Analysis of nuclear factor-κB (NF-κB) essential modulator (NEMO) binding to linear and lysine-linked ubiquitin chains and its role in the activation of NF-κB
Authors: Kazuhiro Iwai
Tobias Kensche
Ivan Dikic
Fumiyo Ikeda
Eiji Goto
Fuminori Tokunaga
Journal: Journal of Biological Chemistry (2012)
Discipline: BIOLOGY & BIOCHEMISTRY
Keywords: NF-κB; NEMO; ubiquitin chains; IKK complex; UBAN domain
Affiliations: Buchmann Institute for Molecular Life Sciences and Institute of Biochemistry II, Goethe University School of Medicine, Theodor-Stern-Kai 7, D-60590 Frankfurt, Main, Germany.

Abstract:  Nuclear factor-κB (NF-κB) essential modulator (NEMO), a component of the inhibitor of κB kinase (IKK) complex, controls NF-κB signaling by binding to ubiquitin chains. Structural studies of NEMO provided a rationale for the specific binding between the UBAN (ubiquitin binding in ABIN and NEMO) domain of NEMO and linear (Met-1-linked) di-ubiquitin chains. Full-length NEMO can also interact with Lys-11-, Lys-48-, and Lys-63-linked ubiquitin chains of varying length in cells. Here, we show that purified full-length NEMO binds preferentially to linear ubiquitin chains in competition with lysine-linked ubiquitin chains of defined length, including long Lys-63-linked deca-ubiquitins. Linear di-ubiquitins were sufficient to activate both the IKK complex in vitro and to trigger maximal NF-κB activation in cells. In TNFα-stimulated cells, NEMO chimeras engineered to bind exclusively to Lys-63-linked ubiquitin chains mediated partial NF-κB activation compared with cells expressing NEMO that binds to linear ubiquitin chains. We propose that NEMO functions as a high affinity receptor for linear ubiquitin chains and a low affinity receptor for long lysine-linked ubiquitin chains. This phenomenon could explain quantitatively distinct NF-κB activation patterns in response to numerous cell stimuli. 

Retracted: No

PubPeer comments:
  Figure 5. Inhibition of miR-100 aggravated apoptosis and autophagy of MPP+-intoxicated SH-SY5Y cells by targeting ATG10. ... (B) Flow cytometry showed apoptosis of SH-SY5Y cells after different treatments. Upper row only. I have stretched the second panel by 106% horizontally for comparison with the 3rd panel, to emphasise the similarities between the hair-ball cell-clouds in the 3rd quadrants. ![file] , 
 Fig 2.  Suppression of HAGLROS attenuated apoptosis and autophagy in MPTP-induced PD mouse model and in MPP+-intoxicated SH-SY5Y cells.... (F) Flow cytometry showed apoptosis of SH-SY5Y cells after different treatments. Two of the 3rd-quadrant hairball cell-clouds have very similar sections. ![file] , 
 Fig 1.  (D) Flow cytometry showed that MPP+ treatment promoted apoptosis of SH-SY5Y cells in a dose-dependent manner.  Here are 1(D), 2(F) and 3(B). The hairballs all seem to be variations on a small number of themes. ![file] , 
 This paper belongs to a set of over 400 papers (as per February 2020) that share very similar Western blots with tadpole-like shaped bands, the same background pattern, and striking similarities in title structures, paper layout, bar graph design, and - in a subset - flow cytometry panels. Despite these similarities, these papers are authored by researchers from different departments and institutes, with almost no overlap in authors. The list of these papers is available here: https: docs.google.com spreadsheets d 1KXqTAyl4j-jVorFPMD2XRpr76LcIKJ0CVyIvRj0exYQ edit?usp=sharing A more detailed description of this set of papers, suspected to all be generated by a common source, a paper mill , can be found here: * https: forbetterscience.com 2020 01 24 the-full-service-paper-mill-and-its-chinese-customers (January 2020) * https: scienceintegritydigest.com 2020 02 21 the-tadpole-paper-mill (February 2020) The same paper mill has been described in these papers: * Jana Christopher - Systematic fabrication of scientific images revealed - FEBS Letters (2018) - https: febs.onlinelibrary.wiley.com doi full 10.1002 1873-3468.13201 * Jennifer A Byrne and Jana Christopher - Digital magic, or the dark arts of the 21st centuryu2014how can journals and peer reviewers detect manuscripts and publications from paper mills? - FEBS Letters (2020) - https: febs.onlinelibrary.wiley.com doi full 10.1002 1873-3468.13747 , 
 Expression of Concern published on Mar. 17, 2020 https: www.tandfonline.com doi full 10.1080 21691401.2020.1741841 We, the Publisher and Editor of Artificial Cells, Nanomedicine, and Biotechnology, are issuing an Expression of Concern for the following article: Article title: Long noncoding RNA HAGLROS regulates apoptosis and autophagy in Parkinsonu2019s disease via regulating miR-100 ATG10 axis and PI3K Akt mTOR pathway activation Authors: Tao Peng, Xiaoyan Liu, Jingtao Wang, Yu Liu, Zhenqiang Fu, Xingrong Ma, Junmin Li, Guifang Sun, Yangfei Ji, Jingjing Lu, Wencui Wan and Hong Lu Journal: Artificial Cells, Nanomedicine, and Biotechnology Bibliometrics: Volume 47, Number 01, pages 2764u20132774 DOI: https: doi.org 10.1080 21691401.2019.1636805 After publication of this article, questions about the scientific integrity of the article content were brought to the Publisher and Editoru2019s attention. We have reached out to the authors requesting that they supply information that would confirm the articleu2019s integrity, but the authors have not responded to our queries within the requested timeframe. Therefore, as we continue to work through the issues raised, we advise readers to interpret the information presented in the article with due caution. , 
 Statement of Retraction, 10 August 2021, https: www.tandfonline.com doi full 10.1080 21691401.2021.1951972  We, the Editors, Authors and Publisher of the journal Artificial Cells, Nanomedicine, and Biotechnology, have retracted the following article: Tao Peng, Xiaoyan Liu, Jingtao Wang, Yu Liu, Zhenqiang Fu, Xingrong Ma, Junmin Li, Guifang Sun, Yangfei Ji, Jingjing Lu, Wencui Wan Hong Lu (2019) Long noncoding RNA HAGLROS regulates apoptosis and autophagy in Parkinsonu2019s disease via regulating miR-100 ATG10 axis and PI3K Akt mTOR pathway activation. Artificial Cells, Nanomedicine, and Biotechnology, 47:1, 2764u20132774, DOI: 10.1080 21691401.2019.1636805 Since publication, the authors continued their study and found that the original experimental results were unverifiable. The authors checked their data and confirmed there are fundamental errors present. Therefore, they have agreed to the retraction of this article. The authors apologise for this oversight. We have been informed in our decision-making by our policy on publishing ethics and integrity and the COPE guidelines on retractions. The retracted article will remain online to maintain the scholarly record, but it will be digitally watermarked on each page as u2018Retractedu2019. ,