Table 1. Nonproteolytic ubiquitylation: Selected substrates of E3 ubiquitin ligases that operate in an unperturbed cell cycle.
| Phase and substrate | E3 ligase | Chain topology | Evidence | Role of ubiquitylation (or deubiquitylation, if indicated) | Counteracting DUB | Reference |
|---|---|---|---|---|---|---|
| G1 | ||||||
| PALB2 | CRL3KEAP1 | MultimonoUb? | vv (uPD), int, vt, m | Prevents BRCA1-PALB2-BRCA2 complex assembly, inhibiting homology-directed DNA repair | USP11 | Orthwein et al., 2015 |
| S | ||||||
| Histone H2A | RING1A,B | MonoUb | vv (ChIP, IF) | Pericentromeric DNA replication | Multiple; not tested for this function | Bravo et al., 2015; Lim et al., 2016 |
| Histone H2B | BRE1 | MonoUb | vv (ChIP), m | Promotes nucleosome reassembly and/or stability | — | Trujillo and Osley, 2012 |
| Histone H3 | Rtt101Mms22 (Sc); CRL4? | MultimonoUb | vv (sIP), vv (Wb, ChIP), int, vt, m | Promote H3 deposition in newly synthesized DNA | — | Han et al., 2013 |
| MCM3 | CRL3KEAP1 | MultimonoUb? | vv (sIP), int | Undetermined | — | Mulvaney et al., 2016 |
| MCM7 | SCFDia2 (Sc), CRL2LRR1 (Xl) | K48-linked (degradation uncertain) | vv (sIP, uPD), vt | Replication termination: Disassembly of the replicative CMG helicase | — | Maric et al., 2014; Moreno et al., 2014; Dewar et al., 2017 |
| MCM10 | ? (Sc) | DimonoUb | vv (sIP) | Promote PCNA recruitment for elongation during DNA replication | — | Das-Bradoo et al., 2006 |
| SLBP | CRL4WDR23 | MultimonoUb | vv (K-GG), vt, m, int | Promote histone mRNA expression | — | Brodersen et al., 2016 |
| Spt16 | Rtt101 (Sc) | K63-linked chain | vv (sIP, uPD), int, vt | Stabilizes FACT complex at replication origins to promote MCM binding | — | Han et al., 2010 |
| S and G2 | ||||||
| Aurora A | CRL3KLHL18 | ? | vv (sIP), int, vt | Activation of centrosomal Aurora A to promote mitotic entry | — | Moghe et al., 2012 |
| TOP2A | BRCA1 | K63-linked chain? | vv (sIP), int | Increase decatenation activity of topoisomerase IIα | — | Lou et al., 2005 |
| TOP2A | RNF168 | K63-linked chain | vv (sIP), int, vt, m | Promote DNA decatenation by increasing topoisomerase IIα chromatin association | USP10 | Guturi et al., 2016 |
| Mitosis | ||||||
| Aurora B | CRL3KLHL21 | MonoUb? | int, vt, m | Promote UBASH3B-dependent Aurora B translocation to the spindle midzone in anaphase | — | Maerki et al., 2009; Krupina et al., 2016 |
| Cyclin B1 | ? | K63-linked chain | vv (sIP), int | Stabilize cyclin B1 | — | Zhang et al., 2015 |
| Dishevelled DVL3 | ? | K63-linked chain | DUBa: vv (sIP, uIP), m | DUB: Promotes spindle orientation, by promoting correct localization of NuMA/dynein at the cell cortex | CYLD | Yang et al., 2014 |
| NuMA | BRCA1? | K63-linked chain | DUBa: vv (sIP) | DUB: Promotes spindle assembly by stimulating the incorporation of NuMA into spindle poles | BRISC complex | Yan et al., 2015 |
| PLK1 | CRL3KLHL22 | MonoUb? | int, vt, m | Remove PLK1 from the kinetochore upon chromosome bi-orientation | USP16 | Beck et al., 2013; Zhuo et al., 2015 |
| Survivin | ? | K63-linked chain | DUBa: vv (sIP) | DUB: Dissociates Survivin and the CPC from centromeres | USP9X | Vong et al., 2005 |
| Late M/early G1 | ||||||
| CENP-A (Dm) | CRL3RDX | ? | vv (uIP), vt | Stabilize CENP-A to promote its incorporation into centromeres | — | Bade et al., 2014 |
| CENP-A | CRL4COPS8, CRL4RBBP7? | MonoUb | vv (sIP), vt, m | Promote interaction with the HJURP histone chaperone and CENP-A loading at centromeres | — | Mouysset et al., 2015; Niikura et al., 2015 |
Shown substrates are not thought to be targeted for proteasomal degradation. Depicted E3 ligase/substrate pairs refer to human proteins, unless indicated. If known, the type of ubiquitylation topology is indicated. A question mark denotes unknown information or a speculative hypothesis. ChIP, chromatin immunoprecipitation; Dm, Drosophila melanogaster; IF, immunofluorescence; int, E3 ligase interaction with substrate; K-GG, ubiquitin profiling; m, mutagenesis of ubiquitylated sites (lysine to arginine); monoUb, monoubiquitylation; Sc, Saccharomyces cerevisiae; sIP, substrate immunoprecipitation and ubiquitin detection; uPD or uIP, ubiquitin pull-down or immunoprecipitation and substrate detection; vt, in vitro ubiquitylation assays; vv, in vivo (method indicated between parentheses); Wb, Western blot; Xl, Xenopus laevis; —, not described.
Available evidence designates the function of the DUB, not an E3 ligase.
Table 1. Nonproteolytic ubiquitylation: Selected substrates of E3 ubiquitin ligases that operate in an unperturbed cell cycle.
| Phase and substrate | E3 ligase | Chain topology | Evidence | Role of ubiquitylation (or deubiquitylation, if indicated) | Counteracting DUB | Reference |
|---|---|---|---|---|---|---|
| G1 | ||||||
| PALB2 | CRL3KEAP1 | MultimonoUb? | vv (uPD), int, vt, m | Prevents BRCA1-PALB2-BRCA2 complex assembly, inhibiting homology-directed DNA repair | USP11 | Orthwein et al., 2015 |
| S | ||||||
| Histone H2A | RING1A,B | MonoUb | vv (ChIP, IF) | Pericentromeric DNA replication | Multiple; not tested for this function | Bravo et al., 2015; Lim et al., 2016 |
| Histone H2B | BRE1 | MonoUb | vv (ChIP), m | Promotes nucleosome reassembly and/or stability | — | Trujillo and Osley, 2012 |
| Histone H3 | Rtt101Mms22 (Sc); CRL4? | MultimonoUb | vv (sIP), vv (Wb, ChIP), int, vt, m | Promote H3 deposition in newly synthesized DNA | — | Han et al., 2013 |
| MCM3 | CRL3KEAP1 | MultimonoUb? | vv (sIP), int | Undetermined | — | Mulvaney et al., 2016 |
| MCM7 | SCFDia2 (Sc), CRL2LRR1 (Xl) | K48-linked (degradation uncertain) | vv (sIP, uPD), vt | Replication termination: Disassembly of the replicative CMG helicase | — | Maric et al., 2014; Moreno et al., 2014; Dewar et al., 2017 |
| MCM10 | ? (Sc) | DimonoUb | vv (sIP) | Promote PCNA recruitment for elongation during DNA replication | — | Das-Bradoo et al., 2006 |
| SLBP | CRL4WDR23 | MultimonoUb | vv (K-GG), vt, m, int | Promote histone mRNA expression | — | Brodersen et al., 2016 |
| Spt16 | Rtt101 (Sc) | K63-linked chain | vv (sIP, uPD), int, vt | Stabilizes FACT complex at replication origins to promote MCM binding | — | Han et al., 2010 |
| S and G2 | ||||||
| Aurora A | CRL3KLHL18 | ? | vv (sIP), int, vt | Activation of centrosomal Aurora A to promote mitotic entry | — | Moghe et al., 2012 |
| TOP2A | BRCA1 | K63-linked chain? | vv (sIP), int | Increase decatenation activity of topoisomerase IIα | — | Lou et al., 2005 |
| TOP2A | RNF168 | K63-linked chain | vv (sIP), int, vt, m | Promote DNA decatenation by increasing topoisomerase IIα chromatin association | USP10 | Guturi et al., 2016 |
| Mitosis | ||||||
| Aurora B | CRL3KLHL21 | MonoUb? | int, vt, m | Promote UBASH3B-dependent Aurora B translocation to the spindle midzone in anaphase | — | Maerki et al., 2009; Krupina et al., 2016 |
| Cyclin B1 | ? | K63-linked chain | vv (sIP), int | Stabilize cyclin B1 | — | Zhang et al., 2015 |
| Dishevelled DVL3 | ? | K63-linked chain | DUBa: vv (sIP, uIP), m | DUB: Promotes spindle orientation, by promoting correct localization of NuMA/dynein at the cell cortex | CYLD | Yang et al., 2014 |
| NuMA | BRCA1? | K63-linked chain | DUBa: vv (sIP) | DUB: Promotes spindle assembly by stimulating the incorporation of NuMA into spindle poles | BRISC complex | Yan et al., 2015 |
| PLK1 | CRL3KLHL22 | MonoUb? | int, vt, m | Remove PLK1 from the kinetochore upon chromosome bi-orientation | USP16 | Beck et al., 2013; Zhuo et al., 2015 |
| Survivin | ? | K63-linked chain | DUBa: vv (sIP) | DUB: Dissociates Survivin and the CPC from centromeres | USP9X | Vong et al., 2005 |
| Late M/early G1 | ||||||
| CENP-A (Dm) | CRL3RDX | ? | vv (uIP), vt | Stabilize CENP-A to promote its incorporation into centromeres | — | Bade et al., 2014 |
| CENP-A | CRL4COPS8, CRL4RBBP7? | MonoUb | vv (sIP), vt, m | Promote interaction with the HJURP histone chaperone and CENP-A loading at centromeres | — | Mouysset et al., 2015; Niikura et al., 2015 |
Shown substrates are not thought to be targeted for proteasomal degradation. Depicted E3 ligase/substrate pairs refer to human proteins, unless indicated. If known, the type of ubiquitylation topology is indicated. A question mark denotes unknown information or a speculative hypothesis. ChIP, chromatin immunoprecipitation; Dm, Drosophila melanogaster; IF, immunofluorescence; int, E3 ligase interaction with substrate; K-GG, ubiquitin profiling; m, mutagenesis of ubiquitylated sites (lysine to arginine); monoUb, monoubiquitylation; Sc, Saccharomyces cerevisiae; sIP, substrate immunoprecipitation and ubiquitin detection; uPD or uIP, ubiquitin pull-down or immunoprecipitation and substrate detection; vt, in vitro ubiquitylation assays; vv, in vivo (method indicated between parentheses); Wb, Western blot; Xl, Xenopus laevis; —, not described.
Available evidence designates the function of the DUB, not an E3 ligase.