title: Phylogenomics reveals an anomalous distribution of USP genes in metazoans.
abstract: Members of the universal stress protein (USP) family were originally identified in stressed bacteria on the basis of a shared domain, which has since been reported in a phylogenetically diverse range of prokaryotes, fungi, protists, and plants. Although not previously characterized in metazoans, here we report that USP genes are distributed in animal genomes in a unique pattern that reflects frequent independent losses and independent expansions. Multiple USP loci are present in urochordates as well as all Cnidaria and Lophotrochozoa examined, but none were detected in any of the available ecdysozoan or non-urochordate deuterostome genome data. The vast majority of the metazoan USPs are short, single-domain proteins and are phylogenetically distinct from the prokaryotic, plant, protist, and fungal members of the protein family. Whereas most of the metazoan USP genes contain introns, with few exceptions those in the cnidarian Hydra are intronless and cluster together in phylogenetic analyses. Expression patterns were determined for several cnidarian USPs, including two genes belonging to the intronless clade, and these imply diverse functions. The apparent paradox of implied diversity of roles despite high overall levels of sequence (and implied structural) similarity parallels the situation in bacteria. The absence of USP genes in ecdysozoans and most deuterostomes may be a consequence of functional redundancy or specialization in taxon-specific roles.
authors.affiliation: ARC Centre of Excellence in Coral Reef Studies and Comparative Genomics Centre, James Cook University, Townsville, Queensland, Australia.
authors.forename: Sylvain
authors.initials: S
authors.lastname: Forêt
authors.forename: François
authors.initials: F
authors.lastname: Seneca
authors.forename: Danielle
authors.initials: D
authors.lastname: de Jong
authors.forename: Annette
authors.initials: A
authors.lastname: Bieller
authors.forename: Georg
authors.initials: G
authors.lastname: Hemmrich
authors.forename: Rene
authors.initials: R
authors.lastname: Augustin
authors.forename: David C
authors.initials: DC
authors.lastname: Hayward
authors.forename: Eldon E
authors.initials: EE
authors.lastname: Ball
authors.forename: Thomas C G
authors.initials: TC
authors.lastname: Bosch
authors.forename: Kiyokazu
authors.initials: K
authors.lastname: Agata
authors.forename: Monika
authors.initials: M
authors.lastname: Hassel
authors.forename: David J
authors.initials: DJ
authors.lastname: Miller
mesh_terms: D000595:Amino Acid Sequence; D000818:Animals; D001499:Bayes Theorem; D015870:Gene Expression; D023281:Genomics / Q000379:methods*; D006360:Heat-Shock Proteins / Q000145:classification / Q000235:genetics*; D006801:Humans; D006829:Hydra / Q000033:anatomy & histology / Q000145:classification / Q000235:genetics; D017403:In Situ Hybridization; D008969:Molecular Sequence Data; D010802:Phylogeny; D016415:Sequence Alignment
chemical_list: D006360:Heat-Shock Proteins