Chemical Synthesis of Structurally Defined Phosphorylated Ubiquitins Suggests Impaired Parkin Activation by Phosphorylated Ubiquitins with a Non-Phosphorylated Distal Unit

Pan, Man; Zheng, Qin; Gao, Shuai; Qu, Qian; Yu, Yuanyuan; Wu, Ming; Lan, Hongbo; Li, Yulei; Liu, Sanling; Li, Jiabin; Sun, Degang; Lu, Lan; Wang, Tian; Zhang, Wenhao; Wang, Jiawei; Li, Yiming; Hu, Honggang; Tian, Changlin; Liu, Lei

doi:10.31635/ccschem.019.20190001

Cited by 33 publications

(22 citation statements)

References 48 publications

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“…Next, we refolded the product using a standard dialysis method and collected the circular dichroism (CD) spectrum of the final product ( Extended Data Fig.1c ). The CD spectrum of the synthesized K29-linked diUb showed an ellipticity near identical to that of the ubiquitin monomer (monoUb), suggesting correct folding of the diUb 40 .…”

Section: Resultsmentioning

confidence: 85%

K29-Linked Ubiquitin Signaling Regulates Proteotoxic Stress Response and Cell Cycle

Yu¹,

Zheng

Erramilli³

et al. 2020

Preprint

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Protein ubiquitination, one of the most common posttranslational modifications, is involved in numerous cellular processes. It shows remarkable topological and functional diversity, a phenomenon known as the ubiquitin code, through the polymerization of ubiquitin via different linkages. Deciphering the cellular ubiquitin code is of central importance to understanding the physiology of the cell. Among the eight possible linkages, K29-linked polyubiquitin is a relatively abundant type of polyubiquitin in both human and yeast cells (Tsuchiya et al., 2018). Despite previous studies, the lack of specific binders as tools to detect K29-linked polyubiquitin has prevented further understanding of its function. In this study, we screened and characterized a synthetic antigen-binding fragment (named sAB-K29) that can specifically recognize K29-linked polyubiquitin. We determined the crystal structure of sAB-K29 bound to K29-linked diubiquitin (diUb), which revealed the molecular basis of sAB-K29 specificity. Using sAB-K29 as a tool, we identified the involvement of K29-linked ubiquitination in RNA processing, the proteotoxic stress response and cell cycle regulation. In particular, we showed that K29-linked ubiquitination is enriched in the midbody at the telophase of mitosis and that downregulation of the K29-linked ubiquitination signal arrests cells in G1/S phase.

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Section: Resultsmentioning

confidence: 85%

K29-Linked Ubiquitin Signaling Regulates Proteotoxic Stress Response and Cell Cycle

Yu¹,

Zheng

Erramilli³

et al. 2020

Preprint

Self Cite

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“…Despite these advances in recent years, some questions still need to be further answered, for example, how the remodeling activity of SMARCAD1 is activated by ubiquitinated nucleosomes or ssDNA and how SMARCAD1 removes the obstacles (such as 53BP1 and nucleosomes) through its histone dimer exchange activity. Take advantage of the recent advances in chemical protein synthesis ( McGinty et al, 2008 ; Fang et al, 2011 , 2012 ; Fierz et al, 2011 ; Siman et al, 2013 ; Li et al, 2014 , 2018 ; Morgan et al, 2016 ; Ai et al, 2019 ; Chu et al, 2019 ; Pan et al, 2019 ) and cryo-electron microscopy techniques, the biochemical and structural studies of ubiquitinated nucleosomes have recently received increasing attention ( Zhou L. et al, 2016 ; Anderson et al, 2019 ; Hsu et al, 2019 ; Jang et al, 2019 ; Park et al, 2019 ; Valencia-Sanchez et al, 2019 ; Worden and Wolberger, 2019 ; Worden et al, 2019 ; Xue et al, 2019 ; Yao et al, 2019 ; Dao et al, 2020 ). Both the in vitro reconstruction experiments and the structural analysis of the SMARCAD1-nucleosome complex may provide new insights into the remodeling mechanism of SMARCAD1.…”

Section: Discussionmentioning

confidence: 99%

The Mechanism of Chromatin Remodeler SMARCAD1/Fun30 in Response to DNA Damage

Tong

2020

Front. Cell Dev. Biol.

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DNA packs into highly condensed chromatin to organize the genome in eukaryotes but occludes many regulatory DNA elements. Access to DNA within nucleosomes is therefore required for a variety of biological processes in cells including transcription, replication, and DNA repair. To cope with this problem, cells employ a set of specialized ATP-dependent chromatin-remodeling protein complexes to enable dynamic access to packaged DNA. In the present review, we summarize the recent advances in the functional and mechanistic studies on a particular chromatin remodeler SMARCAD1 Fun30 which has been demonstrated to play a key role in distinct cellular processes and gained much attention in recent years. Focus is given to how SMARCAD1 Fun30 regulates various cellular processes through its chromatin remodeling activity, and especially the regulatory role of SMARCAD1 Fun30 in gene expression control, maintenance and establishment of heterochromatin, and DNA damage repair. Moreover, we review the studies on the molecular mechanism of SMARCAD1 Fun30 that promotes the DNA end-resection on double-strand break ends, including the mechanisms of recruitment, activity regulation and chromatin remodeling.

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“…Furthermore, E2 discharge experiment showed that Ub-K6-Ub S65Pi could not transfer the Ub thioester from E2∼Ub to Parkin WT. Combination with previous works (Shiba-Fukushima et al, 2012;Koyano et al, 2014), the models of the activation of Parkin WT and phosphorylated Parkin by di-ubiquitin chains were proposed in mitophagy ( Figure 4B) (Pan et al, 2019).…”

Section: Synthesis Of Phosphorylated Di-ubiquitin and Their Applicatimentioning

confidence: 53%

“…Liu and co-workers synthesized the phosphorylated K6-linked di-ubiquitin by hydrazide-based NCL ( Figure 4A) (Pan et al, 2019). To apply this strategy, di-ubiquitin was divided into two segments, ubiquitin G76C (Ub G76C) and ubiquitin K6C (Ub K6C).…”

Section: Synthesis Of Phosphorylated Di-ubiquitin and Their Applicatimentioning

confidence: 99%

Chemical Biology of Autophagy-Related Proteins With Posttranslational Modifications: From Chemical Synthesis to Biological Applications

Luo

Jiang

et al. 2020

Front. Chem.

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Macroautophagy (hereafter referred to as autophagy) is an evolutionarily conserved lysosomal degradation pathway in all eukaryotic cells, which is critical for maintaining cell homeostasis. A series of autophagy-related (ATG) proteins are involved in the regulation of autophagy. The activities of ATG proteins are mainly modulated by posttranslational modifications (PTMs), such as phosphorylation, lipidation, acetylation, ubiquitination, and sumoylation. To tackle molecular mechanisms of autophagy, more and more researches are focusing on the roles of PTMs in regulation of the activity of ATG proteins and autophagy process. The protein ligation techniques have emerged as powerful tools for the chemical engineering of proteins with PTMs, and provided effective methods to elucidate the molecular mechanism and physiological significance of PTMs. Recently, several ATG proteins with PTM were prepared by protein ligation techniques such as native chemical ligation (NCL), expressed protein ligation (EPL), peptide hydrazide-based NCL, and Sortase A-mediated ligation (SML). More importantly, the synthesized ATG proteins are successfully used to probe the mechanism of autophagy. In this review, we summarize protein ligation techniques for the preparation of ATG proteins with PTMs. In addition, we highlight the biological applications of synthetic ATG proteins to probe the autophagy mechanism.

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Chemical Synthesis of Structurally Defined Phosphorylated Ubiquitins Suggests Impaired Parkin Activation by Phosphorylated Ubiquitins with a Non-Phosphorylated Distal Unit

Cited by 33 publications

References 48 publications

K29-Linked Ubiquitin Signaling Regulates Proteotoxic Stress Response and Cell Cycle

K29-Linked Ubiquitin Signaling Regulates Proteotoxic Stress Response and Cell Cycle

The Mechanism of Chromatin Remodeler SMARCAD1/Fun30 in Response to DNA Damage

Chemical Biology of Autophagy-Related Proteins With Posttranslational Modifications: From Chemical Synthesis to Biological Applications

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