Tardigrade workbench: comparing stress-related proteins, sequence-similar and functional protein clusters as well as RNA elements in tardigrades

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urn:nbn:de:bvb:355-epub-306486 Copy

Förster, Frank ; Liang, Chunguang ; Shkumatov, Alexander V. ; Beisser, Daniela ; Engelmann, Julia C. ; Schnölzer, Martina ; Frohme, Marcus ; Müller, Tobias ; Schill, Ralph O. ; Dandekar, Thomas

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Date of publication of this fulltext: 18 Aug 2014 08:53

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Details

Item type:	Article
Journal or Publication Title:	BMC genomics
Publisher:	BioMed Central
Volume:	10
Page Range:	p. 469
Date:	October 2009
Institutions:	Medicine > Institut für Funktionelle Genomik > Lehrstuhl für Statistische Bioinformatik (Prof. Spang)
Identification Number:	Value Type 18978020 PubMed ID 10.1186/1471-2164-10-469 DOI
Classification:	Notation Type 5' Untranslated Regions MESH Animals MESH Cluster Analysis MESH Invertebrates/genetics MESH Multigene Family MESH RNA Stability MESH RNA, Messenger/genetics MESH Sequence Analysis, RNA MESH Species Specificity MESH
Dewey Decimal Classification:	500 Science > 500 Natural sciences & mathematics 500 Science > 570 Life sciences 600 Technology > 610 Medical sciences Medicine
Status:	Published
Refereed:	Yes, this version has been refereed
Created at the University of Regensburg:	Partially
Item ID:	30648

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Abstract

BACKGROUND: Tardigrades represent an animal phylum with extraordinary resistance to environmental stress. RESULTS: To gain insights into their stress-specific adaptation potential, major clusters of related and similar proteins are identified, as well as specific functional clusters delineated comparing all tardigrades and individual species (Milnesium tardigradum, Hypsibius dujardini, Echiniscus ...

Abstract

BACKGROUND:
Tardigrades represent an animal phylum with extraordinary resistance to environmental stress.
RESULTS:
To gain insights into their stress-specific adaptation potential, major clusters of related and similar proteins are identified, as well as specific functional clusters delineated comparing all tardigrades and individual species (Milnesium tardigradum, Hypsibius dujardini, Echiniscus testudo, Tulinus stephaniae, Richtersius coronifer) and functional elements in tardigrade mRNAs are analysed. We find that 39.3% of the total sequences clustered in 58 clusters of more than 20 proteins. Among these are ten tardigrade specific as well as a number of stress-specific protein clusters. Tardigrade-specific functional adaptations include strong protein, DNA- and redox protection, maintenance and protein recycling. Specific regulatory elements regulate tardigrade mRNA stability such as lox P DICE elements whereas 14 other RNA elements of higher eukaryotes are not found. Further features of tardigrade specific adaption are rapidly identified by sequence and/or pattern search on the web-tool tardigrade analyzer http://waterbear.bioapps.biozentrum.uni-wuerzburg.de. The work-bench offers nucleotide pattern analysis for promotor and regulatory element detection (tardigrade specific; nrdb) as well as rapid COG search for function assignments including species-specific repositories of all analysed data.
CONCLUSION:
Different protein clusters and regulatory elements implicated in tardigrade stress adaptations are analysed including unpublished tardigrade sequences.

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Metadata last modified: 02 Jun 2018 07:43

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