Evolution of the highly networked deubiquitinating enzymes USP4, USP15, and USP11
© Vlasschaert et al. 2015
Received: 5 June 2015
Accepted: 17 October 2015
Published: 26 October 2015
USP4, USP15 and USP11 are paralogous deubiquitinating enzymes as evidenced by structural organization and sequence similarity. Based on known interactions and substrates it would appear that they have partially redundant roles in pathways vital to cell proliferation, development and innate immunity, and elevated expression of all three has been reported in various human malignancies. The nature and order of duplication events that gave rise to these extant genes has not been determined, nor has their functional redundancy been established experimentally at the organismal level.
We have employed phylogenetic and syntenic reconstruction methods to determine the chronology of the duplication events that generated the three paralogs and have performed genetic crosses to evaluate redundancy in mice.
Our analyses indicate that USP4 and USP15 arose from whole genome duplication prior to the emergence of jawed vertebrates. Despite having lower sequence identity USP11 was generated later in vertebrate evolution by small-scale duplication of the USP4-encoding region. While USP11 was subsequently lost in many vertebrate species, all available genomes retain a functional copy of either USP4 or USP15, and through genetic crosses of mice with inactivating mutations we have confirmed that viability is contingent on a functional copy of USP4 or USP15. Loss of ubiquitin-exchange regulation, constitutive skipping of the seventh exon and neural-specific expression patterns are derived states of USP11. Post-translational modification sites differ between USP4, USP15 and USP11 throughout evolution.
In isolation sequence alignments can generate erroneous USP gene phylogenies. Through a combination of methodologies the gene duplication events that gave rise to USP4, USP15, and USP11 have been established. Although it operates in the same molecular pathways as the other USPs, the rapid divergence of the more recently generated USP11 enzyme precludes its functional interchangeability with USP4 and USP15. Given their multiplicity of substrates the emergence (and in some cases subsequent loss) of these USP paralogs would be expected to alter the dynamics of the networks in which they are embedded.
Overexpression of these DUBs has been noted in various human cancers, which may be attributable to their collective regulation of oncogenic proteins. For instance, all three paralogs regulate the type I TGF-β receptor while USP15 and USP11 also regulate several of its downstream effectors [4, 12, 13]. Conversely, whereas USP4 and USP15 target p53-inhibiting ligases ARF-BP1  and MDM2 , respectively, USP11 stabilizes p53  as well as several other tumor suppressors including PML , BRCA2  and Mre11 complex members MRE11 & RAD50 . In sum, though these paralogs are functionally redundant in some capacities, each appears to have undergone substantial subfunctionalization and neofunctionalization. A summary of their known protein interactions is presented in Table 2.
To understand the evolutionary changes in sequence, structure, and function among these paralogs, it is very important to know the temporal sequence of duplication. This enables us to determine which are the ancestral states and which are the derived states that potentially represent adaptation in response to an ancient environment. This motivated us to do phylogenetic studies to characterize the branching pattern and the timing of duplication events. An integrative in silico approach probing these systematic changes in a comparative genomic framework was employed to trace the duplication and subsequent radiation of USP4, USP15 and USP11. We first quantified and characterized USP paralogs in a set of representative metazoan genomes and delineated their divergence times in reference to known whole genome duplication events. We then evaluated ortholog variability to gain insight into the evolutionary processes that gave rise to the three paralogs observable in humans.
Phylogenetics based on aligned nucleotide and amino acid sequence
List of coding sequences analyzed with corresponding accession numbers
Little brown bat
Green sea turtle
The branching pattern of Figs. 3 and 4 enables us to infer an approximate time for gene duplication events. The USP15 lineage splits from (USP4,USP11) during the period between the divergence of vertebrates from primitive chordates (from 581 to 460.6 millions of years ago, or MYA ) and the branching of shark from teleost (462.5 to 421.75 MYA ), corresponding to the timing of a known whole genome duplication event . A second gene duplication leads to the USP4/USP11 split which occurred in the common ancestor of bony fishes represented by gar, fugu, zebrafish and coelacanth (421.75 to 416 MYA ). USP11 is absent in shark. Given that the shark genome has evolved little , we may infer that the absence is ancestral instead of secondary loss, i.e., the USP4/USP11 split occurs after the divergence of shark from the ancestor of teleosts.
Synteny of USP11 and USP4 loci supports duplication in a Euteleostome ancestor
Summary of USP4, USP15 and USP11 interaction partners
Signature features of USP paralogs
First let us consider the molecular signatures of structured regions in USP4, USP15, and USP11. The “domain in USP” (DUSP) and “ubiquitin-like” (UBL) structured regions form the N-terminal domain that distinguishes this subgroup of USPs. DUSP-UBL domains mediate some enzyme-substrate interactions [9, 33–35] and confer intrinsic regulatory capacities that have been structurally modeled for mammalian USP4, USP15 and USP11 [20, 32, 35, 36]. For instance, USP4 dimerization occurs in equilibrium through this domain, while neither USP15 nor USP11 are expected to dimerize in vivo . The DUSP-UBL domain of USP4 also regulates ubiquitin active- site binding dynamics through its association with the unstructured insert region , though the absence of key residues impedes this regulatory function in human USP11 [32, 35]. The enzyme kinetics of USP15 are more similar to that of USP4 . Given our derivation of their duplication chronology, it seems likely that the loss of ubiquitin-exchange regulation in USP11 is a derived and not ancestral state, though structural information is available only for mammalian proteins. Fig. 7a presents an alignment of the DUSP-UBL domains of an ancestral USP with the signature sequences of USP4, USP15 and USP11. Lancelet was selected as the ancestral species because it is the closest single-copy relative (Fig. 2). In addition, the domain sequence is identical in Branchiostoma floridae and the newly sequenced B. belcheri, two lancelets that have experienced a high degree of protein evolution , suggesting that it is an accurate depiction of a pre-duplication USP. USP signature sequences indicate residues that are conserved in a majority of members from each phylogenetic clade (elimination of species-specific substitutions). While the key residues are largely conserved in USP4, USP15, and the ancestral USP, disruption of the hydrophobic pocket and shortening of DUSP-UBL linker [32, 35] are signatures of USP11. This derived state implies that USP11 has had a different mode of action throughout time.
The two parts of the structured catalytic domain of these USPs, D1 and D2, are the most highly conserved regions among paralogs and orthologs (Fig. 1). Both are required for catalytic activity, and their conservation extends beyond the USPs under current consideration to the entire USP subfamily of deubiquitinating enzymes.
Distinctive spliced isoforms
Whereas the seventh exon (E7) is alternatively spliced in USP4 and USP15, a corresponding exon is absent in USP11. The flexible linker region separating the DUSP-UBL and catalytic domains is roughly 20 residues long in USP11, its length in USP4 and USP15 short isoforms and the minimal length required for the aforementioned domain interaction . Shark USP4 and the lancelet single-copy USP, ancestral to USP11, contain E7; what is more, both long and short isoforms have been reported in chondrichthyes. Thus, the “permanent skipping” of E7 in all USP11 represents a derived state. Alterations in the stoichiometry of USP4 isoforms have been reported for a rare bone disease , though the functional consequences of E7 alternative splicing have not been studied. In all species, the polypeptides encoded by USP4 and USP15 E7 are serine-rich, and many serve as putative post-translational modification (PTM) sites as identified in large-scale studies on human proteins . In sum, the loss of E7 is a signature derived state of USP11 with potential functional or regulatory implications.
Altered cellular regulation
Post-translational modification (PTM) regulation can differ among gene duplicates. Some PTM sites are well conserved while others stably differentiate the USP paralogs in question. For one, Ser445 (a known Akt phosphorylation site ), there is conservation in all USP4, USP11, USP15 and ancestral homologs. There are, on the other hand, multiple cases wherein a putative phosphorylation site has been lost or gained in USP11 relative to its ancestor, USP4. Within the insert region, USP4 Ser675 and Ser680 (identified phosphorylation substrates in multiple studies [40–48]) are conserved in USP15 but absent from USP11. Similarly, in an alignment of all USPs, putative phosphorylation site USP4 Tyr539  is conserved in USP4 and USP15 while it is substituted by Phe in USP11. Slightly downstream, USP11 has Tyr551 (a reported phosphorylation site ) and Tyr554 whereas His and Phe, respectively, are universally present in USP4 and USP15. Still within the insert region, at positions 607 and 608, there exists in USP11 a pair of tyrosines that have been identified as phosphorylation sites in several large-scale studies . The region in question aligns poorly with other paralogs, though there are two reported, albeit low confidence, serine phosphorylation sites in USP4 and none in USP15. As previously mentioned, the alternatively spliced exon, lost in USP11, contains several reported phosphorylated serines in USP4 and USP15 .
The N and C-termini are remarkably different among USP4, USP11 and USP15. The N-terminus of USP11 is longer, more disordered and more hydrophobic (rich in alanine). In addition, the C-termini of all gnathostome USP15 present a segment rich in aspartic acid, glutamatic acid and asparagine (e.g. human: 962-DEDSNDNDNDIENEN-976; shark: 978-DEDCNENDVENEN-990), except those of teleost fish, which instead have C-terminal segment(s) exceptionally rich in glutamate (e.g. zebrafish: 775-EKEEEEEDEDEEDVNDSEQEED-795; tongue sole: 966-DEEDEEEEEEEEGEVEEEDEEEEEGRE-981, 1015-NEREDEEEEEEEEEEEEEEEQE-1035). A poly-E repetitive sequence is also found in USP11 of various organisms, including teleost fish, some reptiles, the opossum and the Chinese hamster. These regions are schematically highlighted in Fig. 2. Aspartic acid and asparagine residues can be hydroxylated , though it remains to be seen whether any hydroxylation of such residues occurs within the acidic domains of the USPs. In addition, the D- & N- rich C-terminus of non-teleost fish USP15 presents two validated serine phosphorylation sites [39, 50–55], absent from USP4, whereas human USP11 has seven of these sites [39, 50, 55–57] within its final 20 residues that are conserved among mammals. While many of these conserved and differential phosphorylation sites remain to be functionally characterized, most are all located within unstructured regions, namely the insert, linker, and C-terminal regions. This is consistent with reports that disordered region often serve as PTM substrates [58–61] and changes in PTM regulation contributes to the functional divergence of paralogs . In addition to phosphorylation and hydroxylation the disordered regions of the USPs may be subject to a number of other modifications including acetylation, methylation, and/or the addition of peptide moieties such as ubiquitin or SUMO. The contribution of this growing repertoire of PTMs to USP4, USP15, and USP11 regulation has yet to be established.
In sum, each paralog has distinctive signature features that represent common evolutionary categories namely structure-function innovations, distinctive spliced isoforms and altered cellular regulation. The fourth common differentiating trait, different spatiotemporal expression patterns, will be discussed in a later section.
Variable mechanisms of USP11 loss
In vivo demonstration of a minimal requirement for USP4 or USP15
Pooled progeny of USP4- and USP15-null mouse crosses
In the present work we have established the duplication chronology of a subgroup of highly networked ubiquitin-specific proteases, USP4, USP15 and USP11, and have characterized their subsequent radiation. According to the widely accepted 2R theory , vertebrate genomes have undergone two rounds of whole genome duplication (WGD). While it was conventionally assumed that these WGD events predated the divergence of jawless and jawed vertebrates , recent analysis of the elephant shark genome  placed at least one WGD event median to cyclostome and gnathostome divergence. In fact, subsequent studies have suggested that the 2R events occurred independently in cyclostomes and gnathostomes [63, 64], and that the former expansion was further shaped by an additional, lamprey-specific WGD. Thus, the USP15-like duplicate in lampreys is likely not orthologous to gnathostome USP4; rather, USP4 and USP15 appear to be ohnologs derived from WGD in a jawed vertebrate ancestor. In addition, the USP15-likeness of the lamprey version suggests that this paralog is the ancestral sequence, though there is no consensus among invertebrates as to whether their single copy most resembles USP4 or USP15 (Fig. 2). The issue cannot be settled by genomic synteny reconstruction, which is considerably more difficult in earlier species due to increased divergence time and the present lack of chromosomal assembly data for many species. In contrast, well-conserved intragenomic synteny points to the emergence of USP11 as the result of a more recent duplication event that does not coincide with any reported WGD event; it is likely the product of a small-scale duplication (SSD). The characterization of USP4/15 and USP4/11 duplications as WGD and SSD, respectively, corroborates well with reported trends for these phenomena: SSD-derived paralog sequences tend to evolve faster and are more functionally divergent .
Several notable differences in USP composition exist between and within clades. Primate species appear to have inconsistent USP repertoires: USP15 was inactivated by insertion of a LINE1 element in the gibbon, while erasure of USP11 and reduction of unstructured USP4 domains can both be observed in the gorilla. USP11 was also lost in the avian ancestor, inferred by the consistent absence of its genomic locus in all bird genomes (Fig. 8). Curiously, avian USP4 presents notable deviations from the signatures of this paralog: of the six bird genomes surveyed, all bear mutations in crucial residues for the ubiquitin-exchange mechanism , i.e. Arg40 and/or Met24 mutated in all, disruption of DUSP-UBL linker residues (a.a. 88–92) in chicken, QQD box region deleted in duck, and so on. In fact, USP4 is also more divergent in other species where USP11 was lost, which lead for example to the consistently incorrect branching patterns for frog and gorilla USP4 (Figs. 3 and 4; Additional file 1: Figure S1 and Additional file 2: Figure S2). What is more, avian USP4 adopts some USP11 signatures: these have collectively lost the Ser675 and Ser680 phosphorylation sites, while USP4 of the pigeon and zebra finch have also lost E7. The loss of these features that define all other USP4 (and USP15) is a derived state of USP11 and may thus represent a homoplastic convergence of avian USP4 toward the USP11 sequence.
Most of the signature features distinguish USP11 from USP4 and USP15, though the divergence of these last two is of practical interest due to their high protein sequence identity (Fig. 1), functional overlap (Table 2), and capacity for reciprocal rescue at the organismal level (Table 3). USP4 and USP15 differ in their codon usage: USP15, located in GC-poor isochores, employs more AT-ending codons than USP4. Low GC content is common in germ-line specific genes . USP15 is in fact expressed at notably elevated levels in mature oocytes  (oocytes being the cell type for which its expression is the highest in mice ) while USP4 is at low abundance throughout oocyte maturation . USP4 is predominantly expressed in somatic cells, particularly those of the immune system . The distinct spatiotemporal expression patterns of USP4 and USP15 could explain why these redundant proteins have been maintained: vertebrate genomes could optimally encode two versions of an ancestral protein to accommodate its important roles in germ and somatic cells. While we show that one functional copy of USP4 or USP15 is a minimum requirement for viability (Table 3), the observed departure from Mendelian ratios may arise from a functional deficiency in oocytes haploinsufficient for USP15. Planned experiments (including in vitro culture of early embryos) should be informative in this regard. The expansion of TGF-β pathway substrates in USP15 may reflect an enhanced role in the regulation of oocyte development [69–71], while USP4 may have become the USP of greater importance in innate immunity pathways, as reflected by an increased number of substrates (Table 2). Further, an inserted in-frame zebrafish-specific repetitive element has modified the USP15 catalytic domain coding sequence of this species. While it remains to be seen whether the enzymatic activity of USP15 has been altered or inactivated by this insertion, we anticipate that perturbation of USP15 will provide insights into DUB network rewiring in the zebrafish. As a model system that is amenable to the testing of hypotheses through genome manipulation, the zebrafish should be ideal for future investigations of the respective roles and expression patterns of USP4 and USP15. The expression pattern of USP11 is notably distinct: without exception in human, mouse, rat, and pig its expression is predominantly neuronal . In contrast to its paralogs , USP11 exerts a protective effect in glioma  as it stabilizes many tumor suppressors (Table 2).
Identification and proper annotation of homologs in an array of species is a first essential step in studying the evolution of duplicated genes. Coding sequences were retrieved from GenBank  and from genome project databases [62, 73, 74] using the well-annotated human sequences for USP4, USP15 and USP11 as tBLASTn queries . Reciprocal Best BLAST Hit (RBBH) annotation transfer was applied to unannotated genomes. Accession IDs for all sequences are below.
GC content analysis
The seqinr package in R was employed to generate plots for the GC content of the third codon positions (GC3) of the Homo sapiens USP4, USP15 and USP11 coding sequences using a sliding window of width 10. A heatmap of GC3 content was generated using Circos .
Species tree reconstruction
A taxonomic phylogeny was generated using PhyloT . Paralog affiliations were attributed as per their RBBH (described in Sequence retrieval). Putative non-processed pseudogene loci were confirmed using GenScan . The SynMap function in CoGe  enabled comparison of the synteny of USP neighbouring regions in Anolis carolinensis, Homo sapiens, and Gallus gallus, which was visualized using Circos.
USP4, USP15 and USP11 codon sequences were aligned using MUSCLE . The maximum-likelihood method using estimated transition/transversion ratio and F84 model, as implemented in DAMBE , was used to derive a phylogeny rooted on Amphimedon queenslandica. Molecular clock analyses were also conducted using DAMBE .
Codon alignments were produced by the MUSCLE algorithm using default GBlocks parameters as implemented in TranslatorX . AIC and LRT nucleotide substitution model tests in DAMBE  designated the Generalized Time Reversible (GTR) as most appropriate for all alignments. BEAST v.1.8.2 , a Bayesian Markov chain Monte Carlo (MCMC)-based phylogenetic dating program, was employed to quantify USP age-calibrated divergence times. All analyses used a log normal relaxed molecular clock. The USP4/USP11 analysis used six calibration points obtained from TimeTree  (in millions of years): Dog-Cow[USP4,USP11]: 60, Human-Opossum[USP4]: 112, Human-Anole [USP4, USP11]: 320 & Gar-Human [USP4]: 418. The RBM5/RBM10 analysis employed four pairs of calibration points: Human-Gorilla [RBM5,RBM10]: 8, Mouse-Rat[RBM5,RBM10]: 10.4, Human-Anole[RBM5,RBM10]: 320 & Human-Zebrafish [RBM5,RBM10]: 425. Tracer was used to verify similar convergence after 20 million steps for 3 runs in each case.
Mouse genetic crosses
TF2497 and TF2834 strains were purchased from Taconic Laboratories (Germantown, New York, USA), and were housed in a barrier facility at the University of Ottawa under protocol ME-305, approved by the Animal Care Committee, University of Ottawa. The strains were crossed to obtain mice heterozygous for proviral insertions in both the Usp4 and Usp15 genes. Eight pairs of compound heterozygous mice were mated under standard conditions, and progeny were obtained for genotyping. Genotyping was performed at 3–4 weeks of age, using tissue from ear punches. DNA was prepared using the REDExtract-N-Amp™ Tissue PCR Kit (Sigma-Aldrich Canada, Oakville, Ontario) and polymerase chain reaction was performed using the kit reagents. For genotyping of USP4 the forward primer used was derived from the third exon (upstream of the proviral insertion site): 5′- CCAGCAGCCTATTGTCAGAA -3′, where reverse primers were derived from the third intron (downstream of the proviral insertion site): 5′- TCAGTACTTAGGGATCTCTGA -3′ or from the neomycin phosphotransferase gene within the provirus: 5′- AACCTGCGTGCAATCCATCT -3′. Amplification conditions for USP4 were as follows: initial denaturation at 95C for 3 min followed by 30 cycles of 95C for 30 s, 57C for 30 s and 72C for 60 s and a final cycle at 72C for 5 min. A PCR product of approximately 250 base pairs was generated from the wild type gene, whereas the disrupted gene generated a product of approximately 1000 bp as detected by ethidium bromide staining of 1 % agarose gels. For USP15 a similar strategy was adopted using the forward primer: 5′ – GGTTTGAAGGATAACGTAGGC -3′, and reverse primers 5′ – ATAAACCCTCTTGCAGTTGCATC -3′ and 5′- GAGTACCTAACAGGCACTTGAGACG -3′. USP15 PCR conditions were similar except that annealing was done at 55C for 30 s and elongation at 72C was reduced to 45 s.
Availability of supporting data
This work was supported by the Natural Sciences and Engineering Research Council of Canada through grant RGPIN-2015-05879 (awarded to DAG). Caitlyn Vlasschaert was the recipient of a Frederick Banting and Charles Best Scholarship from the Canadian Institutes of Health Research. We thank Dr. Stéphane Aris-Brosou for his time and guidance in troubleshooting the BEAST phylogenetic analyses. We are grateful to David Cook for his help with Circos, and acknowledge the kind assistance of Tim Ramsay in the statistical analysis of mouse crosses.
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