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Proteomics. 2016 May;16(10):1486-98. doi: 10.1002/pmic.201500177. Epub 2016 Apr 27.

Disordered nucleiome: Abundance of intrinsic disorder in the DNA- and RNA-binding proteins in 1121 species from Eukaryota, Bacteria and Archaea.

Wang C1,2, Uversky VN3,4,5, Kurgan L1,2.

Author information

1
Department of Computer Science, Virginia Commonwealth University, Richmond, VA, USA.
2
Department of Electrical and Computer Engineering, University of Alberta, Edmonton, Canada.
3
Department of Molecular Medicine and USF Health Byrd Alzheimer's Research Institute, Morsani College of Medicine, University of South Florida, Tampa, FL, USA.
4
Institute for Biological Instrumentation, Russian Academy of Sciences, Pushchino, Moscow Region, Russian Federation.
5
Department of Biology, Faculty of Science, King Abdulaziz University, Jeddah, Kingdom of Saudi Arabia.

Abstract

Intrinsically disordered proteins (IDPs) are abundant in various proteomes, where they play numerous important roles and complement biological activities of ordered proteins. Among functions assigned to IDPs are interactions with nucleic acids. However, often, such assignments are made based on the guilty-by-association principle. The validity of the extension of these correlations to all nucleic acid binding proteins has never been analyzed on a large scale across all domains of life. To fill this gap, we perform a comprehensive computational analysis of the abundance of intrinsic disorder and intrinsically disordered domains in nucleiomes (∼548 000 nucleic acid binding proteins) of 1121 species from Archaea, Bacteria and Eukaryota. Nucleiome is a whole complement of proteins involved in interactions with nucleic acids. We show that relative to other proteins in the corresponding proteomes, the DNA-binding proteins have significantly increased disorder content and are significantly enriched in disordered domains in Eukaryotes but not in Archaea and Bacteria. The RNA-binding proteins are significantly enriched in the disordered domains in Bacteria, Archaea and Eukaryota, while the overall abundance of disorder in these proteins is significantly increased in Bacteria, Archaea, animals and fungi. The high abundance of disorder in nucleiomes supports the notion that the nucleic acid binding proteins often require intrinsic disorder for their functions and regulation.

KEYWORDS:

DNA-binding proteins; Intrinsically disorder; Intrinsically disordered proteins; Nucleiome; RNA-binding proteins; Systems biology

PMID:
27037624
DOI:
10.1002/pmic.201500177
[Indexed for MEDLINE]

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