Prediction of functionally important phospho-regulatory events in xenopus laevis oocytes
File(s)
Published version
Author(s)
Type
Journal Article
Abstract
The African clawed frog Xenopus laevis is an important model organism for studies in developmental
and cell biology, including cell-signaling. However, our knowledge of X. laevis protein
post-translational modifications remains scarce. Here, we used a mass spectrometrybased
approach to survey the phosphoproteome of this species, compiling a list of 2636
phosphosites. We used structural information and phosphoproteomic data for 13 other species
in order to predict functionally important phospho-regulatory events. We found that the
degree of conservation of phosphosites across species is predictive of sites with known
molecular function. In addition, we predicted kinase-protein interactions for a set of cellcycle
kinases across all species. The degree of conservation of kinase-protein interactions
was found to be predictive of functionally relevant regulatory interactions. Finally, using
comparative protein structure models, we find that phosphosites within structured domains
tend to be located at positions with high conformational flexibility. Our analysis suggests
that a small class of phosphosites occurs in positions that have the potential to regulate protein
conformation.
and cell biology, including cell-signaling. However, our knowledge of X. laevis protein
post-translational modifications remains scarce. Here, we used a mass spectrometrybased
approach to survey the phosphoproteome of this species, compiling a list of 2636
phosphosites. We used structural information and phosphoproteomic data for 13 other species
in order to predict functionally important phospho-regulatory events. We found that the
degree of conservation of phosphosites across species is predictive of sites with known
molecular function. In addition, we predicted kinase-protein interactions for a set of cellcycle
kinases across all species. The degree of conservation of kinase-protein interactions
was found to be predictive of functionally relevant regulatory interactions. Finally, using
comparative protein structure models, we find that phosphosites within structured domains
tend to be located at positions with high conformational flexibility. Our analysis suggests
that a small class of phosphosites occurs in positions that have the potential to regulate protein
conformation.
Date Issued
2015-08-01
Date Acceptance
2015-05-27
Citation
PLOS Computational Biology, 2015, 11 (8)
ISSN
1553-734X
Publisher
Public Library of Science
Journal / Book Title
PLOS Computational Biology
Volume
11
Issue
8
Copyright Statement
© 2015 Johnson et al. This is an open
access article distributed under the terms of the
Creative Commons Attribution License, which permits
unrestricted use, distribution, and reproduction in any
medium, provided the original author and source are
credited.
access article distributed under the terms of the
Creative Commons Attribution License, which permits
unrestricted use, distribution, and reproduction in any
medium, provided the original author and source are
credited.
Identifier
http://gateway.webofknowledge.com/gateway/Gateway.cgi?GWVersion=2&SrcApp=PARTNER_APP&SrcAuth=LinksAMR&KeyUT=WOS:000360824500016&DestLinkType=FullRecord&DestApp=ALL_WOS&UsrCustomerID=1ba7043ffcc86c417c072aa74d649202
Subjects
Science & Technology
Life Sciences & Biomedicine
Biochemical Research Methods
Mathematical & Computational Biology
Biochemistry & Molecular Biology
PROTEIN POSTTRANSLATIONAL MODIFICATIONS
CYCLIN-DEPENDENT KINASE
LARGE-SCALE ANALYSIS
PHOSPHORYLATION SITES
CROSS-TALK
GLOBAL ANALYSIS
SPECIFICITY
PHOSPHOPROTEOME
EVOLUTION
DATABASE
Animals
Female
Mass Spectrometry
Models, Molecular
Oocytes
Phosphoproteins
Phosphorylation
Protein Interaction Maps
Proteomics
Xenopus laevis
Bioinformatics
06 Biological Sciences
08 Information And Computing Sciences
01 Mathematical Sciences
Publication Status
Published
Article Number
ARTN e1004362