Ubiquitination-mediated degradation of cell cycle-related proteins by F-box proteins

Zheng, Nana; Wang, Zhiwei; Wei, Wenyi

doi:10.1016/j.biocel.2016.02.005

Cited by 54 publications

(38 citation statements)

References 188 publications

(197 reference statements)

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“…This gene has been previously reported to have a key role in homologous chromosome pairing, synapsis, DNA recombination and accurate chromosome segregation during meiosis in maize [ 84 ], Arabidopsis [ 85 ] and wheat [ 59 ]. Other hub genes identified in modules 28 and 41 encoded for the high mobility group proteins [ 86-90 ], histone deacetylase [ 91-94 ], and F-box proteins [ 95 ].…”

Section: Resultsmentioning

confidence: 99%

A co-expression network in hexaploid wheat reveals mostly balanced expression and lack of significant gene loss of homeologous meiotic genes upon polyploidization

Alabdullah

Borrill

Martín

et al. 2019

Preprint

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14Polyploidization has played an important role in plant evolution. However, upon polyploidization the 15 process of meiosis must adapt to ensure the proper segregation of increased numbers of chromosomes 16 to produce balanced gametes. It has been suggested that meiotic gene (MG) duplicates return to a 17 single copy following whole genome duplication to stabilise the polyploid genome. Therefore, upon 18 the polyploidization of wheat, a hexaploid species with three related (homeologous) genomes, the 19 stabilization process may have involved rapid changes in content and expression of MGs on 20 homeologous chromosomes (homeologs). To examine this hypothesis, sets of candidate MGs were 21 identified in wheat using co-expression network analysis and orthology informed approaches. In total, 22 130 RNA-Seq samples from a range of tissues including wheat meiotic anthers were used to define 23 co-expressed modules of genes. Three modules were significantly correlated with meiotic tissue 24 samples but not with other tissue types. These modules were enriched for GO terms related to cell 25 cycle, DNA replication and chromatin modification, and contained orthologs of known MGs. Overall 26 74.4 % of genes within these meiosis-related modules had three homeologous copies which was 27 similar to other tissue-related modules. Amongst wheat MGs identified by orthology, rather than co-28 expression, the majority (93.7 %) were either retained in hexaploid wheat at the same number of 29 copies (78.4 %) or increased in copy number (15.3%) compared to ancestral wheat species. 30 Furthermore, genes within meiosis-related modules showed more balanced expression levels between 31 homeologs than genes in non-meiosis-related modules. Taken together our results do not support 32 extensive gene loss nor changes in homeolog expression of MGs upon wheat polyploidization. The 33 construction of the MG co-expression network allowed identification of hub genes and provided key 34 targets for future studies. 35 36 Author summary 37 All flowering plants have undergone a polyploidization event(s) during their evolutionary history. One 38of the biggest challenges faced by a newly-formed polyploid is meiosis, an essential event for sexual 39 reproduction and fertility. This process must adapt to discriminate between multiple related 40 chromosomes and to ensure their proper segregation to produce fertile gametes. The meiotic 41 mechanisms responsible for the stabilisation of the extant polyploids remain poorly understood except 42 in wheat, where there is now a better understanding of these processes. It has been proposed that 43 meiotic adaptation in established polyploids could involve meiotic gene loss following the event of 44 polyploidization. To test this hypothesis in hexaploid wheat, we have computationally predicted sets 45 of hexaploid wheat meiotic genes based on expression data from different tissue types, including 46 meiotic anther tissue, and orthology informed approaches. We have calculated homeolog expression 47 patterns and numbe...

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Section: Resultsmentioning

confidence: 99%

A co-expression network in hexaploid wheat reveals mostly balanced expression and lack of significant gene loss of homeologous meiotic genes upon polyploidization

Alabdullah

Borrill

Martín

et al. 2019

Preprint

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“…The Caenorhabditis elegans homolog, UBC-18, is implicated in developmental processes through its cooperation with the RBR E3 ARI-1 (3). UBCH7 has been shown to regulate S-phase transition of the cell cycle in human cell culture (4); however, to date, it is mainly the multisubunit RING-type E3s known as Cullin-RING ligases (CRLs) associated with substrate ubiquitination that control cell cycle progression (5)(6)(7). Because UBCH7 is unable to work directly with RING E3s, including the CRLs, how it performs its role during regulation of the cell cycle is unclear.…”

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confidence: 99%

Two functionally distinct E2/E3 pairs coordinate sequential ubiquitination of a common substrate in Caenorhabditis elegans development

Dove

Kemp

Bona

et al. 2017

Proc. Natl. Acad. Sci. U.S.A.

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Ubiquitination, the crucial posttranslational modification that regulates the eukaryotic proteome, is carried out by a trio of enzymes, known as E1 [ubiquitin (Ub)-activating enzyme], E2 (Ub-conjugating enzyme), and E3 (Ub ligase). Although most E2s can work with any of the three mechanistically distinct classes of E3s, the E2 UBCH7 is unable to function with really interesting new gene (RING)-type E3s, thereby restricting it to homologous to E6AP C-terminus (HECT) and RING-in-between-RING (RBR) E3s. The Caenorhabditis elegans UBCH7 homolog, UBC-18, plays a critical role in developmental processes through its cooperation with the RBR E3 ARI-1 (HHARI in humans). We discovered that another E2, ubc-3, interacts genetically with ubc-18 in an unbiased genome-wide RNAi screen in C. elegans. These two E2s have nonoverlapping biochemical activities, and each is dedicated to distinct classes of E3s. UBC-3 is the ortholog of CDC34 that functions specifically with Cullin-RING E3 ligases, such as SCF (Skp1-Cullin-F-box). Our genetic and biochemical studies show that UBCH7 (UBC-18) and the RBR E3 HHARI (ARI-1) coordinate with CDC34 (UBC-3) and an SCF E3 complex to ubiquitinate a common substrate, a SKP1-related protein. We show that UBCH7/HHARI primes the substrate with a single Ub in the presence of CUL-1, and that CDC34 is required to build chains onto the Ub-primed substrate. Our study reveals that the association and coordination of two distinct E2/E3 pairs play essential roles in a developmental pathway and suggests that cooperative action among E3s is a conserved feature from worms to humans.

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“…It is noteworthy that the E3 can specifically determine the substrates for ubiquitination and more than 600 E3 ligases have been reported in human genome. 26,27 Among these E3 enzymes, the CRLs are the largest E3 ligase family in eukaryotes. 28 It has been known that Cullins act as a scaffold protein, and its C-terminus is associated with the RING finger protein RBX1/ROC1 or RBX2/ROC2.…”

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confidence: 99%

A new layer of degradation mechanism for PR-Set7/Set8 during cell cycle

et al. 2016

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Set8 is critically involved in transcription regulation, cell cycle progression and genomic stability. -dependent Set8 destruction also contributes to the tight control of cell proliferation and cell cycle progression, in response to UV irradiation. Here, we summarize our new findings regarding the crucial role of b-TRCP in CKI-mediated Set8 degradation, which could provide new evidence to support that dysregulation of a tight regulatory network of Set8 could lead to aberrant cell cycle process.

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Ubiquitination-mediated degradation of cell cycle-related proteins by F-box proteins

Cited by 54 publications

References 188 publications

A co-expression network in hexaploid wheat reveals mostly balanced expression and lack of significant gene loss of homeologous meiotic genes upon polyploidization

A co-expression network in hexaploid wheat reveals mostly balanced expression and lack of significant gene loss of homeologous meiotic genes upon polyploidization

Two functionally distinct E2/E3 pairs coordinate sequential ubiquitination of a common substrate in Caenorhabditis elegans development

A new layer of degradation mechanism for PR-Set7/Set8 during cell cycle

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