title: Tardigrade workbench: comparing stress-related proteins, sequence-similar and functional protein clusters as well as RNA elements in tardigrades.
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.
  
  
  CONCLUSIONS
  Different protein clusters and regulatory elements implicated in tardigrade stress adaptations are analysed including unpublished tardigrade sequences.
authors.affiliation: Dept of Bioinformatics, Biocenter University of Würzburg, 97074 Würzburg, Germany. frank.foerster@biozentrum.uni-wuerzburg.de
authors.forename: Frank
authors.initials: F
authors.lastname: Förster
authors.forename: Chunguang
authors.initials: C
authors.lastname: Liang
authors.forename: Alexander
authors.initials: A
authors.lastname: Shkumatov
authors.forename: Daniela
authors.initials: D
authors.lastname: Beisser
authors.forename: Julia C
authors.initials: JC
authors.lastname: Engelmann
authors.forename: Martina
authors.initials: M
authors.lastname: Schnölzer
authors.forename: Marcus
authors.initials: M
authors.lastname: Frohme
authors.forename: Tobias
authors.initials: T
authors.lastname: Müller
authors.forename: Ralph O
authors.initials: RO
authors.lastname: Schill
authors.forename: Thomas
authors.initials: T
authors.lastname: Dandekar
mesh_terms: D020121:5' Untranslated Regions; D000818:Animals; D016000:Cluster Analysis; D007448:Invertebrates / Q000235:genetics*; D005810:Multigene Family; D020871:RNA Stability; D012333:RNA, Messenger / Q000235:genetics*; D017423:Sequence Analysis, RNA; D013045:Species Specificity
chemical_list: D020121:5' Untranslated Regions; D012333:RNA, Messenger