Functional characterization of the Arabidopsis <i>ubiquitin‐specific protease</i> gene family reveals specific role and redundancy of individual members in development

<jats:title>Summary</jats:title><jats:p>Ubiquitin‐specific proteases (UBPs) are a highly conserved family of proteins in eukaryotes, and play critical roles in protein de‐ubiquitination. Here we report a systematic genetic and expression profiling analysis of the <jats:italic>UBP</jats:italic> gene family in the <jats:italic>Arabidopsis thaliana</jats:italic> genome. Mutation analysis of 25 of the 27 member genes representing 13 of the 14 sub‐families of the <jats:italic>UBP</jats:italic> gene family revealed that single‐gene mutants of three genes in two sub‐families exhibit visible phenotypes. Two of these three genes belonging to the <jats:italic>UBP15</jats:italic> sub‐family were selected for further characterization. The <jats:italic>ubp15</jats:italic> mutants display narrower, serrated and flat rosette leaves, partially due to a defect in cell proliferation, as well as other phenotypes such as early flowering, weak apical dominance and reduced fertility, while the line over‐expressing <jats:italic>UBP15</jats:italic> shows opposite phenotypes. We demonstrated that UPB15 has UBP activity <jats:italic>in vitro</jats:italic>, and that this biochemical activity is essential for its <jats:italic>in vivo</jats:italic> function. A genetic interaction analysis among members of this sub‐family revealed that UBP15 and UBP16, but not UBP17, have functional redundancy. Our data thus suggest that distinct UBPs, even within a closely related sub‐family, can function in different developmental pathways. Although there are clearly functional redundancies among related sub‐family members, those redundancies cannot be inferred simply based on the amino acid identity of the family members.</jats:p>