Promiscuous Interactions of gp78 E3 Ligase CUE Domain with Polyubiquitin Chains

Liu, Shan; Chen, Yinghua; Li, Jess; Huang, Tao; Tarasov, Sergey G.; King, Aaren; Weissman, Allan M.; Byrd, R. Andrew; Das, Ranabir

doi:10.1016/j.str.2012.09.020

Cited by 33 publications

(86 citation statements)

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“…Protein ubiqutination has emerged as a key mechanism involved in growth and development as well as immunity in animals and plants (Liu et al ., ; You et al ., ). Recognition of ubiquitin or specific ubiquitin chains by ubiquitin‐binding domains (UBDs) is vital for deciphering ubiquitin‐mediated signalling pathways (Liu et al ., ). Among a handful of types of characterized UBDs, the coupling of ubiquitin conjugation to endoplasmic reticulum (ER) degradation (CUE) domains consisting of 42–43 amino acid sequences have been identified and characterized based on similarity to the region of the yeast Cue1 protein, which is implicated in yeast ER‐associated degradation (ERAD; Shih et al ., ); however, their roles in ERAD remain poorly understood (Li et al ., ; Liu et al ., ; Shideler et al ., ).…”

Section: Introductionmentioning

confidence: 97%

“…In animals, some CUE domain‐containing (CUEDC) proteins have been implicated in programmed cell death (PCD) and immunity. For examples, the CUEDC protein, ERAD E3 gp78, is a regulator of liver homeostasis and a tumour suppressor in liver, and its CUE domain interacts with ubiquitin and diubiquitin and functions to facilitate substrate binding and processivity in ubiquitination (Liu et al ., ; Zhang et al ., ); another CUEDC protein, CUEDC2, suppresses glioma tumorigenicity by inhibiting the activation of STAT3 and NF‐κB, and its CUE domain is essential for functional interactions with both monoubiquitin and polyubiquitin (Li et al ., ). In plants, the reported CUECD proteins are the duplicated pair of Arabidopsis RING‐finger E3 ligases, RIN2 and RIN3, which each possess a RING‐finger domain in association with a CUE domain; however, the CUE domain was rarely characterized for its roles in the E3 ligases (Kawasaki et al ., ).…”

Section: Introductionmentioning

confidence: 99%

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Disruption of gene SPL35, encoding a novel CUE domain‐containing protein, leads to cell death and enhanced disease response in rice

Wang

et al. 2019

Plant Biotechnology Journal

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Summary Lesion mimic mutants that exhibit spontaneous hypersensitive response ( HR )‐like necrotic lesions are ideal experimental systems for elucidating molecular mechanisms involved in plant cell death and defence responses. Here we report identification of a rice lesion mimic mutant, spotted leaf 35 ( spl35 ), and cloning of the causal gene by TAIL ‐ PCR strategy. spl35 exhibited decreased chlorophyll content, higher accumulation of H 2 O 2 , up‐regulated expression of defence‐related marker genes, and enhanced resistance to both fungal and bacterial pathogens of rice. The SPL 35 gene encodes a novel CUE (coupling of ubiquitin conjugation to ER degradation) domain‐containing protein that is predominantly localized in cytosol, ER and unknown punctate compartment(s). SPL 35 is constitutively expressed in all organs, and both overexpression and knockdown of SPL 35 cause the lesion mimic phenotype. SPL 35 directly interacts with the E2 protein Os UBC 5a and the coatomer subunit delta proteins Delta‐ COP 1 and Delta‐ COP 2 through the CUE domain, and down‐regulation of these interacting proteins also cause development of HR ‐like lesions resembling those in spl35 and activation of defence responses, indicating that SPL 35 may be involved in the ubiquitination and vesicular trafficking pathways. Our findings provide insight into a role of SPL 35 in regulating cell death and defence response in plants.

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Section: Introductionmentioning

confidence: 97%

Section: Introductionmentioning

confidence: 99%

Disruption of gene SPL35, encoding a novel CUE domain‐containing protein, leads to cell death and enhanced disease response in rice

Wang

et al. 2019

Plant Biotechnology Journal

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“…The ability of the NESTA algorithm to reconstruct weak NOESY peaks in a 4D CCNOESY spectrum was examined for a small protein domain, CUE, from the ubiquitin E3 ligase gp78 (Liu et al 2012). The sample was 2 H, 13 C, 15 N-labeled with the exception that Ileδ1, Leu, Val methyl groups were protonated ( 1 H).…”

Section: Resultsmentioning

confidence: 99%

“…Experimental data were collected on three different proteins: (1) a 1 mM sample of the 8 kDa CUE domain containing residues 453–504 from human gp78 (Liu et al 2012); (2) a 330 μM sample of the 15 kDa PH domain of ASAP1, which contains residues 339–451 (Luo et al 2008); and (3) a 400 μM sample of the 32 kDa two domain construct (ZA) of ASAP1 containing residues 441–724 (Luo et al 2008). Isotope labeling was performed by expressing and purifying the proteins from E. coli using standard techniques to produce either uniform 13 C, 15 N-labeled protein, uniform 2 H, 13 C, 15 N-labeled protein (DCN), or uniform 2 H, 13 C, 15 N, 13 C 1 H 3 -methyl (Ileδ1, Leu, Val) labeled protein (DCN-ILV) or 2 H, 15 N, 13 C 1 H 3 -methyl (Ileδ1, Leu, Val) labeled protein (DC methyl N-ILV).…”

Section: Methodsmentioning

confidence: 99%

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Efficient and generalized processing of multidimensional NUS NMR data: the NESTA algorithm and comparison of regularization terms

Sun

Gill

et al. 2015

J Biomol NMR

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The advantages of non-uniform sampling (NUS) in offering time savings and resolution enhancement in NMR experiments have been increasingly recognized. The possibility of sensitivity gain by NUS has also been demonstrated. Application of NUS to multidimensional NMR experiments requires the selection of a sampling scheme and a reconstruction scheme to generate uniformly sampled time domain data. In this report, an efficient reconstruction scheme is presented and used to evaluate a range of regularization algorithms that collectively yield a generalized solution to processing NUS data in multidimensional NMR experiments. We compare l1-norm (L1), iterative re-weighted l1-norm (IRL1), and Gaussian smoothed l0-norm (Gaussian-SL0) regularization for processing multidimensional NUS NMR data. Based on the reconstruction of different multidimensional NUS NMR data sets, L1 is demonstrated to be a fast and accurate reconstruction method for both quantitative, high dynamic range applications (e.g. NOESY) and for all J-coupled correlation experiments. Compared to L1, both IRL1 and Gaussian-SL0 are shown to produce slightly higher quality reconstructions with improved linearity in peak intensities, albeit with a computational cost. Finally, a generalized processing system, NESTA-NMR, is described that utilizes a fast and accurate first-order gradient descent algorithm (NESTA) recently developed in the compressed sensing field. NESTA-NMR incorporates L1, IRL1, and Gaussian-SL0 regularization. NESTA-NMR is demonstrated to provide an efficient, streamlined approach to handling all types of multidimensional NMR data using proteins ranging in size from 8 to 32 kDa.

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Comparison of native and non-native ubiquitin oligomers reveals analogous structures and reactivities

et al. 2016

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Ubiquitin (Ub) chains regulate a wide range of biological processes, and Ub chain connectivity is a critical determinant of the many regulatory roles that this post-translational modification plays in cells. To understand how distinct Ub chains orchestrate different biochemical events, we and other investigators have developed enzymatic and non-enzymatic methods to synthesize Ub chains of well-defined length and connectivity. A number of chemical approaches have been used to generate Ub oligomers connected by non-native linkages; however, few studies have examined the extent to which non-native linkages recapitulate the structural and functional properties associated with native isopeptide bonds. Here, we compare the structure and function of Ub dimers bearing native and non-native linkages. Using small-angle X-ray scattering (SAXS) analysis, we show that scattering profiles for the two types of dimers are similar. Moreover, using an experimental structural library and atomistic simulations to fit the experimental SAXS profiles, we find that the two types of Ub dimers can be matched to analogous structures. An important application of non-native Ub oligomers is to probe the activity and selectivity of deubiquitinases. Through steady-state kinetic analyses, we demonstrate that different families of deubiquitinases hydrolyze native and non-native isopeptide linkages with comparable efficiency and selectivity. Considering the significant challenges associated with building topologically diverse native Ub chains, our results illustrate that chains harboring non-native linkages can serve as surrogate substrates for explorations of Ub function.

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Promiscuous Interactions of gp78 E3 Ligase CUE Domain with Polyubiquitin Chains

Cited by 33 publications

References 43 publications

Disruption of gene SPL35, encoding a novel CUE domain‐containing protein, leads to cell death and enhanced disease response in rice

Disruption of gene SPL35, encoding a novel CUE domain‐containing protein, leads to cell death and enhanced disease response in rice

Efficient and generalized processing of multidimensional NUS NMR data: the NESTA algorithm and comparison of regularization terms

Comparison of native and non-native ubiquitin oligomers reveals analogous structures and reactivities

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