SIRT6 regulates Ras-related protein R-Ras2 by lysine defatty-acylation

Zhang, Xiaoyu; Spiegelman, Nicole A; Nelson, Ornella D.; Jing, Hui; Lin, Hening

doi:10.7554/elife.25158

Cited by 69 publications

(92 citation statements)

References 40 publications

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“…After optimizing the NEM capping, biotinylation, Neutravidin enrichment and NH 2 OH elution conditions (SI Figure 12-14), we found that inclusion of Rapigest, a MS-compatible detergent was essential for efficient thioester hydrolysis, solubility and final elution of transmembrane proteins (CANX and IFITM3) from the beads (Si figure S14A). However, elution of RAS from beads was not complete, suggesting that alk-16 could have been metabolized or incorporated to another residue than Cys, consistent with recent report of Nε-Lys fatty-acylation of Ras isoforms 42 . VCP was used as a control to confirm that the elution was thiol-specific (Figure 3).…”

Section: Resultssupporting

confidence: 88%

Selective Enrichment and Direct Analysis of Protein S-Palmitoylation Sites

et al. 2018

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S-fatty-acylation is the covalent attachment of long chain fatty acids, predominately palmitate (C16:0, S-palmitoylation), to cysteine (Cys) residues via a thioester linkage on proteins. This post-translational and reversible lipid modification regulates protein function and localization in eukaryotes and is important in mammalian physiology and human diseases. While chemical labeling methods have improved the detection and enrichment of S-fatty-acylated proteins, mapping sites of modification and characterizing the endogenously attached fatty acids are still challenging. Here, we describe the integration and optimization of fatty acid chemical reporter labeling with hydroxylamine-mediated enrichment of S-fatty-acylated proteins, and direct tagging of modified Cys residues to selectively map lipid modification sites. This afforded improved enrichment and direct identification of many protein S-fatty-acylation sites compared to previously described methods. Notably, we directly identified the S-fatty-acylation sites of IFITM3, an important interferon-stimulated inhibitor of virus entry, and further demonstrated that the highly conserved Cys residues are primarily modified by palmitic acid. The methods described here should facilitate the direct analysis of protein S-fatty-acylation sites and their endogenously attached fatty acids in diverse cell types and activation states important for mammalian physiology and diseases.

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Section: Resultssupporting

confidence: 88%

Selective Enrichment and Direct Analysis of Protein S-Palmitoylation Sites

et al. 2018

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“…The two models are not mutually exclusive, or contradictory, since it is possible that HDAC11's deacetylase activity could be increased upon chromatin binding which allows for deacetylation of histones, while it functions efficiently as defatty-acylase in the cytosol. A similar mechanistic function has been reported for SIRT6, a member of the NAD + -dependent HDAC 31,32 .…”

Section: Discussionsupporting

confidence: 76%

“…Our study presented here indicate that SHMT2 is regulated by lysine fatty acylation, which has only been known to occur on a few proteins in mammalian cells. [28][29][30][31] Our data suggest that lysine fatty acylation does not alter the enzymatic activity of SHMT2, but instead promotes the recruitment of the BRISC complex to IFNR1 ( Figure 5F). .…”

Section: Discussionmentioning

confidence: 72%

“…Subcellular fractionation was performed following our previous report with minimal modifications 31 . Briefly, cells were suspended in 500 μL of fractionation buffer (250 mM Sucrose, 20 mM pH 7.4 HEPEs, 10 mM KCl, 2 mM MgCl2, 1 mM, EDTA, 1 mM EGTA, and protease inhibitor cocktail) and passed through a 25G needle 20 times using a 1 mL syringe.…”

Section: Detection Of Lysine Fatty Acylation On Endogenous Shmt2 By Wmentioning

confidence: 99%

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HDAC11 regulates type I interferon signaling through defatty-acylation of SHMT2

Cao

Sun

Aramsangtienchai

et al. 2017

Preprint

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The smallest histone deacetylase (HDAC) and the only class IV HDAC member, HDAC11, is reported to regulate immune activation and tumorigenesis, yet its physiological function is largely unknown. Here we identify HDAC11 as an efficient lysine defatty-acylase that is >10,000-fold more efficient than its deacetylase activity. Through proteomics studies, we identified SHMT2 as a defatty-acylation substrate of HDAC11.HDAC11-catalyzed defatty-acylation did not affect the enzymatic activity of SHMT2.Instead, it affects the ability of SHMT2 to regulate type I interferon receptor ubiquitination and internalization. Correspondingly, HDAC11 depletion increased type I interferon signaling in both cell culture and mice. This study is the first time a zinc-dependent HDAC is found to have an activity that is much more efficient than the corresponding deacetylase activity. The finding expands the physiological functions of HDAC11 and protein lysine fatty acylation, and opens up opportunities to develop HDAC11-specific inhibitors as therapeutics to modulate immune responses.

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“…Structural studies of MT-bound MAPs typically reveal conformational changes in the MAP on interaction with the MT lattice. In the most extreme cases, unstructured proteins such as members of the tau/MAP2 family and the mitotic regulatory protein TPX2, become at least partially ordered when in contact with MTs 36,37 . A recent study of the plant MAP Companion of Cellulose synthase 1 also showed similar behaviour in its disordered N-terminus on binding MTs 38 .…”

Section: Discussionmentioning

confidence: 99%

Structural determinants of microtubule minus end preference in CAMSAP CKK domains

Atherton

Luo

Yang

et al. 2019

Preprint

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CAMSAP/Patronins regulate microtubule minus-end dynamics. Their end specificity is mediated by their CKK domains, which we proposed recognise specific tubulin conformations found at minus ends. To critically test this idea, we compared the human CAMSAP1 CKK domain (HsCKK) with a CKK domain from Naegleria gruberi (NgCKK), which has lost minus-end specificity. Near-atomic cryo-electron microscopy structures of HsCKK-and NgCKK-microtubule complexes show that these CKK domains share the same protein fold, bind at the intradimer interprotofilament tubulin junction, but exhibit subtly different footprints on microtubules. Whereas NgCKK binding does not alter the microtubule architecture, HsCKK remodels its microtubule interaction site and changes the underlying polymer structure because the tubulin lattice conformation is not optimal for its binding. NMR experiments show that HsCKK is remarkably rigid, supporting this remodelling ability. Thus, in contrast to many MAPs, CKK domains can differentiate subtly specific tubulin conformations to enable microtubule minus-end recognition.

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SIRT6 regulates Ras-related protein R-Ras2 by lysine defatty-acylation

Cited by 69 publications

References 40 publications

Selective Enrichment and Direct Analysis of Protein S-Palmitoylation Sites

Selective Enrichment and Direct Analysis of Protein S-Palmitoylation Sites

HDAC11 regulates type I interferon signaling through defatty-acylation of SHMT2

Structural determinants of microtubule minus end preference in CAMSAP CKK domains

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