A Conserved Deubiquitinating Enzyme Uses Intrinsically Disordered Regions to Scaffold Multiple Protein Interaction Sites

Reed, Benjamin J.; Locke, Melissa N.; Gardner, Richard G.

doi:10.1074/jbc.m115.650952

Cited by 24 publications

(25 citation statements)

References 47 publications

(89 reference statements)

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“…This function is mediated by the N-terminus of Ubp10, which is recruited by the SIR complex to subtelomeric regions (Emre et al, 2005;Gardner et al, 2005;Zukowski et al, 2018). The silencing and global H2B ubiquitination functions of Ubp10 appear to be separable, as expression of N-terminal truncations of Ubp10 can restore wild type levels of H2B ubiquitination but are still defective in regulation of subtelomeric silencing (Reed et al, 2015). A recent study (Zukowski et al, 2018) reported that Sir2/Sir4, a subset of the SIR complex, stimulates the activity of GST-Ubp10 on both human nucleosomes and H2A/H2B-Ub heterodimers containing a hydrolyzable non-native linkage between ubiquitin and H2B.…”

Section: Discussionmentioning

confidence: 99%

“…Ubp10 contains an unstructured region rich in Asp/Glu that is N-terminal to the catalytic USP domain (residues 362 -733) (Reed et al, 2015) ( Figure 3A). The Nterminal unstructured region contains residues that interact with the Sir3/Sir4 silencing proteins and recruit Ubp10 to subtelomeric regions (Emre et al, 2005;Gardner et al, 2005;Zukowski et al, 2018).…”

Section: Fact Stimulation Does Not Correlate With Ubp10 Nucleosome-bimentioning

confidence: 99%

“…Both yeast H2B-Ub DUBs are conserved in humans. USP36, the human homologue of Ubp10, can complement the effects on global H2B-Ub of a ubp10 deletion in yeast (Reed et al, 2015) and USP22, the homologue of Ubp8, is a subunit of human SAGA (Zhang et al, 2008). Yeast in which both Ubp10 and Ubp8 have been deleted showed a synergistic increase in the steady-state levels of global H2B-Ub, as well as growth defects (Emre et al, 2005).…”

Section: Introductionmentioning

confidence: 99%

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FACT and Ubp10 collaborate to modulate H2B deubiquitination and nucleosome dynamics

Nune

Morgan

Connell

et al. 2018

Preprint

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Monoubiquitination of histone H2B (H2B-Ub) plays a role in transcription and DNA replication, and is required for normal localization of the histone chaperone, FACT.In yeast, H2B-Ub is deubiquitinated by Ubp8, a subunit of SAGA, and Ubp10. Although they target the same substrate, loss of Ubp8 and Ubp10 causes different phenotypes and alters the transcription of different genes. We show that Ubp10 has poor activity on yeast nucleosomes, but that addition of FACT stimulates Ubp10 activity on nucleosomes and not on other substrates. Consistent with a role for FACT in deubiquitinating H2B in vivo, a FACT mutant strain shows elevated levels of H2B-Ub.Combination of FACT mutants with deletion of Ubp10, but not Ubp8, confers increased sensitivity to hydroxyurea and activates a cryptic transcription reporter, suggesting that FACT and Ubp10 may coordinate nucleosome assembly during DNA replication and transcription. Our findings reveal unexpected interplay between H2B deubiquitination and nucleosome dynamics.

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Section: Discussionmentioning

confidence: 99%

Section: Fact Stimulation Does Not Correlate With Ubp10 Nucleosome-bimentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

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FACT and Ubp10 collaborate to modulate H2B deubiquitination and nucleosome dynamics

Nune

Morgan

Connell

et al. 2018

Preprint

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“…The Sir4 PAD also interacts with the integrase of the Ty5 retrotransposon to integrate Ty5 into heterochromatic regions at telomeres and silent mating-type loci. Finally, an N-terminal region of the Ubp10 deubiquitinase (residues 109-133) has been shown to interact with the Sir4 PAD to remove H2B ubiquitin marks, a prerequisite for heterochromatin formation (Reed et al, 2015;Zukowski et al, 2018). Furthermore, Ty5 binding to Sir4 is mediated by post-translational modifications, such as phosphorylation (Zou et al, 1996;Dai et al, 2007;Brady et al, 2008).…”

Section: Introductionmentioning

confidence: 99%

“…Furthermore, Ty5 binding to Sir4 is mediated by post-translational modifications, such as phosphorylation (Zou et al, 1996;Dai et al, 2007;Brady et al, 2008). Finally, an N-terminal region of the Ubp10 deubiquitinase (residues 109-133) has been shown to interact with the Sir4 PAD to remove H2B ubiquitin marks, a prerequisite for heterochromatin formation (Reed et al, 2015;Zukowski et al, 2018).…”

Section: Introductionmentioning

confidence: 99%

The Sir4 H‐ BRCT domain interacts with phospho‐proteins to sequester and repress yeast heterochromatin

et al. 2019

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In Saccharomyces cerevisiae, the silent information regulator (SIR) proteins Sir2/3/4 form a complex that suppresses transcription in subtelomeric regions and at the homothallic mating‐type (HM) loci. Here, we identify a non‐canonical BRCA1 C‐terminal domain (H‐BRCT) in Sir4, which is responsible for tethering telomeres to the nuclear periphery. We show that Sir4 H‐BRCT and the closely related Dbf4 H‐BRCT serve as selective phospho‐epitope recognition domains that bind to a variety of phosphorylated target peptides. We present detailed structural information about the binding mode of established Sir4 interactors (Esc1, Ty5, Ubp10) and identify several novel interactors of Sir4 H‐BRCT, including the E3 ubiquitin ligase Tom1. Based on these findings, we propose a phospho‐peptide consensus motif for interaction with Sir4 H‐BRCT and Dbf4 H‐BRCT. Ablation of the Sir4 H‐BRCT phospho‐peptide interaction disrupts SIR‐mediated repression and perinuclear localization. In conclusion, the Sir4 H‐BRCT domain serves as a hub for recruitment of phosphorylated target proteins to heterochromatin to properly regulate silencing and nuclear order.

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Functional analysis of the N‐terminal region of acetylxylan esterase from Caldanaerobacter subterraneus subsp. tengcongensis

et al. 2022

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Acetylxylan esterase from Caldanaerobacter subterraneus subsp. tengcongensis (TTE0866) has an N-terminal region (NTR; residues 23-135) between the signal sequence (residues 1-22) and the catalytic domain (residues 136-324), which is of unknown function. Our previous study revealed the crystal structure of the wild-type (WT) enzyme containing the NTR and the catalytic domain. Although the structure of the catalytic domain was successfully determined, that of the NTR was undetermined, as its electron density was unclear. In this study, we investigated the role of the NTR through functional and structural analyses of NTR truncation mutants. Based on sequence and secondary structure analyses, NTR was confirmed to be an intrinsically disordered region. The truncation of NTR significantly decreased the solubility of the proteins at low salt concentrations compared with that of the WT. The NTR-truncated mutant easily crystallized in a conventional buffer solution. The crystal exhibited crystallographic properties comparable with those of the WT crystals suitable for structural determination. These results suggest that NTR plays a role in maintaining the solubility and inhibiting the crystallization of the catalytic domain.Acetylxylan esterase (AXE; EC3.1.1.72) hydrolyzes the acetyl groups from acetylated xylan [1,2]. AXE has been proposed to be the initial enzyme in the biodegradation process of cellulose acetate (CA), a plastic used for membrane materials, by decreasing the degree of substitution (DS) by acetate [3][4][5].We studied AXE from Caldanaerobacter subterraneus subsp. tengcongensis (a synonym for Thermoanaerobacter tengcongensis MB4; TTE0866) because this enzyme can uniquely deacetylate CA with a high DS of up to 2.45 [6]. TTE0866 is classified as a carbohydrate esterase family 4 (CE4) by carbohydrate-active Abbreviations AEX, anion-exchange chromatography; AXE, acetylxylan esterase; BSA, bovine serum albumin; CA, cellulose acetate; CD, circular dichroism; CE, carbohydrate esterase; DS, degree of substitution; GlcNAc, N-acetylglucosamine; HIC, hydrophobic interaction chromatography; IDR, intrinsically disordered region; IMAGEJ, image processing and analysis in java; Ni-NTA, nickel-nitrilotriacetic acid affinity chromatography; NTR, N-terminal region; PONDR, predictor of naturally disordered regions; SEC, size exclusion chromatography; WT, wild-type.

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A Conserved Deubiquitinating Enzyme Uses Intrinsically Disordered Regions to Scaffold Multiple Protein Interaction Sites

Cited by 24 publications

References 47 publications

FACT and Ubp10 collaborate to modulate H2B deubiquitination and nucleosome dynamics

FACT and Ubp10 collaborate to modulate H2B deubiquitination and nucleosome dynamics

The Sir4 H‐ BRCT domain interacts with phospho‐proteins to sequester and repress yeast heterochromatin

Functional analysis of the N‐terminal region of acetylxylan esterase from Caldanaerobacter subterraneus subsp. tengcongensis

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