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Bioinformatics. 2014 Apr 15;30(8):1095-1103. Epub 2014 Jan 7.

Correlations between predicted protein disorder and post-translational modifications in plants.

Author information

1
RIKEN Center for Sustainable Resource Science 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama 230-0045, Japan, Department of Biotechnology and Life Science, Faculty of Technology, Tokyo University of Agriculture and Technology, 2-24-16 Naka-cho, Koganei, Tokyo 184-8588, Japan and Research Center for Environmental Genomics, Kobe University, 1-1 Rokko dai, Nada, Kobe 657-8501, Japan RIKEN Center for Sustainable Resource Science 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama 230-0045, Japan, Department of Biotechnology and Life Science, Faculty of Technology, Tokyo University of Agriculture and Technology, 2-24-16 Naka-cho, Koganei, Tokyo 184-8588, Japan and Research Center for Environmental Genomics, Kobe University, 1-1 Rokko dai, Nada, Kobe 657-8501, Japan.
2
RIKEN Center for Sustainable Resource Science 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama 230-0045, Japan, Department of Biotechnology and Life Science, Faculty of Technology, Tokyo University of Agriculture and Technology, 2-24-16 Naka-cho, Koganei, Tokyo 184-8588, Japan and Research Center for Environmental Genomics, Kobe University, 1-1 Rokko dai, Nada, Kobe 657-8501, Japan.

Abstract

MOTIVATION:

Protein structural research in plants lags behind that in animal and bacterial species. This lag concerns both the structural analysis of individual proteins and the proteome-wide characterization of structure-related properties. Until now, no systematic study concerning the relationships between protein disorder and multiple post-translational modifications (PTMs) in plants has been presented.

RESULTS:

In this work, we calculated the global degree of intrinsic disorder in the complete proteomes of eight typical monocotyledonous and dicotyledonous plant species. We further predicted multiple sites for phosphorylation, glycosylation, acetylation and methylation and examined the correlations of protein disorder with the presence of the predicted PTM sites. It was found that phosphorylation, acetylation and O-glycosylation displayed a clear preference for occurrence in disordered regions of plant proteins. In contrast, methylation tended to avoid disordered sequence, whereas N-glycosylation did not show a universal structural preference in monocotyledonous and dicotyledonous plants. In addition, the analysis performed revealed significant differences between the integral characteristics of monocot and dicot proteomes. They included elevated disorder degree, increased rate of O-glycosylation and R-methylation, decreased rate of N-glycosylation, K-acetylation and K-methylation in monocotyledonous plant species, as compared with dicotyledonous species. Altogether, our study provides the most compelling evidence so far for the connection between protein disorder and multiple PTMs in plants.

CONTACT:

tokmak@phoenix.kobe-u.ac.jp or tetsuya.sakurai@riken.jp Supplementary information: Supplementary data are available at Bioinformatics online.

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