The N-recognin UBR4 of the N-end rule pathway is required for neurogenesis and homeostasis of cell surface proteins

Sung Tae Kim; Yoon Jee Lee; Takafumi Tasaki; Joonsung Hwang; Min Jueng Kang; Eugene C Yi; Bo Yeon Kim; Yong Tae Kwon

doi:10.1371/journal.pone.0202260

The N-recognin UBR4 of the N-end rule pathway is required for neurogenesis and homeostasis of cell surface proteins

PLoS One. 2018 Aug 29;13(8):e0202260. doi: 10.1371/journal.pone.0202260. eCollection 2018.

Authors

Sung Tae Kim^{1

2}, Yoon Jee Lee¹, Takafumi Tasaki³, Joonsung Hwang⁴, Min Jueng Kang⁵, Eugene C Yi⁵, Bo Yeon Kim⁴, Yong Tae Kwon^{1

6}

Affiliations

¹ Protein Metabolism Medical Research Center and Department of Biomedical Sciences, College of Medicine, Seoul National University, Seoul, Republic of Korea.
² Center for Pharmacogenetics and Department of Pharmaceutical Sciences, School of Pharmacy, University of Pittsburgh, Pittsburgh, PA, United States of America.
³ Medical Research Institute, Kanazawa Medical University, Ishikawa, Japan.
⁴ World Class Institute, Anticancer Agents Research Center, Korea Research Institute of Bioscience and Biotechnology, Ochang, Cheongwon, Republic of Korea.
⁵ Department of Molecular Medicine and Biopharmaceutical Sciences, School of Convergence Science and Technology and College of Medicine or College of Pharmacy, Seoul National University, Seoul, Republic of Korea.
⁶ Ischemic/Hypoxic Disease Institute, College of Medicine, Seoul National University, Seoul, Republic of Korea.

Abstract

The N-end rule pathway is a proteolytic system in which single N-terminal amino acids of proteins act as a class of degrons (N-degrons) that determine the half-lives of proteins. We have previously identified a family of mammals N-recognins (termed UBR1, UBR2, UBR4/p600, and UBR5/EDD) whose conserved UBR boxes bind N-degrons to facilitate substrate ubiquitination and proteasomal degradation via the ubiquitin-proteasome system (UPS). Amongst these N-recognins, UBR1 and UBR2 mediate ubiquitination and proteolysis of short-lived regulators and misfolded proteins. Here, we characterized the null phenotypes of UBR4-deficient mice in which the UBR box of UBR4 was deleted. We show that the mutant mice die around embryonic days 9.5-10.5 (E9.5-E10.5) associated with abnormalities in various developmental processes such as neurogenesis and cardiovascular development. These developmental defects are significantly attributed to the inability to maintain cell integrity and adhesion, which significantly correlates to the severity of null phenotypes. UBR4-loss induces the depletion of many, but not all, proteins from the plasma membrane, suggesting that UBR4 is involved in proteome-wide turnover of cell surface proteins. Indeed, UBR4 is associated with and required to generate the multivesicular body (MVB) which transiently store endocytosed cell surface proteins before their targeting to autophagosomes and subsequently lysosomes. Our results suggest that the N-recognin UBR4 plays a role in the homeostasis of cell surface proteins and, thus, cell adhesion and integrity.

Publication types

Research Support, Non-U.S. Gov't

MeSH terms

Animals
Autophagosomes / metabolism
Calmodulin-Binding Proteins / genetics
Calmodulin-Binding Proteins / metabolism*
Cell Adhesion / physiology
Cell Line, Tumor
Cell Membrane / metabolism*
Cytoskeletal Proteins / genetics
Cytoskeletal Proteins / metabolism*
Endocytosis / physiology
Fibroblasts / metabolism
HEK293 Cells
HeLa Cells
Homeostasis / physiology*
Humans
Lysosomes / metabolism
Mice, Knockout
Microtubule-Associated Proteins / genetics
Microtubule-Associated Proteins / metabolism*
Multivesicular Bodies / metabolism
Neurogenesis / physiology*
Proteome
Ubiquitin-Protein Ligases / genetics
Ubiquitin-Protein Ligases / metabolism*

Substances

Calmodulin-Binding Proteins
Cytoskeletal Proteins
Microtubule-Associated Proteins
Proteome
UBR4 protein, human
Ubiquitin-Protein Ligases
Ubr4 protein, mouse

Grants and funding

This work was supported by grants from the Seoul National University (SNU) Nobel Laureates Invitation Program (http://www.snu.ac.kr), the National Research Foundation of Korea (NRF; http://www.nrf.re.kr) funded by the Ministry of Science and ICT (MSIT) (NRF-2016R1A2B3011389 to Y.T.K., NRF-2015M3A9B6073835 to E.C.Y., NRF-2014M39Ab5073938 to B.Y.K., and NRF-2015-Global PhD Fellowship to Y.J.L.), the Brain Korea 21 PLUS (to SNU; http://bkplus.nrf.re.kr), SNU Hospital (to Y.T.K.; http://www.snuh.org), the Bio and Medical Technology Development Program (project no. 2012M3A9B6055305 to B.Y.K.) through the MSIT (http://www.msit.go.kr), the R&D Convergence Program (CAP-16-03-KRIBB) of National Research Council of Science & Technology (NST; http://www.nst.re.kr/nst), Korea Research Institute of Bioscience and Biotechnology (KRIBB; http://www.kribb.re.kr) Research Initiative Program (NRF-2014M39Ab5073938 to B.Y.K.), and Grant for Promoted Research from Kanazawa Medical University (http://www.kanazawa-med.ac.jp) (S2016-13, S2017-6 to T.T.) and by JSPS KAKENHI (https://www.jsps.go.jp) Grant Number JP25430119 and JP18K06119 (to T.T.). The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.