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

Abstract

<p>Abstract</p> <p>Background</p> <p>Tardigrades represent an animal phylum with extraordinary resistance to environmental stress.</p> <p>Results</p> <p>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 (<it>Milnesium tardigradum</it>, <it>Hypsibius dujardini</it>, <it>Echiniscus testudo</it>, <it>Tulinus stephaniae</it>, <it>Richtersius coronifer</it>) 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 <url>http://waterbear.bioapps.biozentrum.uni-wuerzburg.de</url>. 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.</p> <p>Conclusion</p> <p>Different protein clusters and regulatory elements implicated in tardigrade stress adaptations are analysed including unpublished tardigrade sequences.</p