs) from Hypsibius dujardini, revealing major pathways involved in resistance against extreme environmental conditions. ESTs are available on the Tardigrade Workbench along with software and databank updates. Our analysis reveals that RNA stability motifs for M. tardigradum are different from typical motifs known from higher animals. M. tardigradum and H. dujardini protein clusters and conserved domains imply metabolic storage pathways for glycogen, glycolipids and specific secondary metabolism as well as stress response pathways (including heat shock proteins, bmh2, and specific repair pathways). Redox-, DNA-, stress- and protein protection pathways complement specific repair capabilities to achieve the strong robustness of M. tardigradum. These pathways are partly conserved in other animals and their manipulation could boost stress adaptation even in human cells. However, the unique combination of resistance and repair pathways make tardigrades and M. tardigradum in particular so highly stress resistant. Keywords: RNA, expressed sequence tag, cluster, protein family, adaptation, tardigrada, transcriptome
    Keywords: Glycogen -- Physiological Aspects ; Nuclear Radiation -- Physiological Aspects ; Anopheles -- Physiological Aspects ; Radiation (Physics) -- Physiological Aspects ; Software -- Physiological Aspects ; Proteins -- Physiological Aspects ; Rna -- Physiological Aspects ; Heat Shock Proteins -- Physiological Aspects ; Plant Lipids -- Physiological Aspects ; Polysaccharides -- Physiological Aspects ; Cells (Biology) -- Physiological Aspects ; Dna -- Physiological Aspects ; Wildlife Conservation -- Physiological Aspects ; Glucose Metabolism -- Physiological Aspects
    ISSN: 1177-9322
    Source: Cengage Learning, Inc.
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  • 8
    Language: English
    In: Bioinformatics and Biology Insights, January 2012, Vol.6
    Description: Tardigrades have unique stress-adaptations that allow them to survive extremes of cold, heat, radiation and vacuum. To study this, encoded protein clusters and pathways from an ongoing transcriptome study on the tardigrade Milnesium tardigradum were analyzed using bioinformatics tools and compared to expressed sequence tags (ESTs) from Hypsibius dujardini, revealing major pathways involved in resistance against extreme environmental conditions. ESTs are available on the Tardigrade Workbench along with software and databank updates. Our analysis reveals that RNA stability motifs for M. tardigradum are different from typical motifs known from higher animals. M. tardigradum and H. dujardini protein clusters and conserved domains imply metabolic storage pathways for glycogen, glycolipids and specific secondary metabolism as well as stress response pathways (including heat shock proteins, bmh2, and specific repair pathways). Redox-, DNA-, stress- and protein protection pathways complement specific repair capabilities to achieve the strong robustness of M. tardigradum. These pathways are partly conserved in other animals and their manipulation could boost stress adaptation even in human cells. However, the unique combination of resistance and repair pathways make tardigrades and M. tardigradum in particular so highly stress resistant.
    Keywords: RNA ; Expressed Sequence Tag ; Cluster ; Protein Family ; Adaptation ; Tardigrada ; Transcriptome ; Biology
    E-ISSN: 1177-9322
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  • 9
    Language: English
    In: Bioinformatics and Biology Insights, 01 April 2012, Vol.2012(6), pp.69-96
    Keywords: Biology
    ISSN: 1177-9322
    E-ISSN: 1177-9322
    Source: Directory of Open Access Journals (DOAJ)
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