Cooperation of Sumoylated Chromosomal Proteins in rDNA Maintenance

Takahashi, Yoshimitsu; Dulev, Stanimir; Liu, Xianpeng; Hiller, Natalie Jasmin; Zhao, Xiaolan; Strunnikov, Alexander

doi:10.1371/journal.pgen.1000215

Cited by 64 publications

(88 citation statements)

References 62 publications

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“…Finally, we and others have shown that sumoylation of the SMC family proteins are preferentially controlled by Mms21 (4,6,38). Sumoylation of MCM has been reported previously (6,36), although how the SUMO pathway regulates MCM sumoylation is largely unknown.…”

Section: Discussionmentioning

confidence: 56%

Molecular Circuitry of the SUMO (Small Ubiquitin-like Modifier) Pathway in Controlling Sumoylation Homeostasis and Suppressing Genome Rearrangements

Albuquerque

Liang

Gaut

et al. 2016

Journal of Biological Chemistry

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Small ubiquitin-like modifier (SUMO) E3 ligases are known to have a major role in preventing gross chromosomal rearrangements (GCRs); however, relatively little is known about the role of SUMO isopeptidases in genome maintenance and their role in controlling intracellular sumoylation homeostasis. Here we show the SUMO isopeptidase Ulp2 in Saccharomyces cerevisiae does not prevent the accumulation of GCRs, and interestingly, its loss causes subunit-specific changes of sumoylated minichromosome maintenance (MCM) helicase in addition to drastic accumulation of sumoylated nucleolar RENT and inner kinetochore complexes. In contrast, loss of Ulp1 or its mis-localization from the nuclear periphery causes substantial accumulations of GCRs and elevated sumoylation of most proteins except for Ulp2 targets. Interestingly, the E3 ligase Mms21, which has a major role in genome maintenance, preferentially controls the sumoylation of Mcm3 during DNA replication. These findings reveal distinct roles for Ulp1 and Ulp2 in controlling homeostasis of intracellular sumoylation and show that sumoylation of MCM is controlled in a subunit-specific and cell cycle dependent manner.Protein sumoylation is an essential post-translational modification in eukaryotes (1, 2). Two families of enzymes control reversible sumoylation of specific substrates, including SUMO 3 (small ubiquitin-like modifier) E3 ligases and SUMO isopeptidases. Three SUMO E3 ligases Siz1, Siz2, and Mms21 have been identified in Saccharomyces cerevisiae and are shown to have distinct, but partially overlapping roles in catalyzing substratespecific sumoylation (3-6). Siz1 and Siz2 are paralogs, and they redundantly catalyze the bulk of sumoylation in cells (5, 6). Mms21 catalyzes sumoylation of fewer substrates but plays a more important role in genome maintenance than Siz1 and Siz2 (6, 7). Deletion of SIZ1 and SIZ2 is lethal in cells lacking Mms21 E3 ligase activity (4, 5). Moreover, deletion of either SIZ1 or SIZ2 causes further accumulation of gross chromosome rearrangements (GCRs) in cells lacking Mms21 E3 ligase activity (6). These findings suggest that the functions of these E3 ligases are partially redundant, which correlates with their partially overlapping roles in catalyzing intracellular sumoylation (5, 6).Besides SUMO E3 ligases, homeostasis of intracellular sumoylation is also regulated by SUMO isopeptidases, which catalyze the removal of SUMO from its targets. Two SUMO isopeptidases Ulp1 and Ulp2 have been identified in S. cerevisiae (8 -10). Ulp2 is not required for cell viability; however, its loss causes accumulation of poly-SUMO chains, resulting in pleiotropic effects including slow growth and sensitivity to higher temperature (9, 11). Moreover, overexpression of ULP2

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Section: Discussionmentioning

confidence: 56%

Molecular Circuitry of the SUMO (Small Ubiquitin-like Modifier) Pathway in Controlling Sumoylation Homeostasis and Suppressing Genome Rearrangements

Albuquerque

Liang

Gaut

et al. 2016

Journal of Biological Chemistry

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“…Sumoylation has also been implicated in the function of condensin in ribosomal DNA (rDNA) maintenance (Takahashi et al 2008) and kinetochore localization (BachellierBassi et al 2008) in budding yeast. It is noteworthy that, unlike the case of cohesin, no specialized loading or dissociating factors have, so far, been identified for condensins.…”

Section: Condensin I Associates With Chromosomes In Prometaphase and mentioning

confidence: 99%

Chromosome Dynamics during Mitosis

Hirano

2015

Cold Spring Harb Perspect Biol

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The primary goal of mitosis is to partition duplicated chromosomes into daughter cells. Eukaryotic chromosomes are equipped with two distinct classes of intrinsic machineries, cohesin and condensins, that ensure their faithful segregation during mitosis. Cohesin holds sister chromatids together immediately after their synthesis during S phase until the establishment of bipolar attachments to the mitotic spindle in metaphase. Condensins, on the other hand, attempt to "resolve" sister chromatids by counteracting cohesin. The products of the balancing acts of cohesin and condensins are metaphase chromosomes, in which two rod-shaped chromatids are connected primarily at the centromere. In anaphase, this connection is released by the action of separase that proteolytically cleaves the remaining population of cohesin. Recent studies uncover how this series of events might be mechanistically coupled with each other and intricately regulated by a number of regulatory factors.

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“…The STUbL localizes at various sites within the nucleus as well, such as DNA replication forks and the NPC (Torres-Rosell et al 2007;Nagai et al 2008;Cook et al 2009). The SUMO pathway has been linked to the nucleolus, the cellular hub for the initial stages of ribosome assembly (Strunnikov et al 2001;D'Amours et al 2004;Panse et al 2006;Takahashi et al 2008;Srikumar et al 2013b). To maintain robust ribosome production, cells have numerous ribosomal DNA (rDNA) copies, even though repeated DNA is prone to aberrant homologous recombination.…”

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confidence: 99%

SUMO Pathway Modulation of Regulatory Protein Binding at the Ribosomal DNA Locus inSaccharomyces cerevisiae

Gillies

Hickey

et al. 2016

Genetics

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In this report, we identify cellular targets of Ulp2, one of two Saccharomyces cerevisiae small ubiquitin-related modifier (SUMO) proteases, and investigate the function of SUMO modification of these proteins. PolySUMO conjugates from ulp2D and ulp2D slx5D cells were isolated using an engineered affinity reagent containing the four SUMO-interacting motifs (SIMs) of Slx5, a component of the Slx5/Slx8 SUMO-targeted ubiquitin ligase (STUbL). Two proteins identified, Net1 and Tof2, regulate ribosomal DNA (rDNA) silencing and were found to be hypersumoylated in ulp2D, slx5D, and ulp2D slx5D cells. The increase in sumoylation of Net1 and Tof2 in ulp2D, but not ulp1ts cells, indicates that these nucleolar proteins are specific substrates of Ulp2. Based on quantitative chromatin-immunoprecipitation assays, both Net1 and Tof2 lose binding to their rDNA sites in ulp2D cells and both factors largely regain this association in ulp2D slx5D. A parsimonious interpretation of these results is that hypersumoylation of these proteins causes them to be ubiquitylated by Slx5/ Slx8, impairing their association with rDNA. Fob1, a protein that anchors both Net1 and Tof2 to the replication-fork barrier (RFB) in the rDNA repeats, is sumoylated in wild-type cells, and its modification levels increase specifically in ulp2D cells. Fob1 experiences a 50% reduction in rDNA binding in ulp2D cells, which is also rescued by elimination of Slx5. Additionally, overexpression of Sir2, another RFBassociated factor, suppresses the growth defect of ulp2D cells. Our data suggest that regulation of rDNA regulatory proteins by Ulp2 and the Slx5/Slx8 STUbL may be the cause of multiple ulp2D cellular defects. KEYWORDS SUMO; Ulp2; rDNA; RENT complex; Fob1 P OST-TRANSLATIONAL protein modifications provide a common mechanism for regulating protein-protein interactions, protein localization, and protein degradation. The small ubiquitin-related modifier (SUMO) protein family modifies target proteins through covalent attachment to lysine side chains (Johnson 2004). The function of substrate "sumoylation" varies with the protein that is sumoylated, but a common role is to modulate the assembly of large protein complexes either by creating additional binding sites or by blocking existing sites (Kerscher 2007).Protein sumoylation occurs through an enzymatic cascade similar to ubiquitylation (Johnson 2004). In Saccharomyces cerevisiae, a single gene, SMT3, codes for SUMO, and as in most species, SUMO ligation is essential for viability. Removal of SUMO from target proteins is also an important regulatory step. S. cerevisiae has two SUMO proteases, Ulp1 and Ulp2 (Hickey et al. 2012). Most Ulp1 is bound to the nuclear pore complex (NPC), and the enzyme is essential for cell-cycle progression. NPC tethering regulates Ulp1 activity by restricting its access to sumoylated proteins (Li and Hochstrasser 2003;Panse et al. 2003). Ulp1 also processes the SUMO precursor by removing its last three residues, thereby exposing the C-terminal Gly-Gly motif required for SU...

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Cooperation of Sumoylated Chromosomal Proteins in rDNA Maintenance

Cited by 64 publications

References 62 publications

Molecular Circuitry of the SUMO (Small Ubiquitin-like Modifier) Pathway in Controlling Sumoylation Homeostasis and Suppressing Genome Rearrangements

Molecular Circuitry of the SUMO (Small Ubiquitin-like Modifier) Pathway in Controlling Sumoylation Homeostasis and Suppressing Genome Rearrangements

Chromosome Dynamics during Mitosis

SUMO Pathway Modulation of Regulatory Protein Binding at the Ribosomal DNA Locus inSaccharomyces cerevisiae

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