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Phylogenetic analysis of ubiquitins (polyubiquitin and ubiquitin extension protein) in marine sponges

The complete nucleotide sequence of two Suberites domuncula cDNAs and one Sycon raphanus cDNA, all encoding ubiquitin, have been determined. One cDNA from S. domuncula codes for polyubiquitin with four tandemly repeated monomeric units and the second cDNA encodes ubiquitin fused to a ribosomal protein of 78 amino acids. S. domunclula possesses at least one additional polyubiquitin gene, from which the last two monomers were also sequenced. All analysed genes from s. domuncula encode identical ubiquitin protein, with only one aa difference (Ala 19) to the human/higher animal ubiquitin (Pro19). Ubiquitin in S. domuncula is identical with the ubiquitin found in another Demospongia, Geodia cydonium. The cDNA from S. raphanus encodes polyubiquitin with seven tandemly repeated units. All these gene monomers code for the same ubiquitin, which differ from the human/higher animals ubiquitin only at position 24 (Asp in Sycon, Glu in others). However, ubiquitin from S. raphanus (Calcarea) shows two aa difference (position 19 and 24) when compared with the ubiquitin sequence from the two Demospongiae. In a phylogenetic tree constructed by multiple sequence alignment of all sponge ubiquitin gene monomers so far identified, all monomers from the same species cluster together, with the clear exception of the monomer from S. domuncula ribosomal protein fusion gene. This monomer branches off first from the tree and forms a separate line; this gives evidence for a very ancient split of ubiquitin-ribosomal-protein fusion genes from polyubiquitin encoding genes and their long separate coexistence in eukaryotes. The ubiquitin extension protein from S. domuncula is 78 aa long, displays all characteristics of 76-81 aa long ribosomal fusion proteins and shows 78% identity in the first 73 aa with the humal S27a protein. However, its C-terminal sequence: 69-GLTYVYKKSD-78 is more similar to the plant consensus than to the higher animal consensus. This protein isolated from the sponge, belonging to the phylogenetically oldest multicellular animals, the Porifera, branches off first from the phylogenetic tree of metazoan ubiquitin extension proteins of the small ribosomal subunits.

Porifera; Ribosomal protein; Metazoa; Phylogeny

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