Database homology searches with the reported
USP25 [
14] have led to the characterization of a new UBP member in the human genome, named
USP28, which maps at 11q23. Structural comparisons at the genomic and protein levels of
USP25 and
USP28, and the deubiquitinating enzymatic assays, allowed the definition of a new UBP subfamily.
Sequence alignments of UBPs have been hindered by the few shared conserved segments, which need specific computer programs to be identified. Nonetheless, several UBP subfamilies have been reported so far. DUB1 and DUB2, with 88.4% amino acid identities, is one of those. Similarly, alignments of UBP41, UBP46, UBP52 and UBP66 from chick skeletal muscle suggest a new subfamily. In our case, the alignment of the newly reported USP28 with USP25 showed homologies beyond the conserved UBP domains and amino acid identities amounting to 51%. In addition, the extensive alignment at the amino-terminal segment supports the proposed USP28 translation initiation site. USP25 and USP28 share the exon-intron distribution and those intron positions with an inaccurate match, located between exons 1-2, 13-14 and 17-18 (Figure ), could be explained by slippage of the donor or acceptor splice sites. All these data strongly support a common ancestry for USP25 and USP28, and suggest that the minor variations observed may contribute to functional differences.
Northern analysis showed abundant
USP28 expression in adult skeletal muscle and heart (Figure ). The transcript size (4.5 kb approximately) was longer than expected from cDNA analysis, although this variability could be due to distinct polyadenylation and transcription initiation sites, as reported for
USP25 and other UBPs [
17].
The high specificity attributed to individual members of the ubiquitin proteolytic system and the structural complexity of
USP25 and
USP28 prompted us to analyze the tissue-specific mRNA isoforms and the cellular localization of the proteins. Alternative splicing had been also reported for other UBP members, such as
USP3 [
17],
USP4 (previously named
UnpEL-UnpES [
13]),
USP5 (previously named
ISOT-1/2 [
18,
19,
20]),
USP9X (previously named
DFFRX [
15]) and
USP15 [
9]. Some cDNA clones of
USP25 and
USP28 contained additional exons that introduced in-frame stop codons, similarly to what has been reported for
USP15 and
USP3. These transcripts most probably originated from splicing errors and were fortuitously cloned, as they did not appear after northern or RT-PCR analyses. Besides, the absence of the conserved domains in the truncated proteins would compromise functionality. Nonetheless, the
USP25 RT-PCR assays in testis produced comparable amplification levels of sequences containing either exons 10-10b-11 (10b introduces an in-frame stop codon) or exons 10-11. This argues in favor of a tissue-specific function for the truncated protein, possibly related to substrate availability and/or enzyme activity.
Exon 19b is present in all
USP28 transcripts in all the assayed tissues. In constrast, exon 19b from
USP25 is present in all tissues but not in all transcripts, thus constituting an alternatively spliced exon. The high degree of sequence homology of exon 19b from both genes supports its functional relevance. In addition, the tissue specificity shown for exon 19a of
USP25 (muscle and heart) and
USP28 (muscle, heart and brain) could confer the enzyme a tissue specificity to deubiquitinate a ubiquitous substrate. This would apply to a widely expressed gene whose function was only relevant in some tissues, as suggested for
Fam [
20]. Alternatively, the tissue-specific exon would bestow on the enzyme the ability to recognize a tissue-specific substrate, as suggested for Faf [
20].
The specific subcellular localization reported for some deubiquitinating enzymes may imply spatial restriction of either the locus of action or the accessibility to the substrate but it might also indicate regulation of cellular processes where ubiquitylation plays a role unrelated to protein degradation (for a recent review see [
21]). In our case, preliminary subcellular localization experiments with protein fusions to GFP showed that USP25 was cytosolic (data not shown) and did not support an involvement outside the ubiquitin-proteasome pathway.
Although several deubiquitinating enzymes have been shown to contribute to development and differentiation (that is, Faf (
Drosophila Fat facets) [
15] and UBP43 [
22]), the specific function of most family members remains unknown. Homology searches of the domains conserved between different UBPs would help to elucidate the function of new members and define the substrate-specific domains. The contribution of
USP25 to Down syndrome pathogenesis is still unclear. However, its overexpression (1.7-fold ± 0.13,
P < 0.05 according to the Mann-Whitney test) in Down syndrome with respect to control fetal brain samples would support its involvement in the pathology. In fact, several UBPs have shown gene-dosage effects, such as USP9Y (whose gene is located in the Y-chromosome pseudoautosomal region and is involved in male azoospermia [
23]) and other USPs related to aneuploidy syndromes: DFFRX in Turner syndrome [
15] and USP18 in DiGeorge syndrome [
24]. On the other hand,
in vitro overexpression or inhibition of some ubiquitin-specific proteases has led to programmed cell death, supporting the idea that their activity is dose dependent [
25].