Construction of human activity‐based phosphorylation networks

Molecular Systems Biology

Robert H Newman⁸  Jianfei Hu³  Hee-Sool Rho⁸  Zhi Xie³  Crystal Woodard⁸  John Neiswinger⁸  Christopher Cooper⁷  Matthew Shirley⁸  Hillary M Clark⁸  Shaohui Hu⁸  Woochang Hwang³  Jun Seop Jeong⁸  George Wu¹¹  Jimmy Lin¹⁴  Xinxin Gao⁸  Qiang Ni⁸  Renu Goel²  Shuli Xia⁶  Hongkai Ji¹¹  Kevin N Dalby⁵  Morris J Birnbaum¹²  Philip A Cole⁸  Stefan Knapp^1,8  Alexey G Ryazanov^8,9  Donald J Zack³  Seth Blackshaw^8,10  Tony Pawson^8,13  Anne-Claude Gingras^8,13  Stephen Desiderio⁷  Akhilesh Pandey⁷  Benjamin E Turk^4,8  Jin Zhang⁸  Heng Zhu⁸ 

[1] Nuffield Department of Clinical Medicine, Structural Genomics Consortium, University of Oxford, Oxford, UK;Institute of Bioinformatics, International Tech Park, Bangalore, India;Department of Ophthalmology, Johns Hopkins School of Medicine, Baltimore, MD, USA;Department of Pharmacology, Yale University School of Medicine, New Haven, CT, USA;Division of Medicinal Chemistry, College of Pharmacy, University of Texas at Austin, Austin, TX, USA;Hugo W. Moser Kennedy Krieger Institute, Baltimore, MD, USA;Department of Molecular Biology and Genetics, Johns Hopkins School of Medicine, Baltimore, MD, USA;Department of Pharmacology and Molecular Sciences, Johns Hopkins School of Medicine, Baltimore, MD, USA;Department of Pharmacology, University of Medicine and Dentistry of New Jersey, Piscataway, NJ, USA;Center for High-Throughput Biology, Johns Hopkins School of Medicine, Baltimore, MD, USA;Department of Biostatistics, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD, USA;Department of Medicine, University of Pennsylvania School of Medicine, Philadelphia, PA, USA;Centre for Systems Biology, Samuel Lunenfeld Research Institute, Mount Sinai Hospital Toronto, ON, Canada;The Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins School of Medicine, Baltimore, MD, USA

关键词: phosphorylation;    signaling networks;    systems biology;   

DOI  :  10.1038/msb.2013.12

来源: Wiley

【 摘 要 】

Abstract

The landscape of human phosphorylation networks has not been systematically explored, representing vast, unchartered territories within cellular signaling networks. Although a large number of in vivo phosphorylated residues have been identified by mass spectrometry (MS)-based approaches, assigning the upstream kinases to these residues requires biochemical analysis of kinase-substrate relationships (KSRs). Here, we developed a new strategy, called CEASAR, based on functional protein microarrays and bioinformatics to experimentally identify substrates for 289 unique kinases, resulting in 3656 high-quality KSRs. We then generated consensus phosphorylation motifs for each of the kinases and integrated this information, along with information about in vivo phosphorylation sites determined by MS, to construct a high-resolution map of phosphorylation networks that connects 230 kinases to 2591 in vivo phosphorylation sites in 652 substrates. The value of this data set is demonstrated through the discovery of a new role for PKA downstream of Btk (Bruton's tyrosine kinase) during B-cell receptor signaling. Overall, these studies provide global insights into kinase-mediated signaling pathways and promise to advance our understanding of cellular signaling processes in humans.

Synopsis

A high-resolution map of human phosphorylation networks was constructed by integrating experimentally determined kinase-substrate relationships with other resources, such as in vivo phosphorylation sites.

• High-quality kinase-substrate relationships (KSRs) were determined using an integrated approach that combines protein microarray technology and bioinformatics analysis.
• Phosphorylation motifs were predicted for 284 human kinases, representing 55% of the human kinome.
• A high-resolution map of human phosphorylation networks was constructed that connects 230 kinases to 2591 in vivo phosphorylation sites in 652 substrates.
• A new role for PKA downstream of Btk (Bruton's tyrosine kinase) during B-cell receptor signaling was discovered based on KSRs identified in the phosphorylation networks.

【 授权许可】

CC BY-NC-SA   
Copyright © 2013 EMBO and Macmillan Publishers Limited

Creative Commons Attribution License, which permits distribution, and reproduction in any medium, provided the original author and source are credited. This license does not permit commercial exploitation without specific permission.