Dataset Information

Comparative proteome analysis of Milnesium tardigradum in early embryonic state versus adults in active and anhydrobiotic state.

ABSTRACT: 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.

SUBMITTER: Schokraie E

PROVIDER: S-EPMC3459984 | biostudies-literature | 2012

REPOSITORIES: biostudies-literature

ACCESS DATA

Publications

Comparative proteome analysis of Milnesium tardigradum in early embryonic state versus adults in active and anhydrobiotic state.

Schokraie Elham E Warnken Uwe U Hotz-Wagenblatt Agnes A Grohme Markus A MA Hengherr Steffen S Förster Frank F Schill Ralph O RO Frohme Marcus M Dandekar Thomas T Schnölzer Martina M

PloS one 20120927 9

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-throughpu ...[more]

PMID: 23029181

Similar Datasets

Project description:BACKGROUND: The phenomenon of desiccation tolerance, also called anhydrobiosis, involves the ability of an organism to survive the loss of almost all cellular water without sustaining irreversible damage. Although there are several physiological, morphological and ecological studies on tardigrades, only limited DNA sequence information is available. Therefore, we explored the transcriptome in the active and anhydrobiotic state of the tardigrade Milnesium tardigradum which has extraordinary tolerance to desiccation and freezing. In this study, we present the first overview of the transcriptome of M. tardigradum and its response to desiccation and discuss potential parallels to stress responses in other organisms. RESULTS: We sequenced a total of 9984 expressed sequence tags (ESTs) from two cDNA libraries from the eutardigrade M. tardigradum in its active and inactive, anhydrobiotic (tun) stage. Assembly of these ESTs resulted in 3283 putative unique transcripts, whereof approximately 50% showed significant sequence similarity to known genes. The resulting unigenes were functionally annotated using the Gene Ontology (GO) vocabulary. A GO term enrichment analysis revealed several GOs that were significantly underrepresented in the inactive stage. Furthermore we compared the putative unigenes of M. tardigradum with ESTs from two other eutardigrade species that are available from public sequence databases, namely Richtersius coronifer and Hypsibius dujardini. The processed sequences of the three tardigrade species revealed similar functional content and the M. tardigradum dataset contained additional sequences from tardigrades not present in the other two. CONCLUSIONS: This study describes novel sequence data from the tardigrade M. tardigradum, which significantly contributes to the available tardigrade sequence data and will help to establish this extraordinary tardigrade as a model for studying anhydrobiosis. Functional comparison of active and anhydrobiotic tardigrades revealed a differential distribution of Gene Ontology terms associated with chromatin structure and the translation machinery, which are underrepresented in the inactive animals. These findings imply a widespread metabolic response of the animals on dehydration. The collective tardigrade transcriptome data will serve as a reference for further studies and support the identification and characterization of genes involved in the anhydrobiotic response.

Project description:BackgroundMany tardigrade species are capable of anhydrobiosis; however, mechanisms underlying their extreme desiccation resistance remain elusive. This study attempts to quantify the anhydrobiotic transcriptome of the limno-terrestrial tardigrade Milnesium tardigradum.ResultsA prerequisite for differential gene expression analysis was the generation of a reference hybrid transcriptome atlas by assembly of Sanger, 454 and Illumina sequence data. The final assembly yielded 79,064 contigs (>100 bp) after removal of ribosomal RNAs. Around 50% of them could be annotated by SwissProt and NCBI non-redundant protein sequences. Analysis using CEGMA predicted 232 (93.5%) out of the 248 highly conserved eukaryotic genes in the assembly. We used this reference transcriptome for mapping and quantifying the expression of transcripts regulated under anhdydrobiosis in a time-series during dehydration and rehydration. 834 of the transcripts were found to be differentially expressed in a single stage (dehydration/inactive tun/rehydration) and 184 were overlapping in two stages while 74 were differentially expressed in all three stages. We have found interesting patterns of differentially expressed transcripts that are in concordance with a common hypothesis of metabolic shutdown during anhydrobiosis. This included down-regulation of several proteins of the DNA replication and translational machinery and protein degradation. Among others, heat shock proteins Hsp27 and Hsp30c were up-regulated in response to dehydration and rehydration. In addition, we observed up-regulation of ployubiquitin-B upon rehydration together with a higher expression level of several DNA repair proteins during rehydration than in the dehydration stage.ConclusionsMost of the transcripts identified to be differentially expressed had distinct cellular function. Our data suggest a concerted molecular adaptation in M. tardigradum that permits extreme forms of ametabolic states such as anhydrobiosis. It is temping to surmise that the desiccation tolerance of tradigrades can be achieved by a constitutive cellular protection system, probably in conjunction with other mechanisms such as rehydration-induced cellular repair.

Project description:BACKGROUND: Tardigrades are multicellular organisms, resistant to extreme environmental changes such as heat, drought, radiation and freezing. They outlast these conditions in an inactive form (tun) to escape damage to cellular structures and cell death. Tardigrades are apparently able to prevent or repair such damage and are therefore a crucial model organism for stress tolerance. Cultures of the tardigrade Milnesium tardigradum were dehydrated by removing the surrounding water to induce tun formation. During this process and the subsequent rehydration, metabolites were measured in a time series by GC-MS. Additionally expressed sequence tags are available, especially libraries generated from the active and inactive state. The aim of this integrated analysis is to trace changes in tardigrade metabolism and identify pathways responsible for their extreme resistance against physical stress. RESULTS: In this study we propose a novel integrative approach for the analysis of metabolic networks to identify modules of joint shifts on the transcriptomic and metabolic levels. We derive a tardigrade-specific metabolic network represented as an undirected graph with 3,658 nodes (metabolites) and 4,378 edges (reactions). Time course metabolite profiles are used to score the network nodes showing a significant change over time. The edges are scored according to information on enzymes from the EST data. Using this combined information, we identify a key subnetwork (functional module) of concerted changes in metabolic pathways, specific for de- and rehydration. The module is enriched in reactions showing significant changes in metabolite levels and enzyme abundance during the transition. It resembles the cessation of a measurable metabolism (e.g. glycolysis and amino acid anabolism) during the tun formation, the production of storage metabolites and bioprotectants, such as DNA stabilizers, and the generation of amino acids and cellular components from monosaccharides as carbon and energy source during rehydration. CONCLUSIONS: The functional module identifies relationships among changed metabolites (e.g. spermidine) and reactions and provides first insights into important altered metabolic pathways. With sparse and diverse data available, the presented integrated metabolite network approach is suitable to integrate all existing data and analyse it in a combined manner.

Project description:The open space is a hostile environment for all lifeforms not only due to vacuum, high radiation, low atmospheric pressure, and extremely low temperature, but also the absence of the geomagnetic field. The geomagnetic field protects Earth mainly from corpuscular radiation, that is, solar wind and cosmic radiation, but above all it influences organisms, including their cells, tissues and organs. Moreover, numerous studies conducted on plants and animals confirmed that hypomagnetic conditions (the term referring to all situations when the magnetic field is weaker than the typical geomagnetic field) have significant influence on the metabolism of living organisms. Although many studies dealt with a variety of aspects related mainly to the influence of hypomagnetic conditions on human health. Very few studies have considered the influence of hypomagnetic conditions on extremophiles. Astrobiologists have long been testing different extremofiles to find out if any multicellular organisms are able to survive in extreme conditions of open space. Among all multicellular extremophiles fit for such research, water bears (Tardigrada) are the most interesting. Not only are they one of the most resistant organisms on Earth, but results obtained from studies on these invertebrates can be extrapolated or applied to vertebrates (including humans). Despite this, studies on the influence of hypomagnetic conditions on tardigrades are rare, so far. In the present study, to test the influence of hypomagnetic conditions on the process of anhydrobiosis while entering and returning from anhydrobiosis, we used two terrestrial anhydrobiotic species that are Echiniscus testudo and Milnesium inceptum. To exclude the ambient magnetic field, experiments were carried out in a special magnetic field shielding chamber. In total, three experiments were conducted: (a) tardigrades in anhydrobiosis, (b) tardigrades entering anhydrobiosis and (c) tardigrades returning to active life. The obtained results clearly showed that even partial isolation from the geomagnetic field, that is, hypomagnetic conditions, has negative influence on anhydrobiotic abilities of both tested tardigrade species. In both species we observed lower survivability rate while entering anhydrobiosis, in anhydrobiotic state and returning to the active state. What is more, we observed a higher mortality rate in Ech. testudo than Mil. inceptum which suggest that different species response to the hypomagnetic conditions in different way. In conclusion, while current knowledge on the influence of hypomagnetic conditions on mortality of invertebrates is very limited, our results suggest that the presence of the magnetic field is a very important factor which should be considered in further research focused on potential survival of Earth organisms in outer space, spacecrafts or different planets and moons.

Dataset Information

Comparative proteome analysis of Milnesium tardigradum in early embryonic state versus adults in active and anhydrobiotic state.

Publications

Comparative proteome analysis of Milnesium tardigradum in early embryonic state versus adults in active and anhydrobiotic state.

Similar Datasets

OmicsDI is part of the ELIXIR infrastructure

Tweets