skip to main content
DOE PAGES title logo U.S. Department of Energy
Office of Scientific and Technical Information

Title: Genetic and structural studies of RABL3 reveal an essential role in lymphoid development and function

Abstract

The small GTPase RABL3 is an oncogene of unknown physiological function. Homozygous knockout alleles of mouse Rabl3 were embryonic lethal, but a viable hypomorphic allele (xiamen [xm]) causing in-frame deletion of four amino acids from the interswitch region resulted in profound defects in lymphopoiesis. Impaired lymphoid progenitor development led to deficiencies of B cells, T cells, and natural killer (NK) cells in Rabl3xm/xm mice. T cells and NK cells exhibited impaired cytolytic activity, and mice infected with mouse cytomegalovirus (MCMV) displayed elevated titers in the spleen. Myeloid cells were normal in number and function. Further, biophysical and crystallographic studies demonstrated that RABL3 formed a homodimer in solution via interactions between the effector binding surfaces on each subunit; monomers adopted a typical small G protein fold. RABL3xm displayed a large compensatory alteration in switch I, which adopted a β-strand configuration normally provided by the deleted interswitch residues, thereby permitting homodimer formation. Dysregulated effector binding due to conformational changes in the switch I–interswitch–switch II module likely underlies the xm phenotype. One such effector may be GPR89, putatively an ion channel or G protein-coupled receptor (GPCR). RABL3, but not RABL3xm, strongly associated with and stabilized GPR89, and an N-ethyl-N-nitrosourea (ENU)-induced mutation (explorer) inmore » Gpr89 phenocopied Rabl3xm.« less

Authors:
 [1];  [1]; ORCiD logo [1];  [1];  [1];  [1];  [1];  [1];  [1];  [1];  [1];  [1]; ORCiD logo [1]; ORCiD logo [1]
  1. Univ. of Texas Southwestern Medical Center, Dallas, TX (United States)
Publication Date:
Research Org.:
Argonne National Lab. (ANL), Argonne, IL (United States). Advanced Photon Source (APS)
Sponsoring Org.:
National Institutes of Health (NIH); USDOE Office of Science (SC), Biological and Environmental Research (BER)
OSTI Identifier:
1618488
Grant/Contract Number:  
R01 AI125581; U19 AI100627; AC02-06CH11357; S10OD025018
Resource Type:
Accepted Manuscript
Journal Name:
Proceedings of the National Academy of Sciences of the United States of America
Additional Journal Information:
Journal Volume: 117; Journal Issue: 15; Journal ID: ISSN 0027-8424
Publisher:
National Academy of Sciences
Country of Publication:
United States
Language:
ENGLISH
Subject:
59 BASIC BIOLOGICAL SCIENCES; small GTPase; lymphopoiesis; GPR89; X-ray crystallography

Citation Formats

Zhong, Xue, Su, Lijing, Yang, Yi, Nair-Gill, Evan, Tang, Miao, Anderton, Priscilla, Li, Xiaohong, Wang, Jianhui, Zhan, Xiaoming, Tomchick, Diana R., Brautigam, Chad A., Moresco, Eva Marie Y., Choi, Jin Huk, and Beutler, Bruce. Genetic and structural studies of RABL3 reveal an essential role in lymphoid development and function. United States: N. p., 2020. Web. https://doi.org/10.1073/pnas.2000703117.
Zhong, Xue, Su, Lijing, Yang, Yi, Nair-Gill, Evan, Tang, Miao, Anderton, Priscilla, Li, Xiaohong, Wang, Jianhui, Zhan, Xiaoming, Tomchick, Diana R., Brautigam, Chad A., Moresco, Eva Marie Y., Choi, Jin Huk, & Beutler, Bruce. Genetic and structural studies of RABL3 reveal an essential role in lymphoid development and function. United States. https://doi.org/10.1073/pnas.2000703117
Zhong, Xue, Su, Lijing, Yang, Yi, Nair-Gill, Evan, Tang, Miao, Anderton, Priscilla, Li, Xiaohong, Wang, Jianhui, Zhan, Xiaoming, Tomchick, Diana R., Brautigam, Chad A., Moresco, Eva Marie Y., Choi, Jin Huk, and Beutler, Bruce. Fri . "Genetic and structural studies of RABL3 reveal an essential role in lymphoid development and function". United States. https://doi.org/10.1073/pnas.2000703117. https://www.osti.gov/servlets/purl/1618488.
@article{osti_1618488,
title = {Genetic and structural studies of RABL3 reveal an essential role in lymphoid development and function},
author = {Zhong, Xue and Su, Lijing and Yang, Yi and Nair-Gill, Evan and Tang, Miao and Anderton, Priscilla and Li, Xiaohong and Wang, Jianhui and Zhan, Xiaoming and Tomchick, Diana R. and Brautigam, Chad A. and Moresco, Eva Marie Y. and Choi, Jin Huk and Beutler, Bruce},
abstractNote = {The small GTPase RABL3 is an oncogene of unknown physiological function. Homozygous knockout alleles of mouse Rabl3 were embryonic lethal, but a viable hypomorphic allele (xiamen [xm]) causing in-frame deletion of four amino acids from the interswitch region resulted in profound defects in lymphopoiesis. Impaired lymphoid progenitor development led to deficiencies of B cells, T cells, and natural killer (NK) cells in Rabl3xm/xm mice. T cells and NK cells exhibited impaired cytolytic activity, and mice infected with mouse cytomegalovirus (MCMV) displayed elevated titers in the spleen. Myeloid cells were normal in number and function. Further, biophysical and crystallographic studies demonstrated that RABL3 formed a homodimer in solution via interactions between the effector binding surfaces on each subunit; monomers adopted a typical small G protein fold. RABL3xm displayed a large compensatory alteration in switch I, which adopted a β-strand configuration normally provided by the deleted interswitch residues, thereby permitting homodimer formation. Dysregulated effector binding due to conformational changes in the switch I–interswitch–switch II module likely underlies the xm phenotype. One such effector may be GPR89, putatively an ion channel or G protein-coupled receptor (GPCR). RABL3, but not RABL3xm, strongly associated with and stabilized GPR89, and an N-ethyl-N-nitrosourea (ENU)-induced mutation (explorer) in Gpr89 phenocopied Rabl3xm.},
doi = {10.1073/pnas.2000703117},
journal = {Proceedings of the National Academy of Sciences of the United States of America},
number = 15,
volume = 117,
place = {United States},
year = {2020},
month = {3}
}

Journal Article:
Free Publicly Available Full Text
Publisher's Version of Record

Save / Share:

Works referenced in this record:

NLRP3 activation and mitosis are mutually exclusive events coordinated by NEK7, a new inflammasome component
journal, December 2015

  • Shi, Hexin; Wang, Ying; Li, Xiaohong
  • Nature Immunology, Vol. 17, Issue 3
  • DOI: 10.1038/ni.3333

Syndromic immune disorder caused by a viable hypomorphic allele of spliceosome component Snrnp40
journal, August 2019


Recent developments in classical density modification
journal, March 2010


The Buccaneer software for automated model building. 1. Tracing protein chains
journal, August 2006


Formation of the Ras Dimer Is Essential for Raf-1 Activation
journal, February 2000

  • Inouye, Kaoru; Mizutani, Shin; Koide, Hiroshi
  • Journal of Biological Chemistry, Vol. 275, Issue 6
  • DOI: 10.1074/jbc.275.6.3737

Diffraction data analysis in the presence of radiation damage
journal, March 2010

  • Borek, Dominika; Cymborowski, Marcin; Machius, Mischa
  • Acta Crystallographica Section D Biological Crystallography, Vol. 66, Issue 4
  • DOI: 10.1107/S0907444909040177

Overview of the CCP 4 suite and current developments
journal, March 2011

  • Winn, Martyn D.; Ballard, Charles C.; Cowtan, Kevin D.
  • Acta Crystallographica Section D Biological Crystallography, Vol. 67, Issue 4
  • DOI: 10.1107/S0907444910045749

The Structural GDP/GTP Cycle of Rab11 Reveals a Novel Interface Involved in the Dynamics of Recycling Endosomes
journal, December 2003

  • Pasqualato, Sebastiano; Senic-Matuglia, Francesca; Renault, Louis
  • Journal of Biological Chemistry, Vol. 279, Issue 12
  • DOI: 10.1074/jbc.M310558200

The Ras superfamily at a glance
journal, March 2005


HKL -3000: the integration of data reduction and structure solution – from diffraction images to an initial model in minutes
journal, July 2006

  • Minor, Wladek; Cymborowski, Marcin; Otwinowski, Zbyszek
  • Acta Crystallographica Section D Biological Crystallography, Vol. 62, Issue 8
  • DOI: 10.1107/S0907444906019949

Humoral Responses against Coimmunized Protein Antigen but Not against Alphavirus-Encoded Antigens Require Alpha/Beta Interferon Signaling
journal, July 2006

  • Hidmark, Åsa S.; Nordström, Eva K. L.; Dosenovic, Pia
  • Journal of Virology, Vol. 80, Issue 14
  • DOI: 10.1128/JVI.02579-05

bMERB domains are bivalent Rab8 family effectors evolved by gene duplication
journal, August 2016


Features and development of Coot
journal, March 2010

  • Emsley, P.; Lohkamp, B.; Scott, W. G.
  • Acta Crystallographica Section D Biological Crystallography, Vol. 66, Issue 4
  • DOI: 10.1107/S0907444910007493

Rab GTPases and their interacting protein partners: Structural insights into Rab functional diversity
journal, July 2017


The structure and function of G-protein-coupled receptors
journal, May 2009

  • Rosenbaum, Daniel M.; Rasmussen, Søren G. F.; Kobilka, Brian K.
  • Nature, Vol. 459, Issue 7245
  • DOI: 10.1038/nature08144

PHENIX: a comprehensive Python-based system for macromolecular structure solution
journal, January 2010

  • Adams, Paul D.; Afonine, Pavel V.; Bunkóczi, Gábor
  • Acta Crystallographica Section D Biological Crystallography, Vol. 66, Issue 2, p. 213-221
  • DOI: 10.1107/S0907444909052925

Negative Regulation of Rho Family GTPases Cdc42 and Rac2 by Homodimer Formation
journal, October 1998


Real-time resolution of point mutations that cause phenovariance in mice
journal, January 2015

  • Wang, Tao; Zhan, Xiaowei; Bu, Chun-Hui
  • Proceedings of the National Academy of Sciences, Vol. 112, Issue 5
  • DOI: 10.1073/pnas.1423216112

Identification of patterns in diffraction intensities affected by radiation exposure
journal, December 2012

  • Borek, Dominika; Dauter, Zbigniew; Otwinowski, Zbyszek
  • Journal of Synchrotron Radiation, Vol. 20, Issue 1
  • DOI: 10.1107/S0909049512048807

Measurement errors and their consequences in protein crystallography
journal, October 2003

  • Borek, Dominika; Minor, Wladek; Otwinowski, Zbyszek
  • Acta Crystallographica Section D Biological Crystallography, Vol. 59, Issue 11
  • DOI: 10.1107/S0907444903020924

GPHR is a novel anion channel critical for acidification and functions of the Golgi apparatus
journal, September 2008

  • Maeda, Yusuke; Ide, Toru; Koike, Masato
  • Nature Cell Biology, Vol. 10, Issue 10
  • DOI: 10.1038/ncb1773

Structure of the small GTPase Rab27b shows an unexpected swapped dimer
journal, June 2007

  • Chavas, Leonard M. G.; Torii, Seiji; Kamikubo, Hironari
  • Acta Crystallographica Section D Biological Crystallography, Vol. 63, Issue 7
  • DOI: 10.1107/S0907444907019725

Mutations in RABL3 alter KRAS prenylation and are associated with hereditary pancreatic cancer
journal, August 2019


A forward genetic screen reveals roles for Nfkbid, Zeb1, and Ruvbl2 in humoral immunity
journal, July 2012

  • Arnold, C. N.; Pirie, E.; Dosenovic, P.
  • Proceedings of the National Academy of Sciences, Vol. 109, Issue 31
  • DOI: 10.1073/pnas.1209134109

Generation of T-cell receptor retrogenic mice
journal, June 2006

  • Holst, Jeff; Szymczak-Workman, Andrea L.; Vignali, Kate M.
  • Nature Protocols, Vol. 1, Issue 1
  • DOI: 10.1038/nprot.2006.61

The Ras protein superfamily: Evolutionary tree and role of conserved amino acids
journal, January 2012

  • Rojas, Ana Maria; Fuentes, Gloria; Rausell, Antonio
  • The Journal of Cell Biology, Vol. 196, Issue 2
  • DOI: 10.1083/jcb.201103008

Multiparametric scaling of diffraction intensities
journal, April 2003

  • Otwinowski, Zbyszek; Borek, Dominika; Majewski, Wladyslaw
  • Acta Crystallographica Section A Foundations of Crystallography, Vol. 59, Issue 3
  • DOI: 10.1107/S0108767303005488

Crystal structure of Rab9 complexed to GDP reveals a dimer with an active conformation of switch II
journal, May 2004


The overexpression of Rabl3 is associated with pathogenesis and clinicopathologic variables in hepatocellular carcinoma
journal, April 2017


LMBR1L regulates lymphopoiesis through Wnt/β-catenin signaling
journal, May 2019


Phaser crystallographic software
journal, July 2007

  • McCoy, Airlie J.; Grosse-Kunstleve, Ralf W.; Adams, Paul D.
  • Journal of Applied Crystallography, Vol. 40, Issue 4
  • DOI: 10.1107/S0021889807021206

A Single Sublingual Dose of an Adenovirus-Based Vaccine Protects against Lethal Ebola Challenge in Mice and Guinea Pigs
journal, November 2011

  • Choi, Jin Huk; Schafer, Stephen C.; Zhang, Lihong
  • Molecular Pharmaceutics, Vol. 9, Issue 1
  • DOI: 10.1021/mp200392g