Expanded Interactome of the Intrinsically Disordered Protein Dss1

Schenstrøm, Signe M.; Rebula, Caio A.; Tatham, Michael H.; Hendus-Altenburger, Ruth; Jourdain, Isabelle; Hay, Ronald T.; Kragelund, Birthe B.; Hartmann‐Petersen, Rasmus

doi:10.1016/j.celrep.2018.09.080

Cited by 15 publications

(55 citation statements)

References 37 publications

(58 reference statements)

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“…Further, our context-dependent prediction of protein disorder using the IUPred2A program (78) revealed the presence of an intrinsically disordered region (IDR) within CBC. Such an IDR might be involved in regulating multiple functions of CBC, as IDR has been implicated as a versatile platform to interact with multiple target proteins (e.g., Sem1/Dss1 [79]). Thus, CBC is likely to regulate its multiple tasks via its IDR, distinct, and/or overlapping domains, but this remains to be elucidated.…”

Section: Discussionmentioning

confidence: 99%

Distinct Functions of the Cap-Binding Complex in Stimulation of Nuclear mRNA Export

Sen

Barman

Kaja

et al. 2019

Molecular and Cellular Biology

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Cap-binding complex (CBC) associates cotranscriptionally with the cap structure at the 5= end of nascent mRNA to protect it from exonucleolytic degradation. Here, we show that CBC promotes the targeting of an mRNA export adaptor, Yra1 (forming transcription export [TREX] complex with THO and Sub2), to the active genes and enhances mRNA export in Saccharomyces cerevisiae. Likewise, recruitment of Npl3 (an hnRNP involved in mRNA export via formation of export-competent ribonuclear protein complex [RNP]) to the active genes is facilitated by CBC. Thus, CBC enhances targeting of the export factors and promotes mRNA export. Such function of CBC is not mediated via THO and Sub2 of TREX, cleavage and polyadenylation factors, or Sus1 (that regulates mRNA export via transcription export 2 [TREX-2]). However, CBC promotes splicing of SUS1 mRNA and, consequently, Sus1 protein level and mRNA export via TREX-2. Collectively, our results support the hypothesis that CBC promotes recruitment of Yra1 and Npl3 to the active genes, independently of THO, Sub2, or cleavage and polyadenylation factors, and enhances mRNA export via TREX and RNP, respectively, in addition to its role in facilitating SUS1 mRNA splicing to increase mRNA export through TREX-2, revealing distinct stimulatory functions of CBC in mRNA export.

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Section: Discussionmentioning

confidence: 99%

Distinct Functions of the Cap-Binding Complex in Stimulation of Nuclear mRNA Export

Sen

Barman

Kaja

et al. 2019

Molecular and Cellular Biology

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“…This kind of antibody can be easily cloned and has the advantage of being specific, soluble, stable, and having high affinity ( Cortez-Retamozo et al, 2004 ; Muyldermans, 2013 ; Liu WS et al, 2018 ). For example, an anti-GFP nanobody has now been applied successfully in co-IP for many interactome studies ( Baymaz et al, 2014 ; Schenstrom et al, 2018 ).…”

Section: Strategies For Studying Interactomes With Mass Spectrometrmentioning

confidence: 99%

Mass spectrometry-based protein-protein interaction techniques and their applications in studies of DNA damage repair

Chen

2021

J. Zhejiang Univ. Sci. B

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Proteins are major functional units that are tightly connected to form complex and dynamic networks. These networks enable cells and organisms to operate properly and respond efficiently to environmental cues. Over the past decades, many biochemical methods have been developed to search for protein-binding partners in order to understand how protein networks are constructed and connected. At the same time, rapid development in proteomics and mass spectrometry (MS) techniques makes it possible to identify interacting proteins and build comprehensive protein-protein interaction networks. The resulting interactomes and networks have proven informative in the investigation of biological functions, such as in the field of DNA damage repair. In recent years, a number of proteins involved in DNA damage response and DNA repair pathways have been uncovered with MS-based protein-protein interaction studies. As the technologies for enriching associated proteins and MS become more sophisticated, the studies of protein-protein interactions are entering a new era. In this review, we summarize the strategies and recent developments for exploring protein -protein interaction. In addition, we discuss the application of these tools in the investigation of protein-protein interaction networks involved in DNA damage response and DNA repair.

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“…37,38 Although these binding partners share the presence of PCI folds and therefore are structurally similar, structural data have demonstrated distinct conformations of DSS1 in different PCI domaincontaining protein complexes. 17,33,36,39 DSS1 also engages with other proteins and protein complexes that do not have PCI domains, including BRCA2 39,40 and the singlestrand DNA binding complex RPA, 41,42 involved in DNA repair. Further, S. pombe DSS1 interacts with ubiquitin independently of its association with the proteasome lid subunits and may serve as a ubiquitin receptor for the proteasome.…”

Section: Introductionmentioning

confidence: 99%

“…41 Interestingly, deletion of the α-helix does not eliminate its multi-specificity, but modulates ligand preference. 42 The COP9 signalosome (CSN) is conserved in eukaryotic cells and acts as a regulator of a large family of E3 ligases called Cullin-RING ubiquitin ligases (CRL). 44,45 Like the proteasome lid, several CSN subunits contain PCI domains.…”

Section: Introductionmentioning

confidence: 99%

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The disordered PCI‐binding human proteins CSNAP and DSS1 have diverged in structure and function

et al. 2021

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Intrinsically disordered proteins (IDPs) regularly constitute components of larger protein assemblies contributing to architectural stability. Two small, highly acidic IDPs have been linked to the so-called PCI complexes carrying PCI-domain subunits, including the proteasome lid and the COP9 signalosome. These two IDPs, DSS1 and CSNAP, have been proposed to have similar structural propensities and functions, but they display differences in their interactions and interactome sizes. Here we characterized the structural properties of human DSS1 and CSNAP at the residue level using NMR spectroscopy and probed their propensities to bind ubiquitin. We find that distinct structural features present in DSS1 are completely absent in CSNAP, and vice versa, with lack of relevant ubiquitin binding to CSNAP, suggesting the two proteins to have diverged in both structure and function. Our work additionally highlights that different local features of seemingly similar IDPs, even subtle sequence variance, may endow them with different functional traits. Such traits may underlie their potential to engage in multiple interactions thereby impacting their interactome sizes.

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Expanded Interactome of the Intrinsically Disordered Protein Dss1

Cited by 15 publications

References 37 publications

Distinct Functions of the Cap-Binding Complex in Stimulation of Nuclear mRNA Export

Distinct Functions of the Cap-Binding Complex in Stimulation of Nuclear mRNA Export

Mass spectrometry-based protein-protein interaction techniques and their applications in studies of DNA damage repair

The disordered PCI‐binding human proteins CSNAP and DSS1 have diverged in structure and function

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