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Investigating the Proteome of Tardigrades: Towards a Better Understanding of Molecular Mechanisms during Anhydrobiosis

Schokraie, Elham (2011)
Investigating the Proteome of Tardigrades: Towards a Better Understanding of Molecular Mechanisms during Anhydrobiosis.
Technische Universität Darmstadt
Dissertation, Erstveröffentlichung

Kurzbeschreibung (Abstract)

Tardigrades have fascinated researchers for more than 300 years because of their amazing capability to undergo anhydrobiosis. In extreme states of dehydration, anhydrobiotic tardigrades undergo a metabolic dormancy, in which metabolism decreases to a non-measurable level and life comes to a reversible standstill until activity is resumed under more favourable conditions. In the anhydrobiotic (tun) state, tardigrades are extraordinary tolerant to physical extremes including high and subzero temperatures, high pressure, and extreme levels of ionizing radiation. Possessing the ability to enter this ametabolic state at any developmental stage, tardigrades are capable of surviving for a very long time and extend their lifespan significantly. Anhydrobiosis seems to be the result of dynamic processes and appears to be mediated by protective systems that prevent lethal damage. However, the survival mechanisms of tardigrades are still poorly understood. This is mainly caused by notable absence of detailed analysis concerning the proteome and genome of these organisms. FUNCRYPTA (Functional Analysis of Dynamic Processes in Cryptobiotic Tardigrades) project consisting of four research groups has been established to fill this gap by performing a broad range of investigations and analyses. As Funcrypta´s cooperation partner specialized in proteomics field we started with establishing optimal protocols for extraction of proteins from tardigrades, performing high resolution gel electrophoresis and high throughput protein identification and quantification. Since the presence of a comprehensive protein database is a prerequisite for protein identification, a M. tardigradum sequencing project has been initiated in parallel to our proteomic study by our genomic cooperation partner. The first tardigrade protein database translated from expressed sequence tags (ESTs), that have been generated by Sanger sequencing contained 3318 sequences. This protein database allowed us to develop the first proteome map of tardigrades utilizing 2D gel electrophoresis. The second protein database based on 454 sequencing with a high number of 24679 protein sequences provided us the basis for protein identification and quantification in a large scale. This resulted for the first time in a broad characterization of proteins expressed in tardigrades. More than 3000 unique proteins of M. tardigradum in three different states (early embryonic state and adults in active and anhydrobiotic states) have been identified with high sequence coverage using 1D electrophoresis in combination with high sensitive nanoLC ESI-MS/MS on a LTQ-Orbitrap mass spectrometer. Among the broad range of identified protein families, proteins known to be associated with desiccation tolerance were identified. This includes proteins with antioxidant activity, chaperones in particular heat shock proteins, aquaporins and Late Embryogenesis Abundant (LEA) proteins. Furthermore the present study provides a semi-quantitative analysis of proteins expressed in early embryonic state and adults in active and anhydrobiotic states using a label-free approach based on Exponentially Modified Protein Abundance Index (emPAI). This method allowed the classification of proteins present in one state in major and minor components and furthermore a quantitative analysis of differentially expressed proteins in each state. The semi-quantitative analysis delivered consequential results in comparing early embryonic state and adults, which will be of importance in the field of developmental biology. Using this approach we quantitatively analyzed the expressed heat shock proteins in active and tun states. The success of the analysis could be confirmed, by the published gene expression analysis of some heat shock proteins performed by our cooperation partner, which delivered similar results. The semi-quantitative analysis of active versus tun state demonstrated up-regulation of proteins in tun state that are mainly not annotated, since they are tardigrade specific and the homology search delivered no result. The functional analysis of these specific proteins in future investigations will be of major importance in regard to investigating anhydrobiosis. Analyzing the proteins that are only identified in tun state, leads to the assumption that not only proteins such as chaperones play important roles in protection mechanisms during anhydrobiosis, but also further processes and mechanisms are associated such as phosphorylation and activation of intracellular signalling cascades. Therefore optimal protocols for analyzing phosphoproteins in tardigrades have been developed and first experiments in detecting phosphoproteins on 2D gels using fluorescent dye (ProQ Diamond) have been performed. This comprehensive study from the first step of developing optimized protocol for protein extraction to the large scale protein identification and quantification builds the basis for future investigations in the field of anhydrobiotic organisms in regard to isolation and functional characterization of proteins, which are associated with protection mechanisms during anhydrobiosis. Understanding the desiccation-tolerance in anhydrobiotic tardigrades will probably enable us to develop new strategies for long-term stabilization and preservation of biological macromolecules in the future, which will be immensely important in medical field as well as in pharmaceutical industry.

Typ des Eintrags: Dissertation
Erschienen: 2011
Autor(en): Schokraie, Elham
Art des Eintrags: Erstveröffentlichung
Titel: Investigating the Proteome of Tardigrades: Towards a Better Understanding of Molecular Mechanisms during Anhydrobiosis
Sprache: Englisch
Referenten: Dencher, Prof. Dr. Norbert A. ; Kaldenhoff, Prof. Dr. Ralf ; Bischoff, Priv. Doz. Ralf
Publikationsjahr: 25 August 2011
Datum der mündlichen Prüfung: 8 November 2010
URL / URN: urn:nbn:de:tuda-tuprints-27355
Kurzbeschreibung (Abstract):

Tardigrades have fascinated researchers for more than 300 years because of their amazing capability to undergo anhydrobiosis. In extreme states of dehydration, anhydrobiotic tardigrades undergo a metabolic dormancy, in which metabolism decreases to a non-measurable level and life comes to a reversible standstill until activity is resumed under more favourable conditions. In the anhydrobiotic (tun) state, tardigrades are extraordinary tolerant to physical extremes including high and subzero temperatures, high pressure, and extreme levels of ionizing radiation. Possessing the ability to enter this ametabolic state at any developmental stage, tardigrades are capable of surviving for a very long time and extend their lifespan significantly. Anhydrobiosis seems to be the result of dynamic processes and appears to be mediated by protective systems that prevent lethal damage. However, the survival mechanisms of tardigrades are still poorly understood. This is mainly caused by notable absence of detailed analysis concerning the proteome and genome of these organisms. FUNCRYPTA (Functional Analysis of Dynamic Processes in Cryptobiotic Tardigrades) project consisting of four research groups has been established to fill this gap by performing a broad range of investigations and analyses. As Funcrypta´s cooperation partner specialized in proteomics field we started with establishing optimal protocols for extraction of proteins from tardigrades, performing high resolution gel electrophoresis and high throughput protein identification and quantification. Since the presence of a comprehensive protein database is a prerequisite for protein identification, a M. tardigradum sequencing project has been initiated in parallel to our proteomic study by our genomic cooperation partner. The first tardigrade protein database translated from expressed sequence tags (ESTs), that have been generated by Sanger sequencing contained 3318 sequences. This protein database allowed us to develop the first proteome map of tardigrades utilizing 2D gel electrophoresis. The second protein database based on 454 sequencing with a high number of 24679 protein sequences provided us the basis for protein identification and quantification in a large scale. This resulted for the first time in a broad characterization of proteins expressed in tardigrades. More than 3000 unique proteins of M. tardigradum in three different states (early embryonic state and adults in active and anhydrobiotic states) have been identified with high sequence coverage using 1D electrophoresis in combination with high sensitive nanoLC ESI-MS/MS on a LTQ-Orbitrap mass spectrometer. Among the broad range of identified protein families, proteins known to be associated with desiccation tolerance were identified. This includes proteins with antioxidant activity, chaperones in particular heat shock proteins, aquaporins and Late Embryogenesis Abundant (LEA) proteins. Furthermore the present study provides a semi-quantitative analysis of proteins expressed in early embryonic state and adults in active and anhydrobiotic states using a label-free approach based on Exponentially Modified Protein Abundance Index (emPAI). This method allowed the classification of proteins present in one state in major and minor components and furthermore a quantitative analysis of differentially expressed proteins in each state. The semi-quantitative analysis delivered consequential results in comparing early embryonic state and adults, which will be of importance in the field of developmental biology. Using this approach we quantitatively analyzed the expressed heat shock proteins in active and tun states. The success of the analysis could be confirmed, by the published gene expression analysis of some heat shock proteins performed by our cooperation partner, which delivered similar results. The semi-quantitative analysis of active versus tun state demonstrated up-regulation of proteins in tun state that are mainly not annotated, since they are tardigrade specific and the homology search delivered no result. The functional analysis of these specific proteins in future investigations will be of major importance in regard to investigating anhydrobiosis. Analyzing the proteins that are only identified in tun state, leads to the assumption that not only proteins such as chaperones play important roles in protection mechanisms during anhydrobiosis, but also further processes and mechanisms are associated such as phosphorylation and activation of intracellular signalling cascades. Therefore optimal protocols for analyzing phosphoproteins in tardigrades have been developed and first experiments in detecting phosphoproteins on 2D gels using fluorescent dye (ProQ Diamond) have been performed. This comprehensive study from the first step of developing optimized protocol for protein extraction to the large scale protein identification and quantification builds the basis for future investigations in the field of anhydrobiotic organisms in regard to isolation and functional characterization of proteins, which are associated with protection mechanisms during anhydrobiosis. Understanding the desiccation-tolerance in anhydrobiotic tardigrades will probably enable us to develop new strategies for long-term stabilization and preservation of biological macromolecules in the future, which will be immensely important in medical field as well as in pharmaceutical industry.

Alternatives oder übersetztes Abstract:
Alternatives AbstractSprache

Tardigraden haben seit mehr als 300 Jahren die Forscher durch ihre einzigartige Fähigkeit, Anhydrobiose einzugehen, fasziniert. Anhydrobiose wird durch extreme Trocknung ausgelöst. Dabei ändern Tardigraden ihre Körperform, ziehen sich zusammen und bilden ein Tönnchen, in dem keinerlei Metabolismus mehr nachweisbar ist. Im anhydrobiotischen (Tönnchen-) Stadium zeigen Tardigraden eine außergewöhnliche Toleranz gegenüber physikalischen Extremen wie hohem Druck, hohen oder niedrigen Temperaturen und ionisierender Strahlung. Durch die Fähigkeit in jeder Entwicklungsphase Anhydrobiose einzugehen, können Tardigraden ihre Lebensdauer deutlich verlängern. Die molekularen Schutz- und Reparatur-Mechanismen während der Anhydrobiose sind aufgrund fehlender fundamentalen Untersuchungen im genomischen und proteomischen Bereich noch unklar. Die molekularen Prozesse während der Anhydrobiose und die involvierten Mechanismen können nur dann geklärt werden, wenn die Grundlagen erforscht sind und für weitergehende Experimente zur Verfügung stehen. Das FUNCRYPTA (Funktionelle Analyse Dynamischer Prozesse in Anhydobiotischer Tardigraden) Projekt bestehend aus vier Forschungsgruppen hat sich zum Ziel gesetzt, diese Grundlagen zu erforschen. Als Kooperationspartner spezialisiert in Proteomiks haben wir in der folgenden Studie optimierte Protokolle für Proteinextraktion, Gelelektrophorese mit hoher Auflösung und Protein-identifikation und -quantifizierung etabliert. Da eine der wichtigsten Vorraussetzungen für die Proteome-Analyse die Existenz einer möglichst vollständigen Proteindatenbank ist, wurde zunächst von unseren Kooperationspartnern eine spezifische Proteindatenbank aus EST-Sequenzen, die durch Sanger-Sequenzierung erzeugt waren, entwickelt. Diese erste Proteindatenbank, die 3318 Proteinsequenzen enthielt, ermöglichte uns die Entwicklung der ersten Proteomkarte vom M. tardigradum. Die zweite Proteindatenbank, die auf 454 Sequenzierung basiert und 24679 Proteinsequenzen beinhaltet, lieferte eine gute Basis für umfangreiche Identifizierung und Quantifizierung der Proteine. Mehr als 3000 einzelne Proteine konnten durch 1D-Elektrophorese in Kombination mit hoch sensitiven massenspektrometrischen Methoden in drei verschiedenen Lebenszuständen der Tardigraden (Embryonen im Frühstadium, erwachsenen Tiere im Aktiv- und Tönnchen-Zustand) identifiziert werden. Diverse Proteinfamilien involviert in ein breites Spektrum biologischer Prozesse sind in den Ergebnissen erhalten. Es konnten vor allem einige Proteine, deren Assoziation mit Anhydrobiose bereits in anderen Organismen untersucht worden sind, in Tardigraden identifiziert werden. Dazu gehören Proteine mit Antioxidant-Aktivität, „Chaperone“-Proteine wie Hitzeschock-Proteine und weiterhin LEA (Late Embryogenesis Abundant) Proteine und Aquaporine. Zusätzlich wurde in der folgenden Studie eine semi-quantitative Analyse der vorhandenen Proteine in drei verschiedenen Lebensstadien (Embryonen, erwachsenen Tiere in Aktiv- und Tönnchen-Zustand) durchgeführt. Der Vergleich und die Quantifizierung identifizierter Proteine durch eine label-freien Methode lieferte aufschlussreiche Ergebnisse über exprimierten Proteine im Embyonen-Frühstadium und Hinweise über mögliche Proteine und Mechanismen, die dem Prozess der Anhydrobiose assoziiert sind. Der Erfolg dieser Quantifizierungsmethode für ausgewählte Hitzeschock-Proteine konnte durch publizierte Gen-Expressionsdaten von unserem Kooperationspartner bestätigt werden. Die semi-quantitative Analyse der exprimierten Proteinen in Aktiv- versus Tönnchen-Zustand zeigte die Hochregulation vieler Proteine, die durch Homologie-Suche nicht annotiert werden konnten. Die funktionelle Analyse und Charakterisierung dieser Tardigraden spezifischen Proteine ist der nächste wichtige Schritt in der Tardigraden-Forschung. Die funktionelle Analyse der Proteine, die nur im Tönnchen-Zustand identifiziert wurden, führte zur Annahme, dass Prozesse wie Phosphorylierung und Aktivierung der intrazellulären Kaskaden eine wichtige Rolle während der Anhydrobiose spielen können. Aus diesem Grund wurde in ersten Experimenten die Phosphorylierung als posttranslationale Modifikation untersucht. Dazu wurden Protokolle zur Detektion der Phosphoproteine in 2D-Gelen durch den Fluoreszenz-Farbstoff ProQ Diamond optimiert. Die proteomischen Ergebnisse zusammen mit erzielten genetischen und bioinformatischen Untersuchungen und Auswertungen stellen nicht nur die fundamentalen Grundlagen der Tardigraden-Forschung dar, sondern liefern viele neue Erkenntnisse auf dem Weg zur Aufklärung der involvierten Schutz-Mechanismen bei der Anhydrobiose. Dies kann in Zukunft zur Entwicklung neuer Methoden und Strategien für die Konservierung und Stabilisierung biologischer Materialien führen, die einen wichtigen Beitrag im Bereich Medizin und Pharma liefern.

Deutsch
Freie Schlagworte: Proteomik, Gel-Elektrophorese, DIGE-Technik, Tardigraden, Anhydrobiose, Protein-Identifizierung, Protein-Quantifizierung, Embryonen-Frühstadium, Tönnchen-Zustand, EST-Sequenzen, FUNCRYPTA-Projekt
Schlagworte:
Einzelne SchlagworteSprache
Shotgun proteomics, gel electrophoresis, DIGE technology, high throughput protein identification, label free quantification, Tardigrades, anhydrobiosis, anhydrobiotic state, early embryonic state, EST sequences, Funcrypta projectEnglisch
Zusätzliche Informationen:

Links to publications: http://www.plosone.org/article/info:doi%2F10.1371%2Fjournal.pone.0009502 http://onlinelibrary.wiley.com/doi/10.1111/j.1439-0469.2010.00608.x/suppinfo

Sachgruppe der Dewey Dezimalklassifikatin (DDC): 500 Naturwissenschaften und Mathematik > 500 Naturwissenschaften
500 Naturwissenschaften und Mathematik > 540 Chemie
500 Naturwissenschaften und Mathematik > 570 Biowissenschaften, Biologie
500 Naturwissenschaften und Mathematik > 590 Tiere (Zoologie)
Fachbereich(e)/-gebiet(e): 07 Fachbereich Chemie
Hinterlegungsdatum: 06 Sep 2011 08:35
Letzte Änderung: 05 Mär 2013 09:54
PPN:
Referenten: Dencher, Prof. Dr. Norbert A. ; Kaldenhoff, Prof. Dr. Ralf ; Bischoff, Priv. Doz. Ralf
Datum der mündlichen Prüfung / Verteidigung / mdl. Prüfung: 8 November 2010
Schlagworte:
Einzelne SchlagworteSprache
Shotgun proteomics, gel electrophoresis, DIGE technology, high throughput protein identification, label free quantification, Tardigrades, anhydrobiosis, anhydrobiotic state, early embryonic state, EST sequences, Funcrypta projectEnglisch
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