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BMC Genomics. 2019 May 22;20(1):403. doi: 10.1186/s12864-019-5755-5.

EcRBPome: a comprehensive database of all known E. coli RNA-binding proteins.

Author information

1
National Centre for Biological Sciences, Tata Institute of Fundamental Research, Bellary Road, Bangalore, Karnataka, 560 065, India.
2
Present address: International Institute of Molecular and Cell Biology in Warsaw, Księcia Trojdena 4, 02-109, Warsaw, Poland.
3
Faculty of Science and Technology, University of Nantes, Rue de la Houssinière, BP 92208, 44322, Nantes Cedex 3, France.
4
National Centre for Biological Sciences, Tata Institute of Fundamental Research, Bellary Road, Bangalore, Karnataka, 560 065, India. mini@ncbs.res.in.

Abstract

The repertoire of RNA-binding proteins (RBPs) in bacteria play a crucial role in their survival, and interactions with the host machinery, but there is little information, record or characterisation in bacterial genomes. As a first step towards this, we have chosen the bacterial model system Escherichia coli, and organised all RBPs in this organism into a comprehensive database named EcRBPome. It contains RBPs recorded from 614 complete E. coli proteomes available in the RefSeq database (as of October 2018). The database provides various features related to the E. coli RBPs, like their domain architectures, PDB structures, GO and EC annotations etc. It provides the assembly, bioproject and biosample details of each strain, as well as cross-strain comparison of occurrences of various RNA-binding domains (RBDs). The percentage of RBPs, the abundance of the various RBDs harboured by each strain have been graphically represented in this database and available alongside other files for user download. To the best of our knowledge, this is the first database of its kind and we hope that it will be of great use to the biological community.

KEYWORDS:

Cross-genome comparison; Database; Escherichia coli; Genome-wide survey; Pathotypes; Proteomes; RNA-binding proteins

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